Characteristics of CO3(2-)-water hydrogen bonds in aqueous solution: insights from HF/MM and B3LYP/MM MD simulations

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, have been performed to investigate the local hydration structure and dynamics of carbonate (CO(3)(2-)) in dilute aqueous solution. With respect to the QM/MM scheme, the QM region, which contains the CO(3)(2-) and its surrounding water molecules, was treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set, while the rest of the system is described by classical MM potentials. For both the HF/MM and B3LYP/MM simulations, it is observed that the hydrogen bonds between CO(3)(2-) oxygens and their nearest-neighbor waters are relatively strong, i.e., compared to water-water hydrogen bonds in the bulk, and that the first shell of each CO(3)(2-) oxygen atom somewhat overlaps with the others, which allows migration of water molecules among the coordinating sites to exist. In addition, it is observed that first-shell waters are either "loosely" or "tightly" bound to the respective CO(3)(2-) oxygen atoms, leading to large fluctuations in the number of first-shell waters, ranging from 1 to 6 (HF/MM) and 2 to 7 (B3LYP/MM), with the prevalent value of 3. Upon comparing the HF and B3LYP methods in describing this hydrated ion, the latter is found to overestimate the hydrogen-bond strength in the CO(3)(2-)-water complexes, resulting in a slightly more compact hydration structure at each of the CO(3)(2-) oxygens.     

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 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.     

Ab initio calculation of the MgO(100) interaction with He and Ne: a HF + MP2 and HF + MP2(B3LYP) comparison

Second order Rayleigh Schr?dinger perturbation theory is applied to calculate the correlation energy contribution to the London dispersion interaction to approximate the interaction of the He and Ne with the MgO(100) surface; single particle orbitals using either Hartree-Fock theory or hybrid-exchange density functional theory are used as the reference state.     

Solvent effects on peroxynitrite structure and properties from QM/MM simulations

We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the solvent was described using the mean-field TIP4P and the polarizable TIP4P-FQ force fields. The choice of basis sets, functionals and force field parameters has been validated by performing calculations on isolated peroxynitrite and on small peroxynitrite-water complexes. Poor values for isolated peroxynitrite structural properties and vibrational frequencies are found for most ab initio methods, particularly regarding the ON-OO(-) bond distance and the harmonic stretching frequency, probably due to the singlet-triplet instability found in the HF wave function. On the other hand, DFT methods yield results in better agreement with high level CCSD(T) ab initio calculations. We have computed the vibrational spectrum for aqueous peroxynitrite by calculating the Fourier transform of the velocity autocorrelation function extracted from the QM-MM molecular dynamics simulations. Our computational scheme, which allows for the inclusion of both anharmonicity and solvent effects, is able to clarify previous discrepancies regarding the experimental spectra assignments and to shed light on the subtle interplay between solvation and peroxynitrite structure and properties.     

DFT:B3LYP ab initio molecular dynamics study of the Zundel and Eigen proton complexes, H5O2+ and H9O4+, in the triplet state in gas phase and solution

DFT:B3LYP ab initio molecular dynamics (MD) approach is used to elucidate the properties of the Zundel and Eigen, H5O2+ and H9O4+, proton complexes in the triplet state. The simulation considers the complexes in the gas phase (isolated complexes) and inside the clusters composed of 32, 64, and 128 water molecules, mimicking the behavior of aqueous solutions. MD simulations reveal three distinct periods. For the complex in solutions, the periods are smoothed out. The H5O2+ and H9O4+ complexes in the triplet state undergo structural rearrangements, which eventually result in hydrogen elimination. For the H5O2+, the hydrogen is eliminated from the center of the water cluster, whereas for the H9O4+ it is removed from a near-surface water molecule. The rate of hydrogen elimination decreases with increasing the number of water molecules surrounding the complex.     

