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Question: <p>If I have some synthetic DNA sequence (<=20 bp long), is there a way for me to reliably insert this sequence next to some n-bp motif? I'd like for this to be possible in humans. If so, are there any restrictions on the size of n? </p>
<p>I have explored the use of CRISPR/Cas9 for this end, but it is limited in the sense that the gRNA target sequence must be adjacent to a PAM sequence. Attempts have been made to solve this problem (<a href="http://www.nature.com/nature/journal/v523/n7561/full/nature14592.html#affil-auth" rel="nofollow">http://www.nature.com/nature/journal/v523/n7561/full/nature14592.html#affil-auth</a>), but they fall short of full generality for n. Are there any better approaches?</p>
Answer:
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https://biology.stackexchange.com/questions/41516/insertion-of-synthetic-dna-sequence
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Question: <p>So I was reading up on articles to do a project about cloning but there were no places in the article where It states the tool used to take the gene out of the nucleus and insert it into plasmids ? can anyone accurately tell me what the tool is. I don't mean the process but the actual names of the tools like CRISPR etc.</p>
<p>As a reference The article was the wiki <a href="https://en.wikipedia.org/wiki/Molecular_cloning" rel="nofollow">https://en.wikipedia.org/wiki/Molecular_cloning</a></p>
Answer:
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https://biology.stackexchange.com/questions/42877/what-tools-are-used-in-animal-cloning
|
Question: <p>I am struggling to set up a project proposal for validation of a known treatment for metastatic colorectal cancer in mouse models.
I want to see how SNPs in patients contribute to their drug resistance and/or toxicity. For the validation of these SNPs as predictive biomarkers, I will use cell lines and mouse models. But, how am I supposed to "induce" these specific SNPs in the mice? CRISPR/Cas9 can be used for the alteration of bigger parts.
Any idea is a useful idea!</p>
Answer:
|
https://biology.stackexchange.com/questions/68626/treatment-validation-on-mouse-models
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Question: <p>In eukaryotes, microRNAs and small interfering RNAs, as part of protein complexes, can attack specific messenger RNAs with complementary sequences, thereby inhibiting translation. However, RNA can also complement DNA. So, do any regulatory RNAs directly bind to DNA (with a protein complex or alone)?</p>
<p>I am only interested in regulation, not modifying DNA (like CRISPR does). I assume that means I am asking if any regulatory RNAs persistently bind to DNA, blocking RNA polymerases?</p>
<p>This question is for either or both eukaryote and prokaryotes. </p>
Answer: <p>Yes there are reports of RNA directly inhibiting transcription. </p>
<p><a href="https://en.wikipedia.org/wiki/RNA-induced_transcriptional_silencing" rel="nofollow noreferrer">RNA induced transcriptional silencing (RITS)</a> is a well known pathway in <em>Schizosaccharomyces pombe</em> (fission yeast). Initial heterochromatinization is dependent on the RNA (as a DNA identfication module) that guides other functional proteins to the target (Also see <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797062/" rel="nofollow noreferrer">Djupedal et al., 2009</a>).</p>
<p>piRNA in higher eukaryotes are known to cause methylation of target DNA regions and thereby the repression of genes at these loci (<a href="http://dx.doi.org/10.1101/gad.1669408" rel="nofollow noreferrer">Aravin and Bourc'his, 2008</a>).</p>
<p>Some classes of <a href="http://www.wormbook.org/chapters/www_endoRNAipathwys/endoRNAipathwys.html" rel="nofollow noreferrer">small RNAs in <em>C.elegans</em></a> (such as 22G RNA) are also known to cause transcriptional silencing.</p>
<p>Many lncRNAs are known to inhibit transcription of their target genes. The most famous example would be that of <a href="https://en.wikipedia.org/wiki/XIST_(gene)" rel="nofollow noreferrer">XIST</a> which causes epigenetic silencing of one of the X-chromosomes in the female. </p>
<p>On a purely biochemical note, RNAs can also form triplex with target DNA regions and impede transcription and replication (<a href="http://dx.doi.org/10.1371/journal.pgen.1005696" rel="nofollow noreferrer">Bacolla et al., 2015</a>).</p>
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https://biology.stackexchange.com/questions/54380/do-any-rnas-directly-inhibit-transcription
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Question: <p>I know this probably sounds rather hypothetical and not very feasible but I would very like an answer telling why it is possible or not possible and why.</p>
<p>With the advancement of crispr and other dna technologies, I have been wondering whether it is possible for us to use a virus, which would easily pass through the gaps of the placenta and infect the developing fetus to alter its genomic materials for the creation of designer babies. Since Zika can alter the genome of a baby to cause deformities, is something opposite also possible, like using a similar virus to develop favourable genes in a fetus.</p>
<p>Also, what are the chances of the virus actually purposely acting under orders of genetic engineering to intentionally deliver the genes through transduction? </p>
<p>Putting all ethical and moral issues aside is such a principle feasible and if no, why not? </p>
Answer: <h2>Zika doesn't alter the host genome at all.</h2>
<blockquote>
<p>Since Zika can alter the genome of a baby to cause deformities</p>
</blockquote>
<p>Zika virus is incapable of altering the host genome. The exact mechanism by which Zika virus infection causes microcephaly is still unclear, but basically it depletes the neural stem cells at a point when the brain is developing, meaning brain development is more limited (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516183/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516183/</a>).</p>
<h2>Some viruses do alter the host genome and are candidate technologies for gene therapy</h2>
<p>Retroviruses are RNA viruses that copy their genetic material into DNA which is then integrated into a host genome. As such, and as you note, this can potentially be exploited to deliver new genetic material into an organism's genome. I'm not sure what you meant by transduction above, but the term is 'retroviral vector-mediated gene delivery'.</p>
<p>Retroviruses have been trialled for gene therapy for decades. See this sad report on a 2002 trial that apparently succeeded but had unexpected side effects <a href="http://www.nature.com/nature/journal/v420/n6912/full/420116a.html)" rel="nofollow noreferrer">here</a>. However, CRISPR is probably an easier method to use.</p>
<h2>You wouldn't attempt to modify a fetus</h2>
<p>Some terminology here: a fetus is what an embryo grows into; it's getting bigger and more complex. And as illustrated by Zika-related microcephaly, any messing about with fetal development can have nasty side effects. There are also more cells to modify and you're likely to end up with a 'mosaic' where some cells are genetically different to others within the same organism. If you're attempting to modify the somatic cells of one organ, you might as well do it after the baby is born; if you're attempting to modify every cell in a human (including germ line cells) you'd do it to an egg or embryo.</p>
<p><a href="http://www.nature.com/news/crispr-fixes-disease-gene-in-viable-human-embryos-1.22382" rel="nofollow noreferrer">This study</a> describes a successful attempt to modify embryos using CRISPR. They saw only 1 mosaic in 58 embryos.</p>
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https://biology.stackexchange.com/questions/67408/is-it-possible-to-use-virus-for-genetic-modification-of-embryos-during-the-fetus
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Question: <p><a href="http://www.bbc.com/news/science-environment-40585299" rel="noreferrer">BBC News recently published an article</a> saying that:</p>
<blockquote>
<p>An image and short film has been encoded in DNA, using the units of inheritance as a medium for storing information ...
The team sequenced the bacterial DNA to retrieve the gif and the image, verifying that the microbes had indeed incorporated the data as intended. </p>
</blockquote>
<p><a href="https://i.sstatic.net/uG4SB.jpg" rel="noreferrer"><img src="https://i.sstatic.net/uG4SB.jpg" alt="This is the image:"></a></p>
<p>The news article shows an image of a hand (shown above) and a short film (not shown here) of a horse rider that was encoded into the DNA <em>"using a genome editing tool known as Crispr [sic]"</em>. </p>
<p>My question is, what does this mean? Did the scientists break down an image into 0's and 1's and (install?) it into bacteria? How does a scientist (download?) an image into bacteria and then (redownload?) the image later? How does DNA hold information of a picture that can be (downloaded)?</p>
Answer: <p>Just to add what might have been missing in the beautiful answer by @iayork. I just want to give a more simple picture of the encoding done in the <em>E. coli</em> DNA.</p>
<ul>
<li><p>First for the <strong>rigid strategy</strong> in which 4 pixel colors were each specified by a different base, suppose we have a sequence:</p>
<p>AAGCCCTGGTCAGCT</p>
<p>Ignore the first AAG and start with C. Now, each base of DNA can represent a 2-digit binary number, and each number then corresponds to a color, like:</p>
<p>C = 00</p>
<p>T = 01</p>
<p>A = 10</p>
<p>G = 11</p>
<p>With this strategy in mind, the sequence CCCT would give 00000001 pixet (or pixel set), and so on as the sequence grows. This pixet would define the color of four pixels in the image. Thus, each base corresponds to a pixel in the image, and the base defines the color of the pixel in a 4-color image.</p></li>
<li><p>Now, lets come to the <strong>flexible strategy</strong>. To begin with, see the table again:</p>
<p><a href="https://i.sstatic.net/ZPOGS.png" rel="noreferrer"><img src="https://i.sstatic.net/ZPOGS.png" alt="flexibe strategy table"></a></p>
<p>Here we are using standard 3-base codons. From the predefined value for each color (1 to 21), we can find the color using the codon. For example, from the same sequence:</p>
<p>AAGCCCTGGTCAGCT</p>
<p>Ignore AAG again and start with CCC. From the table, CCC encodes a value of 1. Move to next, TGG encodes a value of 16, TCA encodes 10 and GCT encodes 7, and so on for longer sequences. So, now we get an image with 4 pixels i.e. 2 x 2 with the pixels having color code 1, 16, 10, 7. In this way, each pixel can have a color from predefined values. On extracting this data, the image comes out as (from <a href="http://gizmodo.com/scientists-code-an-animated-gif-into-dna-1796848053" rel="noreferrer">gizmodo</a>):</p></li>
</ul>
<p><a href="https://i.sstatic.net/gPmSg.jpg" rel="noreferrer"><img src="https://i.sstatic.net/gPmSg.jpg" alt="image"></a></p>
<p>The above part talked mostly about the single image of a hand. Now, talking about the horse-riding GIF, the process is almost the same. Here, we have to encode 5 images instead of one. Scientists encoded these 5 images in 5 different cells. After culturing them for some generations, they extracted the information of all images (using standard bioinformatics tools) and compiled them to get the GIF back. The initial and final GIFs look like this (from <a href="http://www.wired.com/story/scientists-upload-a-galloping-horse-gif-into-bacteria-with-crispr" rel="noreferrer">wired.com</a>):</p>
<p><a href="https://i.sstatic.net/247eN.gif" rel="noreferrer"><img src="https://i.sstatic.net/247eN.gif" alt="GIF"></a></p>
<p><strong>What do these <em>rigid</em> and <em>flexible</em> mean?</strong></p>
<p>In this technique, the terms <em>rigid</em> and <em>flexible</em> are more about individual base rather than the codon. In the <em>rigid</em> strategy, the value of each base is fixed i.e. rigid. For example, in any sequence, C will encode the value '00', whatever the next or previous base is. This means that in both CCCT and GGTC, C has its rigid value '00'. So, for a 4-color image, where each base rigidly corresponds to the color of a pixel, we get as many pixels as the bases in the sequence.</p>
<p>On the other hand, in the <em>flexible</em> strategy, the individual bases do not have a fixed value, and the overall value of a pixet is defined by all the bases encoding that pixet. For example, TCC encodes a value of 6 while CCC encodes 1. The value of individual base is degenerate (or <em>flexible</em>), hence the name <em>flexible strategy</em>.</p>
<p>Thus, in a nutshell, while the rigid strategy is more efficient since one pixel is defined by one base (whereas in flexible strategy, one pixel is defined by one codon), the flexible strategy is better suited for getting more colored images since you get more color options by increasing the number of bases in a codon (whereas you only get 4 colors in rigid strategy, defined by 4 bases).</p>
<p><strong>Why are we ignoring AAG?</strong></p>
<p>As @canadianer points out in their answer, AAG is a <strong>PAM</strong> i.e. Protospacer Adjacent Motif. According to <a href="https://en.wikipedia.org/wiki/Protospacer_adjacent_motif" rel="noreferrer">Wikipedia</a>:</p>
<blockquote>
<p>Protospacer adjacent motif (PAM) is a 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system. PAM is a component of the invading virus or plasmid, but is not a component of the bacterial CRISPR locus.</p>
</blockquote>
<p>In simple terms (avoiding technical details), PAM is required for the CRISPR to function, but is not a part of the sequence itself. Much like a punctuation, it is necessary for proper functioning of CRISPR, but it is not to be read for encoding/decoding purpose. For the Cas9 found in <em>E. coli</em> (and is the most popular one), the sequence AAG serves as a PAM and is thus not used for encoding purpose here. Scientists also avoided to use AAG in their pixets so that there wouldn't be more than one recognition site for integration (ignore this point if you're unaware of the working of CRISPR).</p>
<p><strong>Reference:</strong> <a href="https://www.nature.com/nature/journal/vaop/ncurrent/full/nature23017.html" rel="noreferrer">Shipman, S., Nivala, J., Macklis, J. and Church, G. (2017). CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. <em>Nature.</em> http://dx.doi.org/10.1038/nature23017
</a></p>
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https://biology.stackexchange.com/questions/62641/what-does-it-mean-to-write-an-image-and-gif-into-the-dna-of-bacteria
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Question: <p>Reading this study
<a href="http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html" rel="nofollow">http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html</a></p>
<p>They writing</p>
<blockquote>
<p>Multiple <strong>exogenous</strong> and endogenous genes can be simultaneously activated
by CRISPR-on</p>
<p>We tested single, double and triple activation of a TetO::tdTomato
transgene and the endogenous SOX2 and IL1RN genes (Figure 3A) in
HEK293T cells carrying the stably integrated TetO::tdTomato transgene</p>
</blockquote>
<p>Could you please help me to understand: They talking about exogenous gene. But saying "carrying the stably integrated". Does that mean that this gene (TetO::tdTomato) is in the cell genome (integrated to genome)? If so, what is the meaning of exogenous here?</p>
<p>Thank you!</p>
Answer: <p>According to Merriam Webster, an exogeneous gene is defined as " introduced from or produced outside the organism or system; specifically : not synthesized within the organism or system—compare endogenous".</p>
<p>I believe they refer to the tetO::tdTomato transgene as an exogeneous, or not originating from the species of study</p>
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https://biology.stackexchange.com/questions/31751/what-does-it-mean-carrying-the-stably-integrated-gene
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Question: <p>Is taking AAS a form of gene-editing? Steroids alter genes in some way since they allow people to build more muscle than what's naturally possible -- so they sort of "break" natural genetics somehow.</p>
<p>Given this, would this be considered a form of genetic-engineering on living humans/etc.? What about relative things like myostatin-inhibiting to prevent muscle growth cell limitation or HGH use?</p>
<p>In summary: does the use of AAS/performance enhancing drugs/etc. constitute gene editing? If not, why -- and if so, why and how is it comparable to things like CRISPR and stem-cell/etc. methods?</p>
Answer: <h3>Steroids are not a form of gene editing</h3>
<p>A gene is a sequence of DNA. Gene editing means changing this DNA sequence, kind of like changing the letters in a book.</p>
<p>Essentially all drugs, steroids included, affect the body without changing DNA sequence. Often they bind to a protein, which is the product of a gene, and alter its function. Steroids bind and alter the activity of <em>transcriptiton factors</em>, which are kind of like switches that turn certain genes on and off.</p>
<p>If gene editing is like rewriting a book, taking a drug would be like changing how, when, or where someone reads from the book, without altering the text itself.</p>
<p>If you are interested in how all of this works, you can check out some great free online courses like this:
<a href="https://www.khanacademy.org/science/biology#intro-to-biology" rel="nofollow noreferrer">https://www.khanacademy.org/science/biology#intro-to-biology</a></p>
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https://biology.stackexchange.com/questions/78772/are-androgenic-anabolic-steroids-a-form-of-gene-editing
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Question: <p>From this article <a href="https://ui.adsabs.harvard.edu/abs/2005Sci...308.1909S/abstract" rel="nofollow noreferrer">https://ui.adsabs.harvard.edu/abs/2005Sci...308.1909S/abstract</a></p>
<p>“We created transgenic mice that overexpress human catalase localized in the peroxisome, nucleus, or mitochondria (MCAT).”</p>
<p>How exactly do such changes occur step by step? Those. how did they find which genes needed to be changed in order to get the result in overexpression of catalase and in mitochondria?</p>
<p>I am new to biology, and although I understand, for example, how CRISPR works, it’s not clear where people get such data "this gene in the mouse is responsible for the expression of catalase in mitochondria. "Where to find such data?</p>
Answer: <p>Hi Potion and welcome to Biology Stack Exchange and biology in general!</p>
<p>To answer your questions, these changes do not occur. The authors of the publication have engineered "new" genes (also called transgenes in this context). </p>
<p>They have done so by fusion a portion of a of another gene (also called domain) to the beginning or the end of the sequence of the catalase gene. If your gene of interest is localized to a given organelle (for example mitochondria), you can also swap the domain which is responsible for the targeting to this particular organelle with one from a different gene you know goes for let's say peroxisomes.</p>
<p>If you want to know more details for this particular work I encourage you to check the supplementary material here: <a href="https://science.sciencemag.org/content/sci/suppl/2005/06/23/1106653.DC1/Schriner.SOM.pdf" rel="nofollow noreferrer">https://science.sciencemag.org/content/sci/suppl/2005/06/23/1106653.DC1/Schriner.SOM.pdf</a></p>
<p>Hope that helps!</p>
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https://biology.stackexchange.com/questions/90987/where-do-biologists-get-information-about-mouse-genes
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Question: <p>CRISPR-Cas13 equipped with crRNA (complementary to transcripts of interest) can be designed to target ssRNA transcripts in cells. </p>
<p>Upon successful crRNA and ssRNA binding, a fluorescent domain on Cas13 generates a signal, indicating that target has been found. </p>
<p>As far as I know, this method has been used to find one ssRNA target at a time. If we use different wavelength fluorophores for distinct Cas13-crRNA targets, is it theoretically possible to mix them all in the same reaction and distinguish the presence of different targets based on the different fluorescence wavelengths generated during target binding?</p>
<p>In <a href="http://Nucleic%20acid%20detection%20with%20targeted%20RNAs%20(10).%20This%20crRNA-programmed%20collateral-cleavage%20activity%20allows%20Cas13a%20to%20detect%20CRISPR-Cas13a/C2c2%20thepresenceofaspecificRNAinvivobytriggering%20programmed%20cell%20death%20(10)%20or%20in%20vitro%20by%20non-" rel="nofollow noreferrer">this paper</a> one fluorescently labeled crRNA is used to detect cleavage of one RNA target through complimentary binding. So is it theoretically possible to use several crRNA, each labeled with a different fluorophore, to cleave and detect several target RNAs? </p>
Answer: <p>Answer is no. Because each CRIPSR-Cas(xx) system works as a ribonucleoproteic complex, so they needs to be loaded with a crRNA in order to be working. Functionality is guaranteed while each of the Cas endonuclease domain is associated with a crRNA. You maybe could use multiple Cas13 with multiple crRNA.
In molecular diagnosis is common to use orthogonal CRISPR enzymes with different crRNA, as can be seen in <a href="https://science.sciencemag.org/content/360/6387/439.abstract" rel="nofollow noreferrer">this</a> original research.</p>
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https://biology.stackexchange.com/questions/84841/can-cas13-be-used-with-multiple-crrnas-in-the-same-reaction
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Question: <p>If I understand correctly, the steps of gene editing with CRISPR-Cas9 are roughly as follows</p>
<blockquote>
<ul>
<li>Cas9 nuclease and guide RNA form a complex.</li>
<li>Cas9+guide RNA complex scans genomic DNA and recognizes the sequences homologous to the guide RNA</li>
<li>Induces a double strand break in DNA upstream of the PAM sequence (only breaks when the homologous sequence of the guide RNA is in the vicinity of the PAM).</li>
<li>Genetic modification using the mechanism of DNA repair (NHEJ, HDR) after double-strand break.</li>
</ul>
</blockquote>
<p>If so, in the gene editing with CRISPR-Cas9 , gene editing is likely to continue as long as the Cas9 does not lose its activity, am I right?</p>
<p><strong>My question</strong></p>
<blockquote>
<ul>
<li>When does the Cas lose its activity?</li>
<li>What was the logic of the experiment that identified the timing? / If the matter itself is unexplored, what kind of experiments could be done to find out the timing when the Cas lose its activity?</li>
</ul>
</blockquote>
<p>As <a href="https://www.youtube.com/watch?v=4YKFw2KZA5o" rel="nofollow noreferrer">this movie</a> shows, if the gene editing occurs successfully, it will indeed introduce a mutation in the target gene.</p>
<p>However, even if it does,-this is just my guess from here on out- it is likely to remain complementary to the target gene, at least upstream of the guide RNA. However, even if the target gene is mutated, <strong>there is likely to remain complementary sequence to the guide RNA</strong>, at least upstream of the mutation. So, even if one successful gene edit is completed, I think it's possible that gene editing could happen again in the same location. Moreover, even if the targeted site is successfully edited, there is still the possibility of subsequent off-target editing elsewhere. That's why I think the tools exist to stop CAS.</p>
<p><a href="https://i.sstatic.net/YYNGC.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/YYNGC.jpg" alt="enter image description here" /></a><br>
A guide RNA binds to the target gene that has been bitten by CAS. The strand opposite the strand to which the guide RNA was bound has just been cleaved.
Quoted from this <a href="https://www.youtube.com/watch?v=4YKFw2KZA5o" rel="nofollow noreferrer">video</a>.</p>
<p><strong>An idea for an experiment to detect when CAS goes quiet<br></strong>
If a single cell colony was created from a gene-edited population and there was genetic variation in the cells born from that colony, then I think that would mean that there would have been Cas9 activity even after the single cell colony was started in culture. Is this idea correct? Could there be a smarter experiment?</p>
Answer: <p>Regarding the loss of Cas9 activity, you are already touching on the answer in your question. Cas9 as a nuclease/enzyme is always active, and will continue to cleave double-stranded DNA as long as there are complementary target sites and guide RNAs to guide it there. If the target site is <em>not</em> mutated or completely removed after cleavage, Cas9 can indeed cleave the same site again.</p>
<blockquote>
<p>However, even if the target gene is mutated, there is likely to remain complementary sequence to the guide RNA, at least upstream of the mutation.</p>
</blockquote>
<p>I'm not sure if I misunderstand the point you are trying to make here, but the introduction of mutations is <em>usually</em> enough to prevent recurrent cleavage of the same site (although <a href="https://pubmed.ncbi.nlm.nih.gov/25513782/" rel="nofollow noreferrer">studies of off-target effects</a> clearly show that this is not always the case):</p>
<p>Both <a href="https://pubmed.ncbi.nlm.nih.gov/24529477/" rel="nofollow noreferrer"><em>Streptococcus pyogenes</em></a> and <a href="https://pubmed.ncbi.nlm.nih.gov/26317473/" rel="nofollow noreferrer"><em>Staphylococcus aureus</em></a> Cas9 cleave their target sites between positions -3 and -4, counting from the end of the 20-nt guide sequence (see attached figure below). The double-stranded break can then be repaired either via non-homologous end joining (NHEJ), or via template-driven homologous recombination (HR).</p>
<p><a href="https://i.sstatic.net/RKzc9.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/RKzc9.png" alt="CRISPR/Cas9 cleavage" /></a></p>
<p>In the former case (NHEJ), double-stranded breaks are <em>sometimes</em> repaired with small errors. These errors <em>usually</em> accumulate near the break site (<a href="https://en.wikipedia.org/wiki/Non-homologous_end_joining" rel="nofollow noreferrer">read about NHEJ to understand why</a>), and such mutations will typically destroy the gRNA recognition site. Note, however, that <strong>not all</strong> (in fact, very few) NHEJ repair events will result in the introduction of mutations, and "perfectly repaired" breaks both can and will be re-cleaved by Cas9. But since repeated cleavage is lethal to the cell, there is a selective advantage for mutations that prevent re-cleavage of a target site. Also note that the introduction of mutations (and thereby gene editing) via NHEJ is a random process, with no direct control by the researcher.</p>
<p>In the latter case (HR), the DNA template used for repairing the double-stranded break can typically be chosen by the researcher. It can for example be a chemically synthesized DNA fragment or PCR product with at least some sequence homology to regions flanking the cleavage site. But since there is no specific sequence requirement for the region <em>in between</em> the homology regions, this interspacing region can be designed such that it partly or completely replaces the original recognition and/or PAM sequence (violet region in figure below).</p>
<p><a href="https://i.sstatic.net/B0CL8.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/B0CL8.png" alt="Repair of double-stranded break via HR" /></a></p>
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https://biology.stackexchange.com/questions/96975/when-does-the-cas9-nuclease-stop
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Question: <p>In lectures, we have discussed Michaelis Menten enzyme kinetics, but from lectures it was clear that this was not the only type of kinetics.</p>
<p>After looking into this, I have found enzymes that give a sigmoid curve relating initial rate of reaction to substrate concentration.</p>
<p>So so far I have:</p>
<ol>
<li>Michaelis Menten Kinetics</li>
</ol>
<p>For which I think the only conditions are that the enzyme reaction follows</p>
<p><a href="https://i.sstatic.net/GpbA4.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/GpbA4.jpg" alt="enter image description here"></a></p>
<p>and the enzyme does not bind more than one substrate molecule (isn't allosterically binding)</p>
<ol start="2">
<li>'sigmoidal' kinetics</li>
</ol>
<p>Where the enzyme is an allosteric enzyme and binding of more substrate to the enzyme increases the enzyme's affinity for the substrate.</p>
<p><a href="https://i.sstatic.net/gCUqf.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/gCUqf.png" alt="enter image description here"></a></p>
<p>Are these the only two main types of enzyme kinetics?</p>
Answer: <p>The issue with Michaelis menten curves, is that they presume only one pathway the enzyme can act by. Therefore if an enzyme has multiple pathways the presumptions fail. An example of this is monoamine oxidase, (Ramsay, R. R., Olivieri, A. & Holt, A. An improved approach to steady-state analysis of monoamine oxidases. J. Neural Transm. 118, 1003–1019 (2011).) This paper has the enzyme specific kinetics for monoamine oxidase - the development of the models is incredibly complicated but if you look at the equations you can see how there are multiple pathways. </p>
<p>They also presume only one substrate, so multi-susbtrate reactions need to have the kinetics modified as such. For that the mechanism are: Ping-pong, ternary- ordered and random, all of which impact on the kinetics.If the concentration of the intermediate complex is presumed not to change with time, then another model is the Briggs-Haldane model, known as quasi-steady state kinetics. </p>
<p>Then there are the kinetic models for inhibition. Of which the michaelis menten, where the kinetics vary according to how the inhibitors binds. But as is seen with the above MAO paper, can vary depending on the pathways and binding affinities. If an enzyme is irreversible then the kinetics also differ (Mcdonald, A. G. & Dublin, T. C. Enzymes : Irreversible Inhibition. 1–17 (2012). doi:10.1002/9780470015902.a0000601.pub2). </p>
<p>It is also worth noting, it is better to use non-linear regression to analyze kinetics as linearizing the data can lead to calculation errors (despite admittedly being the easier and clearer option). </p>
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https://biology.stackexchange.com/questions/54496/enzyme-kinetics-types
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Question: <p>I can't understand how to study enzyme kinetics. Say I have a lipase and want to study the kinetics of this lipase using a fluorogenic substrate, how would I do this? From what I understand I would use a 96 or so well plate and in each increase the amount of substrate or increase the amount of enzyme and use a fluorescence microscope or a spectrophotometer? </p>
Answer: <p>I'm going to try to lay out some basic definitions here in as plain language as I can find. </p>
<p>Its difficult to study enzymes when they are outside the cell, where they may behave quite differently in different contexts. We categorize a given enzyme in its class by <em>kcat</em>, <em>Km</em> and by mechanism (the sort of reaction they catalyze. </p>
<p><em>kcat</em> is sort of a maximum velocity of the enzyme - when there is a lot of substrate around - what is the rate of catalysis. Ideally there will be zero product present. </p>
<p><em>Km</em> is sort of the inverse affinity of the enzyme for its substrate, but at half the maximum velocity of the reaction. </p>
<p>The mechanism, which has a couple of definition basically asks how many substrates are bound and in what order, which products are released and in what order, and any intermediates in the reaction which might appear, and in what order. </p>
<blockquote>
<p>e.g.: A -> A* -> B* -> B
A + B -> C + D </p>
</blockquote>
<p>I say 'sort of' because you might never see an enzyme operate at maximum rate in living cells. Substrates are usually rate controlled there - they only have enough of any given compound as they need. </p>
<p>The context that all of these numbers and designations are used is often taxonomical - that is to say you can categorize and sort, and describe what the enzyme does. In practice large differences in the numbers can describe how useful one enzyme is over another, but it doesn't necessarily tell you how an enzyme will definitely behave <em>in vivo</em> or entirely how it will work in an industrial application. Its just a start.</p>
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https://biology.stackexchange.com/questions/17053/enzyme-kinetics
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Question: <p>I measured some enzyme kinetics in a practical course using a substrate-based FRET assay. Unfortunately some of my plots show weird effects. There was always a decrease in signal after 35 minutes. But the curve always regained.
