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.     

New Insights into the Jahn–Teller Effect through ab initio Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulations of CuII in Water

The Cu^II hydration shell structure has been studied by means of classical molecular dynamics (MD) simulations including three-body corrections and hybrid quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations at the Hartree–Fock level. The copper(II ) ion is found to be six-fold coordinated and [Cu(H₂O)₆]²⁺ exhibits a distorted octahedral structure. The QM/MM MD approach reproduces correctly the experimentally observed Jahn–Teller effect but exhibits faster inversions (<200 fs) and a more complex behaviour than expected from experimental data. The dynamic Jahn–Teller effect causes the high lability of [Cu(H₂O)₆]²⁺ with a ligand-exchange rate constant some orders of magnitude higher than its neighbouring ions Ni^II and Zn^II. Nevertheless, no first-shell water exchange occurred during a 30-ps simulation. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and various angular distributions and the dynamical properties as librational and vibrational motions and reorientational times were evaluated, which lead to detailed information about the first hydration shell. Second-shell water-exchange processes could be observed within the simulation time scale and yielded a mean ligand residence time of ≈20 ps.     

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.     

Increasing the time step with mass scaling in Born‐Oppenheimer ab initio QM/MM molecular dynamics simulations

Born‐Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state‐of‐the‐art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass‐scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born‐Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass‐scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

La3Ru8B6 and Y3Os8B6, new members of a homologous series R(A)nM3n−1B2n

Two new compounds, La₃Ru₈B₆ and Y₃Os₈B₆, were synthesized by arc melting the elements. Their structural characterization was carried out at room temperature on as-cast samples by using X-ray diffractometry. According to X-ray single-crystal diffraction results these borides crystallize in Fmmm space group (no. 69), Z=4, a=5.5607(1) Å, b=9.8035(3) Å, c=17.5524(4) Å, ρ=8.956 Mg/m³, μ=25.23 mm⁻¹ for La₃Ru₈B₆ and a=5.4792(2) Å, b=9.5139(4) Å, c=17.6972(8) Å, ρ=13.343 Mg/m³, μ=128.23 mm⁻¹ for Y₃Os₈B₆. The crystal structure of La₃Ru₈B₆ was confirmed from Rietveld refinement of X-ray powder diffraction data. Both La₃Ru₈B₆ and Y₃Os₈B₆ compounds are isotypic with the Ca₃Rh₈B₆ compound and their structures are built up from CeCo₃B₂-type and CeAl₂Ga₂-type structural fragments taken in ratio 2:1. They are the members of structural series R(A)_nM_3n−1B_2n with n=3 (R is the rare earth metal, A the alkaline earth metal, and M the transition metal). Structural and atomic parameters were also obtained for La_0.94Ru₃B₂ compound from Rietveld refinement (CeCo₃B₂-type structure, P6/mmm space group (no. 191), a=5.5835(9) Å, c=3.0278(6) Å).     

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 crystal chemistry of fluorite-related Bi38Mo7O78 from single crystal X-ray diffraction and ab initio calculations

The floating-zone furnace method was used to synthesize single crystals of the fluorite-related δ-Bi₂O₃-type phase Bi₃₈Mo₇O₇₈ for the first time. Single crystal synchrotron X-ray diffraction data, in conjunction with ab initio (density functional theory) calculations, were used to solve, optimize, and refine the 5×3×3 commensurate superstructure of fluorite-type δ-Bi₂O₃ in Pbcn (a=28.7058(11) Å, b=16.8493(7) Å and c=16.9376(6) Å, Z=4, R_F=11.26%, wR_I=21.67%). The structure contains stepped channels of Mo⁶⁺ in tetrahedral environments along the b axis and chains of Mo⁶⁺ in octahedral environments along the ac plane. The role of the stepped channels in oxide ion conduction is discussed. The simultaneous presence of both tetrahedral and octahedral coordination environments for Mo⁶⁺, something not previously observed in Mo⁶⁺-doped δ-Bi₂O₃-type phases, is supported by charge balance considerations in addition to the results of crystallographic and ab initio analysis.     

