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Solvent models

About: Solvent models is a(n) research topic. Over the lifetime, 746 publication(s) have been published within this topic receiving 100600 citation(s). more


Journal ArticleDOI: 10.1063/1.445869
Abstract: Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint. more

Topics: Water model (53%), Solvent models (52%), Water dimer (51%) more

29,424 Citations

Journal ArticleDOI: 10.1021/JP973084F
Abstract: New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume... more

Topics: Ab initio (59%), Force field (chemistry) (53%), Solvation (53%) more

12,333 Citations

Journal ArticleDOI: 10.1021/CR9904009
26 Jul 2005-Chemical Reviews
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072 more

11,599 Citations

Journal ArticleDOI: 10.1002/JCC.10349
Yong Duan1, Chun Wu1, Shibasish Chowdhury1, Mathew C. Lee1  +11 moreInstitutions (3)
Abstract: Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of e = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999–2012, 2003 more

Topics: Molecular dynamics (58%), Force field (chemistry) (56%), Solvent models (56%) more

3,858 Citations

Journal ArticleDOI: 10.1021/JA00172A038
Abstract: sorption results9 revealed that the iron surface was mostly covered by promoter oxides of AI, Ca, and K. Postreaction XPS results also revealed a C( Is) XPS peak of weak to moderate intensity centered at 284.1-283.7 eV. This binding energy approaches those (ca. 283.5 eV) reported for iron cat bide^.^^*'^ More convincing evidence for carbide formation was obtained from TPHT results collected after reaction studies like those displayed in Figure 1 in which methane was the only product. After reaction at temperatures below 340 OC, only small amounts of reactive carbon could be distinguished with maximum methane desorption rates near 300 OC. However, for higher reaction temperatures, large amounts of methane were produced with a maximum rate just above 400 OC. Since XPS results revealed only small amounts of carbonaceous residue on top of the catalyst surface, this reactive carbon must be associated with carbiding of the catalyst. Consequently, it appears that the active carbon incorporation catalyst is carbided iron. This conclusion is well supported by bulk carbon to iron stoichiometries of 0.1-0.25 estimated from the TPHT peak areas which were adequate to represent 40-60'36 conversion to bulk carbides such as Fe,C or FeSC2. Moreover, preliminary results from studies using bona fide iron carbides have shown similar catalytic b e h a ~ i o r . ~ more

Topics: Implicit solvation (68%), Solvation (59%), Solvent models (54%) more

3,390 Citations

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Topic's top 5 most impactful authors

Thomas Simonson

9 papers, 1.3K citations

J. Andrew McCammon

8 papers, 460 citations

Petr Bouř

7 papers, 316 citations

Ken A. Dill

7 papers, 610 citations

David A. Case

7 papers, 1.7K citations

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