Theoretical study of the acetic acid dimer, its microhydration and its behavior in water and chloroform solution
was performed. To characterize the system, we adopted ab initio methods at the DFT and RI MP2 (the resolution
of the identity approximation MP2) levels for the gas-phase calculations, PCM (polarizable continuum model)
approximation using the polarizable conductor calculation model (COSMO) for description of solvent, and
constant energy (NVE) and constant temperature (NVT) molecular dynamics simulations for gas phase and
explicit solvent calculations, respectively. The cyclic structure of the acetic acid dimer is the most stable in
the gas phase only. During microhydration, the water molecules are incorporated in the dimer leading to
water-separated structures. This conclusion is based on ab initio quantum chemical calculations, as well as
on molecular dynamics simulations. The fact that the cyclic structure does not appear in water solution is in
agreement with previous theoretical and experimental results. Extending the search also on other acetic acid
dimer structures, we concluded that acetic acid does not form any dimer structure in water solution. The
cyclic structure is also supposed to be stable in chloroform solution.
Rotating polar linker groups in the cubic metal-organic framework single crystal known as IRMOF-2 were investigated for freedom of motion, response to an external electric field, and effects of dipole-dipole interactions. The crystals consist of octahedrally coordinated zinc oxide clusters linked by the bromoterephthalate group, which contains a rotatable bromo-p-phenylene moiety. We confirmed the rotation by dielectric spectroscopy and found a 7.3 kcal mol(-1) barrier. The non-polar analog, IRMOF-1, containing terephthalic acid, was used as a control system. DFT and MP2 computations of the rotational barrier yield results in agreement with the observation, with B3LYP/SDD being the best. A Monte Carlo analysis of the equilibrium polarization fluctuations was used to assess the possibility of polar ordering and the potential for electro-optic applications.
Different integrator time steps in NVT and NVE simulations of protein and nucleic acid systems are tested with the GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple SWitching) methods. The simulation stability and energy conservation is investigated in relation to the agreement with the Poisson theory. It is found that very close agreement between generalized Born methods and the Poisson theory based on the commonly used sharp molecular surface definition results in energy drift and simulation artifacts in molecular dynamics simulation protocols with standard 2-fs time steps. New parameters are proposed for the GBMV method, which maintains very good agreement with the Poisson theory while providing energy conservation and stable simulations at time steps of 1 to 1.5 fs.
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