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Journal articles on the topic 'Reference interaction site model theory'

Author: Grafiati

Published: 4 June 2021

Last updated: 8 February 2022

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1

Laria, Daniel, David Wu, and David Chandler. "Reference interaction site model polaron theory of the hydrated electron." Journal of Chemical Physics 95, no. 6 (1991): 4444–53. http://dx.doi.org/10.1063/1.461767.

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2

Hsu, David, and D. Chandler. "Reference interaction site model polaron theory of electron mobility in fluids." Journal of Chemical Physics 93, no. 7 (1990): 5075–83. http://dx.doi.org/10.1063/1.458646.

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3

Munaò, G., D. Costa, and C. Caccamo. "Thermodynamically consistent reference interaction site model theory of the tangent diatomic fluid." Chemical Physics Letters 470, no. 4-6 (2009): 240–43. http://dx.doi.org/10.1016/j.cplett.2009.01.064.

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4

Yoshida, Norio, and Tsuyoshi Yamaguchi. "Development of a solvent-polarizable three-dimensional reference interaction-site model theory." Journal of Chemical Physics 152, no. 11 (2020): 114108. http://dx.doi.org/10.1063/5.0004173.

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5

Sergiievskyi, Volodymyr P., Wolfgang Hackbusch, and Maxim V. Fedorov. "Multigrid solver for the reference interaction site model of molecular liquids theory." Journal of Computational Chemistry 32, no. 9 (2011): 1982–92. http://dx.doi.org/10.1002/jcc.21783.

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6

Mitsutake, Kinoshita, Hirata, and Okamoto. "Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory." Condensed Matter Physics 10, no. 4 (2007): 495. http://dx.doi.org/10.5488/cmp.10.4.495.

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7

Munaò, G., D. Costa, F. Saija, and C. Caccamo. "Simulation and reference interaction site model theory of methanol and carbon tetrachloride mixtures." Journal of Chemical Physics 132, no. 8 (2010): 084506. http://dx.doi.org/10.1063/1.3314296.

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8

Nishiyama, Katsura, Fumio Hirata, and Tadashi Okada. "Solute-structure dependence of solvation dynamics studied by reference interaction-site model theory." Journal of Chemical Physics 118, no. 5 (2003): 2279–85. http://dx.doi.org/10.1063/1.1532345.

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9

Kinoshita, Masahiro, Yuko Okamoto, and Fumio Hirata. "Peptide Conformations in Alcohol and Water: Analyses by the Reference Interaction Site Model Theory." Journal of the American Chemical Society 122, no. 12 (2000): 2773–79. http://dx.doi.org/10.1021/ja993939x.

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10

Freedman, Holly, and Thanh N. Truong. "Coupled reference interaction site model/simulation approach for thermochemistry of solvation: Theory and prospects." Journal of Chemical Physics 121, no. 5 (2004): 2187–98. http://dx.doi.org/10.1063/1.1760741.

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11

Ishizuka, R., S. H. Chong, and F. Hirata. "An integral equation theory for inhomogeneous molecular fluids: The reference interaction site model approach." Journal of Chemical Physics 128, no. 3 (2008): 034504. http://dx.doi.org/10.1063/1.2819487.

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12

Kežić, Bernarda, and Aurélien Perera. "Towards a more accurate reference interaction site model integral equation theory for molecular liquids." Journal of Chemical Physics 135, no. 23 (2011): 234104. http://dx.doi.org/10.1063/1.3666006.

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13

Nishiyama, K., T. Yamaguchi, Fumio Hirata, and T. Okada. "Polar solvation dynamics: A combination of the reference interaction-site model and mode-coupling theories." Pure and Applied Chemistry 76, no. 1 (2004): 71–77. http://dx.doi.org/10.1351/pac200476010071.

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We employ the reference interaction-site model (RISM) theory for solvation dynamics of simple ions in acetonitrile. For the description of time evolution of solvent relaxation, we apply the mode-coupling theory recently developed by Yamaguchi and coworkers [Mol. Phys.101, 1211 (2003)]. The combination of the RISM/mode-coupling theory is used for the calculation of the dynamic response function, SS(t), which measures the relaxation of average energy of the solute-solvent system. SS(t) decays with the Gaussian plus underdamped curves in the time duration of first 1 ps, followed by slow, long-tai

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14

Kinoshita, Masahiro, Yuko Okamoto, and Fumio Hirata. "Singular behavior of the reference interaction site model theory observed for peptide in salt solution." Chemical Physics Letters 297, no. 5-6 (1998): 433–38. http://dx.doi.org/10.1016/s0009-2614(98)01150-6.

