[1] F. Hirata, Molecular Theory of Solvation, vol. 24, Springer Science & Business Media, 2003. [2] B. Mennucci, R. Cammi, Continuum Solvation Models in Chemical Physics: From Theory to Applications, John Wiley & Sons, 2008. [3] J. Tomasi, B. Mennucci, R. Cammi, Quantum mechanical continuum solvation models, Chem. Rev. 105 (8) (2005) 2999-3093. [4] P. Muller, Glossary of terms used in physical organic chemistry (IUPAC Recommendations 1994), Pure Appl. Chem. 66 (5) (1994) 1077. [5] P. Cieplak, P. Bash, U. Chandra Singh, P.A. Kollman, A theoretical study of tautomerism in the gas phase and aqueous solution: A combined use of “stateof-the-art” ab initio quantum mechanics and free energy perturbation methods, J. Am. Chem. Soc. 109 (21) (1987) 6283-6289. [6] C. Biot, R. Wintjens, M. Rooman, Stair motifs at protein — DNA interfaces: Nonadditivity of H-bond, stacking, and cation — π interactions, J. Am. Chem. Soc. 126 (20) (2004) 6220-6221. [7] J. Zhao, R. Zhang, Proton transfer reaction rate constants between hydronium ion (H3O+) and volatile organic compounds, Atmos. Environ. 38 (14) (2004) 2177-2185. [8] J.M. Berg, J.L. Tymoczko, L. Stryer, L. Stryer, Biochemistry; 5th ed, W.H. Freeman, New York, 2002. [9] R. Car, M. Parrinello, Unified approach for molecular dynamics and density-functional theory, Phys. Rev. Lett. 55 (22) (1985) 2471. [10] T. Vreven, M.J. Frisch, K.N. Kudin, H.B. Schlegel, K. Morokuma, Geometry optimization with QM/MM methods II: explicit quadratic coupling, Mol. Phys. 104 (5-7) (2006) 701-714. [11] M. Orozco, F.J. Luque, Theoretical methods for the description of the solvent effect in biomolecular systems, Chem. Rev. 100 (11) (2000) 4187-4226. [12] J. Muñoz, X. Barril, F.J. Luque, J.L. Gelpí, M. Orozco, Partitioning of free energies of solvation into fragment contributions: applications in drug design, in: R. Carbó-Dorca, X. Gironés, P.G. Mezey (Eds.), Fundamentals of Molecular Similarity, Springer US, Boston, MA, 143-168(2001). [13] T. Vreven, K. Morokuma, On the application of the IMOMO (integrated molecular orbital + molecular orbital) method, J. Comput. Chem. 21 (16) (2000) 1419-1432. [14] T. Vreven, K.S. Byun, I. Komáromi, S. Dapprich, J.A. Montgomery, K. Morokuma, M.J. Frisch, Combining quantum mechanics methods with molecular mechanics methods in ONIOM, J. Chem. Theory Comput. 2 (3) (2006) 815-826. [15] K.V. Mikkelsen, P. Jo/Rgensen, H.J.R.A. Jensen, A multiconfiguration selfconsistent reaction field response method, J. Chem. Phys. 100 (9) (1994) 6597-6607. [16] F. Hirata, H. Sato, S. Ten-No, S. Kato, The RISM-SCF/MCSCF approach for chemical processes in solutions, in: Eastern Hemisphere Distrib, CRC Press, Boca Raton, 2001. [17] G.M. Ullmann, Charge transfer properties of photosynthetic and respiratory proteins, in: H.S. Nalwa (Ed.), Supramolecular Photosensitive and Electroactive Materials, Academic Press, San Diego, 525-584(2001). [18] W. Tang, C. Cai, S. Zhao, H. Liu, Development of reaction density functional theory and its application to glycine tautomerization reaction in aqueous solution, J. Phys. Chem. C 122 (36) (2018) 20745-20754. [19] C. Cai, W. Tang, C. Qiao, P. Jiang, C. Lu, S. Zhao, H. Liu, Reaction density functional theory study of solvent effect in prototype SN2 reactions in aqueous solution, Phys. Chem. Chem. Phys. 21 (45) (2019) 24876-24883. [20] L. Qing, Y. Li, W. Tang, D. Zhang, Y. Han, S. Zhao, Dynamic adsorption of ions into like-charged nanospace: A dynamic density functional theory study, Langmuir 35 (12) (2019) 4254-4262. [21] W. Tang, H. Yu, C. Cai, T. Zhao, C. Lu, S. Zhao, X. Lu, Solvent