Structure and dynamics of high-spin Ru in aqueous solution: Ab initio QM/MM molecular dynamics simulation

The structural and dynamical properties of high-spin Ru²⁺ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru²⁺. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru²⁺ and the 6-31G^∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru²⁺–O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru²⁺ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.     

Characterization of the structure and dynamics of an aqueous Hg solution by an ab initio molecular dynamics study

Quantum mechanical charge field (QMCF) MD simulation has been performed to investigate the structure and dynamics of Hg²⁺ hydrate. The first-shell hexacoordinated [Hg(H₂O)₆]²⁺ complex with an average Hg²⁺-O distance of 2.40 Å is dominantly found, which corresponds to the neutron diffraction and extended X-ray absorption fine structure (EXAFS) experiments. Other species, in particular the 7-fold coordinated complexes, can be formed transiently, according to the water exchange processes with an associative interchange (I_a) mechanism. The second hydration shell exhibits a Hg²⁺-O distance of 4.6 Å with a coordination number of ~ 14. The mean residence times (MRTs) of first- and second-shell waters clearly indicate a strong “structure-forming” ability of Hg²⁺ in aqueous solution.     

The Jahn-Teller effect of the Cr(2+) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations

The hydration structure of Cr(2+) 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(H(2)O)(6)](2+) complex was pronounced in the QM/MM MD simulation. The first-shell distances of Cr(2+) are in the range of 1.9-2.8 A, which are slightly larger than those observed in the cases of Cu(2+) and Ti(3+). 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.     

Multiple-layer heterometallic MnII–AgI coordination polymers constructed from [Ag 2I (CN)3]? and [AgI(CN)2]? units

Two multiple-layer heterometallic Mn^II–Ag^I coordination polymers, {Mn^II(ampyz)(H₂O)[Ag₂^I(CN)₃][Ag^I(CN)₂]·ampyz} _n (1) and {[Mn^II(benzim)₂[Ag^I(CN)₂]₂][(benzim)Ag^I(CN)]·H₂O} _n (2) where ampyz = 2-aminopyrazine and benzim = benzimidazole, have been prepared and structurally characterized. Compound 1 reveals a multiple-layer two-dimensional network with strong hexanuclear argentophilic interactions leading to an infinite three-dimensional framework. Compound 2 has an unprecedented double-layer two-dimensional squared grid-type network with (4,4) topology through Ag^I···Ag^I and π–π interactions between two adjacent squared layers. These double-layer networks of 2 are linked to others by π–π interactions, leading to a three-dimensional framework.     

Dynamics and mechanism of structural diffusion in linear hydrogen bond

Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H-bond) chain were studied, using the CH(3)OH(2)(+)(CH(3)OH)(n) complexes, n = 1-4, as model systems. The present investigations used B3LYP/TZVP calculations and Born-Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H-bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(n) complexes, n = 1-4. It was found that the H-bond chains with n = 1 and 3 represent the most active intermediate states and the CH(3)OH(2)(+)(CH(3)OH)(n) complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared-proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared-proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH(3)OH molecules in the H-bond chain, and the quasi-dynamic equilibriums between the shared-proton structure (n = 3) and the close-contact structures (n ≥ 4). The latter prohibits proton transfer reaction in the H-bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared-proton intermediate state.     

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 H_HCl···O_w and Cl_HCl···H_w 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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.     

Quantum mechanical/molecular mechanical simulations of the Tl(III) ion in water

Classical molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) MD simulations have been performed to investigate the structural and dynamical properties of the Tl(III) ion in water. A six-coordinate hydration structure with a maximum probability of the Tl-O distance at 2.21 A was observed, which is in good agreement with X-ray data. The librational and vibrational spectra of water molecules in the first hydration shell are blue-shifted compared with those of pure liquid water, and the Tl-O stretching force constant was evaluated as 148 Nm(-1). Both structural and dynamical properties show a distortion of the first solvation shell structure. The second shell ligands' mean residence time was determined as 12.8 ps. The Tl(III) ion can be classified as "structure forming" ion; the calculated hydration energy of -986 +/- 9 kcal mol agrees well with the experimental value of -986 kcal mol.     

Characterization of structure and dynamics of an aqueous scandium(iii) ion by an extended ab initio QM/MM molecular dynamics simulation

Hydration structure and dynamics of an aqueous Sc(iii) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(iii) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(iii)-O bond length of 2.14 ? was identified for six prism water molecules with one capping water located at around 2.26 ?, reproducing well the X-ray diffraction data. The Sc(iii)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(iii) ion predict a mean ligand residence time of 7.3 ps.     

Iodomethyl phenyl sulfoxide: reactivity and synthetic applications

Lithio iodomethyl phenyl sulfoxides reacted with alkyl halides and carbonyl compounds to give adducts in good to moderate yields. Solvolysis of the carbonyl adducts led to sulfones or the ring expanded product.