Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field

The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn(2+) are derived from gas-phase ab initio calculation of Zn(2+)-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn(2+) have been obtained by comparing the AMOEBA Zn(2+)-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn(2+) solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn(2+)(H(2)O)(n) (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn(2+) in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn(2+)-water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.     

Ab initio based polarizable force field parametrization

Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by approximately 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.     

Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation

We have explored the conformation-dependent interaction energy of the triphosphate moiety, a key constituent of ATP and GTP, with a closed-shell divalent cation, Zn2+, used as a probe. This was done using the SIBFA polarizable molecular mechanics procedure. We have resorted to a previously developed approach in which triphosphate is built out from its elementary constitutive fragments, and the intramolecular, interfragment, interaction energies are computed simultaneously with their intermolecular interactions with the divalent cation. This approach has enabled reproduction of the values of the intermolecular interaction energies from ab initio quantum-chemistry with relative errors <3%. It was extended to the complex of a nonhydrolyzable analog of ATP with the active site of a bacterial enzyme having two Mg2+ cations as cofactors. We obtained following energy-minimization a very close overlap of the ATP analog over its position from X-ray crystallography. For models of the ATP analog-enzyme complex encompassing up to 169 atoms, the values of the SIBFA interaction energies were found to match their DFT counterparts with relative errors of <2%.     

含羧酸镁(钙)官能团的多孔芳香骨架材料储氢性能的预测

用MP2方法,TZVPP基组以及基组重叠误差(BSSE)校正计算了氢分子与修饰在多孔芳香骨架(PAF)上的羧酸镁、羧酸钙官能团的相互作用,并建立了描述这一相互作用的分子力学力场.在此基础上用巨正则系综蒙特卡洛(GCMC)模拟预测了氢气在该种新型PAF材料上的吸附等温线.量子化学计算结果表明,每个羧酸镁、羧酸钙官能团分别可以提供13、14个氢分子吸附位点,与每个氢分子的平均结合能在8kJ·mol-1左右.通过比较不同温度和压力下材料的绝对吸附量和超额吸附量发现,在PAF骨架中引入羧酸镁、羧酸钙官能团可以显著提高材料的综合储氢性能,达到并超过了美国能源部提出的2015年储氢标准.同时该工作还揭示了氢吸附量与材料的表面积、空腔体积和分子作用强度间的复杂关系.     

Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

In this contribution, we focused on the use of polarizable force fields to model the structural, energetic, and thermodynamical properties of lanthanides and actinides in water. In a first part, we chose the particular case of the Th(IV) cation to demonstrate the capabilities of the AMOEBA polarizable force field to reproduce both reference ab initio gas-phase energetics and experimental data including coordination numbers and radial distribution functions. Using such model, we predicted the first polarizable force field estimate of Th(IV) solvation free energy, which accounts for −1,638 kcal/mol. In addition, we proposed in a second part of this work a full extension of the SIBFA (Sum of Interaction Between Fragments Ab initio computed) polarizable potential to lanthanides (La(III) and Lu(III)) and to actinides (Th(IV)) in water. We demonstrate its capabilities to reproduce all ab initio contributions as extracted from energy decomposition analysis computations, including many-body charge transfer and discussed its applicability to extended molecular dynamics and its parametrization on high-level post-Hartree–Fock data.     

Ab initio study of [n.n]paracyclophane (n = 2, 3) complexes with cations: unprecedented through-space substituent effects

Several cation-pi complexes between substituted [n.n]paracyclophanes (n = 2, 3) and cations have been studied using high level ab initio calculations. The chemical substitution at the aromatic ring that is not interacting with the cation has a strong influence upon the binding energy. This strong through-space substituent effect has been studied using the "atoms-in-molecules" theory, which has been found useful to explain the energetic results.     

Solvation of radical cations in water--reactive or unreactive solvation?

The solvation and reaction of ethylene radical cation in aqueous solution has been studied with Car-Parrinello molecular dynamics simulations. All ab initio simulations were performed using a system of 56 water and one ethylene molecule. Using a favorable symmetrically solvated radical cation as the starting point of the simulation a fast addition of water (within 90 fs) to the radical cation is observed. The primary addition product is rapidly deprotonated (within 100 fs) to yield the ethanol-2-yl radical. A second simulation was initiated through vertical ionization of neutral hydrated ethylene, representing a significantly less favorable situation for the addition process. No addition of water can be observed in this second simulation over a time span of 1.7 ps. Taken together the two simulations are indicative of a rearrangement of the solvent shell which represents the major part of the overall reaction barrier. Under these circumstances, the reaction rate of an otherwise spontaneous reaction is limited by the intrinsic solvent relaxation time. This interpretation of the reactivity of hydrated radical cations reconciles previously conflicting experimental condensed phase and theoretical gas phase studies.     

