Computational study on the properties and structure of methyl lactate

A theoretical study on the properties and molecular level structure of the very important green solvent methyl lactate is carried out in the gas phase and methanol and water solutions, with the solvent treated both explicitly and as a continuum. Torsional barriers giving rise to different conformers by rotation of the hydroxyl and methyl groups were analyzed using density functional theory (DFT) to establish the most stable conformer both in gas phase and solution. DFT computations on lactate dimers were also done to study short-range features, and the effect of the surrounding solvent on intra- and intermolecular hydrogen bonding was analyzed according to the polarizable continuum model approach. We have also studied lactate/water and lactate/methanol small clusters together with the corresponding binding energies. Moreover, classical molecular dynamics simulations (MD) were carried out to study medium- and large-range effects at lower computational cost. MD simulations at different pressure and temperature conditions on pure lactate were carried out, and mixtures with water and methanol of different compositions were also studied. Structural information, analyzed through the radial distribution functions, together with dynamic aspects of pure and mixed fluids were considered. The intramolecular hydrogen bonding ability of methyl lactate together with the possibility of homo- and hetero-intermolecular association determines the behavior of this molecule in pure fluids or in mixed.     

Intramolecular and liquid structure of 2,2,2-trifluoroethanol by X-ray diffraction

Intramolecular and liquid structure of 2,2,2-trifluoroethanol (TFE) have been investigated by x-ray diffraction at 25°C. The structural parameters for the skeleton of the molecules in the liquid phase are similar to those in the gas phase. The conformers of TFE molecules in the liquid phase are discussed. The O...O distance at about 284 pm and additional F...O one at about 302 pm were found to be characteristic for the first neighbor interactions. Various models (dimers and trimers) have been examined for analyzing the first neighbor structure. The liquid structure was explained in terms of small clusters consisting of two to three molecules rather than of a more extended polymeric network.Central Research Institute for Chemistry of the Hungarian Academy of Sciences, Budapest, P. O. Box 17, H-1525, Hungary.     

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models

A polarizable model for simulation of liquid methanol, compatible with the COS/G2 water model, has been developed using the Charge-on-Spring (COS) technique. The model consists of three point charges, with one polarizable center on the oxygen atom. The Lennard-Jones parameters on the oxygen atom together with the molecular polarizability were varied to reproduce the experimental heat of vaporization and density of liquid methanol at ambient conditions. We examined the energies of various methanol dimers in the gas phase and compared them with values obtained from ab initio calculations. The model was then used to study the thermodynamic, dynamic, structural, and dielectric properties of liquid methanol as well as of a methanol-water mixture. A microscopic picture of the structure of pure liquid methanol and of the methanol-water mixture is provided. Good agreement was found between the results from our model simulations and available experimental and ab initio calculation data. In particular, the experimental dielectric permittivity of 32 could be reproduced, which had been shown to be difficult when using nonpolarizable models.     

Detailed intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules with C(3v) symmetry: chloroform, bromoform, and methyl-iodide

Analyses of the intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules of the CXY(3)-type are described. The process is composed of the determination of several different distance-dependent orientational correlation functions, including ones that are introduced here. As a result, a complete structure classification could be provided for CXY(3) molecular liquids, namely for liquid chloroform, bromoform, and methyl-iodide. In the present work, the calculations have been conducted on particle configurations resulting from reverse Monte Carlo computer modeling: these particle arrangements have the advantage that they are fully consistent with structure factors from neutron and x-ray diffraction measurements. It has been established that as the separation between neighboring molecules increases, the dominant mutual orientations change from face-to-face to edge-to-edge, via the edge-to-face arrangements. Depending on the actual liquid, these geometrical elements (edges and faces of the distorted tetrahedra) were found to contain different atoms. From the set of liquids studied here, the structure of methyl-iodide was found to be easiest to describe on the basis of pure steric effects (molecular shape, size, and density) and the structure of liquid chloroform seems to be the furthest away from the corresponding "flexible fused hard spheres" like reference system.     

