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Article: Kinetic isotope effect. In physical organic chemistry, a kinetic isotope effect (KIE) is the change in the reaction rate of a chemical reaction when one of the atoms in the reactants is replaced by one of its isotopes. Formally, it is the ratio of rate constants for the reactions involving the light (kL) and t... | Wikipedia - Kinetic isotope effect - Summary | 211 | 956 | null |
Section: Background. KIE is considered one of the most essential and sensitive tools for studying reaction mechanisms, the knowledge of which allows improvement of the desirable qualities of said reactions. For example, KIEs can be used to reveal whether a nucleophilic substitution reaction follows a unimolecular (SN1)... | Wikipedia - Kinetic isotope effect - Background | 298 | 1,340 | null |
Thus, replacing normal hydrogen (1H) with its isotope deuterium (D or 2H), doubles the mass; whereas in replacing carbon-12 with carbon-13, the mass increases by only 8%. The rate of a reaction involving a C–1H bond is typically 6–10x faster than with a C–2H bond, whereas a 12C reaction is only 4% faster than the corre... | Wikipedia - Kinetic isotope effect - Background | 257 | 1,098 | null |
Section: Classification > Primary kinetic isotope effects. A primary kinetic isotope effect (PKIE) may be found when a bond to the isotopically labeled atom is being formed or broken.: 427 Depending on the way a KIE is probed (parallel measurement of rates vs. intermolecular competition vs. intramolecular competition),... | Wikipedia - Kinetic isotope effect - Classification > Primary kinetic isotope effects | 259 | 1,239 | null |
Section: Classification > Secondary kinetic isotope effects. A secondary kinetic isotope effect (SKIE) is observed when no bond to the isotopically labeled atom in the reactant is broken or formed.: 427 SKIEs tend to be much smaller than PKIEs; however, secondary deuterium isotope effects can be as large as 1.4 per 2H ... | Wikipedia - Kinetic isotope effect - Classification > Secondary kinetic isotope effects | 349 | 1,610 | null |
For an SN1 reaction, since the carbon atom is converted into an sp2 hybridized carbenium ion during the transition state for the rate-determining step with an increase in Cα-H(2H) bond order, an IKIE would be expected if only the stretching vibrations were important. The observed large normal KIEs are found to be cause... | Wikipedia - Kinetic isotope effect - Classification > Secondary kinetic isotope effects | 150 | 737 | null |
Section: Theory. Theoretical treatment of isotope effects relies heavily on transition state theory, which assumes a single potential energy surface for the reaction, and a barrier between the reactants and the products on this surface, on top of which resides the transition state. The KIE arises largely from the chang... | Wikipedia - Kinetic isotope effect - Theory | 342 | 1,819 | null |
Also, due to the large relative difference in the mass of 2H and 1H and the attendant differences in vibrational frequency, the isotope effect is larger than for any other pair of isotopes except 1H and 3H, allowing both primary and secondary isotope effects to be easily measured and interpreted. In contrast, secondary... | Wikipedia - Kinetic isotope effect - Theory | 341 | 1,645 | null |
(Strictly speaking, a κ H / κ D {\displaystyle \kappa _{\mathrm {H} }/\kappa _{\mathrm {D} }} term resulting from an isotopic difference in transmission coefficients should also be included.) k H k D = ( σ H σ D ‡ σ D σ H ‡ ) ( M H ‡ M D M D ‡ M H ) 3 2 ( I x H ‡ I y H ‡ I z H ‡ I x D ‡ I y D ‡ I z D ‡ I x D I y D I z ... | Wikipedia - Kinetic isotope effect - Theory | 350 | 732 | null |
{H}}}^{\ddagger }M_{{\ce {D}}}}{M_{{\ce {D}}}^{\ddagger }M_{{\ce {H}}}}}\right)^{\frac {3}{2}}\left({\frac {I_{x{\ce {H}}}^{\ddagger }I_{y{\ce {H}}}^{\ddagger }I_{z{\ce {H}}}^{\ddagger }}{I_{x{\ce {D}}}^{\ddagger }I_{y{\ce {D}}}^{\ddagger }I_{z{\ce {D}}}^{\ddagger }}}{\frac {I_{x{\ce {D}}}I_{y{\ce {D}}}I_{z{\ce {D}}}}{... | Wikipedia - Kinetic isotope effect - Theory | 345 | 477 | null |
}}}{1-e^{-u_{i{\ce {H}}}^{\ddagger }}}}}{\prod \limits _{i=1}^{3N-6}{\frac {1-e^{-u_{i{\ce {D}}}}}{1-e^{-u_{i{\ce {H}}}}}}}}\right)e^{-{\frac {1}{2}}\left[\sum \limits _{i=1}^{3N^{\ddagger }-7}(u_{i{\ce {H}}}^{\ddagger }-u_{i{\ce {D}}}^{\ddagger })-\sum \limits _{i=1}^{3N-6}(u_{i{\ce {H}}}-u_{i{\ce {D}}})\right]}} , wh... | Wikipedia - Kinetic isotope effect - Theory | 350 | 525 | null |
~ i ‡ R T {\displaystyle u_{i}^{\ddagger }:={\frac {h\nu _{i}^{\ddagger }}{k_{\mathrm {B} }T}}={\frac {hcN_{\mathrm {A} }{\tilde {\nu }}_{i}^{\ddagger }}{RT}}} . Here, h = Planck constant; kB = Boltzmann constant; ν ~ i {\displaystyle {\tilde {\nu }}_{i}} = frequency of vibration, expressed in wavenumber; c = speed of ... | Wikipedia - Kinetic isotope effect - Theory | 280 | 869 | null |
The integers N and N‡ are the number of atoms in the reactants and the transition states, respectively. The complicated expression given above can be represented as the product of four separate factors: k H k D = S × M M I × E X C × Z P E {\displaystyle {\frac {k_{{\ce {H}}}}{k_{{\ce {D}}}}}=\mathbf {S} \times \mathbf ... | Wikipedia - Kinetic isotope effect - Theory | 330 | 1,316 | null |
