Solvation Structure, Thermodynamics, and Molecular Conformational Equilibria for n-Butane in Water Analyzed by Reference Interaction Site Model Theory Using an All-Atom Solute Model

Abstract

For the four thermodynamic states: temperature T ) 283. 15, 298.15, 313.15, and 328.15 K and the corresponding bulk water density F ) 0.9997, 0.9970, 0.9922, and 0.9875 g cm -3 , for which experimental data are available, we have studied hydration structure, hydration thermodynamics, and molecular conformational equilibria for n-butane in water at infinite dilution, by means of the hypernetted chain closure reference interaction site model (HNC-RISM) theory with an all-atom solute model. The hydration structures of the trans and the gauche conformers of n-butane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With these radial distribution functions as input, the n-butane conformational average hydration free energies, energies, enthalpies, and entropies are calculated. At room temperature, the normalized equilibrium distribution of n-butane conformers, the water solvent-induced rotational free energy surface and the trans-gauche and trans-cis cavity thermodynamic properties are calculated. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes (Yin, D.; Mackerell, A. D., Jr. J. Comput. Chem. 1998, 19, 334), n-butane hydration thermodynamics and its conformational equilibria in water are well described by the HNC-RISM theory in comparison with the available experimental and computer simulation results. We also calculated the solute density derivatives of the water-water radial distribution functions δh vv , with the optimized CHARMM96 all-atom model, the united-atom OPLS (optimized potentials for liquid simulations), and the all-atom OPLS models for n-butane, respectively. The δh vv (r) reflect the effect of increased pressure disrupting the hydrogen bonding between water molecules. The all-atom model seems to enhance such an effect due to the well-documented shortcoming of the RISM theory in the treatment of the excluded volume of so-called auxiliary sites. I. IntroductionTwo important problems in the study of the aqueous solution behavior of biomolecules are the restructuring of water around the molecules and the solvent influence on the conformational structure of the molecules. Small flexible hydrocarbon molecules have been used as models for studying those problems. 1 Among them, n-butane, which has only one conformational degree of freedom, is perhaps the simplest molecule available for studying the two problems at the same time. n-butane has been studied extensively in the gas phase, 1-8 in the neat liquid, 9-17 and in apolar 15,18-23 and aqueous solutions. 15,16,23-33 There are two kinds of models for representing the n-butane molecule. One is a united-atom model, namely that the methyl and methylene groups are approximately considered as one site of pair interactions, respectively. In this model, the hydrogens of the CH n groups are implicitly treated, the interaction sites for the CH n groups are centered on the carbons, and the CH n groups are all taken as neutral. The other one is an all-...

Alternative Ornstein–Zernike models from the homogeneous electron liquid for density functional theory calculations

“…The DCF is still commonly used in the theory of classical liquids, [103][104][105][106] where it is the key ingredient in referenceinteraction-site-models (RISM) for continuum solvation. [107][108][109][110][111][112][113][114][115][116] It has also been used in the context of electronic structure theory by Case and Manby. [49] In both applications, one is attempting to approximate the many-particle distribution function for a large number of identical particles.…”

An integral equation theory for solvation effects on the molecular structural fluctuation

“…In this study, three models are employed for n-butane. One is a model which modified CHARMM96 31,32 (denoted as Model 1) and the second is OPLS-AA 33 (Model 2). In these all-atom type models, bond lengths of C-H and C-C are, respectively, fixed at 1.09 and 1.53 Å.…”

“…TIP3P-type water model is chosen as a solvent. All the Lennard Jones parameters and atomic charges are taken from the literature [31][32][33]35 and listed in Table I. Non-bonded interaction between groups separated by more than three bonds was added into the intramolecular interaction potential.…”

“…Because the molecule has only one conformational degree of freedom, the hydration effects on n-butane have been investigated by many researchers. 15,31,[37][38][39][40][41][42][43] Fig . 1 displays the intramolecular correlation functions between terminal carbon atoms.…”

Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies

“…Accurate calculation of solvent-solute interactions is an important component of robust molecular simulation including protein structure prediction [1][2][3], conformational ensemble calculations [4][5][6][7], and binding free energy calculations [8][9][10]. Solvation free energy methods for atomically detailed molecular models have a long history of development [11][12][13][14][15][16][17][18][19] and have recently benefited from the curation of experimental small molecule solvation data for blind prediction challenges such as the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge studies [10,[20][21][22][23][24][25].…”