Hydrogen bonding in liquid methanol, methylamine, and methanethiol studied by molecular-dynamics simulations (original) (raw)
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Hydrogen bond dynamics in liquid methanol
The Journal of Chemical Physics, 2003
A Car-Parrinello molecular dynamics simulation has been performed on fully deuterated liquid methanol. The results are compared with the latest available experimental and theoretical data. It is shown that the liquid is aggregated in chains of hydrogen bonded molecules. The structure of the aggregates is characterized and it is found that the dynamics includes a fast and a slow regime. The weak H bond formed by the methyl group hydrogens and oxygen atom of surrounding molecules has been characterized. The importance of inductive effects is shown and discussed in terms of maximally localized Wannier function centers. Special attention is devoted to clarify how the molecular dipole moment depends on the number of H bonds formed by each molecule. The IR spectrum is computed and analyzed in terms of H-bond interactions. Insights on the short time dynamics and on the H-bond network are illustrated.
Molecular dynamics simulations of water-methanol mixtures
Chemical Physics, 1991
Molecular dynamics simulations of two water-methanol mixtures with methanol mole fractions of 0.1 and 0.9 at room temperature have been performed. The interaction potentials are based on flexible three-site models for water and methanol. The structural changes relative to the pure solvents are demonstrated with the help of radial distribution functions and the geometrical arrangement of nearest-neighbor molecules. Differences in thermodynamic properties and in hydrogen bonding between the two mixtures and relative to the pure liquids are discussed. 0301-0104/91/% 03.50 0 1991 Elsevier Science Publishers B.V. All rights reserved.
Thermodynamic and structural properties of various models of liquid methanol are investigated in the framework provided by the reference interaction site model ͑RISM͒ theory of molecular fluids. The theoretical predictions are systematically compared with molecular dynamics simulations both at ambient conditions and along a few supercritical isotherms. RISM results for the liquid-vapor phase separation are also obtained and assessed against available Gibbs ensemble Monte Carlo data. At ambient conditions, the theoretical correlations weakly depend on the specific details of the molecular models and reproduce the simulation results with different degrees of accuracy, depending on the pair of interaction sites considered. The position and the strength of the hydrogen bond are quite satisfactorily predicted. RISM results for the internal energy are almost quantitative whereas the pressure is generally overestimated. As for the liquid-vapor phase coexistence, RISM predictions for the vapor branch and for the critical temperature are quite accurate; on the other side, the liquid branch densities, and consequently the critical density, are underestimated. We discuss our results in terms of intrinsic limitations, and suitable improvements, of the RISM approach in describing the physical properties of polar fluids, and in the perspective of a more general investigation of mixtures of methanol with nonpolar fluids of specific interest in the physics of associating fluids.
Hydrogen bond network topology in liquid water and methanol: a graph theory approach
Physical chemistry chemical physics : PCCP, 2013
Networks are increasingly recognized as important building blocks of various systems in nature and society. Water is known to possess an extended hydrogen bond network, in which the individual bonds are broken in the sub-picosecond range and still the network structure remains intact. We investigated and compared the topological properties of liquid water and methanol at various temperatures using concepts derived within the framework of graph and network theory (neighbour number and cycle size distribution, the distribution of local cyclic and local bonding coefficients, Laplacian spectra of the network, inverse participation ratio distribution of the eigenvalues and average localization distribution of a node) and compared them to small world and Erd + os-Rényi random networks. Various characteristic properties (e.g. the local cyclic and bonding coefficients) of the network in liquid water could be reproduced by small world and/or Erd + os-Rényi networks, but the ring size distribution of water is unique and none of the studied graph models could describe it. Using the inverse participation ratio of the Laplacian eigenvectors we characterized the network inhomogeneities found in water and showed that similar phenomena can be observed in Erd + os-Rényi and small world graphs. We demonstrated that the topological properties of the hydrogen bond network found in liquid water systematically change with the temperature and that increasing temperature leads to a broader ring size distribution. We applied the studied topological indices to the network of water molecules with four hydrogen bonds, and showed that at low temperature (250 K) these molecules form a percolated or nearly-percolated network, while at ambient or high temperatures only small clusters of four-hydrogen bonded water molecules exist. † Electronic supplementary information (ESI) available: : the fraction of bonds between molecules with different numbers of hydrogen bonds; : the histogram of the local bonding coefficient (r b ) for the investigated systems; : spectral density of the Laplace matrix for the investigated systems; : the histogram of the local cyclic coefficient (r c ) for the low-density patch of water at various temperatures (in K). See
Journal of Molecular Liquids, 2020
Methanol-water liquid mixtures have been investigated by high-energy synchrotron X-ray and neutron diffraction at low temperatures. We are thus able to report the first complete sets of both X-ray and neutron weighted total scattering structure factors over the entire composition range (at 12 different methanol concentrations (xM) from 10 to 100 mol%) and at temperatures from ambient down to the freezing points of the mixtures. The new diffraction data may later be used as reference in future theoretical and simulation studies. Measured data are interpreted by molecular dynamics simulations, in which the all atom OPLS/AA force field model for methanol is combined with both the SPC/E and TIP4P/2005 water potentials. Although the TIP4P/2005 water model was found to be somewhat more successful, both combinations provide at least semi-quantitative agreement with measured diffraction data. From the simulated particle configurations, partial radial distribution functions, as well as various distributions of the number of hydrogen bonds have been determined. As a general trend, the average number of hydrogen bonds increases upon cooling. However, the number of hydrogen bonds between methanol molecules slightly decreases with lowering temperatures in the concentration range between ca. 30 and 60 mol % alcohol content. The same is valid for water-water hydrogen bonds above 70 mol % of methanol content, from room temperature down to 193 K.
