United Atom Approach Research Articles

New Force-Field for Organosilicon Molecules in the Liquid Phase.

In this paper, we present a new molecular model that can accurately predict thermodynamic liquid state and phase-change properties for organosilicon molecules including several functional groups (alkylsilane, alkoxysilane, siloxane, and silanol). These molecules are of great importance in geological processes, biological systems, and material science, yet no force field currently exists that is widely applicable to organosilicates. The model is parametrized according to the recent Polarization-Consistent Approach (PolCA), which allows for polarization effects to be incorporated into a nonpolarizable model through post facto correction terms and is therefore consistent with previous parametrizations of the PolCA force field. Alkyl groups are described by the United-Atom approach, bond and angle parameters were taken from previous literature studies, dihedral parameters were fitted to new quantum chemical energy profiles, point charges were calculated from quantum chemical optimizations in a continuum solvent, and Lennard-Jones dispersion/repulsion parameters were fitted to match the density and enthalpy of vaporization of a small number of selected compounds. Extensive validation efforts were carried out, after careful collection and curation of experimental data for organosilicates. Overall, the model performed quite well for the density, enthalpy of vaporization, dielectric constant, and self-diffusion coefficient, but it slightly overestimated the magnitude of self-solvation free energies. The modular and transferable nature of the PolCA force field allows for further extensions to other types of silicon-containing compounds.

Molecular dynamics simulation of amorphous polyethylene (PE) under cyclic tensile-compressive loading below the glass transition temperature

The intensive applications of polymer in many engineering composites have imposed an urgent need on the understanding of the mechanical behavior and deformation mechanism of the polymer under cyclic loading. This paper presents the results of a numerical study on the behavior of amorphous polyethylene (PE) subjected to cyclic tensile and compressive loads using molecular dynamics (MD) simulations, based on a united-atom approach. The effects of polymer chain length, the number of chains and strain rates are studied at first. Hysteresis loops, as well as visco-elastoplastic of PE under cyclic loading predicted by MD simulations are qualitatively in agreement with previous experiments. Three distinct hysteresis loops observed in successive loading-unloading reveal the contribution of elasticity, viscosity and plasticity under different loading strains, respectively. The rubber-like recovery behavior of PE at low temperature is attributed to that the mobility of molecular chains is constrained at low temperature. Energy analysis shows that the van der Waals energy and dihedral angle energy are considered to be the primary factors that affects the cyclic behavior of PE.

Structural Properties of Span 80/Tween 80 Reverse Micelles by Molecular Dynamics Simulations.

The sorbitan monooleate (Span 80)/poly(oxyethylene) sorbitan monooleate (Tween 80) reverse micelles (RMs) in the water-in- n-decane microemulsion were studied using the molecular dynamics simulation. The coexistence of the large RMs with the hydrodynamic radii Rh ∼ 10-20 nm and small RMs with Rh ∼ 1-2 nm was previously specified for this system. Models of both surfactants and decane were based on the united-atom approach to allow us to describe the structural properties of the small RMs. The micelles have been self-assembled from an initially homogeneous mixture of surfactant, water, and decane molecules. The dependence of the shape of the RMs on the relative content of surfactants has been established. The inner structure of Span 80, Tween 80, and Span 80/Tween 80 RMs was quantitatively described. Tween 80 molecules penetrate the water core, whereas Span 80 molecules are located on the surface of the RM. The obtained data show that the hydrogen bonds are formed between the surfactant molecules on the surface of the RM and play an important role in the formation of RMs. The water hydrogen bond density distribution in individual and mixed RMs explains the advantages of the mixed surfactant system compared to an individual surfactant.

Predicting hydrophobic solvation by molecular simulation: 2. New united-atom model for alkanes, alkenes, and alkynes.

Existing united-atom models for non-polar hydrocarbons lead to systematic deviations in predicted solvation free energies in hydrophobic solvents. In this article, an improved set of parameters is proposed for alkane molecules that corrects this systematic deviation and accurately predicts solvation free energies in hydrophobic media, while simultaneously providing a very good description of pure liquid densities. The model is then extended to alkenes and alkynes, again yielding very accurate predictions of solvation free energies and densities for these classes of compounds. For alkynes in particular, this work represents the first attempt at a systematic parameterization using the united-atom approach. Averaging over all 95 solute/solvent pairs tested, the mean signed deviation from experimental data is very close to zero, indicating no systematic error in the predictions. The fact that predictions are robust even for relatively large molecules suggests that the new model may be applicable to solvation of non-polar macromolecules without accumulation of errors. The root mean squared deviation of the simulations is only 0.6 kJ/mol, which is lower than the estimated uncertainty in the experimental measurements. This excellent performance constitutes a solid basis on which a more general model can be parameterized to describe solvation in both polar and non-polar environments. © 2016 Wiley Periodicals, Inc.