During the whole measurement the plate was placed in the reader, and was heated to 37°C.</p>
<p><a href="https://i.sstatic.net/NImxs.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/NImxs.png" alt=" x axis - time, y axis - fluorescence " /></a></p>
<p>My question is: Does someone know how/why this effect occurs?</p>
<p>Thanks for your help!</p>
Answer: <p>Worth considering whether it is an effect of the instrument or the system. What would happen if you preincubated your plate for 10 minutes? Would you have the "dip" after 25 minutes or again 35 minutes?
I know our plate reader will want to calibrate its detector at some intervals, perhaps that coincidences with 35 minutes for your combination of variables?</p>
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https://biology.stackexchange.com/questions/105084/why-such-strange-enzyme-kinetics
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Question: <p>What is the difference between $S_{0.5}$ values and $K_m$ values in enzyme kinetics?</p>
Answer: <p>This expands my comment on the question to an answer. </p>
<p>If an enzyme exhibits Michaelis-Menten kinetics, then it is valid to define a K<sub>M</sub> and this equates to the substrate concentration when reaction velocity is 0.5 * V<sub>max</sub>.</p>
<p>However, many enzymes do not exhibit Michaelis-Menten kinetics. One example is when the enzyme shows a co-operative response to substrate concentration. In these circumstances the substrate concentration when reaction velocity is 0.5 * V<sub>max</sub> is still a useful parameter, but there is no K<sub>M</sub>.</p>
<p>See <a href="http://diabetes.diabetesjournals.org/content/47/3/307.full.pdf" rel="nofollow">this paper</a> for a discussion of the kinetic properties of the glucokinase of pancreatic β cells, which acts as the glucose sensor. This enzyme shows positive co-operativity with respect to its substrate glucose, and the authors develop a kinetic analysis in terms of various parameters. These include an S<sub>0.5</sub> value for glucose, but a K<sub>M</sub> value for ATP (presumably because the kinetics with respect to ATP are simple Michaelis-Menten).</p>
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https://biology.stackexchange.com/questions/5004/s-0-5-vs-k-m-values-in-enzyme-kinetics
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Question: <p>I have had a few biochemistry courses, but I still feel confused and a bit scared each time they try to explain and apply enzyme kinetics or even chemometrics in different situation during class. On our last lecture we had kinetics regarding:</p>
<ul>
<li><p>Pingpong reactions (with two substrates A, B):</p>
<p><span class="math-container">$V_0 = \dfrac{K_{cat}[E]* [A][B]}{K_m^B [A] * [B] * [A][B]} $</span></p>
</li>
<li><p>General reactions (with two substrates A, B):</p>
<p><span class="math-container">$V_0 = \dfrac{K_{cat}[E]* [A][B]}{K_m^B [A] * K_s^A * [B] * [A][B]} $</span></p>
</li>
</ul>
<p>And we also had something about analyzing the "principle component" in multivariate data, from enzyme kinetic measurements (as effect of e.g. pH of temperature).</p>
<p>I really don't understand this, or how I would apply this - or analyze my data if I have two substrates.</p>
<p><strong>Question</strong>: In general, is there a good web site which goes beyond the normal Michaelis menten analysis, or a very good book which explains both the basic and more complex scenarios regarding analysis/application of enzyme kinetics for biochemists?</p>
Answer: <p>I always used the book <a href="http://rads.stackoverflow.com/amzn/click/0716716143" rel="nofollow">"Enzyme Structure and Mechanism"</a> by Alan Fersht. (<a href="http://rads.stackoverflow.com/amzn/click/0716732688" rel="nofollow">Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding</a> is the latest version, published in 1998.) Both in some courses I did and when working on (complex) enzymatic mechanisms. It's a classic (so a bit old maybe), but it covers all the basics and includes most of the common complex mechanisms like ping-pong. I don't know if it will teach you how to analyze multivariate data, so maybe you need something else for that. </p>
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https://biology.stackexchange.com/questions/45450/enzyme-kinetics-recommended-literature-to-grasp-the-concepts-better
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Question: <p>I´m here looking for empirical experience over this revelation, which surely is not so amazing but better call biology experts.</p>
<p>I recently founded the <a href="https://en.wikipedia.org/wiki/Lomax_distribution" rel="nofollow noreferrer">Lomax Probability Distribution</a> and noted that the cumulative distribution function <span class="math-container">$L(x)$</span> has a very similar form related to the Michaelis-Menten Kinetics rate equation <span class="math-container">$v(S)$</span>. This since:</p>
<p><span class="math-container">$$L(x) = P(X \leq x) = 1 - \Big[1+\dfrac{x}{\lambda}\Big] ^{-\alpha}$$</span>
and
<span class="math-container">$$v(S)=\dfrac{V_{max}S}{K_m+S}$$</span></p>
<p>Are, in fact, the same equation with <span class="math-container">$\alpha = 1$</span> and <span class="math-container">$\lambda = K_m$</span> since <span class="math-container">$L(x=S) = \dfrac{v(S)}{V_{max}}$</span>.</p>
<p>Can this equation be used to model <em>enzyme kinetic rates</em>?
Does you have applied it?</p>
<p>P.D. I´ve never heard of an application of Pareto-related distributions in enzyme kinetics, so maybe it is a good start for modeling biochemical processes. Specifically, since <span class="math-container">$\lambda = K_m$</span>, we could use experimental data to model this interaction with more precision (maybe) since a model that allows uncertainty is unlike lambert/regression solutions that are only deterministic.</p>
Answer:
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https://biology.stackexchange.com/questions/115740/does-the-lomax-model-describes-enzyme-kinetics
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Question: <p>I'm interested in any way to do time-resolved study of enzyme kinetics. I am studying some physical variables that may affect kinetics, but I want to study how quickly they take effect, and how long the effect lasts. The time scale of interest is milliseconds or less, so the typical spectrophotometric methods (which usually look at absorption change over fairly long times on the order of minutes) won't work.</p>
<p>Luciferase activity can be monitored by tracking the light emitted, and this has potentially very high time resolution as the time between reaction and light emission is on the order of microseconds. However luciferase is a bit of an odd model, as it is not part of normal metabolism or signalling in most organisms. </p>
<p>Is there a way to track enzyme kinetics of any other enzymes with a similarly fast time resolution?</p>
<p><strong>EDIT</strong> Just discovered one name for what I'm looking for: "transient kinetics". </p>
Answer: <p>Some ATPases can work with <a href="https://www.thermofisher.com/order/catalog/product/M12417" rel="nofollow">MANT-ATP</a> or <a href="http://www.jenabioscience.com/cms/en/1/catalog/1932_adenosine_nucleotides.html?gclid=CjwKEAjwka67BRCk6a7_h_7Pui8SJABcMkWRNTAfZqfQox38Qp6QwL3hyUEDi3yaV9Y4fcOI-AXYiRoCwtfw_wcB" rel="nofollow">similar</a> fluorescent ATP analogs that change their fluorescence properties upon protein binding as well as hydrolysis of their phosphate group. This has been used frequently (see <a href="http://www.pnas.org/content/95/17/9831.short" rel="nofollow">here</a> or <a href="http://www.jbc.org/content/272/2/724.short" rel="nofollow">here</a>) to study enzyme kinetics on fast timescales.</p>
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https://biology.stackexchange.com/questions/48284/ways-to-monitor-enzyme-kinetics-with-very-fast-time-resolution
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Question: <p>I am stumped by two questions:</p>
<ol>
<li>Why do we take only the initial 10%(or may be 9.99999....%) of S conversion as the rate of the enzyme reaction. why not more than 10%?</li>
<li>Why doesn't the velocity keep on increasing linearly until the Vmax is reached (as all the S molecules get exhausted)</li>
</ol>
<p>Research and attempts to answer:</p>
<p>Why v<sub>0</sub>'s 10%?</p>
<ol>
<li><p>Steady state kinetics apply when the [ES] is constant, on reaching 10% [P] (for a uni uni reaction) the backward reaction increases, increasing the [ES]?</p></li>
<li><p>On reaching 10% conversion the rate decreases, so we measure the optimum activity.</p></li>
</ol>
<p>Why doesn't the velocity increase linearly until all the molecules are used up?</p>
<ol>
<li><p><s>Since an enzyme's turnover number (kcat) is constant...</s></p></li>
<li><p>...</p></li>
</ol>
<p>Disclaimer :</p>
<ol>
<li>'have put two Qs together.</li>
<li>Didn't find relevant Q on BioSE.</li>
</ol>
Answer: <p>The answer to the first part of your question is that we don't take the initial 10% of a progress curve (velocity vs <em>time</em>) as a measure of activity, but we measure the <em>initial</em> rate of the reaction. We do this by drawing a tangent at the origin. </p>
<p>It is merely a 'rule of thumb' that progress curves are practically linear provided that not more than 10% of substrate has been used up. If there is significant slowing down before 10% is used up - and there may be if the substrate concentration is way below K<sub>m</sub> value - then it is <em>not</em> valid to draw a line through the points: we must draw the tangent to the curve. That is, it is <em>not</em> acceptable to take the average rate during the first 10% of the progress curve. </p>
<p>For this reason it is desirable to use as sensitive a method as possible when measuring an enzymic rate, and to <em>never</em> rely on a single time point (as is common in radioactive assays) without sufficient controls to justify that it it is the initial rate, and not the average rate (or something else) that is being measured. </p>
<p>The reason we measure initial rates is that is makes things simpler on two fronts. </p>
<p>Firstly, the decrease in rate with time of an enzymic reaction may be due to many factors: product may be inhibiting the reaction, the reverse reaction may become important, the enzyme or substrate may be unstable. It is only during the initial rate period that conditions are accurately known, and such effects may be legitimately ignored. It was <a href="https://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics" rel="noreferrer">Michaelis and Menten</a> that first realized the importance of measuring initial rates, and of the great simplification principle that ensued, in enzyme kinetics. (see Cornish-Bowden, 2004). </p>
<p>Secondly, the rate laws themselves are greatly simplified. Provided that e<sub>o</sub> << S<sub>o</sub> (the initial enzyme concentration is very much less than the initial substrate concentration), we may take the S<sub>o</sub> as being equal to the substrate concentration and 'plug in' this value into our rate law (such as the Michaelis-Menten equation), and ignore the effect of time on the value of S. In addtion, we can set all product terms to zero. This can greatly simplify things. </p>
<p>For example, the rate law for a reversible single-substrate mechanism (see <a href="https://biology.stackexchange.com/a/43832/1136">here</a>) is the following: </p>
<p>$$ v = {
{{{V_{max}^f}\over{K_{m}^s}}\ S\ -{{V_{max}^r}\over{K_{m}^p}}\ P }\over{1 + {{S}\over{K_{m}^s}} + {{P}\over{K_{m}^p}}}}\ \ \ \ \ (1)$$ </p>
<p>This one is not as complicated as it looks: we have just defined a K<sub>m</sub> and V<sub>max</sub> for the forward and reverse directions. But let's set product to zero:</p>
<p>$$ v_i = {
{{{V_{max}^f}\over{K_{m}^s}}\ S_o\ }\over{1 + {{S_o}\over{K_{m}^s}} }}\ \ \ \ \ = \ \ \ {{V_{max}^f S_o}\over{{K_{m}^s} + S_o}}\ \ \ \ (2)$$ </p>
<p>We now obtain the familiar Michaelis-Menten Equation (where $v_i$ is the <em>intial</em> velocity). </p>
<p>The second part of your question is more fundamental. I'll take it to mean the following. Why does an enzymic reaction not follow second-order kinetics at all substrate concentrations? Why doesn't doubling the substrate always double the rate (as is often the case in chemical kinetics)? <a href="https://en.wikipedia.org/wiki/Adrian_John_Brown" rel="noreferrer">A. J. Brown</a> in 1902 suggested that the reason for this is the <em>formation of an enzyme-substrate complex</em> and that at sufficiently high substrate concentration all the enzyme would exist in such a complex and the enzyme would become 'saturated'. The formation of an enzyme-substrate complex, of course, is now a cornerstone of enzyme kinetics. One of the early key pieces of evidence for an enzyme-substrate complex was the observation that an enzyme is much more heat-stable in the presence of its substrate than in its absence. </p>
<p>Finally, it is probably worth pointing out that some enzyme operate way below K<sub>m</sub> values and at 'physiological' concentration of substrates <em>do</em> obey (to all intents and purposes) second-order kinetics. Catalase, for example, has a K<sub>m</sub> for hydrogen peroxide of about 1 Molar (<a href="http://www.sciencedirect.com/science/article/pii/0003986155902915?via%3Dihub" rel="noreferrer">Ogura</a>, 1955), and one assumes that physiological concentrations never reach this level. (We need to be a little careful about catalase, however: it is one of the few enzymes that is inactivated by substrate). </p>
<p>A great reference on enzyme assays is the following:</p>
<ul>
<li><a href="https://books.google.ie/books?id=W-KAirjgqdQC&pg=PA1&lpg=PA1&dq=Enzyme+assays+and+kinetic+studies&source=bl&ots=ucAs8WP00u&sig=OgVWUgZSLjDx0se0pCxwB05xSCY&hl=ga&sa=X&ved=0ahUKEwi-ncKenJLSAhUYOsAKHYxQBDQQ6AEIITAC#v=onepage&q=Enzyme%20assays%20and%20kinetic%20studies&f=false" rel="noreferrer">Principles of enzyme assay and kinetic studies</a> by K. F. Tipton in <a href="https://rads.stackoverflow.com/amzn/click/0199638209" rel="noreferrer">Enzyme Assays: A practical approach</a></li>
</ul>
<p>For an introduction to enzyme kinetics, and the early history of enzymology, I like the following:</p>
<ul>
<li>Cornish-Bowden (2004) Fundamentals of Enzyme Kinetics 3<sup>rd</sup> Edn. Portland Press, London.</li>
</ul>
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https://biology.stackexchange.com/questions/65525/enzyme-kinetics-at-the-chemical-level
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Question: <p>I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation.</p>
<p>I searched through some database </p>
<p>yeast metabolome database <a href="http://www.ymdb.ca/" rel="nofollow">http://www.ymdb.ca/</a>
brenda and other enzyme databases for enzmye conc
and also did some literature search</p>
<p>but couldn't find much of data</p>
<p>where possibly i can get these data ??
is there any other way to do simulation without data.</p>
Answer: <p>You should take a look at SGD (the <a href="http://www.yeastgenome.org/" rel="nofollow">Saccharomyces Genome Database</a>), and in particular <a href="http://pathway.yeastgenome.org/overviewsWeb/celOv.shtml" rel="nofollow">YeastCyc</a>. Some protein information pages at SGD give estimates of molecules per cell taken from <a href="http://www.nature.com/nature/journal/v425/n6959/pdf/nature02046.pdf" rel="nofollow">this Nature paper</a>.</p>
<p><em><strong>Added later in response to some comments:</em></strong></p>
<p>The question asks about levels of metabolites and of enzymes, not of transcripts. Microarray data can be, at best, only a guide to levels of proteins. Estimating the levels of metabolites from microarray data is a complete non-starter since there are entire layers of regulation that will be ignored. Just to give one example of a pitfall in this approach: you could have high levels of transcript from which you could you could infer high levels of enzyme, but that enzyme could be inactivated by a post-translational modification.</p>
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https://biology.stackexchange.com/questions/8864/modeling-yeast-biochemical-pathway-using-enzyme-kinetics
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Question: <p>What is the typical effect of enzyme immobilization on the kinetic parameters of an enzyme's activity? </p>
<p>Can one assume that they'd stay approximately the same or is there a gross change? Any way to estimate the effect? </p>
<p>The native parameters are as follows:</p>
<pre><code>kcat 0.5 1/min
Km 0.6 microM
[E0] 5 micro M
[S] 60 micro M
</code></pre>
<p>Could I expect to retain them after immobilization? Or are these too high for an immobilized enzyme?</p>
<p>If it matters, it is a 500 residue enzyme with a MW of approx. 65,000 Da</p>
Answer: <p>The main factor influencing the kinetics of immobilized enzymes is thought to be the rate of diffusion of substrate and product towards and away from the enzyme, respectively. </p>
<p>This has been discussed on <a href="https://www.researchgate.net/post/What_happens_to_the_enzyme_kinetics_when_in_solution_and_when_immobilized" rel="nofollow">ResearchGate</a> and an article in <a href="https://www.researchgate.net/publication/235907631" rel="nofollow">Process Biochemistry</a> from one of those in the discussion quotes figures for effects on immobilized laccase: approx. 100x increase in Km and 2–5x reduction in Vmax (as noted in the poster’s comment).</p>
<p>There are several theoretical treatments of the question:</p>
<ul>
<li><a href="http://www1.lsbu.ac.uk/water/enztech/summary3.html" rel="nofollow">http://www1.lsbu.ac.uk/water/enztech/summary3.html</a></li>
<li><a href="http://link.springer.com/article/10.1007%2FBF02460071#page-1" rel="nofollow">http://link.springer.com/article/10.1007%2FBF02460071#page-1</a></li>
<li><a href="http://www.amazon.co.uk/gp/search?index=books&linkCode=qs&keywords=9780849369872" rel="nofollow">http://www.amazon.co.uk/gp/search?index=books&linkCode=qs&keywords=9780849369872</a></li>
</ul>
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https://biology.stackexchange.com/questions/44465/enzyme-kinetics-effect-of-immobilization-on-kinetic-parameters
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Question: <p><img src="https://i.sstatic.net/0G3bL.png" alt="Enzyme action graph"></p>
<p>At the very peak, the energy is in a state of activation energy. Here, is the substrate just attaching to the enzyme, or is is substrate already breaking?</p>
Answer: <p>Enzymes are <a href="https://en.wikipedia.org/wiki/Catalysis" rel="nofollow noreferrer">catalysts</a> that lower a reactions activation energy (Ea), and thus increases the rate of the reaction. The diagram above is a Gibbs-Free energy landscape/pathway, where <em><strong>the top of the diagram is the transition state</strong></em> between the substrate and the product. Enzymes speed up chemical reactions by stabilising the transition state, and in effect, lowers the activation energy (Ea) required to transform the substrate into the product. The active site of enzymes are thus specifically 'designed' to be as energetically favourable as possible for the transition state.</p>
<p><a href="https://i.sstatic.net/WjiQJ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/WjiQJ.png" alt="enter image description here" /></a></p>
<p>To understand enzyme kinetics it could also be a good idea to look at (understand on a general level) the <a href="https://en.wikipedia.org/wiki/Arrhenius_equation" rel="nofollow noreferrer">Arrhenius equation</a> and <a href="https://en.wikipedia.org/wiki/Reaction_rate_constant" rel="nofollow noreferrer">reaction rate constants</a> (<em>k</em>), to more completely understand what we mean by activation energy and reactions rate.</p>
<p>This whole topic is taught in basic biochemistry, and thus well described by many educational websites, all biochemistry text books, and even found in educational youtube lectures (which is perfect for a basic understanding before you read more heavy theory). My earlier biology SE question <a href="https://biology.stackexchange.com/questions/45450/enzyme-kinetics-recommended-literature-to-grasp-the-concepts-better">Enzyme kinetics: recommended literature to grasp the concepts better</a> also has some good book recommendations.</p>
<p><strong>Following are also some webpages you can look at.</strong></p>
<p><strong><a href="https://www.khanacademy.org/science/ap-biology/cellular-energetics/enzyme-structure-and-catalysis/a/enzymes-and-the-active-site" rel="nofollow noreferrer">Khan Academy</a>:</strong></p>
<blockquote>
<p>With the catalyst, the activation energy is lower than without. ...
That's because enzymes don't affect the free energy of the reactants
or products. Instead, enzymes lower the energy of the transition
state, an unstable state that products must pass through in order to
become reactant (...)</p>
</blockquote>
<p><strong>Chemistry LibreTexts:</strong> General transition state stabilisation is also a nice keyword that would give you a lot of information, e.g. from <a href="https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Book%3A_Biochemistry_Online_(Jakubowski)/09%3A_Catalysis/9.1%3A_A._Methods_of_Catalysis/A5.__Transition_State_Stabilization" rel="nofollow noreferrer">Chemistry LibreTexts</a>:</p>
<blockquote>
<p>Linus Pauling postulated long ago that the only thing that a catalyst
must do is bind the transition state more tightly than the substrate.
That this must be the case can be seen from the diagram (...)</p>
</blockquote>
<p><strong>Wikipedia</strong>: It could also be a good idea to generally read about <a href="https://en.wikipedia.org/wiki/Catalysis" rel="nofollow noreferrer">catalysts</a>, here from the wikipedia page where they use the classical example chymotrypsin and its oxyanion hole (active site that binds the substrate) that contains the Asp-His-Ser catalytic triad:</p>
<p><a href="https://i.sstatic.net/8z2h5.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/8z2h5.jpg" alt="enter image description here" /></a></p>
<blockquote>
<p>In the presence of chymotrypsin, (...), a nucleophile is used in the
form of the catalytic triad - Asp 102, His 57, Ser 195 side chains.
Moreover, the oxyanion hole, which consists of the backbone -NH-
groups of Gly 193 and Ser 195 of the enzyme, have the N-H groups
positioned in such a way that they will donate strong hydrogen bonds
to the substrate's C=O oxygen, given that the carbon atom is
tetrahedral as found in the transition state. This strains the bonds
of the trigonal planar C=O of the original substrate, helping the
reaction to proceed to the transition state. The hydrogen bonds also
stabilize the formal negative charge on the oxygen atoms. In this way,
the activation energy of the reaction is lowered and the rate of
reaction thus increases.</p>
</blockquote>
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https://biology.stackexchange.com/questions/58944/enzyme-kinetics-what-happens-at-the-peak-of-the-gibbs-energy-graph
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Question: <p><a href="https://i.sstatic.net/0O1vC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/0O1vC.png" alt="Enzyme reacts with substrate to produce a complex" /></a></p>
<p>Enzyme reacts with substrate to produce a complex. And finally the products in a catalysis reaction.</p>
Answer: <p>To answer this question, we need to delve into the world of
<a href="https://en.wikipedia.org/wiki/Dimensional_analysis" rel="nofollow noreferrer">dimensional analysis</a>
and to consider when and how rate constants may be compared.</p>
<p>The OP considers the following simple kinetic mechanism, (which, after defining kinetic constants such as
<span class="math-container">$K_m$</span>
and
<span class="math-container">$k_{cat}$</span>
in terms of rate constants,
gives rise to the
<a href="https://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics" rel="nofollow noreferrer">Michaelis-Menten</a>
equation):</p>
<p><span class="math-container">$$
E + S \xrightleftharpoons[{k_{-1}}]{k_1}
ES
\xrightarrow{k_p}
E + P
\tag{1}
$$</span></p>
<h4>First and Second Order Rate Constants</h4>
<p>As written, <span class="math-container">$k_1$</span> is a <em>second-order</em> rate constant and <span class="math-container">$k_p$</span> is a <em>first-order</em> rate constant.</p>
<p>Therefore <span class="math-container">$k_1$</span> will have units of <span class="math-container">$concentration^{-1}\text{. }time^{-1}$</span>, and <span class="math-container">$k_p$</span> will have units of <span class="math-container">$time^{-1}$</span> (as will <span class="math-container">$k_{-1}$</span>).</p>
<p>For example, <span class="math-container">$k_1$</span> may be spoken of as having a value of
<span class="math-container">$10^9 \text{ M}^{-1}\text{ s}^{-1}$</span> (
<a href="https://bionumbers.hms.harvard.edu/bionumber.aspx?id=103916&ver=2" rel="nofollow noreferrer">here</a>
and
<a href="https://en.wikipedia.org/wiki/Diffusion-limited_enzyme" rel="nofollow noreferrer">here</a>),
or as having a value of
<span class="math-container">$10^9 \text{ L mol}^{-1}\text{s}^{-1}$</span>, and <span class="math-container">$k_p$</span> may be spoken of as having a value of <span class="math-container">$10^6 \text{ s}^{-1}$</span>.</p>
<p>By the laws of
<a href="https://en.wikipedia.org/wiki/Dimensional_analysis" rel="nofollow noreferrer">dimensional analysis</a>,
it is meaningless to compare quantities of different units.
