Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace

Kovalenko, Andriy; Ten‐no, Seiichiro; Hirata, Fumio

doi:10.1002/(sici)1096-987x(19990715)20:9<928::aid-jcc4>3.0.co;2-x

Cited by 233 publications

(207 citation statements)

References 18 publications

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“…30 Stand-alone RISM/HNC equations were performed using the modified direct inversion of iterative subspace convergence technique. 38 AMBER PARM99 force field 36 parameters were used, with the exceptions noted below.…”

Section: Computational Detailsmentioning

confidence: 99%

An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide

Freedman

Truong

2004

The Journal of Chemical Physics

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We present an application of our recently proposed coupled reference interaction site model (RISM) molecular dynamics (MD) solvation free energy methodology [Freedman and Truong, Chem. Phys. Lett. 381, 362 (2003); J. Chem. Phys. 121, 2187 (2004)] to study the conformational stability of alanine dipeptide in aqueous solution. In this methodology, radial distribution functions obtained from a single MD simulation are substituted into a RISM expression for solvation free energy. Consequently, iterative solution of the RISM equation is not needed. The relative solvation free energies of seven different conformations of the alanine dipeptide in aqueous solution are calculated. Results from the coupled RISM/MD methodology are in good agreement with those from earlier simulations using the accurate free energy perturbation approach, showing that the alphaR conformation is most stabilized by solution. This study establishes a framework for applying this coupled RISM/MD method to larger biological systems.

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Section: Computational Detailsmentioning

confidence: 99%

An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide

Freedman

Truong

2004

The Journal of Chemical Physics

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“…The solvent susceptibility v was calculated using the DRISM/ HNC [6,7] method for a modified SPC/E water model [9] (Lennard-Jones (LJ) parameter r of hydrogen set to 1.0 Å [10,11]) at T = 298.15 K, a bulk density of q = 0.03334 Å -3 , and with the dielectric constant set to 78. The equations were solved with the modified direct inversion of iterative subspace (MDIIS) technique [12] on a logarithmically spaced grid [13,14] ranging from 0.0059 to 164.02 Å using the convergence criterion that the maximum residual of the direct correlation functions should decay below 10 -8 . Solute-solvent interactions were described by the sum of LJ (using standard Lorentz-Berthelot mixing rules) and Coulomb terms.…”

Section: Computational Detailsmentioning

confidence: 99%

“…The grid size was determined by adding 12.5 Å in each direction to the site position with the largest distance to the molecule's centroid during EC-RISM iterations, and adding 15 Å in the last step. The MDIIS method [12] was applied during iterations up to a convergence threshold of 10 -6 in the direct correlation functions. The temperature was set to 298.15 K. 3D integrals occurring in free energy evaluations were approximated by discrete sums over the grid.…”

Section: Computational Detailsmentioning

confidence: 99%

Prediction of tautomer ratios by embedded-cluster integral equation theory

Heil

Güssregen

Schmidt

2010

J Comput Aided Mol Des

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The "embedded cluster reference interaction site model" (EC-RISM) approach combines statistical-mechanical integral equation theory and quantum-chemical calculations for predicting thermodynamic data for chemical reactions in solution. The electronic structure of the solute is determined self-consistently with the structure of the solvent that is described by 3D RISM integral equation theory. The continuous solvent-site distribution is mapped onto a set of discrete background charges ("embedded cluster") that represent an additional contribution to the molecular Hamiltonian. The EC-RISM analysis of the SAMPL2 challenge set of tautomers proceeds in three stages. Firstly, the group of compounds for which quantitative experimental free energy data was provided was taken to determine appropriate levels of quantum-chemical theory for geometry optimization and free energy prediction. Secondly, the resulting workflow was applied to the full set, allowing for chemical interpretations of the results. Thirdly, disclosure of experimental data for parts of the compounds facilitated a detailed analysis of methodical issues and suggestions for future improvements of the model. Without specifically adjusting parameters, the EC-RISM model yields the smallest value of the root mean square error for the first set (0.6 kcal mol(-1)) as well as for the full set of quantitative reaction data (2.0 kcal mol(-1)) among the SAMPL2 participants.

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“…The water dielectric constants (input for DRISM calculations) at these thermodynamic conditions were taken from reference 44 and are compiled in Table S1. The DRISM-KH equations were solved iteratively using the MDIIS numerical solver 36,41 up to a relative root mean squared accuracy of 10 -10 in a radial grid containing 8192 points separated by 0.1 Å. were considered in the study of cellulose-cellulose effective interactions. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60…”

Section: Numerical Detailsmentioning

confidence: 99%

Cellulose Aggregation under Hydrothermal Pretreatment Conditions

et al. 2016

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Cellulose, the most abundant biopolymer on Earth, represents a resource for sustainable production of biofuels. Thermochemical treatments make lignocellulosic biomaterials more amenable to depolymerization by exposing cellulose microfibrils to enzymatic or chemical attacks. In such treatments, the solvent plays fundamental roles in biomass modification, but the molecular events underlying these changes are still poorly understood. Here, the 3D-RISM-KH molecular theory of solvation has been employed to analyze the role of water in cellulose aggregation under different thermodynamic conditions. The results show that, under ambient conditions, highly structured hydration shells around cellulose create repulsive forces that protect cellulose microfibrils from aggregating. Under hydrothermal pretreatment conditions, however, the hydration shells lose structure, and cellulose aggregation is favored. These effects are largely due to a decrease in cellulose-water interactions relative to those at ambient conditions, so that cellulose-cellulose attractive interactions become prevalent. Our results provide an explanation to the observed increase in the lateral size of cellulose crystallites when biomass is subject to pretreatments and deepen the current understanding of the mechanisms of biomass modification.

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Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace

Cited by 233 publications

References 18 publications

An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide

An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide

Prediction of tautomer ratios by embedded-cluster integral equation theory

Cellulose Aggregation under Hydrothermal Pretreatment Conditions

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