Rietveld refinement and photoluminescent properties of a new blue-emitting material: Eu activated SrZnP2O7

A new efficient blue phosphor, Eu²⁺ activated SrZnP₂O₇, has been synthesized at 1000 °C under reduced atmosphere and the crystal structure and photoluminescence properties have been investigated. The crystal structure of SrZnP₂O₇ was obtained via Rietveld refinement of powder X-ray diffraction (XRD) pattern. It was found that SrZnP₂O₇ crystallizes in space group of P2₁/n (no. 14), Z=4, and the unit cell dimensions are: a=5.30906(2) Å, b=8.21392(3) Å, c=12.73595(5) Å, β=90.1573(3)°, and V=555.390(3) Å³. Under ultraviolet excitation (200-400 nm), efficient Eu²⁺ emission peaked at 420 nm was observed, of which the luminescent efficiency at the optimal concentration of Eu²⁺ (4 mol%) was estimated to be 96% as that of BaMgAl₁₀O₁₇:Eu²⁺. Hence, the SrZnP₂O₇:Eu²⁺ exhibit great potential as a phosphor in different applications, such as ultraviolet light emitting diode and photo-therapy lamps.     

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.     

An extensible interface for QM/MM molecular dynamics simulations with AMBER

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface. © 2013 Wiley Periodicals, Inc.     

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd²⁺ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd²⁺. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd²⁺ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd²⁺ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.     

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.     

The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics,free energies,and excited state properties

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM–TURBOMOLE is well‐suited for extended QM/MM MD simulations using first principles methods with large (triple‐ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg²⁺(aq), where the MM outer sphere water molecules are represented using the SWM4‐NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg²⁺ and Zn²⁺ were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time‐averaged solution absorption spectrum of indole, the emission spectrum of the indole excited state, and the electronic circular dichroism spectrum of an oxacepham. © 2014 Wiley Periodicals, Inc.     

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.     

A re-investigation of the crystal structure and luminescence of BaCa2MgSi2O8:Eu

Barium calcium magnesium silicate (BaCa₂MgSi₂O₈), a compound whose space group was obtained via X-ray diffraction data, was re-investigated using neutron diffraction techniques. A combined powder X-ray and neutron Rietveld method revealed that BaCa₂MgSi₂O₈ crystallizes in the trigonal space group P3? (Z=1, a=5.42708(5) Å, c=6.79455(7) Å, V=173.310(4) Å³; R_p/R_wp=5.52%/7.63%), instead of the previously believed space group P3?m1. The difference in the two structures arises from the displacement of the O2 atom. Blue emission from Ba_0.98Eu_0.02Ca₂MgSi₂O₈ under 325-nm excitation is ascribed to the 4f⁶5d¹→4f⁷ transitions of Eu²⁺ ions at Ba sites and Ca sites. Site assignment of Eu²⁺ ions in the titled compound was performed by analysis of emission spectra at temperatures in the range of 4.2-300 K.     

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 (H9O4+) 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 (H5O2+) 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 ion's 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, Stoichiometry, and Properties of the Chimney-Ladder Phases Ru2Ge3+x (0<x<1)

The preparation and physical characterization of non-stoichiometric Ru₂Ge_3+x (0≤x≤1) are reported for the first time. The defect TiSi₂-type chimney-ladder structure is maintained for the full stoichiometry range. The resistivity of Ru₂Ge_3+x increases systematically with x from 300 mΩ cm, x=0 -3 Ω cm, x=1 at 300 K. The temperature dependence is consistent with a variable range-hopping mechanism for x≥0.6. The Seebeck coefficients of samples do not evolve simply with x. A low thermal conductivity (κ_{300 K}=0.03 W/K cm) suggests that Ru₂Ge₃ has some of the properties of a phonon-glass-electron-crystal. The low value of the thermoelectric figure of merit ZT=3.2×10⁻³ (T=300 K) calculated for Ru₂Ge₃ is due primarily to a low conductivity.     

An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution

Structural and dynamical properties of Zn(II) in aqueous solution were investigated, based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation at double-zeta Hartree-Fock quantum mechanical level including the first and second hydration shells into the QM region. The inclusion of the second shell in the QM region resulted in significant changes in the properties of the hydrate. The first shell coordination number was found to be 6, the second shell consists of approximately 14 water molecules. The structural properties were determined in terms of RDF, ADF, tilt and theta angle distributions, while dynamics were characterized by mean ligand residence times, ion-ligand stretching frequencies and the vibrational and librational motions of water ligands.