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.

The nature of interactions between ethanol and carbon dioxide has been characterized using simulations via the Car-Parrinello molecular dynamics (CPMD) method. Optimized geometries and energetics of free-standing ethanol-CO2 clusters exhibit evidence for a relatively more stable electron donor-acceptor (EDA) complex between these two species rather than a hydrogen-bonded configuration. This fact has also been confirmed by the higher formation rate of the EDA complex in supercritical carbon dioxide-ethanol mixtures. The probability density distribution of CO2 molecules around ethanol in the supercritical state shows two high probability regions along the direction of the lone pairs on the oxygen atom of ethanol. The EDA interaction between ethanol and CO2 as well as that between CO2 molecules themselves leads to significant deviations from linearity in the geometry of the CO2 molecule. The vibrational spectra of carbon dioxide obtained from the atomic velocity correlation functions in the bulk system as well as from isolated complexes show splitting of the nu2 bending mode that arises largely from CO2-CO2 interactions, with ethanol contributing only marginally because of its low concentration in the present study. The stretching frequency of the hydroxyl group of ethanol is shifted to lower frequencies in the bulk mixture when compared to its gas-phase value, in agreement with experiments.

Composite materials composed of aluminosilicate clays with organic molecules or biomolecules in the interlayer galleries are readily synthesized and have many applications in agriculture, medicine, environmental science, engineering, and geochemistry. Detailed characterization of the molecular-scale structure and dynamics of the interlayer galleries is difficult experimentally because of static and dynamic disorder but can be obtained by molecular dynamics (MD) simulation using classical force fields. This Article presents an MD study of smectite clay montmorillonite (MMT) intercalated with poly(ethylene glycol) (PEG) with and without CO2 also present in the interlayer. Bulk PEG can incorporate large amounts of CO2 under supercritical conditions, and MMT–PEG composites have potential as gas-separation materials. The MD simulations of anhydrous MMT containing interlayer CO2 (MMT–CO2), PEG (MMT–PEG), and PEG + CO2 (MMT–PEG–CO2) provide new atomic-level insight into the molecular ordering of CO2 near the basal surface and CO2-induced changes in the structure, conformation, and energetics of PEG in the interlayer. The results show that the structural arrangement among the CO2 molecules in the MMT–CO2 system is similar to that in supercritical CO2 and is analogous to that of crystalline CO2. All Na ions in this system remain coordinated by the basal oxygens (Ob) but are also coordinated by the oxygens (OCO2 ) of the CO2 molecules, and a few are displaced ∼2 Å above their surface sites. The cooperative motion of the Na ions and CO2 molecules increases the Na diffusion and the CO2 reorientation in the interlayers. The critical interactions among cations, CO2, PEG, and the basal surface in the MMT–PEG–CO2 system result in a layer of CO2 trapped between the basal surface and cation-permeable PEG film formed on the basal surface. In the MMT–PEG and MMT–PEG–CO2 systems, PEG is highly disordered and exhibits conformational and orientational heterogeneity in the interlayer confinement with many of the molecules lying in a layer parallel and close to the basal surface of the clay. Some of the PEG molecules span from one basal surface to the other across the interlayer. Many of the Na ions are displaced from the basal surface and are coordinated by both basal oxygens and oxygens of the PEG. Some are completely displaced from the surface and are dissolved in the PEG. In the MMT–PEG–CO2 system, the CO2 molecules occur in well-defined layers parallel to the basal surface and are most commonly dissolved in the PEG. In the full MMT–PEG–CO2 system, Na ions have few OCO2 nearest neighbors, and the presence of CO2 causes the basal spacing to expand but does not change the conformation of the PEG. The MD results provide detailed and otherwise unobtainable information about the coordination environments and distributions of interatomic distances and angles in the interlayer.

The effect of pressure on supercritical carbon dioxide (scCO2) has been characterized by using Car-Parrinello molecular dynamics simulations. Structural and dynamical properties along an isotherm of 318.15 K and at pressures ranging from 190 to 5000 bar have been obtained. Intermolecular pair correlation functions and three-dimensional atomic probability density map calculations indicate that the local environment of a central CO2 molecule becomes more structured with increasing pressure. The closest neighbors are predominantly oriented in a distorted T-shaped geometry while neighbors separated by larger distances are likely oriented in a slipped parallel arrangement. The structure of scCO2 at high densities has been compared with that of crystalline CO2. The probability distributions of intramolecular distances narrow down with increasing pressure. A marginal but non-negligible effect of pressure on the instantaneous intramolecular OCO angle is observed, lending credence to the idea that intermolecular interactions between CO2 molecules in an inhomogeneous near neighbor environment could contribute to the observed instantaneous molecular dipole moment. The extent of deviation from a perfect linear geometry of the carbon dioxide molecule decreases with increasing pressure. Time constants derived from reorientational time correlation functions of the molecular backbone compare well with experimental data. Within the range of thermodynamic conditions explored here, no significant changes are observed in the frequencies of intramolecular vibrational modes. However, a blue shift is observed in the low-frequency cage rattling mode with increasing pressure.

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.

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.

should be read as the probability distribution of ensemble-averaged intramolecular angles and not that of instantaneous intramolecular angles. The OÀCÀO angles of the 32 CO 2 molecules in the system were averaged in each frame of the Car-Parrinello molecular dynamics (CPMD) trajectory, and Figure 3 is the probability distribution of such values. The authors apologize for any misunderstandings that may have arisen as a result of this error.

This paper reviews experimental nuclear magnetic resonance (NMR) and computational molecular dynamics (MD) investigations of the structural and dynamical behavior of cations, anions, H 2 O, and CO 2 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, H 2 O, CO 2 , 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 10 2 to >10 12 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 T 1 and T 2 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.