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15

Xu, Qinzhi, Jianguo Mi, and Chongli Zhong. "Structure of poly(ethylene glycol)–water mixture studied by polymer reference interaction site model theory." Journal of Chemical Physics 133, no. 17 (2010): 174104. http://dx.doi.org/10.1063/1.3502108.

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16

Cui †, Qizhi, and Vedene H. Smith. "Analysis of K+/Na+selectivity of KcsA potassium channel with reference interaction site model theory." Molecular Physics 103, no. 2-3 (2005): 191–201. http://dx.doi.org/10.1080/00268970512331316201.

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17

Sato, Kazuto, Hiroshi Chuman, and Seiichiro Ten-no. "Comparative Study on Solvation Free Energy Expressions in Reference Interaction Site Model Integral Equation Theory." Journal of Physical Chemistry B 109, no. 36 (2005): 17290–95. http://dx.doi.org/10.1021/jp053259i.

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18

Imai, Takashi, Andriy Kovalenko, and Fumio Hirata. "Partial Molar Volume of Proteins Studied by the Three-Dimensional Reference Interaction Site Model Theory†." Journal of Physical Chemistry B 109, no. 14 (2005): 6658–65. http://dx.doi.org/10.1021/jp045667c.

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19

Schweizer, Kenneth S., and Arun Yethiraj. "Polymer reference interaction site model theory: New molecular closures for phase separating fluids and alloys." Journal of Chemical Physics 98, no. 11 (1993): 9053–79. http://dx.doi.org/10.1063/1.464465.

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20

Iida, Kenji, and Hirofumi Sato. "A two-dimensional-reference interaction site model theory for solvation structure near solid-liquid interface." Journal of Chemical Physics 135, no. 24 (2011): 244702. http://dx.doi.org/10.1063/1.3668468.

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21

Freischmidt, Helen M., Robert A. Shanks, Graeme Moad, and Alfred Uhlherr. "Characterization of polyolefin melts using the polymer reference interaction site model integral equation theory with a single-site united atom model." Journal of Polymer Science Part B: Polymer Physics 39, no. 16 (2001): 1803–14. http://dx.doi.org/10.1002/polb.1155.

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22

Yokogawa, Daisuke, Hirofumi Sato, Sergey Gusarov, and Andriy Kovalenko. "Development of additive isotropic site potential for exchange-repulsion energy, based on intermolecular perturbation theory." Canadian Journal of Chemistry 87, no. 12 (2009): 1727–32. http://dx.doi.org/10.1139/v09-131.

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We have developed an additive spherical site potential for exchange-repulsion energy by applying the local density approximation in Hilbert space, the local-site approximation, and the s-type auxiliary basis set to the equation derived from intermolecular perturbation theory. The method efficiently addresses the decomposition of molecular interactions derived from quantum chemistry into additive spherical site potentials, required as force field input in a statistical-mechanical, reference interaction site model (RISM and 3D-RISM), molecular theory of solvation. The present method reproduces t

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23

Tanimoto, Shoichi, Norio Yoshida, Tsuyoshi Yamaguchi, Seiichiro L. Ten-no, and Haruyuki Nakano. "Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory." Journal of Chemical Information and Modeling 59, no. 9 (2019): 3770–81. http://dx.doi.org/10.1021/acs.jcim.9b00330.

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24

Kinoshita, Masahiro, and Fumio Hirata. "Application of the reference interaction site model theory to analysis on surface‐induced structure of water." Journal of Chemical Physics 104, no. 21 (1996): 8807–15. http://dx.doi.org/10.1063/1.471570.

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25

Cui, Qizhi, and Vedene H. Smith. "K+/Na+ selectivity of KcsA potassium channel analyzed by reference interaction site model (RISM) integral equation theory." Chemical Physics Letters 365, no. 1-2 (2002): 110–16. http://dx.doi.org/10.1016/s0009-2614(02)01426-4.

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26

Kinoshita, Masahiro, Yuko Okamoto, and Fumio Hirata. "Solvation structure and stability of peptides in aqueous solutions analyzed by the reference interaction site model theory." Journal of Chemical Physics 107, no. 5 (1997): 1586–99. http://dx.doi.org/10.1063/1.474511.

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27

Roy, Dipankar, and Andriy Kovalenko. "Application of the Approximate 3D-Reference Interaction Site Model (RISM) Molecular Solvation Theory to Acetonitrile as Solvent." Journal of Physical Chemistry B 124, no. 22 (2020): 4590–97. http://dx.doi.org/10.1021/acs.jpcb.0c03230.

