Isobaric and Isothermal Molecular Dynamics Simulations of Diatomic Systems

Abstract

Isobaric molecular dynamics simulations were carried out for diatomic systems using different algorithms available in the literature. Two-centered Lennard-Jones potentials with and without quadrupolar interactions were used. Thermodynamic properties obtained from the isobaric algorithms compared very well with those of an equivalent simulation in the microcanonical ensemble; however, some differences were observed when similar comparisons were carried out for dynamic properties. More specifically, the constant pressure constraint affects the translational dynamics of the system because of the non-negligible differences between the momenta and the instantaneous velocities of the molecules.

Furthermore, the following studies were carried out using isobaric MD simulations: 1. Low temperature spontaneous FCC-orthorhombic (and vice versa) transition of a diatomic system with quadrupolar interactions as a function of the molecular bond length. 2. Effect of quadrupolar interaction on isobaric melting of a model diatomic system. 3. Effect of pressure on melting properties of a model diatomic system with quadrupolar interactions.     

Thermal Properties of Supercritical Carbon Dioxide by Monte Carlo Simulations

We present simulation results for the volume expansivity, isothermal compressibility, isobaric heat capacity, Joule-Thomson coefficient and speed of sound for carbon dioxide (CO 2 ) in the supercritical region, using the fluctuation method based on Monte Carlo simulations in the isothermal-isobaric ensemble. We model CO 2 as a quadrupolar two-center Lennard-Jones fluid with potential parameters reported in the literature, derived from vapor-liquid equilibria (VLE) of CO 2 . We compare simulation results with an equation of state (EOS) for the two-center Lennard-Jones plus point quadrupole (2CLJQ) fluid and with a multiparametric EOS adjusted to represent CO 2 experimental data. It is concluded that the VLE-based parameters used to model CO 2 as a quadrupolar two-center Lennard-Jones fluid (both simulations and EOS) can be used with confidence for the prediction of thermodynamic properties, including those of industrial interest such as the speed of sound or Joule-Thomson coefficient, for CO 2 in the supercritical region, except in the extended critical region.     

The Second Virial Coefficients for Water from Monte Carlo Integration Using Reduced Effective Charges

Abstract

The reduction of the dipole moment of effective pair potentials of rigid water models enables accurate second virial coefficients to be determined over the whole temperature range. Subsequent Isothermal Isobaric (NPT) ensemble simulations of water vapour have shown that there is a significant difference in vapour densities between the modified water potentials.     

Experimental verification of lipid bilayer structure through multi-scale modeling

Great progress has been made in applying coarse-grain molecular dynamics (CGMD) simulations to the investigation of membrane biophysics. In order to validate the accuracy of CGMD simulations of membranes, atomistic scale detail is necessary for direct comparison to structural experiments. Here, we present our strategy for verifying CGMD lipid bilayer simulations. Through reverse coarse graining and subsequent calculation of the bilayer electron density profile, we are able to compare the simulations to our experimental low angle X-ray scattering (LAXS) data. In order to determine the best match to the experimental data, atomistic simulations are run at a range of areas (in the NP_NAT ensemble), starting from distinct configurations extracted from the CGMD simulation (run in the NPT ensemble). We demonstrate the effectiveness of this procedure with two small, single-component bilayers, and suggest that the greater utility of our algorithm will be for CGMD simulations of more complex structures.     

Molecular simulation of the preferential adsorption of CH4 and CO2 in middle-rank coal

The adsorption of the CO₂/CH₄ mixture in coal affects the CO₂-enhanced coalbed methane recovery project. To gain a better understanding of CH₄ and CO₂ interaction with middle-rank coal, we developed a molecular concept with support for the sorption of CH₄ and CO₂ on Ximing-8 coal (XM-8) (1.8% vitrinite reflectance). A XM-8 coal model was built by using molecular dynamic (MD) simulations. The molecular simulations were established by the Grand Canonical Monte Carlo and MD methods to study the effects of the temperature, pressure, and species bulk mole fraction on the pure component adsorption isotherms, isosteric heat and adsorption selectivity. It turns out that the CO₂ selectivity decreases as the pressure and its own bulk mole fraction increases, but it increases as temperature increases, and the selectivity values are not always greater than 1. The interactions between the small molecules and XM-8 were determined by using density functional theory. It was found that the interactions between the CO₂ and XM-8 surface is greater, particularly for the heteroatoms than CH₄. The adsorption selectivity and interaction were simultaneously used to reveal that the advantageously substituted range is high temperature, low pressure and a high content of heteroatoms.     

