Direct Ab Initio Molecular Dynamics Research Articles

Near-Barrierless Ammonium Bisulfate Formation via a Loop-Structure Promoted Proton-Transfer Mechanism on the Surface of Water.

In the atmosphere, a well-known and conventional pathway toward the formation of ammonium sulfate is through the neutralization of sulfuric acid with ammonia (NH3) in water droplets. Here, we present direct ab initio molecular dynamics simulation evidence of the formation of ammonium bisulfate (NH4HSO4) from the hydrated NH3 and SO3 molecules in a water trimer as well as on the surface of a water droplet. This reaction suggests a new mechanism for the formation of ammonium sulfate in the atmosphere, especially when the concentration of NH3 is high (e.g., ∼10 μg m(-3)) in the air. Contrary to the water monomer and dimer, the water trimer enables near-barrierless proton transfer via the formation of a unique loop structure around the reaction center. The formation of the loop structure promotes the splitting of a water molecule in the proton-transfer center, resulting in the generation a NH4(+)/HSO4(-) ion pair. The loop-structure promoted proton-transfer mechanism is expected to be ubiquitous on the surface of cloud droplets with adsorbed NH3 and SO3 molecules and, thus, may play an important role in the nucleation of aerosol particles (e.g., fine particles PM2.5) in water droplets.

Ionization dynamics of water dimer on ice surface

The solid surface provides an effective two-dimensional reaction field because the surface increases the encounter probability of bi-molecular collision reactions. Also, the solid surface stabilizes a reaction intermediate because the excess energy generated by the reaction dissipates into the bath modes of surface. The ice surface in the universe is one of the two dimensional reaction fields. However, it is still unknown how the ice surface affects to the reaction mechanism. In the present study, to elucidate the specific property of the ice surface reaction, ionization dynamics of water dimer adsorbed on the ice surface was theoretically investigated by means of direct ab-initio molecular dynamics (AIMD) method combined with ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) technique, and the result was compared with that of gas phase reaction. It was found that a proton is transferred from H2O+ to H2O within the dimer and the intermediate complex H3O+(OH) is formed in both cases. However, the dynamic features were different from each other. The reaction rate of the proton transfer on the ice surface was three times faster than that in the gas phase. The intermediate complex H3O+(OH) was easily dissociated to H3O+ and OH radical on the ice surface, and the lifetime of the complex was significantly shorter than that of gas phase (100fs vs. infinite). The reason why the ice surface accelerates the reaction was discussed in the present study.

Enhanced Ab Initio Molecular Dynamics Simulation of the Temperature-Dependent Thermodynamics for the Diffusion of Carbon Monoxide on Ru(0001) Surface

CO diffusion on the metal surface is an elementary process in many heterogeneous catalytic reactions. The thermodynamics and the molecular mechanism of the diffusion process are key factors contributing to the kinetics of the catalysis. Theoretical study based on computer simulations can complement experimental studies to provide much needed thermodynamic and mechanistic information. Here, we report direct ab initio molecular dynamics (MD) simulation to investigate the temperature-dependent thermodynamics of CO diffusion on the Ru(0001) surface combined with an efficient sampling method based on integrated tempering to speed up phase space sampling. We show that reliable and smooth two-dimensional potential of mean force surfaces of CO diffusion can be obtained at different temperatures. As expected, with increasing temperature, the distribution of CO adsorbate at different surface sites becomes more and more uniform, while the height of the free energy barrier to CO diffusion decreases. The simulation results were used to elucidate the physics of the temperature-dependent in-plane diffusion. The good agreement between the results of current simulations and previous theoretical studies demonstrates the effectiveness and reliability of free energy simulation with the enhanced ab initio molecular dynamics in heterogeneous surface processes. For complex situations where a simple harmonic model becomes inappropriate and convergent phase space sampling is required, direct MD simulation with enhanced sampling methods can make important contributions to our understanding of the thermodynamics of the surface catalytic processes.

Direct ab‐initio molecular dynamics study on the radiation effects on catalytic triad composed of Ser‐His‐Glu residues

High energy irradiation to the hydrogen bonded system is important in relevance with the initial process of DNA and enzyme damages. In the present study, the effects of radiation to catalytic triad have been investigated by means of direct ab‐initio molecular dynamics (AIMD) calculation. As a model of the catalytic triad, Ser‐His‐Glu residue, which is one of the important enzymes in the acylation reaction, was examined. The ionization and electron attachment processes in Ser‐His‐Glu were investigated as the radiation effects. The direct AIMD calculation showed that a proton of His is spontaneously transferred to carbonyl oxygen of Glu after the ionization. However, the whole structure of catalytic triad was essentially kept after the ionization. On the other hand, in the case of the electron capture in the model catalytic triad Ser‐His‐Glu, the dissociation of Glu residue from [Ser‐His]− was found as a product channel. The mechanism of ionization and electron capture process in the catalytic triad was discussed on the basis of theoretical results. © 2015 Wiley Periodicals, Inc.

