Structure of an accurate ab initio model of the aqueous Cl- ion at high temperatures

The structure of an accurate ab initio model of aqueous chloride ion was calculated at two high-temperature state points (573 K, 0.725 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure. First, the structure of an approximate model was calculated from a molecular dynamics simulation of the model. Then the difference between the structure of the ab initio model and the approximate model was calculated by non-Boltzmann weighting of a sample of configurations taken from the approximate model simulation. Radial distribution functions, average coordination numbers, the distribution of coordination numbers, an analysis of orientations of water in the first coordination shell, and the free energy of hydration of the chloride ion are reported for both state points. The most common water structure has one hydrogen close to the chloride ion and one pointing away (46% at 573 K and 57% at 723 K). Waters in the first coordination shell that are not strongly bound to the chloride ions are common. Several variations of the method were tested. Models in which the water-water interaction is calculated with ab initio methods predict only a slightly different structure than models in which water-water interactions are determined from the approximate models. Similarly, using the approximate model for solute-water interactions when the water is far from the chloride ion did not affect the results. Uncertainties due to the limited sample of configurations are estimated and found to be small. The results are in qualitative agreement with X-ray and neutron diffraction experiments and with simulations of approximate models.     

Sodium chloride in supercritical water as a function of density: potentials of mean force and an equation for the dissociation constant from 723 to 1073 K and from 0 to 0.9 g/cm(3)

The potential of mean force (PMF) of sodium chloride in water has been calculated by using the ab initio classical free-energy perturbation method at five state points: at 973 K with densities of 0.2796, 0.0935, and 0.0101 g/cm (3) and at 723 K with densities of 0.0897 and 0.0098 g/cm (3). The method is based on a QM-MM model in which Na-H 2O, Cl-H 2O, and Na-Cl interactions are calculated by ab initio methods. The water-water interactions are from the polarizable TIP4P-FQ model. The logarithm of the dissociation constant (log K c) has been calculated from the PMF. These predictions, together with experimental measurements, were used to derive an equation for log K c at densities from 0 to 0.9 g/cm (3) and temperatures from 723 to 1073 K, as well as from 600 to 1073 K for densities from 0.29 g/cm (3) to 0.9 g/cm (3). Extrapolation of the present equation below 723 K for densities less than 0.29 g/cm (3) does not fit the experimental results. This is attributed to long-range changes in the local dielectric constant due to the high compressibility. Comparisons with previous predictions and simulations are presented.     

Characterization of hydrated Na+(phenol) and K+(phenol) complexes using infrared spectroscopy

Hydrated alkali metal ion-phenol complexes were studied to model these species in aqueous solution for M=Na and K. IR predissociation spectroscopy in the O-H stretch region was used to analyze the structures of M+(Phenol)(H2O)n cluster ions, for n = 1-4. The onset of hydrogen bonding was observed to occur at n=4. Ab initio calculations were used to qualitatively explore the types of hydrogen-bonded structures of the M+(Phenol)(H2O)4 isomers. By combining the ab initio calculations and IR spectra, several different structures were identified for each metal ion. In contrast to benzene, detailed in a previous study of Na+(Benzene)n(H2O)m [J. Chem. Phys. 110, 8429 (1999)], phenol is able to bind directly to Na+ even in the presence of four waters. This is likely the result of the sigma-type interaction between the phenol oxygen and the ion. With K+, the dominant isomers are those in which the phenol O-H group is involved in a hydrogen bond with the water molecules, while with Na+, the dominant isomers are those in which the phenol O-H group is free and the water molecules are hydrogen-bonded to each other. Spectra and ab initio calculations for the M+(Phenol)Ar cluster ions for M=Na and K are reported to characterize the free phenol O-H stretch in the M+(Phenol) complex. While pi-type configurations were observed for binary M+(Phenol) complexes, sigma-type configurations appear to dominate the hydrated cluster ions.     

Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.     

Dramatic structural rearrangements in porous coordination networks

With the use of ab initio X-ray powder diffraction, a family of isostructural crystalline porous coordination networks, [(ZnX(2))(3)(TPT)(2)](n)· (solvent) (X = I, Br, Cl), has been studied at elevated temperatures of 573-723 K. Upon heating, all three networks exhibited crystalline-to-amorphous-to-crystalline (CAC) phase transformations to three new networks, [(ZnI(2))(3)(TPT)(2)](n), [(ZnBr(2))(3)(TPT)(2)](n)·(H(2)O) and [(ZnBr(2))(μ-Br)(ZnBr)(TPT)](n), and [(ZnCl(2))(μ-Cl)(ZnCl)(TPT)](n), respectively. A set of control experiments was used to obtain detailed mechanistic aspects of the CAC transformations. We demonstrate how bonds are broken and formed in these significant molecular rearrangements and how the initial arrangement plays a crucial role in the formation of the new networks after the CAC transformations. The structural information in the amorphous phase is retained and passed from a metastable to a more stable crystal, thus, reinforcing the notion that coordination networks are flexible and chemically active.     