Since hydrogen and deuterium tend to be much lighter than most reactants and transition states, there is little difference in the molecular masses and moments of inertia between H and D containing molecules, so the MMI factor is usually also approximated as unity. The EXC factor (containing the product of vibrational p... | Wikipedia - Kinetic isotope effect - Theory | 302 | 1,201 | null |
) 1 2 Δ u i − ∑ i ( T S ) 1 2 Δ u i ‡ ] {\displaystyle {\begin{aligned}{\frac {k_{{\ce {H}}}}{k_{{\ce {D}}}}}&\cong \exp \left\{-{\frac {1}{2}}\left[\sum \limits _{i=1}^{3N^{\ddagger }-7}(u_{i{\ce {H}}}^{\ddagger }-u_{i{\ce {D}}}^{\ddagger })-\sum \limits _{i=1}^{3N-6}(u_{i{\ce {H}}}-u_{i{\ce {D}}})\right]\right\}\\&\c... | Wikipedia - Kinetic isotope effect - Theory | 350 | 584 | null |
}} and Δ u i ‡ := u i H ‡ − u i D ‡ {\displaystyle \Delta u_{i}^{\ddagger }:=u_{i\mathrm {H} }^{\ddagger }-u_{i\mathrm {D} }^{\ddagger }} . The sums in the exponent of the second expression can be interpreted as running over all vibrational modes of the reactant ground state and the transition state. Or, one may interp... | Wikipedia - Kinetic isotope effect - Theory | 318 | 1,250 | null |
As mentioned, especially for 1H/2H substitution, most KIEs arise from the difference in ZPE between the reactants and the transition state of the isotopologues; this difference can be understood qualitatively as follows: in the Born–Oppenheimer approximation, the potential energy surface is the same for both isotopic s... | Wikipedia - Kinetic isotope effect - Theory | 344 | 1,623 | null |
This effect should, in principle, be taken into account all 3N−6 vibrational modes for the starting material and 3N‡−7 vibrational modes at the transition state (one mode, the one corresponding to the reaction coordinate, is missing at the transition state, since a bond breaks and there is no restorative force against ... | Wikipedia - Kinetic isotope effect - Theory | 230 | 826 | null |
Thus, we can readily interpret the factor of 1/2 and the sums of u i = h ν i / k B T {\displaystyle u_{i}=h\nu _{i}/k_{\mathrm {B} }T} terms over ground state and transition state vibrational modes in the exponent of the simplified formula above. For a harmonic oscillator, vibrational frequency is inversely proportio... | Wikipedia - Kinetic isotope effect - Theory | 270 | 743 | null |
Moreover, the reduced mass is approximated by the mass of the light atom of the system, X = H or D. Because mD ≈ 2mH, Δ u i ≅ ( 1 − 1 2 ) h ν i H k B T {\displaystyle \Delta u_{i}\cong \left(1-{\frac {1}{\sqrt {2}}}\right){\frac {h\nu _{i\mathrm {H} }}{k_{\mathrm {B} }T}}} . In the case of homolytic C–H/D bond dissocia... | Wikipedia - Kinetic isotope effect - Theory | 263 | 834 | null |
Nevertheless, it is still generally true that cleavage of a bond with a higher vibrational frequency will give a larger isotope effect. To calculate the maximum possible value for a non-tunneling 2H KIE, we consider the case where the ZPE difference between the stretching vibrations of a C-1H bond (3000 cm−1) and C-2H ... | Wikipedia - Kinetic isotope effect - Theory | 347 | 1,399 | null |
"early" or "late" and linear vs. bent); the extent to which a primary 2H isotope effect approaches this maximum, varies. A model developed by Westheimer predicted that symmetrical (thermoneutral, by Hammond's postulate), linear transition states have the largest isotope effects, while transition states that are "early"... | Wikipedia - Kinetic isotope effect - Theory | 322 | 1,349 | null |
For a SKIE at the α position, rehybridization from sp3 to sp2 produces a normal isotope effect, while rehybridization from sp2 to sp3 results in an inverse isotope effect with a theoretical minimum of kH/kD = 2-0.5 ≈ 0.7. In practice, kH/kD ~ 1.1-1.2 and kH/kD ~ 0.8-0.9 are typical for α SKIEs, while kH/kD ~ 1.15-1.3 a... | Wikipedia - Kinetic isotope effect - Theory | 191 | 639 | null |
The following simple expressions relating 2H and 3H KIEs, which are also known as the Swain equation (or the Swain-Schaad-Stivers equations), can be derived from the general expression given above using some simplifications: ( ln ( k H k T ) ln ( k H k D ) ) s ≅ 1 − m H / m T 1 − m H / m D = 1 − 1 / 3 1 − 1 / 2 ≅ 1... | Wikipedia - Kinetic isotope effect - Theory | 349 | 686 | null |
\left({\frac {k_{{\ce {H}}}}{k_{{\ce {T}}}}}\right)_{s}=\left({\frac {k_{{\ce {H}}}}{k_{{\ce {D}}}}}\right)_{s}^{1.44}} . In deriving these expressions, the reasonable approximation that reduced mass roughly equals the mass of the 1H, 2H, or 3H, was used. Also, the vibrational motion was assumed to be approximated by a... | Wikipedia - Kinetic isotope effect - Theory | 345 | 1,090 | null |
Section: Theory > Tunneling. In some cases, a further rate enhancement is seen for the lighter isotope, possibly due to quantum tunneling. This is typically only observed for reactions involving bonds to hydrogen. Tunneling occurs when a molecule penetrates through a potential energy barrier rather than over it. Though... | Wikipedia - Kinetic isotope effect - Theory > Tunneling | 334 | 1,164 | null |
