Modeling electrified metal/water interfaces from ab initio molecular dynamics: Structure and Helmholtz capacitance

The structure and potential distribution of electric double layers (EDLs) are of close relevance to the performance of electrode materials. In the past years, despite tremendous efforts devoted to this topic, an atomistic picture of the EDL is still lacking, let alone understanding on how the EDL structure is related to the dielectric property of interface water. In this article, we briefly review the recent progress in modeling electrified metal/water interfaces using ab initio molecular dynamics (AIMD). The ab initio methods for EDL modeling is firstly summarized, and then we discuss the structures of interface water on metal electrodes at different potential conditions. Moreover, we illustrate the potential-dependent behavior of chemisorbed water on Pt(111) surface and its relationship with the peak of the differential Helmholtz capacitance observed by experiment. At last, we give some perspective for future development in ab initio modeling of electrochemical interfaces.     

Lithium hydroxide phase transition under high pressure: an ab initio molecular dynamics study.

The high-pressure phase transition in the deuterated lithium hydroxide crystalline state has been studied by Car-Parrinello molecular dynamics simulations, in the constant-pressure, constant-temperature ensemble. The recently developed metadynamics approach has been applied to encourage the system to transform into different phases in an affordable simulation time. A previously not completely characterized high-pressure phase has been obtained. The structural and spectroscopic properties have been studied and compared with the neutron scattering, infrared and Raman measurements. It has been found that the calculated structure differs slightly from the experimental hypothesis, and that the presence of strong hydrogen bonds is the source of the red shift and of the characteristic features of the OD-stretching bands in both IR and Raman spectra.     

Assessing the accuracy of improved force‐matched water models derived from Ab initio molecular dynamics simulations

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force‐matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force‐matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc.     

Exploring the hydration of Pb2+: ab initio studies and first-principles molecular dynamics

Even though lead is a well-known toxicant widely scattered throughout the world since antiquity, its chemistry is poorly documented at the molecular level. Here we investigate the hydration of the Pb(2+) ion by means of first-principles molecular dynamics (Car-Parrinello molecular dynamics, CPMD). We found that the hydrated cation is heptacoordinated in a dynamically holodirected arrangement roughly corresponding to a fluxional distorted pentagonal bipyramid. The time-averaged Pb-O bond length is especially large and amounts to 2.70 A with an associated root-mean-square deviation of 0.26 A. This results from a dynamic exchange between short (<2.6 A), intermediate (2.6-3.0 A) and long (>3.0 A) Pb-O bonds. The latter very long Pb-O distance implies that the determination of the coordination number n(c) from experimental work may not necessarily yield values directly comparable to the theoretical value of n(c)=7, since not all experimental techniques would recognize such a long distance as a bond to the metal cation. Pronounced disorders are evidenced in the second shell, characteristic of a chaotropic cation, and exchanges between the first and second shells cannot be excluded on a timescale of a few tens of picoseconds.     

Wavelet transform analysis of ab initio molecular dynamics simulation: application to core-excitation dynamics of BF3

We propose a novel analysis method of ab initio molecular dynamics (AIMD) simulation using a continuous wavelet transform (c-WT) technique. The c-WT technique, one of the time-frequency signal analysis methods, provides a clear view of the dynamical information in time developments. Combined with the auto-correlation function of velocity by AIMD simulation, c-WT analysis enables us to well understand dynamical distribution, such as the vibrational properties following a change of electronic structure in a molecular system. As a practical application, AIMD simulation of core-excited BF(3) (B1s --> 2a(2) (')) is illustrated. AIMD simulation leads to the change of vibrational motion as well as structural deformation by core-excitation. The c-WT analysis clarifies the relationship between structural deformation and the related significant vibrational modes in core-excitation within 50 fs.     

Efficient evaluation of the accuracy of molecular quantum dynamics on an approximate analytical or interpolated ab initio potential energy surface

Ab initio electronic structure methods have reached a satisfactory accuracy for the calculation of static properties, but remain too expensive for quantum dynamical calculations. Recently, an efficient semiclassical method was proposed to evaluate the accuracy of quantum dynamics on an approximate potential without having to perform the expensive quantum dynamics on the accurate potential. Here, this method is applied for the first time to evaluate the accuracy of quantum dynamics on an approximate analytical or interpolated potential in comparison to the quantum dynamics on an accurate potential obtained by an ab initio electronic structure method. Specifically, the vibrational dynamics of H₂ on a Morse potential is compared with that on the full CI potential, and the photodissociation dynamics of CO₂ on a LEPS potential with that on the excited ¹Π surface computed at the EOM‐CCSD/aug‐cc‐pVDZ level of theory. Finally, the effect of discretization of a potential energy surface on the quantum dynamics is evaluated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2426–2435, 2010     

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order M?ller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.     

Whether proton transition to the triphosphate tail of ATP occurs at protein kinase environment: A Car‐Parrinello ab initio molecular dynamics study

Protonation state of the triphosphate tail of ATP (adenosine triphosphate) in protein environment is a fundamental issue, which has significant impact on the mechanism investigation of biochemical processes with ATP involved. Proton transition from surroundings (water molecule coordinating to magnesium, H_W; amino group of Lys, H_L) to the ATP tail in the catalytic core of protein kinase found recently disproved the commonly accepted deprotonation state of ATP tail. In this account, Car‐Parrinello ab initio molecular dynamics (CP‐AIMD) method has been employed to examine whether the proton transition occurs. To provide a comparison basis for the dynamics simulations, static quantum mechanics (QM), and combined quantum mechanics and molecular mechanics (QM/MM) calculations have also been carried out. Consistent results have been obtained that complete transition of hydrogen from the surroundings to the triphosphate tail of ATP is not allowed. The most dominant conformations correspond to the ones with H_W bonding to O(W) and H‐bonding to O(ATP), [O(W)‐H_W···O(ATP)], H_L bonding to N(Lys) and H‐bonding to O(ATP), [N(Lys)‐H_L···O(ATP)]. Metastable structures with one hydrogen atom bonding with two heavy atoms (hydrogen acceptors) were also located by our dynamic simulations. This bonding mode can satisfy the hungering for hydrogen of the two heavy atoms simultaneously. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.     