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28

Roy, Dipankar, and Andriy Kovalenko. "Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory." International Journal of Molecular Sciences 22, no. 10 (2021): 5061. http://dx.doi.org/10.3390/ijms22105061.

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The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand bin

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29

Yokogawa, D. "Coupled Cluster Theory Combined with Reference Interaction Site Model Self-Consistent Field Explicitly Including Spatial Electron Density Distribution." Journal of Chemical Theory and Computation 14, no. 5 (2018): 2661–66. http://dx.doi.org/10.1021/acs.jctc.8b00168.

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30

Akiyama, Ryo, Masahiro Kinoshita, and Fumio Hirata. "Free energy profiles of electron transfer at water–electrode interface studied by the reference interaction site model theory." Chemical Physics Letters 305, no. 3-4 (1999): 251–57. http://dx.doi.org/10.1016/s0009-2614(99)00372-3.

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31

Kinoshita, Masahiro, and Fumio Hirata. "Analysis of salt effects on solubility of noble gases in water using the reference interaction site model theory." Journal of Chemical Physics 106, no. 12 (1997): 5202–15. http://dx.doi.org/10.1063/1.473519.

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32

Kiyota, Yasuomi, and Mayuko Takeda-Shitaka. "Molecular Recognition Study on the Binding of Calcium to Calbindin D9kBased on 3D Reference Interaction Site Model Theory." Journal of Physical Chemistry B 118, no. 39 (2014): 11496–503. http://dx.doi.org/10.1021/jp504822r.

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33

Cui, Qizhi, and Vedene H. Smith. "Analysis of solvation structure and thermodynamics of methane in water by reference interaction site model theory using an all-atom model." Journal of Chemical Physics 113, no. 22 (2000): 10240–45. http://dx.doi.org/10.1063/1.1313788.

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34

Maruyama, Yutaka. "Correction terms for the solvation free energy functional of three-dimensional reference interaction site model based on the reference-modified density functional theory." Journal of Molecular Liquids 291 (October 2019): 111160. http://dx.doi.org/10.1016/j.molliq.2019.111160.

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35

Schweizer, Kenneth S., and John G. Curro. "Analytic reference interaction site model‐mean spherical approximation theory of flexible polymer blends: Effects of spatial and fractal dimensions." Journal of Chemical Physics 94, no. 5 (1991): 3986–4000. http://dx.doi.org/10.1063/1.460704.

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36

Kinoshita, Masahiro, Takashi Imai, Andriy Kovalenko, and Fumio Hirata. "Improvement of the reference interaction site model theory for calculating the partial molar volume of amino acids and polypeptides." Chemical Physics Letters 348, no. 3-4 (2001): 337–42. http://dx.doi.org/10.1016/s0009-2614(01)01129-0.

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37

Imai, Takashi, Ryusuke Hiraoka, Andriy Kovalenko, and Fumio Hirata. "Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation." Proteins: Structure, Function, and Bioinformatics 66, no. 4 (2006): 804–13. http://dx.doi.org/10.1002/prot.21311.

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38

Yoshida, Norio, and Tsuyoshi Yamaguchi. "Erratum: “Development of a solvent-polarizable three-dimensional reference interaction-site model theory” [J. Chem. Phys. 152, 114108 (2020)]." Journal of Chemical Physics 152, no. 18 (2020): 189904. http://dx.doi.org/10.1063/5.0010622.

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39

Munaò, G., D. Costa, and C. Caccamo. "Reference interaction site model investigation of homonuclear hard dumbbells under simple fluid theory closures: Comparison with Monte Carlo simulations." Journal of Chemical Physics 130, no. 14 (2009): 144504. http://dx.doi.org/10.1063/1.3098551.

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40

Schweizer, Kenneth S., Kevin G. Honnell, and John G. Curro. "Reference interaction site model theory of polymeric liquids: Self‐consistent formulation and nonideality effects in dense solutions and melts." Journal of Chemical Physics 96, no. 4 (1992): 3211–25. http://dx.doi.org/10.1063/1.461965.

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41

Cui, Qizhi, and Vedene H. Smith. "Solvation structure, thermodynamics, and conformational dependence of alanine dipeptide in aqueous solution analyzed with reference interaction site model theory." Journal of Chemical Physics 118, no. 1 (2003): 279–90. http://dx.doi.org/10.1063/1.1524617.

