Be(II) in aqueous solution--an extended ab initio QM/MM MD study

An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation at double-zeta restricted Hartree-Fock (RHF) level was performed at 293.15 K, including first and second hydration shell in the QM region to study the structural and dynamical properties of the Be(II)-hydrate in aqueous solution. The first tetrahedrally arranged hydration shell, with the four water molecules located at a mean Be-O distance of 1.61 A, is highly inert with respect to ligand exchange processes. The second shell, however, consisting in average of approximately 9.2 water ligands at a mean Be-O distance of 3.7 A and the third shell at a mean Be-O distance of 5.4 A with approximately 19 ligands rapidly exchange water molecules between them and with the bulk, respectively. Other structural parameters such as radial and angular distribution functions (RDF and ADF) and tilt- and theta-angle distributions were also evaluated. The dynamics of the hydrate were studied in terms of ligand mean residence times (MRTs) and librational and vibrational frequencies. The mean residence times for second shell and third shell ligands were determined as 4.8 and 3.2 ps, respectively. The Be-O stretching frequency of 658 cm(-1), associated with a force constant of 147 N m(-1) could be overestimated but it certainly reflects the exceptional stability of the ion-ligand bond in the first hydration shell.     

Structure and dynamics of La(III) in aqueous solution – An ab initio QM/MM MD approach

Ab initio QM/MM MD simulations have allowed to clarify some of the ambiguities arising from various studies on the hydrated La(III) ion. Both nine- and ten-coordinated hydrates co-exist and interchange in a dissociative process on the nano- or even subnanosecond scale, and thus much faster than any other trivalent main group or transition metal ions. The weak ion–ligand bond (53 N/m) supplies a reasonable explanation for it. The simulation results for La(III) are also compared to those for the isoelectronic ions Cs(I) and Ba(II) obtained by the same ab initio MD procedure, leading to conclusions on the influence of central ion charge on structural and dynamic properties of hydrate complexes.     

Structure and dynamics of solvated Sn(II) in aqueous solution: an ab initio QM/MM MD approach

Structural and dynamical properties of the hydrated Sn(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at double-zeta HF quantum mechanical level. The results indicate Sn(II)aq to be a rather peculiar, if not unique, case of a hydrated ion: four of its eight first-shell ligands do not take place in the otherwise frequent ligand-exchange processes, forming an approximately tetrahedral cage around the ion. The remaining ligands, however, exchange at a rate that is rather comparable to monovalent than divalent ions. This very surprising behavior of ligand exchange not yet observed in any previous simulation of over 30 hydrated metal ions is consistently confirmed by vibrational spectra, bond lengths, and a detailed analysis of the trajectories of the simulation.     

Structure and dynamics of Au+ ion in aqueous solution: ab initio QM/MM MD simulations

Structure and dynamics of hydrated Au(+) have been investigated by means of molecular dynamics simulations based on ab initio quantum mechanical molecular mechanical forces at Hartree-Fock level for the treatment of the first hydration shell. The outer region of the system was described using a newly constructed classical three-body corrected potential. The structure was evaluated in terms of radial and angular distribution functions and coordination number distributions. Water exchange processes between coordination shells and bulk indicate a very labile structure of the first hydration shell whose average coordination number of 4.7 is a mixture of 3-, 4-, 5-, 6-, and 7-coordinated species. Fast water exchange reactions between first and second hydration shell occur, and the second hydration shell is exceptionally large. Therefore, the mean residence time of water molecules in the first hydration shell (5.6 ps/7.5 ps for t*= 0.5 ps/2.0 ps) is shorter than that in the second shell (9.4 ps/21.2 ps for t*= 0.5 ps/2.0 ps), leading to a quite specific picture of a "structure-breaking" effect.     

Structure-breaking effects of solvated Rb(I) in dilute aqueous solution--an ab initio QM/MM MD approach

Structural properties of the hydrated Rb(I) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at the double-zeta HF quantum mechanical level. The first shell coordination number was found to be 7.1, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and theta-angle distributions allowed the full characterization of the hydration structure of the Rb(I) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions, as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes, and rate constants were also analyzed. The mean ligand residence time for the first shell was determined as tau = 2.0 ps.     

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.     

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.     

Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations

Combined ab initio quantum mechanical and molecular mechanical (QM/MM) simulations coupled with the block-localized wave function energy decomposition (BLW-ED) method have been conducted to study the solvation of two prototypical ionic systems, acetate and methylammonium ions in aqueous solution. Calculations reveal that the electronic polarization between the targeted solutes and water is the primary many-body effect, whereas the charge-transfer term only makes a small fraction of the total solute-solvent interaction energy. In particular, the polarization effect is dominated by the solvent (water) polarization.     

Stability of different zinc(II)-diamine complexes in aqueous solution with respect to structure and dynamics: a QM/MM MD study

In the context of our detailed study of the chemical behavior of aquo- and ammine-Zn(II) complexes, ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations were performed at the Hartree-Fock (HF) level for the zinc(II)-diamine complexes in aqueous solution. The initial structures of cis and trans isomers of the tetraaquodiamminezinc(II) complex were found to transform into the triaquodiamminezinc(II) complex by releasing one water ligand after approximately 6 and approximately 22 ps of simulation time, respectively. The structural and dynamical properties of these three zinc complexes, i.e., cis-[Zn(NH3)2(H2O)4]2+, trans-[Zn(NH3)2(H2O)4]2+, and [Zn(NH3)2(H2O)3]2+, were analyzed in terms of radial distribution functions (RDF), coordination number distributions (CND), angular distribution functions (ADF), tilt and theta angle distributions, ligands' mean residence times (MRTs), and ion-ligand stretching frequencies. One considerably elongated Zn-O bond of 2.43 A was observed in the case of the cis isomer for one of the water ligands located in the trans position to an ammonia ligand. In the trans isomer the average Zn-O bond length was observed to be 2.23 A, while in the triaquodiamminezinc(II) complex two distinct Zn-O bonds, namely 2.12 A for the ligands in the trigonal plane and 2.26 A for axial water molecules, were observed. As both of the octahedral isomers are transformed into the pentacoordinated structure within the picosecond range, they might be regarded as "metastable species or intermediates", while the triaquodiamminezinc(II) complex is the most stable species of the zinc(II)-diamine complex in aqueous solution.     

