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.     

Ab initio molecular dynamics study of carbon dioxide and bicarbonate hydration and the nucleophilic attack of hydroxide on CO2

We apply ab initio molecular dynamics (AIMD) to study the hydration structures of the carbon dioxide molecule and the bicarbonate and carbonate anions in liquid water. We also compute the free energy change associated with the nucleophilic attack of the hydroxide ion on carbon dioxide. CO2 behaves like a hydrophobic species and exhibits weak interactions with water molecules. The bicarbonate and carbonate ions are strongly hydrated and coordinate to an average of 6.9 and 8.7 water molecules, respectively. The energetics for the reaction in the gas phase are investigated using density functional theory and second-order M?ller-Plesset perturbation theory (MP2) in conjunction with high-quality basis sets. Using umbrella sampling techniques, we compute the standard state, aqueous phase free energy difference associated with the reaction CO2+OH--->HCO3- after correcting AIMD energies with MP2 results. Our predictions are in good agreement with experiments. The hydration structures along the reaction coordinate, which give rise to a predicted 9.7 kcal/mol standard state free energy barrier, are further analyzed.     

Oxidation of methanol by FeO2+ in water: DFT calculations in the gas phase and ab initio MD simulations in water solution

We investigate the mechanism of methanol oxidation to formaldehyde by ironoxido ([Fe(IV)O]2+), the alleged active intermediate in the Fenton reaction. The most likely reaction mechanisms are explored with density functional theory (DFT) calculations on microsolvated clusters in the gas phase and, for a selected set of mechanisms, with constrained Car-Parrinello molecular dynamics (CPMD) simulations in water solution. Helmholtz free energy differences are calculated using thermodynamic integration in a simulation box with 31 water molecules at 300 K. The mechanism of the reaction is investigated with an emphasis on whether FeO2+ attacks methanol at a C-H bond or at the O-H bond. We conclude that the most likely mechanism is attack by the oxido oxygen at the C-H bond ("direct CH mechanism"). We calculate an upper bound for the reaction Helmholtz free energy barrier in solution of 50 kJ/mol for the C-H hydrogen transfer, after which transfer of the O-H hydrogen proceeds spontaneously. An alternative mechanism, starting with coordination of methanol directly to Fe ("coordination OH mechanism"), cannot be ruled out, as it involves a reaction Helmholtz free energy barrier in solution of 44 +/- 10 kJ/mol. However, this coordination mechanism has the disadvantage of requiring a prior ligand substitution reaction, to replace a water ligand by methanol. Because of the strong acidity of [FeO(H2O)5]2+, we also investigate the effect of deprotonation of a first-shell water molecule. However, this is found to increase the barriers for all mechanisms.     

Ab initio QM/MM molecular dynamics study on the excited-state hydrogen transfer of 7-azaindole in water solution

Ab initio molecular dynamics (AIMD) simulations for the excited-state hydrogen transfer (ESHT) reaction of 7-azaindole (7AI-(H2O)n; n = 1, 2) clusters in the gas phase and in water are presented. The effective fragment potential (EFP) is employed to model the surrounding water molecules. The AIMD simulations for 7AI-H2O and 7AI-(H2O)2 clusters show an asynchronous hydrogen transfer at t approximately 50 fs after the photoexcitation. While the ESHT mechanism for 7AI-H2O in water does not change appreciably compared with that in the gas phase, the AIMD simulations on 7AI-(H2O)2 in water solution exhibit two different mechanisms. Since the tautomer form is lower in energy compared to the normal form in the S1 state, 7AI and (H2O) n fragments separate from each other after the ESHT. With the use of the results of the AIMD trajectories, the minimum energy conical intersection point in the tautomer region has also been located.     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

The low-temperature dynamic crossover phenomenon in protein hydration water: simulations vs experiments

A super-Arrhenius-to-Arrhenius dynamic crossover phenomenon has been observed in the translational alpha-relaxation time and in the inverse of the self-diffusion constant both experimentally and by simulations for lysozyme hydration water in the temperature range of TL = 223 +/- 2 K. MD simulations are based on a realistic hydrated powder model, which uses the TIP4P-Ew rigid molecular model for the hydration water. The convergence of neutron scattering, nuclear magnetic resonance and molecular dynamics simulations supports the interpretation that this crossover is a result of the gradual evolution of the structure of hydration water from a high-density liquid to a low-density liquid form upon crossing of the Widom line above the possible liquid-liquid critical point of water.     

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.     

Structural correlations in liquid water: a new interpretation of IR spectroscopy

We present a new and alternative interpretation of the structure of the IR vibrational mode (nu(OH) band) of pure water. The re-interpretation is based on the influence of the cooperative hydrogen bonding arising from a network of hydrogen bonds in the liquid. The nu(OH) band has six components that are dominated by differences in their O-H bond lengths but deviate from thermodynamically average values due to interactions with the hydrogen bond network. The physical origin of the structure in the nu(OH) band is directly related to the O-H bond length, and variations in this bond length are caused by the influence of the surrounding hydrogen-bonded network of water molecules.     

