Statistical Mechanics Of Molecular Liquids Research Articles

Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory.

There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.

Theoretical Study of the Solvation Effect on the Reductive Reaction of Vinylene Carbonate in the Electrolyte Solution of Lithium Ion Batteries.

Carbon monoxide generation reaction of vinylene carbonate (VC) in the electrolyte solution of lithium ion batteries (ethylene carbonate (EC) and 1.0 M LiClO4/EC) is studied using the RISM-SCF-SEDD method, a hybrid methodology of statistical mechanics for molecular liquids and quantum chemistry. The analytical treatment of the solvent and lithium salt enables us to treat the complicated composition of the solution such as the concentration of the salt which is difficult for the methods based on the molecular dynamics (MD) simulation. The free energy profile and solvation structure are discussed in order to clarify the effect of the solvent, especially lithium salt on the reaction. The lithium salt strongly stabilizes the system due to the electrostatic interaction compared with the system in which the salt does not exist. The effect of the salt is especially important for considering the ionization process of VC.

Photo absorption of p-coumaric acid in aqueous solution: RISM-SCF-SEDD theory approach.

Photo absorption properties of p-coumaric acid, the chromophore of photoactive yellow protein, in aqueous solution were investigated by means of reference interaction site model self-consistent field with spatial electron density distribution (RISM-SCF-SEDD) method. RISM-SCF-SEDD is a combination methodology of electronic structure theory and statistical mechanics for molecular liquids. Here, time-dependent density functional theory was coupled with RISM equation to study the electronic structure of p-coumaric acid in aqueous system. Excitation energies of the chromophore in its neutral, two monoanionic and dianionic forms were computed to elucidate the effect of the deprotonation and solvation on the spectroscopic properties. We found that solvation strongly affects the excitation character of the chromophore, especially for phenolate anion and dianion. The free energy difference among the four protonation states is also discussed. © 2017 Wiley Periodicals, Inc.

A molecular level study of selective cation capture by a host–guest mechanism for 25,26,27,28-tetramethoxycalix[4]arene in MClO4 solution (M = Na, K)

25,26,27,28-Tetramethoxycalix[4] arene selectively captures cations by changing the conformation. In this study, a hybrid approach of ab initio molecular orbital calculation and statistical mechanics for molecular liquid was utilised to understand the capture mechanism in electrolyte solution phase at molecular level. The association free energy and solvation structure were evaluated on the basis of statistical mechanics for molecular liquids. The selectivity is correctly reproduced by the computation, namely cone conformer captures Na+ while K+ is recognised by the partial-cone conformer.

A modern solvation theory: quantum chemistry and statistical chemistry

This perspective highlights recent developments in the field of statistical mechanics for molecular liquids, i.e. the integral equation (IE) theory, especially focusing on hybrid approaches incorporating quantum chemistry and IE theory. The electronic structure of solvated molecules is characterized, followed by recent developments and applications. The latter includes for some specific systems: evaluation of acidity, basicity, pH and pKa, chemical equilibrium and molecular structure, chemical reactions, ionization and electron transfer reactions, as well as excited states and their free energy.

Electrolytes in biomolecular systems studied with the 3D-RISM/RISM theory

We reviewed our recent studies on the molecular recognition and stability of biomolecules in aqueous solutions, which have been carried out based on the statistical mechanics of molecular liquids, or the 3D-RISM/RISM theory. A special stress is put on roles of electrolytes in determining the stability of biomolecules.

Affinity of small ligands to myoglobin studied by the 3D-RISM theory

The affinity of small ligands including O 2, Xe, NO, CO, H 2S, and H 2O to myoglobin is studied based on the Three-dimensional Reference Interaction Site Model (3D-RISM) theory, the statistical mechanics of molecular liquids. The affinity is evaluated in terms of the coordination number of ligands in cavities in the protein, or the “Xe site,” which can be obtained from the radial distribution function of ligand molecules inside the cavities. It is found that NO, CO, and H 2S show greater affinity to the Xe sites than O 2 does, while the affinity of Xe is lower than that of O 2. A relevance of the results to the physiological activity of the protein is speculated. The physical origin of the difference in affinity among the ligands is discussed.

Aqueous Solvation of p-Aminobenzonitrile in the Excited States: A Molecular Level Theory on Density Dependence

Osawa et al. recently studied density dependence of electronic absorption spectra of p-aminobenzonitrile (ABN) in supercritical and subcritical water. They reported the peak position exhibits a minimum in a specific density. RISM-SCF-SEDD, which is a combination method of ab initio electronic structure theory and a statistical mechanics for molecular liquids, was applied to address the origin of this challenging phenomena. Highly accurate electronic structure theories (CASSCF and MCQDPT2) coupled with microscopic description of hydrogen bonding were employed over a wide range of density condition. We found that the solvation effects on the lower two excited states show different density dependence, suggesting that the turnover is attributed to the difference in sensitivity to solvent of the two states.

