Thermodynamic properties and equilibrium constant of chemical reaction in nanosystem: An theoretical and experimental study

The theoretical relations of thermodynamic properties, the equilibrium constant and reactant size in nanosystem are described. The effects of size on thermodynamic properties and the equilibrium constant were studied using nanosize zinc oxide and sodium bisulfate solution as a reaction system. The experimental results indicated that the molar Gibbs free energy, the molar enthalpy and the molar entropy of the reaction decrease, but the equilibrium constant increases with decreasing reactant size. Linear trends were observed between the reciprocal of size for nano-reactant and thermodynamic variable, which are consistent with the theoretical relations.     

Investigation of the role of the C-PCM solvent effect in reactivity indices

It has been shown recently, how the coupling between electronic degrees of freedom and vibrational modes is reflected in the properties of molecules. The necessary derivatives have been analyzed and their thermodynamic relations were demonstrated. This present work is focused on the analysis of a molecular system, under the influence of C-PCM induced solvent effect. The analysis is based on reactivity indices derived from DFT. The shift of frequency for diatomic molecules has been obtained. It has been identified as chemical force effect. The role of nuclear reactivity indices has been emphasized. This concept has been extended to obtain regional chemical potential values within C-PCM model for polyatomic molecules.     

Mechanical unfolding revisited through a simple but realistic model

Single-molecule experiments and their application to probe the mechanical resistance and related properties of proteins provide a new dimension in our knowledge of these important and complex biological molecules. Single-molecule techniques may not have yet overridden solution experiments as a method of choice to characterize biophysical and biological properties of proteins, but have stimulated a debate and contributed considerably to bridge theory and experiment. Here we demonstrate this latter contribution by illustrating the reach of some theoretical findings using a solvable but nontrivial molecular model whose properties are analogous to those of the corresponding experimental systems. In particular, we show the relationship between the thermodynamic and the mechanical properties of a protein. The simulations presented here also illustrate how forced and spontaneous unfolding occur through different pathways and that folding and unfolding rates at equilibrium cannot in general be obtained from forced unfolding experiments or simulations. We also study the relationship between the energy surface and the mechanical resistance of a protein and show how a simple analysis of the native state can predict much of the mechanical properties of a protein.     

Molecular similarity studies on sandalwood odour molecules: Investigations of the conformational space

Summary Odour differences of some campholene and fencholene derivatives are explained by the analysis of the conformational space and the molecular shape of these molecules. The high flexibility caused by free rotation of some carbon-carbon bonds leads in one case to a large number of energetically possible conformations which have to be taken into account for a study of molecular similarity. In another case, steric restrictions reduce the number of relevant conformations such that no active conformation exists in a thermodynamic equilibrium.Conformational Calculations on Sandalwood Odour XII; for part XI, see Ref. [1]     

Equilibrium and kinetics of water adsorption in carbon molecular sieve: theory and experiment

Measurements of water adsorption equilibrium and kinetics in Takeda carbon molecular sieve (CMS) were undertaken in an effort to characterize fundamental mechanisms of adsorption and transport. Adsorption equilibrium revealed a type III isotherm that was characterized by cooperative multimolecular sorption theory. Water adsorption was found to be reversible and did not display hysteresis upon desorption over the conditions studied. Adsorption kinetics measurements revealed that a Fickian diffusion mechanism governed the uptake of water and that the rate of adsorption decreased with increasing relative pressure. Previous investigations have attributed the observed decreasing trend in the rate of adsorption to blocking of micropores. Here, it is proposed that the decrease is attributed to the thermodynamic correction to Fick's law which is formulated on the basis of the chemical potential as the driving force for transport. The thermodynamically corrected formulation accounted for observations of transport of water and other molecules in CMS.     

