Theoretical models for transition-state structure and catalysis in carbonyl addition

Williams, Ian H.; Spangler, Dale; Femec, Douglas A.; Maggiora, Gerald M.; Schowen, Richard L.

doi:10.1021/ja00541a068

Cited by 45 publications

(18 citation statements)

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“…It is known that the inclusion of water molecules in the calculation of the activation barrier for the hydration of formaldehyde substantially lowers this barrier height. [19][20][21][22][23][24][25][26] We tried to find out how different types of substituents affect this lowering. The equilibrium structures of transition states for the methanediol dehydration (TS7) and those for molecules with electron-donating [Me 2 C(OH) 2 -TS8] and electronwithdrawing [(HOCO)HC(OH) 2 -TS9] substituents with the additional water molecule are depicted in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…18 Numerous theoretical studies of this reaction (mostly the reverse reaction, i.e. the formaldehyde hydration) [19][20][21][22][23][24][25][26] have shown that the inclusion of additional water molecules in the process of proton transfer significantly lowers the barrier and brings the theoretical value close to the experimental one. Although methanediol was not isolated experimentally either in the gas or in condensed phases, other geminal diols, such as 2,2-dihydroxyacetic acid, (HOCQO)CH(OH) 2 , 27 or 1,1-dihydroxypropan-2-one, (CH 3 CQO)CH(OH) 2 , 28 were characterized spectroscopically in the gas phase and some more compounds were detected in the solid state, such as chloral hydrate, CCl 3 CH(OH) 2 , [29][30][31][32] dichloroacetaldehyde hydrate, CHCl 2 CH(OH) 2 , 33 hexachloroacetone hydrate, (CCl 3 ) 2 C(OH) 2 , 34 and ninhydrin.…”

Section: Introductionmentioning

confidence: 99%

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Effect of substituents and hydrogen bonding on barrier heights in dehydration reactions of carbon and silicon geminal diols

Ignatyev

Montejo

Ortega

et al. 2011

Phys. Chem. Chem. Phys.

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Activation barrier heights for the dehydration reaction of geminal carbinols and silanediols R'R″X(OH)(2) (X = C, Si) were estimated at the B3LYP and MP2 levels of theory employing Dunning's correlation-consistent triple-zeta basis sets. It was shown that the barrier height for carbon derivatives steadily decreases upon substitution by R groups, usually termed as electron-donating, such as alkyl and amino groups. Substitution by electron-withdrawing groups leads, however, only to small changes in barrier heights compared to that of methanediol. A similar tendency was also found for silicon derivatives, but high activation barriers of this reaction remain even for amino group substituted silanediols. Introduction of additional water molecules into the reactive space of carbinol dehydration drastically reduces barrier heights and brings the transition state energy for methanediol close to the experimental value. The difference between dehydration barrier heights for both methanediol and carbinols with electron-rich substituents becomes well-defined for dimeric species. The higher acidity of the hydroxyl group protons in molecules containing halogens and C==O groups brings about a noticeable growth in the dehydration barrier heights of these compounds. This difference in barrier heights for oligomeric species may be the reason for the stability of carbinols with electron-rich substituents.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Effect of substituents and hydrogen bonding on barrier heights in dehydration reactions of carbon and silicon geminal diols

Ignatyev

Montejo

Ortega

et al. 2011

Phys. Chem. Chem. Phys.

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“…Tropospheric degradation of the proposed CFC leading to the formation of HFCO might be followed by hydrolysis [27,28]. Williams et al [29][30][31][32][33] investigated theoretically the mechanism and catalysis for a carbonyl addition in which an addition of H 2 O to HXCO yields CHX(OH) 2 (in which X = H, Cl, F), which then decomposes preferentially by 1,2-elimination of HX to produce methanoic acid. These authors proposed this reaction Scheme 1.…”

Section: Introductionmentioning

confidence: 99%

Theoretical study on the reaction pathways of HFCO+H2O

Tsai

2008

Journal of Molecular Structure: THEOCHEM

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“…Calculations show that one or more molecules of water59 or a second molecule of the amine61 can assist in the proton transfer process and lower the barrier significantly. Explicit interaction with a molecule of water also calalyzes the hydrolysis of amides62–69 and the hydration of CO 2 70, 71 and carbonyls 72–78…”

Section: Resultsmentioning

confidence: 99%

Lysine carboxylation in proteins: OXA‐10 β‐lactamase

Cross

Vreven

et al. 2005

Proteins

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An increasing number of proteins are being shown to have an N(zeta)-carboxylated lysine in their structures, a posttranslational modification of proteins that proceeds without the intervention of a specific enzyme. The role of the carboxylated lysine in these proteins is typically structural (hydrogen bonding or metal coordination). However, carboxylated lysines in the active sites of OXA-10 and OXA-1 beta-lactamases and the sensor domain of BlaR signal-transducer protein serve in proton transfer events required for the functions of these proteins. These examples demonstrate the utility of this unusual amino acid in acid-base chemistry, in expansion of function beyond those of the 20 standard amino acids. In this study, the ONIOM quantum-mechanical/molecular-mechanical (QM/MM) method is used to study the carboxylation of lysine in the OXA-10 beta-lactamase. Lys-70 and the active site of the OXA-10 beta-lactamase were treated with B3LYP/6-31G(d,p) density functional calculations and the remainder of the enzyme with the AMBER molecular mechanics force field. The barriers for unassisted carboxylation of neutral lysine by carbon dioxide or bicarbonate are high. However, when the reaction with CO2 is catalyzed by a molecule of water in the active site, it is exothermic by about 13 kcal/mol, with a barrier of approximately 14 kcal/mol. The calculations show that the carboxylation and decarboxylation of Lys-70 are likely to be accompanied by deprotonation and protonation of the carbamate, respectively. The analysis may also be relevant for other proteins with carboxylated lysines, a feature that may be more common in nature than previously appreciated.

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Theoretical models for transition-state structure and catalysis in carbonyl addition

Cited by 45 publications

References 0 publications

Effect of substituents and hydrogen bonding on barrier heights in dehydration reactions of carbon and silicon geminal diols

Effect of substituents and hydrogen bonding on barrier heights in dehydration reactions of carbon and silicon geminal diols

Theoretical study on the reaction pathways of HFCO+H2O

Lysine carboxylation in proteins: OXA‐10 β‐lactamase

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