Ab Initio Molecular Dynamics Method Research Articles

Collision Induced Complex Formation following Electron Capture of SO2–H2O Complex Interacting with Argon Atoms

Electron capture dynamics of SO(2)-H(2)O(Ar)(n) complexes (n = 0-2) have been investigated by means of direct ab initio molecular dynamics (MD) method in order to elucidate the effects of solvent argon on the reaction dynamics of SO(2)-H(2)O. The neutral complex of SO(2)-H(2)O has a C(s) symmetry, and the sulfur of SO(2) interacts with the oxygen of H(2)O with an eclipsed form. In the SO(2)-H(2)O(Ar)(n) complexes, the dipole of H(2)O interacts with the argon atoms in the most stable structure. Following the electron capture of the complex SO(2)-H(2)O, the complex anion SO(2)(-)(H(2)O) is dissociated directly into SO(2)(-) + H(2)O. On the other hand, the electron capture of SO(2)(H(2)O)(Ar)(n) argon complex (n = 1-2) leads to the anion-water complex SO(2)(-)(H(2)O) because the collision of H(2)O with the Ar atom causes a rebound of H(2)O from Ar atom to the SO(2)(-) anion. The argon solvent enhanced the SO(2)(-)(H(2)O) complex formation. The reaction mechanism of SO(2)(H(2)O) in the participation of argon atoms was discussed on the basis of the present results.

Magnetic coupling in dilute magnetic semiconductors: A new perspective

AbstractThe ferromagnetic coupling (FMC) among magnetic impurities in the dilute magnetic semiconductors (DMSs) ZnO and GaN is revisited within a molecular orbital (MO) approximation. In particular, based on computational results obtained by both ab initio and tight binding molecular dynamics methods, we demonstrate that the FMC appears to be the coupling between MOs consisting of MO‐parts confined in the tetrahedra centered at the cationic impurities. This new interpretation links the defect‐induced magnetism in DMSs and TMOs (transition metal oxides) to the previously proposed theories of magnetic organic salts and carbon‐based materials.

Ab initio molecular dynamics simulation of pressure-induced phase transformation in BeO

Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ → RS and ZB → RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ → RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange–correlation functional employed and the way of applying pressure.

Orbital free ab initio simulation of surface freezing in a dilute Ga-Tl alloy

We have used the orbital-free ab initio molecular dynamics method to study the phenomenon of surface freezing in a liquid Ga-Tl alloy (nominal Tl concentration of 0.14). Several thermodynamic states are considered from a high temperature of 675 K to a low temperature of 350 K. At the higher temperature the Tl atoms segregate to the surface and form a liquid layer. Upon cooling the layer eventually crystallizes into a close-packed hexagonal solid layer. These results agree with experiments for a dilute liquid alloy of Tl in Ga, except for some overestimation of the surface freezing temperature. X-ray reflectivity data are also well reproduced. The wavelength of the oscillatory density profile coincides with that deduced from experiments and with that obtained in earlier computer simulation results. We also analyze the consequences of surface freezing on the structure of the liquid in contact with the solid layer, finding no influence whatsoever, as the structure basically coincides with the bulk liquid one.

An investigation of the local structure and dynamic properties of undercooled liquid silicon using the orbital-free ab-initio molecular dynamics method

We present results for the static and dynamic structural properties of undercooled liquid Si, at several temperatures between 1550 K and 1100 K, obtained through orbital-free ab-initio molecular dynamics simulations. The local bond angle distributions show a modest increase in the tetrahedral order upon decreasing the temperature. We also analyze the variation of several dynamic magnitudes and transport properties with temperature, showing a tendency to sustain shear waves for some wavevectors as undercooling is deepened. We compare our orbital-free ab-initio results with the limited experimental data available, as well as with results of other ab-initio simulations.

Atomic and electronic structure of mixed Au-Co nanowires: Ab initio molecular dynamics study

The atomic and electronic structure of uniformly and nonuniformly mixed Au-Co nanowires have been studied using the ab initio molecular dynamics method. The effect of elastic stretching/contraction deformations on the stability and electronic properties of mixed Au-Co nanowires has been studied. It is established that Co dimers are formed in a nonuniformly mixed nanowire. The formation of CO2 dimers results in a non-uniform distribution of the electron density and interactomic distances along the wire and leads to accelerated rupture of the wire between Au atoms under stretching. Only a uniformly mixed Au-Co nanowire composed of regularly alternating Au and Co atoms is stable under stretching up to large interactomic distances.

