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PDB protein crystal structures most of the time lack hydrogen atoms. Usualy I use PyMOL (`h_add`) but it does not always seem to be giving the correct result. What can I use for accurate hydrogen addition? |
Jaroslav already gave you a good hint: Assume full dissociation, which leads to the following equation: $$\ce{CuCl2 <=> Cu^2+ + 2Cl^-}$$
Since you know the initial concentration of copper chloride, $c(\ce{CuCl2})=0.74~\mathrm{mol/L}$, what can you say about the ratio of $n(\ce{CuCl2})/n(\ce{Cu^2+})$ and $n(\ce{CuCl2... |
I've used [Reduce][1] before, which is excellent. I'm not sure what you mean by ' does not always seem to be giving the correct result', though? Perhaps you could file a bug report with the PyMOL team if you think there is a bug in *h_add*.
[1]: http://kinemage.biochem.duke.edu/software/reduce.php |
When is described: "In **normal conditions**, viscose absorbs 11 to 14% of water vapour. In liquid water, they swell and can absorb 80 to 120% of water." (Clothing Technology)
What do they mean with 'normal conditions'? In open air?
|
The answer is merely a matter of definition of "valence electrons".
Many texts define "valence electrons" in a way that explicitly includes d electrons of unfilled (but not filled) d subshells.
For example: [Chemistry structure and dynamics][1] by Spencer et al. at page 125:
>We can define valence electrons... |
The answer is merely a matter of definition of "valence electrons".
Many texts define "valence electrons" in a way that explicitly includes $d$ electrons of unfilled (but not filled) $d$ subshells.
For example: [Chemistry structure and dynamics][1] by Spencer et al. at page 125:
>We can define valence elect... |
Let $R$ be the orthogonal matrix corresponding to an operation in $O(3)$. If
R is a proper rotation, then both vectors $\vec{V}$ and axial vectors $\vec{A}$ are transformed in the same way
$$ \vec{V} \rightarrow \vec{V}' = R\vec{V}$$
$$ \vec{A} \rightarrow \vec{A}' = R\vec{A}$$
if $R$ is an improper rotations... |
If you have the forward reaction $$2X\longrightarrow P$$ at rate $K$, would you have $$\frac{dX}{dt} = -2KX^2, \frac{dP}{dt}=KX^2,$$ or $$\frac{dX}{dt} = -KX^2,\frac{dP}{dt}=KX^2$$? |
If you have the forward reaction $$\ce{2X -> P}$$ at rate $K$, would you have $$\frac{\mathrm{d}[\ce{X}]}{\mathrm{d}t} = -2K[\ce{X}]^2,\ \frac{\mathrm{d}[\ce{P}]}{\mathrm{d}t}=K[\ce{X}]^2,$$ or $$\frac{\mathrm{d}[\ce{X}]}{\mathrm{d}t} = -K[\ce{X}]^2,\ \frac{\mathrm{d}[\ce{P}]}{\mathrm{d}t}=K[\ce{X}]^2$$? |
First, a note: while oxygen has fewer allotropes than sulfur, it sure has [more than two][1]! These include $\ce{O}$, $\ce{O_2}$, $\ce{O_3}$, $\ce{O_4}$, $\ce{O_8}$, metallic $\ce{O}$ and four other solid phases. Many of these actually have a corresponding sulfur variant. However, you are right in a sense that sulfur h... |
Every covalent bond has some ionic character and every ionic bond some covalent character. I can understand why a completely ionic bond is an ideal situation. But completely covalent bonds can exist(?).
Take the case of $\ce{H_2}$ or any other diatomic molecule between identical atoms. How can these have any ionic c... |
Can 100% covalent bonds exist? |
Law of equivalence states that
> One equivalent of an element combines with one equivalent of the other.
