Literature DB >> 26032201

A solvation-free-energy functional: a reference-modified density functional formulation.

Tomonari Sumi1, Ayori Mitsutake2,3, Yutaka Maruyama2.   

Abstract

The three-dimensional reference interaction site model (3D-RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation-free-energy (SFE) for large solute molecules in water. To improve the free-energy density functional for the SFE of solute molecules, we propose a reference-modified density functional theory (RMDFT) that is a general theoretical approach to construct the free-energy density functional systematically. In the RMDFT formulation, hard-sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction-site-model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side-chain analogues as well as for 504 small organic molecules.
© 2015 Wiley Periodicals, Inc.

Entities:  

Keywords:  3D-RISM theory; amino acid side-chain; chignolin; classical density functional theory; salvation-free-energy; water

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Year:  2015        PMID: 26032201     DOI: 10.1002/jcc.23942

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  5 in total

1.  Theoretical analysis on thermodynamic stability of chignolin.

Authors:  Tomonari Sumi; Kenichiro Koga
Journal:  Sci Rep       Date:  2019-03-26       Impact factor: 4.379

2.  Mutation-induced change in chignolin stability from π-turn to α-turn.

Authors:  Yutaka Maruyama; Shunpei Koroku; Misaki Imai; Koh Takeuchi; Ayori Mitsutake
Journal:  RSC Adv       Date:  2020-06-15       Impact factor: 3.361

3.  Accuracy enhancement in the estimation of molecular hydration free energies by implementing the intramolecular hydrogen bond effects.

Authors:  Kee-Choo Chung; Hwangseo Park
Journal:  J Cheminform       Date:  2015-11-25       Impact factor: 5.514

4.  Tracing whale myoglobin evolution by resurrecting ancient proteins.

Authors:  Yasuhiro Isogai; Hiroshi Imamura; Setsu Nakae; Tomonari Sumi; Ken-Ichi Takahashi; Taro Nakagawa; Antonio Tsuneshige; Tsuyoshi Shirai
Journal:  Sci Rep       Date:  2018-11-15       Impact factor: 4.379

5.  Water-mediated interactions destabilize proteins.

Authors:  Tomonari Sumi; Hiroshi Imamura
Journal:  Protein Sci       Date:  2021-08-20       Impact factor: 6.725

  5 in total

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