Analytical energy gradient for reference interaction site model self-consistent field explicitly including spatial electron density distribution

Analytical energy gradient formula was derived for reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD). RISM-SCF-SEDD is a combination method of ab initio electronic structure theory and statistical mechanics for molecular liquids [D. Yokogawa et al., J. Chem. Phys. 126, 244504 (2007)]. As shown previously, RISM-SCF-SEDD is numerically stable and has expanded the applicability of the solvation theory. The energy gradient is an indispensable tool to compute molecular geometry and its implementation further extends the capability of RISM-SCF-SEDD. The present method was applied to chemical systems in aqueous solution; hydration structure and geometry of phosphate anion PO(4) (3-) and tautomerization between 2-pyridone and 2-hydroxypyridine. Compared to available experimental data, the present method correctly reproduced the geometries and relative energies of solvated molecules with microscopic solvent distribution. It is clearly shown that highly sophisticated quantum chemical calculation such as coupled cluster with single and double and perturbative triple excitations coupled with solvation effect is a powerful tool to accurately evaluate molecular properties.

First Principle Theory for pKa Prediction at Molecular Level: pH Effects Based on Explicit Solvent Model

pKa is one of the fundamental properties of molecules and its accurate prediction by theoretical method is indispensable in the current era. At present, the most common approach is based on the free energy difference evaluated in dielectric continuum model for pure water, epsilon=80, which completely ignores ionic influence, i.e., ionic strength. In the present paper, a molecular level theory to predict pKa is proposed based on the reference interaction site model, which is a statistical mechanics for molecular liquids. By regarding an acidic aqueous solution as a three component system including water, proton species (cation), and anion, aqueous solutions with desired pH can be theoretically realized by controlling the number density of the proton species. Using computed free energy changes on the deprotonation of glycine at various pH conditions, a titration curve and pKa can be obtained from the first principle, showing excellent agreement with experimental data. To our best knowledge, this is the first theoretical attempt to directly evaluate pKa under the condition where ionic influence is explicitly taken into account by using statistical molecular theory.

Solvent effect on the nuclear magnetic shielding: ab initio study by the combined reference interaction site model and electronic structure theories

A method for calculating the nuclear magnetic shielding constant of atoms in solution is proposed based on the ab initio electronic structure theory combined with the extended reference interaction site model in statistical mechanics for molecular liquids. The method is applied to a water molecule solvated in water, acetone, chloroform, and carbon tetrachloride. The results for solvation effect demonstrate capability to predict the experimental results. The theory provides a tool to investigate the solvent effect on the nuclear magnetic shielding and its temperature dependence from a molecular viewpoint. The theory takes account for the effect of the electrostatic interaction on the electronic structure of solute, but disregards the electron overlap. The effect of intermolecular overlap of the electron on the nuclear magnetic shieldings is examined using a molecular cluster model.

Ab Initio Study on Molecular and Thermodynamic Properties of Water: A Theoretical Prediction of pKw over a Wide Range of Temperature and Density

The ionic product of water (pKw) has been calculated in a wide range of temperature (0−600 °C) and density (0.6−1.4 g/cm3) by means of ab initio electronic structure theory combined with the extended reference interaction site model in statistical mechanics for molecular liquids (RISM-SCF/MCSCF). We consider the autoionization process (H2O + H2O ⇌ H3O+ + OH-) by regarding H2O, H3O+, and OH- as “solute” molecules in an aqueous solution and evaluate molecular geometries, electronic structure, solvation structure, and free energy components of these species as functions of thermodynamical conditions. The results for pKw obtained from the theory have shown a monotonical decrease with increasing density at all the temperatures investigated, in good accord with the experimental observation. The behavior is determined essentially by the difference in solvation free energies, Δμ(H3O+) + Δμ(OH-) − 2Δμ(H2O), associated with the reaction. The Δμ(OH-) shows the density dependence, which is entirely different from tha...

The syn-/ anti-conformational equilibrium of acetic acid in water studied by the RISM-SCF/MCSCF method

The syn-/ anti-conformational equilibrium of acetic acid in water is studied by the RISM-SCF/MCSCF method, a hybridized method of the ab initio quantum chemistry and the statistical mechanics of molecular liquids. The solvent effect on the two conformers are examined in terms of the solvation free energy. Significant stabilization due to solvation was observed on the anti-conformer, while only slight decrease in the free energy is resulted in the syn-conformer. Due to the greater stabilization in the anti-conformer, the energy gap between the two conformers is dramatically reduced in solution; 1.7 kcal/mol in solution compared with 6.9 kcal/mol in gas phase. The change in the electron density of acetic acid upon transferring the solute from gas phase into aqueous solution is visualized to understand the polarization effects due to solvent.