Gas adsorption and diffusion in a highly CO2 selective metal–organic framework: molecular simulations

Grand canonical Monte Carlo and equilibrium molecular dynamics simulations were used to assess the performance of an rht-type metal–organic framework (MOF), Cu-TDPAT, in adsorption-based and membrane-based separation of CH₄/H₂, CO₂/CH₄ and CO₂/H₂ mixtures. Adsorption isotherms and self-diffusivities of pure gases and binary gas mixtures in Cu-TDPAT were computed using detailed molecular simulations. Several properties of Cu-TDPAT such as adsorption selectivity, working capacity, diffusion selectivity, gas permeability and permeation selectivity were computed and compared with well-known zeolites and MOFs. Results showed that Cu-TDPAT is a very promising adsorbent and membrane material especially for separation of CO₂ and it can outperform traditional zeolites and MOFs such as DDR, MFI, CuBTC, IRMOF-1 in adsorption-based CO₂/CH₄ and CO₂/H₂ separations.     

N-octane diffusivity enhancement via carbon dioxide in silica slit-shaped nanopores – a molecular dynamics simulation

Equilibrium molecular dynamics simulations were conducted to study the competitive adsorption and diffusion of mixtures containing n-octane and carbon dioxide confined in slit-shaped silica pores of width 1.9 nm. Atomic density profiles substantiate strong interactions between CO₂ molecules and the protonated pore walls. Non-monotonic change in n-octane self-diffusion coefficients as a function of CO₂ loading was observed. CO₂ preferential adsorption to the pore surface is likely to attenuate the surface adsorption of n-octane, lower the activation energy for n-octane diffusivity, and consequently enhance n-octane mobility at low CO₂ loading. This observation was confirmed by conducting test simulations for pure n-octane confined in narrower pores. At high CO₂ loading, n-octane diffusivity is hindered by molecular crowding. Thus, n-octane diffusivity displays a maximum. In contrast, within the concentration range considered here, the self-diffusion coefficient predicted for CO₂ exhibits a monotonic increase with loading, which is attributed to a combination of effects including the saturation of the adsorption capacity of the silica surface. Test simulations suggest that the results are strongly dependent on the pore morphology, and in particular on the presence of edges that can preferentially adsorb CO₂ molecules and therefore affect the distribution of these molecules equally on the pore surface, which appears to be required to provide the effective enhancement of n-octane diffusivity.     

Structural and dynamical properties predicted by reactive force fields simulations for four common pure fluids at liquid and gaseous non-reactive conditions

Four common pure fluids were chosen to elucidate the reliability of reactive force fields in estimating bulk properties of selected molecular systems: CH₄, H₂O, CO₂ and H₂. The pure fluids are not expected to undergo chemical reactions at the conditions chosen for these simulations. The ‘combustion’ ReaxFF was chosen as reactive force field. In the case of water, we also considered the ‘aqueous’ ReaxFF model. The results were compared to data obtained implementing popular classic force fields. In the gas phase, it was found that simulations conducted using the ‘combustion’ ReaxFF formalism yield structural properties in reasonable good agreement with classic simulations for CO₂ and H₂, but not for CH₄ and H₂O. In the liquid phase, ‘combustion’ ReaxFF simulations reproduce reasonably well the structure obtained from classic simulations for CH₄, degrade for CO₂ and H₂, and are rather poor for H₂O. In the gas phase, the simulation results are compared to experimental second virial coefficient data. The ‘combustion’ ReaxFF simulations yield second virial coefficients that are not sufficiently negative for CH₄ and CO₂, and slightly too negative for H₂. The ‘combustion’ ReaxFF parameterisation induces too strong an effective attraction between water molecules, while the ‘aqueous’ ReaxFF yields a second virial coefficient that is in reasonable agreement with experiments. The ‘combustion’ ReaxFF parameterisation yields acceptable self-diffusion coefficients for gas-phase properties of CH₄, CO₂ and H₂. In the liquid phase, the results are good for CO₂, while the self-diffusion coefficient predicted for liquid CH₄ is slower, and that predicted for liquid H₂ is about nine times faster than those expected based on classic simulations. The ‘aqueous’ ReaxFF parameterisation yields good results for both the structure and the diffusion of both liquid and vapour water.     