Section: Experiments. Simmons and Hartwig refer to the following three cases as the main types of KIE experiments involving C-H bond functionalization: A) KIE determined from absolute rates of two parallel reactions In this experiment, the rate constants for the normal substrate and its isotopically labeled analogue ar... | Wikipedia - Kinetic isotope effect - Experiments | 341 | 1,635 | null |
Generally, the reaction is halted at low conversion (~5 to 10% conversion) or a large excess (> 5 equiv.) of the isotopic mixture is used. This experiment type ensures that both C-H and C-D bond functionalizations occur under exactly the same conditions, and the ratio of products from C-H and C-D bond functionalization... | Wikipedia - Kinetic isotope effect - Experiments | 328 | 1,535 | null |
However, the results of Experiments B and C will differ if the irreversible binding of the isotope-containing substrate takes place in Experiment B prior to the cleavage of the C-H or C-D bond. In such a scenario, an isotope effect may be observed in Experiment C (where choice of the isotope can take place even after s... | Wikipedia - Kinetic isotope effect - Experiments | 334 | 1,410 | null |
In the intramolecular case, however, the product ratio is determined by the proton transfer that occurs after the nucleophilic attack, a process which has a substantial KIE of 2.6. Thus, Experiments A, B, and C will give results of differing levels of precision and require different experimental setup and ways of analy... | Wikipedia - Kinetic isotope effect - Experiments | 319 | 1,492 | null |
The ratio between the amounts of the two species in the reactants and the products will thus change gradually over the course of the reaction, and this gradual change can be treated as follows: Assume that two isotopic molecules, A1 and A2, undergo irreversible competition reactions: [k_{1}]P1}}\\{\ce {{A2}+{B}+{C}+\cd... | Wikipedia - Kinetic isotope effect - Experiments > Evaluation of rate constant ratios from intermolecular competition reactions | 350 | 782 | null |
of conversions for the isotopic species A1 and A2, respectively. Isotopic enrichment of the starting material can be calculated from the dependence of R/R0 on F1 for various KIEs, yielding the following figure. Due to the exponential dependence, even very low KIEs lead to large changes in isotopic composition of the st... | Wikipedia - Kinetic isotope effect - Experiments > Evaluation of rate constant ratios from intermolecular competition reactions | 192 | 612 | null |
Section: Experiments > Kinetic isotope effect measurement at natural abundance > Single-pulse NMR. Quantitative single-pulse nuclear magnetic resonance spectroscopy (NMR) is a method amenable for measuring kinetic fractionation of isotopes for natural abundance KIE measurements. Pascal et al. were inspired by studies d... | Wikipedia - Kinetic isotope effect - Experiments > Kinetic isotope effect measurement at natural abundance > Single-pulse NMR | 344 | 1,585 | null |
These key observations suggest an asynchronous reaction mechanism for the cycloaddition of isoprene with maleic anhydride. The limitations for determining KIEs at natural abundance using NMR are that the recovered material must have a suitable amount and purity for NMR analysis (the signal of interest should be distinc... | Wikipedia - Kinetic isotope effect - Experiments > Kinetic isotope effect measurement at natural abundance > Single-pulse NMR | 217 | 1,097 | null |
Section: Experiments > Kinetic isotope effect measurement at natural abundance > Organometallic reaction mechanism elucidation examples. Colletto et al. developed a regioselective β-arylation of benzo[b]thiophenes at room temperature with aryl iodides as coupling partners and sought to understand the mechanism of this ... | Wikipedia - Kinetic isotope effect - Experiments > Kinetic isotope effect measurement at natural abundance > Organometallic reaction mechanism elucidation examples | 308 | 1,323 | null |
Section: Experiments > Kinetic isotope effect measurement at natural abundance > DEPT-55 NMR. Though KIE measurements at natural abundance are a powerful tool for understanding reaction mechanisms, the amounts of material needed for analysis can make this technique inaccessible for reactions that use expensive reagents... | Wikipedia - Kinetic isotope effect - Experiments > Kinetic isotope effect measurement at natural abundance > DEPT-55 NMR | 326 | 1,650 | null |
Section: Case studies > Primary hydrogen isotope effects. Primary hydrogen KIEs refer to cases in which a bond to the isotopically labeled hydrogen is formed or broken at a rate- and/or product-determining step of a reaction. These are the most commonly measured KIEs, and much of the previously covered theory refers to... | Wikipedia - Kinetic isotope effect - Case studies > Primary hydrogen isotope effects | 221 | 1,069 | null |