Defect‐Mediated Ordering of Condensed Water Structures in Microporous Zeolites

Ab‐initio molecular dynamics simulations and transmission infrared spectroscopy are employed to characterize the structure of water networks in defect‐functionalized microporous zeolites. Thermodynamically stable phases of clustered water molecules are localized at some of the defects in zeolite Beta, which include catalytic sites such as framework Lewis acidic Sn atoms in closed and hydrolyzed‐open forms, as well as silanol nests. These water clusters compete with ideal gas‐like structures at low water densities and pore‐filling phases at higher water densities, with the equilibrium phase determined by the water chemical potential. The physical characteristics of these phases are determined by the defect identity, with the local binding and orientation of hydroxyl moieties around the defects playing a central role. The results suggest general principles for how the structure of polar solvents in microporous solid acids is influenced by local defect functionalization, and the thermodynamic stability of the condensed phases surrounding such sites, in turn, implies that the catalysis of Lewis acids will be influenced by local water ordering.     

Verification of Onsager's reciprocal relations for evaporation and condensation using non-equilibrium molecular dynamics

Non-equilibrium molecular dynamic (NEMD) simulations have been used to study heat and mass transfer across a vapor-liquid interface for a one-component system using a Lennard-Jones spline potential. It was confirmed that the relation between the surface tension and the surface temperature in the non-equilibrium system was the same as in equilibrium (local equilibrium). Interfacial transfer coefficients were evaluated for the surface, which expressed the heat and mass fluxes in temperature and chemical potential differences across the interfacial region (film). In this analysis it was assumed that the Onsager reciprocal relations were valid. In this paper we extend the number of simulations such that we can calculate all four interface film transfer coefficients along the whole liquid-vapor coexistence curve. We do this analysis both for the case where we use the measurable heat flux on the vapor side and for the case where we use the measurable heat flux on the liquid side. The most important result we found is that the coupling coefficients within the accuracy of the calculation are equal. This is the first verification of the validity of the Onsager relations for transport through a surface using molecular dynamics. The interfacial film transfer coefficients are found to be a function of the surface temperature alone. New expressions are given for the kinetic theory values of these coefficients which only depend on the surface temperature. The NEMD values were found to be in good agreement with these expressions.     

Development of a Unifying Framework for the Restrictions in Multi-component Diffusion Close to Equilibrium

In this work a unifying framework is developed for multi-component diffusion close to equilibrium by proposing additional restrictions for the Fickian diffusion coefficients such as the Onsager reciprocal relations. Moreover, it is shown that these additional restrictions can explain the discrepancy, reported in the literature, of calculating negative concentrations in Fickian ternary free diffusion observed even if the second thermodynamic law constraints and the phase stability criteria are satisfied. It is believed that this work could be used to further investigate multi-component diffusion.     

Characterisation and improvement of sorption materials with molecular modeling for the use in heat transformation applications

In this paper, several materials for sorption heat transformation applications are evaluated on basis of experimental characterisation and molecular simulation methods. With regard to the application, classical zeolites, ion exchanged zeolites, aluminophosphates as well as silica-aluminophosphates have been analysed. Furthermore samples of metal organic frameworks (MOF) have been evaluated for the use in sorption heat transformation applications with very promising results. In order to understand the fundamental relationship between adsorbent microstructure and water adsorption equilibrium, molecular simulation of water adsorption in various adsorbents are employed. As a result of these simulations within the grand canonical ensemble, the number of water molecules adsorbed in thermodynamic equilibrium under given conditions of temperature and chemical potential (resp. pressure) are obtained. These data are compared with adsorption data from thermogravimetric measurements.     

A theory of a curved vapor-liquid separation boundary: The lattice gas model

Molecular theory of curved vapor-liquid interphase boundaries was considered in terms of the lattice gas model. The theory uses the quasi-thermodynamic concept of curved layers of a separation boundary with a large radius. The transition from a rectangular lattice to such layers is performed by the introduction of a variable number of the nearest neighbors. The problems (1) of the transition from distributed molecular models to layer models reflecting macroscopic symmetry of the interphase boundary and (2) of a minimum linear size of the surface region to which thermodynamic approaches are applicable were considered. Equations for the quasi-equilibrium distribution of molecules at the vapor-liquid boundary in a metastable system were constructed in the quasi-chemical approximation taking into account direct correlations between the nearest interacting molecules. A metastable state is maintained by a pressure jump described by the macro-scopic Laplace equation on a separation surface inside the interphase region. Equations for local mean pressure values and normal and tangential pressure tensor components inside the interphase region were constructed. These equations were used to obtain microscopic difference mechanical equilibrium equations for curved boundaries of spherical and cylindrical drops in the metastable state. The relation between the micro-scopic difference mechanical equilibrium equations and similar differential equations and the macroscopic Laplace equation, which described pressure jump in a metastable system, was considered. Various definitions of surface tension are discussed.     