Molecular dynamics simulation of a complex surface reaction: The effect of coverage onH2dissociation on Pd(111)

We develop a strategy based on a molecular dynamics method with reactive force fields for large-scale simulations of reacting systems. The considerably enhanced computational efficiency (${10}^{5}$ times faster than an ab initio molecular dynamics method) opens an avenue to simulating complex chemical reactions that had been previously nontractable. As a demonstration of feasibility, thorough simulations were performed for ${\mathrm{H}}_{2}$ dissociation on H-covered Pd(111), which bring insights into the coverage effect on surface reactivity.

Ab Initio Molecular Dynamics Study of H2 Formation Inside POSS Compounds

The mechanism and dynamics of the formation of a hydrogen molecule by incorporating two hydrogen atoms in a stepwise manner into the cavity of some POSS (polyhedral oligomeric silsesquioxanes) compounds has been investigated by ab initio molecular orbital and ab initio molecular dynamics (AIMD) methods. The host molecules in the present reactions are two types of POSS, T(8) ([HSiO(1.5)](8)) and T(12)(D(2d)) ([HSiO(1.5)](12)). AIMD simulations were performed at the CASSCF level of theory, in which two electrons and two orbitals of the colliding hydrogen atoms are included in the active space. The trajectories were started by inserting the second hydrogen atom into the hydrogen atom-encapsulated-POSS (H + H@T(n) → H(2)@T(n); n = 8 and 12). In many cases, the gradual formation of a hydrogen molecule has been observed after frequent collisions of two hydrogen atoms within the cages. The effect of the introduction of an argon atom in T(12) is discussed as well.

Ab initio theoretical calculations of the electronic excitation energies of small water clusters

A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

Ionization dynamics of a water dimer: specific reaction selectivity

Ionization dynamics of a water dimer have been investigated by means of a direct ab initio molecular dynamics (MD) method. Two electronic state potential energy surfaces of (H(2)O)(2)(+) (ground and first excited states, (2)A'' and (2)A') were examined as cationic states of (H(2)O)(2)(+). Three intermediate complexes were found as product channels. One is a proton transfer channel where a proton of H(2)O(+) is transferred into the H(2)O and then a complex composed of H(3)O(+)(OH) was formed. The second is a face-to-face complex channel denoted by (H(2)O-OH(2))(+) where the oxygen-oxygen atoms directly bind each other. Both water molecules are equivalent to each other. The third one is a dynamical complex where H(2)O(+) and H(2)O interact weakly and vibrate largely with a large intermolecular amplitude motion. The dynamics calculations showed that in the ionization to the (2)A'' state, a proton transfer complex H(3)O(+)(OH) is only formed as a long-lived complex. On the other hand, in the ionization to the (2)A' state, two complexes, the face-to-face and dynamical complexes, were found as product channels. The proton of H(2)O(+) was transferred to H(2)O within 25-50 fs at the (2)A'' state, meaning that the proton transfer on the ground state is a very fast process. On the other hand, the decay process on the first excited state is a slow process due to the molecular rotation. The mechanism of the ionization dynamics of (H(2)O)(2) was discussed on the basis of theoretical results.

Ionization dynamics of aminopyridine dimer: a direct ab initio molecular dynamics (MD) study

The ionization dynamics of an aminopyridine dimer (AP)(2) has been investigated by means of the direct ab initio molecular dynamics (MD) method. It was found that the reaction process was composed of three steps after the vertical ionization of (AP)(2): dimer approach, proton transfer and energy relaxation. The timescales of these processes were 50-100, 10-20, and 200 fs, respectively. The timescale of the dimer approach was dependent on the initial separation between AP(+) and AP. After the ionization, AP approached gradually the ionized AP(+). The proton of AP(+) was transferred to AP at the nearest intermolecular distance, while the potential energy was quickly dropped according to the proton transfer. The energy relaxation of the dimer cation was significantly faster than that of the monomer cation. The mechanism of ionization dynamics of (AP)(2) was discussed on the basis of the theoretical results.