Section: Case studies > Secondary hydrogen isotope effects. Secondary hydrogen isotope effects or secondary KIE (SKIE) arise in cases where the isotopic substitution is remote from the bond being broken. The remote atom nonetheless influences the internal vibrations of the system, which via changes in zero-point energy... | Wikipedia - Kinetic isotope effect - Case studies > Secondary hydrogen isotope effects | 334 | 1,643 | null |
When the hybridization of a carbon atom changes from sp3 to sp2, a number of vibrational modes (stretches, in-plane and out-of-plane bending) are affected. The in-plane and out-of-plane bending in an sp3 hybridized carbon are similar in frequency due to the symmetry of an sp3 hybridized carbon. In an sp2 hybridized car... | Wikipedia - Kinetic isotope effect - Case studies > Secondary hydrogen isotope effects | 338 | 1,479 | null |
More generally the SKIE for reversible reactions can be "normal" one way and "inverse" the other if bonding in the transition state is midway in stiffness between substrate and product, or they can be "normal" both ways if bonding is weaker in the transition state, or "inverse" both ways if bonding is stronger in the t... | Wikipedia - Kinetic isotope effect - Case studies > Secondary hydrogen isotope effects | 325 | 1,495 | null |
Then, analysis of the experimental data for the reaction allowed them to choose which pathway was most likely based on the observed isotope effect. Secondary hydrogen isotope effects from the methylene hydrogens were also used to show that Cope rearrangement in 1,5-hexadiene follow a concerted bond rearrangement pathwa... | Wikipedia - Kinetic isotope effect - Case studies > Secondary hydrogen isotope effects | 165 | 739 | null |
Section: Case studies > Secondary hydrogen isotope effects > Steric isotope effects. The steric isotope effect (SIE) is a SKIE that does not involve bond breaking or formation. This effect is attributed to the different vibrational amplitudes of isotopologues. An example of such an effect is the racemization of 9,10-di... | Wikipedia - Kinetic isotope effect - Case studies > Secondary hydrogen isotope effects > Steric isotope effects | 286 | 1,199 | null |
Section: Case studies > Inverse kinetic isotope effects. Reactions are known where the deuterated species reacts faster than the undeuterated one, and these cases are said to exhibit inverse KIEs (IKIE). IKIEs are often observed in the reductive elimination of alkyl metal hydrides, e.g. ((Me2NCH2)2)PtMe(H). In such cas... | Wikipedia - Kinetic isotope effect - Case studies > Inverse kinetic isotope effects | 333 | 1,113 | null |
Section: Case studies > Carbon-13 isotope effects > Compensating for variations in 13C natural abundance. Often, the largest source of error in a study that depends on the natural abundance of carbon is the slight variation in natural 13C abundance itself. Such variations arise; because the starting materials in the re... | Wikipedia - Kinetic isotope effect - Case studies > Carbon-13 isotope effects > Compensating for variations in 13C natural abundance | 233 | 1,166 | null |
Section: Case studies > Isotope effects with elements heavier than carbon. Interpretation of carbon isotope effects is usually complicated by simultaneously forming and breaking bonds to carbon. Even reactions that involve only bond cleavage from the carbon, such as SN1 reactions, involve strengthening of the remaining... | Wikipedia - Kinetic isotope effect - Case studies > Isotope effects with elements heavier than carbon | 349 | 1,784 | null |
Similarly, combining nitrogen and hydrogen isotope effects was used to show that syn eliminations of simple ammonium salts also follow a concerted mechanism, which was a question of debate before. In the following two reactions of 2-phenylcyclopentyltrimethylammonium ion with ethoxide, both of which yield 1-phenylcyclo... | Wikipedia - Kinetic isotope effect - Case studies > Isotope effects with elements heavier than carbon | 168 | 706 | null |
Section: Case studies > Other examples. Since KIEs arise from differences in isotopic mass, the largest observable KIEs are associated with substitution of 1H with 2H (2× increase in mass) or 3H (3× increase in mass). KIEs from isotopic mass ratios can be as large as 36.4 using muons. They have produced the lightest "h... | Wikipedia - Kinetic isotope effect - Case studies > Other examples | 321 | 1,256 | null |
The KIE leads to a specific distribution of 2H in natural products, depending on the route they were synthesized in nature. By NMR spectroscopy, it is therefore easy to detect whether the alcohol in wine was fermented from glucose, or from illicitly added saccharose. Another reaction mechanism that was elucidated using... | Wikipedia - Kinetic isotope effect - Case studies > Other examples | 325 | 1,314 | null |
Article: Klopman–Salem equation. In the theory of chemical reactivity, the Klopman–Salem equation describes the energetic change that occurs when two species approach each other in the course of a reaction and begin to interact, as their associated molecular orbitals begin to overlap with each other and atoms bearing p... | Wikipedia - Klopman–Salem equation - Summary | 171 | 899 | null |