Equivalent of $\ce{Na}$ is $22.99$ and that of $\ce{O}$ is $8$. By the law of equivalence, $1$ equivalent of $\ce{Na}$ combines with $1$ equivalent of $\ce{O}$. But in $\ce{Na2O2}$, $$ 23 \times 2 ~\text{parts... |
According to Pauling's famous [The Nature of the Chemical Bond][1] , 3rd edition, at page 73:
>In the hydrogen molecule a quantum-mechanical treatment has shown that the two ionic structures H+H- and H-H+ enter into resonance with the extreme covalent structure H-H only to a small extent, each ionic structure contri... |
According to Pauling's famous [The Nature of the Chemical Bond][1] , 3rd edition, at page 73:
>In the hydrogen molecule a quantum-mechanical treatment has shown that the two ionic structures H+H- and H-H+ enter into resonance with the extreme covalent structure H-H only to a small extent, each ionic structure contri... |
According to Pauling's famous [The Nature of the Chemical Bond][1] , 3rd edition, at page 73:
>In the hydrogen molecule a quantum-mechanical treatment has shown that the two ionic structures $\ce{H+H-}$ and $\ce{H- H+}$ enter into resonance with the extreme covalent structure $\ce{H-H}$ only to a small extent, each ... |
In a [paper][1] I have read the term GMEC, which was not further explained.
GMEC stands for Global Minimum Energy Conformation. But what is it?
Is it just the conformation with the lowest energy?
[1]: http://m.bioinformatics.oxfordjournals.org/content/24/13/i196.full |
What is GMEC (Global Minimum Energy Conformation)? |
I'm getting a little confused about the definition of chelation and its implications (I should probably point out I'm only an A2 Chemistry student). The IUPAC defines chelation as
>the formation or presence of two or more separate coordinate bonds between a polydentate (multiple bonded) ligand and a single central at... |
I'm getting a little confused about the definition of chelation and its implications (I should probably point out I'm only an A2 Chemistry student). The IUPAC defines chelation as the following:
>The formation or presence of two or more separate coordinate bonds between a polydentate (multiple bonded) ligand and a sin... |
1) I can understand that we need to supply energy to counter the nuclear attraction when we remove electrons and that is the reason ionisation energy is endothermic.
But why does an atom release energy when we add an electron to it?
2) Coming to ionisation energy, why do we need to supply energy to remove the elect... |
1) I understand that we need to supply energy to counter the nuclear attraction when we remove electrons and that is the reason ionization energy is endothermic. However, why does an atom release energy when we add an electron to it?
2) With respect to ionization energy, why is energy required to remove electrons o... |
There are two proposed mechanisms for this.
The first one is the attack of the $\pi$-bond on the $\ce{Hg(OAc)2}$.
But why does mercuric acetate act as an electrophile here? It is in its most common +II oxidation state. Does this happen only because mercury has empty $6d$ orbitals.
While the second mechanism st... |
There are two proposed mechanisms for Oxymercuration and demercuration.
The first mechanism is concerted (i.e. single transition state connecting reactants and products) characterized by an attack of the $\pi$-bond on the $\ce{Hg(OAc)2}$.
Why does mercuric acetate act as an electrophile in the first mechanism? It... |
The context of my question is rotational spectroscopy (using microwave radiation), where there is the $J = \pm 1$ selection rule. The way I understand spectroscopy is that the sample is irradiated with a range of frequencies. Is it possible, during the irradiation of the sample (say CO), for the molecule to be excited ... |
In spectroscopy, is it possible for the sample to be excited multiple times? |
So, I've been looking into polymer chemistry to model breaking polymers for a biological model, and I've been a bit stumped by the concept of persistence length.
I know that if a polymer is significantly longer than its persistence length, it needs to be treated as though the ends are completely independent of each ... |
What happens if a polymer's length is equal to its persistence length? |
Most places that talk about Hypervalency say that it only occurs from 3rd period downwards. This explains the occurrence of Cl2O7 or chlorine heptoxide. However some 2nd period nonmetals like C and O show Hypervalency.