The First Molecular Wheel: A Theoretical Investigation

ABSTRACTRecently, the first molecular nanowheel was synthesized and characterized from Scanning Tunneling Microscope (STM) experiments. It was demonstrated that a specifically designed hydrocarbon molecule (C44H24) could roll on a copper substrate along the [110] surface direction. In this work we report a preliminary theoretical analysis of the isolated molecule and of its rolling processes on different Cu surfaces. We have used ab initio and classical molecular dynamics methods. The simulations showed that the rolling mechanism is only possible for the [110] surface. In this case, the spatial separation among rows of copper atoms is enough to ‘trap’ the molecule and to create the necessary torque to roll it. Other surface orientations ([111] and [100]) are too smooth and cannot provide the necessary torque for the rolling process.

Predissociation via Conformational Change: Photodissociation of N,N-Dimethylnitrosamine in the S1 State

We investigated the photodissociation mechanism of N,N-dimethylnitrosamine (CH(3))(2)NNO (DMN) by ab intio quantum chemical methods. Inspired by an earlier study we calculated two-dimensional potential energy surfaces of the S(1) state of DMN in its planar and pyramidal conformations. While the planar molecular geometry appears to possess no direct dissociation channel, the pyramidal configuration is dissociative yielding the products NO + (CH(3))(2)N. Using wave packet dynamics on the planar S(1) potential energy surface the experimental absorption spectrum was well reproduced which gives indirect but strong support for the nondissociative nature of this surface. The transition from the planar to the pyramidal conformation of DMN was then investigated by an ab initio molecular dynamics method which revealed the time evolution of the geometrical parameters of the molecule up to the dissociation of the N-N bond. This occurs about 90 fs after photon excitation. The calculated minimum energy path along the N-N coordinate and the structural changes of the molecule along this coordinate provided a detailed picture of this indirect dissociation or, more specific, predissociation process via conformational change.

Quantum wavepacket ab initio molecular dynamics: Generalizations using an extended Lagrangian treatment of diabatic states coupled through multireference electronic structure

We present a generalization to our previously developed quantum wavepacket ab initio molecular dynamics (QWAIMD) method by using multiple diabatic electronic reduced single particle density matrices, propagated within an extended Lagrangian paradigm. The Slater determinantal wavefunctions associated with the density matrices utilized may be orthogonal or nonorthogonal with respect to each other. This generalization directly results from an analysis of the variance in electronic structure with quantum nuclear degrees of freedom. The diabatic electronic states are treated here as classical parametric variables and propagated simultaneously along with the quantum wavepacket and classical nuclei. Each electronic density matrix is constrained to be N-representable. Consequently two sets of new methods are derived: extended Lagrangian-QWAIMD (xLag-QWAIMD) and diabatic extended Lagrangian-QWAIMD (DxLag-QWAIMD). In both cases, the instantaneous potential energy surface for the quantum nuclear degrees of freedom is constructed from the diabatic states using an on-the-fly nonorthogonal multireference formalism. By introducing generalized grid-based electronic basis functions, we eliminate the basis set dependence on the quantum nucleus. Subsequent reuse of the two-electron integrals during the on-the-fly potential energy surface computation stage yields a substantial reduction in computational costs. Specifically, both xLag-QWAIMD and DxLag-QWAIMD turn out to be about two orders of magnitude faster than our previously developed time-dependent deterministic sampling implementation of QWAIMD. Energy conservation properties, accuracy of the associated potential surfaces, and vibrational properties are analyzed for a family of hydrogen bonded systems.

Direct ab initio MD study on the hydrogen abstraction reaction of triplet state acetone from methanol molecule

Solvent re-orientation process of triplet acetone/methanol complex and intermolecular hydrogen atom abstraction reaction on the triplet state energy surface, (CH3)2C=O (T1) + CH3OH → (CH3)2C–OH + CH2OH in gas phase, have been investigated by means of density functional theory (DFT) and direct ab initio molecular dynamics (MD) methods. The static DFT calculation of hydrogen abstraction reaction at the T1 state showed that the transition state is 16.4 and 30.9 kcal/mol lower than the energy levels of S1 and S2 states, respectively, and 9.2 kcal/mol higher than the bottom of T1 state. The product state, (CH3)2C–OH⋯CH2OH, is 8.4 kcal/mol lower in energy than the level of T1 state. The direct ab initio MD calculation showed that the product is rapidly formed within 150 fs and the separated products (CH3)2C–OH + CH2OH were formed. The mechanism of reaction dynamics of the triplet acetone/methanol complex was discussed on the basis of theoretical results.