2 ( ∑ a , b c r a c s b β a b ) 2 E r − E s ) {\displaystyle \Delta E={\Big (}-\sum _{a,b}(q_{a}+q_{b})\beta _{ab}S_{ab}{\Big )}+{\Big (}\sum _{k<\ell }{\frac {Q_{k}Q_{\ell }}{\varepsilon R_{k\ell }}}{\Big )}+{\Big (}\sum _{r}^{\mathrm {occ.} }\sum _{s}^{\mathrm {unocc.} }-\sum _{s}^{\mathrm {occ.} }\sum _{r}^{\mathrm ... | Wikipedia - Klopman–Salem equation - Formulation and interpretation | 350 | 696 | null |
k {\displaystyle Q_{k}} is the total charge on atom k {\displaystyle k} , ε {\displaystyle \varepsilon } is the local dielectric constant, R k ℓ {\displaystyle R_{k\ell }} is the distance between the nuclei of atoms k {\displaystyle k} and l {\displaystyle l} , c r a {\displaystyle c_{ra}} is the coefficient of atomic ... | Wikipedia - Klopman–Salem equation - Formulation and interpretation | 334 | 1,438 | null |
Section: Numeric locants. The International Union of Pure and Applied Chemistry (IUPAC) recommends the use of numeric prefixes to indicate the position of substituents, generally by identifying the parent hydrocarbon chain and assigning the carbon atoms based on their substituents in order of precedence. For example, t... | Wikipedia - Locant - Numeric locants | 331 | 1,455 | null |
Section: Greek letter locants. Another common system uses Greek letter prefixes as locants, which is useful in identifying the relative location of carbon atoms as well as hydrogen atoms to other functional groups. The α-carbon (alpha-carbon) refers to the first carbon atom that attaches to a functional group, such as ... | Wikipedia - Locant - Greek letter locants | 302 | 1,302 | null |
Section: Greek letter locants > Proteins and amino acids. In proteins and amino acids, the α-carbon is the backbone carbon before the carbonyl carbon atom in the molecule. Therefore, reading along the backbone of a typical protein would give a sequence of –[N—Cα—carbonyl C]n– etc. (when reading in the N to C direction)... | Wikipedia - Locant - Greek letter locants > Proteins and amino acids | 255 | 1,080 | null |
Section: Synthesis. The formation of macrocycles by ring-closure is called macrocyclization. The central challenge to macrocyclization is that ring-closing reactions do not favor the formation of large rings. Instead, medium sized rings or polymers tend to form. Early macrocyclizations were achieved ketonic decarboxyla... | Wikipedia - Macrocycle - Synthesis | 269 | 1,221 | null |
Section: Stereocontrol. Macrocyclic stereocontrol refers to the directed outcome of a given intermolecular or intramolecular reaction that is governed by the conformational preference of a macrocycle. Stereocontrol for cyclohexane rings is well established in organic chemistry, in large part due to the axial/equatorial... | Wikipedia - Macrocycle - Stereocontrol | 268 | 1,336 | null |
Significantly, even small conformational preferences, such as those envisioned in floppy macrocycles, can profoundly influence the ground state of a given reaction, providing stereocontrol such as in the synthesis of miyakolide. Reaction classes used in synthesis of natural products under the macrocyclic stereocontrol ... | Wikipedia - Macrocycle - Stereocontrol | 194 | 701 | null |
Section: Stereocontrol > Prominent examples in synthesis > Cladiell-11-ene-3,6,7-triol. The cladiellin family of marine natural products feature 9-membered rings. The synthesis of (−)-cladiella-6,11-dien-3-ol allowed access to a variety of other members of the cladiellin family. The conversion to cladiell-11-ene-3,6,7-... | Wikipedia - Macrocycle - Stereocontrol > Prominent examples in synthesis > Cladiell-11-ene-3,6,7-triol | 201 | 771 | null |
Section: Stereocontrol > Prominent examples in synthesis > (±)-Periplanone B. The synthesis of (±)-periplanone B is a prominent example of macrocyclic stereocontrol. Periplanone B is a sex pheromone of the American female cockroach, and has been the target of several synthetic attempts. Significantly, two reactions on ... | Wikipedia - Macrocycle - Stereocontrol > Prominent examples in synthesis > (±)-Periplanone B | 241 | 993 | null |
Section: Macrocycles in Drug Discovery. Over the last few years, macrocyclic molecules have become increasingly relevant in drug discovery. For a long time, this motif was found almost exclusively in natural products (s. Cyclosporine), but it can now also be found in some completely synthetic molecules (s. Grazoprevir)... | Wikipedia - Macrocycle - Macrocycles in Drug Discovery | 227 | 1,077 | null |
Section: Chemistry. Mauveine is a mixture of four related aromatic compounds differing in number and placement of methyl groups. Its organic synthesis involves dissolving aniline, p-toluidine, and o-toluidine in sulfuric acid and water in a roughly 1:1:2 ratio, then adding potassium dichromate. Mauveine A (C26H23N+4X−)... | Wikipedia - Mauveine - Chemistry | 339 | 1,178 | null |
Section: History. In 1856, William Henry Perkin, then age 18, was given a challenge by his professor, August Wilhelm von Hofmann, to synthesize quinine. In one attempt, Perkin oxidized aniline using potassium dichromate, whose toluidine impurities reacted with the aniline and yielded a black solid, suggesting a "failed... | Wikipedia - Mauveine - History | 300 | 1,333 | null |
Section: Preparation and reactions. For mass spectrometry studies at low pressure, methenium can be obtained by ultraviolet photoionization of methyl radical, or by collisions of monatomic cations such as C+ and Kr+ with neutral methane. In such conditions, it will react with acetonitrile CH3CN to form the ion (CH3)2CN... | Wikipedia - Methenium - Preparation and reactions | 162 | 659 | null |
Section: Nomenclature. The trivial name carbene is the preferred IUPAC name. The systematic names methylidene and dihydridocarbon, valid IUPAC names, are constructed according to the substitutive and additive nomenclatures, respectively. Methylidene is viewed as methane with two hydrogen atoms removed. By default, this... | Wikipedia - Methylene (compound) - Nomenclature | 257 | 1,061 | null |
Section: Nomenclature > Methylidene group. A methylidene group is any part of a molecule that consists of a CH2= group. The group may be represented as =CH2, where the '=' denotes the double bond. In contrast, methylene is connected to the rest of the molecule by two single bonds. The distinction is often important, be... | Wikipedia - Methylene (compound) - Nomenclature > Methylidene group | 199 | 865 | null |
Section: Preparation. Methylene can be prepared by decomposition of compounds with a methylidene or methanediyl group, such as ketene (ethenone) (CH2=CO), diazomethane (linear CH2=N2), diazirine (cyclic [−CH2−N=N−]) and diiodomethane (I−CH2−I). The decomposition can be effected by photolysis, photosensitized reagents (... | Wikipedia - Methylene (compound) - Preparation | 178 | 667 | null |
Section: Chemical properties > Radical character. Many of methylene's electronic states lie relatively close to each other, giving rise to varying degrees of radical chemistry. The ground state is a triplet radical with two unpaired electrons (X̃3B1), and the first excited state is a singlet non-radical (ã1A1). With th... | Wikipedia - Methylene (compound) - Chemical properties > Radical character | 329 | 1,266 | null |
Section: Chemical properties > Structure. The ground state of methylene has an ionisation energy of 10.396 eV. It has a bent configuration, with H–C–H angle of 133.84°, and is thus paramagnetic. (The correct prediction of this angle was an early success of ab initio quantum chemistry.) However conversion to a linear co... | Wikipedia - Methylene (compound) - Chemical properties > Structure | 153 | 607 | null |
Section: Chemical properties > Chemical reactions > Organic chemistry. Neutral methylene complexes undergo different chemical reactions depending on the pi character of the coordinate bond to the carbon centre. A weak contribution, such as in diazomethane, yields mainly substitution reactions, whereas a strong contribu... | Wikipedia - Methylene (compound) - Chemical properties > Chemical reactions > Organic chemistry | 293 | 1,250 | null |
Article: Methylotroph. Methylotrophs are a diverse group of microorganisms that can use reduced one-carbon compounds, such as methanol or methane, as the carbon source for their growth; and multi-carbon compounds that contain no carbon-carbon bonds, such as dimethyl ether and dimethylamine. This group of microorganisms... | Wikipedia - Methylotroph - Summary | 219 | 968 | null |
Section: Metabolism. The key intermediate in methylotrophic metabolism is formaldehyde, which can be diverted to either assimilatory or dissimilatory pathways. Methylotrophs produce formaldehyde through oxidation of methanol and/or methane. Methane oxidation requires the enzyme methane monooxygenase (MMO). Methylotroph... | Wikipedia - Methylotroph - Metabolism | 261 | 990 | null |
Section: Metabolism > Catabolism. Methylotrophs use the electron transport chain to conserve energy produced from the oxidation of C 1 {\displaystyle {\ce {C1}}} compounds. An additional activation step is required in methanotrophic metabolism to allow degradation of chemically-stable methane. This oxidation to methano... | Wikipedia - Methylotroph - Metabolism > Catabolism | 331 | 1,275 | null |
Section: Metabolism > Anabolism. The main metabolic challenge for methylotrophs is the assimilation of single carbon units into biomass. Through de novo synthesis, methylotrophs must form carbon-carbon bonds between 1-Carbon ( C 1 {\displaystyle {\ce {C1}}} ) molecules. This is an energy intensive process, which facult... | Wikipedia - Methylotroph - Metabolism > Anabolism | 233 | 951 | null |
Section: Metabolism > Anabolism > Bacteria > Ribulose bisphosphate (RuBP) cycle. Unlike the other assimilatory pathways, bacteria using the RuBP pathway derive all of their organic carbon from CO 2 {\displaystyle {\ce {CO2}}} assimilation. This pathway was first elucidated in photosynthetic autotrophs and is better kno... | Wikipedia - Methylotroph - Metabolism > Anabolism > Bacteria > Ribulose bisphosphate (RuBP) cycle | 314 | 1,120 | null |