Computing the 7Li NMR chemical shielding of hydrated Li+ using cluster calculations and time-averaged configurations from ab initio molecular dynamics simulations

Ab initio molecular dynamics (AIMD) simulations have been used to predict the time-averaged Li NMR chemical shielding for a Li(+) solution. These results are compared to NMR shielding calculations on smaller Li(+)(H(2)O)(n) clusters optimized in either the gas phase or with a polarizable continuum model (PCM) solvent. The trends introduced by the PCM solvent are described and compared to the time-averaged chemical shielding observed in the AIMD simulations where large explicit water clusters hydrating the Li(+) are employed. Different inner- and outer-coordination sphere contributions to the Li NMR shielding are evaluated and discussed. It is demonstrated an implicit PCM solvent is not sufficient to correctly model the Li shielding, and that explicit inner hydration sphere waters are required during the NMR calculations. It is also shown that for hydrated Li(+), the time averaged chemical shielding cannot be simply described by the population-weighted average of coordination environments containing different number of waters.     

Molecular dynamics simulation of the dielectric constant of water: the effect of bond flexibility

The role of bond flexibility on the dielectric constant of water is investigated via molecular dynamics simulations using a flexible intermolecular potential SPC/Fw [Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. 128, 024503 (2006)]. Dielectric constants and densities are reported for the liquid phase at temperatures of 298.15 K and 473.15 K and the supercritical phase at 673.15 K for pressures between 0.1 MPa and 200 MPa. Comparison with both experimental data and other rigid bond intermolecular potentials indicates that introducing bond flexibility significantly improves the prediction of both dielectric constants and pressure-temperature-density behavior. In some cases, the predicted densities and dielectric constants almost exactly coincide with experimental data. The results are analyzed in terms of dipole moments, quadrupole moments, and equilibrium bond angles and lengths. It appears that bond flexibility allows the molecular dipole and quadrupole moment to change with the thermodynamic state point, and thereby mimic the change of the intermolecular interactions in response to the local environment.     

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.     

Hydration structure of water confined between mica surfaces

We report further molecular dynamics simulations on the structure of bound hydration layers under extreme confinement between mica surfaces. We find that the liquid phase of water is maintained down to 2 monolayer (ML) thick, whereas the structure of the K(+) ion hydration shell is close to the bulk structure even under D = 0.92 nm confinement. Unexpectedly, the density of confined water remains approximately the bulk value or less, whereas the diffusion of water molecules decreases dramatically. Further increase in confinement leads to a transition to a bilayer ice, whose density is much less than that of ice Ih due to the formation of a specific hydrogen-bonding network.     

Vibrational and orientational dynamics of water in aqueous hydroxide solutions

We report the vibrational and orientational dynamics of water molecules in isotopically diluted NaOH and NaOD solutions using polarization-resolved femtosecond vibrational spectroscopy and terahertz time-domain dielectric relaxation measurements. We observe a speed-up of the vibrational relaxation of the O-D stretching vibration of HDO molecules outside the first hydration shell of OH(-) from 1.7 ± 0.2 ps for neat water to 1.0 ± 0.2 ps for a solution of 5 M NaOH in HDO:H(2)O. For the O-H vibration of HDO molecules outside the first hydration shell of OD(-), we observe a similar speed-up from 750 ± 50 fs to 600 ± 50 fs for a solution of 6 M NaOD in HDO:D(2)O. The acceleration of the decay is assigned to fluctuations in the energy levels of the HDO molecules due to charge transfer events and charge fluctuations. The reorientation dynamics of water molecules outside the first hydration shell are observed to show the same time constant of 2.5 ± 0.2 ps as in bulk liquid water, indicating that there is no long range effect of the hydroxide ion on the hydrogen-bond structure of liquid water. The terahertz dielectric relaxation experiments show that the transfer of the hydroxide ion through liquid water involves the simultaneous motion of ~7 surrounding water molecules, considerably less than previously reported for the proton.     

Formation of ice-like water structure on the surface of an antifreeze protein

Antifreeze proteins (AFPs) are found in different species from polar, alpine, and subarctic regions where they serve to inhibit ice crystal growth by adsorption to ice surfaces. Computational methods have the power to investigate the antifreeze mechanism in atomic detail. Molecular dynamics simulations of water under different conditions have been carried out to test our water model for simulations of biological macromolecules in extreme conditions: very low temperatures (200 K) and at the ice/liquid water interface. We show that the flexible F3C water model reproduces properties of water in the solid phase (ice I(h)), the supercooled liquid phase, and at the ice/liquid water interface. Additionally, the hydration of the type III AFP from ocean pout was studied as a function of temperature. Hydration waters on the ice-binding surface of the AFP were less distorted and more tetrahedral than elsewhere on the surface. More ice-like hydrating water structures formed on the ice-binding surface of the protein such that it created an ice-like structure in water within its first hydration layer but not beyond, suggesting that this portion of the protein has high affinity for ice surfaces.     