Alkali metal mediated C-C bond coupling reaction.

Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2](-) was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

Fundamental frequency from classical molecular dynamics.

We give a theoretical validation for calculating fundamental frequencies of a molecule from classical molecular dynamics (MD) when its anharmonicity is small enough to be treated by perturbation theory. We specifically give concrete answers to the following questions: (1) What is the appropriate initial condition of classical MD to calculate the fundamental frequency? (2) From that condition, how accurately can we extract fundamental frequencies of a molecule? (3) What is the benefit of using ab initio MD for frequency calculations? Our analytical approaches to those questions are classical and quantum normal form theories. As numerical examples we perform two types of MD to calculate fundamental frequencies of H2O with MP2/aug-cc-pVTZ: one is based on the quartic force field and the other one is direct ab initio MD, where the potential energies and the gradients are calculated on the fly. From those calculations, we show comparisons of the frequencies from MD with the post vibrational self-consistent field calculations, second- and fourth-order perturbation theories, and experiments. We also apply direct ab initio MD to frequency calculations of C-H vibrational modes of tetracene and naphthalene. We conclude that MD can give the same accuracy in fundamental frequency calculation as second-order perturbation theory but the computational cost is lower for large molecules.

Photo-Reaction Mechanism of the Hydrated Superoxide Anion: A Theoretical Study

Electron detachment dynamics of the hydrated superoxide anion $$ {\text{O}}_2^ - ({\text{H}}_{ 2} {\text{O}})_{n}$$ (n = 2) have been investigated by means of the direct ab initio molecular dynamics method. Two electronic states (triplet and singlet states) were examined for the neutral oxygen molecule after the electron detachment. In both electronic states, the dissociation products O2 + water cluster, were obtained. However, the internal states are essentially different from each other. On the triplet state surface, the O–O stretching mode of O2(3Σ) is excited as a vibrational mode. On the other hand, the internal mode of the product on the singlet state surface is silent. The reaction mechanism is discussed on the basis of theoretical results.

Water-Accelerated OH Addition to Sulfur Dioxide SO2: Direct Ab Initio Molecular Dynamics (AIMD) Study

Ionization dynamics of water microsolvated sulfur dioxide SO2(H2O)n (n = 1-3 and 6) have been investigated by means of direct ab initio molecular dynamics (AIMD) method to elucidate the hydration effects of OH addition reaction to SO2 following the ionization. The calculations showed that the neutral 1:1 complex SO2-H2O has a C(s) symmetry and the sulfur of SO2 interacts with the oxygen of H2O with an eclipsed form. In the case of ionization of SO2-H2O 1:1 complex (n = 1), the cation complex composed of [H2O-SO2](+) with a face-to-face form was obtained as the product. The OH addition reactions to SO2 were found in larger systems (n = 2, 3, and 6) following the ionization. The reaction was expressed as SO2(+)(H2O)n → SO2(OH)···H(+)(H2O)(n-1) (n = 2, 3, and 6). The proton generated as (SO2-H2O)(+) → (HSO3) + H(+) was stabilized by the second water molecule as the reaction: H(+) + H2O → H3O(+). These processes occurred and were completed within the cluster. The OH addition mechanism in SO2(+)(H2O)n cluster was discussed on the basis of the present results.

Mechanism of Dissolution of a Lithium Salt in an Electrolytic Solvent in a Lithium Ion Secondary Battery: A Direct Ab Initio Molecular Dynamics (AIMD) Study

The mechanism of dissolution of the Li(+) ion in an electrolytic solvent is investigated by the direct ab initio molecular dynamics (AIMD) method. Lithium fluoroborate (Li(+)BF4(-)) and ethylene carbonate (EC) are examined as the origin of the Li(+) ion and the solvent molecule, respectively. This salt is widely utilized as the electrolyte in the lithium ion secondary battery. The binding of EC to the Li(+) moiety of the Li(+)BF4(-) salt is exothermic, and the binding energies at the CAM-B3LYP/6-311++G(d,p) level for n=1, 2, 3, and 4, where n is the number of EC molecules binding to the Li(+) ion, (EC)n(Li(+)BF4(-)), are calculated to be 91.5, 89.8, 87.2, and 84.0 kcal mol(-1) (per EC molecule), respectively. The intermolecular distances between Li(+) and the F atom of BF4(-) are elongated: 1.773 Å (n=0), 1.820 Å (n=1), 1.974 Å (n=2), 1.942 Å (n=3), and 4.156 Å (n=4). The atomic bond populations between Li(+) and the F atom for n=0, 1, 2, 3, and 4 are 0.202, 0.186, 0.150, 0.038, and 0.0, respectively. These results indicate that the interaction of Li(+) with BF4(-) becomes weaker as the number of EC molecules is increased. The direct AIMD calculation for n=4 shows that EC reacts spontaneously with (EC)3(Li(+)BF4(-)) and the Li(+) ion is stripped from the salt. The following substitution reaction takes place: EC+(EC)3(Li(+)BF4(-))→(EC)4Li(+)-(BF4(-)). The reaction mechanism is discussed on the basis of the theoretical results.