Molecular electronics—the future of bioelectronics

In the last decade, molecular electronics, as an active frontier of interdisciplinary research areas, has become one of the most rapidly developing fields, and attracted worldwide interests. The fundamental element of molecular electronics is a molecular device or a supramolecular device, which is an organized molecular system constructed mainly by organic molecules or biomolecules that have some specific functions in signal detection, process, storage, and transmission through chemical or physical interactions at molecular or supramolecular levels. A molecular device (MD) can involve chemical information processes, and be relatively easy to realize a large number of links between the molecules. The links can be controlled by the external signals. These are the expected features of molecular computing and directly involve chemical and biological processes. MD may overcome some limitations of the solid-state chips, and can be directly applied to chemical and biological processes. Molecular electronics is a part of bioelectronics. It will play an important and revolutionary role in the next century. This paper intends to review the research activities of molecular electronics in China, particularly in LMBE.     

Statistical mechanical theory of local compositions

The concept of local composition has received much attention during the past few years, much of which has been devoted to justifying the empirical model proposed by Wilson in 1964. In this report the concept of local composition is defined on statiscal mechanical grounds and expressions relating these compositions to thermodynamic properties of equilibrium fluid mixtures are derived. In particular, different local composition approximations are presented and new approximations based on molecular theories of mixtures are derived. Sets of mixing rules consistent with these different local composition approximations result, some of which are density and temperature dependent. Also, relations for partial molar properties in terms of local compositions are derived from the Kirkwood-Buff solution theory. Finally the radius of the sphere of influence of local compositions is formulated on statistical mechanical grounds.     

Statistical mechanics of time independent nondissipative nonequilibrium states

We examine the question of whether the formal expressions of equilibrium statistical mechanics can be applied to time independent nondissipative systems that are not in true thermodynamic equilibrium and are nonergodic. By assuming that the phase space may be divided into time independent, locally ergodic domains, we argue that within such domains the relative probabilities of microstates are given by the standard Boltzmann weights. In contrast to previous energy landscape treatments that have been developed specifically for the glass transition, we do not impose an a priori knowledge of the interdomain population distribution. Assuming that these domains are robust with respect to small changes in thermodynamic state variables we derive a variety of fluctuation formulas for these systems. We verify our theoretical results using molecular dynamics simulations on a model glass forming system. Nonequilibrium transient fluctuation relations are derived for the fluctuations resulting from a sudden finite change to the system's temperature or pressure and these are shown to be consistent with the simulation results. The necessary and sufficient conditions for these relations to be valid are that the domains are internally populated by Boltzmann statistics and that the domains are robust. The transient fluctuation relations thus provide an independent quantitative justification for the assumptions used in our statistical mechanical treatment of these systems.     

Deformation behavior of polymer networks containing or interacting with a solvent

General formalism to describe both equilibrium and nonequilibrium states of polymer networks containing a solvent or interacting with the solvent medium is proposed. Two classes of problems have been formulated. It is necessary to determine the stress-strain state of an inhomogeneously swollen material in one case and that of a statically loaded material occurring in thermodynamic equilibrium with the solvent in the other case. The state of the swollen material is characterized in terms of the global mechanical stress tensor and the solvent chemical potential. In the case of incompressible material and liquid, an osmotic stress tensor is introduced. A method for deriving physical expressions for the mechanical stress tensor, the chemical potential, and the osmotic stress tensor is proposed on the basis of the known free energy relations that follow from different theories of rubber elasticity. The efficacy of the general formalism is demonstrated using particular examples in which the deformation behavior and the equilibrium swelling of mechanically loaded polymer networks are considered.     