On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation.

We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with experimental data. The three CG models predict reasonably well (but only qualitatively) the surface tension of THF, as a function of temperature, from the triple point to the critical temperature. On the other hand, only the TraPPE united-atoms models are able to predict accurately the experimental surface tension of the system in the whole temperature range.

Transferable Anisotropic United-Atom Force Field Based on the Mie Potential for Phase Equilibrium Calculations: n-Alkanes and n-Olefins.

A new transferable force field parametrization for n-alkanes and n-olefins is proposed in this work. A united-atom approach is taken, where hydrogen atoms are lumped with neighboring atoms to single interaction sites. A comprehensive study is conducted for alkanes, optimizing van der Waals force field parameters in 6 dimensions. A Mie n-6 potential is considered for the van der Waals interaction, where for n-alkanes we simultaneously optimize the energy parameters ϵCH3 and ϵCH2 as well as the size parameters σCH3 and σCH2 of the CH3(sp(3)) and CH2(sp(3)) groups. Further, the repulsive exponent n of the Mie n-6 potential is varied. Moreover, we investigate the bond length toward the terminal CH3 group as a degree of freedom. According to the AUA (anisotropic united-atom) force field, the bond length between the terminal CH3 group and the neighboring interaction site should be increased by Δl compared with the carbon-carbon distance in order to better account for the hydrogen atoms. The parameter Δl is considered as a degree of freedom. The intramolecular force field parametrization is taken from existing force fields. A single objective function for the optimization is defined as squared relative deviations in vapor pressure and in liquid density of propane, n-butane, n-hexane, and n-octane. A similar study is also done for olefins, where the objective function includes 1-butene, 1-hexene, 1-octene, cis-2-pentene, and trans-2-pentene. Molecular simulations are performed in the grand canonical ensemble with transition-matrix sampling where the phase equilibrium properties are obtained with the histogram reweighting technique. The 6-dimensional optimization of strongly correlated parameters is possible, because the analytic PC-SAFT equation of state is used to locally correlate simulation results. The procedure is iterative but leads to very efficient convergence. An implementation is proposed, where the converged result is not affected (disturbed) by the analytic equation of state. The resulting transferable anisotropic Mie-potential (TAMie) force field shows average relative deviations in vapor pressure of 1.1% and in liquid density of 0.9% for alkanes, and 2% and 1.5% for olefins, respectively, in a wide range of (reduced) temperature, Tr = 0.55-0.97. For substances that were not members of the objective function, the TAMie force field enables predictions of phase equilibrium properties with good accuracy.

Lennard-Jones force field parameters for cyclic alkanes from cyclopropane to cyclohexane

Lennard-Jones (LJ) force field parameters for cyclic alkanes from cyclopropane to cyclohexane are proposed. The molecular geometry is obtained from quantum mechanical calculations. The united-atom approach is applied by initially locating each site at the carbon atom position and subsequently changing the site–site distance; thereby, the LJ parameters and the site–site distance are optimized to vapor–liquid equilibrium (VLE) data, i.e., vapor pressure, saturated liquid density and enthalpy of vaporization. These new cycloalkane force fields are able to describe the VLE data with deviations of a few percent. Furthermore, self-diffusion coefficient, shear viscosity and thermal conductivity are calculated by molecular dynamics simulation and the Green–Kubo formalism. For the smaller two cycloalkanes, i.e., cyclopropane and cyclobutane, the predicted transport properties are in good agreement with the available experimental data. However, the force fields for cyclopentane and cyclohexane specified in this way do not predict transport properties with the desired accuracy. Therefore, they are re-optimized to experimental data on VLE properties and self-diffusion coefficient simultaneously. Then, also the other transport properties meet the experimental data well.