Example:
CH5 this is unlikely to occur but it does sometimes happen that carbon bonds to 5 atoms in... |
Most places that talk about Hypervalency say that it only occurs from 3rd period downwards. This explains the occurrence of $\ce{Cl2O7}$ or chlorine heptoxide. However some 2nd period nonmetals like C and O show Hypervalency.
Example:
$\ce{CH5}$ this is unlikely to occur but it does sometimes happen that carbon b... |
In my experience, most texts that address hypervalency say that it only occurs from elements in the 3rd period and onwards. This explains the occurrence of $\ce{Cl2O7}$ or chlorine heptoxide. However, some 2nd period nonmetals like $\ce{C}$ and $\ce{O}$ show hypervalency.
**Examples:**
- $\ce{CH5}$ - This is unl... |
According to Pauling's famous [The Nature of the Chemical Bond][1] , 3rd edition, at page 73:
>In the hydrogen molecule a quantum-mechanical treatment has shown that the two ionic structures $\ce{H+H-}$ and $\ce{H- H+}$ enter into resonance with the extreme covalent structure $\ce{H-H}$ only to a small extent, each ... |
Somebody I know insists that the use of a catalyst increases the atom economy. They did chemistry at school, and were told that a catalyst increases the atom economy. He pointed me to several past exams where this was written as a valid answer in mark schemes.
However, I am convinced that this is false. After all, a... |
Does a catalyst increase atom economy? |
So, I've been looking into polymer chemistry to model breaking polymers for a biological model, and I've been a bit stumped by the concept of persistence length.
I know that if a polymer is significantly longer than its persistence length, it needs to be treated as though the ends are completely independent of each ... |
Very technically? Yes.
Realistically? The probability is small enough that even if it does happen, the peaks for the multiple transitions are going to be small enough that we cannot really observe them on the spectrum. The lifetime of a given excited state is so small compared to the analogous time in the ground sta... |
I am trying to repeat an experiment conducted by FDA on Malachite Green (MG).
According to [this paper][1],
Prepare a series of LC calibrants by aliquoting into individual 15 mL graduated
glass or disposable polypropylene centrifuge tubes, 50 µL, 100 µL, and 200 µL
of the 0.1 µg/mL MG2 solution a... |
Role of Acetonitrile and Ammonium Acetate buffer in Leucomalachite Green stock solution? |
The shapes respectively denoted by 'tetrahedron' and 'trigonal pyramid' seem to be the same. Is there a difference between the two? If not, why are the two presented as different concepts in introductory chemistry courses? |
In the [book](http://www.amazon.com/Organic-Chemistry-Jonathan-Clayden/dp/0198503466/ref=sr_1_2?ie=UTF8&qid=1433196245&sr=8-2&keywords=clayden+organic+chemistry) by Clayden et al. you can find a very nice description of the mechanism of the halogenation of enols and the haloform reaction on pp. 533-536. Especially on p... |
Since they're using ACN/ammonium acetate to elute from solid phase extraction cartridges and that's what they're injecting into their LC analysis, they probably want to use the same mixture to avoid problems with unmatched matrices with their standards. The ammonium acetate is the pH buffer. Malachite green has differe... |
what is the most accepted theory for explaining ODD EVEN Effect in LC? Can anyone explain or send the link to the corresponding paper? |
What is the most accepted theory for explaining the *odd even effect* in liquid crystals? Can anyone explain and refer the corresponding paper? |
What is the explanation of the odd even effect in liquid crystals? |
I read everywhere about the explosive reactivity of perchlorate salts (e.g., Na, Ca, NH3 [especially]) when mixed with organic materials or solvents, yet I find no information about its reactivity with Methane.
Can anyone comment please? |
Perchlorate salts: (explosive) reactivity with methane? |
I read everywhere about the explosive reactivity of perchlorate salts (e.g., $\ce{Na}$, $\ce{Ca}$, $\ce{NH3}$ [especially]) when mixed with organic materials or solvents, yet I find no information about its reactivity with methane.
