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Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: convergence toward Born-Oppenheimer trajectories.

A dynamical extension of the "curvy-steps" approach to linear-scaling self-consistent field calculations is presented, which yields an extended-Lagrangian formulation of ab initio molecular dynamics. An exponential parametrization of the one-electron density matrix, expressed in terms of atom-centered Gaussian basis functions, facilitates propagation along the manifold of density matrices in a geometrically correct fashion that automatically enforces idempotency constraints. The extended Lagrangian itself is constraint free, thus neither density matrix purification nor expensive, iterative solution for Lagrange multipliers is required. Propagation is highly efficient, and time steps compare favorably to those used in Car-Parrinello molecular dynamics simulations. The behavior of the method, especially with regard to the maintenance of adiabatic decoupling of nuclei and electrons, is examined for a sequence of diatomic molecules, and comparison is made to trajectories propagated on the converged Born-Oppenheimer surface. Certain claims to the contrary notwithstanding, our results demonstrate that vibrational frequencies may depend on the value of the fictitious mass parameter, even in an atom-centered basis. Light-atom stretching frequencies can be significantly redshifted, even when the nuclear and electronic energy scales are well separated. With a sufficiently small fictitious mass and a short time step, accurate frequencies can be obtained; we characterize appropriate values of these parameters for a wide range of vibrational frequencies.

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Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories.

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.

Amino Acid Sequence↗

The effect of zero-point energy differences on the isotope dependence of the formation of ozone: a classical trajectory study.

The effect of zero-point energy differences (DeltaZPE) between the possible fragmentation channels of highly excited O(3) complexes on the isotope dependence of the formation of ozone is investigated by means of classical trajectory calculations and a strong-collision model. DeltaZPE is incorporated in the calculations in a phenomenological way by adjusting the potential energy surface in the product channels so that the correct exothermicities and endothermicities are matched. The model contains two parameters, the frequency of stabilizing collisions omega and an energy dependent parameter Delta(damp), which favors the lower energies in the Maxwell-Boltzmann distribution. The stabilization frequency is used to adjust the pressure dependence of the absolute formation rate while Delta(damp) is utilized to control its isotope dependence. The calculations for several isotope combinations of oxygen atoms show a clear dependence of relative formation rates on DeltaZPE. The results are similar to those of Gao and Marcus [J. Chem. Phys. 116, 137 (2002)] obtained within a statistical model. In particular, like in the statistical approach an ad hoc parameter eta approximately 1.14, which effectively reduces the formation rates of the symmetric ABA ozone molecules, has to be introduced in order to obtain good agreement with the measured relative rates of Janssen et al. [Phys. Chem. Chem. Phys. 3, 4718 (2001)]. The temperature dependence of the recombination rate is also addressed.

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Quasiclassical trajectory study of formaldehyde unimolecular dissociation: H(2)CO-->H2 + CO, H + HCO.

We report quasiclassical trajectory calculations of the dynamics of the two reaction channels of formaldehyde dissociation on a global ab initio potential energy surface: the molecular channel H(2)CO-->H(2) + CO and the radical H(2)CO-->H + HCO. For the molecular channel, it is confirmed that above the threshold of the radical channel a second, intramolecular hydrogen abstraction pathway is opened to produce CO with low rotation and vibrationally hot H(2). The low-j(CO) and high-nu(H(2) ) products from the second pathway increase with the total energy. The competition between the molecular and radical pathways is also studied. It shows that the branching ratio of the molecular products decreases with increasing energy, while the branching ratio of the radical products increases. The results agree well with very recent velocity-map imaging experiments of Suits and co-workers and solves a mystery first posed by Moore and co-workers. For the radical channel, we present the translational energy distributions and HCO rotation distributions at various energies. There is mixed agreement with the experiments of Wittig and co-workers, and this provides an indirect confirmation of their speculation that the triplet surface plays a role in the formation of the radical products.

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A growing string method for the reaction pathway defined by a Newton trajectory.

The reaction path is an important concept of theoretical chemistry. We use a projection operator for the following of the Newton trajectory (NT) along the reaction valley of the potential energy surface. We describe the numerical scheme for the string method, adapting the proposal of a growing string (GS) by [Peters et al.,J. Chem. Phys. 120, 7877 (2004)]. The combination of the Newton projector and the growing string idea is an improvement of both methods, and a great saving of the number of iterations needed to find the pathway over the saddle point. This combination GS-NT is at the best of our knowledge new. We employ two different corrector methods: first, the use of projected gradient steps, and second a conjugated gradient method, the CG+ method of Liu, Nocedal, and Waltz, generalized by projectors. The executed examples are Lennard-Jones clusters, LJ(7) and LJ(22), and an N-methyl-alanyl-acetamide (alanine dipeptide) rearrangement between the minima C7(ax) and C5. For the latter, the growing string calculation is interfaced with the GASSIAN03 quantum chemical software package.

