Alanine: Then There Was Water

Mullin, Jonathan; Gordon, Mark S.

doi:10.1021/jp901459y

Cited by 58 publications

(66 citation statements)

References 89 publications

(198 reference statements)

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“…Previous work showed that the D-chiral analogs did not significantly alter the relative N f Z energy. 5 Continuum Calculations. The HF+PCM/6-31++G(d,p) continuum method predicts the Z to be lower in energy than the N species; however, this difference is only 0.8 kcal/mol.…”

Section: Resultsmentioning

confidence: 99%

“…4 The authors of the present work studied alanine in the presence of up to 32 effective fragment potential (EFP1)/DFT 11 waters and found ∆H NfZ ) 11.7, 10.1, or 9.1 kcal/mol using MP2//EFP2, MP2(EFP1/DFT), or PCM+MP2//MP2(EFP1/ DFT), respectively, with 32 waters. 5 The aforementioned studies used discrete explicit solvent models to investigate the hydrogen bonded interaction between water molecules and the amino acid, adding a continuum (implicit) solvent as a third layer to simulate complete solvation. This work builds upon the previous analysis that included up to 32 discrete water molecules and additionally explores the importance of including a continuum description of the solvent.…”

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: Introductionmentioning

confidence: 99%

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

Mullin

Gordon

2009

J. Phys. Chem. B

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“…196 Solvation of alanine by increasing number of water molecules was studied by Mullin and Gordon. 457,458 Song et al investigated solvent effects on the conformational potential energy surfaces (gauche versus trans conformations) of acetylcholine and acetylthiocholine ACh and ATCh. 459 The EFP2 model has been used to investigate intermolecular interactions in complex molecular clusters.…”

Section: Homogeneous Clusters and Explicit Solvent Treatmentsmentioning

confidence: 99%

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

et al. 2011

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Theoretical chemists have always strived to perform quantum mechanics (QM) calculations on larger and larger molecules and molecular systems, as well as condensed phase species, that are frequently much larger than the current state-of-the-art would suggest is possible. The desire to study species (with acceptable accuracy) that are larger than appears to be feasible has naturally led to the development of novel methods, including semiempirical approaches, reduced scaling methods, and fragmentation methods. The focus of the present review is on fragmentation methods, in which a large molecule or molecular system is made more computationally tractable by explicitly considering only one part (fragment) of the whole in any particular calculation. If one can divide a species of interest into fragments, employ some level of ab initio QM to calculate the wave function, energy, and properties of each fragment, and then combine the results from the fragment calculations to predict the same properties for the whole, the possibility exists that the accuracy of the outcome can approach that which would be obtained from a full (nonfragmented) calculation. It is this goal that drives the development of fragmentation methods. Disciplines Chemistry CommentsReprinted (adapted) with permission from Chemical Reviews 112 (2012): 632,

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“…The structure of the Ala monomer in water has been studied theoretically by several groups. [56,57,[67][68][69][70][71][72][73][74][75][76][77] The structure of the dimer was optimized here for the Z2 and Z3 conformations, as these conformers are the most stable ones for Gly. The optimized structures in water are displayed in Figure 2.…”

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confidence: 99%

Glycine Dimers: Structure, Stability, and Medium Effects

Friant-Michel

Ruiz‐López

2010

ChemPhysChem

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We report a study on different ionization states and conformations of the bimolecular (Gly)(2) system by means of quantum mechanical calculations. Optimized geometries for energy minima of the glycine dimer, as well as relative energies and free energies were computed as a function of the medium: gas phase, nonpolar polarizable solvent, and aqueous solution. The polarizable continuum model was employed to account for solvation effects. Energy calculations were done using the MP2/aug-cc-pVTZ and B3LYP/6-311+G(2df,2p) methods on B3LYP/6-31+G(d,p) optimized structures (some single-point energy calculations were also done using the B3PW91 and PBE1KCIS methods). Ionized forms of the glycine dimer (either zwitterion-zwitterion or neutral-zwitterion) are predicted to exist in all media, in contrast to amino acid monomers. In aqueous solution, dimerization is an exergonic process (-4 kcal mol(-1)). Thus, according to our results, zwitterion-zwitterion Gly dimers might be abundant in supersaturated glycine aqueous solutions, a fact that has been connected with the structure of α-glycine crystals but that remains controversial in the literature. Another noticeable result is that zwitterion-zwitterion interactions are substantially underestimated when computed using methods based on density functional theory. For comparison, some calculations for the dimer of the simplest chiral amino acid alanine were done as well and differences to the glycine dimer are discussed.

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Alanine: Then There Was Water

Cited by 58 publications

References 89 publications

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

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

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

Glycine Dimers: Structure, Stability, and Medium Effects

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