Can anyone comment please? |
I read everywhere about the explosive reactivity of perchlorate salts (e.g., $\ce{Na}$, $\ce{Ca}$, $\ce{NH4}$ [especially]) when mixed with organic materials or solvents, yet I find no information about its reactivity with methane.
Can anyone comment please? |
- My book says, methyl chloride, methyl bromide, ethyl chloride and some cholorofluromethanes are gases at room temperature, whereas higher members are liquids or solids. Why?
- With this question, I got another question for which the former would be subset. How to determine whether a compound is gas or liquid or ... |
> What is the specific heat of a 20 g substance that releases 979 J of heat when changing from 70 °C to 25 °C.
I started out with the following equation:
$c = \frac{Q}{m\Delta T}$
$Q = 979\ \mathrm{J}$
$m = 20\ \mathrm{g}$
$\Delta T = 45\ \mathrm{^\circ C}$
My final answer was $2202.75\ \mathrm{J}$
... |
- My book says, methyl chloride, methyl bromide, ethyl chloride and some cholorofluromethanes are gases at room temperature, whereas higher members are liquids or solids. Why?
- With this question, I got another question for which the former would be subset. How to determine whether a compound is gas or liquid or ... |
**Problem:** $\ce{N2O}$ falls apart in oxygen gas and nitrogen gas according to a first order reaction rate. If you know that the rate constant is $0.38 s^{-1}$ at $760$ degrees Celsius, compute then the initial rate for the decomposition of $3.00$g $\ce{N_2 O}$ in a barrel of $5.0$ L. When the initial concentration do... |
**Problem:** $\ce{N2O}$ falls apart in oxygen gas and nitrogen gas according to a first order reaction rate. If you know that the rate constant is $0.38\ \mathrm{s^{-1}}$ at $760\ \mathrm{^\circ C}$, compute then the initial rate for the decomposition of $3.00\ \mathrm{g}$ $\ce{N2O}$ in a barrel of $5.0\ \mathrm{L}$. W... |
How can shorter bonds between C-H be easier to break than longer ones?
For example, consider the length of the C-H bonds in Ethane, Ethene and Ethyne, and the corresponding acidities.
Ethane: BL= 1.102Å & pka= 50
Ethene: BL= 1.085Å & pka= 44
Ethyne: BL= 1.061Å & pka= 25 |
Bond Length and Acidity? |
So, I've been looking into polymer chemistry to model breaking polymers for a biological model, and I've been a bit stumped by the concept of persistence length.
I know that if a polymer is significantly longer than its persistence length, it needs to be treated as though the ends are completely independent of each ... |
First of all somebody in the world explain me what proton is? Then I wanna know that how its energy is directly proportional to frequency of light (please don't tell that it is because E=hv relation ) ? |
The first answer is correct. If the reaction is $\ce{2X->P}$, then two units of $\cf{X}$ should disappear for every unit of $\cf{P}$ formed. Only the first possibility meets this criterion.
The rate law for the reaction could be anything. In your example you have apparently assumed that it is a second order reacti... |
At high temperatures nitrogen dioxide decomposes into nitrogen oxide and oxygen gas according to $$\ce{2 NO_2 -> 2 NO + O_2}$$
I have a question now. Let's say at a certain temperature I'm given data for the formation of $\ce{O_2}$. For example:
At $t = 0$ we have $[\ce{O_2}] = 0$ mol/L, at $t = 50$, $[\ce{O_2}] = ... |
First of all somebody in the world explain me what photon is? Then I wanna know that how its energy is directly proportional to frequency of light (please don't tell that it is because E=hv relation ) ? |
okay, I think I'm making this more complicated than it needs to be, but here it is:
I have 7 drug solutions, all 1 mg/mL which need to have the following concentration in urine:
A: 25,000 ng/ml
B: 25,000 ng/ml
C: 100,000 ng/ml
D: 100,000 ng/ml
E: 10,000 ng/ml
F: 1000 ng/ml
G: 1000 ng/ml
How much of each... |
Is Na a single electron species and can I apply Bohr's Model on it?
