A QM/MM study on the correlation between the polarisations of and electrons in a hydrated benzene

References

• Tamres M, Searles S, Leighly EM, et al. Hydrogen bond formation with pyridines and aliphatic amines. J Am Chem Soc. 1954;76:3983–3985.
   Web of Science ®Google Scholar
• Nishio M, Hirota M, Umezawa Y. The CH/π interaction. New York (NY): Willey-VCH; 1998.
   Google Scholar
• Tsuzuki S, Honda K, Uchimaru T, et al. Origin of attraction and directionality of the π/π interaction: model chemistry calculations of benzene dimer interaction. J Am Chem Soc. 2002;124:104–112.
   PubMed Web of Science ®Google Scholar
• Desiraju GR, Steiner T. The weak hydrogen bond. New York (NY): Oxford University Press; 1999.
   Google Scholar
• Chakrabarti P, Bhattacharyya R. Geometry of nonbonded interactions involving planar groups in proteins. Prog Biophys Mol Biol. 2007;95:83–137.
   PubMed Web of Science ®Google Scholar
• Levitt M, Perutz MF. Aromatic rings act as hydrogen bond acceptors. J Mol Biol. 1988;201:751–754.
   PubMed Web of Science ®Google Scholar
• Meyer EA, Castellano RK, Diederich F. Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed. 2003;42:1210–1250.
   PubMed Web of Science ®Google Scholar
• Sun H, Tottempudi UK, Mottishaw JD, et al. Strengthening π-π interactions while suppressing Csp2-H…π (T-shaped) interactions via perfluoroalkylation: a crystallographic and computational study that supports the beneficial formation of 1-D π-π stacked aromatic materials. Cryst Growth Des. 2012;12:5655–5662.
   Web of Science ®Google Scholar
• Fujii A, Shibasaki K, Kazama T, et al. Experimental and theoretical determination of the accurate interaction energies in benzene-halomethane: the unique nature of the activated CH/π interaction of haloalkynes. Phys Chem Chem Phys. 2008;10:2836–2843.
   PubMed Web of Science ®Google Scholar
• Steiner T, Schreurs AMM, Kanters JA, et al. Water molecules hydrogen binding to aromatic acceptors of amino acids: the structure of Tyr-Tyr-Phe dihydrate and a crystallographic database study on peptides. Acta Cryst D. 1998;54:25–31.
   PubMedGoogle Scholar
• Tóth G, Watts CR, Murphy RF, et al. Significance of aromatic-backbone amide interactions in protein structure. Proteins Struct Funct Genet. 2001;43:373–381.
   PubMed Web of Science ®Google Scholar
• Hudson KL, Bartlett GJ, Diehl RC, et al. Carbohydrate-aromatic interactions in proteins. J Am Chem Soc. 2015;137:15152–15160.
   PubMed Web of Science ®Google Scholar
• Makhatadze GI, Privalov PL. Energetics of interactions of aromatic hydrocarbons with water. Biophys Chem. 1994;50:285–291.
   PubMed Web of Science ®Google Scholar
• Gallicchio E, Zhang LY, Levy RM. The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem. 2002;23:517–529.
   PubMed Web of Science ®Google Scholar
• Takahashi H, Suzuoka D, Morita A. Why is benzene soluble in water? Role of OH/π interaction in solvation. J Chem Theory Comput. 2015;11:1181–1194.
   PubMed Web of Science ®Google Scholar
• Takahashi H, Matubayasi N, Nakahara M, et al. A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation. J Chem Phys. 2004;121:3989–3999.
   PubMed Web of Science ®Google Scholar
• Takahashi H, Omi A, Morita A, et al. Simple and exact approach to the electronic polarization effect on the solvation free energy: formulation for quantum-mechanical/ molecular-mechanical system and its applications to aqueous solutions. J Chem Phys. 2012;136:214503.
   PubMed Web of Science ®Google Scholar
• Warshel A, Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol. 1976;103:227–249.
   PubMed Web of Science ®Google Scholar
• Warshel A. Computer modeling of chemical reactions in enzymes and solutions. New York (NY): Willey; 1991.
   Google Scholar
• Gao J, Xia X. A priori evalution of aqueous polarization effects through Monte Carlo QM-MM simulations. Science. 1992;258:631–635.
   PubMed Web of Science ®Google Scholar
• Matubayasi N, Nakahara M. Theory of solutions in the energetic representation. I. Formulation. J Chem Phys. 2000;113:6070–6081.