The pathway to reorientation in ammonium fluoride

Two alternative transition states for ammonium ion rotation in crystalline NH₄F have been characterised using ab initio calculations. In one all the cations rotate in phase, while in the other the rotating ions are isolated from each other by non-rotated ions. These two transition states are characterised by the cation displacement and changes in the bond lengths and bond angles within the ammonium ion. The pathway for passing over the barrier was investigated by low temperature molecular dynamics runs from each transition state. In both cases the order of events in passing from the ground state to the transition state is first cation displacement towards a neighbouring fluoride ion, secondly, lengthening of the NH bond pointing to this ion, and thirdly, rotation about this bond.     

Jahn-teller distortions in XH4+ radical cations (X = Si,Ge, Sn). an ab initio CI study

The Jahn-Teller effect in XH₄⁺ radical cations (X = Si, Ge, Sn) has been studied by ab initio CI calculations, using pseudopotentials. These cations undergo important distortions to C_2v and C_3v symmetries, from both structural and energetic points of view. C_2v and C_3v structures lie very close in energy in the stannane cation, the C_2v geometry being slightly more stable, while the energy gap between both geometries is more significant in the silane and germane cations.     

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.     

Quasiclassical trajectory study of the collision-induced dissociation dynamics of Ar + CH3SH+ using an ab initio interpolated potential energy surface

Classical trajectory calculations have been performed to investigate the collision-induced dissociation (CID) of the CH(3)SH(+) cation with Ar atoms. A new intramolecular potential energy surface for the CH(3)SH(+) cation is evaluated by interpolation of 3000 ab initio data points calculated at the MP2/6-311G(d,p) level of theory. The new potential energy surface includes seven accessible dissociation channels of the cation. The present QCT calculations show that migration of hydrogen atoms, leading to the rearrangement CH(3)SH(+) <--> CH(2)SH(2)(+), is significant at the collision energies considered (6.5-34.7 eV) and that the formation of CH(3)(+), CH(3)S(+), and CH(2)(+) cations takes place primarily by a "shattering" mechanism in which the products are formed just after the collision. The theoretical product abundances are found to be in qualitative agreement with the experimental data. However, at high collision energies, the calculated total cross sections for the formation of CH(3)(+) and CH(2)SH(+) cations are noticeably larger than the experimental determinations. Several features of the dynamics of the CID processes are discussed.     

Interpreting ultrafast molecular fragmentation dynamics with ab initio electronic structure calculations

High-level ab initio electronic structure calculations are used to interpret the fragmentation dynamics of CHBr(2)COCF(3), following excitation with an intense ultrafast laser pulse. The potential energy surfaces of the ground and excited cationic states along the dissociative C-CF(3) bond have been calculated using multireference second order perturbation theory methods. The calculations confirm the existence of a charge transfer resonance during the evolution of a dissociative wave packet on the ground state potential energy surface of the molecular cation and yield a detailed picture of the dissociation dynamics observed in earlier work. Comparisons of the ionic spectrum for two similar molecules support a general picture in which molecules are influenced by dynamic resonances in the cation during dissociation.     

Pentazole-based energetic ionic liquids: a computational study

The structures of protonated pentazole cations (RN5H+), oxygen-containing anions such as N(NO2)2-, NO3-, and ClO4- and the corresponding ion pairs are investigated by ab initio quantum chemistry calculations. The stability of the pentazole cation is explored by examining the decomposition pathways of several monosubstituted cations (RN5H+) to yield N2 and the corresponding azidinium cation. The heats of formation of these cations, which are based on isodesmic (bond-type conserving) reactions, are calculated. The proton-transfer reaction from the cation to the anion is investigated.     

Ab initio calculations of the melting temperatures of refractory bcc metals

We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.     

Molecular simulation study of some thermophysical and transport properties of triazolium-based ionic liquids