Gd(III) polyaminocarboxylate chelate: realistic many-body molecular dynamics simulations for molecular imaging applications

Realistic molecular dynamics simulations of polyaminocarboxylate complexes of gadolinium (III) ion in water are performed, providing coordination numbers and average residence times in quantitative agreement with available experimental data. A theoretical analysis, based on fitting a fluctuating charges model on ab initio data, also indicates that charge transfer between the ion and the ligand is significant.     

A polarizable ion model for the structure of molten CuI

The results are reported of the molecular dynamics simulations of the coherent static structure factor of molten CuI at 938 K using a polarizable ion model. This model is based on a rigid ion potential to which the many body interactions due to the anions induced polarization are added. The calculated structure factor reproduces the clear sharp prepeak observed in neutron diffraction data. The corresponding partial structure factors and the related radial distribution functions calculated by molecular dynamics are compared with those found in the literature derived from a combination of neutron and x-ray diffraction data with the aid of the reverse Monte Carlo simulation technique, as well as those calculated by ab initio MD simulations.     

Electronic structure and normal vibrations of CH3(OCH2CH2)nOCH3-M+-CF3SO3- (n = 2-4, M = Li, Na, and K)

Electronic structure and the vibrational frequencies of CH(3)(OCH(2)CH(2))(n)OCH(3)-M(+)-CF(3)SO(3)(-) (n = 2-4, M = Li, Na, and K) complexes have been derived from ab initio Hartree-Fock calculations. The metal ion shows varying coordination from 5 to 7 in these complexes. In tetraglyme-lithium triflate, Li(+) binds to one of the oxygens of CF(3)SO(3)(-) (triflate or Tf(-)) unlike for potassium or sodium ions, which possess bidentate coordination. Structures of glyme-MTf complexes thus derived agree well with those determined from X-ray diffraction experiments. The metal ion binds more strongly to ether oxygens of tetraglyme than its di- or triglyme analogues and engenders contraction of SO (for oxygens binding to metal ion) bonds with consequent frequency upshift for the corresponding vibration in the complex relative to those in the free MTf ion pairs. Complexation of the diglyme with LiTf engenders the largest downshift (91 cm(-1)) for the SO(2) stretching vibration of the free anion, which suggests stronger binding of lithium to the diglyme than the tri- (79 cm(-1)) or tetraglyme (70 cm(-1)). A frequency shift in the opposite direction for the SO (where oxygens do not coordinate to the metal) and CF(3) stretchings, which stems from the ion-polymer and anion-ion interactions, has been noticed. These frequency shifts have been analyzed using natural bond orbital analysis and difference electron density maps coupled with molecular electron density topography.     

Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.     

Ab initio model potential and molecular dynamics simulation of Ag6 clusters

We present an approach to generate a model potential with parameters fitted to ab initio energetic surfaces. The potential includes two-, three- and four-body terms. Each of them consists of an exponential exchange and dispersion terms. The analytical form of the latter was taken from perturbation theory up to fourth order. We illustrate the present approach by constructing an ab initio model potential for the Ag₆ cluster. A molecular dynamics simulation using this potential reveals interesting features in the isomerization of the C _2v structure. A two step isomerization transition is observed: First, at temperatures around 350 K, the cluster structures fluctuate between two-dimensional isomers. At higher temperatures (450 K), fast transitions occur between two- and three-dimensional cluster configurations.     

Solvation of Na+ in argon clusters

The structures and stabilities of Ar(n)Na+ clusters (n < or = 54) are investigated using atomistic potentials fitted to reproduce ab initio calculations performed at the coupled-cluster level on the smaller clusters. Polarization effects are described using either the interaction between dipoles induced by the sodium ion, or a small charge transfer in the framework of a fluctuating charges model. In both models, extra three-body contributions of the Axilrod-Teller type are also included between the sodium ion and all pairs of argon atoms. The two models predict essentially similar growth patterns, and a transition in the metal ion coordination from 8 (square antiprism) to 12 (icosahedron) is seen to occur near n = 50, in response to the intrasolvent constraints.     

Calculations on the competition between association and reaction for C3H(+) + H2

A potential energy surface has been calculated for the competing associative and reactive ion-molecule processes involving the reactants C3H(+) + H2. Our ab initio results show that the linear ion C3H+ and H2 can directly access the deep potential well of the propargyl ion H2CCCH+, which is calculated to lie 390 kJ mol-1 below the zero-point energy of the reactants. Isomerization between the propargyl ion and the lower energy, cyclic C3H3+ ion, calculated to lie 501 kJ mol-1 below the zero-point energy of reactants, can subsequently occur via two pathways. One of these pathways involves a transition state lying 22 kJ mol-1 below the energy of the reactants while the other, which occurs at much lower energies, involves two transition states and an intermediate. The dissociation of c-C3H3+ into c-C3H2(+) + H is calculated to occur directly, without any intermediate potential energy maximum, but the energy of the products lies 7.3 kJ mol-1 above the energy of the reactants. Using the minimum energy potential pathway and properties of the stationary point structures determined via ab initio methods, we have calculated both the association rate coefficient to produce C3H3+ as a function of density and the branching ratio between the propargyl and cyclic structures of the ion. Our results are in good agreement with some experimental results and in conflict with others. Specifically, we agree with the 1:1 branching ratio measured for the propargyl and cyclic isomers of C3H3+ at 80 and 300 K and we agree with the rate coefficient for radiative association measured at 80 K. We cannot reproduce reported measurements that the reactive channel (C3H2(+) + H) is the dominant channel at 80 K and at low gas densities, or that the association channel at high densities saturates at an effective rate coefficient well below the Langevin value -2x10(-11) cm3 s-1 at 300K and 1x10(-10) cm3 s-1 at 80K.     