The effects of dispersion interactions on the dynamics of hydrogen bonds and vibrational spectral diffusion in liquid methanol are investigated through first principles simulations with a dispersion corrected density functional. Calculations are done at two different temperatures of 300 and 350 K and the results are compared with those of an earlier study where no such dispersion corrections were included. It is found that inclusion of dispersion interactions slightly increases the number of molecules held through non-hydrogen-bonded dispersion interactions in the neighborhood which, in turn, makes the dynamics faster. The inclusion of dispersion corrections gives rise to a faster hydrogen bond dynamics compared to the case when no such dispersion corrections are made. Also, the time scale of vibrational spectral diffusion obtained with the dispersion corrected density functional is found to be in better agreement with experiments.► Ab initio simulation study is performed on deuterated liquid methanol with dispersion corrected density functional. ► The structure, hydrogen bonds and vibrational frequencies are calculated at two different temperatures. ► Calculations are made for the dynamics of hydrogen bonds and frequency fluctuations. ► Vibrational spectral hole dynamics calculations are also performed for selected OD stretch modes. ► Effects of dispersion interactions on hydrogen bond dynamics and vibrational spectral diffusion are discussed.
The Journal of Physical Chemistry B
New X-ray and neutron diffraction experiments have been performed on ethanol−water mixtures as a function of decreasing temperature, so that such diffraction data are now available over the entire composition range. Extensive molecular dynamics simulations show that the all-atom interatomic potentials applied are adequate for gaining insight into the hydrogen-bonded network structure, as well as into its changes on cooling. Various tools have been exploited for revealing details concerning hydrogen bonding, as a function of decreasing temperature and ethanol concentration, like determining the H-bond acceptor and donor sites, calculating the cluster-size distributions and cluster topologies, and computing the Laplace spectra and fractal dimensions of the networks. It is found that 5-membered hydrogen-bonded cycles are dominant up to an ethanol mole fraction x eth = 0.7 at room temperature, above which the concentrated ring structures nearly disappear. Percolation has been given special attention, so that it could be shown that at low temperatures, close to the freezing point, even the mixture with 90% ethanol (x eth = 0.9) possesses a three-dimensional (3D) percolating network. Moreover, the water subnetwork also percolates even at room temperature, with a percolation transition occurring around x eth = 0.5.
Association effects in pure methanol via Monte Carlo simulations. I. Structure
The Journal of Chemical Physics, 2013
A methodology for the determination of the oligomers residing in a pure associated fluid was developed in the framework of the molecular simulation technique. Firstly, the number of hydrogen bonds between each pair of molecules of the fluid is computed by using a specific criterion to define the hydrogen bonding formation. Secondly, sets of molecules linked by hydrogen bonds are identified and classified as linear chains, cyclic aggregates, branched linear chains, branched cyclic aggregates and the rest of clustering. The procedure is applied over all the configurations produced in usual Monte Carlo simulations and allows the computation of the following properties characterizing the structure of the fluid: the fraction of molecules in the monomer or associated state, the fraction of each type of aggregate with a given size (and of molecules belonging to them), and the most probable and the average cluster size for each type. In addition, the degree of branching in branched linear chains and the type of ring in branched cyclic clusters can be obtained. In this work, all these quantities were computed for OPLS methanol using NpT Monte Carlo simulations at atmospheric pressure for 298.15 K (room conditions) and from 800 K to 350 K (gas phase), and along several supercritical isobars: 25, 50, 100, 200, and 500 MPa from 250 K to 1000 K. An analysis of the results has provided a comprehensive structural picture of methanol over the whole thermodynamic state space.