It is absurd, for example, it ask if pH 7 is greater than (or less than) <span class="math-container">$10^\text{o}\text{C}$</span>,
or if 2 mol is greater than (or less than) 5 seconds.</p>
<p>So too with rate constants: it is meaningless to ask if a second-order rate constant is greater than or less than (or is equal to) a first-order rate constant.</p>
<p>The application of dimensional analysis to situations often encountered in enzyme kinetics is well described in
<a href="https://www.wiley.com/en-us/Fundamentals+of+Enzyme+Kinetics%2C+4th+Edition-p-9783527330744" rel="nofollow noreferrer">Fundamentals of Enzyme Kinetics</a>
(Cornish-Bowden, 2013, 4th Ed, Section 1.3) and the relevant section seems to be freely accessible via
<a href="https://books.google.ie/books?id=_3fqaYnrdosC&printsec=frontcover&dq=Fundamentals+of+Enzyme+Kinetics+Athel+Cornish-Bowden&hl=en&sa=X&ved=2ahUKEwiL26iY1OT1AhWYiVwKHSHeDK4Q6AF6BAgJEAI#v=onepage&q=Fundamentals%20of%20Enzyme%20Kinetics%20Athel%20Cornish-Bowden&f=false" rel="nofollow noreferrer">Google Books</a>.</p>
<p>For example, we can multiply and divide quantities of different dimensions, but we
cannot add or subtract them.</p>
<p>Thus, inspection of the numerator of the following equation shows that it is CLEARLY WRONG:</p>
<p><span class="math-container">$$
K_m
=
\frac{k_p + k_{1}}{k_{-1}}
\tag{2}
$$</span></p>
<p>The CORRECT expression for <span class="math-container">$K_m$</span> for the mechanism shown in Eqn (1) is
<em>the sum of the two first-order rate constants, divided by the second-order rate constant</em>:</p>
<p><span class="math-container">$$
K_m
=
\frac{k_p + k_{-1}}{k_{1}}
\tag{3}
$$</span></p>
<p>We can also infer from Eqn (3) that <span class="math-container">${K_m}$</span> has dimensions of molarity,
even if we have no idea as to what the symbol <span class="math-container">${K_m}$</span> refers.</p>
<p><span class="math-container">$$
\frac{\text{s}^{-1}}{\text{M}^{-1}\text{ s}^{-1}} = \text{M}
\tag{4}
$$</span></p>
<p>Application of the rules of dimensional analysis is often useful in 'scanning' the
equations encountered in enzyme kinetics.</p>
<p><span class="math-container">$$
Y=
\frac
{1}
{1 + \frac{[A]}{K_m^A} + \frac{[B]}{K_m^B} + X}
\tag{5}
$$</span></p>
<p>For example, without any prior knowledge as to what <span class="math-container">$X$</span>, <span class="math-container">$Y$</span>, <span class="math-container">$K_m^A$</span> and <span class="math-container">$K_m^B$</span> refer to,
inspection of Eqn (5) allows the following conclusions to be drawn:</p>
<ol>
<li><span class="math-container">$X$</span> is dimensionless</li>
<li>The quantities <span class="math-container">$\frac{[A]}{K_m^A}$</span> and <span class="math-container">$\frac{[B]}{K_m^B}$</span> are dimensionless</li>
<li><span class="math-container">$Y$</span> is dimensionless</li>
</ol>
<h4><em>Pseudo</em> First-Order Rate Constants</h4>
<p>Although <span class="math-container">$k_1$</span> and <span class="math-container">$k_2$</span> have different dimensions,
<span class="math-container">$k_1 \text{[A]}$</span>
has dimensions of a first-order rate constant <span class="math-container">$(time^{-1})$</span> and <em>can</em> be directly compared
with <span class="math-container">$k_p$</span> and <span class="math-container">$k_{-1}$</span>.</p>
<p>The quantity
<span class="math-container">$k_1 \text{[A]}$</span>
is often referred to as a <em>pseudo</em> first-order rate constant. (Personally,
I don't like the term)</p>
<p>Thus, to argue that <span class="math-container">$k_1 \text{[A]}$</span> >> <span class="math-container">$k_p$</span> is perfectly OK from a dimensional
analysis perspective.</p>
<p>Perhaps more importantly, a <em>pseudo</em> first-order rate constant may be added to or
subtracted from a first-order rate constant.</p>
<p>Thus, an equation such as the following presents no problems (again from a dimensionless
analysis point of view):</p>
<p><span class="math-container">$$
Y=
\frac{k_1}
{{k_1} [A] + k_{-1} + {k_p}}
\tag{6}
$$</span></p>
<h4>Common Confusion Concerning Rate Constants: An Example</h4>
<p>It is surprising how often the laws of dimensional analysis are misapplied in
the world of enzyme kinetics.</p>
<p>For example, in a paper published in <em>J. Chem. Educ.</em> in 2011, it is stated "For the classic Michaelis-Menten enzyme,
<span class="math-container">$k{_1} > k_{-1} >> k{_2}$</span>" where "... <span class="math-container">$k_1$</span> is the forward rate constant for the first step, the
fast binding of substrate <span class="math-container">$(S)$</span> to enzyme <span class="math-container">$(E)$</span> to make the non-
covalent enzyme-substrate complex <span class="math-container">$(ES)$</span>, <span class="math-container">$k_{-1}$</span> is the reverse
rate constant for the dissociation of <span class="math-container">$ES$</span> back into <span class="math-container">$E + S$</span>; and <span class="math-container">$k_2$</span>
is the rate constant for the subsequent slow catalytic step converting <span class="math-container">$S$</span> to product".</p>
<p>Let's state it bluntly: <span class="math-container">$k_1$</span> <em>cannot</em> be greater than <span class="math-container">$k_{-1}$</span>, as <span class="math-container">$k_1$</span> is a
second-order rate constant and <span class="math-container">$k_{-1}$</span> is a first-order rate constant.</p>
<p>Furthermore (and very surprisingly), <em>J. Chem. Educ.</em> has not corrected the error.</p>
<p>(In my opinion, the paper is otherwise good).</p>
<h4>Reference</h4>
<p>Cornish-Bowden, Athel (2013)
<a href="https://www.wiley.com/en-us/Fundamentals+of+Enzyme+Kinetics%2C+4th+Edition-p-9783527330744" rel="nofollow noreferrer">Fundamentals of Enzyme Kinetics</a>
4th Ed, Wiley-Blackwell
[ <a href="https://books.google.ie/books?id=_3fqaYnrdosC&printsec=frontcover&dq=Fundamentals+of+Enzyme+Kinetics+Athel+Cornish-Bowden&hl=en&sa=X&ved=2ahUKEwiL26iY1OT1AhWYiVwKHSHeDK4Q6AF6BAgJEAI#v=onepage&q=Fundamentals%20of%20Enzyme%20Kinetics%20Athel%20Cornish-Bowden&f=false" rel="nofollow noreferrer">google books</a> ]</p>
|
https://biology.stackexchange.com/questions/107110/in-enzyme-kinetics-can-the-kp-be-greater-than-k1-in-any-way
|
Question: <p>Wikipedia has this image titled "Pressure Chamber to measure Enzyme Activity under High Pressure"</p>
<p>Made me wonder why do we need to measure Enzyme Activity under high pressure? </p>
<p>Are there enzymes in nature that must work under variable pressure conditions? My impression from my knowledge of conventional chemical kinetics was that in the liquid phase the effect of pressure on chemical kinetics was typically very low simply because of incompressiblity of liquids. Unless Pressures were very very high. Is this not so with enzyme activity? Or are there enzymes that must work under very high pressures?</p>
<p><a href="https://en.wikipedia.org/wiki/Enzyme_assay" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Enzyme_assay</a></p>
<p><a href="https://i.sstatic.net/q9fnY.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/q9fnY.png" alt="enter image description here"></a></p>
Answer: <p>At least one group who have published on the effect of pressure on enzyme activity (Cho and Northrop) are <strong>not</strong> interested in it from a practical point of view, i.e. they are not subjecting enzymic reactions to pressures that they think they encounter naturally. Instead they are using the effects of pressure to test the kinetic and thermodynamic predictions of different models of enzyme catalysis. In particular they believe that pressure effects provide a means of testing the idea, first suggested by Linus Pauling, that an enzyme has a greater affinity for the transition state, rather than for the substrate.</p>
<p>This is explained in a paper on yeast alcohol dehydrogenase, but only the <a href="http://www.ncbi.nlm.nih.gov/pubmed/10360944" rel="nofollow">abstract</a> is freely available. They claim to have evidence against Pauling’s idea, but I am not sure the extent to which this is generally accepted.</p>
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https://biology.stackexchange.com/questions/48673/enzyme-activity-under-high-pressure
|
Question: <p>I mean, I want to practice with challenging exercises and I want to know the theory behind them. So, I started reading:</p>
<ul>
<li>Organic Chemistry: Yurkanis, P.</li>
<li>Enzyme kinetics: Bisswanger, H.</li>
<li>Biotechnology procedures and experiments Handbook: Harisha, S.
But just the first one has problems and not about enzymes at all.</li>
</ul>
<p>So, I looking for a good (theoretic) and complete (challenging with exercises) book about enzymes.</p>
Answer:
|
https://biology.stackexchange.com/questions/87996/looking-for-a-good-and-complete-enzimology-exercises-book
|
Question: <p>I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity <em>in vitro</em>, I would argue that the substrate and enzyme concentrations resemble those <em>in vivo</em>. As a result, conclusions made by such assays do not apply 100% to the naturally occurring reactions. Are there any examples in literature that address this issue? </p>
<p>Along those lines, what is the concentration of fatty acids/nucleic acids in the cell?</p>
Answer: <p>The macromolecule concentration within E Coli is estimated to be around 0.3-0.4 g/ml [1]</p>
<p>The concentrations of your substrate in respect to your enzyme are generally fairly analogous to <em>in vitro</em> studies compared to <em>in vivo</em> studies. However, this is heavily based on the assumption that the diffusion constants for both molecules stay consistent. In many cases that is true and errors can be corrected for using PEG to imitate the crowding effect. And yes, people have begun to look at the question [2]</p>
<p>However, for larger macromolecules like DNA and chromosomes that do see effects from subdiffusive transport, the molecules don't obey diffusive random-wal behavior [3]. The classic model system is the lac repressor which exhibits non-diffusive kinetics due to its interactions with DNA.</p>
<ol>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/1748995">http://www.ncbi.nlm.nih.gov/pubmed/1748995</a></li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21237136">http://www.ncbi.nlm.nih.gov/pubmed/21237136</a></li>
<li><a href="http://prl.aps.org/abstract/PRL/v104/i23/e238102">http://prl.aps.org/abstract/PRL/v104/i23/e238102</a></li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/7317363">http://www.ncbi.nlm.nih.gov/pubmed/7317363</a></li>
</ol>
|
https://biology.stackexchange.com/questions/1134/how-crowded-is-the-bacterial-cell
|
Question: <p>I'm trying to understand enzyme kinetics, the formula for K<sub>m</sub> and K<sub>cat</sub> make sense to me. </p>
<blockquote>
<p><strong>K<sub>m</sub></strong> , the substrate concentration at which the reaction rate is half of V<sub>max</sub></p>
<p><strong>K<sub>cat</sub></strong>, used to describe the limiting rate of any enzyme-catalyzed reaction at saturation. Most of the time
K<sub>cat</sub> just equals K<sub>2</sub> (NOT the case when there are
more reaction steps)</p>
</blockquote>
<p>I can find information about the calculation of the <strong>specificity constant</strong> (K<sub>cat</sub> / K<sub>m</sub>) and what it means: </p>
<blockquote>
<p><strong>specificity constant</strong>,the rate constant for the conversion of E + S to E + P</p>
</blockquote>
<p>However I can't find any detailed explanation WHY you should devide the K<sub>cat</sub> by K<sub>m</sub>. Secondly K<sub>m</sub> is HALF of V<sub>max</sub> (so actullay at half saturation) but K<sub>cat</sub> is at full saturation, deviding these two numbers makes no sense to me. <strong>So to summerize I'm asking : What is the "meaning" of the division of these two consants?</strong></p>
<p><em>definitions are derived/edited from Lehninger principles of biochemistry</em></p>
Answer: <p>Just as $k_{cat}$ represents the rate of reaction at saturating substrate concentration, $k_{cat} / K_m$ represents the rate of the reaction at negligible substrate concentration.</p>
<p>If we take a look at the standard one substrate/one product Michaelis–Menten kinetics rate equation:</p>
<p>$$v = \frac{k_{cat}[E][S]}{K_m + [S]}$$</p>
<p>We can imagine what happens when $[S] \to 0$, we see that when $[S] \ll K_m$, the denomiator can be reduced to $K_m$, and thus the rate equation becomes</p>
<p>$$v = \frac{k_{cat}}{K_m}[E][S]$$</p>
<p>Or in other words, $k_{cat} / K_m$ is the (pseudo-)second order rate constant between the enzyme and the substrate, when $[S] \ll K_m$.</p>
<p>In fact, when you get into more complex rate equations (like inhibitors, pH effects, and kinetic isotope effects) there's a decent argument (one often made by <a href="https://en.wikipedia.org/wiki/W._Wallace_Cleland" rel="nofollow noreferrer">W.W. Cleland</a>) to be made that the two key constants for enzymatic reactions are $k_{cat}$ and $k_{cat} / K_m$, and it's $K_m$ that should be thought of as the "derived" constant. (The fact that we write the rate equation in terms of $k_{cat}$ and $K_m$ is a historical accident - we could have just as easily had $ v = \frac{k_{cat}\Phi [E][S]}{K_m + \Phi [S]}$, where I've arbitrarily chosen $\Phi$ as the symbol for $k_{cat}/K_m$.)</p>
<p>This still leaves the issue of why $k_{cat} / K_m$ is often referred to as the "specificity constant" of the enzyme. The reason for this is that if you have a single enzyme in the presence of two different substrates, you have a competitive inhibition setup. The math is a little dense (see <a href="http://employees.csbsju.edu/hjakubowski/classes/ch331/transkinetics/olinhibition.html" rel="nofollow noreferrer">here</a> or <a href="http://www1.lsbu.ac.uk/water/enztech/inhibition.html" rel="nofollow noreferrer">here</a> for examples), but the end result is that the ratio of reaction rates for the two substrates is related to the ratio of their respective $k_{cat} / K_m$'s:</p>
<p>$$\frac{v_a}{v_b} = \frac{k_{cat,A} / K_{m,A}}{k_{cat,B} / K_{m,B}}\frac{[A]}{[B]}$$</p>
<p>This actually makes intuitive sense, with the right mindset - the only stage where the two substrates are competing (where you make the decision to do reaction A versus reaction B) is when they're binding to free enzyme. "The rate when you only care about free enzyme" is equivalent to the negligible substrate case. With negligible substrate, all you have is free enzyme - there isn't enough substrate to have appreciable amounts of substrate-bound form, and the rate of enzyme-substrate encounter is much lower than the rate of product formation, meaning that in the steady state you don't have appreciable amounts of product-bound form, either. Thus the $k_{cat} / K_m$ for a particular substrate is representing how good the <em>free</em> enzyme is at performing that reaction.</p>
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https://biology.stackexchange.com/questions/53483/what-is-the-meaning-behind-kcat-km
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Question: <p>So I have two substrates for one enzyme and I measured the product formation-> michaelis menten kinetics. The Vmax for both substrates is the same, the Km however is higher on substrate number 2. What can I conclude from this in terms of enzyme-substrate interaction?</p>
Answer: <p>The situation you described is entirely normal. <span class="math-container">$V_{max}$</span> is the same, so when described with a graph of initial reaction rate vs. substrate concentration, both curves will asymptotically approach the same maximum level. <span class="math-container">$K_M$</span> is higher in one than the other, so the exact shape of the curve as it goes from 0 to <span class="math-container">$V_{max}$</span> is different. As you may know, you can interpret <span class="math-container">$K_M$</span> as the substrate concentration that causes the initial reaction rate to be half of <span class="math-container">$V_{max}$</span>. This means the substrate with the higher <span class="math-container">$K_M$</span> will have a shallower first half of the curve. </p>
<p>You can read more about these parameters and initial enzyme kinetics in <a href="https://www.ncbi.nlm.nih.gov/books/NBK22430/" rel="nofollow noreferrer">Berg biochemistry</a> or at <a href="https://www.khanacademy.org/science/biology/energy-and-enzymes/enzyme-regulation/a/basics-of-enzyme-kinetics-graphs" rel="nofollow noreferrer">khanacademy</a>.</p>
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https://biology.stackexchange.com/questions/79016/struggling-to-make-sense-of-km
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Question: <p>I'm doing an experiment for my IB bio EE involving colorimetry. I'm not experienced at all with colorimetry, so I'm having some trouble planning it. The experiment is on enzyme kinetics, and I'm testing the effect of an inhibitor on the rate of digestion of starch by alpha-amylase. Currently, my plan is just to use a starch solution with an iodine indicator, add the amylase and inhibitor and measure the change in absorbance of a certain wavelength over time with the colorimeter, however, I'm worried that when I add the amylase and the inhibitor it'll affect the colour of the solution quite a lot. Will this be an issue, and if so is there a better method I could use to control for it?</p>
<p>Any help would be appreciated, this is my first time actually planning an experiment and I'm finding it difficult :)</p>
Answer: <p>Let's work through the options.</p>
<p>First, the amylase could affect the color of the starch-iodine complex by direct association (rather than gradually digesting the starch). I'd think someone would have noticed that by now, but you could test amylase + starch + iodine versus starch + iodine negative control at "time 0" to see what you think.</p>
<p>Next, your inhibitor could affect the color of the starch-iodine complex. In that case, a starch + iodine negative control will look different from an inhibitor + starch + iodine negative control.</p>
<p>Finally, perhaps amylase binds the inhibitor in some <em>special</em> way that causes the whole complex to hunt out starch-iodine complex and make a strange color. It seems unlikely, yet it's not <em>that</em> unlikely since depending how it works the inhibitor might manage to jam up amylase in mid-bite with the starch attached, and the protein somehow manages to mess with the wrapping of starch around iodine. In that case you need to look at whether (amylase + inhibitor) + starch + iodine looks different from amylase + starch + iodine and/or inhibitor + starch + iodine at "time 0", then consider the color change from there.</p>
<p>For "time 0", you might conceivably need to extrapolate back to that time point after measuring changes after some short time intervals you can accurately measure, if the color change is rapid.</p>
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https://biology.stackexchange.com/questions/86091/will-amylase-inhibitors-affect-the-colorigenic-reaction-between-starch-and-iodin
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Question: <p>I have never heard of straigthforward definitions of these fields in my college lectures, and the Internet searches were not very helpful. However, from what I have learned at different subjects, this what I understand of the following areas.</p>
<ul>
<li><strong>Biochemistry:</strong> The study of metabolic pathways, enzyme kinetics, bioenergetics and the chemical mechanisms of the reactions. It does study molecular structure, but only of small molecules such as monomers, metabolites and coenzymes.</li>
<li><strong>Molecular biology:</strong> The study of information pathways, such as transcription, splicing and replication. It applies as well to techniques such as PCR.</li>
<li><strong>Molecular genetics:</strong> The study of how a genotype creates a particular phenotype. For example, it would be the study of why an allele produces smooth peas while another one produces wrinkled ones.</li>
<li><strong>Structural biology:</strong> Elucidating the structure of macromolecules (proteins, nucleic acids) and their complexes. It uses X-ray crystallography, NMR and cryo-electron microscopy to study them.</li>
</ul>
<p>So, are my definitions accurate? If not, why?</p>
Answer:
|
https://biology.stackexchange.com/questions/84247/what-is-the-difference-among-biochemistry-molecular-biology-molecular-genetics
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Question: <p>I was going through the GRN modelling from <em>Chemical and enzyme kinetics</em>
by D. Gonze & M. Kaufman (<a href="http://mcb111.org/w11/gonze_kinetics.pdf" rel="nofollow noreferrer">PDF</a>). The gene has 2 sites for activator/repressor. It say the DNA <span class="math-container">$D_0$</span> combines with activator/repressor at one of the sites leading to <span class="math-container">$D_1$</span> and then <span class="math-container">$D_1$</span> combines with <span class="math-container">$X$</span> again leading to <span class="math-container">$D_2$</span>. It says then then total DNA is conserved in the reaction leading to <span class="math-container">$D_{Total} = D_0 + 2D_1 + D_2$</span>. I want to ask why is there "2" with <span class="math-container">$D_1$</span> shouldn't it be <span class="math-container">$D_{Total} = D_0 + D_1 + D_2$</span>. What I am talking about is given on page 49 of the document.
<span class="math-container">$$D_0 + X \leftrightarrow D_1$$</span> <span class="math-container">$$D_1 + X \leftrightarrow D_2$$</span>
For first chemical reaction the rates are <span class="math-container">$k_1$</span> and <span class="math-container">$k_{-1}$</span>. For the second reaction the chemical reaction rates are <span class="math-container">$\alpha k_1$</span> and <span class="math-container">$k_{-1}$</span>.
Also, what will be the rate of the reaction for <span class="math-container">$D_2+X\rightarrow D_3$</span> when the DNA has 3 sites instead of 2.</p>
Answer:
|
https://biology.stackexchange.com/questions/100387/conservation-law-in-gene-regulatory-network-modelling
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Question: <p>I have created a <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781438" rel="nofollow noreferrer">convenience kinetics</a><sup>†</sup> model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have read some publications related to this work but can’t get a satisfactory idea of how to do it properly. </p>
<h3>Details</h3>
<p>I've got a pancreatic model for the study on type 2 diabetic patients. It has a few compartments and the reaction pathways; the species are metabolites. All the reactions are convenience kinetics based. Enzyme is a constant factor, so its production and regulation is not considered. From my model, I'll get the V<sub>m</sub> values for all the reactions and then I'm supposed to get the V<sub>m</sub> (V<sub>max</sub> of Michaelis-Menten kinetics) values for the type 2 diabetic patients by somehow integrating the transcriptomics data with it. I was asked to use the fold change values but I couldn't find any relevant publication on this topic (my PI has suggested me these but hasn't worked in this area before).</p>
<p>Any leads or references will be highly appreciated.
<hr>
<sup>† </sup>You can call convenience kinetics rate laws as approximate rate laws or you might have heard about "modular rate laws", they are more or less the same. We use this approximate rate law approach in cases where we don't have the experimental data for all the true rate law parameters.</p>
Answer: <p>I am assuming that in your model, the reactants and products (species) are metabolites and each reaction denotes conversion of one metabolite to another. </p>
<p>From transcriptomics, you will get the relative expression levels of different genes.
When you have two samples from different conditions you can calculate the differential expression. </p>
<p>A model can be as complex as you can make it but we can start with simple assumptions. As you said, enzymes are assumed to be constant with respect to metabolites and are not dynamically changing. I also guess that you are not considering genes other than enzymes to be affecting the metabolic reactions (you might actually want to consider the solute transporters). Also, you are assuming Michaelis-Menten kinetics for all reactions. </p>
<p>In that case your V<sub>max</sub> (i.e. maximum rate of a reaction) would be k<sub>cat</sub> × E<sub>0</sub> where k<sub>cat</sub> is the turnover number and E<sub>0</sub> is the total amount of enzyme. </p>
<p>E<sub>0</sub> can be approximated using the transcriptomics data. However, transcriptomics data is relative and not absolute. If you need absolute quantification, you must have at least one reference whose absolute mRNA copy number is known. Another issue is that the ratio of protein and mRNA expression would not be the same for all genes and it is basically the amount of active protein you need to know. So proteomics would be one step closer.</p>
<p>When you are comparing two conditions, you can use the differential expression (fold change values) to adjust the parameters between the two conditions. For e.g. if you know that phosphofructokinase is 2 fold downregulated in diabetes (compared to healthy case) then you can reduce the V<sub>max</sub> of the corresponding reaction by 2 fold in your diabetes model. However, it all would make sense only if the parameters of your "healthy" model are reasonably close to the biological reality.</p>
<p>Moreover, you still need to know k<sub>cat</sub>. It cannot be obtained from high throughput studies. You may have to either make some guesses or check out papers/databases. Also, your rate is not always V<sub>max</sub>. To estimate the dynamic rate you must know K<sub>M</sub> too (when the substrate is in excess you can ignore K<sub>M</sub>). <a href="https://www.brenda-enzymes.org/index.php" rel="nofollow noreferrer">BRENDA</a> may have some information about these constants for different enzymes. </p>
<p>At a very crude level, you can remove the reactions whose corresponding enzymes have zero expression. </p>
<hr>
<p>These are some articles on integration of transcriptomics data with FBA (not kinetic models):</p>
<ul>
<li><a href="https://dx.doi.org/10.3389%2Ffphys.2012.00299" rel="nofollow noreferrer">Blazier and Papin (2012)</a></li>
<li><a href="https://doi.org/10.1371/journal.pcbi.1003580" rel="nofollow noreferrer">Machado and Herrgård (2014)</a> </li>
<li><a href="https://doi.org/10.1371/journal.pone.0154188" rel="nofollow noreferrer">Guo and Feng (2016)</a></li>
</ul>
<p>Machado and Herrgård actually claim that integration of transcriptomics data does not improve their model predictions:</p>
<blockquote>
<p>Also, it is observed that for many conditions, the predictions
obtained by simple flux balance analysis using growth maximization and
parsimony criteria are as good or better than those obtained using
methods that incorporate transcriptomic data.</p>
</blockquote>
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https://biology.stackexchange.com/questions/85360/how-to-integrate-transcriptomics-data-with-kinetic-metabolic-models
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Question: <p>Quoting Wikipedia: <a href="https://en.wikipedia.org/wiki/Diffusion_limited_enzyme#Mechanism" rel="nofollow noreferrer">"Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible."</a> Which are those enzymes and how can they be so fast?</p>
<p>One example is catalase which <a href="https://www.waterjournal.org/volume-7/milgrom" rel="nofollow noreferrer">Lionel Milgrom discusses in Water Journal no. 7</a>. </p>
Answer:
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https://biology.stackexchange.com/questions/51223/how-can-some-enzymes-work-faster-than-the-diffusion-rates-of-the-molecules-it-ca
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Question: <p>I'm from India and i'm preparing for a competitive exam called the Joint Admissions Test for a Masters admission.</p>
<p>I need help in finding books to read from for these chapters:</p>
<p><strong>General Biology</strong>: Taxonomy and physiology, Pro-and eukaryotic organism; cell organelles and their function; multicellular Organization; energy transformations; internal transport systems of plants; respiration; regulation of body fluids and excretory mechanisms; cellular reproduction; Mendelian genetics and heredity; biology and populations and communities; evolution; genesis and diversity of organism; animal behaviour, plant and animal diseases.</p>
<p><strong>Basics of Biochemistry, Biophysics, Molecular Biology</strong>: Buffers; trace elements in biological systems; enzymes and proteins; vitamins; biological oxidations, carbohydrates and lipids and their metabolisms; digestion and absorption; detoxifying mechanisms; plant and animal hormones and their action, nervous system, nucleic acids, nature of gene and its function, Genetic code, synthesis of nucleic acids and proteins. Enzyme mechanisms and kinetics, nucleic acid metabolism, photo synthesis.</p>
<p><strong>Structure of Biomolecules</strong>: intra and intermolecular forces; thermodynamics and kinetics of biological systems, principles of x-ray diffraction, IR and UV spectroscopy and hydrodynamic techniques.</p>
<p><strong>Microbiology, Cell Biology and Immunology</strong>: Classes of micro-organisms and their characterization, nutrient requirement for growth; laboratory techniques in microbiology, pathogenic micro-organisms and disease; applied microbiology; viruses, Microbial genetics. Innate and adaptive immunity, antigen antibodies.Cell theory; Cell architecture; methods of cell fractionation; cell division; types of chromosome structure; biochemical genetics- inborn errors of metabolisms; viruses and fungi; principles of processes of development.</p>
<p>PS. I've studied biology only until high school.</p>
Answer:
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https://biology.stackexchange.com/questions/40022/what-are-the-best-books-for-the-iit-jam-biological-sciences-exam
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Question: <p>I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in the 21.5. According to this <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1065158/" rel="noreferrer">paper</a>, Fig. 2C, the normalized specific activity of the enzyme is about 70% at pH 6.3 and about 47% at pH 7. If I divide 34 mM at pH 6.3 by 0.7 (which should get me the optimum Km at the optimum pH of 5.5) and then multiply by 0.48, then I get 23 mM. However, the paper says Km is between 30 - 38 mM, so if I divide 30 and 38 separately by 0.7 and multiply by 0.47, I get 20 and 25.6 mM respectively. Because my value falls within this range, this then must mean that I have the right enzyme and the same result as the paper. </p>
<p>So my questions are:</p>
<ol>
<li><p>When the paper says Km is "34 +/- 4 mM", can I assume that means the Km can be anywhere between 30 - 38 mM? I'm surprised to see how wide the range is. I assumed Km is usually just one value with a deviation of at most 0.1.</p></li>
<li><p>Do pH change Km values? I understand that pH changes the shape(s) of the enzyme and/or substrate. Therefore that must affect how much it wants to bind to the substrate. If the enzyme's desire to bind to a substrate decreases due to increase in pH, for example, that would mean more substrates are needed to surround the enzyme, thus increasing Km.</p></li>
<li><p>If pH does change Km, is this how I determine the Km value of a different pH value if the Km value at another pH is already known? I know that specific activity and Michaelis constant are different, but how much product can be converted per minute depends on how much the enzyme likes to bind to a substrate, which is represented by the Michaelis constant. Did my reasoning and calculation arrive at the right conclusion? If not, how is the calculation done?</p></li>
</ol>
Answer: <p>From the derivation of <a href="https://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics" rel="nofollow">Michaelis-Menten kinetics</a> you can see that:</p>
<p>$$K_m=\frac{k_f + k_{cat}}{k_r}$$</p>
<p>Where $k_f$ and $k_r$ are binding and unbinding rate constants (for Enzyme-Substrate binding), respectively, and $k_{cat}$ is the turnover number. This is for the Quasi-Steady-State approximation (QSSA). For the equilibrium approximation:</p>
<p>$$K_m=\frac{k_f}{k_r}$$ which is same as the association constant.</p>
<p>In both the cases pH can affect the rate of binding and unbinding by affecting the affinity between the enzyme and the substrate. For example lets assume that the substrate binding site is negatively charged. Low pH would increase the electrostatic potential of the substrate binding site towards zero by affecting the ionization of the functional groups. </p>
<p>pH can also have indirect effects on the substrate binding site because it can modify the overall structure of the protein.</p>
<p>Many enzyme catalysed reactions involve <a href="https://en.wikipedia.org/wiki/Enzyme_catalysis#Proton_donors_or_acceptors" rel="nofollow">acid-base catalysis</a> i.e. there is a transfer of proton. In reactions like these, pH can affect $k_{cat}$. </p>
<blockquote>
<p>If pH does change Km, is this how I determine the Km value of a
different pH value if the Km value at another pH is already known?</p>
</blockquote>
<p>You can do that by making a <a href="https://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plot" rel="nofollow">Lineweaver-Burk plot</a> for the changed pH.</p>
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https://biology.stackexchange.com/questions/37050/does-ph-affect-michaelis-constant
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Question: <p>I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just trying to test the technique).</p>
<p>Unfortunately, for this technique to work, it is best if there aren't any aromatic amino acids around since it is entirely in the UV range.</p>
<p>I did a quick search in UniProt, and - somewhat surprisingly - there are very few proteins without aromatic amino acids, let alone any enzymes. The yeast protein sequences database contains zero(!) proteins with no aromatic AAs. The human database contains a few proteins (~20): for example many metallothioneins, proline-rich proteins, and HMG proteins have no aromatic AAs. No common enzymes turn up in that search.</p>
<p>Can anyone think of an enzyme - or perhaps a small catalytically active fragment of one - which has no aromatic amino acids?</p>
<p>If not - this is maybe a more general question - what makes aromatic amino acids apparently necessary for most enzymes?</p>
<p>P.S. The yeast results are:
lowest aromatic AA content is 4% in vacuolar ATPase (many DNA/RNA polymerase subunits are also quite low);
median is 11%, many common enzymes eg alcohol dehydrogenase, glutathione oxidoreductase etc fall in that range;
highest is 24% in sterol methyl oxidase</p>
<p><strong>UPDATE</strong> A thorough search of the RefSeq NR protein sequence db does turn up a whole lot of stuff, but it tends to be from weird species, mostly bacteria... eg oxaloacetate decarboxylase from Rubrivivax benzoatilyticus (which - maybe no surprise - eats aromatic compounds). It still seems like there is a strong selective pressure to incorporate aromatic AAs in enzymes</p>
Answer:
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https://biology.stackexchange.com/questions/79295/are-there-any-enzymes-without-aromatic-amino-acids
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Question: <p>It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 <em>grams</em> of DNA. This is clearly absurd and not the case.</p>
<p>Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an <em>upper bound</em> - but even so, a very uninformative one), and in practice, yields will fall far short of it because:</p>
<ul>
<li>Every single duplex of DNA does not denature at each cycle</li>
<li>Primers do not bind to every single molecule of DNA at each cycle</li>
<li>Not every DNA strand gets bound by a polymerase at every cycle</li>
<li>Not every polymerase that binds manages to complete the entire product in time in every cycle</li>
<li>The reaction inhibits itself by depleting dNTPs</li>
<li>The heat denatures the reaction by degrading enzyme</li>
</ul>
<p>In fact, cursory examination of qPCR output often follows saturation kinetics:</p>
<p><img src="https://i.sstatic.net/JlTkp.png" alt="enter image description here"></p>
<p>Mathematical methods for modeling qPCR are obviously well developed.</p>
<p>My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?</p>
<p>For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).</p>
Answer: <p><strong>An expected efficiency for a typical PCR is 80%, meaning each cycle multiplies the copy number of the targeted DNA sequence 1.58 times.</strong></p>
<p>Firstly, it makes more sense to refer to the amount of DNA in a polymerase chain reaction in terms of <em>copy number</em> or in terms of <em>moles</em>; the <em>number of DNA molecules</em> of interest is what the reaction is operating on, and the mass of product generated is a function of the length of the product (and, to a lesser degree, on the composition of the product).</p>
<p>The following discussion is sourced from this URL: <a href="https://www.csun.edu/~hcbio027/biotechnology/lec3/pcr/p.htm" rel="nofollow noreferrer">https://www.csun.edu/~hcbio027/biotechnology/lec3/pcr/p.htm</a></p>
<p>According to Perkin-Elemer, copy-number <strong>amplification of 100,000 fold</strong> of the targeted sequence of DNA can be expected from a PCR with 0.1 ng of Lambda phage DNA (a well-characterized and standard DNA isolate) in a 100 µL reaction with > 25 cycles of denaturation, annealing, and extension.</p>
<p>In the above 100,000-fold amplification example, if the targeted amplicon were to be 500 bp in length, the estimated molecular-weight of duplex DNA of 500bp is 325,000 g/mol (based an average base-pair having a molecular mass of 650 g/mol).</p>
<p>The Lamdba Phage genome is 42,502 base-pairs in length.
