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Over wide temperature and pressure ranges, the molecular dynamics simulation is performed to study the mass transfer of six n-alkanes from n-C5H12 to n-C10H22 in CO2 at infinite dilution by calculating the diffusion coefficients, which have not yet been measured by experiment. Meanwhile, the structural properties of these systems are explored. It is found that under different temperature and pressure conditions, the variation trends of the radial distribution functions of n-alkanes are quite different, while the variation trends of the average coordination number of n-alkanes can be divided into three types. The radius of gyration and the solvent accessible surface area are both affected by temperature and carbon chain length, but their variation trends are different, and it could explain the abnormal variation trends of the radial distribution functions and the average coordination number. [ABSTRACT FROM AUTHOR]

The diffusion coefficients of 14 n-alkanes (ranging from methane to n-tetradecane) in liquid and supercritical methanol at infinite dilution (at a pressure of 10.5 MPa and at temperatures of 299 K and 515 K) were deduced via molecular dynamics simulations. Values for the radial distribution function, coordination number, and number of hydrogen bonds were then calculated to explore the local structure of each fluid. The flexibility of the n-alkane (as characterized by the computed dihedral distribution, end-to-end distance, and radius of gyration) was found to be a major influence and hydrogen bonding to be a minor influence on the local structure. Hydrogen bonding reduces the flexibility of the n-alkane, whereas increasing the temperature enhances its flexibility, with temperature having a greater effect than hydrogen bonding on flexibility. [ABSTRACT FROM AUTHOR]

Infinite dilute diffusion coefficients ( D 12 ) of normal alkanes (C1 to C14) in 1-octanol (C8-OH), as well as primary alkanols (C1-OH to C14-OH) in n-octane (C8) have been studied using molecular dynamics simulation in the temperature range from 298 to 374 K and at atmosphere pressure. Simulated D 12 values for short-chain solute molecules show a good agreement with the experimental ones taken from literature, while for the long-chain solute molecules the overestimation is large. Besides, the structures of solute molecules in above fluid mixtures are investigated by calculating radial distribution functions, radius of gyration, end-to-end distance, and root mean square fluctuation of atomic positions. These results confirm long-chain n -alkanes and n -alkanols molecules are curved and curled up, which we call it flexibility. Moreover, flexibilities for solute molecules (5 ≤ n ≤ 9) are symmetric but for much long-chain solute molecules like n-tetradecane (C14) and 1-tetradecanol (C14-OH) are asymmetric. We believe that strong chain-chain interactions are existed between different long-chain molecules, and it will result in the solute and solvent molecules are intertwisted. The serious overestimation of simulated D 12 for long-chain solute molecules can be reasonably explained by the intertwist effect. [ABSTRACT FROM AUTHOR]

Self-diffusion of methanol, ethanol, 1-propanol and 2-propanol has been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 478 K at pressures up to 300 MPa. The simulation results on self-diffusion of methanol, ethanol and 2-propanol (for 2-propanol, at high temperatures) agree well with experiment, which suggests that the simulation method is a powerful tool to obtain self-diffusion coefficients over wide range of temperature and pressure, under which it is rather difficult for experiments. The local structures of methanol, ethanol and 2-propanol are investigated by calculating the radial distribution functions, H-bond numbers, coordination numbers and the ratios of H-bond number divided by coordination number. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The degree of forming H-bond space network in methanol, ethanol and water is higher than that in 2-propanol, and they are all higher than those in ammonia and methylamine. The simulation results demonstrate that the effect of hydrogen bonding on the translational dynamics in methanol and ethanol is more pronounced than that in 2-propanol. [ABSTRACT FROM PUBLISHER]

The diffusion coefficients of n-alkanes (fromCH4to C14H30) in near critical andsupercritical carbon dioxide at infinite dilution have been studiedby molecular dynamics simulation. The simulation results agree wellwith experiment, which suggests that the simulation method is a powerfultool to obtain diffusion coefficients of solutes in fluids at highpressures. The local structures of such fluids are further investigatedby calculating radial distribution functions and coordination numbers.Meanwhile, the dihedral, end-to-end distance and radius of gyration,which are calculated to characterize the flexibility of n-alkanes, are used to reasonably explain the abnormal trends on radialdistribution functions and coordination numbers. Moreover, it is foundthat the flexibility effects on diffusion in pure n-alkanes and infinitely dilute n-alkane/CO2system are different. The differences in MD simulation results ofmolecular diffusion in such systems could be qualitatively explainedby the flexibility. [ABSTRACT FROM AUTHOR]

