水合锰(Ⅱ)结构的量子化学和ABEEM/MM研究

The microstructures of pure water and aqueous NaCl solutions over a wide range of salt concentrations (0-4 m) under ambient conditions are characterized by X-ray scattering and molecular dynamics (MD) simulations. MD simulations are performed with the rigid SPC water model as a solvent, while the ions are treated as charged Lennard-Jones particles. Simulated data show that the first peaks in the O...O and O...H pair correlation functions clearly decrease in height with increasing salt concentration. Simultaneously, the location of the second O...O peak, the signature of the so-called tetrahedral structure of water, gradually disappears. Consequently, the degree of hydrogen bonding in liquid water decreases when compared to pure fluid. MD results also show that the hydration number around the cation decreases as the salt concentration increases, which is most likely because some water molecules in the first hydration shell are occasionally substituted by chlorine. In addition, the fraction of contact ion pairs increases and that of solvent-separated ion pairs decreases. Experimental data are analyzed to deduce the structure factors and the pair correlation functions of each system. X-ray results clearly show a perturbation of the association structure of the solvent and highlight the appearance of new interactions between ions and water. A model of intermolecular arrangement via MD results is then proposed to describe the local order in each system, as deduced from X-ray scattering data.

Interaction between water molecules and alkali metal ions in aqueous salt solutions has been studied by the oxygen K-edge soft X-ray absorption spectroscopy (XAS) in transmission mode. In the measurement of several alkali halide aqueous solutions with different alkali chlorides (Li, Na, and K) and different sodium halides (Cl, Br, and I), the pre-edge component arising from the hydration water molecules shows a blue shift in peak energy as strongly depending on cations but not on anions. In the temperature dependent measurement, the pre-edge component arising from water molecules beyond the first hydration shell shows the same behavior as that of pure liquid water. On the other hand, the pre-edge component arising from water molecules in the first hydration shell of Li+ ions is not evidently dependent on the temperature, indicating that the hydration water molecules are more strongly bound with Li+ ions than the other water molecules. These experimental results are supported by the results of radial distribution functions of the first hydration shell and their temperature dependence, evaluated by molecular dynamics simulations.

The water structure around hydrophobic groups governs various biochemical processes. There is an ongoing debate on whether water molecules near hydrophobic groups are more ordered with greater participation in water-water hydrogen bonding with respect to water in the pure bulk state. The water structure around six different hydrophobic amino acid side chain analog molecules has been studied in pure water using molecular dynamics simulations. The analysis of water tetrahedral order parameter and the number of hydrogen bonds formed by the individual water molecules in the first hydration shell of the hydrophobic analogs provide evidence that both ordering and hydrogen bonds involving water molecules are to some extent reduced in the hydrophobic hydration shell. It is revealed that the water tetrahedrality in the outer part of the first hydrophobic hydration shell is equivalent to bulk water for all the water models except for the TIP4P-2005 model which shows marginally higher tetrahedrality. However, irrespective of the model employed, water tetrahedrality has always been found to be reduced in the inner part of the first hydration shell, which eventually makes the overall water tetrahedrality in the first hydrophobic hydration shell marginally lower than that observed for pure bulk water. Importantly, it is noticed that the decrease in water structuring exhibits solute size dependencies. Around a small solute like methane, the water tetrahedral ordering or hydrogen bonding propensity is quite similar to that of the bulk state. The effect, reduction in water structuring, is however more pronounced for relatively larger solutes.

The structures of aquo complexes of the curium(III) ion have been systematically studied using quantum chemical and molecular dynamics (MD) methods. The first hydration shell of the Cm3+ ion has been calculated using density functional theory (DFT), with and without inclusion of the conductor-like polarizable continuum medium (CPCM) model of solvation. The calculated results indicate that the primary hydration number of Cm3+ is nine, with a Cm-O bond distance of 2.47-2.48 A. The calculated bond distances and the hydration number are in excellent agreement with available experimental data. The inclusion of a complete second hydration shell of Cm3+ has been investigated using both DFT and MD methods. The presence of the second hydration shell has significant effects on the primary coordination sphere, suggesting that the explicit inclusion of second-shell effects is important for understanding the nature of the first shell. The calculated results indicate that 21 water molecules can be coordinated in the second hydration shell of the Cm3+ ion. MD simulations within the hydrated-ion model suggest that the second-shell water molecules exchange with the bulk solvent with a lifetime of 161 ps.