Theoretical Study for Autoionization of Liquid Water: Temperature Dependence of the Ionic Product (pKw)

The temperature dependence of the ionic product of water (pKw) is investigated theoretically by means of ab initio electronic structure theory combined with the extended reference interaction site method in statistical mechanics of molecular liquids (RISM-SCF/MCSCF method). The chemical equilibrium H2O + H2O ⇌ H3O+ + OH- is studied, in which water molecules, hydronium ions, and hydroxide ions are regarded as “solute” molecules in aqueous solution. Molecular geometries, electronic structures, pair correlation functions, and free energy components of those species as well as their temperature dependence are calculated. It is shown that the hydroxide anion is polarized more easily by surrounding solvent compared to the other species. The solvent-induced electronic structure relaxes toward that in the gas phase as temperature increases. The hydroxide anion exhibits the largest temperature dependence in the electronic structure as well as in solvation structure. It is found that changes in the solvation free e...

Theoretical study for the basicities of methylamines in aqueous solution: A RISM-SCF calculation of solvation thermodynamics

An ab initio quantum chemical calculation combined with the extended reference interaction site method in statistical mechanics of molecular liquids (the RISM-SCF method) is used to examine the basicities of methylamines in aqueous solution. Free energy changes upon protonation are calculated for a series of methylamines in the gas phase and in aqueous solution, respectively. The gas phase results show a monotonical increase in the basicity with successive methyl substitutions in accord with experiment and earlier theoretical studies. In aqueous solution, however, the results show an irregular order in basicity, which is in qualitative agreement with well established experimental data. Several contributions to free energy changes such as those resulting from solvation and from substitutions are analyzed entirely from a microscopic point of view. It is shown that solvation free energies play an essential role in the determination of the basicity in the solution. Further, it is shown that the solvation structures and the solute electronic structures are altered by the self-consistent treatment in the determination of solute-solvent interactions and that such alterations cause substantial effects on the basicity.

The solvent effect on the acidities of haloacetic acids in aqueous solution. A RISM-SCF study

The acidities of acetic, fluoracetic and chloroacetic acids in aqueous solution are calculated by means of the ab initio method combined with the reference interaction site method in the statistical mechanics of molecular liquids (the RISM-SCF method). The inversion in the order of acidities experimentally observed when a series of haloacetic acids is immersed into aqueous solution is reproduced. It is shown that the inversion is caused by competition between substitution and solvation effects. The solvation effect is discussed in molecular detail in terms of the charge distribution of the solute and the solute-solvent radial distribution functions.

A theoretical analysis of the ultraviolet spectrum (180?260 nm) of pure liquid benzene

This paper reports an attempt to understand theoretically the red shifts seen in the benzene ultraviolet spectrum upon changing from gas to the liquid phase. The theoretical analysis is performed through a framework which brings together Quantum Chemistry and Classical Statistical Mechanics of molecular liquids. As it is discussed herein, the influence of the liquid phase on the individual molecular properties is taken into account by means of a perturbation term included in the effective molecular Hamiltonian. Such a perturbation depends explicitly on both the chemical nature and the static structure of the liquid surrounding the molecule under study. In order to simulate the vibronic couplings, which make the benzene |Ddforbidden|DD bands1La and1Lb have nonzero intensity, random displacements of the nuclei of benzene have been employed in this introductory work. The calculations involve the CNDO/S procedure and the atom-atom radial distribution functions of the liquid sample. The results account for the large red shift (≃20 nm) undergone by the band1La.

Liquid phase effects on molecular properties

A theory for environmental effects on molecular properties is developed, founded on a perturbed molecular orbitals model and statistical mechanics of molecular liquids. Some methods for the theoretical calculation of molecular properties in pure liquids or solutions can be derived from this theory. The simplest is applied to carbon disulphide in the liquid phase, computing the atom-atom distribution functions using the Monte Carlo method.

Liquid phase effects on molecular properties

A theory for environmental effects on molecular properties is developed, founded on a perturbed molecular orbitals model and statistical mechanics of molecular liquids. Some methods for the theoretical calculation of molecular properties in pure liquids or solutions can be derived from this theory. The simplest is applied to carbon disulphide in the liquid phase, computing the atom-atom distribution functions using the Monte Carlo method.