effects on a derivative of 1, 3, 4-oxadiazole tautomerization reaction in water: A reaction density functional theory study, Chem. Eng. Sci. 213 (2020) 115380. [22] I.D. Reva, S.G. Stepanian, L. Adamowicz, R. Fausto, Combined FTIR matrix isolation and ab initio studies of pyruvic acid: Proof for existence of the second conformer, J. Phys. Chem. A 105 (19) (2001) 4773-4780. [23] Y. Valadbeigi, H. Farrokhpour, Theoretical study on keto-enol tautomerism and isomerization in pyruvic acid, Int. J. Quantum Chem. 113 (21) (2013) 2372-2378. [24] Y. Liu, S. Zhao, J. Wu, A site density functional theory for water: application to solvation of amino acid side chains, J. Chem. Theory Comput. 9 (4) (2013) 1896-1908. [25] S. Zhao, Z. Jin, J. Wu, New theoretical method for rapid prediction of solvation free energy in water, J. Phys. Chem. B 115 (21) (2011) 6971-6975. [26] W.L. Jorgensen, D.S.M. And, J. Tiradorives, Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc. 118 (45) (1996) 11225-11236. [27] W.L. Jorgensen, P. Schyman, Treatment of halogen bonding in the OPLS-AA force field: application to potent anti-HIV agents, J. Chem. Theory Comput. 8 (10) (2012) 3895-3901. [28] R. Evans, The nature of the liquid-vapour interface and other topics in the statistical mechanics of non-uniform, classical fluids, Adv. Phys. 28 (2) (1979) 143-200. [29] S. Zhao, R. Ramirez, R. Vuilleumier, D. Borgis, Molecular density functional theory of solvation: From polar solvents to water, J. Chem. Phys. 134 (19) (2011) 194102. [30] R.H. Byrd, P. Lu, J. Nocedal, C. Zhu, A limited memory algorithm for bound constrained optimization, SIAM J. Sci. Comput. 16 (5) (1995) 1190-1208. [31] M. Frigo, S.G. Johnson, The design and implementation of FFTW3, Proc. IEEE 93 (2) (2005) 216-231. [32] H.B. Schlegel, Optimization of equilibrium geometries and transition structures, J. Comput. Chem. 3 (2) (1982) 214-218. [33] K. Fukui, The path of chemical reactions -the IRC approach, Acc. Chem. Res. 14 (12) (1981) 471-476. [34] S. Miertus, J. Tomasi, Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes, Chem. Phys. 65 (2) (1982) 239-245. [35] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, Gaussian 09 Revision A.1, in: Gaussian Inc, 2009. [36] S. Zhao, J. Wu, An efficient method for accurate evaluation of the site-site direct correlation functions of molecular fluids, Mol. Phys. 109 (21) (2011) 2553-2564. [37] S. Zhao, H. Liu, R. Ramirez, D. Borgis, Accurate evaluation of the angulardependent direct correlation function of water, J. Chem. Phys. 139 (3) (2013) 034503. [38] Y.X. Yu, J. Wu, Structures of hard-sphere fluids from a modified fundamentalmeasure theory, J. Chem. Phys. 117 (22) (2002) 10156-10164. [39] R. Roth, R. Evans, A. Lang, G. Kahl, Fundamental measure theory for hardsphere mixtures revisited: The White Bear version, J. Phys. Condens. Matter 14 (46) (2002) 12063-12078. [40] B. Chahkandi, S.F. Tayyari, M. Bakhshaei, M. Chahkandi, Investigation of simple and water assisted tautomerism in a derivative of 1,3,4-oxadiazole: A DFT study, J. Mol. Graph. Model. 44 (2013) 120-128. [41] P. Chen, C. Wang, J. Jiang, H. Wang, M. Hayashi, Barrierless proton transfer within short protonated peptides in the presence of water bridges. A density functional theory study, J. Phys. Chem. B 115 (6) (2011) 1485-1490. [42] Y. Ren, M. Li, N. Wong, Prototropic tautomerism of imidazolone in aqueous solution: A density functional approach using the combined discrete/self-consistent reaction field (SCRF) models, J. Mol. Model. 11 (2) (2005) 167-173. |