The structure of the solvation shell of Na + in aqueous solutions

Solvation of Ca 2+ in aqueous methanol—MD simulation studies

Raman spectra of aqueous Ga(III) perchlorate and nitrate solutions were measured at room temperature. From Ga(ClO4)3 solutions, a strongly polarized band at 526 cm−1 and two depolarized modes at 430 and 328 cm−1 were assigned to ν1(a1g), ν2(eg) and ν5(f2g) of the hexaaquagallium(III) ion, [Ga(OH2)63+] (Oh symmetry), respectively. The infrared active mode at 555 cm−1 was assigned to ν3(f1u). The Raman spectroscopic data suggest that the hexaaquagallium(III) ion is thermodynamically stable in perchlorate solutions (no inner‐sphere complex formation). In a supersaturated solution and in concentrated Ga(NO3)3 solutions most of the gallium(III) exists in the form of an outer‐sphere ion pair, [Ga(OH2)63+NO3−], but a small amount of the gallium(III) occurs as an inner‐sphere complex, [Ga(OH2)5ONO2]2+, which could be confirmed using Raman spectroscopy. Upon dilution, the fraction of the weak inner‐sphere nitrato complex diminishes and only the outer‐sphere complex is observable. Ab initio geometry optimizations and wavenumber calculations of [Ga(OH2)63+] were carried out at the Hartree–Fock and second order Møller–Plesset levels of theory, using various basis sets up to 6–31+G*. The global minimum structure of the hexaaqua Ga(III) species corresponds to symmetry Th. The unscaled vibrational wavenumbers of the [Ga(OH2)63+] are reported. The unscaled vibrational wavenumbers of the GaO6 unit are lower than the experimental values (∼15%). Scaling the wavenumbers reproduces only partially the measured values for the GaO6 unit. The theoretical binding enthalpy for [Ga(OH2)63+] was calculated and accounts for ∼60% of the experimental single ion hydration enthalpy for Ga(III). Ab initio geometry optimizations and wavenumber calculations are also reported for a [Ga(OH2)183+] (Ga[6+12]) cluster with six water molecules in the first sphere and 12 water molecules in the second sphere. The global minimum occurs for T symmetry. Calculated wavenumbers of the gallium [6+12] cluster correspond well with the observed wavenumbers in solution. The ν1 GaO6 (unscaled) mode occurs at 524 cm−1, which is in good agreement with the experimental value. The theoretical binding enthalpy for [Ga(OH2)183+] was calculated and is slightly underestimated compared with the experimental single ion hydration enthalpy of Ga(III). The water molecules of the first sphere form strong H‐bonds with water molecules in the second hydration shell because of the strong polarizing effect of the Ga(III) ion. Copyright © 2002 John Wiley & Sons, Ltd.

We study the effects of ions on the structure and dynamics of the hydrogen bonds in liquid water. As a technique we use femtosecond two-color mid-infrared spectroscopy, since this technique allows a clear distinction of the dynamics of the first solvation (hydration) shell of water molecules from the dynamics of bulk water. We find that water molecules in the first hydration shell of the halogenic anions Cl−, Br− and I− show much slower hydrogen-bond dynamics than water molecules in the pure liquid. We also observe that the first hydration shell shows very slow collective orientational dynamics, and forms a rigid, long-living structure. Finally, we find that ions have surprisingly little effect on the hydrogen-bond dynamics of water molecules outside the first hydration shell, which implies that ions do not enhance or weaken the hydrogen-bond network of liquid water.

In this study, we present density functional theory calculations on the properties of proton transfer and electron binding in isolated, mono-, di-, and pentahydrated 9-methylguanine:1-methylcytosine (mG:mC) base pair radical anions. It was found that the proton transfer in mG:mC(*-) is coupled to the interbase propeller-twisting and stretching motions, which cooperatively shorten the proton-transfer distance. Without the propeller-twisting motion, the interbase stretching will be hindered and the proton-transfer distance will become somewhat longer, which in turn, results in rising of the kinetic barrier for proton transfer. The monohydration can assist or resist the proton-transfer reaction, depending on the hydration sites. Inclusion of five water molecules in the first hydration shell around mG:mC(*-) only moderately lowers the proton-transfer barrier from 3.80 to 3.01 kcal mol(-1) and the reaction energy from -3.16 to -6.40 kcal mol(-1) due to the cancellation between opposite influences of H(2)O molecules. A further consideration of bulk hydration using a polarizable continuum model does not affect the proton-transfer energetics. In contrast, both the first hydration shell and bulk hydration were found to play important roles in stabilizing the excess electron in mG:mC; the adiabatic electron affinity of mG:mC increases from 0.302 to 0.645 eV upon inclusion of five water molecules in the first hydration shell, and further increases to 1.813 eV when the bulk hydration is considered. We noticed that the water molecule can enhance electron binding by direct interaction with the nucleobase that accommodates excess electron or through the indirect effect of tuning interbase hydrogen bonds. In addition, the microhydration effects on proton transfer and electron binding were found to be approximately additive.