42,502 bp × 650 grams/mol/bp = 2.762×10^7 grams/mol.</p>
<p>0.1 ng Lambda DNA -> 0.1×10^-9 grams.
0.1×10^-9 g ÷ 2.762×10^7 g/mol = 3.619 × 10^-18 moles.
3.619 × 10^-18 moles × NA (Avogradro's Number) = 2.179×10^6 copies, or 2,179,000 copies.</p>
<p>2.179×10^6 copies × 100,000 = 2.179×10^11 copies.
2.179×10^11 copies ÷ NA × 325,000 g/mol = 1.176×10^-7 grams of sequence.
1.176×10^-7 grams is equal to 0.117 µg or 117 ng.</p>
<p>An amplification yield of 100,000x after 25 cycles would mean at each cycle 1 template would yield 1.58 templates for the next round of synthesis.</p>
<p>How was this calculated? If c is the number of copies made per round of synthesis, then:</p>
<pre><code>c^25 = 100,000 = 10^5
so c^5 = 10
and so 5(log c) = log 10 = 1
so log c = 0.2 and c = 1.58 (approximately)
(Or you could calculate the 25th root of 100,000 on a calculator, if you prefer.)
</code></pre>
<p>If we obtain 1.58 copies instead of the theoretical maximum of 2 copies, then the efficiency of the reaction could be said to be 79% (because 1.58/2.00 = 0.79).</p>
<p>One reason this calculation is important is that a slight loss of efficiency is magnified through the amplification. A reaction may appear to have not worked if the efficiency drops (in each cycle) by just a few percent. Optimization is critically important in the polymerase chain reaction.</p>
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https://biology.stackexchange.com/questions/19081/equation-for-accurate-prediction-of-pcr-yield
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Question: <p>I would like to know about those transporters with <em>alternating-access</em>-type mechanism, <strong>that can only efficiently shuttle molecules in one direction but the other direction is severely kinetically inhibited</strong>. From <a href="https://biology.stackexchange.com/questions/107289/thermodynamics-of-one-directional-passive-membrane-transporters">this question</a> I know that they exist, but Google searches are futile in finding examples. Wikipedia is not much help, either. I also skimmed the seventh chapter of the <a href="https://rads.stackoverflow.com/amzn/click/com/0134093410" rel="nofollow noreferrer" rel="nofollow noreferrer">Campbell biology book</a>, about the structure and function of the cell membrane, but there was no clue.</p>
<p>More generally, I have found examples of enzymes that is inhibited only in one direction, such as F1-ATPase (even without the inhibitory epsilon subunit) with its <a href="https://www.embopress.org/doi/full/10.1038/sj.emboj.7600293" rel="nofollow noreferrer">mechanism of ADP inhibition</a>, which primarily affect ATP hydrolysis and not ATP synthesis. I just have not found examples of this in <em>passive transporters</em> specifically.</p>
<p>Furthermore, is the mechanism of unidirectional inhibition inherent to the transporter domain itself, or does it require a separate domain, as in the case of the voltage-gated ion channels, to sense the gradient flowing in the other direction and then inhibit the transporter domain?</p>
<p>Is there even an universal mechanism?</p>
<p>My guess for an universal mechanism would be the former, as I am aware of the basic kinetics of the active <em>ABC transporters</em>, in that they preferentially open to one side of the membrane.</p>
Answer: <p>Voltage-gated proton channels are passive transmembrane transport proteins that will only transport protons in one direction. These channels will be open when there is a lower pH in the cytoplasm, allowing protons to flow out of the cell, but will close when the pH is higher in the cytoplasm, not allowing protons into the cell. [<a href="https://doi.org/10.1152/physrev.00028.2002" rel="nofollow noreferrer">1</a>] In this case, the protein does not sense the direction of flow, but rather opens only in conditions where one direction of flow is possible.</p>
<p>Most voltage-gated proton channels have a separate voltage-sensing domain from their pore domain. However, H<sub>V</sub>1 does not have separate voltage-sensing and pore domains. [<a href="https://doi.org/10.1085%2Fjgp.201611619" rel="nofollow noreferrer">2</a>] Therefore, neither combined nor separate regulatory and transport domains is universal. I am not aware of the mechanism in either case, or whether their are other proteins with different mechanisms.</p>
<br/>
<ol>
<li>DeCoursey, T. E. (2003). Voltage-gated proton channels and other proton transfer pathways. <em>Physical Rev</em>, <em>83</em>, 475-579. <a href="https://doi.org/10.1152/physrev.00028.2002" rel="nofollow noreferrer">https://doi.org/10.1152/physrev.00028.2002</a></li>
<li>DeCoursey, T. E., Morgan, D., Musset, B., & Cherney, V. V. (2016). Insights into the structure and function of H<sub>V</sub>1 from a meta-analysis of mutation studies. <em>J Gen Physiol</em>, <em>148</em>(2), 97-118. <a href="https://doi.org/10.1085%2Fjgp.201611619" rel="nofollow noreferrer">https://doi.org/10.1085%2Fjgp.201611619</a></li>
</ol>
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https://biology.stackexchange.com/questions/108966/examples-of-passive-membrane-transport-proteins-that-only-transport-in-one-direc
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Question: <p><em>Characteristics of chemical reactions</em> are certain characteristics that tell us whether a chemical reaction has occurred or not.</p>
<p>Some important characteristics of chemical reactions are given below :</p>
<li> Evolution of a gas
<li> Formation of a precipitate
<li> Change in color
<li> Change in temperature
<li> Change in state
<p>I was wondering whether <em>all</em> chemical reactions can be identified by one or more of these characteristics. Since there is an extremely wide range of chemical reactions, I think that these are just the <em>major</em> characteristics of chemical reactions and there may exist some reactions that exhibit none of these characteristics.
<br>
Am I right about this? If yes, what are some examples of chemical reactions that show none of these characteristics?</p>
<p>Thanks!</p>
Answer: <p>I think you are right about this judgment. There are certainly some outliers which show none of these characteristics.</p>
<p>One example I can think about is the catalytic reduction of nitrate to nitrite, by either transition metal catalysts or biocatalysts. And I think some reactions in liquid phase show none of the characteristics you mentioned above.</p>
<p>Still, I think the key here is that chemical reactions always involve the breaking-forming of chemical bonds and the change of electron cloud distribution. I think that's the essential characteristic of chemical reactions.</p>
<p>Thanks! Let me know if you have more questions.</p>
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https://chemistry.stackexchange.com/questions/135659/characteristics-of-chemical-reactions
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Question: <p>I just got in 10th grade and the first chapter in Chemistry in our school curriculum is <em>Chemical Reactions and Equations</em></p>
<p>The chapter is littered with a <strong>lot</strong> of chemical reactions and their equations and most of the teachers I consult say that there is no alternative to revising them but I <strong>hate</strong> to blindly memorize stuff without knowing why it happens in that manner and not in some other way.</p>
<p>Is it really true that there is no other way than to <strong>memorize</strong> the equations?</p>
<p>If there is an alternative, please let me know.</p>
<p>And how can I predict the products of a chemical reaction if its reactants are given. Is it done by understanding the types of chemical reactions.</p>
<p>One of my teachers said that it could be done like this : If you're given two elements as reactants and you know that they will react, then you know that it is a combination reaction, you can figure out the chemical formula of the compound that those two elements will form on combination and then balance the equation. This works for simple reactions like <em>Na + Cl <span class="math-container">$\longrightarrow$</span> NaCl</em> or for some simple decomposition, displacement or double displacement reactions but what about complex reactions like this :</p>
<p><span class="math-container">$2 Pb(NO_ 2)_3$</span> (s) <span class="math-container">$\longrightarrow$</span> <span class="math-container">$2PbO$</span> (s) + <span class="math-container">$4NO_2$</span> (g) + <span class="math-container">$O_2$</span> (g)</p>
<p>I can quite easily visualize a combination reaction as two elements sharing or losing or gaining electrons and combining to form a compound, but how do I visualize these types of reactions</p>
<p>I'm sorry if you find this question silly...
<br>
All answers are welcome</p>
<p>Thanks</p>
Answer:
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https://chemistry.stackexchange.com/questions/132135/understanding-chemical-reactions
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Question: <p>Whats the difference between chemical processes and chemical reactions?
Ive heard that the chemical industries only uses chemical processes to produce new substances, but isnt that also what happens when a chemical reaction occurs? I couldn't find a lot on this topic online except for the wikipedia aricles that only made me more confused.</p>
Answer: <p>According to IUPAC:</p>
<blockquote>
<p><strong>Chemical reaction</strong></p>
<p>A process that results in the interconversion of chemical species.
Chemical reactions may be elementary reactions or stepwise reactions
(It should be noted that this definition includes experimentally
observable interconversions of conformers.) Detectable chemical
reactions normally involve sets of molecular entities as indicated by
this definition, but it is often conceptually convenient to use the
term also for changes involving single molecular entities (i.e.
'microscopic chemical events').</p>
</blockquote>
<p>A chemical reaction is a kind of process in which interconversion of chemical species takes place. Because of this, we can say that a chemical reaction is a chemical process.</p>
<p>Chemical process can be a broad term, which describe any process that is commonly studied by chemists because they are closely related to chemical reactions. It is somewhat diffuse, as boundaries of the field of chemistry.</p>
<p>Industries use a variety of procedures to obtain substances. Chemical processes/reactions take place. If your interest is realising what is done in industries, do not get stuck in these subtleties. Most of the times they are not intentionally distinguished, and their usage is customary in the field.</p>
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https://chemistry.stackexchange.com/questions/51782/chemical-processes-and-chemical-reactions-difference
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Question: <p>What are the chemical reactions and/or chemical processes that take place during SFE(supercritical fluid extraction)? Namely supercritical $\ce{CO2}$.</p>
Answer: <p>Supercritical fluid technology is used primarily to enhance the chemical extraction process. The solubility of a compound in a supercritical solvent increases as the system pressure increases at constant temperature. This is due to the highly pressurized supercritical solvent disrupting the intermolecular attractive forces between the molecules of the compound to be extracted, and replacing those forces with increased attractive forces between the compound and the supercritical solvent. Carbon dioxide is a very common material used for supercritical extraction. It is cheap, not flammable, has low toxicity and, after the extraction is complete you simply return the system to STP, allow the carbon dioxide to evaporate and you are left with only the extracted material. Some examples of commercial uses for supercritical carbon dioxide include caffeine extraction from coffee beans, sterilization of surgical equipment, fracking and dry cleaning.</p>
<p>Chemical reactions involving supercritical carbon dioxide are now being intensely studied. One reaction that has been commercialized involves reaction of supercritical carbon dioxide with hardened, alkaline cements. A harder cement containing carbonate groups throughout the entire volume of cement is formed along with water (environmentally friendly process).</p>
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https://chemistry.stackexchange.com/questions/14122/chemical-reactions-in-sfe
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Question: <p>I'm creating a program, which predicts reactions of compound. So, I need a database of chemical reactions. And I need both inorganic and organic reactions. But I can't use Scifinder or Reaxys because they are not free. Is there any free analogs?</p>
Answer: <p>In the current form the question is addressed, and assuming you took a look at a listing of software already in the field like <a href="https://en.wikipedia.org/wiki/List_of_computer-assisted_organic_synthesis_software" rel="noreferrer">here</a>, I speculate the sheer number of organic reactions (<a href="https://en.wikipedia.org/wiki/List_of_organic_reactions" rel="noreferrer">just some</a>) alone renders such a task as a one-man / one-woman project too large. There is a lot of work associated to create such a database, or software. <a href="http://www.orgsyn.org/" rel="noreferrer">Organic Synthesis</a> is one open-access reference for organic reactions, yet the normal output is a html / pdf of the <em>reaction procedure</em>, and not a <a href="https://en.wikipedia.org/wiki/Chemical_table_file#SDF" rel="noreferrer">*.sdf</a> (or other chemically relevant *.xml-like) format. <a href="http://www.inorgsynth.com/" rel="noreferrer">Inorganic Synthesis</a> is a publication with similar intent as the former, yet not openly accessible.</p>
<p>Nevertheless, if you are interested in this topic, I suggest to consult the recent publications <em>Computer-aided synthesis design: 40 years on</em> (<a href="http://onlinelibrary.wiley.com/doi/10.1002/wcms.61/full" rel="noreferrer">DOI 10.1002/wcms.61</a>) as well as the just about a year old <em>Computer-Assisted Synthetic Planning: The End of the Beginning</em> in <em>Angewandte Chemie</em> (<a href="http://onlinelibrary.wiley.com/doi/10.1002/anie.201506101/abstract" rel="noreferrer">English version DOI: 10.1002/anie.201506101</a>).</p>
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https://chemistry.stackexchange.com/questions/71827/free-chemical-reactions-database
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Question: <p>I am wondering about chemical reactions when the reactants are in a plasma state. Consider hydrogen and oxygen. Heated, these would react to form water.</p>
<p>If hydrogen and oxygen plasma were combined, would the separation of electrons from nuclei prevent normal chemical reactions? Or would the reaction take place in the plasma state?</p>
Answer: <p>Yes, chemical reactions do take place in high-temperature plasmas. In fact, these reactions present some problems in the analytical technique known as Inductively Coupled Plasma - Mass Spectroscopy (ICP-MS), which typically uses an argon plasma. </p>
<p>As noted in the comments, the conditions within a plasma are very different from those in a laboratory at STP, for example. But that just means that the chemical reactions that are observed are different, not that they don't exist. In ICP-MS for example, one is trying to detect the masses of very low concentrations of various elements in the presence of relatively huge quantities of argon, oxygen and hydrogen (the latter assuming that an aqueous sample is being analyzed). Species that are formed within the plasma include $\ce{Ar2+}$, $\ce{ArO+}$ and more. When one of these species has the same mass as the trace isotope of interest, it only takes a very small percentage of these products to interfere with the analysis. </p>
<p>This example of argon plasma can largely be extended to your specific question "If hydrogen and oxygen plasma were combined, would the separation of electrons from nuclei prevent normal chemical reactions?". Depending on the conditions of the plasma (temperature, concentrations, degree of ionization, etc.) the answer is that the reaction would only form some small degree of transient water molecules, as compared to say molecular hydrogen and oxygen gas at high temperatures or in the presence of a catalyst, which would overwhelmingly form water. In other words, the former (plasma state oxygen and hydrogen) would form trace amounts of water, and probably hydrogen peroxide and other oxygen-hydrogen species, where under "normal" conditions the formation of water would be strongly favored (thermodynamically anyway). It's just the nature and definition of a plasma that whatever species you have in your plasma will want to be broken into it's elemental constituents and the formation of molecules will be strongly unfavored.</p>
<p><strong>Summary:</strong><br>
The conditions within a plasma are very different from conditions typically encountered in a non-plasma environment, and thus the chemical reactions are different. The formation of otherwise exotic species like $\ce{Ar2+}$ are relatively commonplace within an argon plasma for example ("common" being a relative term of course, as concentrations of $\ce{Ar2+}$ may still be relatively low, just much higher than would be seen outside of the conditions present in the plasma). Plasma conditions themselves can also vary widely, from conditions where only a small portion of the gas molecules are charged to conditions where the majority are charged. Regardless, the high energy state of a plasma tends to result in the destruction of molecules to their atomic precursors, but occasionally there are reactions to form products that would not be seen outside of a plasma.</p>
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https://chemistry.stackexchange.com/questions/73840/chemical-reactions-in-plasma-state
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Question: <p>I am looking for introduction to modeling of chemical reactions. I think there is the base approach, where concentrations of chemical species are given, plus ratios of each possible reaction / outcome. Is there a paper lightly explaining internal mechanics of such reactions, and their modeling via system of differential equations?</p>
Answer: <p>The topic you are asking about is called <strong>reaction dynamics</strong>, and is closely related to <strong>chemical kinetics</strong> (the former is more focussed on atomistic events, reactive and nonreactive collisions, while the later usually describes the mathematical treatment of the kinetic laws governing species concentrations). It was the topic of the <a href="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1986/index.html" rel="noreferrer">1986 Nobel Prize in Chemistry</a>.</p>
<p>It is covered by most <a href="http://rads.stackoverflow.com/amzn/click/0198792859" rel="noreferrer">physical chemistry</a> textbooks, and more in depth by <a href="http://rads.stackoverflow.com/amzn/click/0137371233" rel="noreferrer">specialized textbooks</a> on that matter. It is sometimes taught together with basics of statistical mechanics or statistical thermodynamics. Check your favorite (or local) university for a list of reading material on this topic!</p>
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https://chemistry.stackexchange.com/questions/2619/introduction-to-modeling-chemical-reactions
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Question: <p>We know that quantum tunneling is the reason behind several natural phenomenon like alpha decay and thermonuclear fusion inside the stars. How can it influence chemical reactions by tunnelling a species through the activation energy? If so how does it influence the kinetics and fraction of molecules taking part in the reaction.</p>
Answer: <p>The probability of tunnelling at an energy $E$ is given by $p(E)\approx e^{-bA\sqrt{m}}$ where $A$ is proportional to the <em>area</em> of the potential energy barrier above energy $E$, i.e. the top part of the potential barrier, $m$ the mass and $b$ some constants, $\pi, \hbar$. etc. Thus for a given mass and energy if the barrier is narrow, so $A$ is small, tunnelling is more likely than if the barrier is wide. At a given energy for the same barrier if the mass is large tunnelling is small. Thus we tend to see tunnelling only with H and D and not Cl atoms for example. Tunnelling is also important in electron transfer reactions.</p>
<p>As there is not just a single energy in a reaction but a distribution of energies, according to the Boltzmann distribution, it is necessary to modify the expression above to average over the energy but the basic result is the same, which is that the reaction rate constant is reduced by the factor $p(E)$.</p>
<p>[If the potential energy barrier is $V(x)$ then $\displaystyle p(E)=\exp\left(-\frac{2\sqrt{m}}{\hbar}\int_{x_1}^{x_2}\sqrt{V(x)-E}\right)$ where $x_{1,2}$ are the points either side of the barrier with energy $E$.]</p>
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https://chemistry.stackexchange.com/questions/99004/tunneling-in-chemical-reactions
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Question: <p>Do reactions whose final outcome is <strong>not even theoretically predictable by any means possible</strong> exist in Nature or does the outcome of all possible chemical reactions can (at least in theory) be <strong>predicted</strong> if we could get enough information about the conditions the reaction system is in?</p>
<p>My question isn't about a well-defined reaction system whose behavior is unknown to a certain degree but about the possibility <em>in principle</em> to discover a chemical reaction or a system of chemical reactions able to produce compounds which can't be predicted even in theory, even if we manage to acquire all the possible information about the system that can be acquired by all experimental means possible? What I want to ask is whether we can, at least <strong>in theory</strong>, know all possible products a reaction system can generate or do we "hit a wall" limiting our ability to predict certain chemical reactions over a certain limit?</p>
<p>I know very well the difference between a stochastic and a deterministic process, but what I'm asking isn't about stochasticity. It is about the possible <strong>predictability</strong> of all chemical reactions that could exist. As far as I know if we use the concept of stochasticity we may be able to derive possible, albeit only <em>probable</em> predictions about the state the system can be in. Therefore we can at least compute some probabilities different compounds can have to emerge under certain conditions. What I'm asking about is the validity of the concept of <a href="https://en.wikipedia.org/wiki/Ergodicity" rel="noreferrer">ergodicity</a>, therefore I want to know is it possible to know the end state and all the reaction products of <strong>all</strong> possible chemical reactions, or there are some which could generate products that are impossible to predict in both theory and reality? Do reactions generating such unpredictable behavior exist in the real world or are they possible only in theory?</p>
Answer: <p><strong>Life is an example of a series of chemical reactions with unpredictable results.</strong></p>
<p>Forget, for a moment, the long term evolution of living creatures and consider the chemistry behind inheritance and selection (at least one sexual activity has started). The key chemical reaction that drives the DNA code for the next generation is random mixing of the genetic material of the parents to generate the DNA of the next generation. This process clearly demonstrates that the result of a chemical reaction is not entirely predictable given the components (the code is written in the same language, but the combination in children is a random combination of the parent's DNA). </p>
<p>Over a longer time period, we can also observe that entirely new types of life emerge via Darwinian random variation and selection. Future life is hard to predict given the existing life at a given point in time. And the underlying process is a chemical reaction involving DNA.</p>
<p>So maybe it isn't natural to think of this as <em>chemistry</em>. But it is built of chemical processes and demonstrates that, in a sufficiently complex system, chemistry can deliver results that are not easily forecastable. Perhaps simpler systems can demonstrate the same point, but this one is staring us in the face as an existence proof.</p>
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https://chemistry.stackexchange.com/questions/84242/do-non-ergodic-chemical-reactions-exist
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Question: <p>I was going to ask whether there are software that could be used to predict the products of any given chemical reaction. However, I then noticed these two earlier questions</p>
<ul>
<li><a href="https://chemistry.stackexchange.com/questions/2808/chemical-software-for-solving-reactions?rq=1">Chemical software for solving reactions</a></li>
<li><a href="https://chemistry.stackexchange.com/questions/8351/software-for-predicting-chemical-reactions?rq=1">Software for predicting chemical reactions</a></li>
</ul>
<p>where it is said such predictions are too difficult to make. What makes the prediction difficult? </p>
Answer: <p>Because you need would need to solve the <a href="http://en.wikipedia.org/wiki/Dirac_equation">Dirac equation</a> (relativistic Schrodinger equation) for all the particles in the system to get a completely accurate result. </p>
<p>Even solving the time independent non-relativistic Schrodinger equation for $\ce{H2+}$ in isolation, where there is only one electron and two protons involves approximating the protons as fixed relative to each other. </p>
<p>Now imagine trying solving a system of $10^{23}$ molecules each having multiple nuclei, and dozens or even hundreds of electrons, and including time dependence!</p>
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https://chemistry.stackexchange.com/questions/24216/why-is-predicting-products-of-chemical-reactions-difficult
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Question: <p>I recently read about Chaos Theory and was wondering if a chemical reaction results in or shows characteristics of chaos (I found a few examples of such reactions <a href="https://www.google.com/amp/s/www.researchgate.net/post/What_are_the_famous_chemical_reactions_yielding_chaos/amp" rel="nofollow noreferrer">here</a>)</p>
<blockquote>
<p>Chaos theory concerns deterministic systems whose behavior can in principle be predicted. Chaotic systems are predictable for a while and then 'appear' to become random.</p>
</blockquote>
<p>If the reaction becomes unpredictable towards the time of attainment of equilibrium we can't possibly determine how the reaction will proceed during the time frame so <strong>will the reaction attain a state of equilibrium</strong> and will it be at the time it should've without chaos being in the picture? </p>
<p><strong>If the equilibrium shifts can we quantify by how much and how much more or less time will it take to attain it in general or we need to take specific reactions and analyze them?</strong></p>
<p><strong>Also after attaining equilibrium can the system again show Chaotic behaviour and if it does what can se say about the state of equilibrium?</strong></p>
Answer: <p>A homogeneous reaction mixture can hardly show macroscopical chaotic behaviour. <a href="https://en.wikipedia.org/wiki/Belousov%E2%80%93Zhabotinsky_reaction" rel="nofollow noreferrer">Well known cyclic counterexamples</a> exist, and practically any reaction which proceeds faster than diffusion or mechanical mixing can homogenise it again (e.g. any reaction that generates a lot of heat!) is liable to show some intermediate chaotic concentration gradients. Its usually hard to notice, and most reactions are perfectly reproducible, if you set them up in the same way (<em>educt impurities!</em>).</p>
<p>If your reaction vessel contains inflows of different chemical composition, then you easily get chaotic behaviour. Think about a tube reactor. I believe chemical engineers are spending a lot of their time trying to control and avoid chaos.</p>
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https://chemistry.stackexchange.com/questions/119571/chaos-in-chemical-reactions
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Question: <p>Most chemical reactions are reversible, and even for so called "irreversible" ones, the equilibrium point lies so far towards the product, that they are effectively irreversible, but even for them, an equilibrium point exists. The products and reactants are in an equilibrium with each other.</p>
<p>Is there any chemical reaction where this is not the case, aka where no backward reaction, from products to reactants occur?</p>
Answer: <p>Reversibility requires several conditions: The first is the attainment of equilibrium. A condition must exist where all the products and reactants are present. With: Appropriate mixing. Sufficient, appropriate energy. A possible mechanism of reaction. No competing side reactions.</p>
<p>The second is that the process must be possible from both directions by the same mechanism. This almost restricts reversibility to elementary, basic reactions or to more complicated reactions that have been changed into a linked set of elementary reactions. The latter are subject to side reactions. Basic reactions are mostly simple acid-base reactions involving electron-pair migration and/or single electron transfer redox reactions. A more complex reaction can possibly be reversible if it is, or can be reduced to, a series of elementary reactions. This is one of the reasons that enzymatic and catalytic reactions can happen effectively.</p>
<p>As examples Cellular respiration and Photosynthesis are complicated chain processes that are desperately trying to attain equilibrium. They each rely on product and heat removal to prevent the almost elementary enzymatic reactions from attaining equilibrium. When these removal processes fail the reactions almost attain equilibrium with dire results. The cyclic almost steady state of glucose oxidation and generation is a complicated many step process that is not an equilibrium because the mechanism[s] in the two directions are entirely different, the energy forms for the reactions are different and, of course, the processes are not intimately mixed.</p>
<p>My answer, an opinion, the only reversible reactions are the elementary steps of a reaction. As these steps accumulate the reaction becomes irreversible for the reasons stated above.</p>
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https://chemistry.stackexchange.com/questions/187690/are-there-any-true-irreversible-chemical-reactions
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Question: <p>In a chemical reaction, is energy always either lost or gained by the reactants? As much as I am concerned, changes in energy can occur during the absorption of heat or the emission of light or heat (these are the most often occurring). Is every chemical reaction accompanied by these conditions? Aren't there any chemical reactions without these conditions? Usually when we observe common chemical reactions (sugar that is melting in the water), we don't see any emissions or absorptions. Are these changes so trifling that we can't feel them (while they actually exist), or there are reactions with no emissions or absorptions?</p>
Answer: <p>your question is good yet lacks the specifics.
