Chinapong Kritayakornupong

Symmetry Breaking and Hydration Structure of Carbonate and Nitrate in Aqueous Solutions: A Study by Ab Initio Quantum Mechanical Charge Field Molecular Dynamics

The ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism was applied to simulate carbonate and nitrate anions in aqueous solution. The out-of-plane (ν(2)) spectra obtained from the velocity autocorrelation functions (VACFs) and the torsion angle-time functions indicate that the symmetry of carbonate is reduced from D(3h) to a lower degree by breaking up the molecular plane, whereas the planarity of nitrate anion is retained. The calculated frequencies are in good agreement with the Raman and IR data. Carbonate shows a stronger molecular hydration shell than the nitrate anion with the average molecular coordination numbers of 8.9 and 7.9, respectively. A comparison with the average number of ion-solvent hydrogen bonds (H-bonds) indicates the extra water molecules within the hydration shell of carbonate (∼2) and nitrate (∼3), readily migrating from one coordinating site to another. The mean residence times for water ligands in general classify carbonate and nitrate as moderate and weak structure-making anions, while the specific values for individual sites of nitrate reveal local weak structure-breaking properties.

Structural and Dynamical Properties and Vibrational Spectra of Bisulfate Ion in Water: A Study by Ab Initio Quantum Mechanical Charge Field Molecular Dynamics

The ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism was applied to simulate the bisulfate ion, HSO4-, in aqueous solution. The averaged geometry of bisulfate ion supports the separation of six normal modes of the O*-SO3 unit with C3v symmetry from three modes of the OH group in the evaluation of vibrational spectra obtained from the velocity autocorrelation functions (VACFs) with subsequent normal coordinate analyses. The calculated frequencies are in good agreement with the observations in Raman and IR experiments. The difference of the averaged coordination number obtained for the whole molecule (8.0) and the summation over coordinating sites (10.9) indicates some water molecules to be located in the overlapping volumes of individual hydration spheres. The averaged number of hydrogen bonds (H-bonds) during the simulation period (5.8) indicates that some water molecules are situated in the molecular hydration shell with an unsuitable orientation to form a hydrogen bond with the ion. The mean residence time in the surroundings of the bisulfate ion classify it generally as a weak structure-making ion, but the analysis of the individual sites reveals a more complex behavior of them, in particular a strong interaction with a water molecule at the hydrogen site.

Molecular modeling of nitrosamines adsorbed on H-ZSM-5 zeolite: an ONIOM study.

AbstractBinding energies of nitrosamine compounds, N-nitrosamine (NA), N-methyl-N-nitrososamine (NMA), N-ethyl-N-nitrososamine (NEA), N,N-dimethyl-N-nitrosoamine (NDMA), N-ethyl-N-methyl-N-nitrosoamine (NEMA) and N,N-diethyl-N-nitrosoamine (NDEA) on the H-ZSM-5 zeolite were obtained using the ONIOM(B3LYP/6–31G(d):AM1) approach. Based on amino and imino isomers of nitrosamines, there are two adsorption configurations on the H-ZSM-5 for NA (as NA_a and NA_i), NMA (as NMA_a and NMA_i) and NEA (as NEA_a and NEA_i). The relative binding energies of nitrosamines are in order: NA_a > NMA_a ~ NEA_a > NA_i > NMA_i ~ NEA_i > NEMA ~ NDEA > NDMA. The order of adsorption selectivity for nitrosamines of the H-ZSM-5 is NA_a ~ NA_i >> NMA_a ~ NEA_a > NDMA ~ NMA_i ~ NEMA > NDEA ~ NEA_i. The selective recognition of the NA by the H-ZSM-5 was obviously found. FigureThe optimized structures of adsorption complexes with the most stable conformers of the N-methyl-N-nitrososamine (NMA), N-ethyl-N-nitrososamine (NEA), N,N-dimethyl-N-nitrososamine (NDMA), N-ethyl-N-methyl-N-nitrososamine (NEMA) and N,N-diethyl-N-nitrososamine (NDEA) on the H-ZSM-5 zeolite

The Jahn‐Teller effect of the Cr2+ ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations

The hydration structure of Cr2+ has been studied using molecular dynamics (MD) simulations including three‐body corrections and combined ab initio quantum mechanical/molecular mechanical (QM/MM) MD simulations at the Hartree‐Fock level. The structural properties are determined in terms of radial distribution functions, coordination numbers, and several angle distributions. The mean residence time was evaluated for describing ligand exchange processes in the second hydration shell. The Jahn‐Teller distorted octahedral [Cr(H2O)6]2+ complex was pronounced in the QM/MM MD simulation. The first‐shell distances of Cr2+ are in the range of 1.9–2.8 Å, which are slightly larger than those observed in the cases of Cu2+ and Ti3+. No first‐shell water exchange occurred during the simulation time of 35 ps. Several water‐exchange processes were observed in the second hydration shell with a mean residence time of 7.3 ps.

