An integrated effective fragment—polarizable continuum approach to solvation: Theory and application to glycine

Bandyopadhyay, Pradipta; Gordon, Mark S.; Mennucci, Benedetta; Tomasi, Jacopo

doi:10.1063/1.1433503

Cited by 124 publications

(130 citation statements)

References 34 publications

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“…Alanine(H 2 O) 16 (Figure 12). When 16 waters are present, Z16-1 is predicted to be the global minimum at all levels of theory, and all four N isomers shown in Figure 12 are higher in energy than the two lowest energy Z isomers.…”

Section: Alanine(h 2 O) 5 (Figure 8)mentioning

confidence: 99%

“…21 In the second study, Monte Carlo simulations with local minimizations were used in order to find a low energy configuration. 16 Cui used a similar approach in order to examine the affects of TIP3P waters. 20 Using the three-layer approach, the Z form is predicted to be more stable than the N species when a reliable continuum method 21 29 and coupled cluster with single and double excitations (CCSD).…”

Section: 68mentioning

confidence: 99%

“…However the long-range interactions may not achieve the desired accuracy. [15][16][17]20,21 Supermolecular complexes have also been studied using DFT/ B3LYP 21 and the composite DFT/B3LYP + Onsager 36 model, but these authors do not discuss configurational sampling. In a separate effort, MC simulations with a molecular mechanics force field were employed to sample the configuration space, with the structures subsequently optimized with semiempirical QM methods.…”

Section: 68mentioning

confidence: 99%

“…Bandyopadhyay et al considered the glycine(H 2 O) 8 complex using three-layer models that combined the effective fragment potential with either the Onsager or PCM models. 16,21 In the first study, eight water molecules in the solvent shell were selected from a previous molecular dynamics calculation, and this structure was optimized. 21 In the second study, Monte Carlo simulations with local minimizations were used in order to find a low energy configuration.…”

Section: 68mentioning

confidence: 99%

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Alanine: Then There Was Water

Mullin

Gordon

2009

J. Phys. Chem. B

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An ab initio study of the addition of successive water molecules to the amino acid l-alanine in both the nonionized (N) and zwitterionic (Z) forms are presented. The main focus is the number of waters needed to stabilize the Z form and how the solvent affects conformational preference. The solvent is modeled by ab initio electronic structure theory, the EFP (effective fragment potential) model, and the isotropic dielectric PCM (polarizable continuum method) bulk solvation techniques. The EFP discrete solvation model is used with a Monte Carlo algorithm to sample the configuration space to find the global minimum. Bridging structures are predicted to be the lowest energy Z minima after 3−5 discrete waters are included in the calculations, depending on the level of theory. Second-order perturbation theory and PCM stabilize the Z structures by ∼3−6 and 7 kcal/mol, respectively, relative to the N global minimum through the addition of up to 8 waters.Subsequently, the contributions of each are ∼1 kcal/mol relative to the N global minimum. The presence of 32 waters appears to be close to converging the N−Z enthalpy difference, ΔHN−Z. Disciplines Chemistry CommentsReprinted (adapted) February 17, 2009; ReVised Manuscript ReceiVed: April 12, 2009 An ab initio study of the addition of successive water molecules to the amino acid L-alanine in both the nonionized (N) and zwitterionic (Z) forms are presented. The main focus is the number of waters needed to stabilize the Z form and how the solvent affects conformational preference. The solvent is modeled by ab initio electronic structure theory, the EFP (effective fragment potential) model, and the isotropic dielectric PCM (polarizable continuum method) bulk solvation techniques. The EFP discrete solvation model is used with a Monte Carlo algorithm to sample the configuration space to find the global minimum. Bridging structures are predicted to be the lowest energy Z minima after 3-5 discrete waters are included in the calculations, depending on the level of theory. Second-order perturbation theory and PCM stabilize the Z structures by ∼3-6 and 7 kcal/mol, respectively, relative to the N global minimum through the addition of up to 8 waters. Subsequently, the contributions of each are ∼1 kcal/mol relative to the N global minimum. The presence of 32 waters appears to be close to converging the N-Z enthalpy difference, ∆H N-Z .

