Moumita Saharay

Ab initio molecular-dynamics study of supercritical carbon dioxide

Car-Parrinello molecular-dynamics simulations of supercritical carbon dioxide (scCO(2)) have been performed at the temperature of 318.15 K and at the density of 0.703 g/cc in order to understand its microscopic structure and dynamics. Atomic pair correlation functions and structure factors have been obtained and good agreement has been found with experiments. In the supercritical state the CO(2) molecule is marginally nonlinear, and thus possesses a dipole moment. Analyses of angle distributions between near neighbor molecules reveal the existence of configurations with pairs of molecules in the distorted T-shaped geometry. The reorientational dynamics of carbon dioxide molecules, investigated through first- and second-order time correlation functions, exhibit time constants of 620 and 268 fs, respectively, in good agreement with nuclear magnetic resonance experiments. The intramolecular vibrations of CO(2) have been examined through an analysis of the velocity autocorrelation function of the atoms. These reveal a red shift in the frequency spectrum relative to that of an isolated molecule, consistent with experiments on scCO(2). The results have also been compared to classical molecular-dynamics calculations employing an empirical potential.

Dehydration-induced amorphous phases of calcium carbonate

Amorphous calcium carbonate (ACC) is a critical transient phase in the inorganic precipitation of CaCO3 and in biomineralization. The calcium carbonate crystallization pathway is thought to involve dehydration of more hydrated ACC to less hydrated ACC followed by the formation of anhydrous ACC. We present here computational studies of the transition of a hydrated ACC with a H2O/CaCO3 ratio of 1.0 to anhydrous ACC. During dehydration, ACC undergoes reorganization to a more ordered structure with a significant increase in density. The computed density of anhydrous ACC is similar to that of calcite, the stable crystalline phase. Compared to the crystalline CaCO3 phases, calcite, vaterite, and aragonite, the computed local structure of anhydrous ACC is most-similar to those of calcite and vaterite, but the overall structure is not well described by either. The strong hydrogen bond interaction between the carbonate ions and water molecules plays a crucial role in stabilizing the less hydrated ACC compositions compared to the more hydrated ones, leading to a progressively increasing hydration energy with decreasing water content.

Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS

The hydrolysis of cellulose is the bottleneck in cellulosic ethanol production. The cellobiohydrolase CelS from Clostridium thermocellum catalyzes the hydrolysis of cello-oligosaccharides via inversion of the anomeric carbon. Here, to examine key features of the CelS-catalyzed reaction, QM/MM (SCCDFTB/MM) simulations are performed. The calculated free energy profile for the reaction possesses a 19 kcal/mol barrier. The results confirm the role of active site residue Glu87 as the general acid catalyst in the cleavage reaction and show that Asp255 may act as the general base. A feasible position in the reactant state of the water molecule responsible for nucleophilic attack is identified. Sugar ring distortion as the reaction progresses is quantified. The results provide a computational approach that may complement the experimental design of more efficient enzymes for biofuel production.

NMR and computational molecular modeling studies of mineral surfaces and interlayer galleries: A review.

Abstract This paper reviews experimental nuclear magnetic resonance (NMR) and computational molecular dynamics (MD) investigations of the structural and dynamical behavior of cations, anions, H2O, and CO2 on the surfaces and in the interlayer galleries of layer-structure minerals and their composites with polymers and natural organic matter (NOM). The interaction among mineral surfaces, chargebalancing cations or anions, H2O, CO2, and NOM are dominated by Coulombic, H-bond, and van der Waals interactions leading to statically and dynamically disordered systems and molecular-scale processes with characteristic room-temperature frequencies varying from at least as small as 102 to >1012 Hz. NMR spectroscopy provides local structural information about such systems through the chemical shift and quadrupolar interactions and dynamical information at frequencies from the subkilohertz to gigahertz ranges through the T1 and T2 relaxation rates and line shape analysis. It is often difficult to associate a specific structure or dynamical process to a given NMR observation, however, and computational molecular modeling is often effective in providing a much more detailed picture in this regard. The examples discussed here illustrate these capabilities of combining experimental NMR and computational modeling in mineralogically and geochemically important systems, including clay minerals and layered double hydroxides.