A Coupled Car-Parrinello Molecular Dynamics and EXAFS Data Analysis Investigation of Aqueous Co 2+ (original) (raw)
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Classical and QM/MM molecular dynamics simulations of Co2+ in water
Chemical Physics, 2003
Classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations have been performed to describe structural and dynamical properties of Co 2þ in water. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at unrestricted Hartree-Fock (UHF) level using the LANL2DZ ECP basis set for Co 2þ and the double-f plus polarization basis set for water. For the rest of the system newly constructed three-body corrected potential functions were used. A well-structured rigid octahedron was observed for the stable first hydration shell showing no first shell water exchange process within a simulation time of 11.9 ps. For second hydration shell ligands, a mean residence time of 28 ps was observed. Librational and vibrational motions as well as the ion-oxygen motion were investigated by means of velocity autocorrelation functions showing significant differences between classical and QM/MM results.
MONTE CARLO SIMULATIONS OF Co (II) IN WATER INCLUDING THREE-BODY CORRECTION
Indonesian Journal of Chemistry, 2010
In order to describe the cobalt-water interaction correctly, a new ab initio potential was developed consisting of pair interaction terms as well as three-body contributions. Within this approach, it was possible to correct for the well-known failures of pair potentials in describing solvation phenomena of such ions. A first-shell coordination number of 6 in agreement with experimental data were obtained from Monte Carlo simulations of a single cobalt (II) ion in water. The structure of hydrated ion is discussed in terms of radial density functions and coordination number, energy and angular distributions.
Journal of Molecular Liquids, 2018
The structural and thermodynamic properties of Na +-Clion-pair association in water-CO2 binary mixtures in supercritical conditions for infinitely dilute solutions are studied using constrained molecular dynamics simulations over a wide range of compositions. It is found that solvation structure varies dramatically with the solvent composition. Contact ion pairs (CIPs) are found to be more stable than all other configurations as seen from the potentials of mean force (PMFs). PMFs of the NaCl ion pair in pure CO2 look almost like the pair potential between the ion pair. Stabilities of CIPs increase with increase in the mole fraction of CO2. An increment in the average number of hydrogen bonds with an increase in the mole fraction of H2O in the bulk as well as in the solvation shell of the ions is observed. Ion-pair association in aqueous CO2 mixtures in supercritical conditions is found to be endothermic and driven by entropy. Preferential solvation analysis shows that both Na + and Clions are preferentially solvated by water and even a small percentage of water in the mixture prevents CO2 molecules from entering the first solvation shell of ions due to the strong hydrophilicity of the ions.
Journal of Molecular Structure: THEOCHEM, 1997
High-level ab initio (MP2/6-311++G (U,2p) geometry, Gaussian-2, MP4(SDTQ) and QCISD(T) binding energies) and density-functional (Becke3LYP/6-311++G(2df,2@')) calculations have been performed on the charge-transfer complex between water and carbon dioxide. The complex appears to have two equivalent non-planar minima of C, symmetry. Minima are separated by transition states with C 1 symmetry, whereas the totally planar structure with Czv symmetry is a second-order transition state. All the critical points lie at approximately the same energy (less than 0.05 kJ mol-' difference). Therefore, the experimentally observable structure should be planar. The best equilibrium intermolecular distance for this complex calculated at the MP2/6_311++G(2d,2p) level is 2.800 A. Our best estimate of the observable intermolecular distance (corrected for anharmonicity) is 2.84 A, in agreement with the experimentally derived value of 2.836 A. Our best estimate of the binding energy at the QCISD(T) level, taking into account the variation of the distance owing to anharmonicity and the use of more sophisticated theoretical treatments, is -12.0 2 0.2 kJ mol-'. Our best estimate of the barrier to internal rotation, also at the MP2/6_311++G(2d,2p) level, is 4.0 kJ mol-', outside the error limits of the experimental determination (3.64 2 0.04 kJ mol-'). Density functional theory at the level employed here gives an equilibrium intermolecular distance that is too large (2.857 A), a binding energy that is too small (8.1 kJ mol-'), attributable neither to geometry nor to the basis set, and also a barrier to internal rotation that is slightly too small (3.39 kJ mol-'). The overall picture is, however, reasonably good.
Molecular Dynamics Simulations of Carbon Dioxide and Water at an Ionic Liquid Interface
The Journal of Physical Chemistry B, 2011
Molecular dynamics simulations using classical force fields were carried out to study the structural and transport properties of clay mineral−water−CO 2 systems at pressure and temperature relevant to geological carbon storage. The simulations show that the degree of swelling caused by intercalation of CO 2 strongly depends on the initial water content in the interlayer space and that CO 2 intercalation stimulates inner-sphere adsorption of the positively charged interlayer ions on the internal clay surfaces, which modifies the wetting properties of the surfaces. DFT-based molecular dynamics simulations were used to interpret the origin of the observed shift in the asymmetric stretch vibration of CO 2 trapped in montmorillonite. The origin of the shift is attributed to the electric field effects on the CO 2 molecules induced by the water molecules.