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Classical trajectory study of collisions of Ar with alkanethiolate self-assembled monolayers: potential-energy surface effects on dynamics.

We have investigated collisions between Ar and alkanethiolate self-assembled monolayers (SAMs) using classical trajectory calculations with several potential-energy surfaces. The legitimacy of the potential-energy surfaces is established through comparison with molecular-beam data and ab initio calculations. Potential-energy surfaces used in previous work overestimate the binding of Ar to the SAM, leading to larger energy transfer than found in the experiments. New calculations, based on empirical force fields that better reproduce ab initio calculations, exhibit improved agreement with the experiments. In particular, polar-angle-dependent average energies calculated with explicit-atom potential-energy surfaces are in excellent agreement with the experiments. Polar- and azimuthal-angle-dependent product translational energies are examined to gain deeper insight into the dynamics of Ar+SAM collisions.

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The triplet channel in the photodissociation of ozone in the Hartley band: classical trajectory surface hopping analysis.

The triplet channel in the photodissociation of ozone in the Hartley band, O3 + hv-->O(3P) + O2(3sigma), is investigated by means of a classical trajectory surface hopping method using ab initio diabatic potential energy surfaces for the B and the R states. Because of the strong recoil in the R state along the breaking O-O bond, O2(3sigma) is produced with a high rotational energy. The nonadiabatic transition probability depends markedly on the coordinate along the crossing seam. As a consequence a unique correlation is found between the internuclear geometry at the crossing and the final vibrational state of O2(3sigma). The calculated distribution of the translational energy is in good accord with the measured distribution.

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Dynamics of the C(1D)+D2 reaction: a comparison of crossed molecular-beam experiments with quasiclassical trajectory and accurate statistical calculations.

In this paper we report a combined experimental and theoretical study on the dynamics of the insertion reaction C((1)D)+D(2) at 15.5 kJ mol(-1) collision energy. Product angular and velocity distributions have been obtained in crossed beam experiments and quasiclassical trajectory (QCT) and rigorous statistical calculations have been performed on the recent and accurate ab initio potential energy surface of Bussery-Honvault, Honvault, and Launay at the energy of the experiment. The molecular-beam results have been simulated using the theoretical calculations. Good agreement between experiment and both QCT and statistical predictions is found.

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A skewed-momenta method to efficiently generate conformational-transition trajectories.

We present a novel computational method, the skewed-momenta method (Skew'M), which applies a bias to the Maxwell distribution of initial momenta used to generate ensembles of trajectories. As a result, conformational transitions are accentuated and kinetic properties are calculated more effectively. The connection to the related puddle jumping method is discussed. A reweighting scheme permits the exact calculation of kinetic properties. Applications are presented for the rapid calculation of rate constants for molecular isomerization, and for the efficient reconstruction of free-energy profiles using a straightforward modification of the Jarzynski identity.

Chemistry, Physical↗

Quasi-classical trajectory study of Si+O2-->SiO+O reaction.

Quasi-classical trajectory calculations for the Si(3P)+O2(X 3Sigmag-)-->SiO(X 1Sigma+)+O(1D) reaction have been carried out using the analytical ground 1A' potential energy surface (PES) recently reported by Dayou and Spielfiedel [J. Chem. Phys. 119, 4237 (2003)]. The reaction has been studied for a wide range of collision energies (0.005-0.6 eV) with O2 in its ground rovibrational state. The barrierless PES leads to a decrease of the total reaction cross section with increasing collision energy. It has been brought to evidence that the reaction proceeds through different reaction mechanisms whose contributions to reactivity are highly dependent on the collision energy range. At low collision energy an abstraction mechanism occurs involving the collinear SiOO potential well. The associated short-lived intermediate complex leads to an inverted vibrational distribution peaked at v'=3 and low rotational excitation of SiO(v',j') with a preferentially backward scattering. At higher energies the reaction proceeds mainly through an insertion mechanism involving the bent and linear OSiO deep potential wells and associated long-lived intermediate complexes, giving rise to nearly statistical energy disposals into the product modes and a forward-backward symmetry of the differential cross section.

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Cross sections of the O+ + H2 --> OH+ + H ion-molecule reaction and isotopic variants (D2, HD): quasiclassical trajectory study and comparison with experiments.