Evidence of complete hydrophobic coating of bombesin by trifluoroethanol in aqueous solution: an NMR spectroscopic and molecular dynamics study

Bombesin is a tetradecapeptide that possesses a random coil structure in pure water. In the presence of 30 % (v/v) 2,2,2-trifluoroethanol (TFE), it adopts a partial helical conformation involving the C-terminal amino acids 6-14. This conformational change, known as the TFE effect, is studied here in terms of the solvation state of the peptide at different TFE concentrations by means of intermolecular homo- and heteronuclear NOE measurements. When an aqueous solution of bombesin is titrated with TFE, a continual decrease in the water/peptide interactions and a concomitant increase in the TFE/peptide interactions is observed, and at 30 % (v/v) TFE no homonuclear NOEs between water and the peptide can be detected. The conformational transition of the bombesin molecule is thus accompanied by a complete surface covering with TFE. A parallel molecular dynamics (MD) study of the peptide in aqueous solution with the single-point charge (SPC) water model and in a 30 % (v/v) TFE/water mixture with a recently developed TFE model has also been performed. The 10 ns simulations were in agreement with the experimental data. The calculations indicate stabilisation of the alpha-helix in the H(2)O/TFE mixture, in contrast to the situation in pure water, and clustering of the TFE molecules around the peptide.     

X-ray scattering and density-functional theory calculations to study the presence of hydrogen-bonded clusters in liquid N-methylacetamide

A structural investigation of liquid N-methylacetamide (NMA) is performed by x-ray scattering and density functional theory (DFT). Experimental data are analyzed to yield the total structure function SM(Q) and the pair correlation function g(r). The DFT calculations, using the standard triple zeta valence basis set augmented by a diffuse function for carbon, nitrogen and oxygen atoms, are performed on the one hand to study the structure and stability of the two possible conformers cis and trans. On the other hand, they are meant to examine some possible clusters which may describe the intermolecular arrangement in liquid NMA. Among two series of dimers and trimers associations, the spectra are particularly interpreted in terms of: Trans NMA dimers and trimers which resemble the short-range crystal structure, mixed cis and trans trimers and cis cyclic trimers. The H-bonding parameters and the intermolecular energy for each model are described.     

A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model

We study the bulk and interfacial properties of methanol via molecular dynamics simulations using a CHARMM (Chemistry at HARvard Molecular Mechanics) fluctuating charge force field. We discuss the parametrization of the electrostatic model as part of the ongoing CHARMM development for polarizable protein force fields. The bulk liquid properties are in agreement with available experimental data and competitive with existing fixed-charge and polarizable force fields. The liquid density and vaporization enthalpy are determined to be 0.809 g/cm3 and 8.9 kcal/mol compared to the experimental values of 0.787 g/cm3 and 8.94 kcal/mol, respectively. The liquid structure as indicated by radial distribution functions is in keeping with the most recent neutron diffraction results; the force field shows a slightly more ordered liquid, necessarily arising from the enhanced condensed phase electrostatics (as evidenced by an induced liquid phase dipole moment of 0.7 D), although the average coordination with two neighboring molecules is consistent with the experimental diffraction study as well as with recent density functional molecular dynamics calculations. The predicted surface tension of 19.66+/-1.03 dyn/cm is slightly lower than the experimental value of 22.6 dyn/cm, but still competitive with classical force fields. The interface demonstrates the preferential molecular orientation of molecules as observed via nonlinear optical spectroscopic methods. Finally, via canonical molecular dynamics simulations, we assess the model's ability to reproduce the vapor-liquid equilibrium from 298 to 423 K, the simulation data then used to obtain estimates of the model's critical temperature and density. The model predicts a critical temperature of 470.1 K and critical density of 0.312 g/cm3 compared to the experimental values of 512.65 K and 0.279 g/cm3, respectively. The model underestimates the critical temperature by 8% and overestimates the critical density by 10%, and in this sense is roughly equivalent to the underlying fixed-charge CHARMM22 force field.     

From molecular clusters to liquid structure in AlCl3 and FeCl3

Melting of aluminum and iron trichloride is accompanied by a structural transition from sixfold to fourfold coordination of the trivalent metal ions, and a widely accepted interpretation of the structure of their melts near freezing is that they mainly consist of strongly correlated dimers formed from two edge-sharing tetrahedra. We carry out classical molecular dynamics simulations to examine how a polarizable-ion force law, determined on isolated molecular monomers and dimers in the gaseous phase of these compounds, fares in accounting for the pair structure of their liquid phase and for mean square displacements and diffusion coefficients of the two species in each melt. The model reproduces the main features of the neutron diffraction structure factor, showing peaks due to intermediate range order and to charge and density short-range order, and accounts for the experimental data at a good semi-quantitative level. We find agreement with the neutron and X-ray diffraction data on metal–halogen and Cl–Cl bond lengths in the melt, and demonstrate the high sensitivity of the results for the width of the first-neighbor shell to truncation in obtaining it by Fourier transform of the neutron-weighted structure factor in momentum space. We also report comparisons with a recent first-principles study of the structure of the AlCl₃ melt by the Car–Parrinello method. Finally, we demonstrate break-up of dimers into monomers upon raising the liquid temperature in the case of AlCl₃.     