Substituent effects on the thermochemistry of thiophenes. a theoretical (G3(MP2)//B3LYP and G3) study

Very good linear correlations between experimental and calculated enthalpies of formation in the gas phase (G3(MP2)//B3LYP and G3) for 48 thiophene derivatives have been obtained. These correlations permit a correction of the calculated enthalpies of formation in order to estimate more reliable "experimental" values for the enthalpies of formation of substituted thiophenes, check the reliability of experimental measurements, and also predict the enthalpies of formation of new thiophenes that are not available in the literature. Moreover, the difference between the enthalpies of formation of isomeric thiophenes with the same substituent in positions 2 and 3 of the ring has been analyzed. Likewise, a comparison of the substituent effect in the thiophene and benzene rings has been established.     

Comparison of HF,HF + MP2, LDA,BLYP, and B3LYP band structures of the homopolypeptides

Ab initio HF, HF + MP2, LDA DFT, BLYP DFT, and B3LYP DFT calculations are compared in the case of 19 homopolypeptides in their β pleated sheet conformation. The results show that the B3LYP method provides good results for the fundamental gaps, as compared with the values estimated on the basis of available UV spectra and intermediate exciton calculations for PolyGly and PolyAla. The HF method gives the best agreement, using Koopman's theorem for the ionization potential, taking the calculated VB_max values in the HF case if one compares them with the experimental ionization potentials of the 19 amino acids measured by mass spectroscopy. Finally, how these methods might be improved to determine the most stable conformations of the homopolypeptides is outlined. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Jet cooled spectroscopy of H2DO+: Barrier heights and isotope-dependent tunneling dynamics from H3O+ to D3O+

The first high resolution spectroscopic data for jet cooled H2DO+ are reported, specifically via infrared laser direct absorption in the OH stretching region with a slit supersonic jet discharge source. Transitions sampling upper (0-) and lower (0+) tunneling states for both symmetric (nu1+ <-- 0+, nu1- <-- 0-, and nu1- <-- 0+) and antisymmetric (nu3+ <-- 0+ and nu3- <-- 0-) OH stretching bands are observed, where +/- refers to wave function reflection symmetry with respect to the planar umbrella mode transition state. The spectra can be well fitted to a Watson asymmetric top Hamiltonian, revealing band origins and rotational constants for benchmark comparison with high-level ab initio theory. Of particular importance are detection and assignment of the relatively weak band (nu1- <-- 0+) that crosses the inversion tunneling gap, which is optically forbidden in H3O+ or D3O+, but weakly allowed in H2DO+ by lowering of the tunneling transition state symmetry from D(3h) to C(2v). In conjunction with other H2DO+ bands, this permits determination of the tunneling splittings to within spectroscopic precision for each of the ground [40.518(10) cm(-1)], nu1 = 1 [32.666(6) cm(-1)], and nu3 = 1 [25.399(11) cm(-1)] states. A one-dimensional zero-point energy corrected potential along the tunneling coordinate is constructed from high-level ab initio CCSD(T) calculations (AVnZ, n = 3,4,5) and extrapolated to the complete basis set limit to extract tunneling splittings via a vibrationally adiabatic treatment. Perturbative scaling of the potential to match splittings for all four isotopomers permits an experimental estimate of DeltaV0 = 652.9(6) cm(-1) for the tunneling barrier, in good agreement with full six-dimensional ab initio results of Rajamaki, Miani, and Halonen (RMH) [J. Chem. Phys. 118, 10929 (2003)]. (DeltaV0 (RMH) = 650 cm(-1)). The 30%-50% decrease in tunneling splitting observed upon nu1 and nu3 vibrational excitations arises from an increase in OH stretch frequencies at the planar transition state, highlighting the transition between sp2 and sp3 hybridizations of the OHD bonds as a function of inversion bending angle.     

ESR studies on heterogeneous processes in irradiated SiO2/B2O3+H2O systems

Effect of B³⁺ (%B₂O₃) percentage ratio in silica gel on the nature and the mechanism of defect formation and yields of paramagnetic radiation centers (PC) have been studied. The nature of paramagnetic radiation centers of electron hole type has been revealed and their behavior has been investigated as a function of temperature changes. It has been found that the interaction between paramagnetic centers formed at SiO₂/B₂O₃ surface with absorbed water molecules (=1) leads to the formation of H and OH radicals. In addition the experiment shows that increased B³⁺ (%B₂O₃) percentage ratio in silica gel results in higher yields of paramagnetic centers and H-radicals. Possible mechanism of formation, localization and annihilation of non-equilibrium charge carriers (NCC) and their energy transfer to the adsorbed phase has been suggested.     