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42

Cui, Qizhi, and Vedene H. Smith. "Analysis of solvation structure and thermodynamics of ethane and propane in water by reference interaction site model theory using all-atom models." Journal of Chemical Physics 115, no. 5 (2001): 2228–36. http://dx.doi.org/10.1063/1.1384421.

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43

Minezawa, Noriyuki. "Excited-state free energy surfaces in solution: Time-dependent density functional theory/reference interaction site model self-consistent field method." Journal of Chemical Physics 138, no. 24 (2013): 244101. http://dx.doi.org/10.1063/1.4811201.

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44

Phongphanphanee, Saree, Norio Yoshida, Shigetoshi Oiki, and Fumio Hirata. "Probing “ambivalent” snug-fit sites in the KcsA potassium channel using three-dimensional reference interaction site model (3D-RISM) theory." Pure and Applied Chemistry 86, no. 2 (2014): 97–104. http://dx.doi.org/10.1515/pac-2014-5018.

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Abstract The potassium channel is highly selective for K+ over Na+, and the mechanism underlying this selectivity remains unclear. We show the three-dimensional distribution functions (3D-DFs) of small cations (Li+, Na+, and K+) and the free energy profile of ions inside the open selectivity filter (SF) of the KcsA channel. Our previous results [S. Phongphanphanee, N. Yoshida, S. Oiki, F. Hirata. Abstract Book of 5th International Symposium on Molecular Science of Fluctuations toward Biological Functions, P062 (2012)] indicate that the 3D-DF for K+ exhibits distinct peaks at the sites formed b

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45

Cui, Qizhi, and Vedene H. Smith. "Solvation Structure, Thermodynamics, and Molecular Conformational Equilibria forn-Butane in Water Analyzed by Reference Interaction Site Model Theory Using an All-Atom Solute Model." Journal of Physical Chemistry B 106, no. 25 (2002): 6554–65. http://dx.doi.org/10.1021/jp020191n.

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46

Munaò, Gianmarco, Dino Costa, and Carlo Caccamo. "Development of molecular closures for the reference interaction site model theory with application to square-well and Lennard-Jones homonuclear diatomics." Journal of Physics: Condensed Matter 28, no. 41 (2016): 414007. http://dx.doi.org/10.1088/0953-8984/28/41/414007.

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47

Omelyan, Igor, Andriy Kovalenko, and Fumio Hirata. "Compressibility oftert-Butyl Alcohol-Water Mixtures: The Rism Theory." Journal of Theoretical and Computational Chemistry 02, no. 02 (2003): 193–203. http://dx.doi.org/10.1142/s0219633603000501.

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The isothermal compressibility χTof binary mixtures of water and tert-butyl alcohol (TBA) is calculated using the reference interaction site model (RISM) integral equation theory. The calculations are performed over the whole concentration from x = 0 to 1 and a wide temperature from T = 283 to 313 K ranges employing the extended point charge model for water and optimized site–site potentials for TBA molecules. The results obtained are compared versus available experimental data. It is demonstrated that, despite an approximate character of the model potentials and closure relation applied, the

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48

Yamaguchi, Tsuyoshi, and Norio Yoshida. "Solvation dynamics in electronically polarizable solvents: Theoretical treatment using solvent-polarizable three-dimensional reference interaction-site model theory combined with time-dependent density functional theory." Journal of Chemical Physics 154, no. 4 (2021): 044504. http://dx.doi.org/10.1063/5.0036289.

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49

Roy, Dipankar, Devjyoti Dutta, and Andriy Kovalenko. "Predicting 1,9-Decadiene−Water Partition Coefficients Using the 3D-RISM-KH Molecular Solvation Theory." Physchem 1, no. 2 (2021): 215–24. http://dx.doi.org/10.3390/physchem1020015.

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The Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko−Hirata (KH) closure is applied to calculate the 1,9-Decadiene/Water partition coefficients for a diverse class of compounds. The liquid state of 1,9-Decadiene is represented with the united atom TraPPE force field parameters. The 3D-RISM-KH computed partition functions are in good agreement with the experimental results. Our computational scheme can be used for a quantitative structure partitioning prediction for decadiene-water system, which has been used in membrane-mimicking of the egg-lecithin/water permeabilit

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50

Yokogawa, Daisuke, Hirofumi Sato, and Shigeyoshi Sakaki. "New generation of the reference interaction site model self-consistent field method: Introduction of spatial electron density distribution to the solvation theory." Journal of Chemical Physics 126, no. 24 (2007): 244504. http://dx.doi.org/10.1063/1.2742380.

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