Improving Far UV Circular Dichroism Calculations of Peptides and Proteins with the Dipole Interaction Model

The dipole interaction model (assembled into the computer package DInaMo) uses a classical electromagnetic theory for calculating the far UV circular dichroism (CD) of peptides and proteins. DInaMo reduces all amide chromophores to a single point with anisotropic polarizability and all nonchomophoric aliphatic atoms to points with isotropic polarizability. By determining interactions among the chomophoric and nonchromoporic parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Polarizabilities are largest for the chromophoric points and smaller for the nonchromophoric points with hydrogens having the smallest polarizabilities. It is possible to collapse hydrogen polarizability onto the atom to which it is bound or ignore it in the CD calculation creating a united atom approach. Ignoring CH3 group hydrogens and treating only the π-π∗ transition reproduces experiment in the region of 180 to 210 nm well, showing bands with similar morphology and absorption maxima for the π-π∗ transition. Recent calculations on small peptides and proteins in which both CH3 and CH2 group hydrogens have been ignored seem to produce better CD results than ignoring only the CH3 group hydrogens. Also, preliminary calculations using the mean polarizability values of the CH3 and CH2 groups show some good prospects of further improving the CD calculations with the DinaMo package. In addition, initial calculations indicate that DInaMo has the potential of including the n-π∗ transition in the CD calculations.

Molecular dynamics simulations of strain-controlled fatigue behaviour of amorphous polyethylene

Fatigue of amorphous polyethylene under low strain was simulated using molecular dynamics. The united atom approach and the Dreiding force field were chosen to describe the interaction between monomers. Molecular dynamics simulations resembling strain-controlled loading fatigue tests in tension-tension mode were performed to study the effect of the R-ratio and mean strain on the mechanical responses. Laboratory fatigue experiments in strain/displacement control were performed at room temperature, and the results were compared to the simulation results. The simulations are able to produce qualitatively similar behaviour to the experimental results, for instance, mean stress relaxation, hysteresis loops in the stress–strain curve, and change in the cyclic modulus. They also show that stress relaxation is enhanced by cyclic loading. The simulations show that cyclic loading changes the total potential energies of the system, especially the van der Waals potential. The changes in the van der Waals potential energy contribute significantly to the increasing of the stiffness of the system. Some changes in dihedral angles with lower energy configurations are observed; however, bond distances and angles do not change significantly. The chains tend to unfold slightly along the loading axis as the fatigue loading progresses.

Computing Theoretical Circular Dichroism of Proteins using the Dipole Interaction Model (DINAMO) with a United Atom Approach

The dipole interaction model is a classical electromagnetic theory for calculating the π-π∗ transitions of peptides and proteins. DInaMo reduces all amide chromophores to single points with anisotropic polarizability and all nonchromophoric aliphatic atoms to points with isotropic polarizability; all other atoms are ignored. By determining interactions among the chromophoric and nonchromphoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of the CD spectrum for each molecule. DInaMo software is being modified to reduce computational demand by collapsing hydrogens into the atoms to which they are bound (i.e., united atom). Crystal structures of proteins containing less than 300 residues are energy minimized using NAMD. Hydrogens attached to various groups (e.g., CH3, CH2, or CH groups) are then deleted programmatically. Deleted hydrogen polarizabilities are either ignored or added to the atom to which they are bound. Theoretically predicted CD for a variety of proteins (26 different structures, examples pictured below) are compared with synchrotron radiation CD data. Theory agrees with experiment showing bands with similar morphology and absorption maxima for the π-π∗ transitions.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Equilibrium and Transport Properties of Primary, Secondary and Tertiary Amines by Molecular Simulation

Using molecular simulation techniques such as Monte Carlo (MC) and molecular dynamics (MD), we present several simulation results of thermodynamic and transport properties for primary, secondary and tertiary amines. These calculations are based on a recently proposed force field for amines that follows the Anisotropic United Atom approach (AUA). Different amine molecules have been studied, including <i>n<i/>-ButylAmine, di-<i>n<i/>-ButylAmine, tri-<i>n<i/>-ButylAmine and 1,4-ButaneDiAmine for primary, secondary, tertiary and multi-functional amines respectively. For the transport properties, we have calculated the viscosity coefficients as a function of temperature using the isothermal-isobaric (NPT) ensemble. In the case of the pure components, we have investigated different thermodynamic properties using NVT Gibbs ensemble simulations such as liquid-vapor phase equilibrium diagrams, vaporization enthalpies, vapor pressures, normal boiling points, critical temperatures and critical densities. We have also calculated the excess enthalpies for water-<i>n<i/>-ButylAmine and <i>n<i/>-heptane-<i>n<i/>-ButylAmine mixtures using Monte Carlo simulations in the NPT ensemble. In addition, we present the calculation of liquid-vapor surface tensions of <i>n<i/>-ButylAmine using a two-phase NVT simulation as well as the radial distribution functions. Finally, we have investigated the physical Henry constants of nitrous oxide (N<sub>2<sub/>O) and nitrogen (N<sub>2<sub/>) in an aqueous solutions of <i>n<i/>-ButylAmine. In general, we found a good agreement between the available experimental information and our simulation results for all the studied properties, ratifying the predictive capability of the AUA force field for amines.