   Web of Science ®Google Scholar
• Suzuoka D, Takahashi H, Morita A. Computation of the free energy due to electron density fluctuation of a solute in solution: a QM/MM method with perturbation approach combined with a theory of solutions. J Chem Phys. 2014;140:134111.
   PubMed Web of Science ®Google Scholar
• Tomasi J, Mennucci B, Cammi R. Quantum mechanical continuum solvation models. Chem Rev. 2005;105:2999–3093.
   PubMed Web of Science ®Google Scholar
• Matubayasi N, Nakahara M. Theory of solutions in the energy representation. II. Functional for the chemical potential. J Chem Phys. 2002;117:3605–3616.
   Web of Science ®Google Scholar
• Sakuraba S, Matubayasi N. Distribution-function approach to free energy computation. J Chem Phys. 2011;135:114108
   PubMed Web of Science ®Google Scholar
• Hansen P, McDonald IR. Theory of simple liquids. 3rd ed. London: Academic; 2006.
   Google Scholar
• Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian 09 revision c01. Wallingford (CT): Gaussian; 2010.
   Google Scholar
• Becke AD. Densityfunctional thermochemistry. III. The role of exact exchange. J Chem Phys. 1993;98:5648–5652.
   Web of Science ®Google Scholar
• Dunning TH. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J Chem Phys. 1989;90:1007–1023.
   Web of Science ®Google Scholar
• Hohenberg P, Kohn W. Inhomogeneous electron gas. Phys Rev. 1989;136:B864–B871.
   Web of Science ®Google Scholar
• Kohn W, Sham LJ. Self-consistent equations including exchange and correlation effects. Phys Rev. 1965;140:A1133–A1138.
   Web of Science ®Google Scholar
• Chelikowsky JR, Troullier N, Saad Y. Finite-difference-pseudopotential method: electronic structure calculations without a basis. Phys Rev Lett. 1994;72:1240–1243.
   PubMed Web of Science ®Google Scholar
• Chelikowsky JR, Troullier N, Wu K, et al. Higher-order finite-difference pseudopotential method: an application to diatomic molecules. Phys Rev B. 1994;50:11355–11364.
   Web of Science ®Google Scholar
• Takahashi H, Hori T, Wakabayashi T, et al. A density functional study for hydrogen bond energy by employing real space grids. Chem Lett. 2000;29:222–223.
   Google Scholar
• Takahashi H, Hori T, Wakabayashi T, et al. Real space ab initio molecular dynamics simulations for the reactions of OH radical/OH anion with formaldehyde. J Phys Chem A. 2001;105:4351–4358.
   Web of Science ®Google Scholar
• Takahashi H, Hori T, Hashimoto H, et al. A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents. J Comput Chem. 2001;22:1252–1261.
   Web of Science ®Google Scholar
• Kleinman L, Bylander DM. Efficacious form for model pseudopotentials. Phys Rev Lett. 1982;48:1425–1428.
   Web of Science ®Google Scholar
• Ono T, Hirose K. Timesaving double-grid method for real-space electronic-structure calculations. Phys Rev Lett. 1999;82:5016–5019.
   Web of Science ®Google Scholar
• Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A. 1988;38:3098–3100.
   PubMed Web of Science ®Google Scholar
• Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B. 1988;37:785–789.
   PubMed Web of Science ®Google Scholar
• Allen MP, Tildesley DJ. Computer simulation of liquids. Oxford: Oxford University Press; 1987.
   Google Scholar
• Frankel D, Smit B. Understanding molecular simulation. London: Academc; 1996.
   Google Scholar
• Berendsen HJC, Grigera JR, Straatsma TP. The missing term in effective pair potentials. J Phys Chem. 1987;91:6269–6271.
   Web of Science ®Google Scholar
• Scott WRP, Hünenberger PH, Tironi IG, et al. The GROMOS biomolecular simulation program package. J Phys Chem A. 1999;103:3596–3607.
   Web of Science ®Google Scholar
• Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996;118:11225–11236.
   Web of Science ®Google Scholar
• Champagne B, Perpete EA, van Gisbergen SJ, et al. Assessment of conventional density functional schemes for computing the polarizabilities and hyperpolarizabilities of conjugated oligomers: an ab initio investigation of polyacetylene chains. J Chem Phys. 1998;109:10489–10498.
   Web of Science ®Google Scholar
• König G, Mei Y, Pickard FC, et al. Computation of hydration free energies using the multiple environment single system quantum mechanical/molecular mechanical method. J Chem Theory Comput. 2016;12:332–344.
   PubMed Web of Science ®Google Scholar