Adsorption of Amphiphilic Dimers at Surfaces

Adsorption of amphiphilic dimers is analyzed in the framework of density functional Ono–Kondo theory. There are three configurations for dimers absorbed at a surface: one parallel to the surface and two perpendicular to the surface (AB and BA, with A or B touching the surface, respectively). Densities of molecules in each configuration are calculated from density functional theory and compared to Monte Carlo simulation data. There is good agreement between theory and simulations. It is shown that the parallel configuration is preferred over the perpendicular configuration, except when there are very strong asymmetries in intermolecular forces. In most cases, the parallel configuration is even preferred over the combination of the two perpendicular configurations.     

Dynamic molecular movements and aggregation structures of lipids in a liquid state

This paper discusses the molecular conformations and the liquid structures of triacylglycerols (TGs) and fatty acids in their melts. Three models for liquid state ordering have been proposed for TG melts to date: the smectic liquid crystal model, the nematic liquid crystal model, and the discotic model. To completely resolve the liquid structure of TGs, further research is required. However, some information on the molecular level has been obtained for fatty acids that are relatively simple compounds. The combination of various spectroscopic and thermodynamic measurements revealed that the hydrogen-bonded dimers of fatty acids are units of intermolecular and intramolecular movements in the liquids and in non-polar solvents. The dimers that construct the clusters resemble the smectic liquid crystal and determine the physicochemical properties of the liquid of the fatty acid. Cholesterol stabilizes the clusters, while ethanol destroys them. Self-diffusion and neutron diffraction measurements revealed that two kinds of fatty acids exist in their binary liquid mixture exist as the homodimers composed of same species.     

Ab initio rigid water: effect on water structure, ion hydration, and thermodynamics

We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ( approximately 8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 A longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.     

Intermolecular Nuclear Relaxations and Molecular Site-Site Pair Correlation Functions in Liquids

Intermolecular nuclear relaxation studies of real liquids and the results of theoretical calculations for model potential functions have provided significant information on the role of molecular interactions in the structure of liquids. The intermolecular proton-proton paircorrelation function (pcf), obtained from the reference interaction site model (RISM) is used as the equilibrium distribution and is used to obtarn an effective force for the calculation of intermolecular proton relaxation rates in liquid benzene, 1,3,5-trideuterobenzene and ethane. For liquid ethane, better agreement with experiment is observed with the pcf obtained from the Monte Carlo simulation than with the RISM result.     

Structure,hydrogen bonding and vibrational spectra of pyruvic acid

The complete vibrational spectra of liquid pyruvic acid and the infrared spectrum of crystalline pyruvic acid at about 20 K have been recorded and analyzed. A vibrational assignment is proposed based on these spectra and comparison with spectra of derivatives of pyruvic acid.The spectra of pyruvic acid can best be interpreted in terms of a cyclic hydrogen-bonded dimer structure in which the two carbonyl groups are in a trans configuration in the pure liquid phase. A similar structure has been reported for crystalline pyruvic acid by X-ray diffraction. In dilute solution the structure appears to be monomeric with an internal hydrogen bond, in essential agreement with the structures of the monomer reported from microwave spectroscopic measurements.     

Negative thermal expansion of water in hydrophobic nanospaces

The density and intermolecular structure of water in carbon micropores (w = 1.36 nm) are investigated by small-angle X-ray scattering (SAXS) and X-ray diffraction (XRD) measurements between 20 K and 298 K. The SAXS results suggest that the density of the water in the micropores increased with increasing temperature over a wide temperature range (20-277 K). The density changed by 10%, which is comparable to the density change of 7% between bulk ice (I(c)) at 20 K and water at 277 K. The results of XRD at low temperatures (less than 200 K) show that the water forms the cubic ice (I(c)) structure, although its peak shape and radial distribution functions changed continuously to those of a liquid-like structure with increasing temperature. The SAXS and XRD results both showed that the water in the hydrophobic nanospaces had no phase transition point. The continuous structural change from ice I(c) to liquid with increasing temperature suggests that water shows negative thermal expansion over a wide temperature range in hydrophobic nanospaces. The combination of XRD and SAXS measurements makes it possible to describe confined systems in nanospaces with intermolecular structure and density of adsorbed molecular assemblies.     