Theoretical investigation of the phase behaviour of mixtures of a novel family of perfluoroalkyl–polyoxyethylene ether diblock surfactants in aqueous solutions of carbon dioxide

The accurate knowledge of the thermodynamic properties, with special emphasis on phase equilibria, of aqueous solutions of carbon dioxide is essential from practical and theoretical points of view. These aqueous mixtures are of great interest in different industrial processes, including its use as supercritical solvents, CO 2 sequestration technologies and oil enhanced recovery, among many different applications. From a theoretical point of view, this mixture exhibits a variety of interactions, including dispersive forces, hydrogen bonding between water molecules, and also dipolar and quadrupolar electrical interactions, which determine its phase behaviour. In particular, the mixture exhibits type III phase behaviour, which leads to large regions of liquid–liquid immiscibility. In a number of practical situations, it is important to make miscible this mixture. This can effectively be done by adding some amount of a selected surfactant that stabilizes the mixture. An ideal candidate would be a surfactant formed by hydrophilic and CO 2-philic parts that interact favourably with water and carbon dioxide molecules, respectively. In this work we study a novel family of diblock amphiphiles, the perfluoroalkyl–polyoxyethylene ether non-ionic diblock surfactants, which have the general formula F(CF 2) i (OCH 2CH 2) j OH or simply F i E j . We employ the sophisticated and versatile Statistical Associating Fluid Theory for potentials of variable range, the so-called SAFT-VR approach, to study the phase behaviour of aqueous solutions of carbon dioxide and the novel surfactants. All molecules are modeled under the united-atom approach, in which different chemical groups are treated as hard-sphere attractive segments. The F i E j surfactant is modelled as a diblock compound, which consists of a perfluorinated alkane chain and a polyoxyethylene ether chain. The optimized molecular parameters for H 2O, CO 2, and the perfluoroalkyl, polyoxyethylene ether and the rest of chemical groups forming the surfactant are taken from previous works from the literature. Unlike interactions between different chemical groups are carefully chosen to reproduce the phase behaviour of similar associating surfactants previously studied in the literature. In this work we study the effect of temperature, pressure and composition of a selection of mixtures to understand the microscopic conditions that determine the stabilization of aqueous solutions of carbon dioxide when this kind of surfactants are added. To our knowledge, this is the first time the phase behaviour of mixtures containing this kind of surfactants is studied using a microscopic modelling approach.

An approach towards understanding the structure of complex molecular systems: the caseof lower aliphatic alcohols

An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applyingreverse Monte Carlo modelling as a method of interpretation of diffraction data, ispresented. The emphasis is on the evaluation of several computational strategies in view oftheir suitability to obtain high quality molecular models via the reverse Monte Carloprocedure. A consistent set of distances of closest approach and fixed neighbour constraintsapplicable to all three investigated systems was developed. An all-atom description iscompared with a united-atom approach. The potentialities of employment of neutrondiffraction data of completely deuterated and isotopically substituted samples, x-raydiffraction data, and results of either molecular dynamics or Monte Carlo calculationswere investigated. Results show that parallel application of x-ray and neutrondiffraction data, the latter being from completely deuterated samples, within anall-atom reverse Monte Carlo procedure is the most successful strategy towardsattaining reliable, detailed, and well-structured molecular models, especially if themodels are subsequently refined with the results of molecular dynamics simulations.