Pseudobond ab initio QM/MM approach and its applications to enzyme reactions

This perspective article mainly focuses on the development and applications of a pseudobond ab initio QM/MM approach to study enzyme reactions. The following aspects of methodology development are discussed: the approaches for the QM/MM covalent boundary problem, an efficient iterative optimization procedure, the methods to determine enzyme reaction paths, and the approaches to calculate free energy change in enzyme reactions. Several applications are described to illustrate the capability of the methods. Finally, future directions are discussed.     

Exploring structure and dynamics of the diaquotriamminezinc(II) complex by QM/MM MD simulation

The structural and dynamical properties of the cis-(O-Zn-O angle approximately 90 degrees) and trans-(O-Zn-O angle approximately 180 degrees) isomers of the model diaquotriamminezinc(II) complex in aqueous solution have been evaluated using the hybrid quantum mechanical/molecular mechanical molecular dynamics simulation approach at ab initio Hartree-Fock level. In both complexes, the first hydration shell contains five ligands (two water and three ammonia molecules) arranged in a trigonal bipyramidal geometry. In the metastable cis-isomer two different bond lengths of 2.34 and 2.13 A are observed for the Zn-Oax and Zn-Oeq bonds, respectively. The trans-isomer shows the maximum of the Zn-O distance at 2.26 A. The Zn-N bond distances in both cases are approximately 2.12 A. A geometrical transformation of the cis-isomer into the trans-isomer was observed after 11.5 ps of simulation, and the trans-isomer then remained stable throughout the whole simulation time of 30 ps. A comparative study for both isomers has been performed in terms of radial distribution functions, coordination number distributions, angular distribution functions, tilt and theta angle distributions, ligands' mean residence time, ion-ligand stretching frequencies, and the vibrational and librational motions of water ligands. The results are compared with the data for the previously studied zinc-monoamine and -diamine complexes.     

Gold(I) in liquid ammonia: ab initio QM/MM molecular dynamics simulation

Structure and dynamics investigations of Au(I) ion in liquid ammonia have been performed by means of a molecular dynamics simulation based on ab initio quantum mechanical/molecular mechanical forces, where the first solvation shell was treated by quantum mechanics at Hartree-Fock level. The outer region of the system was described using a newly constructed classical three-body corrected potential. A rigid structure of the first solvation shell was observed with an average Au-N distance of 2.15 A and a coordination number of 2.0.     

Ab initio QM/MM simulation of Ag+ in 18.6% aqueous ammonia solution: structure and dynamics investigations

Structure and dynamics investigations of Ag(+) in 18.6% aqueous ammonia solution have been carried out by means of the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation method. The most important region, the first solvation shell, was treated by ab initio quantum mechanics at the Restricted Hartree-Fock (RHF) level using double-zeta plus polarization basis sets for ammonia and plus ECP for Ag(+). For the remaining region in the system, newly constructed three-body corrected potential functions were used. The average composition of the first solvation shell was found to be [Ag(NH(3))(2)(H(2)O)(2.8)](+). No ammonia exchange process was observed for the first solvation shell, whereas ligand exchange processes occurred with a very short mean residence time of 1.1 ps for the water ligands. No distinct second solvation shell was observed in this simulation.     

Structure and dynamics of the [Zn(NH3)(H2O)5]2+ complex in aqueous solution obtained by an ab initio QM/MM molecular dynamics study

A model complex of the hexahydrated zinc(ii) cation with one water substituted by ammonia in aqueous solution has been studied by hybrid ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) at the double-zeta Hartree-Fock (HF) quantum mechanical level. The first solvation shell, consisting of 5 + 1 ligand(s) at mean distances of 2.2 and 2.1 A, respectively, from the Zn(ii) ion, was found to remain stable with respect to exchange processes within the simulation time. The labile second shell consists on average of approximately 19 water molecules. For structural elucidation of the pentaaquozinc(ii) amine complex in aqueous solution several data sets such as radial distribution functions (RDF), coordination number distributions (CND) and different angular distributions (ADF, tilt and theta angle) were employed. Dynamics were characterised by the ligands' mean residence time (MRT), ion-ligand stretching frequencies and the vibrational and librational motions of water ligands. The labile second shell's MRT value decreases upon introduction of one NH(3) ligand to 7.2 ps from the 10.5 ps observed for the hexaaquozinc(ii) complex.     

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value.     

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.     

The solvation structure of Pb(II) in dilute aqueous solution: an ab initio quantum mechanical/molecular mechanical molecular dynamics approach

Structural properties of the hydrated Pb(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical molecular dynamics simulations at Hartree-Fock quantum mechanical level. The first shell coordination number was found to be nine, and several other structural parameters such as angular distribution functions, radial distribution functions, and tilt- and theta-angle distributions allow the full characterization of the hydration structure of the Pb(II) ion.     

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.