References
- Ben-Naim A. Solvation thermodynamics. New York (NY): Springer; 1987.
- Lesk AM. Introduction to protein science; architecture, function, and genotics. London: Oxford University Press; 2004.
- Frenkel D, Smit B. Understanding molecular simulation: from algorithms to applications. SanDiego: Academic Press; 2001.
- Allen MP, Tildesley DJ. Computer simulation of liquids. New York (NY): Oxford University Press; 1989.
- Binder K, Heermann D. Monte Carlo simulation in statistical physics: an introduction. New York (NY): Springer; 2010.
- Hansmann UHE, Okamoto Y. The generalized-ensemble approach for protein folding simulations. Annu Rev Comput Phys. 1999;6:129–157.
- McQuarrie DA. Statistical mechanics. New York (NY): Harper Collins Publishers; 1976.
- Hansen JP, McDonald IR. Theory of simple liquids. London: Academic Press; 1976.
- Gray CG, Gubbins KE. Theory of molecular fluids: fundamentals. New York (NY): Oxford University Press; 1985.
- Hirata F, editor. Molecular theory of solvation. Dordrecht: Kluwer Academic Publishers; 2003.
- Chandler D, Andersen HC. Optimized cluster expansions for classical fluids. II. Theory of molecular liquids. J. Chem. Phys. 1972;57:1930–1936.
- Beglov D, Roux B. An integral equation to describe the solvation of polar molecules in liquid water. J Phys Chem B. 1997;101:7821–7826.
- Kovalenko A, Hirata F. Three-dimensionl density profiles of water in contact with a solute of arbitrary shape: a RISM approach. Chem Phys Lett. 1998;290:237–244.
- Du Q, Beglov D, Roux B. Solvation free energy of polar and nonpolar molecules in water: an extended interaction site integral equation theory in three dimensions. J Phys Chem B. 2000;104:796–805.
- Miyata T, Hirata F. Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution. J Comput Chem. 2008;29:871–882.
- Luchko T, Gusarov S, Roe DR, et al. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. J Chem Theory Comput. 2010;6:607–624.
- Imai T, Kovalenko A, Hirata F. Solvation thermodynamics of protein studied by the 3D-RISM theory. Chem Phys Lett. 2004;395:1–6.
- Imai T, Hiraoka R, Kovalenko A, et al. Water molecules in a protein cavity detected by a statistical-mechanical theory. J Am Chem Soc. 2005;127:15334–15335.
- Yoshida N, Phongphanphanee S, Maruyama Y, et al. Selective ion-binding by protein probed with the 3D-RISM theory. J Am Chem Soc. 2006;128:12042–12043.
- Imai T, Hiraoka R, Kovalenko A, et al. Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. PROTEINS. 2007;66:804–813.
- Imai T, Oda K, Kovalenko A, et al. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design. J Am Chem Soc. 2009;131:12430–12440.
- Kiyota Y, Yoshida N, Hirata F. A new approach for investigating the molecular recognition of protein: toward structure-based drug design based on the 3D-RISM theory. J Chem Theory Comput. 2011;7: 3803–3815.
- Sindhikara DJ, Yoshida N, Hirata F. Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase. J Comput Chem. 2012;33:1536–1543.
- Hermans J. The amino acid dipeptide: small but still influential after 50 years. Proc Natl Acad Sci USA. 2011;108:3095–3096.
- Pettitt BM, Karplus M. The potential of mean force surfce for the alanine dipeptide in aqueous solution: a theoretical approach. Chem Phys Lett. 1985;121:194–201.
- Pettitt BM, Karplus M. Conformational free energy of hydration for the alanine dipeptide: thermodynamic analysis. J Phys Chem. 1988;92:3994–3997.
- Takekiyo T, Imai T, Kato M, et al. Temperature and pressure effects on conformational equilibria of alanine dipeptide in aqueous solution. Biopolymers. 2004;73:283–290.
- Tobias DJ, Brooks CL III. Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results. J Phys Chem. 1992;96:3864–3870.