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

AbstractDepending on their environment, polyproline peptides form chiral helices that may be either left‐ (PPII) or right‐handed (PPI). Here, we have characterized both the structure and free energy landscapes of Ace‐(Pro)n‐Nme (n an integer less than 13) peptides, in vacuo and in implicit water environments. Both ab initio and classical molecular dynamics methods were used. In terms of the latter, we used a recently developed Adaptively Biased Molecular Dynamics (ABMD) method in conjunction with three different force fields (ff99, ff99SB, ff03) and two different Generalized Born models for the implicit solvent environment. Specifically, the ABMD method provides for an accurate description of the free energy landscapes in terms of a set of collective variables, which were carefully chosen as to reflect the “slow modes” of the polyproline peptides. These are primarily based on the cis‐trans isomerization associated with the prolyl bonds. In agreement with recent experimental results, the peptides form not only the pure PPII or PPI structures but also a large number of stable conformers having more or less similar free energies, whose distributions we have characterized. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Electron Capture Dynamics of a Water Molecule Connected to a Cyclic Water Trimer: A Direct Ab Initio MD Approach

Electron capture dynamics of the water tetramer (H(2)O)(n) (n = 4) have been investigated by means of a full-dimensional direct ab initio molecular dynamics (MD) method at the MP2/6-311++G(d,p) level. Two structural conformers (branched and cyclic forms of the water tetramer) were examined as neutral water tetramers. The structure of the branched form is that a dangling water molecule binds to the ring composed of a cyclic water trimer. In the case of electron capture of the branched form, first, an excess electron was trapped by the dangling water molecule. Next, rotation of the water molecule located in the ring occurred rapidly, while a hydrogen bond of the ring was broken. The branched structure was gradually changed to a linear one. This change was caused by the increase of the dipole moment of the neutral water tetramer oriented toward the excess electron. The time scale of hydrogen bond breaking and solvation of the excess electron were estimated to be 100 and 400 fs, respectively. In the case of the cyclic water tetramer, a planar structure was only changed to a slight bent form. The mechanism of electron capture of the water tetramer (mainly the branched form) was discussed on the basis of theoretical results.

Free energy calculations using dual-level Born–Oppenheimer molecular dynamics

We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.

Reactive force fields for surface chemical reactions: A case study with hydrogen dissociation on Pd surfaces

An approach based on reactive force fields is applied to the parametrization of potential energy surface (PES) for chemical reactions on surfaces with a benchmark system, H(2)/Pd(111). We show that a simple reactive force field based on the second moment approximation does not allow for obtaining reliable results of reaction dynamics for the considered system. With a more elaborate reactive force field, i.e., reactive bond order (REBO) force field, we succeeded in obtaining a reliable PES for H(2)/Pd(111). The accuracy of the constructed REBO force field is carefully checked through various tests including the comparison not only between energies calculated with density functional theory and those with REBO force field but also between the available results of ab initio molecular dynamics simulations and those with our force field. Moreover, our REBO force field is endowed with some transferability since the force field constructed with a database containing only information on H(2)/Pd(111) allows for obtaining also accurate results for H(2)/Pd(100) and qualitatively correct results for H(2)/Pd(110) without any refitting. With the help of our reactive force field, the molecular dynamics simulation for the dissociation of H(2) on the considered Pd surfaces is speeded up by five orders of magnitude compared to ab initio molecular dynamics method. The demonstrated reliability and the very high computational efficiency of reactive force fields open extremely attractive perspectives for studying large-scale complex reacting systems.

Direct ab initio MD study on the interaction of hydroperoxy radical (HOO) with water molecules

Structures and electronic states of the HOO radical interacting with water molecules, expressed by HOO(H2O)n (n = 1 and 2), have been investigated by means of a direct ab initio molecular dynamics (MD) method. From the static ab initio calculation of HOO-H2O complex, two types of HOO radical were found: i.e., the HOO radical acts as a hydrogen donor or acceptor in the complex (n = 1). The binding energies of former and latter complexes were calculated to be 8.7 and 3.3 kcal mol(-1), respectively, at the QCISD/6-311++G(2d,2p) level. In the case of 1:2 complex HOO(H2O)2, a cyclic structure with a hydrogen donor of HOO was obtained as the stable form. Effects of zero point vibration on the structures and hyperfine coupling constants of the HOO radical were also investigated. The structures and electronic states of HOO(H2O)n (n = 1 and 2) were discussed on the basis of theoretical results.