Please explain why not as it also contains one electron in its outermost shell. |
Is Na a single electronic species? |
I think I'm making this more complicated than it needs to be, but here it is:
I have 7 drug solutions, all 1 mg/mL which need to have the following concentration in urine:
A: 25,000 ng/ml
B: 25,000 ng/ml
C: 100,000 ng/ml
D: 100,000 ng/ml
E: 10,000 ng/ml
F: 1000 ng/ml
G: 1000 ng/ml
How much o... |
Is Na a single electron species and can I apply Bohr's Model on it?
Please explain why not as it also contains one electron in its outermost shell. |
What photon is and how its energy is directly proportional to frequency of light (please don't tell that it is because E=hv relation)? |
What is a photon and how is its energy directly proportional to frequency of light (please don't tell that it is because $E=h\nu$ relation)? |
<sub>Not a duplicate of [Hydrazine synthesis](https://chemistry.stackexchange.com/questions/2759/hydrazine-synthesis) - I know [what hydrazine is](http://fscimage.fishersci.com/msds/11040.htm) and am not going near it voluntarily!</sub>
Looked at this [resource on the Internet](http://www.lookchem.com/Chempedia/Chem... |
The wikipedia [article][1] on trinitromethane claims that:
>There is some evidence that the anion (which obeys the 4n+2 Hückel rule) is aromatic.
Unfortunately the citation is behind a paywall so I can't read it but my first obvious question is how can the trinitromethane anion obey Hückel's rule? Two of the requir... |
Is the conjugate base of trinitromethane aromatic? |
Does anyone have input or experience on passivation of stainless steel, particularly in outdoor environments where submersion of components is not practical due to location or size? Nitric acid (and solutions with sodium dichromate) typically call for submersion for extended periods of time based on the concentration o... |
Is passivation of stainless steel feasible in the field? |
The wikipedia [article][1] on trinitromethane claims that:
>There is some evidence that the anion (which obeys the 4n+2 Hückel rule) is aromatic.
Unfortunately the citation is behind a paywall so I can't read it but my first obvious question is how can the trinitromethane anion obey Hückel's rule? Two of the requir... |
Is the conjugate base of trinitromethane aromatic (What is Y-aromaticity)? |
how does the delocalized electron hold metal atom together? What is the forces of attraction between the atom and electron called ? |
What turns clear liquid soap blue? |
<sub>Not a duplicate of [Hydrazine synthesis](https://chemistry.stackexchange.com/questions/2759/hydrazine-synthesis) - I know [what hydrazine is](http://fscimage.fishersci.com/msds/11040.htm) and am not going near it voluntarily!</sub>
Looked at this [resource on the Internet](http://www.lookchem.com/Chempedia/Chem... |
I want to address two exceptions in the trend of ionization energy across the period, that are causing me problems:
Taking the second period as an example :![Consider only the second period][1]
The two exceptions from the general trend are the ionization energies of B lesser than Be and that of O less than N.... |
The wikipedia [article][1] on trinitromethane claims that:
>There is some evidence that the anion (which obeys the 4n+2 Hückel rule) is aromatic.
Unfortunately the citation is behind a paywall so I can't read it but my first obvious question is how can the trinitromethane anion obey Hückel's rule? Two of the requir... |
I want to address two exceptions in the trend of ionization energy across the period, that are causing me problems:
Taking the second period as an example :![Consider only the second period][1]
The two exceptions from the general trend are the ionization energies of B lesser than Be and that of O less than N.... |
I want to address two exceptions in the trend of ionization energy across the period, that are causing me problems:
Taking the second period as an example :![Consider only the second period][1]
The two exceptions from the general trend are the ionization energies of B lesser than Be and that of O less than N.... |
I want to address two exceptions in the trend of ionization energy across the period, that are causing me problems:
Taking the second period as an example :![Consider only the second period][1]
The two exceptions from the general trend are the ionization energies of B lesser than Be and that of O less than N.... |
One of the great successes of the Bohr model was the ability to explain the emission spectrum of hydrogen (and hydrogen-like monoelectronic ions), by allowing a simple theoretical derivation of the experimentally determined and remarkably accurate [Rydberg formula](http://en.wikipedia.org/wiki/Rydberg_formula):
$$\f... |
One of the great successes of the Bohr model was the ability to explain the emission spectrum of hydrogen (and hydrogen-like monoelectronic ions), by allowing a simple theoretical derivation of the experimentally determined and remarkably accurate [Rydberg formula](http://en.wikipedia.org/wiki/Rydberg_formula):
$$\f... |
I was trying to synthesize 1-iodo-4-nitrobenzene in the lab today – however, the appearance of my product really confused me.