Electron detachment dynamics of O2−(H2O): direct ab initio molecular dynamics (AIMD) approach

Electron detachment dynamics of the hydrated superoxide anion O2−(H2O) have been investigated by means of direct ab initio molecular dynamics (AIMD) methods. Two potential energy surfaces were examined as electronic states of oxygen molecule after the electron detachment of the hydrated superoxide anion: O2(3Σ)(H2O) and O2(1Δ)(H2O). In both electronic states, the dissociation products, O2 + H2O, were obtained. However, the internal states of O2 were essentially different from each other. On the triplet state surface, the O–O stretching mode of O2(3Σ) was excited, whereas that of O2(1Δ) was silent. The reaction mechanism was discussed on the basis of theoretical results.

Solvent Stripping Dynamics of Lithium ion solvated by ethylene carbonates: A direct ab-initio molecular (AIMD) Study

Solvent dissociation dynamics from solvated lithium ion solvated by ethylene carbonates (EC) have been investigated by means of direct ab-initio molecular dynamics (AIMD) method. The lithium ion was solvated by four EC molecules as the first solvation shell. It was found that the solvation number of lithium ion is drastically changed from 4 to 1 when the solvated lithium ion accepts an excess electron. The binding energy of Li-EC decreased to a one-tenth. Finally, the contact ion pair composed of Li+ and EC− was formed as the product. The mechanism of solvent dissociation was discussed on the basis of theoretical results.

Double π–π stacking dynamics of benzene trimer cation: direct ab initio molecular dynamics (AIMD) study

Mechanism of π–π double stacking process of benzene trimer cation has been investigated by means of direct ab initio molecular dynamics method. It was found that H-shaped form of neutral benzene trimer is drastically changed to the π–π double stacking form composed of benzene trimer cation following the ionization. Absorption spectrum of charge resonance band of (Bz) 3 + was gradually blueshifted as a function of time. Time scale of the double stacking process (the formation of trimer cation from the H-shaped form) was calculated to be 0.7–1.5 ps, which is comparable to that of dimer cation formation. After the ionization of benzene trimer, (Bz)(Bz)c(Bz′), the hole is distributed around three benzene molecules with a branching ratio of (Bz)+0.3(Bz)c+0.4(Bz′)+0.3, and the structure of (Bz)c+ was rapidly deformed due to the Jahn–Teller effect. Next, the molecular rotation of central benzene (Bz)c+ occurred gradually. Immediately, both benzene molecules in the wing positions were also rotated synchronicity. Finally, the π–π double stacking form composed of benzene trimer cation was formed. The formation mechanism of benzene trimer cation was discussed on the basis of theoretical results.

Ab initiodynamics trajectory study of the heterolytic cleavage of H2 by a Lewis acid [B(C6F5)3] and a Lewis base [P(tBu)3

Activation of H2 by a "frustrated Lewis pair" (FLP) composed of B(C6F5)3 and P(tBu)3 species has been explored with high level direct ab initio molecular dynamics (AIMD) simulations at finite temperature (T = 300 K) in gas phase. The initial geometrical conditions for the AIMD trajectory calculations, i.e., the near attack conformations of FLP + H2, were devised using the host-guest model in which suitable FLP conformations were obtained from the dynamics of the B(C6F5)3∕P(tBu)3 pair in gas phase. AIMD trajectory calculations yielded microscopic insight into effects which originate from nuclear motion in the reacting complex, e.g., the alternating compression∕elongation of the boron-phosphorous distance and the change of the pyramidality of boron in B(C6F5)3. The ensemble averaged trajectory analysis has been compared with the minimum energy path (MEP) description of the reaction. Similar to MEP, AIMD shows that an attack of the acid∕base pair on the H-H bond gives rise to the polarization of the H2 molecule and as a consequence generates a large dipole moment of the reacting complex. The MEP and AIMD portrayals of the reaction are fundamentally different in terms of the magnitude of the motion of nuclei in B(C6F5)3 and P(tBu)3 during the H2 cleavage. In the AIMD trajectory simulations, geometries of B(C6F5)3 and P(tBu)3 appear as nearly "frozen" on the short time scale of the H2 cleavage. This is contrary to the MEP picture. Several of the concepts which arise from this work, e.g., separation of time scales of nuclear motion and the time-dependence of the donor-acceptor interactions in the reacting complex, are important for the understanding of chemical reactivity and catalysis.