Evaluation of cross sections for Lα x-ray production by up to 4 MeV protons in representative elements from silver to uranium

Over the last two decades, Lα x-ray production cross sections have been fitted with a number of empirical formulae. Cross sections obtained from these formulae are averaged and fitted to a new empirical formula. These new empirical cross sections are compared with the results of the plane-wave Born approximation and the ECPSSR theory of Brandt and Lapicki (1981 Phys. Rev. A 23 1717). They are also gauged by the ECPSSR theory that has been corrected with a united atom approach in slow collisions, evaluated with Dirac–Hartree–Slater instead of screened hydrogenic wavefunctions, modified for intra-shell couplings as well as the change of the atomic parameters due to multiple ionizations. The effects of appropriately normalized intra-shell coupling factors and of multiple ionization were found to be small and essentially offset each other. The role of different sets of atomic parameters in conversion of the predictions of these ionization theories for Lα x-ray production in elements from the 47 ⩽ Z2 ⩽ 92 range of target atoms bombarded by up to 4 MeV protons is examined, and the selection of the optimal combination of ionization theory and atomic parameters for a reliable data base for PIXE analysis of elements heavier than palladium is discussed.

Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations.

The energy and its first and second geometrical derivatives obtained by DFT calculations for a number of conformations of a single molecule are used to parametrize intramolecular force fields, suitable for computer simulations. A systematic procedure is proposed to adequately treat either fully atomistic or more simplified force fields, as within the united atom approach or other coarse grained models. The proposed method is tested and validated by performing molecular dynamics simulations on several different molecules, comparing the results with literature force fields and relevant experimental data. Particular emphasis is given to the united atom approach for flexible molecules characterized by "soft" torsional potentials which are known to retain a high degree of chemical specificity.

Probing Molecular Structure at Interfaces for Comparison with Bulk Solution Behavior: Water/2-Propanol Mixtures Monitored by Vibrational Sum Frequency Spectroscopy

The orientation of the isopropyl group at the liquid/vapor interface in 2-propanol/water binary mixtures was studied by vibrational sum frequency spectroscopy. The CH(3) stretch modes of the two methyl groups were used to determine the molecule's orientation by employing a novel united atom approach to model the (CH(3))(2)X moiety. For this purpose, the changes in the molecular susceptibility of the isopropyl group stretches were derived in the laboratory frame as a function of the tilt and twist angles. The results indicated that the methyl groups lay down on the surface at low alcohol mole fraction and gradually twisted with increasing mole fraction. At the azeotrope, x(iso) = 0.68, one of the methyl groups aligned approximately parallel to the surface normal, whereas the other was nearly parallel with the liquid/vapor interface. When the mole fraction of 2-propanol was higher than 0.68, the orientation of 2-propanol remained almost constant. The change in the alcohol's orientation with 2-propanol mole fraction closely tracked changes in its bulk activity coefficient. Such results lead to a picture in which the surface structure and bulk properties of the system are closely linked.

Single-file motion of polyatomic molecules in one-dimensional nanoporous materials

In a continuation of the study of the mobility of fluids adsorbed in nanoporous materials, molecular dynamics simulations are used to investigate the behaviour of polyatomic ethane molecules adsorbed in AlPO4-5. The current work is based on the use of the united atom approach as a better model than the single-centre ethane used to date. Ethane molecules are modelled as rigid diatoms, and as a result the molecules have more degrees of freedom in the form of the rotational components that are absent in the single-centre ethane model. This represents a more sophisticated model for ethane and is used in the simulations to test earlier findings. Simulations with binary mixtures of methane and ethane also have been conducted with three mixture compositions. The transition from ordinary diffusion to single-file motion for a finite residence time is found to occur at a methyl group diameter of 4.75 Å. This is identical to the ethane diameter in the earlier study. Thus, only the minimum dimension determines the transition size. Also it is shown that the diatomic molecules undergo free rotation within the channel even when they are in the single-file mode of motion. In the case of binary mixtures, the methane molecules still undergo ordinary diffusion. Ethane molecules exhibit single-file motion at a methyl group diameter of 4.75 Å. The diffusion coefficient of methane decreases with increasing ethane size, while the trends in the single-file mobility of ethane as a function of methyl group diameter are nonlinear.