Product spin-orbit state resolved dynamics of the H+H2O and H+D2O abstraction reactions

The product state-resolved dynamics of the reactions H+H(2)O/D(2)O-->OH/OD((2)Pi(Omega);v',N',f )+H(2)/HD have been explored at center-of-mass collision energies around 1.2, 1.4, and 2.5 eV. The experiments employ pulsed laser photolysis coupled with polarized Doppler-resolved laser induced fluorescence detection of the OH/OD radical products. The populations in the OH spin-orbit states at a collision energy of 1.2 eV have been determined for the H+H(2)O reaction, and for low rotational levels they are shown to deviate from the statistical limit. For the H+D(2)O reaction at the highest collision energy studied the OD((2)Pi(3/2),v'=0,N'=1,A') angular distributions show scattering over a wide range of angles with a preference towards the forward direction. The kinetic energy release distributions obtained at 2.5 eV also indicate that the HD coproducts are born with significantly more internal excitation than at 1.4 eV. The OD((2)Pi(3/2),v'=0,N'=1,A') angular and kinetic energy release distributions are almost identical to those of their spin-orbit excited OD((2)Pi(1/2),v'=0,N'=1,A') counterpart. The data are compared with previous experimental measurements at similar collision energies, and with the results of previously published quasiclassical trajectory and quantum mechanical calculations employing the most recently developed potential energy surface. Product OH/OD spin-orbit effects in the reaction are discussed with reference to simple models.     

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.     

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.     

Proton dynamics in the perchloric acid clathrate hydrate HClO4.5.5H2O

In the perchloric acid clathrate hydrate HClO4.5.5H2O, the perchlorate anions are contained inside an aqueous host crystalline matrix, positively charged because of the presence of delocalized acidic protons. Our experimental results demonstrate that the microscopic mechanisms of proton conductivity in this system are effective on a time scale ranging from nanosecond to picosecond. In the present paper, we discuss more specifically on the relaxation processes occurring on a nanosecond time scale by combining high-resolution quasielastic neutron scattering and 1H pulse-field-gradient nuclear magnetic resonance experiments. The combination of these two techniques allows us to probe proton dynamics in both space and time domains. The existence of two types of proton dynamical processes has been identified. The slowest one is associated to long-range translational diffusion of protons between crystallographic oxygen sites and has been precisely characterized with a self-diffusion coefficient of 3.5 x 10(-8) cm2/s at 220 K and an activation energy of 29.2+/-1.4 kJ/mol. The fastest dynamical process is due to water molecules' reorientations occurring every 0.7 ns at 220 K with an activation energy of 17.4+/-1.5 kJ/mol. This powerful multitechnique approach provides important information required to understand the microscopic origin of proton transport in an ionic clathrate hydrate.     

Hybrid QM/MM molecular dynamics simulations for an ionic SN2 reaction in the supercritical water: OH- + CH3Cl --> CH3OH + Cl-

A hybrid real space quantum mechanical/molecular mechanical (RS-QM/MM) method has been applied to an ionic S(N)2 reaction (OH- + CH3Cl --> CH3OH + Cl-) in water solution to investigate dynamic solvation effects of the supercritical water (SCW) on the reaction. It has been demonstrated that the approaching process of OH- to methyl group is prevented by water molecules in the ambient water (AW), while the reaction takes place easily in the gas phase. Almost the same solvation effect on the dynamics of OH- is observed in the SCW, though the bulk density of water is substantially reduced compared with that of the AW. It has been shown that the solvation of the SCW around the OH anion is locally identical to that of the AW due to the strong ion-dipole interactions between OH- and water molecules. At the transition state, the QM/MM simulations have revealed that the excess electron is quite flexible, and the charge volume, as well as the fractional charges on atoms, vary seriously depending on the instantaneous solvent configurations. However, it has been found that the solvation energy in the SCW can be qualitatively related to the HOMO volume of the system by Born's equation.     