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Section: Alanine(h 2 O) 5 (Figure 8)mentioning

confidence: 99%

Section: 68mentioning

confidence: 99%

Section: 68mentioning

confidence: 99%

Section: 68mentioning

confidence: 99%

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Alanine: Then There Was Water

Mullin

Gordon

2009

J. Phys. Chem. B

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“…Some threelayer approaches have been developed that combine the microsolvation and continuum approaches. [38][39][40][41][42][43][44] These methods may reduce the number of explicit solvent molecules required (and hence the computational cost) and may allow for an accurate description of long-range interactions.…”

Section: Introductionmentioning

confidence: 99%

Incremental Solvation of Nonionized and Zwitterionic Glycine

2006

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Microsolvation and combined microsolvation−continuum approaches are employed in order to examine the structures and relative energies of nonionized (N) and zwitterionic (Z) glycine clusters. Bridging structures are predicted to be the global minima after 3−5 discrete water molecules are included in the calculations. Calculations incorporating electron correlation stabilize the zwitterionic structures by about 7−9 kcal/mol relative to the N structures regardless of the number of discrete water molecules considered. Continuum calculations stabilize the Z structures relative to N structures; this effect decreases as the number of discrete water molecules is increased. Eight water molecules do not appear to fully solvate glycine. Disciplines Chemistry CommentsReprinted (adapted) Abstract: Microsolvation and combined microsolvation-continuum approaches are employed in order to examine the structures and relative energies of nonionized (N) and zwitterionic (Z) glycine clusters. Bridging structures are predicted to be the global minima after 3-5 discrete water molecules are included in the calculations. Calculations incorporating electron correlation stabilize the zwitterionic structures by about 7-9 kcal/mol relative to the N structures regardless of the number of discrete water molecules considered. Continuum calculations stabilize the Z structures relative to N structures; this effect decreases as the number of discrete water molecules is increased. Eight water molecules do not appear to fully solvate glycine.

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Calculation of Reduction Potential and p K _a

Jensen

2005

Encyclopedia of Inorganic Chemistry

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Three methods, quantum mechanical and molecular mechanical polarizable continuum model (QM/MM/PCM), QM/PCM, and empirical, were developed and applied to calculate protein reduction potential ( E 0 ) and p K a values. In the QM/MM/PCM calculation of Lys55 p K a of turkey ovomucoid third domain (OMTKY3), the MP2/6‐31 + G(2d,p) method was used to describe the QM region consisting of ∼45 atoms; the rest of the protein was modeled either with ab initio‐derived electric multipole points or atomic charges from standard force field methods; and the aqueous solvation effect was described with the polarizable continuum model (PCM). The calculated Lys55 p K a values are in good agreement with experiments. QM/PCM methods were used to calculate p K a values of various proteins and the E 0 of type‐1 Cu centers. For solvent‐exposed p K a sites, QM/PCM (MP2/6‐31 + G(2d,p) for ∼100 atoms, PCM with dielectric = 78.39 for aqueous solution) methods can often reproduce experimental p K a values. For type‐1 Cu E 0 , because of protein burial, the desolvation effect becomes significant: it was found that Cu‐ligand interactions and desolvation can potentially change the E 0 by ∼300 and ∼400 mV, respectively, using the CPCM/B3LYP/6‐311++G(2df,p) method and model molecules of ∼100 atoms. An empirical method, PROPKA, was developed for protein p K a calculation and analysis, which is able to calculate the p K a values of a protein within ∼1 s.

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An integrated effective fragment—polarizable continuum approach to solvation: Theory and application to glycine

Cited by 124 publications

References 34 publications

Alanine: Then There Was Water

Alanine: Then There Was Water

Incremental Solvation of Nonionized and Zwitterionic Glycine

Calculation of Reduction Potential and p K _a

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An integrated effective fragment—polarizable continuum approach to solvation: Theory and application to glycine

Cited by 124 publications

References 34 publications

Alanine: Then There Was Water

Alanine: Then There Was Water

Incremental Solvation of Nonionized and Zwitterionic Glycine

Calculation of Reduction Potential and p K a

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Calculation of Reduction Potential and p K _a