- Chipot C, Pohorille A. Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study, J Phys Chem B. 1998;102:281–290.
- Apostolakis J, Ferrara P, Carfish A. Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water. J Chem Phys. 1999;110:2099–2108.
- Liu P, Kim B, Friesner RA, et al. Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc Natl Acad Sci USA. 2005;102:13749–13754.
- Cruz V, Ramos J, Martinez-Salazar J. Water-mediated conformation of the alanine dipeptide as revealed by distributed Umbrella Sampling. J Phys Chem B. 2011;115:4880–4886.
- Ferguson AL, Panagiotopoulos AZ, Debenedetti PG, et al. Integrating diffusion maps with umbrella sampling: application to alanine dipeptide. J Chem Phys. 2011;134(135103):1–15.
- Kovalenko A. Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials. A Pure Appl Chem. 2013;85:159–199.
- Kovalenko A. Multiscale modeling of solvation. In: Breitkopf C, Swider-Lyons K, editors. Springer handbook of electrochemical energy. Berlin Heidelberg: Springer-Verlag; 2017. p. 95–139.
- Okumura H, Okamoto Y. Temperature and pressure dependence of alanine dipeptide studied by multibaric-multithermal molecular dynamics simulations. J Phys Chem B. 2008;111:12038–12049.
- Okumura H. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent. Phys Chem Chem Phys. 2011;13:114–126.
- Iwasaki H, Gyoubu S, Kawatsua T, et al. A 3D-RISM integral equation study of a hydrated dipeptide. Mol Simul. 2015;41:1015–1020.
- Kollman PA, Dixon R, Cornell W, et al. The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: Wilkinson A, Weiner P, van Gunstern WF, editors. Computer simulation of biomolecular system. Vol. 3. Berlin Heidelberg: Springer-Verlag; 1997. p. 83–96.
- Hornak V, Abel R, Okur A, et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters. PROTEINS. 2006;65:712–725.
- Lincoff J, Sasmal S, Head-Gordon T. Comparing generalized ensemble methods for sampling of systems with many degrees of freedom. J Chem Phys. 2016;145:174107–174117.
- Yang YI, Zhang J, Che X, et al. Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling. J Chem Phys. 2016;144:094105–094115.
- Kovalenko A, Hirata F. Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model. J Chem Phys. 1999;110:10095–10112.
- Hirata F, Rossky PJ. An extended rism equation for molecular polar fluids. Chem Phys Lett. 1981;83:329–334.
- Case DA, Babin V, Berryman JT, et al. AMBER 14. San Francisco: University of California; 2014.
- Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935.
- Kell GS. Density, thermal expansivity, and compressibility of liquid water from 0° to 150°C: correlations and tables for atmospheric pressure and saturation reviewed and expressed on 1968 temperature scale. J Chem Eng Data. 1975;20:97–105.
- Perkyns JS, Pettitt BM. A site-site theory for finite concentration saline solutions. J Chem Phys. 1992;97:7656–7666.
- Hasted JB. Liquid water: dielctric properties. In: Franks F, editor. Water a comprehensive treatise. New York (NY): Plenum press; 1972. p. 255–263.
- Torrie GM, Valleau JP. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J Comput Phys. 1977;23:187–199.
- Kumar S, Bouzida D, Swendsen RH, et al. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem. 1992;13:1011–1021.
- Mezei M, Mehrotra PK, Beveridge DL. Monte Carlo determination of the free energy and internal energy of hydration for the ala dipeptide at 25°. J Am Chem Soc. 1985;107:2239–2245.
- Roterman IK, Lambert MH, Gibon KD, et al. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N’-methyl amide: comparisons, contrasts and simple experimental tests. J Biomol Struct Dyn. 1989;78:421–453.
- Madison V, Kopple KD. Solvent-dependent conformational distributions of some dipeptides. J Am Chem Soc. 1980;15:4855–4863.
- Smith DE, Haymet ADJ. Free energy, entropy, and internal energy of hydrophobic interactions: computer simulations. J Chem Phys. 1993;98:6445–6454.