Ab initio molecular dynamics with discrete variable representation basis sets: techniques and application to liquid water

Finite temperature ab initio molecular dynamics (AIMD), in which forces are obtained from "on-the-fly" electronic structure calculations, is a widely used technique for studying structural and dynamical properties of chemically active systems. Recently, we introduced an AIMD scheme based on discrete variable representation (DVR) basis sets, which was shown to have improved convergence properties over the conventional plane wave (PW) basis set [Liu,Y.; et al. Phys. Rev. B 2003, 68, 125110]. In the present work, the numerical algorithms for the DVR based AIMD scheme (DVR/AIMD) are provided in detail, and the latest developments of the approach are presented. The accuracy and stability of the current implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The structural information obtained from the present work is in good agreement with the result of recent AIMD simulations with a PW basis set (PW/AIMD). Advantages of using the DVR/AIMD scheme over the PW/AIMD method are discussed. In particular, it is shown that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points.     

Numerical Study of Vibrational Energy Relaxation of O-H Bending inLiquid H2O

The relaxation of O-H bending of water molecule H2O in the liquid phase was studied with the molecular dynamics simulation approach. Both rigid and fexible solvents were used to identify the di?erent channels for the vibrational energy relaxation. It was observed that the relaxation time for the O-H bend overtone is 174 fs in the rigid solvent while it is 115 fs in the fexible solvent. The main pathway of the O-H bend overtone is transition to the bend fundamental. The relaxation time of the O-H bend fundamental was calculated as 204 fs which is comparable to the experimental value 170 fs.     

A molecular dynamics study of small water clusters comparing two flexible models for water

We report results from a molecular dynamics study of small water clusters, (H₂O) _n=2,3,4,6,8, comparing the recent polarizable, dissociable (PD) model of Halley et al. with the central force Stillinger-Rahman (SR) model. Dynamics calculations in the microcanonical ensemble quantified short-time averaged temperatures and RMS bond length fluctuations, which, in combination with simulated thermal quenching, identified structures and structural and phase changes of the clusters. Both models generally pointed to similar global minimum energy configurations, but local minima configurations, relative energies, and RMS bond length fluctuations varied more significantly. The PD model, with its incorporation of many-body effects, more accurately reproduced the structural features of clusters predicted from ab initio calculations, although it over-estimated the binding energies. Solid-like, pre-melting, and liquid-like states were identified based upon RMS bond length fluctuations for the O-O, O-H and H-H pairs. The SR and PD models yielded very similar trends in melting temperature as a function of cluster size. This suggests that general trends in the melting phenomenon do not depend strongly upon details of the models. The melting temperatures for the dimer and tetramer closely resembled the bulk melting temperature, while those for other sizes were considerably lower.     

Orientational dynamics for an amphiphilic-solvent solution

In this work, we performed Monte Carlo simulations on a lattice model for spontaneous amphiphilic aggregation, in order to study the orientational and hydrogen-bonding dynamics of water on different regions inside the micellar solution. We employed an associating lattice gas model that mimics the aqueous solvent, which presents a rich phase diagram with first- and second-order transition lines. Even though this is a simplified model, it makes possible to investigate the orientational dynamics of water in an equilibrium solution of amphiphiles, as well as the influence of the different phases of the solvent in the interfacial and bulk water dynamics. By means of extensive simulations, we showed that, at high temperatures, the behavior of the orientational relaxation and hydrogen bonding of water molecules in the bulk, first, and second hydration shells are considerable different. We observe the appearance of a very slow component for water molecules in the first hydration shell of micelles when the system reaches a high-density phase, consistent with previous theoretical and experimental studies concerning biological water. Also, at high temperatures, we find that water molecules in the second hydration shell of micelles have an orientational decay similar to that of bulk water, but with a generally slower dynamics. Otherwise, at low temperatures, we have two components for the orientational relaxation of bulk water in the low density liquid phase, and only a single component in the high density liquid (HDL) phase, which reflect the symmetry properties of the different phases of the solvent model. In the very dense region of water molecules in the first hydration shell of micelles at low temperatures, we find two components for the orientational relaxation on both liquid phases, one of them much slower than that in the single component of bulk water in the HDL phase. This happens even though our model does not present any hindrance to the water rotational freedom caused by the presence of the amphiphiles.     

Dynamical properties of the water molecules in the hydration shells of Fe(II) and Fe(III) ions: ab initio QM/MM molecular dynamics simulations

Dynamical properties, librational and vibrational motions of water molecules in the first and second hydration shells of the Fe(II) and Fe(III) ion were evaluated by means of velocity autocorrelation functions obtained by combined quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. The frequencies of rotation around three principal axes and the frequencies of intramolecular vibration of the water molecules in the first hydration shells obtained from the simulations are blue-shifted for both ions compared to those observed experimentally for liquid water. The intramolecular geometry of water molecules in the quantum mechanically treated region (ion plus first hydration shell) shows shorter O–H bonds and wider H–O–H angles than the bulk solvent.