Ionization dynamics of the water trimer: A direct ab initio MD study

Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ∼15fs after the ionization). In complex channel, an ion–radical contact pair (H3O+–OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50–100fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results.

Hole capture dynamics of phenyl-capped thiophene: Direct ab-initio molecular dynamics study

Hole capture dynamics of phenyl-capped thiophene (DPT) have been investigated by means of density functional theory (DFT) and direct ab-initio molecular dynamics (AIMD) calculations. DPT has been utilized as a part of organic solar cells. The direct AIMD calculations showed that the twist angle of DPT vibrates periodically after hole capture.

Diffusion dynamics of lithium ion and atom on graphene surfaces

Recent theoretical studies of the diffusion dynamics of lithium ions and atoms (Li + and Li) in carbon materials have been reviewed. Graphene, graphene flakes, and fullerene (C 60 ) were examined as the carbon materials. The direct ab initio molecular dynamics (MD) method, used in the present study, is a hybrid technique composed of ab initio molecular orbital and MD methods. The diffusion of Li + ions (atoms) and their interaction with the carbon materials are treated at the quantum mechanical level. The diffusion path and reaction mechanism obtained by the direct ab initio MD method were significantly different from those of a usual classical MD calculation. Details of the diffusion dynamics of the lithium were discussed on the basis of theoretical results.

Electron detachment dynamics of Cu−(H2O)n (n = 1–3): a direct ab initio MD study

Direct ab initio molecular dynamics (MD) has been applied to the electron detachment dynamics of Cu−(H2O)n (n = 1–3). The initial structures of Cu(H2O)n were generated randomly around the equilibrium point of anionic complex Cu−(H2O)n and then trajectories were run from the vertical electron detachment points of Cu−(H2O)n. It was found that three reaction channels compete with each other when n = 1: dissociation channel (the product is Cu + H2O) and complex formation channel (the product is neutral CuH2O complex). The complex channel is further classified to two kind of complexes: a strongly bound (I) complex and a weakly bound (II) complex. The dissociation channel occurred from an inner Franck–Condon (FC) region where the distance Cu−–H2O is shorter than the equilibrium point. On the other hand, the complex formation channel occurred from the wide FC region. In case of n = 2 and 3, dissociation channels were the main products. The mechanism of the electron detachment dynamics was discussed on the basis of the theoretical results.

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.

Direct ab initio molecular dynamics (MD) study of the ionization on a benzene dimer

The ionization dynamics of a benzene dimer have been investigated by means of a direct ab initio molecular dynamics (MD) method in order to elucidate the reaction mechanism. Following the ionization, the T-shaped neutral benzene dimer was gradually changed to a π-stacked benzene dimer cation. The structural change and time evolution of the electronic absorption spectrum were completely visualized for the first time. The time scale of the dimer formation was estimated to be 1.0–1.5 ps. First, the benzene molecule at the stem position (Bz′) was ionized, and the structure of Bz′+ was rapidly deformed due to the Jahn–Teller effects. Next, the rotation of (Bz′)+ gradually occurred relative to Bz. Finally, a π-stacked benzene dimer cation was formed. TD-DFT calculations indicated that the absorption spectrum of (Bz)2+ is blue-shifted as a function of time. The formation mechanism of the benzene dimer cation was discussed on the basis of the theoretical results.

Melting temperature of tungsten from twoab initioapproaches

We have calculated the melting temperature of tungsten by two ab initio approaches. The first approach can be divided into two steps. In the first step, we simulate a large coexisting solid and liquid system by the classical embedded-atom method potential and obtain an approximate melting temperature. In the second step, we compute the accurate melting temperature by performing the ab initio free-energy corrections. The second approach is to perform a direct ab initio molecular-dynamics simulation for the coexisting solid and liquid system using the constant particle number, pressure, and enthalpy ensemble. In the second approach, the simulation is carried out entirely using a density-functional theory Hamiltonian, and no other approximations are imposed. However, the simulation is performed using a relatively small supercell. The results obtained from two ab initio approaches can provide a check for each other. Our results show that they are in good agreement with each other and also in reasonably good agreement with the experimental value.