Online resource for theoretical study of hydration of biopolymers

An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.     

Online resource for theoretical study of hydration of biopolymers

An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.     

Characterization of the high-pressure structural transition and thermodynamic properties in sodium chloride: a computational investigation on the basis of the density functional theory

Using first-principles calculations, the elastic constants, the thermodynamic properties, and the structural phase transition between the B1 (rocksalt) and the B2 (cesium chloride) phases of NaCl are investigated by means of the pseudopotential plane-waves method. The calculations are performed within the generalized gradient approximation to density functional theory with the Perdew-Burke-Ernzerhof exchange-correlation functional. On the basis of the third-order Birch-Murnaghan equation of states, the transition pressure Pt between the B1 phase and the B2 phase of NaCl is determined. The calculated values are generally speaking in good agreement with experiments and with similar theoretical calculations. From the theoretical calculations, the shear modulus, Young's modulus, rigidity modulus, and Poisson's ratio of NaCl are derived. According to the quasi-harmonic Debye model, we estimated the Debye temperature of NaCl from the average sound velocity. Moreover, the pressure derivatives of elastic constants, partial differentialC11/partial differentialP, partial differentialC12/partial differentialP, partial differentialC44/partial differentialP, partial differentialS11/partial differential P, partial differentialS12/partial differentialP, and partial differentialS44/partial differentialP, for NaCl crystal are investigated for the first time. This is a quantitative theoretical prediction of the elastic and thermodynamic properties of NaCl, and it still awaits experimental confirmation.     

缔合溶液热力学性质与谱学性质的关联

缔合溶液具有与理想溶液显著不同的热力学和谱学性质,对于热力学和谱学的研究,有助于我们理解缔合溶液的特殊行为.谱学技术中核磁共振(NMR)、红外(IR)和拉曼(Raman)光谱是研究分子间相互作用和溶液结构等微观性质的有效方法,谱学已成为分子热力学研究体系"四面体结构"中的第四个顶点.本文对缔合溶液中热力学(汽液平衡和焓)和谱学(NMR,IR和Raman)联系的最新研究进展进行了综述,着重介绍相关的模型,如化学缔合模型、局部组成(LC)、格子流体氢键(LFHB)理论以及统计缔合流体理论(SAFT).     

Thermodynamics of tri-n-octyltin chloride+hydrocarbon mixtures by gas-liquid chromatography

Gas liquid chromatography was employed to measure the activity coefficients of a group of hydrocarbons at infinite dilution in tri-n-octyltin chloride at 40, 45, 50, 55 and 60°C. The partial molar excess thermodynamic quantities are interpreted by means of the Flory-Patterson theory, and compared with the results obtained for the same group of solutes in tetra-n-octyltin as the solvent. The alkanes activity coefficients and excess enthalpies in both phases are linearly related. Enthalpyentropy compensation in both solvents is discussed.     

The determination of the thermodynamic characteristics of Lennard-Jones fluids under isobaric conditions by the method of molecular functions

Integral equation theory for partial distribution functions was used to suggest an effective method for calculating the derivative of radial distribution function with respect to temperature under isobaric conditions. The thermodynamic expansion, compression, and pressure coefficients and isobaric and isochoric heat capacities were calculated for Lennard-Jones fluids. The calculation results were in close agreement with the known thermodynamic relations.     

The thermodynamic limit of linear gradient chromatography

The thermodynamic limit of the elution profile for solutes in linear gradient chromatography is obtained from the analytical solution of the equation for the ideal model of chromatography, Eq. (12). This limit is of great interest in both preparative and analytical chromatographies because it specifies the maximum possible concentration profile that can be achieved at elution. Elution profiles that are obtained from simulated experiments of the equilibrium dispersive model, Eq. (8), are compared with predictions made by the presented theory as well as the theory by Poppe [11]. It is found that for short injection times the simulated experimental peak is Gaussian like and its width agrees very well with the theory of Poppe. When the injection time increases, the experimental elution profile gradually approaches the profile that is obtained as the thermodynamic limit.     

Finite-temperature full configuration interaction

The exact basis-set values of various thermodynamic potentials of a molecule are evaluated by the finite-temperature full configuration-interaction (FCI) method using ab initio molecular integrals over Gaussian-type orbitals. The thermodynamic potentials considered are the grand partition function, grand potential, internal energy, entropy, and chemical potential in the grand canonical ensemble as well as the partition function, Helmholtz energy, internal energy, and entropy in canonical ensemble. Approximations to FCI that are accurate at low and high temperatures are proposed, implemented, and tested. The results of finite-temperature FCI and its approximations are compared with one another as well as with the results of finite-temperature zeroth-order many-body perturbation theory, in which the Fermi–Dirac statistics is exact. Analytical asymptotic properties in the low- or high-temperature limits of some of these thermodynamic potentials are also given.     

Geometrical thermodynamic field theory

A manifestly covariant, coordinate independent reformulation of the thermodynamic field theory (TFT) is presented. The TFT is a covariant field theory that describes the evolution of a thermodynamic system, extending the near‐equilibrium theory established by Prigogine in 1954. We introduce the minimum rate of dissipation principle, which applies to any system relaxing toward a steady state. We also derive the thermodynamic field equations, which in the case of α–α and β–β processes have already appeared in the literature. In more general cases, the equations are notably simpler than those previously encountered, and they extend beyond the weak‐field regime. Finally, we derive the equations that determine the steady states as well as the critical values of the control parameters beyond which a steady state becomes unstable. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Monte carlo simulation and thermodynamic perturbation theory for mixtures of diatomic molecules

The thermodynamic properties and site—site distribution functions of mixtures of non-spherical molecules are obtained by Monte Carlo simulation. A non-spherical reference-system perturbation theory based on the RISM equation is developed to predict these results. The agreement between theory and simulation for the thermodynamic properties is encouraging. Important differences in the relative peak heights of the site—site distribution functions from theory and simulation are attributed to the role of attractive forces in determining local structure in the fluid mixtures, where the volumes of the components are similar but the well depths differ.     