Journal of Chemical Theory and Computation, 2012
Extracting reliable thermochemical parameters from molecular dynamics simulations of chemical reactions, although based on ab initio methods, is generally hampered by difficulties in reproducing the results and controlling the statistical errors. This is a serious drawback with respect to the quantum-chemical description based on potential energy surfaces. This work is an attempt to fill this gap. We apply molecular dynamics, based on density functional theory (DFT) and empowered by path metadynamics (MTD), to simulate the reaction of CO 2 with (one, two, and three) water molecules in the gas phase. This study relies on a strategy that ensures a precise control of the accuracy of the reaction coordinates and of the reconstructed freeenergy surface on this space, namely, on (i) fully reversible MTD simulations, (ii) a committor probability analysis for the diagnosis of the collective variables, and (iii) a cluster analysis for the characterization of the reconstructed free-energy surfaces. This robust procedure permits a meaningful comparison with more traditional calculations of the potential energy surfaces that we also perform within the same DFT computational scheme. This comparison shows in particular that the reactants and products of systems with only three water molecules can no longer be understood in terms of one structure but must be described as statistical configuration ensembles. Calculations carried out with different prescriptions for the exchange-correlation functionals also allow us to establish their quantitative effect on the activation barriers for the formation and the dissociation of carbonic acid. Their decrease induced by the addition of one water molecule (catalytic effect) is found to be largely independent of the specific functional.
Journal of Chemical Theory and Computation, 2009
Composition-dependent solvation dynamics around the probe coumarin 153 (C153) have been explored in CO 2-expanded methanol and acetone with molecular dynamics (MD) simulations. Solvent response functions are biexponential with two distinct decay time scales: a rapid initial decay (∼0.1 ps) and a long relaxation process. Solvation times in both expanded solvent classes are nearly constant at partition compositions up to 80% CO 2. The extent of solvation beyond this composition has the greatest tunability and sensitivity to bulk solvent composition. Solvent rotational correlation functions (RCFs) have also been used to explore rotational relaxation. Rotations have a larger range of time scales and are dependent on a number of factors including bulk composition, solvent-solvent interactions, particularly hydrogen bonding, and proximity to C153. The establishment of the solvation structure around a solute in a GXL is clearly a complex process. With respect to the local solvent domain around C153, it was seen to be primarily affected by a nonlinear combination of the rotational and diffusive transport dynamics.
Journal of Molecular Liquids, 2020
In this work, the theoretical solubility of CO 2 into different choline chloride and phosphonium based deep eutectic solvents (DESs) was successfully calculated using COSMO-RS method. FTIR spectrums of the seven DESs were calculated in order to investigate and check out their structure. There was a good agreement between the predicted values and the experimental results reported in the literature. The Sigma profiles analysis showed the possibility of formation of H-bonding between CO 2 and the DESs which favors increasing the solubility of CO 2. Molecular dynamics simulation was performed to investigate the molecular interaction between the different DESs and CO 2. The actual approach can be used in the estimation of different physicochemical properties of DESs especially the capture of undesirable molecules like H 2 S, NOx, H 2 O and CO 2 .
Industrial & Engineering Chemistry Research, 2009
The correlation and prediction of the solubility of gases in (nonelectrolyte as well as in electrolyte) aqueous/ organic solvent mixtures is an important topic in many areas of chemical engineering. Despite the importance of that field, comparatively little attention has been given to that area in both classical thermodynamics (i.e., correlation methods that are based on semiempirical expressions for the excess Gibbs energy) and molecular simulation (where gas solubility can be predicted from intermolecular pair potentials). In the work presented here, recently published experimental data for the solubility of carbon dioxide in aqueous solutions of acetone (covering temperatures from 313 to 395 K at pressures ranging up to about 9 MPa) are used for testing a semiempirical, classical method (for the correlation of such gas solubility phenomena) as well as the Gibbs ensemble Monte Carlo method (GEMC) (for predicting the solubility of carbon dioxide in aqueous solutions of acetone from published intermolecular pair potentials without using any adjustable binary interaction parameter). The correlation method reproduces the experimental data (nearly) within experimental uncertainty, as was expected. The predictions by the GEMC method also agree well with the experimental data.
Molecular dynamics simulation of CO2 hydrates: Prediction of three phase coexistence line
The Journal of chemical physics, 2015
The three phase equilibrium line (hydrate-liquid water-liquid carbon dioxide) has been estimated for the water + carbon dioxide binary mixture using molecular dynamics simulation and the direct coexistence technique. Both molecules have been represented using rigid nonpolarizable models. TIP4P/2005 and TIP4P/Ice were used for the case of water, while carbon dioxide was considered as a three center linear molecule with the parameterizations of MSM, EPM2, TraPPE, and ZD. The influence of the initial guest occupancy fraction on the hydrate stability has been analyzed first in order to determine the optimal starting configuration for the simulations, paying attention to the influence of the two different cells existing in the sI hydrate structure. The three phase coexistence temperature was then determined for a pressure range from 2 to 500 MPa. The qualitative shape of the equilibrium curve estimated is correct, including the high pressure temperature maximum that determines the hydrat...