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Register a new userA classical reactive potential for molecular clusters of sulphuric acid and water
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We present a two-state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent.
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We evaluate the grand potential of a cluster of two molecular species, equivalent to its free energy of formation from a binary vapour phase, using a nonequilibrium molecular dynamics technique where guide particles, each tethered to a molecule by a harmonic force, move apart to disassemble a cluster into its components. The mechanical work performed in an ensemble of trajectories is analysed using the Jarzynski equality to obtain a free energy of disassembly, a contribution to the cluster grand potential. We study clusters of sulphuric acid and water at 300 K, using a classical interaction scheme, and contrast two modes of guided disassembly. In one, the cluster is broken apart through simple pulling by the guide particles, but we find the trajectories tend to be mechanically irreversible. In the second approach, the guide motion and strength of tethering are modified in a way that prises the cluster apart, a procedure that seems more reversible. We construct a surface representing the cluster grand potential, and identify a critical cluster for droplet nucleation under given vapour conditions. We compare the equilibrium populations of clusters with calculations reported by Henschel et al. [J. Phys. Chem. A 118, 2599 (2014)] based on optimised quantum chemical structures.
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR relaxation times $T_{1,2}$ in the fast motion regime where $T_1 = T_2$ agree with measured (de-oxygenated) $T_2$ data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion $D_T$ coefficients calculated using simulation configurations are well-correlated with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.
We report on the successful synthesis and hyperpolarization of N unprotected {alpha} amino acid ethyl acrylate esters and extensively, on an alanine derivative hyperpolarized by PHIP (4.4$pm$1% $^{13}$C-polarization), meeting required levels for in vivo detection. Using water as solvent increases biocompatibility and the absence of N-protection is expected to maintain biological activity.
Room Temperature Ionic Liquids (RTILs) have attracted much of the attention of the scientific community in the past decade due the their novel and highly customizable properties. Nonetheless their high viscosities pose serious limitations to the use of RTILs in practical applications. To elucidate some of the physical aspects behind transport properties of RTILs, extensive classical molecular dynamics (MD) calculations are reported. Bulk viscosities and ionic conductivities of butyl-methyl-imidazole based RTILs are presented over a wide range of temperatures. The dependence of the properties of the liquids on simulation parameters, e.g. system size effects and choice of the interaction potential, is analyzed.
MOLSCAT is a general-purpose program for quantum-mechanical calculations on nonreactive atom-atom, atom-molecule and molecule-molecule collisions. It constructs the coupled-channel equations of atomic and molecular scattering theory, and solves them by propagating the wavefunction or log-derivative matrix outwards from short range to the asymptotic region. It then applies scattering boundary conditions to extract the scattering matrix (S matrix). Built-in coupling cases include atom + rigid linear molecule, atom + vibrating diatom, atom + rigid symmetric top, atom + asymmetric or spherical top, rigid diatom + rigid diatom, rigid diatom + asymmetric top, and diffractive scattering of an atom from a crystal surface. Interaction potentials may be specified either in program input (for simple cases) or with user-supplied routines. For the built-in coupling cases, MOLSCAT can loop over partial wave (or total angular momentum) to calculate elastic and inelastic cross integral sections and spectroscopic line-shape cross sections. Post-processors are available to calculate differential cross sections, transport, relaxation and Senftleben-Beenakker cross sections, and to fit the parameters of scattering resonances. MOLSCAT also provides an interface for plug-in routines to specify coupling cases (Hamiltonians and basis sets) that are not built in; plug-in routines are supplied to handle collisions of a pair of alkali-metal atoms with hyperfine structure in an applied magnetic field. For low-energy scattering, MOLSCAT can calculate scattering lengths and effective ranges and can locate and characterize scattering resonances as a function of an external variable such as the magnetic field.
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