Anan Tongraar

The hydration shell structure of Li+ investigated by Born–Oppenheimer ab initio QM/MM dynamics

Abstract A combined ab initio quantum mechanical (QM) and molecular mechanical (MM) molecular dynamics simulation has been applied to study the non-additive contributions to the surroundings of Li + in water. The first hydration sphere of Li + is treated by Born–Oppenheimer ab initio quantum mechanics, while the rest is described by classical pair potentials. A tetrahedral structure of four water molecules in the first solvation shell of Li + is found by this combined QM/MM method with a valence double-zeta basis set, in contrast to the octahedral structure obtained by the traditional simulation using pair potentials.

The hydration structures of F− and Cl− investigated by ab initio QM/MM molecular dynamics simulations

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations have been performed to investigate the hydration shell properties of F− and Cl−. The chemically most relevant region, the hydration sphere of the anions, was treated by Born–Oppenheimer ab initio quantum mechanics using D95V+, 6-31+G and D95V++ basis sets for F−, Cl− and water, respectively, while the remaining part was described by classical pair potentials. The QM/MM simulations have predicted average coordination numbers of 4.6±0.2 for F− and 5.6±0.1 for Cl−, in contrast to the corresponding values of 5.8±0.1 and 5.9±0.1 resulting from classical pair potential simulations. Within the first hydration shell of F−, the QM/MM results indicate more flexibility of the hydration complex in which the F−⋯H–O bond appears to be linear. For the case of Cl−, a combination of linear and bridged forms, together with a competition between the solvation of the ion and hydrogen bonding among water molecules, are observed.

Structure of the hydrated Ca2+ and Cl−: Combined X-ray absorption measurements and QM/MM MD simulations study

A combination of X-ray absorption spectroscopy (XAS) measurements and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations has been applied to elucidate detailed information on the hydration structures of Ca(2+) and Cl(-). The XAS spectra (extended X-ray absorption fine structure, EXAFS, and X-ray absorption near-edge structure, XANES) measured from aqueous CaCl(2) solution were analyzed and compared to those generated from snapshots of QM/MM MD simulations of Ca(2+) and Cl(-) in water. With regard to this scheme, the simulated QM/MM-EXAFS and QM/MM-XANES spectra, which correspond to the local structure and geometrical arrangement of the hydrated Ca(2+) and Cl(-) at molecular level show good agreement with the experimentally observed EXAFS and XANES spectra. From the analyses of the simulated QM/MM-EXAFS spectra, the hydration numbers for Ca(2+) and Cl(-) were found to be 7.1 +/- 0.7 and 5.1 +/- 1.3, respectively, compared to the corresponding values of 6.9 +/- 0.7 and 6.0 +/- 1.7 derived from the measured EXAFS data. In particular for XANES results, it is found that ensemble averages derived from the QM/MM MD simulations can provide reliable QM/MM-XANES spectra, which are strongly related to the shape of the experimental XANES spectra. Since there is no direct way to convert the measured XANES spectrum into details relating to geometrical arrangement of the hydrated ions, it is demonstrated that such a combined technique of XAS experiments and QM/MM MD simulations is well-suited for the structural verification of aqueous ionic solutions.

The role of non-additive contributions on the hydration shell structure of Mg2+ studied by Born–Oppenheimer ab initio quantum mechanical/molecular mechanical molecular dynamics simulation

Abstract An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate the effects of non-additive contributions on the hydration shell structure of Mg 2+ . The active-site region, the sphere including the second hydration shell of Mg 2+ , was treated by Born–Oppenheimer ab initio quantum mechanics, while the rest is described by classical pair potentials. A hydration complex with six inner shell waters and 12 second shell waters was observed. It was also found that the effects of non-additive terms play an important role in the preferential orientation of water molecules inside the hydration sphere of Mg 2+ .

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.

Molecular dynamics simulations of a potassium ion and an iodide ion in liquid ammonia

Abstract The systems consisting of one K+ with 215 ammonia and one I− with 215 ammonia molecules have been investigated by molecular dynamics simulations at an average temperature of 240 K, using a flexible ammonia model. K+-ammonia and I−-ammonia pair potentials were constructed from ab initio calculations with basis set superposition error (BSSE) correction. Eventual non-additivity of the K+-ammonia potential has been also examined. Structural properties of the solutions were investigated through radial distribution functions (RDFs) and their running integration numbers, leading to coordination numbers of 8.7 and for 12–15 K+ and I−, respectively. Velocity autocorrelation functions and their Fourier transforms, describing the dynamical properties of the solutions, are in good agreement with available theoretical and experimental data.

Preferential solvation of Ca2+ in aqueous ammonia solution: Classical and combined ab initio quantum mechanical/molecular mechanical molecular dynamics simulations

Classical and combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations have been performed to investigate the solvation structure of Ca2+ in 18.4% aqueous ammonia solution. The classical molecular dynamics simulation has been carried out based on pairwise additive potentials. For the QM/MM scheme, the first solvation sphere of Ca2+ is treated by Born–Oppenheimer ab initio quantum mechanics using LANL2DZ basis sets, while the rest of the system is described based on classical pairwise additivity. The results indicate the importance of the QM treatment in obtaining a reliable geometrical arrangement as well as the correct coordination number of the solvated ion. Within the first solvation sphere of Ca2+, the QM/MM simulation reveals a polyhedral structure with an average coordination number of 7.2, consisting of 5.2 water and 2 ammonia molecules, compared to the corresponding value of 9.7 composed of 6.7 water and 3 ammonia molecules obtained by classical pair potential simulation. The preference for ligands is discussed on the basis of detailed simulation results.

QM/MM MD simulations of iodide ion (I(-)) in aqueous solution: a delicate balance between ion-water and water-water H-bond interactions.

The characteristics of an iodide ion (I(-)) in aqueous solution were investigated by means of HF/MM and B3LYP/MM molecular dynamics simulations, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels using the LANL2DZdp and D95 V+ basis sets for I(-) and water, respectively. According to both the HF/MM and B3LYP/MM results, the ion-water interactions are relatively weak, compared to the water-water hydrogen bonds, thus causing an unstructured nature of the hydration shell. Comparing the HF and B3LYP treatments for the description of this hydrated ion, the overestimation of the ion-water hydrogen-bond strength by the B3LYP method is recognizable, yielding a remarkably more compact and too rigid ion-water complex.

Ab initio QM/MM dynamics of H3O+ in water.

A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6–8 water molecules. It is treated at the Hartree‐Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O  4+ ) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O  2+ ) structure. Besides the three nearest‐neighbor water molecules directly hydrogen‐bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ions hydration shell indicate that such next‐nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton.

Structure and dynamics of hydrated NH 4+: An ab initio QM/MM molecular dynamics simulation

A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate solvation structure and dynamics of NH  4+ in water. The most interesting region, the sphere includes an ammonium ion and its first hydration shell, was treated at the Hartree–Fock level using DZV basis set, while the rest of the system was described by classical pair potentials. On the basis of detailed QM/MM simulation results, the solvation structure of NH  4+ is rather flexible, in which many water molecules are cooperatively involved in the solvation shell of the ion. Of particular interest, the QM/MM results show fast translation and rotation of NH  4+ in water. This phenomenon has resulted from multiple coordination, which drives the NH  4+ to translate and rotate quite freely within its surrounding water molecules. In addition, a “structure‐breaking” behavior of the NH  4+ is well reflected by the detailed analysis on the water exchange process and the mean residence times of water molecules surrounding the ion.