Section: Metabolism > Anabolism > Bacteria > Ribulose monophosphate (RuMP) cycle. A new pathway was suspected when RuBisCO was not found in the methanotroph Methylmonas methanica. Through radio-labelling experiments, it was shown that M. methanica used the ribulose monophosphate (RuMP) pathway. This has led researchers... | Wikipedia - Methylotroph - Metabolism > Anabolism > Bacteria > Ribulose monophosphate (RuMP) cycle | 271 | 1,005 | null |
Section: Metabolism > Anabolism > Bacteria > Serine cycle. Unlike the other assimilatory pathways, the serine cycle uses carboxylic acids and amino acids as intermediates instead of carbohydrates. First, 2 molecules of formaldehyde are added to 2 molecules of the amino acid glycine. This produces two molecules of the a... | Wikipedia - Methylotroph - Metabolism > Anabolism > Bacteria > Serine cycle | 206 | 820 | null |
Section: Metabolism > Anabolism > Yeasts > Dihydroxyacteone (DHA) cycle. The dihydroxyacetone (DHA) pathway, also known as the xylulose monophosphate (XuMP) pathway, is found exclusively in yeast. This pathway assimilates three molecules of formaldehyde into 1 molecule of DHAP using 3 molecules of xylulose 5-phosphate ... | Wikipedia - Methylotroph - Metabolism > Anabolism > Yeasts > Dihydroxyacteone (DHA) cycle | 198 | 719 | null |
Section: Environmental Implications. As key players in the carbon cycle, methylotrophs work to reduce global warming primarily through the uptake of methane and other greenhouse gases. In aqueous environments, methanogenic archaea produce 40-50% of the world's methane. Symbiosis between methanogens and methanotrophic b... | Wikipedia - Methylotroph - Environmental Implications | 328 | 1,607 | null |
Because these compounds are volatile and impact the climate and atmosphere, research on the interaction of these bacteria with these one-carbon compounds can also help understanding of air-sea fluxes of these compounds, which impact climate predictions. For example, it is uncertain whether the ocean acts as a net sourc... | Wikipedia - Methylotroph - Environmental Implications | 342 | 1,611 | null |
These types of studies will contribute to further understanding of deep sea carbon cycling and the connectivity between deep ocean and surface carbon cycling. The expansion of omics technologies has accelerated research on the diversity of methylotrophs, their abundance and activity in a variety of environmental niches... | Wikipedia - Methylotroph - Environmental Implications | 335 | 1,778 | null |
Article: Moiety (chemistry). In organic chemistry, a moiety ( MOY-ə-tee) is a part of a molecule that is given a name because it is identified as a part of other molecules as well. Typically, the term is used to describe the larger and characteristic parts of organic molecules, and it should not be used to describe or ... | Wikipedia - Moiety (chemistry) - Summary | 185 | 870 | null |
Section: Measurement. The α and β anomers are diastereomers of each other and usually have different specific rotations. A solution or liquid sample of a pure α anomer will rotate plane polarised light by a different amount and/or in the opposite direction than the pure β anomer of that compound. The optical rotation o... | Wikipedia - Mutarotation - Measurement | 337 | 1,349 | null |
Article: N-linked glycosylation. N-linked glycosylation is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein), in a process called N-glycosylation, studied i... | Wikipedia - N-linked glycosylation - Summary | 216 | 839 | null |
Section: Energetics of bond formation. There are two types of bonds involved in a glycoprotein: bonds between the saccharides residues in the glycan and the linkage between the glycan chain and the protein molecule. The sugar moieties are linked to one another in the glycan chain via glycosidic bonds. These bonds are t... | Wikipedia - N-linked glycosylation - Energetics of bond formation | 319 | 1,297 | null |
Section: Biosynthesis. The biosynthesis of N-linked glycans occurs via three major steps: Synthesis of dolichol-linked precursor oligosaccharide En bloc transfer of precursor oligosaccharide to protein Processing of the oligosaccharide Synthesis, en bloc transfer and initial trimming of precursor oligosaccharide occurs... | Wikipedia - N-linked glycosylation - Biosynthesis | 241 | 1,045 | null |
Section: Biosynthesis > Synthesis of precursor oligosaccharide. The process of N-linked glycosylation starts with the formation of dolichol-linked GlcNAc sugar. Dolichol is a lipid molecule composed of repeating isoprene units. This molecule is found attached to the membrane of the ER. Sugar molecules are attached to t... | Wikipedia - N-linked glycosylation - Biosynthesis > Synthesis of precursor oligosaccharide | 225 | 944 | null |
Section: Biosynthesis > Transfer of glycan to protein. Once the precursor oligosaccharide is formed, the completed glycan is then transferred to the nascent polypeptide in the lumen of the ER membrane. This reaction is driven by the energy released from the cleavage of the pyrophosphate bond between the dolichol-glycan... | Wikipedia - N-linked glycosylation - Biosynthesis > Transfer of glycan to protein | 329 | 1,330 | null |
Section: Biosynthesis > Processing of glycan. N-glycan processing is carried out in endoplasmic reticulum and the Golgi body. Initial trimming of the precursor molecule occurs in the ER and the subsequent processing occurs in the Golgi. Upon transferring the completed glycan onto the nascent polypeptide, two glucose re... | Wikipedia - N-linked glycosylation - Biosynthesis > Processing of glycan | 344 | 1,454 | null |
These modifications are catalyzed by glycosyltransferases and glycosidases respectively. In the cis-Golgi, a series of mannosidases remove some or all of the four mannose residues in α-1,2 linkages. Whereas in the medial portion of the Golgi, glycosyltransferases add sugar residues to the core glycan structure, giving ... | Wikipedia - N-linked glycosylation - Biosynthesis > Processing of glycan | 306 | 1,234 | null |
Section: Function. N-linked glycans have intrinsic and extrinsic functions. Within the immune system, the N-linked glycans on an immune cell's surface will help dictate that migration pattern of the cell, e.g. immune cells that migrate to the skin have specific glycosylations that favor homing to that site. The glycosy... | Wikipedia - N-linked glycosylation - Function | 191 | 781 | null |
Section: Importance in therapeutic proteins. Many therapeutic proteins in the market are antibodies, which are N-linked glycoproteins. For example, Etanercept, Infliximab and Rituximab are N-glycosylated therapeutic proteins. The importance of N-linked glycosylation is becoming increasingly evident in the field of phar... | Wikipedia - N-linked glycosylation - Importance in therapeutic proteins | 323 | 1,377 | null |
However, glycans produced in these systems can differ from glycans produced in humans, as they can be capped with both N-glycolylneuraminic acid (Neu5Gc) and N-acetylneuraminic acid (Neu5Ac), whereas human cells only produce glycoproteins containing N-acetylneuraminic acid. Furthermore, animal cells can also produce gl... | Wikipedia - N-linked glycosylation - Importance in therapeutic proteins | 217 | 895 | null |
Section: Energy barrier. The identity of the inverting atom has a dominating influence on the barrier. Inversion of ammonia is rapid at room temperature, inverting 30 billion times per second. Three factors contribute to the rapidity of the inversion: a low energy barrier (24.2 kJ/mol; 5.8 kcal/mol), a narrow barrier w... | Wikipedia - Pyramidal inversion - Energy barrier | 219 | 893 | null |
Section: Biradicals. The simplest non-Kekulé molecules are biradicals. A biradical is an even-electron chemical compound with two free radical centres which act independently of each other. They should not be confused with the more general class of diradicals. One of the first biradicals was synthesized by Wilhelm Schl... | Wikipedia - Non-Kekulé molecule - Biradicals | 184 | 768 | null |
Section: Biradicals > Quinodimethanes and PAHs. Other examples of non-Kekulé molecules are the biradicaloid quinodimethanes, that have a six-membered ring with methylene substituents. Non-Kekulé polynuclear aromatic hydrocarbons are composed of several fused six-membered rings. The simplest member of this class is tria... | Wikipedia - Non-Kekulé molecule - Biradicals > Quinodimethanes and PAHs | 314 | 1,226 | null |
Section: Classification. Non-Kekulé molecules with two formal radical centers (non-Kekulé diradicals) can be classified into non-disjoint and disjoint by the shape of their two non-bonding molecular orbitals (NBMOs). Both NBMOs of molecules with non-disjoint characteristics such as trimethylenemethane have electron den... | Wikipedia - Non-Kekulé molecule - Classification | 251 | 1,075 | null |
Section: Examples. Historically, nonclassical ions were invoked to explain unusually fast solvolyses of steroidal, norbornyl, and cyclopropyl halides. Explanations for these rates was once controversial. The 2-norbornyl cation is one of the best characterized carbonium ions: C7H10 + H+ → C7H+11 In fact, it has emerged ... | Wikipedia - Nonclassical ion - Examples | 202 | 786 | null |
Article: Nucleofuge. In chemistry, a nucleofuge (from nucleo- 'atomic nucleus' and fuge 'to run away/escape') is a leaving group which retains the lone pair of electrons from its previous bond with another species. For example, in the SN2 mechanism, a nucleophile attacks an organic compound containing the nucleofuge (t... | Wikipedia - Nucleofuge - Summary | 160 | 683 | null |
Article: On-water reaction. On-water reactions are a group of organic reactions that take place as an emulsion in water and have an unusual reaction rate acceleration compared with (i) the same reaction in an organic solvent, or (ii) the corresponding dry media reaction. This effect has been known for many years but in... | Wikipedia - On-water reaction - Summary | 336 | 1,570 | null |
Section: Examples. In one study a coupling reaction between an indole and a quinone takes place at room temperature without catalyst in water in 82% chemical yield even though reactants and products are insoluble in this medium. The reaction is much less efficient in homogeneous systems such as dichloromethane, toluene... | Wikipedia - On-water reaction - Examples | 251 | 998 | null |
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