Structural and dynamical properties of the V(3+) ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation.

A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree‐Fock level has been performed to investigate structural and dynamical parameters of the V3+ ion in dilute aqueous solution. A distorted octahedral structure with the average V3+‐O distance of 1.99 Å is evaluated from the QM/MM simulation, which is in good agreement with the X‐ray data. Several structural parameters such as angular distribution functions, θ‐ and tilt‐angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V3+. The Jahn‐Teller distortions of the V3+ ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell.

Active site of the solvated thiosulfate ion characterized by hydration structures and dynamics

The reactivity of the terminated sulfur atom within the thiosulfate ion (S2O3(2-)) when it is involved in chemical reactions was investigated through the properties of the molecular hydration shell, obtained from the ab initio quantum mechanical change field molecular dynamics (QMCF MD) simulation. The average geometry indicated the significant effect of explicit water on the reduction of the S-S length, which was reflected in the splitting peaks of the spectrum for the stretching mode of this bond (ν(SS)). A further investigation on a simple model with various theoretical levels exhibited the hydrophobicity of the S-S bond. The evaluation of the molecular coordination number was sensitive to the radii of the atomic hydration spheres, which were obtained from the vague boundaries of the first peak in the atomic radial distribution functions. The number of actual contacts specified 6.8 water molecules interacting with the thiosulfate ion, and 2.4 extra waters located in the molecular hydration shell, forming a H-bonding network with the bulk water. The mean residence times for the water ligands distinguished the asymmetric strength of the hydration shell into a weaker sulfur and three stronger oxygen sites, instigating the terminated sulfur atom as the active site that is involved in chemical reactions.

Determination of structure and dynamics of the solvated bisulfide (HS-) ion by ab initio QMCF molecular dynamics.

The hydration structure of the bisulfide (HS(-)) ion in dilute aqueous solution was characterized by means of an ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level employing Dunning double-ζ plus polarization function (DZP) basis sets. An average H-S bond distance of 1.35 Å resulted from the simulation and a hydration shell located at 2.42 Å S(HS(-))···H(w) and 3.97 Å HS(-) distances, respectively. At the sulfur site, the average coordination number is 5.9 ± 1.1, while the value for the hydrogen site is 9.2 ± 1.6. The calculated H(HS(-))-S(HS(-)) stretching frequency of 2752 cm(-1) obtained from the QMCF MD simulation is in good agreement with that reported from the Raman spectrum (2570 cm(-1)) only if a scaling factor of 0.89 is applied. The stability of the nondissociated HS(-) structure is reflected by the force constants of 436.1 and 4.5 N/m determined for the H(HS(-))-S(HS(-)) and H(HS(-))···O(w) bonds, respectively. A weak structure-making effect of the hydrated HS(-) ion results from the mean residence times of 1.5 and 2.1 ps of coordinated water molecules at the sulfur and hydrogen sites of the HS(-) ion, respectively.

Structural and Dynamical Properties of Hydrogen Fluoride in Aqueous Solution : An ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation

The novel ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level has been employed to investigate hydration structure and dynamics of hydrogen fluoride in aqueous solution. The average H-F bond length of 0.93 A obtained from the QMCF MD simulation is in good agreement with the experimental data. The HHF...Ow distance of 1.62 A was evaluated for the first hydration shell, and 2.00 A was observed for the FHF...Hw distance. The stability of hydrogen bonding is more pronounced in the hydrogen site of hydrogen fluoride, with a single water molecule in this part of the first hydration shell. A wide range of coordination numbers between 3 and 9 with an average value of 5.6 was obtained for the fluorine site. The force constants of 819.1 and 5.9 N/m were obtained for the HHF-FHF and HHF...Ow interactions, respectively, proving the stability of the nondissociated form of hydrogen fluoride in aqueous solution. The mean residence times of 2.1 and 2.5 ps were determined for ligand exchange processes in the neighborhood of fluorine and hydrogen atoms of hydrogen fluoride, respectively, indicating a weak structure-making effect of hydrogen fluoride in water. The corresponding H-bond lifetimes attribute this effect to the H atom site of HF.

An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution

An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree‐Fock level in conjunction with Dunning double‐ζ plus polarization function basis sets. The simulation predicts an average HCl bond distance of 1.28 Å, which is in good agreement with the experimental value. The HHCl···Ow and ClHCl···Hw distances of 1.84 and 3.51 Å were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure‐making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively.