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.     

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     

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.     

Influence of end-capped group on structural and electronic properties of the At-π-Ac-π-At small molecule donor for high-performance organic solar cells

Structural Chemistry - To achieve high efficient donors for organic solar cells, structural, electronic, and optical properties of the At-π-Ac-π-At small molecules were systematically...     

Ab initio quantum mechanical charge field (QMCF) molecular dynamics: a QM/MM – MD procedure for accurate simulations of ions and complexes

A new formalism for quantum mechanical / molecular mechanical (QM/MM) dynamics of chemical species in solution has been developed, which does not require the construction of any other potential functions except those for solvent–solvent interactions, maintains all the advantages of large simulation boxes and ensures the accuracy of ab initio quantum mechanics for all forces acting in the chemically most relevant region. Interactions between solute and more distant solvent molecules are incorporated by a dynamically adjusted force field corresponding to the actual molecular configuration of the simulated system and charges derived from the electron distribution in the solvate. The new formalism has been tested with some examples of hydrated ions, for which accurate conventional ab initio QM/MM simulations have been previously performed, and the comparison shows equivalence and in some aspects superiority of the new method. As this simulation procedure does not require any tedious construction of two-and three-body interaction potentials inherent to conventional QM/MM approaches, it opens the straightforward access to ab initio molecular dynamics simulations of any kind of solutes, such as metal complexes and other composite species in solution.     

Tl(I)‐the strongest structure‐breaking metal ion in water? A quantum mechanical/molecular mechanical simulation study

Structural and dynamical properties of the Tl(I) ion in dilute aqueous solution have been investigated by ab initio quantum mechanics in combination with molecular mechanics. The first shell plus a part of the second shell were treated by quantum mechanics at Hartree-Fock level, the rest of the system was described by an ab initio constructed potential. The radial distribution functions indicate two different bond lengths (2.79 and 3.16 A) in the first hydration shell, in good agreement with large-angle X-ray scattering and extended X-ray absorption fine structure spectroscopy results. The average first shell coordination number was found as 5.9, and several other structural parameters such as coordination number distributions, angular distribution functions, and tilt- and theta-angle distributions were evaluated. The ion-ligand vibration spectrum and reorientational times were obtained via velocity auto correlation functions. The Tl-O stretching force constant is very weak with 5.0 N m(-1). During the simulation, numerous water exchange processes took place between first and second hydration shell and between second shell and bulk. The mean ligand residence times for the first and second shell were determined as 1.3 and 1.5 ps, respectively, indicating Tl(I) to be a typical "structure-breaker". The calculated hydration energy of -84 +/- 16 kcal mol(-1) agrees well with the experimental value of -81 kcal mol(-1). All data obtained for structure and dynamics of hydrated Tl(I) characterize this ion as a very special case among all monovalent metal ions, being the most potent "structure-breaker", but at the same time forming a distinct second hydration shell and thus having a far-reaching influence on the solvent structure.