there are different so called "energy fields" in which changes occur (entropy, potential ,gibes and so forth).
the thermodynamic field is endless and can be spanned with any variables (using maxwells equations and Legendre transformation)
there is
a sort of an axiom that states that all matter will try to find a way to a lower state of energy.
but that said its not to scientific. </p>
<p>now for the question:
every reaction creates some amounts of electromagnetic waves (as a price for electron "movement") some can be seen with the naked eye as they emit waves in the Uv-vis spectrum some are just infrared radiations of inner states of electron decay to a lower energetic state via vibrational relaxation. </p>
<p>ideally no reaction will occur in the ideal zero as there is no energy to "pay" for any kind of a reaction.</p>
<p>for further read:
quantitive chemical analysis by harris
chapter 17 fundamentals of spectrophotometry.</p>
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https://chemistry.stackexchange.com/questions/77339/energy-in-a-chemical-reaction
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Question: <p><a href="https://en.wikipedia.org/wiki/Halogen" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Halogen</a></p>
<p>Can Halogens react with each other?</p>
<p>Examples :</p>
<p>Chlorine + Flourine</p>
<p>Flourine + Iodine</p>
<p>Iodine + Bromine</p>
<p>Chlorine + Bromine</p>
<p>and so on.</p>
<p>Permutations and Combinations.</p>
<p>Chlorine + Flourine =</p>
<p>Chlorine + Bromine =</p>
<p>Chlorine + Iodine =</p>
<p>Flourine + Bromine =</p>
<p>Flourine + Iodine =</p>
<p>Bromine + Iodine =</p>
<p>What will be the chemical reactions & applications?</p>
Answer: <p>There is plenty of information about all these compounds if you look at "Interhalogen compounds" through Google. All these compounds are known :</p>
<p>AX- type : ClF, BrF, BrCl, ICl, IBr</p>
<p>AX3-type: ClF3, BrF3, (ICl3)2,</p>
<p>AX5-type: ClF5, BrF5, IF5,</p>
<p>AX7-type: IF7.</p>
<p>Their synthesis, structures and properties are nicely described, much better than what I could do here.</p>
<p>And please note that the symbol F describes the element <strong>fluorine</strong>, and not <strong>flourine</strong>. Its compounds are <strong>fluorides</strong>, and not <strong>flourides</strong>.</p>
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https://chemistry.stackexchange.com/questions/141917/halogens-chemical-reactions-with-each-other
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Question: <p>I've always wondered what the chemistry behind fire is. What are the basic chemical reactions behind a simple wood fire, and how do they manifest into this phenomenon?</p>
Answer: <p>Even though fire is one of the <a href="http://en.wikipedia.org/wiki/Classical_element#Classical_elements_in_Greece" rel="nofollow noreferrer">Greek classical elements</a>, it is the only one that is not matter in our current understanding. What we experience as fire is the energy (in the form of light and heat) given off by the exothermic combustion of (usually) organic materials, like wood. The large amounts of thermal energy released by combustion often cause the gases in the fire to <a href="http://en.wikipedia.org/wiki/Incandescence" rel="nofollow noreferrer">incandesce</a>, that is, some of the kinetic energy produced by the fire is converted into electromagnetic radiation that we see (visible) and feel (infrared). </p>
<p>The chemical reaction for combustion is pretty simple. Take, for example, the combustion of n-octane $\ce{C8H18}$, which produces more than 5 MJ of energy per mole during combustion (from <a href="http://webbook.nist.gov/cgi/cbook.cgi?ID=C111659&Units=SI&Mask=2#Thermo-Condensed" rel="nofollow noreferrer">webbook.nist.gov</a>). </p>
<p>$$\ce{2C8H18 +25O2->16CO2 +18H2O} \space\space \Delta_cH^o=-5430 \text{ kJ/mol} $$</p>
<p>The combustion of wood is more complex. The majority of the organic mass of dry dead wood is lignin and cellulose. <a href="http://en.wikipedia.org/wiki/Lignin" rel="nofollow noreferrer">Lignin</a> is a highly-cross-linked copolymer of p-coumaryl alcohol, $\ce{C9H10O2}$, <a href="http://en.wikipedia.org/wiki/Coniferyl_alcohol" rel="nofollow noreferrer">coniferyl alcohol</a>, $\ce{C10H12O3}$, and <a href="http://en.wikipedia.org/wiki/Sinapyl_alcohol" rel="nofollow noreferrer">sinapyl alcohol</a>, $\ce{C11H14O4}$. <a href="http://en.wikipedia.org/wiki/Cellulose" rel="nofollow noreferrer">Cellulose</a> is a linear polymer of <a href="http://en.wikipedia.org/wiki/Glucose" rel="nofollow noreferrer">glucose</a>, with formula $\ce{(C6H10O5)}_n$.</p>
<p>Different species will have different ratios of lignin to cellulose, different cross-link densities in the lignin, and different ratios of coumaryl to coniferyl to sinapyl alcohols. The formula for lignin could be expressed then as $\ce{(C9H10O2)}_x \cdot \ce{(C10H12O3)}_y \cdot \ce{(C11H14O4)}_z$.</p>
<p>The equation for the combustion reaction for cellulose is:
$$\ce{(C6H10O5)}_n +6n\ce{O2->}+6n\ce{CO2}+5n\ce{H2O} $$</p>
<p>Since lignin is more complex, its combustion equation is more complex:
$$2[\ce{(C9H10O2)}_x \cdot \ce{(C10H12O3)}_y \cdot \ce{(C11H14O4)}_z]+(21x+23y+25z)\ce{O2}\\ \ce{->}(18x+20y+22z)\ce{CO2}+(10x+12y+14z)\ce{H2O}$$</p>
<p>And assuming the variable composition of wood as a ratio (A:B) of cellulose to lignin, the overall combustion reaction becomes the following monstrosity:</p>
<p>$$A\ce{(C6H10O5)}_n +2B[\ce{(C9H10O2)}_x \cdot \ce{(C10H12O3)}_y \cdot \ce{(C11H14O4)}_z]+[6An+B(21x+23y+25z)]\ce{O2}\\ \ce{->}[6An+B (18x+20y+22z)]\ce{CO2}+[5An+B(10x+12y+14z)]\ce{H2O}$$</p>
<p>Given the number of variables ($A, B, n, x, y, z$), the $\Delta_cH^o$ for this reaction is difficult to determine (but not impossible, assuming we know some thermochemical reference data). Whatever its value, it is exothermic enough to induce incandescence. </p>
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https://chemistry.stackexchange.com/questions/1254/what-are-the-chemical-reactions-behind-fire
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Question: <p>My question concerns how energy is used in chemical reactions. I am working with a reaction between magnesium and hydrochloric acid in a class (although this is not a homework question). What I've found is that the magnesium gives away its valence electrons to either the hydrogen or to the chloride. But in the second case, the chloride ions would first give their valence electrons to the hydrogen, and then they would accept the electrons from a magnesium atom. As I was thinking about which of the cases was more probable, I started thinking about the energy involved. For example, I would think that moving the electrons first from the chloride ions to the hydrogen, and then from the magnesium to the chloride, would use much more energy than the magnesium just giving its electrons to the hydrogen ions. </p>
<p>My question is, as a general rule of thumb, although I wouldn't mind a detailed answer, are reactions that, like this one (as far as I know), have multiple "ways" of reacting going to take the way that uses the minimal amount of energy? Or are the electrons free to move to whichever atom is closest?</p>
Answer: <p>Magnesium cannot give one or two electrons to the chloride ion. Because Chloride ions have the maximum number of 8 electrons in their external shells. There is no possibility for a new electron to stay on a Chloride ion. And the Chloride ion will be reluctant to accept or to loose one of its electrons, because it has the ideal conformation (8 outer electrons). So there are no "multiple ways" of reacting, as you imagine. The only thing that may happen is for magnesium to loose two electrons per atom, because at the end of this departure, it will have 8 outer electrons, and this seems to be to ultimate goal for all atoms. These electrons will be caught by <span class="math-container">$H^+$</span> ions, which are transformed into <span class="math-container">$H$</span> atoms and then into <span class="math-container">$H_2$</span> molecules. </p>
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https://chemistry.stackexchange.com/questions/127186/energy-in-chemical-reactions
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Question: <p>I recently came across a question in which an option is 'Breaking a chemical bond is the first step in any chemical reaction', which lead me to think of reactions which do not involve bond breaking. The only reaction I can think of is dimer formation, but a Google search reveals no more. Surely this cannot be the only example?</p>
Answer: <p>The reaction of a Lewis acid with a Lewis base results only in bond formation. Your question gets at the essence of chemistry, though. A chemical reaction is the rearrangement of electrons between atoms. So generally, most reactions will involve breaking bonds. Even for monomers (e.g. alkenes) to polymerize, $\pi$-bonds within the monomers have to be broken to form $\sigma$-bonds in the polymer. You seldom have one without the other.</p>
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https://chemistry.stackexchange.com/questions/99967/which-chemical-reactions-dont-involve-bond-breaking
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Question: <p>I want to show a schematic representation of chemical reactions from start to finish in a way that will include more detailed preparation instructions than a plain chemical formula: volumes, concentrations, waiting time, temperature, etc.</p>
<p>Is there a graphical language for this kind of thing? I'm looking for something more sophisticated than a typical flow chart, and more targeted towards chemical reactions.</p>
Answer:
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https://chemistry.stackexchange.com/questions/36924/is-there-a-generic-graphical-language-to-represent-chemical-reactions
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Question: <p>I've seen before chemistry demonstrations where solutions are mixed with one another and subsequently where the resulting product goes through periodic color changes: for example blue to orange and back to blue again. The reaction seems to go on for awhile at a regular period.</p>
<p>My question - can this reaction be considered resonance in the sense that energy is flowing back and forth between two chemical states? In such reactions are there actually two chemical species between the color changes or just energy level/temperature differences?</p>
Answer: <p>A couple of points:</p>
<p>The demo is probably an oscillating chemical reaction, in which the concentration of a given species increases and decreases repeatedly over time. However, the energy of the overall system is dissipating as that is happening - not oscillating.</p>
<p>Resonance, on the other hand, is a (widely misunderstood) concept that applies to a single chemical species and not a bulk reaction mixture. Resonance does not consist of energy flowing back and forth between two chemical states, but rather is meant to represent a single energy state that is a hybrid between two (or more) classical Lewis structures. A double headed arrow between the two classical structures indicates <em>resonance stabilization</em> — mostly resulting from delocalization of electrons relative to the classical structures. The double headed arrow <strong>does not</strong> indicate oscillation between those two structures.</p>
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https://chemistry.stackexchange.com/questions/31383/periodically-oscillating-chemical-reactions
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Question: <p>I am looking for a complete directory of chemical reactions. It should be searchable by element or substance and also the various factors (pressure, temperature, catalyst, etc) should be mentioned. Is there something like this? Thanks!</p>
Answer:
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https://chemistry.stackexchange.com/questions/57323/is-there-a-database-of-known-chemical-reactions
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Question: <p>Why is the Gibbs free energy (G) considered a spontaneity criterion for phase transformations and chemical reactions? Why are other thermodynamic parameters such as enthalpy (H), entropy (S), and Helmholtz free energy (A) not accepted as spontaneity criteria?</p>
Answer: <p>Spontaneity is simply a system not at equilibrium (this is regardless of direction) with a possible mechanism to reach equilibrium.</p>
<p>Before getting upset note that reactions involving only standard conditions do not reach equilibrium in <em>either</em> direction, so one direction will be spontaneous and the other not. This is incorrect both directions are from the standard states to equilibrium [JG].</p>
<p>For a multistep reaction each elementary step should be considered in turn. At equilibrium forward and reverse reactions are at the same rate and the chemical activities satisfy the equilibrium constant. The equilibrium constant value determines the extent of reaction in each direction.</p>
<p>The energetics of a reaction are determined by the energy change <em>and</em> the entropy change, not by only one of the two. The functions that combine these properly are the Gibbs free energy</p>
<p><span class="math-container">$$G = H - TS, \tag{1}$$</span></p>
<p>especially useful at constant pressure; and the Helmholtz free energy</p>
<p><span class="math-container">$$A = E - TS, \tag{2}$$</span></p>
<p>especially useful at constant volume.</p>
<p>There are cases where either <span class="math-container">$H$</span> or <span class="math-container">$S$</span> is much larger and seems to dominate the process. But if one thinks it through, that is true when the conditions are far from equilibrium. At equilibrium</p>
<p><span class="math-container">$$\Delta G = 0 = \Delta H - T\,\Delta S\quad\implies\quad \Delta H = T\,\Delta S. \tag{3}$$</span></p>
<p>This means at equilibrium an infinitesimal change in either will perturb the equilibrium in the appropriate direction with an appropriate change in the other to satisfy the equilibrium condition. If energy is added, <span class="math-container">$\Delta H > 0$</span>; bonds break increasing particles, <span class="math-container">$\Delta S > 0$</span>; <span class="math-container">$\Delta G = 0.$</span></p>
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https://chemistry.stackexchange.com/questions/166821/spontaneity-criterion-for-phase-transformations-and-chemical-reactions
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Question: <p>I am a mathematician working on real-life models in ordinary differential equations. I want to know if there are any models of oscillatory chemical reactions that consist of three ordinary differential equations where one variable is much slower than the other two. In particular I am interested in bursting behavior, which consists of alternating trains of fast oscillations with periods of rest.</p>
<p>I have been searching and I couldn't find what I am looking for. I found about the Belousov-Zhabotinsky reaction, but in this case we have one fast variable and two slow variables, while I'm looking for two fast variables and one slow variable.</p>
Answer:
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https://chemistry.stackexchange.com/questions/166898/mathematical-models-of-oscillatory-chemical-reactions
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Question: <p>Suppose only a set of chemical formulas is given. How can you find all mathematically possible chemical equations whose educts and products are only from this set?</p>
<p>Take e.g. the set <span class="math-container">$\{ \ce{C, H2, O2, N2, CO, CO2, H2O, NH3, NO, NO2, NO3}\}$</span>.</p>
<p>Or consider e.g. the example in <a href="https://math.stackexchange.com/questions/1752609/finding-all-chemical-equations-linear-algebra">MathStackexchange: Finding all chemical equations (Linear Algebra)</a>.</p>
<p>To find all combinations and partial reactions between such given species by hand, is possibly incredibly tedious or near impossible for more complex chemical reaction systems.</p>
<p>I guess these methods are topic of Mathematical Chemistry, Computer Chemistry or Chemoinformatics.</p>
Answer: <p>The purely combinatorial methods are a first step in modeling chemical reactions. They alone however cannot consider the possibility of the chemical reactions and the chemical stability of the reaction products.<br>
<span class="math-container">$\ $</span></p>
<p>1.)</p>
<p>You can build all combinations of at least two formulas, all from the original set of given chemical formulas, and treat this as your set of given formulas. But you can also treat the whole original set of given chemical formulas.</p>
<p>I demonstrate the method with the first example given in the question:</p>
<p><span class="math-container">$$\{ \ce{C, H2, N2, O2, CO, CO2, H2O, NH3, NO, NO2, NO3}\}$$</span></p>
<p>We set up one chemical equation with all chemical formulas that are in the given set. Let the stoichiometric factors in the chemical equation be denoted by <span class="math-container">$\nu$</span>. Because we don't know which of the given substances will be educt and which of them will be product, we write the chemical equation without reaction arrow. Instead, a negative stoichiometric factor will later mark an educt, a positive a product: </p>
<p><span class="math-container">$$\nu_1\ce{C}+\nu_2\ce{H2}+\nu_3\ce{N2}+\nu_4\ce{O2}+\nu_5\ce{CO}+\nu_6\ce{CO2}+\nu_7\ce{H2O}+\nu_8\ce{NH3}+\nu_9\ce{NO}+\nu_{10}\ce{NO2}+\nu_{11}\ce{NO3}$$</span></p>
<p>We have to obey one of the first fundamental laws of chemistry: the <a href="https://en.wikipedia.org/wiki/Law_of_multiple_proportions" rel="nofollow noreferrer">Law of multiple proportions</a>. To fulfill this law, the total sum of each chemical element in our chemical equation has to be <span class="math-container">$0$</span>. And if ions are among our given chemical formulas, the total sum of all electric charges has to be <span class="math-container">$0$</span> also. But no electric charges are involved in our given example. </p>
<p>We will now build a mathematical model of our chemical problem.</p>
<p>For each of the given chemical elements, we have to set up its balance equation from our chemical equation above:</p>
<p><span class="math-container">$\ce{C}:\ \ \ \nu_1+\nu_5+\nu_6=0$</span><br>
<span class="math-container">$\ce{H}:\ \ \ 2\nu_2+2\nu_7+3\nu_8=0$</span><br>
<span class="math-container">$\ce{N}:\ \ \ 2\nu_3+\nu_8+\nu_9+\nu_{10}+\nu_{11}=0$</span><br>
<span class="math-container">$\ce{O}:\ \ \ 2\nu_4+\nu_5+2\nu_6+\nu_7+\nu_9+2\nu_{10}+3\nu_{11}=0$</span></p>
<p>This is a linear equation system. In the general case, too, a linear equation system results. It consists of the coefficients (the numbers above) and the stoichiometric factors <span class="math-container">$\nu_i$</span>, which are sought. In our example, the equation system has 4 equations (the number of different chemical elements and the electric charge) and 11 unknowns (the number of chemical formulas in the given set). </p>
<p>Linear Algebra says how a linear equation system can be handled. We use here the matrix presentation.</p>
<p>Each of the 11 given chemical formulas is presented by a column vector which contains the frequency of occurence of each chemical element in the chemical formula in a prescribed order. Each of the 4 given chemical elements is presented by a row vector which contains the frequency of occurence of the chemical element in the chemical formulas in a prescribed order.</p>
<p>All 11 column vectors or all 4 raw vectors of the equation system are combined to give the coefficient matrix <span class="math-container">$A$</span>. Our 11 wanted stoichiometric coefficients build the solution vector <span class="math-container">$x$</span>, which is sought. The matrix representation of our linear equation system is than:</p>
<p><span class="math-container">$$A\cdot x=\emptyset,$$</span> </p>
<p>wherein <span class="math-container">$\emptyset$</span> is the zero column vector with 4 rows. It is written out:</p>
<p><span class="math-container">$$\left(
\begin{array}{}
1&0&0&0&1&1&0&0&0&0&0\\
0&2&0&0&0&0&2&3&0&0&0\\
0&0&2&0&0&0&0&1&1&1&1\\
0&0&0&2&1&2&1&0&1&2&3
\end{array}
\right)
\cdot
\left(
\begin{array}{}
\nu_1\\\nu_2\\\nu_3\\\nu_4\\\nu_5\\\nu_6\\\nu_7\\\nu_8\\\nu_9\\\nu_{10}\\\nu_{11}
\end{array}
\right)
=\left(\begin{array}{}0\\0\\0\\0\end{array}\right)$$</span></p>
<p>The solution vector <span class="math-container">$x$</span> can be found by solving the linear equation system by methods of Linear Algebra.</p>
<p>The solution vector of our example is:</p>
<p><span class="math-container">$$x=\left(
\begin{array}{c}
2\nu_4+\nu_6+\nu_7+\nu_9+2\nu_{10}+3\nu_{11}\\-\nu_7+3\nu_3+\frac{3}{2}\nu_9+\frac{3}{2}\nu_{10}+\frac{3}{2}\nu_{11}\\\nu_3\\\nu_4\\-2\nu_4-2\nu_6-\nu_7-\nu_9-2\nu_{10}-3\nu_{11}\\\nu_6\\\nu_7\\-2\nu_3-\nu_9-\nu_{10}-\nu_{11}\\\nu_9\\\nu_{10}\\\nu_{11}
\end{array}
\right)$$</span></p>
<p>The different combinatorially possible chemical equations are obtained by choosing suitable values for the free variables <span class="math-container">$\nu_3,\nu_4,\nu_6,\nu_7,\nu_9,\nu_{10},\nu_{11}$</span>.<br>
<span class="math-container">$\ $</span></p>
<p>2.)</p>
<p>Further investigations could be made by searching the solutions that don't contain any other solution. That are the minimal solutions, that means the solutions that are linearly independent of the other solutions.</p>
<p>I found 663 chemical equations and 83 minimal solutions for the example above.</p>
<p>Generating only the minimal solutions in polynomial time needs particular algorithms:</p>
<p>Schay, G.; Pethö, Á.: Über die mathematischen Grundlagen der Stöchiometrie. Acta Chim. Acad. Sci. Hung. 32 (1962) 59-67</p>
<p>Pethö, Á.: Zur Theorie der Stöchiometrie Chemischer Reaktionssysteme. Wissenschaftl. Zeitschr. 6 (1964) 13-15</p>
<p>Pethö, Á.: Algebraic treatment of a class of chemical reactions in stoichiometry. Acta Chim. Acad. Sci. Hung. 54 (1967) 107-117</p>
<p>Pethö, Á.: On a class of solutions of algebraic homogeneous linear equations. Acta Math. Acad. Sci. Hung. 18 (1967) 19-23</p>
<p>Pethö, Á.: Kémiai reakciók egy osztályának algebrai elemzése. Magyar Kémiai Folyóirat 74 (1968) 488-491</p>
<p>Kumar, S.; Pethö, Á: Note on a combinatorial problem for the stoichiometry of chemical reactions. Int. Chem. Eng. 25 (1985) 767-769</p>
<p>Pethö, Á.: The linear relationship between stoichiometry and dimensional analysis. Chem. Eng. Technol. 13 (1990) 328-332</p>
<p>Szalkai, I.: Generating minimal reactions in stoichiometry using linear algebra. Hung. J. Ind. Chem. 19 (1991) 289-292<br>
<strong>with a software code at the end of the article</strong></p>
<p>Pethö, Á.: Mathematical discussion of the application of Hess‘s law. Hung. J. Ind. Chem. 21 (1993) 35-38</p>
<p>Pethö, Á.: Further remarks on the linear relationship between stoichiometry and dimensional analysis. Chem. Eng. Techn. Chem. Eng. Tech. 17 (1994) (1) 47-49</p>
<p>Pethö, Á.: Further remarks on the analogy between stoichiometry and dimensional analysis: The valuation operation. Hung. J. Ind. Chem. 23 (1995) 229-231</p>
<p>Laflamme, C.; Szalkai, I.: Counting simplexes in <span class="math-container">$R^n$</span>. Hung. J. Ind. Chem. 23 (1995) 237-240</p>
<p>Laflamme, C.; and I. Szalkai, I.: Counting simplexes in <span class="math-container">$R^3$</span> Electron. J. Combin. 5 (1998) (1) #R40 11. Printed version in: J. Combin. 5 (1998) 597-607</p>
<p>Szalkai, I.: Handling multicomponent systems in <span class="math-container">$R^n$</span> I Theoretical results. J. Math. Chem. 25 (1999) 31-46</p>
<p>Szalkai, I.: On valuation operators in stoichiometry and in reaction syntheses. J. Math. Chem. 27 (2000) 377-386</p>
<p>Szalkai, I.: A new general algorithmic method in reaction syntheses using linear algebra. J. Math. Chem. 28 (2000) 1-34</p>
<p>Szalkai, B.; Szalkai, I.: Counting minimal reactions with specific conditions in <span class="math-container">$R^4$</span> J. Math. Chem. 49 (2011) 1071-1085</p>
<p>Szalkai, I.; Dósa, G; Tuza, Z.; Szalkai, B.: On minimal solutions of systems of linear equations with applications. Miskolc Mathematical Notes 13 (2012) (2) 529-541</p>
<p>Szalkai, B.; Szalkai, I.: Simplexes and their applications - A short survey. Miskolc Math. Notes 14 (2013) (1) 279-290</p>
<p>Szalkai, I.; Tuza, Z.: Minimum Number of Affine Simplexes of Given Dimension. Discr. Appl. Math. 180 (2015) 141-149</p>
<p>Szalkai, I.: Reakciómechanizmusok algoritmikus és matematikai vizsgálata (Algorithmic and Mathematical Examination of Reaction Mechanisms). PhD thesis, University of Pannonia, Veszprém, Hungary, 2014</p>
<p><strong><a href="http://konyvtar.uni-pannon.hu/doktori/2014/Szalkai_Istvan_theses_en.pdf" rel="nofollow noreferrer">Szalkai, I: An algorithmical and mathematical investigation of reactions. English extract of the author's PhD thesis, 2014</a></strong><br>
<strong>See the examples and references therein.</strong></p>
<p><strong>Tóth , J.: Reaction Kinetics: Exercises, Programs and Theorems. Springer, 2018</strong><br>
<span class="math-container">$ $</span></p>
<p>3.)</p>
<p>The answer above treats overall reactions. The underlying elementary reaction steps (<a href="https://en.wikipedia.org/wiki/Elementary_reaction" rel="nofollow noreferrer">elementary reactions</a>) can be generated by working with the Ugi-Dugundji model: The chemical formulas are presented as graphs together with their graph matrices (Bond-Electron matrices (BE-matrices) and Reaction matrices (R-matrices)). The single elementary reaction steps will be generated successively by stepwise shifts of electrons or bonds in the set of given chemical formulas by stepwise shifting of single edges in the reaction matrix.</p>
<p>Ugi, I.; Gillespie, P.; Gillespie, C.: Chemistry, a finite metric topology - synthetic planning, an exercise in algebra. Trans. New York Acad. Sci. II 34 (1972) 416-432</p>
<p>Dugundji, J.; Ugi, I.: An algebraic model of constitutional chemistry as a basis for chemical computer programs. Top. Curr. Chem. 39 (1973) 19-64 </p>
<p>Dugundji, J.; Gillespie, P. D.; Marquarding, D.; Ugi, I.; Ramirez, F.: Metric spaces and graphs representing the logical structure of chemistry. in: Chemical applications of graph theory. Balaban, A. T. (Ed.), Academic Press, London 1976, 107-174</p>
<p>Brandt, J.; Friedrich, J.; Gasteiger, J.; Jochum, C.; Wolfgang Schubert, W.; Ugi, I.: Computer programs for the deductive solution of chemical problems on the basis of a mathematical model of chemistry. in: Wipke, W. T.; Howe, W. J.: Computer-Assisted Organic Synthesis. American Chemical Society 1977, chapter 2, 33-59 </p>
<p><a href="https://www.degruyter.com/view/j/pac.1978.50.issue-11-12/pac197850111303/pac197850111303.xml" rel="nofollow noreferrer">Ugi, I.; Brandt, J.; Friedrich, J.; Gasteiger, J.; Jochum, C.; Lemmen, P.; Wolfgang Schubert, W.: The deductive solution of chemical problems by computer programs on the basis of a mathematical model of chemistry. Pure Appl. Chem. 50 (1978) 1303-1318</a></p>
<p><a href="https://www.researchgate.net/publication/239270108_Computer_Programs_for_the_Deductive_Solution_of_Chemical_Problems_on_the_Basis_of_a_Mathematical_Model_of_Chemistry" rel="nofollow noreferrer">Ugi, I.; Brandt, J.; Friedrich, J.; Gasteiger, J.; Jochum, C.; Lemmen, P.; Schubert, W.: Computer Programs for the Deductive Solution of Chemical Problems on the Basis of a Mathematical Model of Chemistry. Pure Appl. Chem. 50 (1978) (11-12) 1303-1318</a></p>
<p>Behnke, C.; Bargon, J.: Computer-assisted topological analysis and completion of chemical reactions. J. Chem. Inf. Comput. Sci. 30 (1990) (3) 228-237 </p>
<p>Ugi, I; Dengler, A.: The algebraic and graph theoretical completion of truncated reaction equations. J. Math. Chem. 9 (1992) (1) 1-10</p>
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https://chemistry.stackexchange.com/questions/111375/finding-all-chemical-reactions-given-products-and-reactants
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Question: <p>While studying enthalpy <span class="math-container">$H=U+PV$</span> and its changes, I realized I am not clear on the following: chemical reactions happen with the <strong>external</strong> pressure being constant and equal to the atmospheric pressure <span class="math-container">$P_{atmos}$</span>. But, in general, the system's internal pressure <span class="math-container">$P_{gas}$</span> would seem to be different from <span class="math-container">$P_{atmos}$</span> and variable during a reaction...
The change in enthalpy <span class="math-container">$\Delta H= Q$</span>, where <span class="math-container">$Q$</span> is thermal energy, only when the gas internal pressure matches the environment external pressure: <span class="math-container">$P_{gas}=P_{external}=constant$</span> Under those circumstances, the emitted or absorbed thermal energy <span class="math-container">$Q$</span> goes into change #H# while the gas expands/contracts. The work <span class="math-container">$PV$</span> done by the gas is perfectly matched by the <span class="math-container">$PV$</span> work done on it by the environment.</p>
<p>How common is for the gas internal pressure to be constant and equal to <span class="math-container">$P_{atmos}$</span> during chemical reactions to justify <span class="math-container">$\Delta H = Q$</span>?</p>
Answer: <p>What happens during a reaction is important insofar as reversibility is concerned (a reversible path being a special way of performing a reaction in which equilibrium is sustained throughout), but not when computing <span class="math-container">$\Delta H$</span>. The condition <span class="math-container">$\Delta H = q$</span> is derived from the basic law of conservation of energy and the definition of enthalpy. Because H is a state function, to compute the change in its value you need to know only the initial and final states of the system (and of course the values of H corresponding to those states). For <span class="math-container">$\Delta H = q$</span> to hold requires that (1) only expansion (pV) work be performed and that (2) the initial and final pressures of the system equal each other.</p>
<p>You can dream up scenarios in which you start at mechanical equilibrium (balanced pressure) between surroundings and system but end up at a constrained system volume (rigid). For instance, if an explosion moves a piston to a constrained setting within a cylinder. In that case it is not true that the enthalpy change and heat are equal. On the other hand, if the explosion is constrained such that the volume can expand until pressures balance (and external constraining pressure is constant), then enthalpy change and heat are equal.</p>
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https://chemistry.stackexchange.com/questions/144598/do-most-chemical-reactions-happen-at-constant-pressure
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Question: <p>I'm reading a paper entitled <a href="https://arxiv.org/pdf/1508.04125.pdf" rel="nofollow noreferrer">Reachability Problems for Continuous Chemical Reaction Networks</a> and as I was reading it I realized: I have no idea what the difference is between a continuous chemical reaction network (CCRN) and a chemical reaction network (CRN). The paper does distinguish between the two, so they aren't two terms for the same thing. The <a href="https://en.wikipedia.org/wiki/Chemical_reaction_network_theory" rel="nofollow noreferrer">wikipedia article</a> doesn't distinguish/give a definition for a CCRN. Most of the results when I search google are papers that are way over my head - the one I'm reading right now is to be quite honest over my head. </p>
<p>Any help would be appreciated. Thanks!</p>
Answer: <p>I suspect that the distinction is that a CRN considers <em>discrete</em> species concentrations whereas a CCRN considers <em>continuous</em> species concentrations: "The CCRN model is continuous, dealing with <em>real-valued concentrations of species</em>...". More precisely, whereas a CRN deals with concentrations $x(t), y(t) \in \mathbb{Q}$, a CCRN deals with concentrations $x(t), y(t) \in \mathbb{R}$.</p>
<p>On a microscopic level, it's easy to see why $x(t), y(t)$ should be elements of $\mathbb{Q}$: a microscopic concentration is simply a ratio of the number of one molecule to the total number of molecules in the system, and the numerator and denominator must thus be integral. </p>
<p>For macroscopic systems, however, since the denominator---the total number of molecules in the system---is so large, it becomes a very good approximation to take $x(t), y(t) \in \mathbb{R}$. Moving to $\mathbb{R}$ is convenient, since then by physical considerations $x(t)$ and $y(t)$ are continuous, and we can, under mild assumptions, take derivatives and return to a rate-law formalism involving differential equations rather than difference equations.</p>
<hr>
<p><em>Remark.</em> I'm not familiar with this field, and I don't know how common the CRN/CCRN distinction is. Indeed, the Wikipedia article assumes differentiability of $x(t), y(t)$ and hence that $x(t), y(t) \in \mathbb{R}$. </p>
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https://chemistry.stackexchange.com/questions/74727/continuous-chemical-reaction-network-versus-chemical-reaction-network-differen
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Question: <p>There are <a href="http://faculty.sdmiramar.edu/fgarces/zCourse/All_Year/Ch100_OL/aMy_FileLec/04OL_LecNotes_Ch100/05_CompoundBonding/505_IMF_Water/505_pic/descriptionIMF.gif" rel="nofollow">various chemical reactions</a> that can occur between materials.</p>
<ol>
<li>Which chemical reactions occur with the tongue?</li>
<li>How come all reactions are reversible (nothing sticks to my tongue)?</li>
<li>What's special about the tongue-water interaction that makes it tasteless?</li>
</ol>
Answer: <p>1) I would guess that all of the different interactions are possible except for ionic and covalent because those are much stronger than the rest and it would be difficult for the food molecules to disassociate from the taste receptors to be used again. Enzymes in saliva break down complex food molecules to smaller and simpler ones.</p>
<p>2) Started explaining in 1, molecules are not usually permanently bound to the taste receptor in order for the taste receptor to be used again (another molecule being able to bind to it). Some toxins form covalent bonds to receptors, such as curare. I'm not sure what kinds of receptors taste ones are but toxins target different specific receptors. Curare binds to nicotinic acetylcholine receptors, found in muscles.</p>
<p>3) We don't taste things unless a molecule binds to a taste receptor.</p>
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https://chemistry.stackexchange.com/questions/24905/which-chemical-reactions-occur-between-my-tongue-and-the-food-i-eat
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Question: <p>Is it possible that some chemical reactions can't be balanced through the redox method? Because it seems to me that the elements on the reactants side have the same oxidation states with the product side.</p>
Answer: <p>Sometimes you aren't able to use the redox method to balance a chemical equation. This is because the redox method is only used to balanced an equation where a element gets oxidised or reduced. However if there is a chemical equation where no element is getting oxidised or reduced, then you won't be able to use the redox method to balance the equation. However, fortunately most of the time these type of equations can be easily balanced. Consider the following unbalanced equation: $$\ce{Ba(OH)2.8H2O (s) + NH4SCN (s) -> Ba(SCN)2 (s) + H2O (l) + NH3 (g)}$$</p>
<p>Here none of the elements are reduced or oxidised, hence you would not be able to balance this equation using the redox method.</p>
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https://chemistry.stackexchange.com/questions/34935/is-the-redox-method-applicable-to-all-chemical-reactions
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Question: <p>I am rather a newb in the GAMESS field but finally, learned to make input files for most molecular simulations and could even use TD-DFT for excited states (special thanks to Geoff Hutchison for his help).</p>
<p>Now I want to start simulating simple chemical reactions. I looked at the GAMESS manual and think I need to make transition states and find the least energy pathways but have no idea how to make an input file for that.</p>
<p>Can anyone give me a simple input file example for a simple reaction?</p>
Answer: <p>As in geometry optimization, you are searching for a stationary point on the potential energy surface (PES). Not for local minimum, but for saddle point, therefore in GAMESS, you specify <code>RUNTYP=SADPOINT</code>. You would also need the correct (non-guess) Hessian matrix, which you can calculate separately with <code>RUNTYP=HESSIAN</code>. In the transition state (TS), you should have zero gradients (stationary point) and one imaginary eigenvalue of Hessian (the reaction coordinate in TS).</p>
<p>For a working example, see e.g. <a href="http://molecularmodelingbasics.blogspot.de/2009/08/finding-transition-state-sn2-reaction.html" rel="nofollow noreferrer" title="SN2 reaction">S<sub>N</sub>2 transition state</a>. In principle, you need a very good guess at TS geometry, which you obtain by scanning along some chosen coordinate. The point highest in energy should be reasonably similar to the TS, and you optimize to a saddle point starting from there. Already at the guess geometry, you must have one imaginary Hessian eigenvalue (resembling the reaction you are looking for, not methyl rotation somewhere else).</p>
<p>But beware, finding the transition states is one of the most difficult topics in computational chemistry and you are not guaranteed to find one, no matter how hard you try. One of the biggest problems is solvation, as you often wish to find a reaction barrier in solvent (where the majority of the chemistry happens), but you can calculate only in a vacuum. Just think of how carefully the workbench chemist finds the correct solvent for a given reaction, on the computer you have only very crude approximations to it (and most often just vacuum).</p>
<p>That said, it is great fun and rewarding to find the transition states. For best results, use the simplest theory available, as it is better to have smooth and well-behaved PES, even though it is slightly wrong, so it is no harm to start with HF or BLYP (or B3LYP). To get some ideas, start with simple reactions, i.e. where no charged species are involved, so electrocyclic reactions are probably the best choice, e.g. Diels–Alder.</p>
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https://chemistry.stackexchange.com/questions/20003/how-to-simulate-chemical-reactions-in-gamess
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Question: <p>We might have a half cell consisting of the redox couple <span class="math-container">$\ce{Ag+}/\ce{Ag}$</span>, which for example's sake might be fixed to be at the cathode (i.e. undergoing reduction).</p>
<p>The reaction at the cathode is then</p>
<p><span class="math-container">$$\ce{Ag+ + e- -> Ag}$$</span></p>
<p>The standard electrode potential of the <span class="math-container">$\ce{Ag+}/\ce{Ag}$</span> couple is <span class="math-container">$+0.80\ \mathrm V$</span> with respect to SHE. I've seen the above reaction written as such:</p>
<p><span class="math-container">$$\ce{Ag+ + e- <=> Ag} \quad E = +0.80\ \mathrm V$$</span></p>
<p>I'm confused as to why we write this electrode potential next to the reaction, considering that the electrode potential of a redox couple is reasonably disjoint to the concept of the chemical reaction. Although, at the end of the day, the chemical reaction results in the interfacial potential difference which causes the electrode potential, <span class="math-container">$E$</span> is a property of the electrode, not the chemical reaction.</p>
<p>Is it perhaps just because we want to write the equation of the reaction occurring at a certain electrode <em>and</em> the electrode potential of the electrode on the same line?</p>
<p>I'm aware that for associating potentials with written reactions, there exist two different conventions: European, where all reactions are labelled with the reduction potentials of the couple, and American, where oxidation reactions are labelled with the oxidation potentials of the redox couple and likewise reductions with reduction potentials. However, my question is why we need to attach the electrode potential to the chemical reaction in the first place! </p>
<p>That is, ultimately, aren't redox potentials associated with redox couples/electrodes, not reactions?</p>
Answer: <p>Your question is a valid question, and ignore downvotes. They don't mean anything.</p>
<p>Your understanding is very good and that you realized that the electrode potential is a property of the electrode and it really does not care how the reaction is written. However, a equation is <span class="math-container">$needed$</span> to keep track of the electrons lost or gained in the Nernst equation. So as a <em>tradition</em> and a matter of convenience, electrode potentials are quoted along with a balanced half-cell.</p>
<p>Another very important thing to remember (even some university teachers and PhDs lack this understanding), that the sign of the electrode potential in invariant. It does not care how the reaction is written. It is the electrostatic sign of the electrode. This part takes care of the European and American conventions. American convention is due to Gibbs and Latimer and no longer used. Most international electrochemists have agreed to stick to the European convention i.e., write all half reactions as reduction. </p>
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https://chemistry.stackexchange.com/questions/129088/why-do-we-write-electrode-potentials-next-to-chemical-reactions
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Question: <p>I posted the following question in Physics SE and was advised to transfer it to Chemistry SE.</p>
<hr>
<p>I studied physics in college ten years ago and I recently started to learn biochemistry. I enjoy finding out that some familiar concepts in physics play important roles in biochemistry such as entropy and the Gibbs free energy. </p>
<p>For example, as a (ex-)student of physics, I am happy to know that the Gibbs free energy determines the directions of chemical reactions. I feel this is a good example where a sort of fundamental law of physics determines how a phenomenon looks like.</p>
<p>However, I still can not understand why the chemical reactions in a body need to be so complex. Many chemical systems consist of more than several steps to achieve their purposes. According to <a href="https://en.m.wikipedia.org/wiki/Glycolysis" rel="noreferrer">Wikipedia</a>, glycolysis takes ten steps through its process. Why are so many steps necessary?</p>
<p>I tried to find out a physical law that prohibit the glycolysis process from being achieved in one or two steps, but I could not find an answer. I would like to know (or discuss) whether there is a physical law that makes chemical systems so complex (many steps required).</p>
<p>My assumption is that some physical law prohibit the existence of an enzyme that realizes a one-step process of glycolysis.</p>
Answer: <p><strong>There is no fundamental law preventing simple chemical reactions: things are complex because of the combinatorial complexity of chemical compounds</strong></p>
<p>The complexity of many chemical reactions is a byproduct of the fact that there is a very, very large variety of possible chemicals. Much of that complexity happens because of the almost infinite way even some simple elements can be combined together to give complicated structures (carbon being the archetypal example). Theoretically, for example (theoretical because not all of the examples can exist in 3D space) there are 366,319 ways to build different alkane compounds from just 20 carbon atoms and hydrogen atoms (see <a href="https://chemistry.stackexchange.com/q/16135/81">this question here</a> and <a href="http://oeis.org/A000602/list" rel="noreferrer">this entry</a> in the Encyclopaedia of integer sequences). And this number drastically understates the real complexity as it ignores mirror images and more complicated ways of joining the carbon atoms together (like in rings, for example). The complexity just gets more mind boggling if you start adding other elements to the mix.</p>
<p>No physical law prevent us making any possible compound in one step. But the sheer complexity of the end products makes simple ways to reach many of them extraordinarily unlikely from the laws of probability alone, never mind the specific ways chemical components can be easily joined up to make more complex things.</p>
<p>Here is a simple analogy. Let's say you want to assemble a <a href="https://shop.lego.com/en-GB/Death-Star-75159" rel="noreferrer">Lego model of the Star Wars Death Star weapon</a>. There are 4,016 pieces of lego that have to be assembled in the right combination and the right order. There is no <em>physical</em> law that says you couldn't somehow do that in a single step. But no sane person's intuition would assume that this was easy or likely. It isn't physical law that prevents one step assembly: it is <em>combinatorial complexity</em>. Chemistry is, do I really need to say this, more <em>complicated</em> than Lego: not least because atoms can be joined up in many more complex ways than the simple, standard-sized physical pins that join Lego bricks together.</p>
<p>Both nature and synthetic chemists have explored many ways to achieve particular end products from simpler building blocks. Sometimes new chemical Death Star equivalents (like the geometrically beautiful hydrocarbon dodecahedrane, which, incidentally, has 20 carbons but isn't counted in the list of 20 carbon alkanes) are made only after long sequences of reactions. The <a href="https://en.wikipedia.org/wiki/Dodecahedrane" rel="noreferrer">original synthesis of dodecahedrane</a> took 29 steps but others found better, higher yielding, routes that took only 20. Many important drugs are first synthesised in long sequences of reactions but are later found to be available via much shorter routes (there is nothing like the economics of manufacturing cost to encourage creativity).</p>
<p>So the reason many chemical reactions take multiple steps isn't <em>physical</em> laws but probability theory. There are just too many possible chemicals and too many ways to combine things for single step routes to most given products to be likely to work. Doing one thing at a time (just like you would if building the Lego Death Star) is the way to get what you want.</p>
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https://chemistry.stackexchange.com/questions/98490/why-do-some-chemical-reactions-require-many-steps
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Question: <p>Is there somewhere where I can find an authoritative list of chemical reactions, energy requirements, known catalysts, etc.? If not, how do you know if and how to transform substance A to substance B? What references do you use?</p>
Answer:
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https://chemistry.stackexchange.com/questions/23452/is-there-an-authoritative-list-of-chemical-reactions-transformations
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Question: <p>I have always been confused about the role of slash in chemical reactions.</p>
<p>In some reactions, e.g. $\ce{NaBH4}/\ce{OH-}$ it means we use both compounds, right?</p>
<p>And in reactions where we write $\ce{Pt/Pd/Ni}$ do we mean platinum or palladium or nickel?</p>
Answer: <p>The ambiguity seems to come not so much from Chemistry, but from English punctuation. <a href="http://www.thepunctuationguide.com/slash.html" rel="nofollow noreferrer">Slashes</a> are often used in place of "and", "or", or the latin "cum" (meaning combined with). It seems that it unfortunately is just context dependent, though I would argue its use as a replacement for "or" is most consistent grammatically and defining this to be the meaning of the slash would eliminate ambiguity in these situations.</p>
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https://chemistry.stackexchange.com/questions/41492/what-is-the-role-of-the-slash-in-chemical-reactions
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Question: <p>I wondered if it was possible to predict the product(s) of a reaction (or even the equilibrium) based on the reactants and the temperature/pressure.</p>
<p>I found an answer to a similar question <a href="https://chemistry.stackexchange.com/a/2809/4447">here</a>:</p>
<blockquote>
<p>No, there is no such thing as chemical reaction are not that easily
predictable. You can get result right in some cases, but it is
impossible to count all factors.</p>
</blockquote>
<p>What (significant) factors also influence a reaction? Is it the arrangement or state of the chemicals? Is it too related to other physical properties to ignore them?</p>
<p>Please name the most important ones.</p>
Answer: <p>For predicting chemical reaction you should use classical mechanics to take in account the simple interactions between the molecules and quantum mechanical for all the aspects concerning the molecule itself and complex interactions.
Knowing the principal parameter such as temperature and pressure that could describe the system with the classical mechanics (kinetic energy etc. etc.) is not enough for predicting the reaction with <em>ab initio</em> methods.
Adding the quantum mechanical contribute is mandatory and quite hard to do. A amateur chemist do not have neither the skills nor the computation power require to make such calculations. For the moment you can't do that with any software but the last Nobel was won by three theoretical chemists who are dealing with this topic. Have a look <a href="http://www.scientificamerican.com/article/2013-chemistry-nobel-for-molecule-computer-models/" rel="noreferrer">here</a> for more information.</p>
<p>In your case where the reactions are well known you can use a chemical reactions database like <a href="http://kinetics.nist.gov/kinetics/KineticsSearchForm.jsp" rel="noreferrer">the NIST one</a>.
This is a simple query:
<img src="https://i.sstatic.net/ERUYx.png" alt="enter image description here"></p>
<p>And this is the...</p>
<p><img src="https://i.sstatic.net/xx7cu.png" alt="enter image description here"></p>
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https://chemistry.stackexchange.com/questions/8351/software-for-predicting-chemical-reactions
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Question: <p>In my thermodynamics course, we introduced the chemical potential as a modification of the first + second law of thermodynamics in the case of a system that can exchange particles with its surroundings (consider only PV work):</p>
<p><span class="math-container">\begin{equation}
dU = TdS - pdV + \sum_{j=1}\mu_j dN_j
\end{equation}</span>
where the sum is over all the components of the system. This makes sense to me - even if we keep everything else constant, just by adding more matter to the system the energy should increase. Now, this should be true for a closed system undergoing a chemical reaction, so the 3rd term on the RHS could be non-zero. If we consider a quasistatic process, we can identify the first and second terms on the RHS as the heat and work. So the chemical potential term appears to represent some sort of energy transfer separate from heat and work, but how is this possible? Aren't heat and work the only ways to transfer energy?</p>
<p>And if the chemical potential term represents some sort of work in this case, how come the term which we defined to just explain the increase of the internal energy with the increase of the amount of matter in the system also coincidentally can now be interpreted as a work term?</p>
<p>In other words, my question is how do I physically interpret the chemical potential term?</p>
<p>I asked this question in Physics Stack Exchange (I am a physics student), but I wasn't able to obtain an answer that made complete sense to me (I was told that internal energy doesn't include bond energy, but I couldn't find a source that confirms this).</p>
Answer:
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https://chemistry.stackexchange.com/questions/160446/meaning-of-chemical-potential-in-chemical-reactions
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Question: <p>Are there chemical reactions that could cool down an average sized room by a noticeable amount (say 5 °C)?</p>
<p>I would like to investigate if it is possible to have a situation where I can mix 2 reagents at room temperature and pressure and in open air then they should react and become colder than room temperature without evaporation of some type, with an eye to making a noticeable drop in the room temperature.</p>
Answer: <p>The reaction between ammonium thiocyanate and barium hydroxide octahydrate is endothermic. It absorbs heat from the surroundings.</p>
<p><a href="http://www.youtube.com/watch?v=MyAzjSdc3Fc" rel="nofollow">http://www.youtube.com/watch?v=MyAzjSdc3Fc</a></p>
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https://chemistry.stackexchange.com/questions/1238/chemical-reactions-with-a-room-scale-cooling-effect
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Question: <p>I have heard that chemical reactions create energy. I wanted to know how this energy was created (specifically light energy) and how this energy came about. I wanted to know if the energy produced was made of particles (for example, light energy is made of photons).</p>
<p><strong>My answer</strong> I already knew about heat, kinetic, potential, and sound energy. What I was really looking for was light energy, which is caused by a phenomenon known as chemiluminescence. </p>
Answer: <p>Usually it's radiation. Depending on how exotermic reaction was, in which medium was it done, result is light staring with infra-red up to v.short ultra-violet. You can't generate particles like electrons because the low of Charge conservation must be obeyed (you transferring the electrons from one substance to the other). </p>
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https://chemistry.stackexchange.com/questions/5440/what-is-the-energy-released-in-chemical-reactions
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Question: <p>I wanted to know some common parameters which decide the feasibility of any chemical reaction.
And can we make a non favourable reaction favourable.</p>
Answer: <p>Because a reaction is thermodynamically favoured does not mean that it will be a fast reaction. So 'yes' they always proceed but possibly infinitesimally slowly. Temperature is the most common way of quickening a reaction. Of course a catalyst also does so but this generally by changing the way the reaction occurs, i.e. the mechanism is different using a catalyst but the product is the same. Enzymes are natures catalysts, in synthetic chemistry (and in you car exhaust) metal based compounds are often used.</p>
<p>All reactions have an activation energy $E_a$ between reactants and products and a small increase in the size of this can slow a reaction exponentially. Experimentally, the rate constant is generally found be of the form $k=k_0 exp(-E_a/RT) $, which is the Arrhenius equation, with <em>R</em> the gas constant and <em>T</em> the temperature in Kelvin. </p>
<p>The Boltzmann thermal distribution explains why this type of equation applies. This shows that as temperature increases molecules have more energy and so surmount the activation energy more frequently and so reaction rate increases,</p>
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https://chemistry.stackexchange.com/questions/54722/do-thermodynamically-favourable-chemical-reactions-always-proceed
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Question: <p>I got interested in Chemical Reaction Theory by studying the lecture notes of Feinberg and related papers for my bachelor thesis and want to dive deeper into that subject.</p>
<p>Are there any books you would recommend for doing so? I would really appreciate it. I'm looking for something which emphasizes the mathematical aspects but also gives good actual chemistry examples or references. </p>
<p>So far I found a book by Peter Érdi & Janos Tóth from 1989 called "<em>Mathematical Models of Chemical Reactions: Theory and Applications of Deterministic and Stochastic Models</em>", which does just that. However I fear it is a little outdated as it seems there has been quite some progress in that field recently. So maybe there isn't even a book out yet as the theory seems relatively fragmented.</p>
<p>Do you know more?</p>
Answer: <p>If you are up for some fun and want to learn about unimolecular reactions (e.g., rearrangements decompositions after energy absorption) then you should try <em>Theory of unimolecular and recombination reactions</em> by RG Gilbert, SC Smith. <em>Oxford: Blackwell Scientific Publications</em> (<strong>1990</strong>).</p>
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https://chemistry.stackexchange.com/questions/69280/books-on-chemical-reaction-theory
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Question: <p>Can anybody give me a schematic representation of how quantum tunneling allows chemical reactions to occur at very low temperatures like in the interstellar medium.</p>
Answer:
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https://chemistry.stackexchange.com/questions/34858/effect-of-quantum-tunnelling-on-chemical-reactions-at-very-low-temperature
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Question: <p>I know this kind of question has been asked many times but I think this is a bit different.</p>
<p>We have $G = H - TS$. Here I am talking about chemical reactions at constant pressure and temperature. We can write $\Delta G = Q - Q_\mathrm{rev} = \Delta H - T \Delta S$.</p>
<p>For an irreversible chemical reaction, for example an exothermic one, if $q = -10~\mathrm{kJ~mol^{-1}}$ (exothermic), then $Q_\mathrm{rev}$ could be $-9$, $-8$, $-7$, etc. The difference $(Q – Q_\mathrm{rev})$ would be negative ($-1$, $-2$, $-3$, etc.). This represents the portion of $Q$ that can be converted into non-PV work. The remainder of the heat is dispersed into the surrounding and is wasted. Right?</p>
<p>So here $Q$ as absolute value is more than $Q_\mathrm{rev}$, so we have more heat generated than a reversible chemical reaction that can be used as work ($Q = 8~\mathrm{kJ~mol^{-1}}$ and $Q_\mathrm{rev} = 2~\mathrm{kJ~mol^{-1}}$). So why is it said that a reversible reaction produces more useful heat? Again, I am talking about chemical reaction and not mechanical process.</p>
Answer:
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https://chemistry.stackexchange.com/questions/41057/gibbs-free-energy-in-chemical-reaction
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Question: <p>I know that one current area of research is ways to protect astronauts from ionizing radiation when they venture out of the atmosphere of Earth, but would that same ionizing radiation be a cause of concern when performing chemical reactions in space or in the atmosphere of planets with little atmosphere?</p>
<p>I'm aware that radiation like ultraviolet, which is present in sunlight here on Earth, is used in organic chemistry for the homolytic fission of halides, but I'm not sure how much higher energy radiation might affect other reactions.</p>
Answer: <p>It depends....</p>
<p>First let's define the "problem space". </p>
<p>Chemical reactions are typically driven by a few eV (electron volts). "Ionizing radiation" can be keV or MeV which is vastly excessive. In fact that amount of energy is so massive that it would "rip up" the chemical bonding in any material. Only solid metals would be somewhat stable since the 3D lattice locks the atoms into place. $\ce{NaCl}$ for example could decompose to Na metal and $\ce{Cl_2}$ gas. </p>
<p>Any sort of chemical reaction in space has to have a container of some sort which would mitigate the penetration of the ionizing radiation somewhat. But it surely won't stop all of the ionizing radiation. There are nuclear experiments that are conducted a mile underground to try to remove cosmic particles. </p>
<p>The primary source of ionizing radiation in our solar system is the sun. So more distance from the sun is your friend. </p>
<p>"Performing chemical reactions in space" sort of implies that a human is doing the reactions. A biological entity is going to be more effected than any vat of chemicals. So in an environment which humans or plants could safely operate, then performing chemical reactions won't be a problem. </p>
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https://chemistry.stackexchange.com/questions/30787/radiation-in-space-and-its-effects-on-chemical-reactions
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Question: <p>Considering energy-releasing devices such as bombs or batteries which operate on chemical reactions and not nuclear (i.e. strong/weak) forces, what are the upper bounds on the amount of chemical potential energy that can be contained in 1kg or 1m<sup>3</sup> of ordinary matter at RTP?</p>
<p>Here I'm not asking for the energy density of known compounds, necessarily, but rather an answer of the type "no conceivable compound could exceed X J/kg because ..."</p>
<p>Extra kudos if you can add insight into limits on the rate of energy release and efficiency considerations.</p>
Answer:
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https://chemistry.stackexchange.com/questions/57434/whats-the-limit-on-energy-density-for-chemical-reactions
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Question: <p>Every day we use chemical reactions to perform mechanical work by creating either heat (e.g. in a piston engine) or electricity (batteries). I know muscles perform work by taking stored chemical energy and converting it directly into mechanical force.</p>
<p>Other than in organic chemistry, are there any examples of chemical reactions that we use to perform mechanical work without the intermediate step of harnessing the heat or electrical potential created by the reaction?</p>
Answer:
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https://chemistry.stackexchange.com/questions/14431/are-there-practical-chemical-reactions-that-do-mechanical-work-without-heat-or-e
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Question: <p>I'm a geology student completing a project on chemical staining and was after some chemistry help on some of the reactions taking place. I am using various different stains to identify carbonate and feldspar minerals. </p>
<p>One of the stains, in particular, is alizarin red S (1,2-dihydroxyanthraquinone) and is used to stain calcite ($\ce{CaCO3}$) red and Fe-calcite/Fe-dolomite blue. The stain powder is mixed with a weak (2%) HCl solution to react with the carbonate and produce the stain. However, I am just unsure about what reactions are taking place between the stain solution and the mineral that produce the precipitate on the surface of the grains. </p>
<p>I'm not finding literature on this reaction - probably because it has been mainly used by geologists without a solid chemistry background. Any help would be much appreciated.</p>
Answer: <p>Alizarin red S can stain calcium deposits through interaction of its sulfonic acid and hydroxy groups with calcium ions.</p>
<p>I found a reference for you: <a href="http://jhc.sagepub.com/content/17/2/110.full.pdf+html" rel="nofollow">http://jhc.sagepub.com/content/17/2/110.full.pdf+html</a></p>
<p>Interestingly, however, this research seems to suggest using a solution of pH $\approx$ 9, stating that solutions of acetic acid (pH 5) did not work that well.</p>
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https://chemistry.stackexchange.com/questions/34291/chemical-reactions-involved-in-staining
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Question: <p>"In reversible reactions, as the reactants react with other reactants to form products, the products are reacting with other products to form reactants."
<a href="http://chemwiki.ucdavis.edu/Physical_Chemistry/Equilibria/Chemical_Equilibria/Reversible_vs._Irreversible_Reactions" rel="nofollow">http://chemwiki.ucdavis.edu/Physical_Chemistry/Equilibria/Chemical_Equilibria/Reversible_vs._Irreversible_Reactions</a></p>
<p>Inside an ideal battery, the chemical reaction is reversible (at equilibrium), thus the oxydation-reduction reaction Zn + Cu2+ = Zn2+ + Cu is happening in both direction at the same rate right?</p>
<p>Now, for a real battery, there's resistivity inside it due to many factors, thus the chemical reaction is irreversible. My question is, during the irreversible reaction, is the reaction happening in both directions but at different rate due to resistivity inside the battery or it is just like the combustion reaction happening in one direction?</p>
Answer:
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https://chemistry.stackexchange.com/questions/41074/irreversible-chemical-reaction-in-a-battery
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Question: <p>Chemical transformation alters the chemical properties of a material, which includes reactivity with various chemical species. The new specials thus formed have different characteristics from the initials.</p>
<p>The chemical reaction breaks bonds, forms bonds, or both. Basically, the atoms within the species reorganize into a new combination, producing a new chemical species with different chemical properties.</p>
<p>Can a chemical reaction happen without a transformation? There is a chemical balance that pH and chemical properties do not change ...</p>
<p>If there is a chemical reaction in which there is no transformation, what example can you give me?</p>
Answer: <p>What you are looking for describes the state of thermodynamic equilibrium. Many examples you've been presented are reactions of the form <span class="math-container">$$\ce{A^* +B<->B^* +A}$$</span> which do not "transform" the properties of the system as a whole. The reactions permute the arrangement of atoms into chemically identical arrangements. From a thermodynamic standpoint they are equivalent initial and final states.</p>
<p>If you look at a collection of molecules in aggregate you might identify other reactions called <a href="https://en.wikipedia.org/wiki/Isomerization" rel="nofollow noreferrer">isomerizations</a>, including <a href="https://en.wikipedia.org/wiki/Tautomer" rel="nofollow noreferrer">tautomerizations</a>, that involve rapid changes in the structure of a molecule between various structural forms. In a given sample you will encounter all such isomers in equilibrium concentrations, and if you focus on just one single molecule you will see it sample all of the possible isomers, provided you wait long enough. During that time, if the system is in equilibrium, the properties of the sample as a whole will not change and the relative proportions of the different isomers will be preserved.</p>
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https://chemistry.stackexchange.com/questions/136415/is-there-a-chemical-reaction-without-a-chemical-change
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Question: <blockquote>
<p>Chemical reactions occur at constant temperature and pressure.</p>
</blockquote>
<p>Consider a gaseous, equilibrium reaction: <span class="math-container">$\ce{2NO2(g) <=> N2O4(g)}$</span>. Most questions/textbooks formulate such questions by stating: <em>The reaction happens at (<span class="math-container">$T$</span>) temperature and (<span class="math-container">$P$</span>) pressure.</em></p>
<p>This gives the impression that the surrounding Temperature and pressure are constant.</p>
<ul>
<li>The first confusion that then arises is: For thermodynamic quantities such as <em>enthalpy</em> that involve pressure, which pressure should we use, internal or external?</li>
</ul>
<p>After reading some chem.SE answers, it seems to me that <span class="math-container">$P_{sys}=P_{surr}$</span> is a basic assumption. However this doesn't seem to go well with the example I mentioned: Since the pressure of the system will be given by <span class="math-container">$(n_1)RT/V + (n_2)RT/v$</span>, where <span class="math-container">$n_1$</span> and <span class="math-container">$n_2$</span> are the moles of <span class="math-container">$\ce{NO2}$</span> and <span class="math-container">$\ce{N2O4}$</span>. Clearly, as the reaction progresses, (<span class="math-container">$n_1+n_2$</span>) changes, and thus,the pressure of the system changes. If the surrounding pressure is kept constant, this beaks the "assumption": <span class="math-container">$P_{sys}=P_{surr}$</span>.</p>
<p>Am I missing something?</p>
Answer: <p>You have correctly stated the pressure of the system is <span class="math-container">$$p = \frac {(n_1 + n_2)RT}{V}$$</span></p>
<p>But at the end of your question you incorrectly imply the volume is constant and the pressure changes. That is not true. Constant pressure means the external constant pressure ( like the atmospheric one ) keeps the system pressure constant. Imagine there is a massless, frictionless piston, ensuring <span class="math-container">$p_\mathrm{ext} = p_\mathrm{sys}$</span>. It is similar as a thermostatic water bath keeps the system temperature constant.</p>
<p>So less confusing is to rewrite the ideal gas state equation :</p>
<p><span class="math-container">$$V = \frac {(n_1 + n_2)RT}{p}$$</span></p>
<p>There are 4 variables: <span class="math-container">$p, V, T, n_\mathrm{tot}=n_1 + n_2$</span>.
But there are just 3 degress of freedom = 3 independent variables.</p>
<p>Either <span class="math-container">$V, n_\mathrm{tot}, T$</span> are given, and <span class="math-container">$p=f(V, n_\mathrm{tot},T)$</span>,<br />
either <span class="math-container">$p, V, T$</span> are given, and <span class="math-container">$n_\mathrm{tot}=f(p,V,T)$</span>,<br />
either <span class="math-container">$p, n_\mathrm{tot}, T$</span> are given, and <span class="math-container">$V=f(p,n_\mathrm{tot},T)$</span>,<br />
either <span class="math-container">$p, n_\mathrm{tot}, V$</span> are given, and <span class="math-container">$T=f(p,n_\mathrm{tot},V)$</span>.</p>
<p>We have already given 2 variables: <span class="math-container">$p, T$</span>, with <span class="math-container">$n_\mathrm{tot},V$</span> remaining free.<br />
But there is the equilibrium relation</p>
<p><span class="math-container">$$K_p = \frac {p_{\ce{N2O4}}} {({p_{\ce{NO2}} )}^2}=\frac {p \cdot ( 1 - x_{\ce{NO2}}) } {({p \cdot x_{\ce{NO2}} )}^2}$$</span></p>
<p><span class="math-container">$$K_p \cdot p \cdot {({x_{\ce{NO2}} )}^2} + x_{\ce{NO2}} - 1 = 0$$</span></p>
<p>Solving the quadratic equation we would finally get <span class="math-container">$n_\mathrm{tot}$</span>, so all 3 degrees of freedom are saturated with given values for <span class="math-container">$p, T, n_\mathrm{tot}$</span>.</p>
<p>So in our case, the following applies:</p>
<p><span class="math-container">$p, n_\mathrm{tot}, T$</span> are given, and <span class="math-container">$V=f(p,n_\mathrm{tot},T)=\dfrac {n_\mathrm{tot}RT}{p}$</span></p>
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https://chemistry.stackexchange.com/questions/138417/thermodynamics-of-chemical-reactions-at-constant-pressure
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Question: <p>what are some of the original examples of uses of differential equations for modeling and analyzing chemical reactions, particularly those relevant to biochemistry, involving proteins and enzymes? Michaelis and Menten's work in 1910s is one example. </p>
<p>What are the earlier examples or antecedents to this work? (references to good historical accounts of this modeling endeavor would also be helpful).</p>
Answer:
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https://chemistry.stackexchange.com/questions/97810/origin-of-use-of-differential-equations-for-modeling-chemical-reactions
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Question: <p>Tell me the requirements and procedure for <strong>producing black smoke using chemical reactions</strong>.</p>
Answer: <p>When ignited, mixtures of potassium chlorate, charcoal and anthracene (or naphthalene) produce black smoke.</p>
<p><strong>However, note that milling and grinding dry mixtures of potassium chlorate and charcoal is a well-known method to cause an explosion and severely harm or kill yourself!</strong> </p>
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https://chemistry.stackexchange.com/questions/24806/how-to-produce-black-smoke-using-chemical-reaction
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Question: <p>I was a college student of physics ten years ago, and recently started to learn biochemistry. I enjoy finding out that some familiar concepts in physics play important roles in biochemistry such as Entropy and Gibbs free energy. </p>
<p>For example, as a (ex-)student of physics, I am happy to know that Gibbs free energy helps to decide the directions of chemnical reactions. I feel this is a good example where a sort of fundamental law of physics determines how phenomenon looks like.</p>
<p>However, I still can not understand why the chemical reactions in a body need to be so complex. Many chemnical systems consists of more than several steps to acheive their purposes. According to <a href="https://en.m.wikipedia.org/wiki/Glycolysis" rel="nofollow noreferrer">wikipedia</a>, glycolysis takes ten steps through its process. Why so many steps are necessary?</p>
<p>I tried to find out a physical law which prohibit that glycolysis process is achieved by one or two steps. But I could not find an answer.</p>
<p>I would like to know (or discuss) whether there is a physical law which makes the chemical system such a complex one (many steps required).</p>
<p>My assumption is that some physical law prohibit the existence of a enzyme which realize a one-step process of glycolysis.</p>
Answer: <p>The number of steps required to model a reaction really depends on what time scales you are interested in looking at. Let's take the process of burning natural gas with air. If you only care about the final products of the combustion after a really long time, like let's say hours, then a single step reaction would be a perfectly good model. In fact, in situations where you only care about the global heat release and maybe the speed of the reaction at one particular condition, single-step or few-step reactions are just fine. </p>
<p>But let's say you are really interested in what's happening. When we look at a global reaction, let's say:</p>
<p>$$ O_2 + 2H_2 \rightarrow 2H_2 O $$</p>
<p>We'll assume this is in air, but the nitrogen doesn't really react. Nice and simple, right? Well, for the reactions to occur, you need some $O_2$ molecules to collide with $H_2$ molecules. But it's not enough that they collide. They need to collide with enough energy to break the bonds between them. And it's possible that one of the molecules breaks at lower energy than the the other. When they break, they break into 2 O's or 2 H'2. So our simple reaction really starts out as:</p>
<p>$$ O_2 + M \rightarrow 2 O + M $$
and
$$ H_2 + M \rightarrow 2 H + M $$</p>
<p>where $M$ is any other molecule. Okay, so now we've got a mixture of $H$, $O$, $H_2$, $O_2$, and $N_2$ floating around and bumping into each other. If they bump together with enough energy, we can start forming other things. Things like $HO_2$, $OH$, $H_2O_2$ and of course, $H_2O$. </p>
<p>Because these reactions rely on collisions, you need to form some things before you can form other things. So before an $O$ and an $H$ can collide to form $OH$, the $O_2$ and $H_2$ have to collide with other things and break apart. So there's finite time scales with all of the reactions, and they tend to cascade through a series of reactions before reaching the final product. If you are looking at time scales similar to those of the reactions, then these details really matter. </p>
<p>Hydrogen reactions are super simple. Imagine how complex organic molecules are. Even things like methane or propane have hundreds or thousands of steps to go from the complex molecule through all of the radicals to the final species. And the time scales the reactions occur over are all based on how frequently the collisions between them occur, and how much energy those collisions have. </p>
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https://chemistry.stackexchange.com/questions/98637/why-do-some-chemical-reactions-require-many-steps
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Question: <p>I have come across many questions like: "if electron had 3 spins (-1/2,0,+12) then what change will be there in the periodic table?", also sometimes " if the capacity of each orbital becomes 5 then in what period or group will the particular element be?" So what is the relation between quantum no. and the periodic table?</p>
Answer: <p>If electrons could have $m_s = -1/2, 0,$ and $1/2$, then the entire structure of the Periodic Table would be different. The s-block would have 3 elements instead of the 2 that we see now, because each s orbital can accommodate 3 electrons, and similarly the p-block would have 9 elements instead of 6.</p>
<p>It is not possible to say, for example, "sodium would be in so-and-so position in the new Periodic Table" because in such a universe, the element sodium would not even exist the way it does in our universe. The new Periodic Table would not have an element with the electronic configuration $\mathrm{(1s)^2(2s)^2(2p)^6(3s)^1}$. What I am basically saying is, there is no one-to-one correspondence between the elements in our universe and the elements in such a hypothetical universe (<em>mathematically</em> speaking, you can, but it would not make any <em>chemical</em> sense). Nevertheless, you could say that sodium is defined to be the element with 11 protons and 11 electrons. In that case, it would have a configuration of $\mathrm{(1s)^3(2s)^3(2p)^5}$ and it would be the fifth element in the Period 2 p-block.</p>
<p>Actually, there is no evidence that the aufbau principle should still hold true in such a universe: the large repulsion that arises from putting 3 electrons into the same orbital might well make filling the 2s orbital before the 1s orbital more favourable. So, our hypothetical "sodium" might have a weird electronic configuration of $\mathrm{(1s)^2(2s)^2(2p)^7}$. The Periodic Table is useful partly because it groups elements with similar electron configurations - which implies similar chemical properties - together. However, if these elements do not obey the aufbau principle, then there is no guarantee that the elements in the same group should have similar chemical properties, and therefore no guarantee that a Periodic Table in such a hypothetical universe would even be useful.</p>
<p>I should end off by saying that the laws of quantum mechanics stipulate that the different values of $m_s$ must increase in steps of $1$. Therefore, it is not actually <em>possible</em> that $m_s$ could ever take on values of $-1/2, 0$, and $1/2$, since these increase in steps of $1/2$. You might say: "Ah! But we could say, what happens if $m_s = -1, 0, 1$." Well, in that case, you have much more to worry about than just the orbital occupancy. Without going into too much detail, the Pauli exclusion principle would no longer apply to electrons, and you would have more problems than just "one orbital can fit 3 electrons".</p>
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https://chemistry.stackexchange.com/questions/40377/periodic-table-quantum-numbers
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Question: <p>The periodic table I understand is arranged by order of increasing atomic number after Henry Moseley's X-ray experiment. </p>
<p>But I also learned that the periodic table also has its shape due to the types of subshells present in certain sections called blocks of the table.</p>
<p>However, I still do not understand who shaped the modern periodic table so it mimics the filling of lattermost subshells of atoms of each element (in order of increasing number of electrons- from left to right as well as top to bottom for the elements.) </p>
<p>My Question is : was the periodic table Mendeleev and Moseley devised not in a shape that can be used to predict the filling order of each elements, and that the periodic table was later adapted to fit this concept of orbitals in? </p>
Answer: <p>Mendeleev was the first to realize that properties recur among the elements. To highlight this, he devised the early periodic table <strong>based on atomic masses</strong>. Moseley came along and stated that the periodic properties of elements was a function of their <strong>atomic numbers</strong> rather than their atomic masses. </p>
<p><a href="https://i.sstatic.net/g4v1N.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/g4v1N.png" alt="Mendeleev's periodic table"></a></p>
<p>It was <strong>Niels Bohr</strong> who came up with the idea of shells and subshells. He developed his own take on the periodic table, which looked somewhat like this:</p>
<p><a href="https://i.sstatic.net/y3ejD.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/y3ejD.jpg" alt="Bohr's representation"></a></p>
<p>Finally, coming to your question, A lot of derivatives of the periodic table were made by various scientists during the 1920's - 1940's. The version we use today was made by <strong>Glenn T. Seaborg</strong> and his colleagues.</p>
<blockquote>
<p>Seaborg and collaborators had synthetically produced several new elements with atomic numbers beyond uranium, the last naturally occurring element in the table. Seaborg saw that these elements, the transuranics (plus the three elements preceding uranium) demanded a new row in the table, something Mendeleev had not foreseen. Seaborg’s table added the row for those elements beneath a similar row for the rare earth elements, whose proper place had never been quite clear, either.</p>
</blockquote>
<p><strong>Further reading:</strong></p>
<ul>
<li><a href="https://www.sciencenews.org/article/periodic-table-history-chemical-elements-150-anniversary" rel="nofollow noreferrer">How the periodic table went from a sketch to an enduring masterpiece</a></li>
<li><a href="https://en.wikipedia.org/wiki/Periodic_table#Second_version_and_further_development" rel="nofollow noreferrer">Further development of the Periodic Table - Wikipedia</a></li>
</ul>
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https://chemistry.stackexchange.com/questions/125276/structure-of-the-periodic-table
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Question: <p>I am not a chemist, but I am interested in Science in a general sense. Can anybody explain why the periodic table is periodic in nature? I would appreciate links for further reading.</p>
Answer: <p>Elements interact with the rest of the world through their electrons. How those electrons interact with other atoms (or electromagnetic radiation) determines how that atom behaves.</p>
<p>You see this with isotopes. Different elements are distinguished from each other by the number of protons in their nucleus. Changing the number of neutrons has little effect on their properties. Why is this? It's not the protons themselves which change the properties, instead it's how the change in total positive charge of the nucleus changes how many electrons the atom can hold and how they behave that changes the properties. Different numbers of electrons - and specifically different numbers of electrons with respect to the net charge on the atom - change the properties of the atom. Changing the number of neutrons changes the nucleus, but has little effect on how the electrons behave, so has little effect on the chemistry of the atom.</p>
<p>So what does that have to do with "periodicity" of the periodic table? Well, there's a structure to how the electrons are "stored" in an atom. These are orbitals. For a bunch of quantum mechanical reasons that are rather advanced for this question, there are repeating patterns in these orbitals. Most particularly, in the <em>l</em> <a href="https://www.angelo.edu/faculty/kboudrea/general/quantum_numbers/Quantum_Numbers.htm" rel="nofollow noreferrer">quantum number</a> which determines the shape of the orbital. Each period corresponds (roughly) to the <em>n</em> quantum number. For each <em>n</em>, there are a set of <em>l</em>s which go along. (Because of tradition, orbitals with different <em>l</em> quantum numbers get letter labels: <em>s</em>, <em>p</em>, <em>d</em>, <em>f</em>, ...)</p>
<p>This is why you see periodic trends. Having exactly filled <em>s</em> and <em>p</em> orbitals is the most stable, and each <em>n</em> has its own set of <em>s</em> and <em>p</em>. So each time you get a filled <em>s</em> and <em>p</em>, you get an inert noble gas. For halogens (like chlorine and bromine), you need just one extra electron to fill the <em>s</em> and <em>p</em> orbitals, so they really like taking a single electron from other elements. In contrast, the alkali metals (like sodium and potassium) can most easily get to a completely filled <em>s</em> and <em>p</em> orbital state by <em>losing</em> a single electron, resulting in their propensity for a positive charge. It's how close the atoms are to filled <em>s</em> and <em>p</em> orbitals - regardless of their <em>n</em> quantum number - and what it takes to get there which provides the bulk of the "periodicity" of the periodic table. </p>
<p>It turns out that the <em>s</em> and <em>p</em> orbitals are the most "exposed", so what's going on there contributes the majority of the behavioral change between elements. Elements that differ only in how the electrons in their <em>d</em> orbitals are situated have much less property differences (this is why most transition metals have similar properties). Elements which differ only in <em>f</em> orbitals (like the Lanthanides) are even more alike. There certainly are differences here, but they tend to rely on more subtle effects than those that cause the alkali/chalcogen/halogen/noble gas differences.</p>
<p>Note that this sort of orbital-based periodicity breaks down as you get lower in the periodic table. That's because you actually start to get <a href="https://chemistry.stackexchange.com/questions/16633/why-is-gold-golden">relativistic effects</a>, and how the orbitals behave starts to change. Periodic trends are just that - trends - and aren't absolute.</p>
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https://chemistry.stackexchange.com/questions/43869/why-is-the-periodic-table-periodic
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Question: <p>I there a <em>Good</em> Version of a printable Periodic table Which is minimalistic and gives <strong>necessary</strong> information only such as -</p>
<ul>
<li>At. Number</li>
<li>Element Name</li>
<li>At. weight</li>
<li>Shell configuration </li>
<li>color coding of various groups or Series</li>
</ul>
Answer: <p>The <a href="https://iupac.org/what-we-do/periodic-table-of-elements/" rel="noreferrer">IUPAC periodic table</a> (<a href="http://iupac.org/cms/wp-content/uploads/2015/07/IUPAC_Periodic_Table-28Nov16.pdf" rel="noreferrer">2016-pdf</a>) is good because it quantifies the accuracy of the natural abundance atomic weights, but it doesn't give electron configuration. </p>
<p>The <a href="http://www.nist.gov/pml/data/periodic.cfm" rel="noreferrer">NIST periodic table</a> has electron configuration, and probably is closest to what you want.</p>
<p><img src="https://i.sstatic.net/dkIFU.png" alt="enter image description here"></p>
<p>The NIST table is also good from a copyright point of view, because you can reproduce it without worrying about copyright infrigment, as <a href="http://www.usa.gov/copyright.shtml" rel="noreferrer">US government works are generally not subject to copyright protection</a>. </p>
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https://chemistry.stackexchange.com/questions/24606/periodic-table-for-printing
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Question: <p>Why do we find big spaces in the periods of the Periodic Table between $\ce{H}$ and $\ce{He}$, $\ce{Be}$ and $\ce{B}$, and $\ce{Mg}$ and $\ce{Al}$? </p>
<p>What is the logic of such organization of the periods?</p>
Answer: <p>From a historical perspective, this was done to account for the commonalities between how the various elements behaved. In other words, the Alkali metals all exhibited a strong reaction with $H_2O$, the noble gasses all exhibited inertness in reactions, and so on.</p>
<p>This is explained in modern day science via the quantum description of electronic structure which indicates that elements within the same group tend to have the same number of valence electrons in the valence shell. Simply put, the reason why there are such gaps between $H$ and $He$; $Be$ and $B$, and otherwise is because there are simply different quantum arrangements of the electrons which are readily accessible to the element. That is, the ground state of $He$ has both accessible $l=0$ states occupied by electrons, which constitutes the valence shell and so is in an energetically favorable state to remain inert - becoming of the noble gasses. Hence, it’s moved far to the right from $H$ to the 8th group; consistent with the historical structure of the table.</p>
<p>That’s a crude description, but about what’s happening here. I agree however that the chemists may feel more at home discussing the periodic table. I’ll stick to the chart of nuclides.</p>
<p>Also, the Wikipedia article is fairly informative on this topic:
<a href="http://en.wikipedia.org/wiki/Periodic_table" rel="nofollow noreferrer">http://en.wikipedia.org/wiki/Periodic_table</a></p>
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https://chemistry.stackexchange.com/questions/28769/organisation-in-periodic-table
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Question: <p>Several people have said that the key to understanding chemistry is through memorizing the periodic table.</p>
<p>I want to ask if there is a simple technique to learn it, or if I just have to remember every element as it is?</p>
Answer: <p>You can memorize the periodic table in one night, simply by emulating best-practice memorization techniques and doing what memory experts do. Common sense, right?</p>
<p>Memory experts and world champion memory ‘athletes’ activate the enormous natural power of their visual memory by using visualization and association mnemonic techniques. </p>
<p>That’s a fancy way of saying they create mental pictures and link them together in their mind. It’s incredibly simple but amazingly fast and effective.</p>
<p>Watch <a href="https://www.youtube.com/watch?v=0nFkQ4cQhME">YouTube’s #1 “How to Memorize” video</a> and you’ll probably amaze yourself with how easily you can remember and recall 15 random words in order, using one of these techniques.</p>
<p>The foundation technique most memory experts use is the Method of Loci (or Memory Palace or Journey Method). Think of a particular journey you take every day, and picture certain locations along the way. </p>
<p>For example, imagine leaving home in the morning and travelling to work or school. You might walk out your front door, through the front gate, and get on a bus. </p>
<p>At each location you visualize an object that represents what you’re trying to remember. Because the chemical elements themselves can be difficult to visualize, you substitute them with an object that you will naturally associate or link to the element itself. </p>
<p>For example, ‘hydrogen’ sounds similar to ‘hydrant’, so when you visualize a hydrant sitting at your front door, you’ll be prompted to remember ‘hydrogen’. When you picture a large helium balloon tied to your front gate, you’ll remember helium. And when your bus begins talking with a ‘lithp’ (how people with a lisp pronounce ‘lisp’), you’ll be prompted to recall lithium.</p>
<p>These established memory techniques have been proven by over 50 years of academic research in fields like cognitive psychology. Google ‘memory palace’ or ‘world memory champion’ and you’ll discover they’re the fastest and most effective methods to memorize a deck of playing cards and a lot of other geeky things.</p>
<p>The method used in the video above is called the Link and Story Method, and is based on the same principles of visualization and association. The weakness of this method compared to the Memory Palace is the amount of time it takes to create the (intentionally) bizarre and crazy story to link all the words (or chemical elements) together.</p>
<p>But all the work has already been done for you at <a href="https://www.memorizeperiodictable.com/">How to Memorize the Periodic Table</a>. This animated video course is the fastest way to memorize the periodic table because it uses best-practice visual memory techniques. </p>
<p>All the mental images and association links described above have already been created, and transformed into engaging whiteboard animation videos. You just need to sit back and watch, and let the amazing natural power of your visual memory do its thing.</p>
<p>What about other techniques? </p>
<p>Most other methods people suggest to memorize the periodic table rely on verbal memory, but don’t activate the enormous power of your visual memory.</p>
<p>Flashcards or equivalent apps are convenient but don’t provide an association or link between chemical element names, meaning they rely on rote memorization. Repetition by itself is not meaningful, takes an unnecessarily long time and effective retention is low.</p>
<p>Acronyms and acrostics are ‘first letter mnemonics’. You could use the acronym HHeLiBeBCNOF (pronounced ‘heeliebeb kernoff’) to remember the first nine elements. It's a nonsense word, but it condenses nine names into one mental prompt or cue.</p>
<p>Or the acrostic “<strong>H</strong>ere <strong>He</strong> <strong>Li</strong>es <strong>Be</strong>neath <strong>B</strong>ed <strong>C</strong>lothes, <strong>N</strong>othing <strong>O</strong>n, <strong>F</strong>eeling <strong>Ne</strong>rvous” would equate to H He Li Be B C N O F Ne.</p>
<p>Acronyms chunk words together, which is good (even if they are nonsense) and acrostics use more meaning, but either way you'll only have the first letter or two to remind you of each element's full name. That's tough for 118 elements!</p>
<p>The first letter cues don’t prompt you enough to recall the complete element name, so acronyms and acrostics can be great for the first 20 elements, but not for all 118.</p>
<p>Songs are also popular, whether you’re a fan of Tom Lehrer or ASAP Science. A catchy tune gives better association and meaning than acronyms and acrostics, but you still have to rely on bucketloads of repetition. They’re a great way to make repetition fun, but songs only tap into your verbal memory, not your powerful visual memory.</p>
<p>Bottom line, you should play to your natural strengths. Your brain loves pictures. And that makes visual memory techniques 10X more powerful than verbal memory techniques (like songs and acronyms) to memorize the periodic table.</p>
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https://chemistry.stackexchange.com/questions/24723/memorizing-the-periodic-table
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Question: <p>The groups go from 1 to 18 in the periodic table. When looking at the transition metals in the periodic table, You see roman numerals labelled with 'B,' in the order of III, IV, V, VI, VII, VIII, VIII, VIII, I, II.
Why does III - VIII come before I and II? And why does VIII get repeated three times? </p>
<p>Also, what is the difference in the groups labelled A and B, besides the fact that the B groups are the transition metals?</p>
Answer: <p>Even though your question get downvoted, I think it is an legitimate question for people to understand the trend. I believe I-VIII Roman numeral nomenclature belong to CAS system while 1-18 Arabic numeral groups are recommended by IUPAC (Ref.1). The IUPAC recommended Periodic Table is given below (ignore the Roman numerals, which I put in there to explain):</p>
<p><a href="https://i.sstatic.net/puhjb.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/puhjb.jpg" alt="The Periodic Table of Elements" /></a></p>
<p>According to Ref.1, the confusion of Periodic Table of Elements has been addressed as follows:</p>
<blockquote>
<p>H.G. Deming used the long periodic table in his textbook General Chemistry (See following diagram with Roman numerals only; Ref.2), which appeared in the USA for the first time in 1923, and designated the first two and the last five Main Groups with the notation "A", and the intervening Transition Groups with the notation "B". The numeration was chosen so that the characteristic oxides of the B groups would correspond to those of the A groups. The iron, cobalt, and nickel groups were designated neither A nor B. The Noble Gas Group was originally attached by Ueming to the left side of the periodic table. The group was later switched to the right side and usually labeled as Group VlllA. This version of the periodic table was distributed for many years by the Sargent-Welch Scientific Company, Skokie, Illinois, USA. <span class="math-container">$[\cdot\cdot\cdot]$</span></p>
<p>The designations A and B have been extensively and rather arbitrarily used in the meantime in textbooks and in publications. An investigation of the application of the subgroup designations A and B in all articles, which appeared between 1972 and 1981 and covered by Chemical Abstracts, revealed a completely arbitrary use of the designation. Moreover, more than 10% of the articles it was nearly impossible, from the wording of the text, to recognize which elements were being discussed without further information (Ref.3).</p>
</blockquote>
<p><a href="https://i.sstatic.net/n1wPp.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/n1wPp.jpg" alt="Deming’s long periodic table" /></a></p>
<p>The IUPAC Commission on the Nomenclature of Inorganic Chemistry (CNIC) proposed the designations of groups by Arabic numerals in 1984 (Ref.4), which was approved by the Nomenclature Commission of the American Chemical Society (ACS) and rest is history.</p>
<p>Thus, it is safe to say that this nomenclature is now outdated and not worth discussing.</p>
<hr />
<p><strong>References:</strong></p>
<ol>
<li>E. Fluck, “New notations in the periodic table,” <em>Pure and Applied Chemistry</em> <strong>1988</strong>, <em>60(3)</em>, 431-436 (<a href="https://dx.doi.org/10.1351/pac198860030431" rel="nofollow noreferrer">https://dx.doi.org/10.1351/pac198860030431</a>).</li>
<li>Horace Grove Deming, <em>General Chemistry</em>; J. Wiley & Sons, Inc.: New York, NY, 1923.</li>
<li>W. C. Fernelius, W. H. Powell, “Confusion in the periodic table of the elements,” <em>J. Chem. Educ.</em> <strong>1982</strong>, <em>59(6)</em>, 504-504 (<a href="https://doi.org/10.1021/ed059p504" rel="nofollow noreferrer">https://doi.org/10.1021/ed059p504</a>).</li>
<li>K. L. Loening, “Recommended Format for the Periodic Table of the Elements,” <em>J. Chem. Educ.</em> <strong>1984</strong>, <em>61(2)</em>, 136-136 (<a href="https://doi.org/10.1021/ed061p136" rel="nofollow noreferrer">https://doi.org/10.1021/ed061p136</a>).</li>
</ol>
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https://chemistry.stackexchange.com/questions/133155/groups-of-the-periodic-table
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Question: <p>What are the blocks of the periodic table? What is the purpose of naming the elements per block group? What do they signify?</p>
Answer: <p>Below is a picture of the 4 blocks in the Periodic Table. The elements in a block all use the same orbital to hold their valence or outer shell electrons. For example, all of the elements in block 1 have their valence electrons in an $\ce{s}$ orbital, those in block 2 have their valence electrons in a $\ce{p}$ orbital, block 3 the $\ce{d}$ orbitals and block 4 the $\ce{f}$ orbitals.</p>
<p><img src="https://i.sstatic.net/e9Pmg.gif" alt="enter image description here"></p>
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https://chemistry.stackexchange.com/questions/13958/block-on-the-periodic-table
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Question: <p>How does reactivity change as you move from one side of the periodic table to the other or if you move from the top to the bottom?</p>
Answer: <p>I'm assuming you're asking about how the CHARACTER changes as we move all about the periodic table, and based on that how does the reactivity change.</p>
<p>As we move from left to right, the electropositive character decreases, and the electronegative character increases. For example, take the 3rd period. Sodium's reactivity is pretty high, because it readily gives away an electron to get a stable configuration. As we move towards the right, the reactivity decreases, but again it starts rising and reaches a high vue when we get to chlorine, which readily accepts an electron to get a stable configuration.</p>
<p>When we go down a group, electropositive character increases, but electronegative character decreases. Thus, if we may see the Li-family, reactivity increases down the group, but if we look at the halogen family, i.e. the F-family, reactivity decreases. </p>
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https://chemistry.stackexchange.com/questions/57111/reactivity-change-of-periodic-table
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Question: <p>In my Chemistry course, we must <strong>memorize a list of common polyatomic ions</strong>. Is their an easy way of memorizing ions such as Sulfate $\ce{SO4^2-}$ by looking at just the <strong>periodic table</strong>. I listed the ones we have to memorize bellow. I know that if they contain oxygen (which is most of them) they usually end in "<strong>ate</strong>" or "<strong>ite</strong>." But how do I know how many Oxygen an ion will contain and its charge. My teacher said the only reference table we can use on our test is the Periodic Table of Elements. <a href="https://i.sstatic.net/p9qxD.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/p9qxD.png" alt="enter image description here"></a></p>
<p>I have to memorize the name and the formulas of the ions. Any methods will be much appreciated. I guess the real question is their any trends in the periodic table that helps predict the charge and number of oxygens and polyatomic ions will have? So if I have Sulfate for example, Can I predict the formula by looking at Sulfur on the periodic table</p>
<p><strong>Update</strong>: My question is <strong>not a duplicate of <a href="https://chemistry.stackexchange.com/questions/32962/when-to-use-ate-and-ite-for-naming-oxyanions">When to use -ate and -ite for naming oxyanions?</a></strong> because my question wants to **use the periodic table to identify and memorize polyatomic ion **. Voldemorts question had nothing to do with memorization what so ever!</p>
<blockquote>
<p>But, what I don't understand is how does the book know that NO−3 is Nitrate: how does the book know that NO−3 is "the most common oxyanion for the element". How does it know that a charge of −1 and 3 oxygen atoms create "the most common" Nitrogen oxyanion?</p>
</blockquote>
<p>His question had nothing do with specifically looking for patterns in the periodic table to help him or her memorize the polyatomic ions. In fact he or she wasn't even asking for a technique or method to memorize polyatomic ions, but rather figure out which form of a polyatomic ion is "most common." For Example: He wanted to find out how the author of his book knows $\ce{NO3^-}$ is more common than $\ce{NO2^-}$</p>
Answer: <p><strong>Number of oxygens:</strong></p>
<p>If your anion is in:</p>
<ul>
<li>the 2nd period;</li>
<li>the VIIth main group/the 17th group/a halogen; or</li>
<li>is silicon:</li>
</ul>
<p>then the <em>-ate</em> anion will have three oxygens.</p>
<p>All other <em>-ate</em> elemental anions will have four oxygens.</p>
<p>(Take note of ‘aluminate’ which I haven’t physically <em>seen</em> in that form yet but your teacher seems to insist be $\ce{AlO2-}$; disregarding this general trend.)</p>
<p>From the <em>-ate</em> anion, remove one oxygen to arrive at the <em>-ite</em>, remove two for <em>hypo-ite</em>. Add one for <em>per-ate</em>.</p>
<p><strong>Charge:</strong></p>
<p>Start at an anion with the most oxygens. (Note: Usually this is the <em>-ate</em> but because the halogens and permanganate are special they have the <em>per-ate</em> anion which is more oxygen-rich and important here.) Assume the maximum possible oxidation state for the non-oxygen atom. Assume $-\mathrm{II}$ oxidation state for every oxygen. Add up and take the negative value to arrive at the charge.</p>
<p>A <em>hydrogen-</em> will add $\ce{H}$ and lower the charge by one.</p>
<p>A <em>thio-</em> means one oxygen is replaced by sulphur.</p>
<p>A <em>di-</em> means <em>take two of the (hydrogenated) anion and subtract water.</em> <em>Pyro</em> means the same thing.</p>
<p><strong>Memorise all the remaining!</strong> That is most importantly:</p>
<ul>
<li>Chromite. Similar to aluminate I’ not sure if I ever saw it out in the real world.</li>
<li>Cyanide/cyanate. Thiocyanate is just like thiosulphate.</li>
<li>Oxalate, acetate and tartrate. Organic ions that will never fit into this scheme nicely.</li>
<li>Peroxide and superoxide. But those are <em>-ide</em>s anyway.</li>
<li>Permanganate; which is almost like a perhalogenate. Luckily, molybdate and chromate fall into a category described above.</li>
</ul>
<p><strong>Periodic Table</strong></p>
<p><a href="https://i.sstatic.net/S4Wbb.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/S4Wbb.png" alt="enter image description here"></a></p>
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https://chemistry.stackexchange.com/questions/39265/memorizing-polyatomic-ions-using-periodic-table
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Question: <p>Can we know the reaction between any two elements in the periodic table? If yes then can we know the reaction between any three or more elements in the periodic table?</p>
Answer: <p>We don't even know completely the reaction of one element with itself. </p>
<p>For example, consider carbon. There are constantly new forms of carbon being discovered. </p>
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https://chemistry.stackexchange.com/questions/24897/reaction-between-elements-in-a-periodic-table
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Question: <p>Dmitri Mendeleev noticed patterns in elements which allowed him to design the periodic table which ultimately led to the modern periodic table.</p>
<p>How were elements organized before this? Was there any method that served as a crude standard?</p>
Answer: <p>Aaron J. Ihde's <a href="https://books.google.com/books?id=89BIAwAAQBAJ" rel="nofollow noreferrer"><em>The Development of Modern Chemistry</em></a> (DMC) has an entire chapter entitled "Classification of the Elements," which includes a very nice overview of the attempts before Mendeleev to bring order to the elements. All quotations below are from Chapter 9 (pp236-243, specifically) of the 1984 Dover edition of DMC, itself "an unabridged, slightly corrected republication of the third printing (1970) of the work originally published by Harper & Row, Publishers, Inc., in 1964" (front matter). The section and sub-section headers are generally those of DMC, with exceptions marked with an asterisk.</p>
<p><strong>It is important to bear in mind when considering some of these systems that the best values of the atomic weights of many elements at the time were incorrect</strong>, either (a) due to simple experimental error, or (b) due to systematic misinterpretation of the available data, due to the limited state of knowledge at the time. For example, the best-regarded atomic weights of many elements were one-half the accepted values of today because the values were derived from measurements on compounds whose formulas were erroneous $($e.g., the atomic weight of oxygen was calculated based on experiments with water, which was thought to have the formula $\ce{HO})$. </p>
<p>For interest, a short article on Aaron J. Ihde can be found on the <a href="https://de.wikipedia.org/wiki/Aaron_J._Ihde" rel="nofollow noreferrer">German language Wikipedia</a>.</p>
<hr>
<h2>Early Attempts at Classification</h2>
<h3>Döbereiner's Triads</h3>
<p>As already <a href="https://chemistry.stackexchange.com/a/74225/">noted</a> by Buttonwood in his answer, <a href="https://en.wikipedia.org/wiki/Johann_Wolfgang_D%C3%B6bereiner" rel="nofollow noreferrer">Johann Wolfgang Döbereiner</a> appears to have been the first to attempt to systematize the elements, after:</p>
<blockquote>
<p>he observed that the atomic weight of strontium appeard to be $50$, the mean of the then accepted values for calcium $(27.5)$ and barium $(72.5)$.</p>
<p>...</p>
<p>His triads included elements with similar properties, the atomic weight of the central member being the mean of the other two atomic weights.</p>
</blockquote>
<p>The Döbereiner triads (some which he was unable to complete at the time) included in DMC (using modern atomic symbols) are:</p>
<p>$$
\require{begingroup}\begingroup
\begin{array}{cccccccc}
\hline
\ce{Li} & \ce{Ca} & \ce{Cl} & \ce{S} & \ce{Mn} & \ce{B} & \ce{Be} & \ce{Y} \\
\ce{Na} & \ce{Sr} & \ce{Br} & \ce{Se} & \ce{Cr} & \ce{?} & \ce{?} & \ce{?} \\
\ce{K} & \ce{Ba} & \ce{I} & \ce{Te} & \ce{Fe} & \ce{Si} & \ce{Al} & \ce{Cs} \\
\hline
\end{array}
$$</p>
<p>DMC notes further:</p>
<blockquote>
<p>Magnesium he considered as an isolated element, not part of a triad. Fluorine, as yet undiscovered but its existence clearly known, he did not include in the halogen triad. Although the atomic weight of nitrogen fell exactly between that of carbon and oxygen, Döbereiner regarded the three elements as isolated non-metals rather than as members of a triad. He also treated hydrogen as an isolated element.</p>
</blockquote>
<h3>Other Numerical Classification Systems</h3>
<ul>
<li><p>Similarity defined by an atomic weight difference of $8$:</p>
<blockquote>
<p>P. Kremers [no further identification given] observed that the atomic weights of certain [elements he regarded as] non-metals in which he saw similarity differed by $8$; i.e., $\ce{O} = 8$, $\ce{S} = 16$, $\ce{Ti} = 24.12$, $\ce{P} = 32$, $\ce{Se} = 39.62$.</p>
</blockquote></li>
<li><p>Atomic weights as odd vs. even multiples of four:</p>
<blockquote>
<p>At the same time, [Kremers observed that] the atomic weights of certain metals fell between those of successive non-metals; i.e., $\ce{Mg} = 12$, $\ce{Ca} = 20$, $\ce{Fe} = 28$. When divided by $4$, the atomic weights of the non-metals were an even number, those of the metals an odd number.</p>
</blockquote></li>
<li><p>Groupings of elements suggested by <a href="https://en.wikipedia.org/wiki/John_Hall_Gladstone" rel="nofollow noreferrer">John Hall Gladstone</a> based on (a) similar atomic weights, and atomic weights in (b) geometric and (c) arithmetic progression:</p>
<ul>
<li><p>(a) $\ce{Cr/Mn/Fe/Co/Ni}$ all near $28$; $\ce{Pd/Rh/Ru}$ all near $52$</p></li>
<li><p>(b) $\ce{Pd}$ group $(52)$, $\ce{Pt}$ group $(99)$, and $\ce{Au}$ $(197)$; separated by multiplicative factors of approximately two</p></li>
<li><p>(c) $\ce{Li}$ $(7)$, $\ce{Na}$ $(23)$, and $\ce{K}$ $(39)$; separated by an additive factor of $16$</p></li>
</ul>
<blockquote>
<p>The first type [Gladstone] compared with <a href="https://en.wikipedia.org/wiki/Allotropy" rel="nofollow noreferrer">allotropy</a>; the second, with <a href="https://en.wiktionary.org/wiki/polymerism" rel="nofollow noreferrer">polymerism</a> in organic chemistry; the third, with <a href="https://en.wikipedia.org/wiki/Homologous_series" rel="nofollow noreferrer">homologous series</a>.</p>
</blockquote></li>
<li><p>Classifications based on arbitrary mathematical progressions:</p>
<ul>
<li><blockquote>
<p><a href="https://en.wikipedia.org/wiki/Josiah_Parsons_Cooke" rel="nofollow noreferrer">Josiah Parsons Cooke</a> (1827-1894) of Harvard developed a classification based upon six series of elements, each series derived from the atomic weight by a mathematical formula. For example, the sixth series, composed of hydrogen and the alkali metals, was based on the formula $1+(n\times 3)$. Thus: $$\begin{array}{ccc}
\ce{H}~(1) = 1 + (0 \times 3) & ~~~ & \ce{Na}~(23) = 1 + (7 \times 3) \\
\ce{Li}~(7) = 1 + (2 \times 3) & ~~~ & ~\ce{K}~(39) = 1 + (13 \times 3) \end{array}$$</p>
</blockquote></li>
<li><p><a href="https://en.wikipedia.org/wiki/Jean-Baptiste_Dumas" rel="nofollow noreferrer">Jean Baptiste André Dumas</a> (1800-1884) posited several arithmetic progressions in series of elements, roughly analogous to homologous series in organic compounds, in the vein of J.H. Gladstone's third type of grouping above (series names are my descriptors):</p>
<blockquote>
<p>$$\def\dumhc#1#2{\ce{#1} &= 1 + (#2 \times 14)}
\textbf{Hydrocarbon Radicals} \\
\begin{align}
\dumhc{H}{0} \\
\dumhc{CH3}{1} \\
\dumhc{C2H5}{2} \\
\dumhc{C3H7}{3} \\
\dumhc{C4H9}{4} \\
\textit{general}\dumhc{}{n}
\end{align}
$$
$$
\textbf{Halogens} \\
\begin{align}
\ce{F} &= 19 \phantom{+2~~\times 16.5)+(2~~\times 28) + 19} = \,19 \\
\ce{Cl} &= 19 + \phantom{(2~~\times} 16.5 \phantom{)+(2~~\times 28)+19} = \,35.5 \\
\ce{Br} &= 19 + (2 \times 16.5) + \phantom{(2~~\times} 28\phantom{)~+19} = \, 80 \\
\ce{I} &= 19 + (2\times 16.5) + (2\times 28) + 19 = 127
\end{align}
$$
$$
\textbf{Chalcogenides} \\
\begin{align}
\ce{O} &= 8 \phantom{+(4~~\times 8)} = \,8 \\
\ce{S} &= 8 + \phantom{(4~~\times} 8\phantom{)} = 16 \\
\ce{Se} &= 8 + (4\times 8) = 40 \\
\ce{Te} &= 8 + (7\times 8) = 64
\end{align}
$$
$$
\textbf{Pnictogens} \\
\begin{align}
\ce{N} &= 14 \phantom{+17+(2~~\times 44)} = ~14 \\
\ce{P} &= 14 + 17 \phantom{+(2~~\times 44)} = ~31 \\
\ce{As} &= 14+17+ \phantom{(2~~\times} 44 \phantom{)} = ~75 \\
\ce{Sb} &= 14+17+(2\times 44) = 119 \\
\ce{Bi} &= 14+17+(4\times 44) = 207
\end{align}
$$
$$
\textbf{Alkaline Earths}\textit{ (mostly)} \\
\begin{align}
\ce{Mg} &= 12 \phantom{+(10~~\times 8)} = \,12 \\
\ce{Ca} &= 12 + \phantom{(10~~\times} 8\phantom{)} = \,20 \\
\ce{Sr} &= 12 + \phantom{1}(4\times 8) = \, 44 \\
\ce{Ba} &= 12 + \phantom{1}(7\times 8) = \, 68 \\
\ce{Pb} &= 24 + (10\times 8) = 104
\end{align}
$$ </p>
</blockquote>
<p>Interestingly, Dumas interpreted these "trends" as being potential evidence (obviously not borne out by subsequent investigation) for the feasibility of <a href="https://en.wikipedia.org/wiki/Nuclear_transmutation#Alchemy" rel="nofollow noreferrer">transmutation</a> among specific groups of related elements.</p></li>
</ul></li>
</ul>
<h2>Immediate Precursors of the Periodic Table</h2>
<h3>De Chancourtois' Telluric Helix</h3>
<p>As <a href="https://chemistry.stackexchange.com/questions/74216/what-organizational-methods-predate-the-periodic-table#comment140409_74225">noted</a> by Buttonwood, <a href="https://en.wikipedia.org/wiki/Alexandre-%C3%89mile_B%C3%A9guyer_de_Chancourtois" rel="nofollow noreferrer">Alexandre-Émile Béguyer de Chancourtois</a> (1820-1886):</p>
<blockquote>
<p>... conceived the idea of plotting the elements according to atomic weights on the surface of a cylinder. The circumference of the cylinder was divided into sixteen sections since the atomic weight of oxygen was $16$. The elements were plotted on a line or helix that descended at an angle of $45^\circ$ with the top of a cylinder. There was a striking resemblance in elements that were on the same vertical line.</p>
<p>... [H]e observed that atomic weights followed the formula $n+16n'$, the value of $n$ frequently being $7$ or $16$ [noting that none of the noble gases had yet been discovered]. ... Gaps in the helix were considered as indicating not unknown elements but different varieties of known elements. He believed, for example, that there was a form of carbon whose atomic weight was $44$.</p>
</blockquote>
<p>In particular, the above Wikipedia article on de Chancourtois emphasizes that he "was the first scientist to see the periodicity of elements when they were arranged in order of their atomic weights." A public domain image of his "Telluric Helix" is also available at the <a href="https://en.wikipedia.org/wiki/Alexandre-%C3%89mile_B%C3%A9guyer_de_Chancourtois#Organizing_the_elements" rel="nofollow noreferrer">Wikipedia page</a>, and reproduced below (click to enlarge):</p>
<p><a href="https://i.sstatic.net/l2Q7R.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/l2Q7Rm.png" alt="de Chancourtois classification scheme"></a></p>
<h3>Newlands' Law of Octaves</h3>
<p>Again as <a href="https://chemistry.stackexchange.com/questions/74216/what-organizational-methods-predate-the-periodic-table#comment140409_74225">noted</a> by Buttonwood, <a href="https://en.wikipedia.org/wiki/John_Newlands_(chemist)" rel="nofollow noreferrer">John Alexander Reina Newlands</a> (1837-1898):</p>
<blockquote>
<p>... was the other major precursor of <a href="https://en.wikipedia.org/wiki/Dmitri_Mendeleev" rel="nofollow noreferrer">Mendeleev</a> and <a href="https://en.wikipedia.org/wiki/Julius_Lothar_Meyer" rel="nofollow noreferrer">Lothar Meyer</a>. ... Newlands' first publication dealing with the classification of the elements appeared in 1863. It was essentially a reworking of <a href="https://en.wikipedia.org/wiki/Jean-Baptiste_Dumas" rel="nofollow noreferrer">Dumas'</a> ideas, for Newlands was looking for numerical relationships between elements. A year later he adopted the atomic weights recommended by <a href="https://en.wikipedia.org/wiki/Stanislao_Cannizzaro" rel="nofollow noreferrer">Cannizzaro</a> and published a table of 37 elements subdivided into ten families. A crude repetitive character was evident, and blank spaces were left for undiscovered elements. In a table in a subsequent paper he assigned numbers to the elements [precursors to the modern <a href="https://en.wikipedia.org/wiki/Atomic_number" rel="nofollow noreferrer">atomic numbers</a>], which were listed in order of increasing atomic weights. He used numbers for the elements in all his work thereafter. In August, 1865, he published an eight-column table listing 62 elements in order of increasing atomic weights; they were subdivided into seven horizontal families. It was in this table that he saw an analogy to the octave in music. The eighth element resembled the first element, the fifteenth resembled the first and the eighth; in other words, an interval of seven elements separated similar elements. Soon afterwards he suggested that the numerical relationships observed by earlier chemists were due to this law of octaves.</p>
<p>...</p>
<p>Newlands must be credited for taking a pioneering step toward the discovery of the periodic law, for he detected the repetition of properties when elements are arranged according to increasing atomic weights. He noted that this relation was evident only if Cannizzaro's atomic weights were used. he used blank spaces for unknown elements but failed to do this consistently, holding that perhaps the interval between repetitions was eight or nine and that this could be dealt with as new elements were discovered.</p>
</blockquote>
<p>As with de Chancourtois, the Wikipedia article on Newlands <a href="https://en.wikipedia.org/wiki/John_Newlands_(chemist)#References" rel="nofollow noreferrer">includes</a> a public domain image of his periodic chart, which is reproduced here for reference:</p>
<p><a href="https://i.sstatic.net/5SPnS.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/5SPnS.png" alt="Newlands table of the elements"></a></p>
<p>$\endgroup$</p>
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