Ab initio molecular-dynamics study of supercritical carbon dioxide

Car-Parrinello molecular-dynamics simulations of supercritical carbon dioxide (scCO2) 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 CO2 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 CO2 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 scCO2. The results have also been compared to classical molecular-dynamics calculations employing an empirical potential

Persistence in an antiferromagnetic Ising model with conserved magnetisation

We obtain the persistence exponents for an antiferromagnetic Ising system in which the magnetisation is kept constant. This system belongs to Model C (system with non-conserved order parameter with a conserved density) and is expected to have persistence exponents different from that of Model A (system with no conservation) but independent of the conserved density. Our numerical results for both local persistence at zero temperature and global persistence at the critical temperature however indicate that the exponents are dependent on the conserved magnetisation in both two and three dimensions. This nonuniversal feature is attributed to the presence of the conserved field and is special to the persistence phenomena.Comment: 8 pages, to be published in Physica A (Proceedings of the Statphys-Kolkata IV, 2002

Enhanced molecular multipole moments and solvent structure in supercritical carbon dioxide

Understanding the green solvent: The solvent structure and molecular electrostatic multipole moments of supercritical carbon dioxide (scCO2) were studied using ab initio molecular dynamics simulations. Blue, cyan, and orange (see graphic) represent the increasing probability of finding an oxygen atom, which belongs to a neighboring molecule, in the first coordination shell of CO2

Electron donor-acceptor interactions in ethanol-CO<SUB>2</SUB> mixtures: an ab Initio molecular dynamics study of supercritical carbon dioxide

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 ν2 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

Evolution of intermolecular structure and dynamics in supercritical carbon dioxide with pressure: an ab initio molecular dynamics study

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

Ab initio molecular dynamics investigations of structural, electronic and dynamical properties of water in supercritical carbon dioxide

Ab initio molecular dynamics simulations of a solitary perdeuterated water molecule solvated in supercritical carbon dioxide have been performed along an isotherm at three different densities. Electron donor-acceptor interactions between the oxygen atom of water and the carbon atom of CO2 as well as hydrogen bonded interactions between the two molecules have been shown to play a dominant role in the solvation. The mean dipole moment of the water molecule increases with the density of the solution, from a value of 1.85 D at low density to around 2.15 D at the highest density. The increase in the solvent density causes the water molecule to exhibit a range of behavior, from a free molecule to one that interacts strongly with CO2. A blue shift in the bending mode of water has been observed with increasing solvent density. The carbon dioxide molecules which are present in the first neighbor shell of water are found to exhibit larger propensity to deviate from a linear geometry in their instantaneous configurations

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

Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations

The utilization of microbial cellulase enzymes for transforming plant biomass into biofuel or bioethanol, which can serve as a substitute for fossil fuel, is a subject of growing interest. Nonetheless, large-scale production of biofuel using cellulases is not economically feasible as the extraction of these enzymes from diverse microorganisms is an expensive process. To address this issue, immobilizing the enzyme to a substrate material, e.g., carbon nanotubes (CNTs), to recycle without a significant decline in its catalytic activity is a promising solution. Due to the hydrophobic nature of CNTs, we employed molecular docking and network analysis methodologies to identify potential CNT-binding sites on the outer surface of a wild-type cellulase enzyme, CelS. Classical molecular dynamics simulations of CNT-bound CelS through one of the selected binding sites resulted in negligible changes in the secondary structure of the enzyme and its catalytic domain, implying the least possible effect on the catalytic activity post-immobilization. Furthermore, our study reveals that while the unfolding near the CNT-binding region in CelS is more pronounced when the enzyme is interacting with a wider CNT, resulting in enhanced contact area and improved binding affinity, its impact on the overall CelS structure is relatively less significant when compared to thinner CNTs. Particularly, CNTs of diameter ∼12 Å can serve as a favorable option for substrate materials in cellulase immobilization. Our study also provides critical insights into the binding mechanisms between cellulase and CNTs, which could lead to the development of more efficient biocatalysts for biofuel production