Interaction of CO with Kr: Potential energy surface and bound states

The first ab initio potential energy surface of the Kr-CO complex is developed using single and double excitation coupled-cluster theory with noniterative treatment of triple excitations. Mixed basis sets, aug-cc-pVQZ for the C and O atoms and aug-cc-pVQZ-PP for the Kr atom, with an additional (3s3p2d2f1g) set of midbond functions are used. The computed interaction energies in 336 configurations are analytically fitted to a two-dimensional potential model by a least squares fit. The potential has a minimum of -119.68 cm(-1) with Re=7.35a 0 at an approximate T-shaped geometry (theta e=98.5 degrees ). Bound state energies are calculated up to J=12, thus enabling a comprehensive comparison between theory and available experimental data as well as providing detailed guidance for future spectroscopic investigations of higher-lying states. The predicted transition frequencies and spectroscopic constants are in good agreement with the experimental results.     

An analysis of the electrostatic interaction between nucleic acid bases

Results from several commonly used approximate methods of evaluating electrostatic interactions have been compared to the rigorous, nonexpanded electrostatic energies at both uncorrelated and correlated levels of theory. We examined a number of energy profiles for both hydrogen bonded and stacked configurations of the nucleic acid base pairs. We found that the penetration effects play an extremely important role and the expanded electrostatic energies are significantly underestimated with respect to the ab initio values. Apart from the inability to reproduce the magnitudes of the ab initio electrostatic energy, there are other problems with the available approximate electrostatic models. For example, the distributed multipole analysis, one of the most advanced methods, is extremely sensitive to the basis set and level of theory used to evaluate the multipole moments. Detailed ab initio results are provided that other researchers could use to test their approximate models.     

On the simulation of photoelectron spectra in molecules with conical intersections and spin-orbit coupling: the vibronic spectrum of CH3S

A method to simulate photoelectron spectra for states coupled by conical intersections and the spin-orbit interaction is reported. The algorithm is based on the multimode vibronic coupling model and treats the spin-orbit interaction in a nonperturbative manner. Since the algorithm is not dependent on molecular symmetry, the approach is generally applicable to accidental conical intersections as well as the symmetry required intersections found in Jahn-Teller molecules. The method is also computationally efficient using energy gradient and derivative coupling information to limit the number of nuclear configurations at which ab initio data are required. This approach is applied to simulate the negative ion photoelectron spectrum of the methylthio radical. The two-state Hamiltonian employed to describe this system was determined employing ab initio gradients and derivative couplings at only 17 nuclear configurations.     

Ab initio molecular dynamics studies of ionic dissolution and precipitation of sodium chloride and silver chloride in water clusters, NaCl(H2O)n and AgCl(H2O)n, n = 6, 10, and 14

An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H(2)O)(n) and AgCl(H(2)O)(n) with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H(2)O)(n) is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ mol(-1)), are identifiable on the free energy profiles of NaCl(H(2)O)(n) for n = 10 and 14 at 300 K, with the Na(+)/Cl(-) pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ mol(-1)). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H(2)O)(n) clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure.     

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.     

IR-UV double resonance spectroscopy of guanine-H2O clusters

We present the IR-UV double resonance spectrum of guanine monohydrate in the region 3100 cm(-1) to 3800 cm(-1) along with the energies and frequencies of these structures calculated at the non-empirical correlated ab initio RI-MP2/cc-pVDZ level. We assign the structures of guanine-water clusters by comparing the experimental spectra with the ab initio calculations and with the IR spectra of the bare guanine monomer. We find two clusters with guanine in the enol-amino tautomeric form and one structure with guanine in the keto-amino form.     

Incidence of partial charges on ion selectivity in potassium channels

Potassium channels are membrane proteins known to select potassium over sodium ions at a high diffusion rate. We conducted ab initio calculations on a filter model of KcsA of about 300 atoms at the Hartree-Fock level of theory. Partial charges were derived from the quantum mechanically determined electrostatic potential either with Merz-Kollman or Hinsen-Roux schemes. Large polarization and/or charge transfer occur on potassium ions located in the filter, while the charges on sodium ions remain closer to unity. As a result, a weaker binding is obtained for K(+) ions. Using a simplified version of a permeation model based on the concerted-motion mechanism for ion translocation within the single-file ion channel [P. H. Nelson, J. Chem. Phys. 117, 11396 (2002)], we discuss how differences in polarization effects in the adducts with K(+) and Na(+) can play a role as for ionic selectivity and conductance.