Results of a molecular dynamics study of several triazolium-based ionic liquids are reported. Triazolium cations include 1,2,4-triazolium, 1,2,3-triazolium, 4-amino-1,2,4-triazolium, and 1-methyl-4-amino-1,2,4-triazolium. Each cation was paired with a nitrate or perchlorate anion. These materials are part of a class of ionic compounds that have been synthesized recently but for which little physical property data are available. Properties of the more common ionic liquid, 1-n-butyl-3-methylimidazolium nitrate, are also computed and compared with the properties of the triazolium-based compounds. A molecular mechanics force field was developed for these materials using a mix of ab initio calculations and parameter fitting using the molecular compound 1H-1,2,4-triazole as a basis for the triazolium cations. Liquid-phase properties that were computed include heat capacities, cohesive energy densities, gravimetric densities/molar volumes as a function of temperature and pressure, self-diffusivities, rotational time constants, and various pair correlation functions. In the solid phase, heat capacities and lattice parameters were computed. Of all of these properties, only lattice parameters have been measured experimentally (and only for four of the triazolium compounds). The agreement with the experimental crystal structures was good. When compared with that of the imidazolium-based ionic liquid, the triazolium-based materials have much smaller molar volumes, higher cohesive energy densities, and larger specific heat capacities. They also tend to be less compressible, have a higher gravimetric density, and have faster rotational dynamics but similar translational dynamics.     

Classical simulations with the POLIR potential describe the vibrational spectroscopy and energetics of hydration: divalent cations, from solvation to coordination complex

POLIR, a polarizable water potential optimized for vibrational and intermolecular spectroscopy in pure water but not optimized for solvation, is used to describe solutions of the divalent metal cations Ca(2+), Mg(2+), and Cu(2+). The spectral shifts in the O-H stretch region obtained from classical simulations are in agreement with experiment. The water-ion binding energies are dominated by classical electrostatics, even though the Cu(2+) case might be considered to involve an intermediate-strength chemical bond. Three-body energies of the ion with the first solvation shell are in agreement with ab initio calculations. Our results indicate the importance of polarization in the development of accurate, transferable, force fields and the power of classical methods when it is carefully included.     

Unusual "amphiphilic" association of hydrated protons in strong acid solution

The solvation structure of the hydrated excess proton in concentrated aqueous HCl solution is studied using the self-consistent iterative multi-state empirical valence bond method. At 0.43-0.85 M concentrations, hydronium cations are found to form unusual cation pairs. This behavior is consistent with our earlier finding that hydronium cations can have an "amphiphilic" character due in part to the asymmetric nature of their hydrogen bonding to nearby water molecules. The existence of these hydronium amphiphilic pairs is further supported by a Car-Parrinello ab initio molecular dynamics simulation at 1.0 M HCl concentration. It is also found that the hydronium cation pairs are stabilized by a delocalization of the hydrated excess proton charge defects involving additional water molecules. At the higher concentrations of 1.68 and 3.26 M, the abundance of such hydronium pairs decreases, and the analysis of the radial distribution functions indicates the possible formation of an aggregate structure with longer-ranged order.     

On the performance of molecular polarization methods. II. Water and carbon tetrachloride close to a cation

Our initial study on the performance of molecular polarization methods close to a positive point charge [M. Masia, M. Probst, and R. Rey, J. Chem. Phys. 121, 7362 (2004)] is extended to the case in which a molecule interacts with a real cation. Two different methods (point dipoles and shell model) are applied to both the ion and the molecule. The results are tested against high-level ab initio calculations for a molecule (water or carbon tetrachloride) close to Li+, Na+, Mg2+, and Ca2+. The monitored observable is in all cases the dimer electric dipole as a function of the ion-molecule distance for selected molecular orientations. The moderate disagreement previously obtained for point charges at intermediate distances, and attributed to the linearity of current polarization methods (as opposed to the nonlinear effects evident in ab initio calculations), is confirmed for real cations as well. More importantly, it is found that at short separations the phenomenological polarization methods studied here substantially overestimate the dipole moment induced if the ion is described quantum chemically as well, in contrast to the dipole moment induced by a point-charge ion, for which they show a better degree of accord with ab initio results. Such behavior can be understood in terms of a decrease of atomic polarizabilities due to the repulsion between electronic charge distributions at contact separations. It is shown that a reparametrization of the Thole method for damping of the electric field, used in conjunction with any polarization scheme, allows to satisfactorily reproduce the dimer dipole at short distances. In contrast with the original approach (developed for intramolecular interactions), the present reparametrization is ion and method dependent, and corresponding parameters are given for each case.     

Gradients of the polarization energy in the effective fragment potential method

The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermolecular interaction parameters are obtained from preparative ab initio calculations on isolated molecules. The polarization energy in the EFP method is modeled with asymmetric anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbitals of the molecules. Analytic expressions for the translational and rotational gradients (forces and torques) of the EFP polarization energy have been derived and implemented. Periodic boundary conditions (the minimum image convention) and switching functions have also been implemented for the polarization energy, as well as for other EFP interaction terms. With these improvements, molecular dynamics simulations can be performed with the EFP method for various chemical systems.     

Ab initio Ehrenfest dynamics

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2-4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2C=NH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2C=NH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation.