Incremental Solvation of Nonionized and Zwitterionic Glycine

Aikens, Christine M.; Gordon, Mark S.

doi:10.1021/ja062842p

Cited by 184 publications

(252 citation statements)

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“…The importance of including electron correlation has been demonstrated in previous studies. [3][4][5] A MP2+PCM/6-31++G-(d,p) single point calculation at the HF+PCM geometry predicts the Z to be 1.8 kcal/mol lower in energy. MP2 may alter the gradient and, consequently, the geometry as well.…”

Section: Resultsmentioning

confidence: 99%

“…The PCM contributes ∼1.5 kcal/mol to this energy difference. The addition of PCM has a large (9.4 kcal/mol) stabilizing effect on the energy of Z36-2 relative to Z36-1 stemming from a difference in the contribution of the hydrogen bonding pairs of COO -and NH 3 + surface areas to the PCM cavity. The higherenergy N species N36-3 and N36-4 are both examples of mostly solvated neutral alanine isomers that are 15-20 kcal/mol higher in energy than the lowest energy N structure.…”

Section: Resultsmentioning

confidence: 99%

“…The two lowest-energy Z structures, Z48-1 and Z48-2, differ by only 2.4 kcal/mol at the highest level of theory and have similar, fully solvated structures. In Z48-1 the water molecules that sit below the NH 3 + group are arranged approximately in a prism structure, while in Z48-2 these six waters are arranged in a chairlike conformation. In both cases, Z48-1 and Z48-2, these six waters appear to be the beginning of a second solvent shell.…”

Section: Resultsmentioning

confidence: 99%

“…These authors determined 1.8 and 6.0 kcal/mol enthalpies for the process N f Z (∆H NfZ ) using MP2// RHF/6-31++G(d,p) and MP2+PCM//RHF/6-31++G(d,p), respectively, with eight water molecules. 3 Aikens and Gordon noted that convergence had probably not been achieved at this number of water molecules. Chuchev and BelBruno found a 6.6 and 5.2 kcal/mol enthalpy for the alanine N f Z transition (∆H NfZ ) using density functional theory (DFT/B3LYP) 10 and MP2 single points, respectively, at the DFT geometry for 10 waters.…”

Section: Introductionmentioning

confidence: 99%

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Water and Alanine: From Puddles(32) to Ponds(49)

Mullin

Gordon

2009

J. Phys. Chem. B

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The solvation of alanine is investigated, with a focus on adding a sufficient number of discrete water molecules to determine the first solvation shell for both the nonionized (N) and zwitterionic (Z) forms to converge the enthalpy of solvation and the enthalpy difference for the two forms of alanine. Monte Carlo sampling was employed using the generalized effective fragment potential (EFP) method to determine the global minimum of both conformers, with the number of EFP water molecules ranging from 32−49. A subset of sampled geometries were optimized with second-order perturbation theory (MP2) using the 6-31++G(d,p) basis set. Single point energies were calculated at these geometries using the polarizable continuum model (PCM). The predicted 298.15 K enthalpy of solvation ranges for MP2/6-31++G(d,p) and MP2+PCM//MP2/ 6-31++G(d,p) are 10.0−13.2 kcal/mol and 10.1−12.6 kcal/mol, respectively. Disciplines Chemistry CommentsReprinted (adapted) ReceiVed: May 23, 2009; ReVised Manuscript ReceiVed: August 26, 2009 The solvation of alanine is investigated, with a focus on adding a sufficient number of discrete water molecules to determine the first solvation shell for both the nonionized (N) and zwitterionic (Z) forms to converge the enthalpy of solvation and the enthalpy difference for the two forms of alanine. Monte Carlo sampling was employed using the generalized effective fragment potential (EFP) method to determine the global minimum of both conformers, with the number of EFP water molecules ranging from 32-49. A subset of sampled geometries were optimized with second-order perturbation theory (MP2) using the 6-31++G(d,p) basis set. Single point energies were calculated at these geometries using the polarizable continuum model (PCM). The predicted 298.15 K enthalpy of solvation ranges for MP2/6-31++G(d,p) and MP2+PCM//MP2/6-31++G(d,p) are 10.0-13.2 kcal/mol and 10.1-12.6 kcal/mol, respectively.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Water and Alanine: From Puddles(32) to Ponds(49)