The various interactions occurring between pyrrole and benzene are a particularly appropriate model, as they are viewed as better X-H···π examples. A combined and sequential use of Quantum Mechanical (QM) calculations and Molecular Dynamics (MD) simulations was applied to investigate the different intermolecular interactions for benzene and pyrrole as clusters and its liquid mixture. All the cluster structures were fully optimized by the B2PLYP-D methods (including dispersion correction) with jun-cc-pVTZ (a revised aug-cc-pVTZ basis set). MD simulation with OPLS-AA force field was used to study the liquid mixture of benzene/pyrrole at different temperatures. Two types of N-H···π hydrogen bonds are preferred interactions compared with C-H···π interactions, either as clusters or as its liquid mixture. Based on the QM results, we clarify the difference in red-shifts of N-H bond of N-H···π hydrogen bonds observed by Jet FT-IR (Phys Chem Chem Phys 10: 2827, ). Meanwhile, the nature of various X-H···π interactions is unveiled by atoms in molecules (AIM), natural bond orbital and energy decomposition analysis (EDA). Furthermore, in light of QM results, MD simulation results further characterize the behavior and structural properties of these interactions. Finally, we proposed an original idea to explain the strength variation of different N-H···π hydrogen bond in liquid mixture based on AIM and EDA analysis. Graphical Abstract: [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

A combined and sequential use of quantum mechanical (QM) calculations and classical molecular dynamics (MD) simulations was made to investigate the σ and π types of hydrogen bond (HB) in benzene-water and pyrrole-water as clusters and as their liquid mixture, respectively. This paper aims at analyzing similarities and differences of these HBs resulted from QM and MD on an equal footing. Based on the optimized geometry at ωb97xD/aug-cc-pVTZ level of theory, the nature and property of σ and π types of HBs are unveiled by means of atoms in molecules (AIM), natural bond orbital (NBO) and energy decomposition analysis (EDA). In light of the above findings, MD simulation with OPLS-AA and SPC model was applied to study the liquid mixture at different temperatures. The MD results further characterize the behavior and structural properties of σ and π types HBs, which are somewhat different but reasonable for the clusters by QM. Finally, we provide a reasonable explanation for the different solubility between benzene/water and pyrrole/water. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Self-diffusion and structural properties of n-alkanes have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 600 K at pressures up to 300 MPa. The simulated results of lower n-alkanes are in good agreement with the existing experimental data, and support the reliability of results of the simulations of self-diffusion coefficients obtained at the extreme conditions. We predict the self-diffusion coefficients for methane, ethane, propane and n-butane at the similar reduced temperatures and pressures to draw a comparison between them. Then the correlation between self-diffusion and structural properties are further investigated by calculating the coordination numbers. Moreover, we define four distances and their corresponding relative deviations to characterize the flexibility of long-chain n-alkanes. The simulated results show that the self-diffusion of n-alkane molecules is mainly affected by the close packing, and the flexibility has a strong impact on the self-diffusion of longer n-alkane molecules. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

The N–H ··· π H-bond interactions of clusters and liquid formed by pyrrole molecules were investigated by Quantum Mechanics (QM) and classical Molecular Dynamics (MD), respectively. Based on the optimized geometry at the B97-D/aug-cc-pVTZ level of theory including dispersion correction, the nature and the origin of N–H ··· π H-bond interactions were unveiled by atoms in molecules (AIM), natural bond orbital (NBO), and energy decomposition analysis (EDA). Among them, the AIM analysis gives evidence to the presence of N–H ··· π H-bond interactions, the NBO examination reveals that π → σ* donor-acceptor orbital interaction is of great importance. EDA study indicates that N–H ··· π interactions are governed by the electrostatic and dispersion term. Meanwhile, MD simulation with OPLS-AA (optimized potentials for liquid simulations all-atom) was applied to study the pure liquid pyrrole at different temperature. The results confirm the existence of the N–H ··· π H-bond in the pure liquid pyrrole, and further characterized the structures of this H-bond which is somewhat different to the clusters. [ABSTRACT FROM AUTHOR]