A quasichemical model for comb-like aggregation of monohydric alcohols: supramolecular structure and macroscopic properties

A new quasichemical model of the supramolecular structure of the liquid consisting of chain-like and comb-like hydrogen-bonded aggregates with branches of unit length has been developed. Analytical expressions for structural characteristics (size and structure distributions of aggregates), dielectric (permittivity, dipole correlation factor), optic (mean molecular anisotropy in liquid, optic correlation factor, anisotropic Rayleigh light scattering ratio) and thermodynamic (energy of intermolecular interactions in liquid, vaporisation enthalpy) properties of the liquid as functions of structural and thermodynamic aggregation parameters have been derived. The analytical model developed creates the foundation for studying the role of branched aggregates in the supramolecular structure of liquids and various macroscopic properties determined by different molecular parameters. The model is applied to pure methanol at ambient conditions. The dependence of structural characteristics of liquid, dipole correlation factor, permittivity, mean molecular anisotropy in liquid, vaporisation enthalpy on the equilibrium constants of chain-like and branched aggregation is studied. The results are compared with experimental data and computer simulation. The influence of branching degree of aggregates on different physicochemical properties of liquid is revealed and discussed.     

Molecular simulation of the high-pressure phase equilibria of binary atomic fluid mixtures using the exponential-6 intermolecular potential

Molecular simulation results using the exponential-6 intermolecular potential are reported for the phase behaviour of the atomic binary mixtures of neon+xenon, helium+neon, helium+argon and helium+xenon. These binary mixtures exhibit both vapour–liquid and liquid–liquid phase equilibria up to very high pressures. Comparison with experiment indicates good overall agreement. The results indicate that the exponential-6 intermolecular potential is a useful generic potential for molecular simulation.     

Environment-induced stabilization of hydrogen-bonded dimers in crystal of lysine (5-methyl-1H-[1,2,4]triazol-3ylsulfanyl)-acetate

Crystal and molecular structure of lysine (5-methyl-1H-[1,2,4]triazol-3-ylsulfanyl)-acetate was determined and intermolecular interactions between ions in crystal were investigated by quantum-chemical methods (MP2 and B3LYP-D). COSMO solvation method was used to account crystal field effects. While the gas-phase calculations significantly overestimate attraction between similarly charged and repulsion between oppositely charged ions, COSMO method provides results which are consistent with interaction energies estimated from AIM analysis of electron density distribution. Also, all hydrogen-bonded dimers found in crystal are intrinsically stable if modeled with COSMO method, contrary to gas phase calculations.     

The role of intermolecular hydrogen bond on dielectric properties in hydrogen-bonded material 5-bromo-9-hydroxyphenalenone: theoretical investigation

Dielectric properties of the hydrogen-bonded material, 5-bromo-9-hydroxyphenalenone (C(13)H(7)O(2)Br; BrHPLN), are investigated theoretically by means of electronic structure calculations and Monte Carlo simulations. The density functional calculations of BrHPLN crystals have revealed that the polarization per one molecule can be about 1.7 times larger than that of the isolated monomer. It is also found that there exists significant electron density (0.01 e bohr(-3)) in an intermolecular C-H···O region, which, together with the interatomic distances of 2.39 ? for H···O and 3.34 ? for C···O, suggests the existence of intermolecular weak hydrogen bonding that may enhance the molecular polarization. The induced polarization effects in various intermolecular configurations are evaluated with the Fragment Molecular Orbital method. In addition to the π-π stacking interactions, two types of "in plane" intermolecular weak hydrogen-bonding configurations are found to affect the molecular dipole moment most significantly. These effects are efficiently included in a Monte Carlo simulation method in terms of "dipole corrections" as functions of both the intermolecular arrangements and the intramolecular proton configurations. The application to the dielectric phase transition of a BrHPLN crystal shows that the dipole corrections almost double the transition temperature, toward better agreement with experiments, and qualitatively affect the temperature dependence of the dielectric constant. Discussions are given to support that the results will remain adequate and consistent even after explicit inclusion of the quantum tunneling effects.