At first, I added conc. sulphuric acid to water and 4-nitroaniline.
This was followed by diazotising the amine sulphate with sodium nitrite and water. (This was done at temperatures of belo... |
Is $\ce{Na}$ a single electron species and can I apply Bohr's Model on it?
Please explain why not as it also contains one electron in its outermost shell. |
Can the Bohr atomic model be applied to sodium and other single valence electron species? |
TL;DR version is the question title. Some context and data follow.
I was creating an assignment for my organic chemistry students in which they would need to draw as many isomers as they could from a simple formula, for example $\ce{C3H6O}$ (which fits 7 structures - 9 if you count minor enol tautomers and 11 if you... |
Why do cyclic ethers have higher boiling points than their acyclic isomers? |
this can be very useful for people who are afraid of spontaneous human conbustion! But seriously, I heard there are non-harmful chemicals used in some fire extinguishers, so can they maybe be put on our skin, clothes etc in advance to prevent ever catching fire? |
Are there substances people can put on themselves to prevent catching fire? |
**Does the activity of a solid or liquid change over the course of a reaction?**
The density of a solid or liquid reactant doesn't change over the course of a reaction. The mass and volume do as it is consumed, but the ratio of the two is constant. If the reaction causes a temperature change then there are small cha... |
It depends *how long* one is exposed to heat, and *how hot* the source is, but yes, there are "fire retardants" for skin:
1. A mix of alcohol (ethanol or isopropanol) and water or [butane in soap sud can be set afire on your palm without burning you][1], if done **very carefully**. The water soaks up heat energy bot... |
This can be very useful for people who are afraid of spontaneous human combustion! But seriously, I heard there are non-harmful chemicals used in some fire extinguishers, so can they maybe be put on our skin, clothes, etc. in advance to prevent ever catching fire? |
What role does H2O2 have in copper (II) acetate formation? |
A maximum of 1.89 mg of AgCl will dissolve in 1.00 L of solution at 25.00C. A maximum of 5.26 mg of AgCl will dissolve in 1.00 L of solution at 50.00C. Use this information to calculate ΔH(naught) and ΔS(naught) for the following reaction.
AgCl (s) > Ag+ (aq) + Cl- (aq)
Assume that ΔH and ΔS are independe... |
**So, assuming I am able to extract an unknown chemical of some specified group from a plant, is there any way for me to determine the chemical's structure?**
Yes.
**I don't really have access to these tools as student over the summer. I am willing to spend a small amount of money on this project, but no more tha... |
>A maximum of $1.89~\mathrm{mg}$ of $\ce{AgCl}$ will dissolve in $1.00~\mathrm{L}$ of solution at $25.00~^\circ\mathrm{C}$. A maximum of $5.26~\mathrm{mg}$ of $\ce{AgCl}$ will dissolve in $1.00~\mathrm{L}$ of solution at $50.00~^\circ\mathrm{C}$. Use this information to calculate $\Delta H^\circ$ and $\Delta S^\circ$... |
How to find the standard enthalpy and entropy for the dissolution of silver chloride? |
If 50.0 mg of CO3^2- and 50.0 mg of Ca^+2 are present in 1 liter of water , what will be the final (equilibrium) concentration of Ca^+2 expressed in moles per liter? |
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