Short-time Fourier transform analysis of ab initio molecular dynamics simulation: collision reaction between CN and C4H6

Collision reactions between cyano radical (CN) and dimethylacetylene (C4H6) are thought to occur in the atmosphere of Saturn's moon Titan. However, it is difficult to reproduce reactions occurring in unique environments to study their dynamical processes. In this study, collision reactions between CN and C4H6 were investigated using ab initio molecular dynamics (AIMD) simulations. The simulation results were categorized into three kinds: nonreactive collision, incorporation, and substitution. Short-time Fourier transform analysis of velocity autocorrelation functions obtained by the AIMD simulations, which has been recently developed by our research group, was performed to examine the nonequilibrium condition of the vibrational states. Spectrograms, which correspond to the time evolution of power spectra, clarify the relationship between the three reaction channels and the dynamical changes of the vibrational states.     

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.     

Ab initio molecular dynamics study of prebiotic production processes of organic compounds at meteorite impacts on ocean

Recent experiments concerning prebiotic materials syntheses suggest that the iron-bearing meteorite impacts on ocean during Late Heavy Bombardment provided abundant organic compounds associated with biomolecules such as amino acids and nucleobases. However, the molecular mechanism of a series of chemical reactions to produce such compounds is not well understood. In this study, we simulate the shock compression state of a meteorite impact for a model system composed of CO₂, H₂O, and metallic iron slab by ab initio molecular dynamics combined with multiscale shock technique, and clarify possible elementary reaction processes up to production of organic compounds. The reactions included not only pathways similar to the Fischer–Tropsch process known as an important hydrocarbon synthesis in many planetary processes but also those resulting in production of a carboxylic acid. It is also found that bicarbonate ions formed from CO₂ and H₂O participated in some forms in most of these observed elementary reaction processes. These findings would deepen the understanding of the full range of chemical reactions that could occur in the meteorite impact events. © 2018 Wiley Periodicals, Inc.     

New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).     

Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations

The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer (5'-GCGTACACATGCG-3') have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl and 3-methylisocarbostyril. The stabilization energy of the model system (model A) consisting of a central base pair (base-analogue pair) and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set. The geometry of the model was averaged from structures determined by MD simulations. The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system (model B) which also contained a sugar-phosphate backbone. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair (model A) were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The selectivity of the base-analogue pair was reproduced (model B) when their desolvation energy was included with the interaction energy of both strands determined by the approximate SCC-DFTB-D method.     

Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations

L ‐2‐haloacid dehalogenase (L ‐DEX) catalyzes the hydrolytic dehalogenation of L ‐2‐haloalkanoic acids to produce the corresponding D ‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L ‐DEX from Pseudomonas sp. YL (L ‐DEX YL) by using molecular modeling. The complexes of wild‐type L ‐DEX YL and its K151A and D180A mutants with its typical substrate, L ‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L ‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L ‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Exploration of the (ethanol)4–water heteropentamers potential energy surface by simulated annealing and Ab initio molecular dynamics

A DFT electronic structure study of the (ethanol)₄–water heteropentamers at the B3LYP/6‐31+G(d) model chemistry was carried out. To get determine possible configurations, the potential energy surface (PES) was explored with two methods: simulated annealing and ab initio molecular dynamics. The results suggest that the PES is very flat. A total of 81 stable structures were determined. These structures were classified into 16 different geometric patterns according to geometric criteria like the number of hydrogen bonds and their spatial arrangement: cyclic, bicyclic, or lineal patterns. Thermodynamic stability was used for defining the order of such classification. Hydrogen bonds are mutually disturbed due to the existence of cooperative effects. Cooperativity affects the nature of the hydrogen bonds and the overall stability of the ethanol–water system given that the strongest interactions are markedly covalent and the most stable geometric pattern corresponds to the pentagonal arrangement. These observations were supported by the analysis of the loss of atomic charge of the hydrogen atoms involved in hydrogen bonds. These hydrogen bonds were classified as primary and secondary hydrogen bonds: O? H ··· O and C? H ··· O, respectively. For comparative purposes, some (ethanol)₅, (methanol)₅, and (methanol)₄–water clusters were characterized in this study. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Ab initio calculation and quasi‐classical dynamics study of the two lowest potential energy surfaces of the O(1D)+HBr system*

The lowest singlet 1¹A′ and 1¹A″ potential energy surfaces (PES) of the O(¹D)+HBr system have been ab initio computed. The complete active space self‐consistent field (CASSCF) method was used in most of the calculations, considering all the valence orbitals as active. The calculations were complemented with both analytical gradient calculations to characterize the stationary points and multireference configuration interaction (MRCI) calculations at selected nuclear geometries to improve the determination of the barrier heights and of the energetics. Electronic energy values for both PESs were then independently fitted by polynomial expansions in bond order coordinates. On the fitted surfaces quasi‐classical trajectories were separately run. Single‐surface calculations behave qualitatively different for the ground and the excited PES at low collision energies. A satisfactory agreement with existing experimental data was obtained by using the ground PES while calculations performed on the excited 1¹A″ PES worsened the agreement. However, when collision energy is increased, detailed experimental distributions are less well reproduced by calculations on the ground PES. This may imply the participation via nonadiabatic transitions of the 2¹A′ PES at higher energies while the adiabatic ground singlet PES well describes reactive scattering at low collision energy. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001