A simple thermodynamic model of the liquid-ordered state and the interactions between phospholipids and cholesterol

A theoretical model is proposed to describe the heat capacity function and the phase behavior of binary mixtures of phospholipids and cholesterol. The central idea is that the liquid-ordered state (L_o) is a thermodynamic state or an ensemble of conformations of the phospholipid, characterized by enthalpy and entropy functions that are intermediate between those of the solid and the liquid-disordered (L_d) states. The values of those thermodynamic functions are such that the L_o state is not appreciably populated in the pure phospholipid, at any temperature, because either the solid or the L_d state have much lower free energies. Cholesterol stabilizes the L_o state by nearest-neighbor interactions, giving rise to the appearance of the L_o phase. The model is studied by Monte Carlo simulations on a lattice with nearest-neighbor interactions, which are derived from experiment as much as possible. The calculated heat capacity function closely resembles that obtained by calorimetry. The phase behavior produced by the model is also in agreement with experimental data. The simulations indicate that separation between solid and L_o phases occurs below the melting temperature of the phospholipid (T_m). Above T_m, small L_d and L_o domains do exist, but there is no phase separation.     

The thermal properties of binary structure sI clathrate hydrate from molecular dynamics simulation

In this work, we present temperature dependence of lattice parameter and normalised lattice parameter in the atmospheric pressure and 120 bar and also pressure dependence of unit cell volume and normalised unit cell volume at 150 and 250?K for variety guests with different size, polarity and guest–host hydrogen bonding capability such as trimethylene oxide (TMO), ethylene oxide (EO), formaldehyde (FA), cyclobutane (CB), cyclopropane (CP) and ethane (Et) in the large cages with CH₄ in small cages of sI clathrate hydrates by molecular dynamics simulations. The obtained values of lattice parameters for the guest species are compatible with the experimental values. These clathrate hydrates are simulated with TIP4P/ice four-site water potential. Herein, isobaric thermal expansivity and isothermal compressibility are calculated at a temperature range of 50–250?K and a wide pressure range. These structural properties have been compared for guests which they are isoelectronic and have similar masses but with different size and polarity. We use molecular dynamics simulations to relate microscopic guest properties, like guest–host hydrogen bonding to macroscopic sI clathrate hydrate properties. The temperature dependence of thermodynamic properties such as constant-volume and constant-pressure heat capacity is presented in the atmospheric pressure for these guest species.     

Application of Gibbs Ensemble and NPT Monte Carlo Simulation to the Development of Improved Processes for H2S-rich Gases

The design of improved processes for producing hydrogen sulphide (H₂S)-rich natural gases faces a general scarcity of experimental data, because of the high toxicity and corrosive character of H₂S. We present here a prospective application of Monte Carlo simulation to predict desired fluid properties.

A first step was the selection of intermolecular potentials for water, H₂S, carbon dioxide (CO₂) and methane on the basis of pure component properties (vapour pressures, vapourisation enthalpies, liquid densities, supercritical densities at high pressure). A second step involved the prediction of phase diagrams of binary and ternary mixtures of the methane–H₂S–water system, using two-phase and three-phase Gibbs ensemble simulations. In a third step the density and excess enthalpy of the CO₂–H₂S system were computed for a large range of pressure, temperature and compositions.

Comparison with available experimental data showed that all investigated properties could be consistently predicted without needing parameter calibration on binary data. The results also provided a qualitative understanding of water solubility in H₂S-rich fluids based on molecular self-association.     

Electrodissociation of clathrate-like structures

In the present work, we develop molecular dynamics (MD) simulations in the NPT (isobaric–isothermic) ensemble to analyse the effect of an external electrostatic field over a cubic methane hydrate crystallite. The amplitude of the field is in the range 0.5–3.0 V/nm. For the simulations, we used the SPC/E rigid water model and a single-site model for methane at a temperature of 248 K and a pressure of 20 bar. When the external electrostatic field is applied, the water dipoles are oriented in such a way that the methane molecules can diffuse far away from the water cages, hence the clathrate dissociation takes place. This last phenomenon was observed for intensities above 1.5 V/nm. Taking the final configuration of each run as input, we develop a new set of MD simulations, and we observe that the stable clathrate is not recovered immediately when the external electrostatic field is turned off due to limitations in the simulation time.     

Monte Carlo Study of Structural and Thermodynamic Properties of Liquid Chloroform Using a Five Site Model

A five site potential model combining Lennard–Jones plus Coulomb potential functions has been developed for chloroform molecule. The partial charges needed for Coulombic interactions were derived using the chelpg procedure implemented in the gaussian 92 program. These calculations were performed at the MP2 level with MC-311G* basis set for Cl and 6-311G** for C and H atoms. The parameters for the Lennard–Jones potentials were optimized to reproduce experimental values for the density and enthalpy of vaporization of the pure liquid at 298 K and 1 atm. The statistical mechanics calculations were performed with the Monte Carlo method in the isothermic and isobaric (NpT) ensemble. Besides the values obtained for density, ρ, and molar enthalpy of vaporization at constant pressure, Δ H_V, for liquid chloroform, results for molar volume, V_m, molar heat capacity, C_p, isobaric thermal expansivity, α_p, and isothermal compressibility, κ_T, for this pure liquid are also in very good agreement with experimental observations. Size effects on the values of thermodynamic properties were investigated. The potential model was also tested by computing the free energy for solvating one chloroform molecule into its own liquid at 298 K using a statistical perturbation approach. The result obtained compares well with the experimental value. Site–site pair correlation functions were calculated and are in good accordance with theoretical results available in the literature. Dipole–dipole correlation functions for the present five site model were also calculated at different carbon–carbon distances. These correlations were compared to those obtained using the four site model reported in the literature. An investigation of the solvent dependence of the relative free energy for cis/trans conversion of a hypothetical solute in TIP4P water and chloroform was accomplished. The results show strong interaction of water and chloroform molecules with the gauche conformer. The value obtained for the free energy barrier for cis/trans rotation in TIP4P water is higher than that for chloroform. This result is in agreement with the continuous theory for solvation as the conformer with higher dipole moment is more favoured by the solvent with higher dieletric constant. The results also show an increase in entropy as the solute goes from the cis to the trans geometry and this result is more appreciable in the aqueous solution. This revised version was published online in June 2006 with corrections to the Cover Date.     

Carbon dioxide enrichment alleviates heat stress by improving cellular redox homeostasis through an ABA‐independent process in tomato plants

Plant responses to elevated CO₂ and high temperature are critically regulated through a complex network of phytohormones and redox homeostasis. However, the involvement of abscisic acid (ABA) in plant adaptation to heat stress under elevated CO₂ conditions has not been thoroughly studied. This study investigated the interactive effects of elevated CO₂ (800 μmol·mol^?1) and heat stress (42 °C for 24 h) on the endogenous level of ABA and the cellular redox state of two genotypes of tomato with different ABA biosynthesis capacities. Heat stress significantly decreased maximum photochemical efficiency of PSII (Fv/Fm) and leaf water potential, but also increased levels of malondialdehyde (MDA) and electrolyte leakage (EL) in both genotypes. Heat‐induced damage was more severe in the ABA‐deficient mutant notabilis (not) than in its parental cultivar Ailsa Craig (Ailsa), suggesting that a certain level of endogenous ABA is required to minimise the heat‐induced oxidative damage to the photosynthetic apparatus. Irrespective of genotype, the enrichment of CO₂ remarkably stimulated Fv/Fm, MDA and EL in heat‐stressed plants towards enhanced tolerance. In addition, elevated CO₂ significantly strengthened the antioxidant capacity of heat‐stressed tomato seedlings towards a reduced cellular redox state for a prolonged period, thereby mitigating oxidative stress. However, elevated CO₂ and heat stress did not alter the endogenous level of ABA or the expression of its biosynthetic gene NCED2 in either genotype, indicating that ABA is not involved in elevated CO₂‐induced heat stress alleviation. The results of this study suggest that elevated CO₂ alleviated heat stress through efficient regulation of the cellular redox poise in an ABA‐independent manner in tomato plants.     