Water and aqueous solutions: simple non-speculative model approach

Different ways of molecular modeling of water are analyzed and their similarities and differences identified. An up-to-date summary of achievements of a general approach to common rigid site-site interaction models of molecular fluids applied to water and aqueous solutions is then presented and discussed. The method is based on considering only a short-range part of a total realistic potential (such as SPC/E or TIPxP) which determines the structure of water (and fluids in general). A simplification of the interactions at short intermolecular separations leads then to simple models, called primitive models. Quite accurate results in an analytic form for the thermodynamic properties of the models are obtained using the thermodynamic perturbation theory. It is shown that the properly constructed primitive models reproduce, qualitatively, anomalies of pure water and basic characteristics of hydrophobic hydration. The concept of an extended excluded volume, based on pseudo-hard bodies, is introduced and exemplified by considering the partial molar volume of apolar solutes. Potential future development towards a theory of water based on the primitive models as a reference with the long-range contributions added as a perturbation is discussed.     

Stability of the polar NiO(111) surface

Based on density functional theory and thermodynamic model, we compile a phase diagram for the polar NiO(111) surface as a function of temperature and oxygen pressure. The electronic correlation between Ni-3d electrons has also been included in the form of GGA+U method. Consistent with recent experiments, present GGA+U calculation indicates that over a broad range of oxygen partial pressure, the most stable phases are the oxygen and Ni terminated octopolar structures, which are almost degenerate in energy. We also show that the stabilization of the NiO(111) surface goes together with remarkable changes in the geometrical and electronic structure.     

立方体纳米氧化亚铜反应动力学的理论及实验研究

为了探究纳米多相反应过程的动力学行为,本文通过液相还原法可控合成了粒度为55 nm的立方体氧化亚铜（Cu₂O）。基于纳米与块体Cu₂O的区别,采用原位微量热技术获取Cu₂O体系与HNO₃反应过程的热动力学精细信息,结合热动力学原理及动力学过渡态理论计算得到Cu₂O反应动力学参数,并建立立方体动力学模型讨论并佐证动力学实验结果。结果表明,纳米Cu₂O的反应速率常数大于块体,而表观活化能、指前因子、活化焓、活化熵和活化Gibbs自由能均小于块体;随着温度的升高,纳米Cu₂O的反应速率常数和活化Gibbs自由能均增大。动力学模型表明影响反应动力学参数的主要因素为：偏摩尔表面焓影响表观活化能,偏摩尔表面熵影响指前因子,偏摩尔表面Gibbs自由能影响反应速率常数。本文为纳米材料多相反应动力学参数的获取和分析应用提供了一种普适的理论模型和实验方法。     

Thermodynamic properties underlying the alpha-helix-to-beta-sheet transition, aggregation, and amyloidogenesis of polylysine as probed by calorimetry, densimetry, and ultrasound velocimetry

In this work, we performed a detailed thermodynamic study of an aggregation-prone polypeptide, polylysine, to gain a deeper insight into the scenario of physicochemical events during its unfolding, aggregation, and amyloidogenesis. The precise and simultaneous determination of the partial molar volume, the heat capacity, and the coefficients of thermal expansion, as well as adiabatic and isothermal compressibility of the protein upon unfolding and aggregation, yields a thermodynamic picture of the aggregation process highlighting the importance of volume fluctuations during unfolding and amyloidogenesis of proteins.     

Determination of hydrogen atom positions in basic lead carbonate hydrocerussite by quantum chemical methods and simulation of the vibrational spectra

Positions of hydrogen atoms in the crystal structure of basic lead carbonate hydrocerussite are determined by the PM5 quantum chemical method. Raman and infrared spectra as well as thermodynamic functions are calculated for this compound by the theory of crystal lattice dynamics.     

Prediction of thermodynamic properties of sodium dodecyl sulfate aqueous solutions through the hetero-SAFT equation of state

A special version of statistical associating fluid theory (SAFT), the so-called hetero-segmented SAFT equation of state, has been extended to calculate the thermodynamic properties of sodium dodecyl sulfate aqueous solutions. The predicted properties were included the vapor pressure as well as second thermodynamic properties, such as speed of sound. Evaluation of the model has been done through comparison of the calculated vapor pressure with experimental data in the range of 298.15–313.15 K. The hetero-SAFT model is found to be able to correctly describe the thermodynamic derivative properties as well as pVT and VLE properties of ionic surfactant solutions.     

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.     

Thermodynamic studies of binary methanol and ethanol solutions of 1-dodecanol and 1-tetradecanol at 25°C

The osmotic coefficients of binary methanol and ethanol solutions of 1-dodecanol and 1-tetradecanol wer measured at 25°C up to 8 mol-kg^–1 in methanol and 5.5 mol-kg^–1 in ethanol. The activity coefficients of the solute were calculated from Bjerrum's relation. From the osmotic and activity coeficients the excess Gibbs energies of solution as well as the respective partial molar functions of solute and solvent and the virial pair interaction coefficients for the excess Gibbs energies were calculated. In addition, the difference in the Gibbs energy of solvation for the solvent in solution relative to the pure solvent was calculated, as well as the partial molar volumes and excess partial molar volumes of solutes at infinite dilution, and the coefficients of pairwise contributions to the excess volume were determined. The thermodynamic parameters obtained are discussed on the basis of solute-solvent and solute-solute interactions.