Mullin

Gordon

2009

J. Phys. Chem. B

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“…Schematic of a multifunctionalized mesoporous silica system. as solvated glycine 21 and alanine, 22 for which the structure of the surrounding water has a significant impact on the relative stabilities of the nonionic and zwitterionic species. The EFP/ MM method by Nemukhin et al also only has two regions: a QM region and an EFP region.…”

Section: Introductionmentioning

confidence: 99%

An Interface between the Universal Force Field and the Effective Fragment Potential Method

et al. 2008

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In order to properly describe reactions in heterogeneous catalyst systems, the reactants, solvent, and bulk effects of the surface must be taken into account. Embedded-cluster QM (quantum mechanics)/MM (molecular mechanics) methods can treat reactions on surfaces (the gas−surface interface), and the effective fragment potential method (EFP) can accurately treat the solvent effects on reactions (the gas−liquid interface). In order to create a QM/MM/EFP hybrid method for treatment of heterogeneous catalytic systems in the presence of a solvent (the liquid−surface interface), an EFP−MM interaction potential has been developed. Example calculations on small clusters of silica and water have been carried out. Disciplines Chemistry CommentsReprinted (adapted) ReceiVed: June 5, 2008; ReVised Manuscript ReceiVed: July 29, 2008 In order to properly describe reactions in heterogeneous catalyst systems, the reactants, solvent, and bulk effects of the surface must be taken into account. Embedded-cluster QM (quantum mechanics)/MM (molecular mechanics) methods can treat reactions on surfaces (the gas-surface interface), and the effective fragment potential method (EFP) can accurately treat the solvent effects on reactions (the gas-liquid interface). In order to create a QM/MM/EFP hybrid method for treatment of heterogeneous catalytic systems in the presence of a solvent (the liquid-surface interface), an EFP-MM interaction potential has been developed. Example calculations on small clusters of silica and water have been carried out.

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Solution‐Phase Organic Chemistry

Bachrach

2014

Computational Organic Chemistry

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Standard quantum chemical computations are performed on a single molecule or complex. This isolated species represents a molecule in the gas phase. While gas-phase chemistry comprises an important chemical subdiscipline, the vast majority of chemical reactions occur in solution. Perhaps most critical is that all of biochemistry takes place in an aqueous environment, and so if computational chemistry is to be relevant for biochemical applications, treatment of the solvent is imperative.Neglecting solvent effects is extremely hazardous. Equilibria and kinetics can be dramatically altered by the nature of the solvent. For example, the rate of nucleophilic substitution reactions spans 20 orders of magnitude in going from the gas phase to polar and nonpolar solvents. 1 -3 A classical example of a dramatic solvent effect on equilibrium is the tautomerism between 1 and 2. In the gas phase, the equilibrium lies far to the left, while in the solution phase, 2 dominates because of its much larger dipole moment. 4 Another classical example is that the trend in gas-phase acidity of aliphatic alcohols is reverse of the well-known trend in the solution phase; in other words, in the solution phase, the relative acidity trend is R 3 COH < R 2 CHOH < RCH 2 OH, but the opposite is true in the gas phase. 5,6 1 2Through the 1980s, computational chemists did neglect solvent effects, because they either hoped it would not matter or had no real way to effectively treat solvation. In terms of the former case, modeling reactions involving nonpolar molecules with nonpolar transition states (TSs) in nonpolar solvents as gas-phase chemistry might be appropriate. This, however, comprises a very small subset of chemistry, and even small changes in charge distribution can manifest themselves in large solvent effects.

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Incremental Solvation of Nonionized and Zwitterionic Glycine

Cited by 184 publications

References 68 publications

Water and Alanine: From Puddles(32) to Ponds(49)

Water and Alanine: From Puddles(32) to Ponds(49)

An Interface between the Universal Force Field and the Effective Fragment Potential Method

Solution‐Phase Organic Chemistry

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