Simone Raugei

An ab initio study of water molecules in the bromide ion solvation shell

The solvation shell structure and dynamics of Br− in an aqueous solution of HBr (1.6 M) was studied, under ambient conditions, by ab initio molecular dynamics using the Car–Parrinello approach. The present calculations indicate that Br− is asymmetrically solvated by water. The calculated residence time of water in the inner Br− anion solvation shell agrees well with the most recent experimental estimate. Analysis indicates that the large anion scarcely influences the molecular dipole moment of solvation shell molecules.

INTERMOLECULAR INTERACTIONS IN THE N2-N2 DIMER

Intermolecular interactions at the MP2 level for the nitrogen dimer are reported. The results are compared with density functional calculations, showing the limits of the approximation adopted for the exchange and correlation functionals. Preliminary results of ab initio molecular dynamics on solid nitrogen are reported.

Ab-initio molecular dynamics study of theSN2 reaction Cl−+ ClCH2CN

Ab-initio molecular dynamics has been used to investigate the SN2 reaction Cl− + ClCH2CN using two different exchange-correlation functionals. The results have been compared with available experimental data and with calculations at the MP2/6-311 + G(d,p) level of theory. As a reference, comparison has also been made with calculations for the Cl− + CH3Cl reaction, for which accurate experimental data and higher level ab-initio calculations are available. The ∽0 K energy profile has been calculated. It has been found that the minimum energy reaction pathway is characterized by the formation of a strong H-bond. Differences in the electron distribution along the pathway of the two reactions have also been discussed.

Ab Initio Raman Spectra of β-Lactamase Inhibitor Intermediates Bound to E166A SHV β-Lactamase.

The assignment and the analysis of the experimental vibrational Raman spectra of enzyme bound β-lactamase inhibitors may be of help to understand the mechanisms responsible for bacterial drug resistance. We present a computational study of the structural and vibrational properties of clavulanic acid and tazobactam intermediates, two important β-lactamase inhibitors, bound to the singly mutated E166A SHV β-lactamase in aqueous solution by hybrid molecular mechanics/quantum mechanics (QM/MM) simulations at ambient conditions. We compare the Raman spectra obtained from the time autocorrelation function of polarizability tensor as obtained from a QM/MM protocol to those obtained from the instantaneous normal modes analysis performed on top of the QM/MM trajectory in order to establish the accuracy of these two computational methods and to review the previously made assignments. It is shown that the O═C-C═C-NH- trans-enamine moiety symmetric and asymmetric stretchings are strongly coupled with the N-H in-plane rocking and originate the band structure between 1600 cm(-1) and 1640 cm(-1). Results indicate also that to properly describe Raman scattering properties of the trans-enamine intermediate, it is crucial to include both mechanical (beyond the second derivative of the potential energy at equilibrium) and electrical (beyond the first derivative of polarizability) anharmonicity. In addition, we show that the environment electrostatic field dynamically modulates the Raman activity, enhancing or inhibiting it.

Orientational ordering in the mixed crystal Ar1-x (N2)x: a molecular dynamics study.

The mixed crystal Ar1−x(N2)x was studied by molecular dynamics simulations in the NPT ensemble for three selected concentrations. The α↔β transition was not observed, instead the low temperature α phase shows a transition to a plastic fcc phase. The mixed crystals with fcc arrangement tend to form orientationally ordered crystals. An orientational glass was obtained and characterized for x≃0.7 and with an hcp structure in agreement with the experimental observations.

Structure of the strongly associated liquid antimony pentafluoride: An ab initio molecular dynamics study

Under ambient conditions, pure antimony pentafluoride (SbF5) is a strongly associated liquid. Early NMR works established that the molecules oligomerize via cis-fluorine chains. We have employed ab initio molecular dynamics to investigate the structure of liquid SbF5. The simulation confirms the strong tendency of molecules to oligomerize via a barrierless, diffusion-limited process. The nature of the SbF5 chemical bond and the experimentally observed propensity to form cis-fluorine chains has been analyzed in terms of Wannier localized orbital functions. The calculation indicated a very strong ionic character for the Sb–F bond.

A MOLECULAR DYNAMICS SIMULATION OF THE VIBRATIONAL PROPERTIES OF THE AR1-X(N2)X CRYSTAL

A classical molecular dynamics calculation of the vibrational properties (and in particular of the infrared and Raman response) of the Ar1−x(N2)x mixed crystal is presented based on an intermolecular interaction potential including electrostatic terms. The lattice and internal vibration region are discussed separately. The vibrational properties are correlated with the structural properties and with the orientational ordering in the crystals.