The average OH stretching vibrational frequency for the water molecules in the first hydration shell around a Li(+) ion in a dilute aqueous solution was calculated by a hybrid molecular dynamics + quantum-mechanical ("MD + QM") approach. Using geometry configurations from a series of snapshots from an MD simulation, the anharmonic, uncoupled OH stretching frequencies were calculated for 100 first-shell OH oscillators at the B3LYP and HF/6-31G(d,p) levels of theory, explicitly including the first shell and the relevant second shell water molecules into charge-embedded supermolecular QM calculations. Infrared intensity-weighting of the density-of-states (DOS) distributions by means of the squared dipole moment derivatives (which vary by a factor of 20 over the OH stretching frequency band at the B3LYP level), changes the downshift from approximately -205 to -275 cm(-1) at the B3LYP level. Explicit inclusion of relevant third-shell water molecules in the supermolecular cluster leads to a further downshift by approximately -30 cm(-1). Our final estimated average downshift is approximately -305 cm(-1). The experimental value lies somewhere in the range between -290 and -420 cm(-1). Also, the absolute nu(OH) frequency is well reproduced in our calculations. "In-liquid" instantaneous correlation curves between nu(OH) and various typical H-bond strength parameters such as R(O...O), R(H...O), the intramolecular OH bond length, and the IR intensity are presented. Some of these correlations are robust and persist also for the rather distorted instantaneous geometries in the liquid; others are less so.

Water exchange between the coordination shells of metal cations in aqueous solutions is fundamental in understanding their role in biochemical processes. Despite the importance, the microscopic mechanism of water exchange in the first hydration shell of Mg2+ has not been resolved since the exchange dynamics is out of reach for conventional all-atom simulations. To overcome this challenge, transition path sampling is applied to resolve the kinetic pathways, to characterize the reaction mechanism and to provide an accurate estimate of the exchange rate. The results reveal that water exchange involves the concerted motion of two exchanging water molecules and the collective rearrangement of all water molecules in the first hydration shell. Using a recently developed atomistic model for Mg2+, water molecules remain in the first hydration shell for about 40 ms, a time considerably longer compared to the 0.1 ms predicted by transition state theory based on the coordinates of a single water molecule. The discrepancy between these timescales arises from the neglected degrees of freedom of the second exchanging water molecule that plays a decisive role in the reaction mechanism. The approach presented here contributes molecular insights into the dynamics of water around metal cations and provides the basis for developing accurate atomistic models or for understanding complex biological processes involving metal cations.

Ion solvation and water structure in potassium halide aqueous solutions

The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.

The energy surface for Na(+)/NH3 has been evaluated by means of ab initio SCF calculations at extended basis-set level, and a six-center Na(+)/NH3 analytical pair potential has been derived, which consists of Coulomb interaction terms, exponential and 1/r2 terms. A Monte Carlo simulation has been carried out for an ammonia–water mixture (18.45 mol% NH3) containing one Na(+) ion at 20.0°C and 1.0 atm. From the resultant total radical distribution functions, two solvation shells were recognized. The first shell contains 4.0 ammonia and 2.4 water molecules. The ammonia molecules point with the lone-pair site mostly towards the ion; the angular orientation of the water molecules, however, varies significantly owing to the influence of neighbouring ammonia molecules. Intermediate peaks appear between the first and second shell in Na–H2O radical distribution functions, containing 3.4 water molecules. The second solvation shell contains ca. seven water molecules, whereas only two ammonia molecules are found. Ammonia molecules in the second solvation shell are independent from the central ion and are influenced in their molecular orientation mostly by neighbouring water molecules.

At 20°C, transfer ribonucleic acid (tRNA) binds manganese ions cooperatively. The binding sites are studied by spin relaxation of the water protons in a solution of the Mn2+–tRNA complex, as a function of temperature and proton NMR frequency. Below room temperature the frequency dependence of the proton relaxation shows that the correlation time τc of the ion–proton dipolar interaction is limited by electron spin relaxation. Hence τc is not in these conditions an indicator of molecular motion. This explains why the relaxation effects of Mn2+ bound to different polynucleotides were previously observed to be quite similar. This also shows that the rotational correlation time is long (> 2 × 10−9 sec) and hence there is rigidity in the binding of the ion to tRNA. The “effective” number, pw, of water molecules in the first hydration shell, taking into account possible anisotropies of the molecular movements, is equal to two. This may indicate that the first hydration shell contains only two water molecules, the other ligands being groups from tRNA. PolyA also has pw = 2, whereas polyU has five water molecules in the first hydration shell. Above room temperature, the rotational correlation time decreases with an enthalpy of ∼ 15 kcal/mol, which is similar to that observed in optical absorption. Therefore the large-scale movements observed by proton relaxation correlate with the near-neighbor geometry which governs hypochromism. There seems to remain some structure up to 100°C. These results reinforce the proposition that strongly bound divalent cations play a role in the macromolecule's tertiary structure. They are discussed with reference to recent models of tRNA.