A dynamics study [cross section and microscopic mechanism versus collision energy (E(T))] of the reaction O+ + H2 --> OH+ + H, which plays an important role in Earth's ionosphere and interstellar chemistry, was conducted using the quasiclassical trajectory method, employing an analytical potential energy surface (PES) recently derived by our group [R. Martinez et al., J. Chem. Phys. 120, 4705 (2004)]. Experimental excitation functions for the title reaction, as well as its isotopic variants with D2 and HD, were near-quantitatively reproduced in the calculations in the very broad collision energy range explored (E(T) = 0.01-6.0 eV). Intramolecular and intermolecular isotopic effects were also examined, yielding data in good agreement with experimental results. The reaction occurs via two microscopic mechanisms (direct and nondirect abstraction). The results were satisfactorily interpreted based on the reaction probability and the maximum impact parameter dependences with E(T), and considering the influence of the collinear [OHH]+ absolute minimum of the PES on the evolution from reactants to products. The agreement between theory and experiment suggests that the reaction mainly occurs through the lowest energy PES and nonadiabatic processes are not very important in the wide collision energy range analyzed. Hence, the PES used to describe this reaction is suitable for both kinetics and dynamics studies.

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Effective chromophore potential, dissipative trajectories, and vibrational energy relaxation: Br2 in Ar matrix.

The intramolecular wave packet dynamics on the electronic B (3pi0) potential of Br2 in solid argon is induced and interrogated by femtosecond pump-probe spectroscopy. An effective potential of the chromophore in the solid is derived from the wave packet period for different excitation photon energies. Deep in the potential well, it is consistent with vibrational energies from wavelength-resolved spectra. It extends to higher energies, where the vibrational bands merge to a continuum, and even beyond the dissociation limit, thus quantifying the cage effect of the argon matrix. This advantage of pump-probe spectroscopy is related to a reduced contribution of homogeneous and inhomogeneous line broadenings. The vibrational energy relaxation rates are determined by a variation of the probe window spatial position via the probe quantum energy. A very large energy loss in the first excursion of the wave packet is observed near the dissociation limit. This strong interaction with the argon matrix is directly displayed in an experimental trajectory.

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A classical trajectory study of the photodissociation of T1 acetaldehyde: the transition from impulsive to statistical dynamics.

Previous experimental and theoretical studies of the radical dissociation channel of T(1) acetaldehyde show conflicting behavior in the HCO and CH(3) product distributions. To resolve these conflicts, a full-dimensional potential-energy surface for the dissociation of CH(3)CHO into HCO and CH(3) fragments over the barrier on the T(1) surface is developed based on RO-CCSD(T)/cc-pVTZ(DZ) ab initio calculations. 20,000 classical trajectories are calculated on this surface at each of five initial excess energies, spanning the excitation energies used in previous experimental studies, and translational, vibrational, and rotational distributions of the radical products are determined. For excess energies near the dissociation threshold, both the HCO and CH(3) products are vibrationally cold; there is a small amount of HCO rotational excitation and little CH(3) rotational excitation, and the reaction energy is partitioned dominantly (>90% at threshold) into relative translational motion. Close to threshold the HCO and CH(3) rotational distributions are symmetrically shaped, resembling a Gaussian function, in agreement with observed experimental HCO rotational distributions. As the excess energy increases the calculated HCO and CH(3) rotational distributions are observed to change from a Gaussian shape at threshold to one more resembling a Boltzmann distribution, a behavior also seen by various experimental groups. Thus the distribution of energy in these rotational degrees of freedom is observed to change from nonstatistical to apparently statistical, as excess energy increases. As the energy above threshold increases all the internal and external degrees of freedom are observed to gain population at a similar rate, broadly consistent with equipartitioning of the available energy at the transition state. These observations generally support the practice of separating the reaction dynamics into two reservoirs: an impulsive reservoir, fed by the exit channel dynamics, and a statistical reservoir, supported by the random distribution of excess energy above the barrier. The HCO rotation, however, is favored by approximately a factor of 3 over the statistical prediction. Thus, at sufficiently high excess energies, although the HCO rotational distribution may be considered statistical, the partitioning of energy into HCO rotation is not.

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Equilibrium free energies from fast-switching trajectories with large time steps.

Jarzynski's [Phys. Rev. Lett. 78, 2690 (1997)] identity for the free-energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase-space mappings. Solving a system's equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free-energy differences that are in principle exact. Numerical simulations show that Newton's equation can be discretized to low order over very large time steps (limited only by the computer's ability to represent resulting values of dynamical variables) without sacrificing thermodynamic accuracy. For computing the reversible work required to move a particle through a dense liquid, these calculations are more efficient than conventional fast-switching simulations by more than an order of magnitude. We also explore consequences of the phase-space mapping perspective for systems at equilibrium, deriving an exact expression for the statistics of energy fluctuations in simulated conservative systems.

