3DRISM multigrid algorithm for fast solvation free energy calculations

Volodymyr P. Sergiievskyi, Maxim V. Fedorov

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter 2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarlcing of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good correlation between calculated and experimental results for solvation free energies of aqueous solutions of small organic compounds (correlation coefficient 0.97, root-mean-square deviation <1 kcal/mol).

LanguageEnglish
Pages2062-2070
Number of pages9
JournalJournal of Chemical Theory and Computation
Volume8
Issue number6
DOIs
Publication statusPublished - 12 Jun 2012

Fingerprint

Solvation
Free energy
solvation
free energy
organic compounds
Organic compounds
molecular theory
Molecules
Molecular modeling
personal computers
correlation coefficients
Personal computers
Hydration
Integral equations
hydration
integral equations
molecules
solutes
grids
aqueous solutions

Keywords

  • solvation
  • 3DRISM multigrid algorithm
  • free energy calculations

Cite this

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title = "3DRISM multigrid algorithm for fast solvation free energy calculations",
abstract = "In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter 2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarlcing of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good correlation between calculated and experimental results for solvation free energies of aqueous solutions of small organic compounds (correlation coefficient 0.97, root-mean-square deviation <1 kcal/mol).",
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3DRISM multigrid algorithm for fast solvation free energy calculations. / Sergiievskyi, Volodymyr P.; Fedorov, Maxim V.

In: Journal of Chemical Theory and Computation , Vol. 8, No. 6, 12.06.2012, p. 2062-2070.

Research output: Contribution to journalArticle

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