The Extrapolation of Vapour–liquid Equilibrium Curves of Pure Fluids in Alternative Gibbs Ensemble Monte Carlo Implementations

Extrapolation schemes based on Taylor series expansion to determine the vapour–liquid equilibrium (VLE) curves of pure molecular fluids are presented for the NpH and μVL versions of the Gibbs ensemble Monte Carlo (GEMC) simulations. The coexistence curves of the various configurational quantities can be expressed as Taylor series around the simulated equilibrium point as a function of pressure in the NpH version and chemical potential in the μVL version. The coefficients of the Taylor series are calculated from single GEMC simulations using Clapeyron-like equations and fluctuation formulas. A Padè approximant is used to widen the range where the extrapolation is accurate. These methods are demonstrated on atomic Lennard-Jones fluid. The procedure is found to be an accurate and useful tool to calculate wide sections of the VLE curves. With this procedure the saturation heat capacity can be directly determined using the calculated derivatives.     

The Folding Transition-State Ensemble of a Four-Helix Bundle Protein: Helix Propensity as a Determinant and Macromolecular Crowding as a Probe

The four-helix bundle protein Rd-apocyt b₅₆₂, a redesigned stable variant of apocytochrome b₅₆₂, exhibits two-state folding kinetics. Its transition-state ensemble has been characterized by Φ-value analysis. To elucidate the molecular basis of the transition-state ensemble, we have carried out high-temperature molecular dynamics simulations of the unfolding process. In six parallel simulations, unfolding started with the melting of helix I and the C-terminal half of helix IV, and followed by helix III, the N-terminal half of helix IV and helix II. This ordered melting of the helices is consistent with the conclusion from native-state hydrogen exchange, and can be rationalized by differences in intrinsic helix propensity. Guided by experimental Φ-values, a putative transition-state ensemble was extracted from the simulations. The residue helical probabilities of this transition-state ensemble show good correlation with the Φ-values. To further validate the putative transition-state ensemble, the effect of macromolecular crowding on the relative stability between the unfolded ensemble and the transition-state ensemble was calculated. The resulting effect of crowding on the folding kinetics agrees well with experimental observations. This study shows that molecular dynamics simulations combined with calculation of crowding effects provide an avenue for characterize the transition-state ensemble in atomic details.     

Energetic assessment of fixation of CO<Subscript>2</Subscript> and subsequent biofuel production using <Emphasis Type="Italic">B. cereus</Emphasis> SM1 isolated from sewage treatment plant

The ongoing work on global warming resulting from green house gases (GHGs) has led to explore the possibility of bacterial strains which can fix carbon dioxide (CO₂) and can generate value-added products. The present work is an effort in this direction and has carried out an exhaustive batch experiments for the fixation of CO₂ using B. Cereus SM1 isolated from sewage treatment plant (STP). The work has incorporated 5-day batch run for gaseous phase inlet CO₂ concentration of 13 ± 1 % (%v/v). 84.6 (±5.76) % of CO₂ removal was obtained in the gaseous phase at mentioned CO₂ concentration (%v/v). Energetic requirement for CO₂ fixation was assessed by varying Fe[II] ion concentration (0–200 ppm) on the per-day basis. The cell lysate obtained from CO₂ fixation studies (Fe[II] ion = 100 ppm) was analyzed using Fourier transformation infrared spectroscopy (FTIR) and gas chromatography-mass spectroscopy (GC–MS). This analysis confirmed the presence of fatty acids and hydrocarbon as valuable products. The hydrocarbons were found in the range of C₁₁–C₂₂ which is equivalent to light oil. The obtained fatty acids were found in the range of C₁₁–C₁₉. The possibility of fatty acid conversion to biodiesel was explored by carrying out the transesterification reaction. The yield of biodiesel was obtained as 86.5 (±0.048) % under the transesterification reaction conditions. Results of this research work can provide the valuable information in the implementation of biomitigation of CO₂ at real scenario.