Thermodynamic parameters of the activation of glycine zwitterion protonation reactions

Slifkin, M.A.; Ali, S. Mubarik

doi:10.1016/0167-7322(84)80025-2

Cited by 42 publications

(61 citation statements)

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“…Amino acids have been the subject of a variety of experimental [1][2][3][4][5][6][7][8][9] and theoretical studies 10-68 because of its central role in metabolism as building blocks of proteins. Especially, among 20 amino acids, glycine has been usually preferred as a subject of theoretical studies due to its small size and the existence of experimental data.…”

Section: Introductionmentioning

confidence: 99%

“…Especially, among 20 amino acids, glycine has been usually preferred as a subject of theoretical studies due to its small size and the existence of experimental data. [1][2][3][4][5][6][7][8][9] High-level ab initio studies demonstrated that the neutral form (NE) of glycine exists in the gas phase but the zwitterionic form (ZW) is unstable in vacuo. [11][12][13][14][15][16][17][18][19][20]27,[30][31][32][33] However, as is well known, the ZW of glycine predominates in crystalline or in aqueous solution, 2 and hence the solvent (or environmental) effects should be included in the theoretical studies to explore the glycine chemistry correctly.…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study

Kim¹,

Park²,

Lee³

et al. 2011

Bulletin of the Korean Chemical Society

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The stable conformers of glycine and the inter-conversions between them were studied theoretically at various levels of theory, B3LYP, MP2, CCSD and CCSD(T), in the gas phase and in aqueous solution. In aqueous solution, the structures examined by use of the conductor-like polarizable continuum model (CPCM) with various cavity models, UA0, UAHF, UAKS, UFF, BONDI and PAULING, and by use of a discrete/continuum solvation model with eight water clusters. The Gibbs free energy differences between the neutral (NE) and zwitterionic conformers (ZW), ΔG Z-N [= G ZW -G NE ], in aqueous solution were well reproduced by using the BONDI and PAULING cavity models. However the ΔG Z-N values were underestimated in other cavity models, although the ZW conformers existed as stable species in aqueous solution. In the studies of a discrete/ continuum solvation model with eight water clusters, gas phase results are still insufficient to reproduce the experimental findings. However the ΔG Z-N values calculated by use of CPCM method in aqueous solution agreed well with the experimental ones.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study

Kim¹,

Park²,

Lee³

et al. 2011

Bulletin of the Korean Chemical Society

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“…9 One of the reasons for this may be the insufficiency of the theoretical level used to calculate the solute energy change along the route. The solute energies of the intermediate steps of hydrogen atom transfer may depend on the theory used: MP2 level may not be good enough in the current case.…”

Section: ¹1mentioning

confidence: 99%

“…9 Recently, we have shown in the quantum mechanical/molecular mechanical framework with Metropolis Monte Carlo method (QM/MM-MC method) that the free energy barrier height of a water-mediated tautomerization path is higher than that of the direct tautomerization path in aqueous environment and that it is not "proton" but "hydrogen atom" that transfers.…”

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confidence: 99%

“…17 Experimentally, the free energy of Z form was estimated to be 7.27 kcal mol ¹1 lower than that of N form, 8 and the free energy barrier height from Z to N was estimated to be 14.6 kcal mol ¹1 . 9 Recently, we have shown in the quantum mechanical/molecular mechanical framework with Metropolis Monte Carlo method (QM/MM-MC method) that the free energy barrier height of a water-mediated tautomerization path is higher than that of the direct tautomerization path in aqueous environment and that it is not "proton" but "hydrogen atom" that transfers. 7 In the current work, we aim at performing the quantitative calculation of the NZ free energy difference of glycine in aqueous solution.…”

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confidence: 99%

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Helmholtz Energy Change between Neutral and Zwitterionic Forms of Glycine in Aqueous Solution Using Ab Initio Expanded QM/MM-MC with QM Solvent

Miyamoto

Aida

2013

Chemistry Letters

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We present an extended methodology of the quantum mechanical/molecular mechanical framework with Metropolis Monte Carlo method (QM/MM-MC), in which close surrounding solvent molecules are included in QM subsystem to evaluate quantitatively the solvation free energy change. The neutral (N) and zwitterionic (Z) structures of glycine in aqueous solution were optimized in the combination procedure of simulated annealing with MC at MM level and QM/MM-vib geometry optimization. Helmholtz energy change between N and Z forms of glycine in aqueous solution was calculated stepwise with expanded QM/MM-MC method, and the computational result was in good agreement with the experimental value.Glycine is a molecule that can form an intramolecular hydrogen bond and may convert from a neutral (N) form to a zwitterionic (Z) form in an aqueous solution. Since the conversion between N and Z of glycine can be considered as a prototype of the tautomerization of amino acid, the process and the energy profile of the NZ conversion have been extensively studied.17 Experimentally, the free energy of Z form was estimated to be 7.27 kcal mol ¹1 lower than that of N form, 8 and the free energy barrier height from Z to N was estimated to be 14.6 kcal mol ¹1 . 9 Recently, we have shown in the quantum mechanical/molecular mechanical framework with Metropolis Monte Carlo method (QM/MM-MC method) that the free energy barrier height of a water-mediated tautomerization path is higher than that of the direct tautomerization path in aqueous environment and that it is not "proton" but "hydrogen atom" that transfers. 7In the current work, we aim at performing the quantitative calculation of the NZ free energy difference of glycine in aqueous solution. To this end, we present an extended QM/MM-MC method to calculate the Helmholtz free energy change. Solvation effect cannot be elucidated simply by taking account of only a few solvent molecules in a few selected configurations of the solvent, even if high level of theory is used. It is necessary to treat many solvent molecules and many solvent configurations explicitly. This is why several methods such as QM/MM-MC method have been adopted. If MC simulations are to be performed to sample solvent configurations satisfactorily, a lower level of theory must be used. If a lower level of theory is used throughout for free energy calculations, however, a resultant computational value may not be reliable. In this Letter, the following three points are addressed to evaluate quantitatively the free energy change in aqueous solution. The first is how to obtain a solute structure in aqueous solution, which may be largely different from that in the gas phase. The second is how to include close surrounding water molecules in QM subsystem in free energy calculations. We present a new methodology here, which we call the "expanded QM/MM-MC method." The last is how to treat the solute with higher level QM in the free energy evaluation. Thus, we present the multistage evaluation of Helmholtz energy change.At the beginning, ...

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Conformers of Zwitterionic Glycine in Aqueous Phase

Ghosh

Choi

2018

Bulletin Korean Chem Soc

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Zwitterionic glycine was investigated for its major conformers and their isomerizations in aqueous phase by QM/MM‐MD. The rotameric barrier of zwitterionic glycine along C−C bond is approximately 2 kcal/mol higher than that of non‐ionized one. It can be attributed to the strong electrostatic effects of zwitterion, which attracts water solvents more tightly. Unlike the previous quantum mechanical calculations, our QM/MM‐MD found that only the gauche conformer as stable minima along the C−N bond rotation. Overall, the preferred conformers in real solution are different from those found with limited clusters, necessitating the use of QM/MM‐MD.

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Thermodynamic parameters of the activation of glycine zwitterion protonation reactions

Cited by 42 publications

References 3 publications

Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study

Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study

Helmholtz Energy Change between Neutral and Zwitterionic Forms of Glycine in Aqueous Solution Using Ab Initio Expanded QM/MM-MC with QM Solvent

Conformers of Zwitterionic Glycine in Aqueous Phase

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