Analysis by Means of <Superscript>1</Superscript>H NMR Spectroscopy of Heteroassociaion in Water Solution of Antitumor Antibiotics Daunomycin and Actinomycin D

Heteroassociation of aromatic antitumor antibiotics daunomycin (DAU) and actinomycin D (AMD) was investigated using 1D and 2D ¹H NMR spectroscopy (at 500 MHz) and molecular mechanics procedure with the goal of establishing the mechanism of the combined action of antibiotics in the system AMD-DAU. The experimental data were processed applying a modified statistical and thermodynamic model of the molecules heteroassociation. Proceeding from this model the values were obtained of induced proton chemical shifts, equilibrium constant and thermodynamic parameters of complexing reaction between DAU and AMD. By means of molecular mechanics with the use of X-PLOR software and of the analysis results of the induced proton chemical shifts in the molecules the most probable spatial structure, 1:1, was established for the heterocomplex of DAU and AMD. Heterocomplexes of daunomycin and actinomycin D form due to stacking interaction between the aromatic chromophores with possible additional stabilization of the complexes by an intermolecular hydrogen bond.     

Supramolecular Stabilization of Metastable Tautomers in Solution and the Solid State

This work presents a successful application of a recently reported supramolecular strategy for stabilization of metastable tautomers in cocrystals to monocomponent, non‐heterocyclic, tautomeric solids. Quantum‐chemical computations and solution studies show that the investigated Schiff base molecule, derived from 3‐methoxysalicylaldehyde and 2‐amino‐3‐hydroxypyridine ( ap ), is far more stable as the enol tautomer. In the solid state, however, in all three obtained polymorphic forms it exists solely as the keto tautomer, in each case stabilized by an unexpected hydrogen‐bonding pattern. Computations have shown that hydrogen bonding of the investigated Schiff base with suitable molecules shifts the tautomeric equilibrium to the less stable keto form. The extremes to which supramolecular stabilization can lead are demonstrated by the two polymorphs of molecular complexes of the Schiff base with ap . The molecules of both constituents of molecular complexes are present as metastable tautomers (keto anion and protonated pyridine, respectively), which stabilize each other through a very strong hydrogen bond. All the obtained solid forms proved stable in various solid‐state and solvent‐mediated methods used to establish their relative thermodynamic stabilities and possible interconversion conditions.     

1H nmr study of heteroassociation of caffeine with acridine orange in aqueous solution

The molecular mechanism of the action of caffeine (CAF) as a complexing interceptor of aromatic ligands intercalated in DNA is considered using a typical intercalant — acridine orange (AO) dye. Hetero-association of CAF and AO was investigated by one- and two-dimensional H NMR spectroscopy (500 MHz). The concentration (at 298 and 308 K) and temperature dependences of the proton chemical shifts of molecules in aqueous solution were measured. The equilibrium constants of the CAF-AO hetero-association reactions at different temperatures and the limiting chemical shifts of the protons of the aromatic ligands of the associates were determined. The most plausible structure of the 1:1 CAF-AO helerocomplex in aqueous solution is suggested based on the calculated values of the induced proton chemical shifts of the molecules and the quantum mechanical screening curves for CAF and AO. The thermodynamic parameters of CAF-AO helerocomplex formation art calculated. The structural and thermodynamic analyses indicate that dispersion forces and hydrophobic interactions play a significant role in heterocomplex formation in aqueous salt solution. The relative contents of different types of associate in a mixed solution containing CAF and AO are estimated. The equilibrium of CAF-AO heteroassociates in solution is characterized in relation to temperature. Heteroassociation of CAF and AO molecules leads to decreased effective concentration of intercalant in solution and hence to decreased mutagenic activity of the dye. Translated from Zhumal Struktumoi Khimii, Vol. 41, No. 1, pp. 86-96, January–February, 2000.