Trapping dynamics of isobutane, n-butane, and neopentane on Pt(111): Effects of molecular weight and structure

The molecular adsorption dynamics of isobutane, n-butane, and neopentane on Pt(111) was investigated using supersonic molecular beam techniques and stochastic trajectory calculations. Using the united atom approach, a single, pairwise-additive Morse Potential for methyl (methylene)–plantinum interactions quantitatively simulates the dependence of the initial trapping probability, α, on the initial translational energy, ET, and angle of incidence, θi, for each alkane. For both isobutane and n-butane, the dependence of α on ET and θi best scales with ET cos0.8θi, which is similar to that found previously for ethane and propane trapping on Pt(111). The initial trapping probability of neopentane exhibits a more pronounced dependence on θi, which scales according to ET cos1.3θi. The simulations suggest that the enhanced angular dependence of α for neopentane is related to its molecular weight. As the mass of the incident species is increased, momentum transfer to the surface becomes more efficient than the interconversion of incident parallel and normal momentum due to corrugation of the surface potential. The net effect is an increase in the trapping probability at glancing incidence compared to lighter molecules, and a resulting shift in the angular dependence of α towards normal energy scaling. The calculations also predict that collisional energy transfer to rotation is important in promoting adsorption. For each molecule, rotational excitation is determined to be the most effective energy transfer process that discriminates trapping from scattering. In addition, translational energy transfer to torsional vibration about the central C–C bond is highly efficient for n-butane, and greatly facilitates adsorption. Less excitation is predicted for C–C–C bending modes for all of these molecules.

Computer simulation of liquid tetramethylurea and its aqueous solution

Thermodynamic properties and correlation functions for the pure liquid 1,1,3,3-tetramethylurea (TMU) and its aqueous solution were obtained by Monte Carlo simulation in the isothermic and isobaric (NPT) ensemble at 25°C and 1.0 atm. An eight site potential model combining Lennard-Jones plus coulombic functions was developed to calculate intermolecular interaction between TMU molecules. In this model the methyl groups are represented by a united atom approach. The partial charges needed for Coulomb interactions and the geometry of the TMU molecule were calculated at the HF level using a 6-31g* basis set with the CHELPG formalism. The parameters needed for the Lennard-Jones potential functions were optimised to reproduce experimental values for the density and enthalpy of vaporisation of the pure liquid at 298 K and 1.0 atm. The results obtained for density, enthalpy of vaporisation and other thermodynamic properties for the pure liquid TMU are in good agreement with experimental data. Radial distribution functions (rdf) obtained for liquid TMU are broad indicating a low degree of molecular organisation. Dipole–dipole correlation shows a preference for anti-parallel molecular orientation at short distances. Therefore, the present results are consistent with experimental data indicating the formation of dimers due to dipole–dipole interaction. A further test for the potential model was also provided by studying the hydration of TMU on TIP4P water. Potential functions for water–TMU intermolecular interaction were obtained by standard combining rules. The value obtained for the free energy of hydration using statistical perturbation theory was ΔG=-16.82 kJ mol-1, to be compared with the value ΔG=-56.48 kJ mol-1 obtained for urea. Radial distribution functions for water–TMU interaction show features indicating hydrogen bonding between the TMU oxygen site and hydrogen of water. Compared to pure water, our results shows that the water–TMU hydrogen bonding is more stable. The results also show that in dilute TMU–water solution the influence of TMU on the energetics of water–water hydrogen bonding is negligible. Contrasting with gas phase results for the TMU–water dimer the present results do not indicate the formation of hydrogen bonding interaction with the nitrogen site of TMU in aqueous solution. This finding is in agreement with previous hydration studies of dimethylformamide and also with the hydrophobic behaviour of TMU observed in experiments. Dipole–dipole correlation results obtained for TMU and water molecules in the water–TMU solution exhibit significant differences when compared to the ones for the pure liquids.

Temperature dependence of the properties of simulated PCH5

We present the results of molecular dynamics simulation studies of 4-(trans-4'-pentylcyclohexyl)- benzonitrile (PCH5) at different temperatures in the isotropic and nematic phases within the united atom approach. Special attention is paid to the electrostatic interactions. Different methods of determining point charges are compared and the effect of the electrostatic interactions on the molecular distribution is considered. Their decisive influence on local molecular packing and phase transition temperature is shown. We analyse various static and dynamic properties, being specially interested in the reliability of the simulation results, to check to which extent they are distorted by the confinements adopted during the simulations (and especially the size of the system). Using realistic molecular interaction models in contrast to simple model ellipsoids, we find that the number of molecules and the lengths of the simulation runs have to be increased considerably when studying macroscopic properties like the phase transition temperature and the order parameter. Much easier to access are single particle and local properties such as translational dynamics and local ordering, but also the relative dependence of the order parameters of various ranks.