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A quasiclassical trajectory study for the N(4S)+O2(X 3Sigmag-)-->NO(X 2Pi)+O(3P) reaction on the new 2A' and 4A' potential-energy surfaces.

A quasiclassical trajectory study with the sixth-order explicit symplectic algorithm of the N(4S)+O2(X 3Sigmag-)-->NO(X 2Pi)+O(3P) atmospheric reaction has been performed by employing the new 2A' and 4A' potential-energy surfaces reported by Sayos et al. [J. Chem. Phys. 117, 670 (2002)]. For the translational temperature considered up to 10,000 K, the larger relative translational energy and the higher rovibrational levels of O2 molecule with respect to the previous works have been taken into account, and a clearer database about the character of the total reaction cross section has been presented in this work. The dependence of microscopic rate constants on the vibrational level of O2 molecule at T=3000, 5000, and 10,000 K has been exhibited, and we can see that the values of log10 k(T,v,J) vary almost linearly with the vibrational level of O2 molecule. The thermal rate constants at the translational temperature between 300 and 10,000 K have been evaluated and compared with the experimental and previous theoretical results. It is found that the thermal rate constants determined in this work have a better agreement with the experimental data and can provide a more valid theoretical reference at the translational temperature considered for the title reaction.

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Dynamics of the O(3P) + H2 reaction at low temperatures: comparison of quasiclassical trajectory with quantum scattering calculations.

Quasiclassical trajectory and quantum-mechanical scattering calculations are reported for the O((3)P) + H(2)(X (1)Sigma(g) (+);upsilon = 1-3,j = 0)-->OH(X (2)Pi) + H((2)S) reaction at energies close to the reaction threshold. The dynamics of the reaction have been investigated for zero total angular momentum using the lowest (3)A" potential-energy surface developed by Rogers et al. [J. Phys. Chem. A 104, 2308 (2000)] and its recent extensions by Brandao et al. [J. Chem. Phys. 121, 8861 (2004)] which provide an improved description of the van der Waals interaction. Good agreement is observed for this system between quasiclassical and quantal results for incident kinetic energies above the tunneling regime. Quantum-mechanical calculations also confirm recent theoretical predictions of a strong collision-energy dependence of the OH(v(') = 0)OH(v' = 1) product branching ratio in the O((3)P) + H(2)(v = 1) reaction, which explains the differences observed in OH vibrational populations between experiments using different O((3)P) sources.

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Quantum mechanical and quasiclassical trajectory scattering calculations for the C(1D) + H2 reaction on the second excited 1 1A" potential energy surface.

Time-independent quantum mechanical (QM) and quasiclassical trajectory (QCT) scattering calculations have been carried out for the C(1D) + H2 --> CH + H reaction at a collision energy of 80 meV on a newly developed ab initio potential energy surface [B. Bussery-Honvault et al., Phys. Chem. Chem. Phys. 7, 1476 (2005)] of 1 1A" symmetry, corresponding to the second singlet state 1 1B1 of CH2. A general good agreement has been found between the QM and QCT rotational distributions and differential cross sections (DCSs). In both cases, DCSs are strongly peaked in the forward direction with a small contribution in the backward direction in contrast with those obtained on the 1 1A' surface, which are nearly symmetric. Rotational distributions obtained on the 1 1A" surface are somewhat colder than those calculated on the 1 1A' surface. The specific dynamics and the contribution of the 1 1A" surface to the overall reactivity of this system are discussed.

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Generalized trajectory surface hopping method based on the Zhu-Nakamura theory.

We present a generalized formulation of the trajectory surface hopping method applicable to a general multidimensional system. The method is based on the Zhu-Nakamura theory of a nonadiabatic transition and therefore includes the treatment of classically forbidden hops. The method uses a generalized recipe for the conservation of angular momentum after forbidden hops and an approximation for determining a nonadiabatic transition direction which is crucial when the coupling vector is unavailable. This method also eliminates the need for a rigorous location of the seam surface, thereby ensuring its applicability to a wide class of chemical systems. In a test calculation, we implement the method for the DH(2) (+) system, and it shows a remarkable agreement with the previous results of C. Zhu, H. Kamisaka, and H. Nakamura, [J. Chem. Phys. 116, 3234 (2002)]. We then apply it to a diatomic-in-molecule model system with a conical intersection, and the results compare well with exact quantum calculations. The successful application to the conical intersection system confirms the possibility of directly extending the present method to an arbitrary potential of general topology.

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