Stationary points on the energy hypersurface of the reaction O3 + H•→ [•O3H]* ⇆ O2 + •OH and thermodynamic functions of •O3H at G3MP2B3, CCSD(T)-CBS (W1U) and MR-ACPF-CBS levels of theory

The relative enthalpies, ΔH^o (0) and ΔH^o (298.15), of stationary points (four minimum and three transition structures) on the ^•O₃H potential energy surface were calculated with the aid of the G3MP2B3 as well as the CCSD(T)–CBS (W1U) procedures from which we earlier found mean absolute deviations (MAD) of 3.9 kJ mol⁻¹ and 2.3 kJ mol⁻¹, respectively, between experimental and calculated standard enthalpies of the formation of a set of 32 free radicals. For CCSD(T)-CBS (W1U) the well depth from O₃ + H^• to trans-^•O₃H, ΔH^o_well(298.15) = −339.1 kJ mol⁻¹, as well as the reaction enthalpy of the overall reaction O₃ + H^•→O₂ + ^•OH, Δ_rH^o(298.15) = −333.7 kJ mol⁻¹, and the barrier of bond dissociation of trans-^•O₃H → O₂ + ^•OH, ΔH^o(298.15) = 22.3 kJ mol⁻¹, affirm the stable short-lived intermediate ^•O₃H. In addition, for radicals cis-^•O₃H and trans-^•O₃H, the thermodynamic functions heat capacity C^o_p(T), entropy S^o (T), and thermal energy content H^o(T) − H^o(0) are tabulated in the range of 100 − 3000 K. The much debated calculated standard enthalpy of the formation of the trans-^•O₃H resulted to be Δ_fH^o(298.15) = 31.1 kJ mol ⁻¹ and 32.9 kJ mol ⁻¹, at the G3MP2B3 and CCSD(T)-CBS (W1U) levels of theory, respectively. In addition, MR-ACPF-CBS calculations were applied to consider possible multiconfiguration effects and yield Δ_fH^o(298.15) = 21.2 kJ mol ⁻¹. The discrepancy between calculated values and the experimental value of −4.2 ± 21 kJ mol⁻¹ is still unresolved. Note added in proof: Yu-Ran Luo and J. Alistair Kerr, based on the discussion in reference 12, recently presented an experimental value of Δ_fH^o(298.15) = 29.7 ± 8.4 kJ mol⁻¹ in the 85th edition of the CRC Handbook of Chemistry and Physics (in progress).     

Full-dimensional quantum dynamics study of the H + H2O and H + HOD exchange reactions

The initial state-selected time-dependent wave packet approach is employed to study the H' + H(2)O → H'OH + H and H' + HOD → H'OD + H, HOH' + D exchange reactions with both OH bonds in the H(2)O reactant and OH(D) bond in the HOD reactant treated as reactive bonds. The total reaction probabilities for different partial waves, as well as the integral cross sections, which are the exact CC (coupled-channel) results, are first obtained in this study for the H(2)O(HOD) reactant initially in the ground rovibrational state. Because of the shallow C(3v) minimum along the reaction path, the reaction probabilities for the three reactions present several resonance peaks, with one dominant resonance peak just above the threshold. The cross sections for the H' + HOD → HOH' + D reaction are substantially smaller than those for the H' + H(2)O → H'OH + H and H' + HOD → H'OD + H reactions, indicating that the H'/H exchange reactions are much more favored. In the CC calculations, the resonance peaks in the reaction probabilities diminish quickly with the increase in total angular momenta J, resulting in the existence of a clear step-like feature just above the threshold in the cross sections for the title reactions, which manifests the signature of shape resonances in these reactions. In the CS calculations, the resonance peaks on reaction probabilities persist in many partial waves, and thus the resonance structures can no longer survive the partial-wave summation and are washed out completely in the CS cross sections for the title reactions.