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PubMed2004

Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation.

For two methods commonly used to achieve canonical-ensemble sampling in a molecular-dynamics simulation, the Langevin thermostat and the Andersen [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)] thermostat, we observe, as have others, synchronization of initially independent trajectories in the same potential basin when the same random number sequence is employed. For the first time, we derive the time dependence of this synchronization for a harmonic well and show that the rate of synchronization is proportional to the thermostat coupling strength at weak coupling and inversely proportional at strong coupling with a peak in between. Explanations for the synchronization and the coupling dependence are given for both thermostats. Observation of the effect for a realistic 97-atom system indicates that this phenomenon is quite general. We discuss some of the implications of this effect and propose that it can be exploited to develop new simulation techniques. We give three examples: efficient thermalization (a concept which was also noted by Fahy and Hamann [S. Fahy and D. R. Hamann, Phys. Rev. Lett. 69, 761 (1992)]), time-parallelization of a trajectory in an infrequent-event system, and detecting transitions in an infrequent-event system.

Algorithms↗
PubMed2004

Classical trajectory calculations of intramolecular vibrational energy redistribution. I. Methanol-water complex.

Intramolecular vibrational energy redistributions of the O-H stretching (nuOH) vibration for the methanol monomer and its water complex, the methanol-water dimer, are investigated by using ab initio full-dimensional classical trajectory calculations. For the methanol monomer, in the high-energy regime of the 5nuOH overtone, the time dependence of the normal-mode energies indicates that energy flowed from the initial excited O-H stretching mode to the C-H stretching mode. This result confirms the experimental observation of energy redistribution between the O-H and C-H stretching vibrations [L. Lubich et al., Faraday Discuss. 102, 167 (1995)]. Furthermore, a lot of dynamical information in the time domain is contained in the power spectra, whose density is given by the Fourier transformation of the total momentum obtained from trajectory calculations. For the methanol-water hydrogen-bonded complex, at the high-energy level of the 5nuOH overtone, the calculated power spectrum shows considerable splitting and broadening, indicating significant energy redistribution through strong coupling between the O-H stretching vibration and other vibrations. It is thus clear that the A-H...B hydrogen-bond formation facilitates energy redistribution subsequent to the vibrational excitation of the hydrogen-bonded A-H stretching mode.

Journal Article↗
PubMed2004

Photodissociation of CCH: classical trajectory calculations involving seven electronic states.

The photodissociation dynamics of ethynyl radical, C(2)H, involving seven electronic states is studied by classical trajectory calculations. Initial values of the trajectories are selected based on relative absorption intensities calculated by Mebel et al. The energies and the derivatives are interpolated by three-dimensional cubic spline interpolator using an extended data pool. Mean square errors and standard deviations in interpolation of energies for 450 data points are found to be in the range 3.1 x 10(-6)-1.4 x 10(-5) and 1.7 x 10(-3)-3.8 x 10(-3) hartrees, respectively. The photofragments of C(2) and H are produced mainly in the X (1)Sigma(g) (+), a (3)Pi(u), b (3)Sigma(g) (-), c (3)Sigma(u) (+), A (1)Pi(u), B (1)Delta(g) electronic states of C(2) as product. The avoided crossings do not appear to be in the main dissociation pathways. The internal distributions are in good accord with the experimental results where comparison is possible, suggesting that the fragmentation mechanism of C(2)H(2) into C(2) and H is a two step process involving C(2)H radical as an intermediate with a life time long enough to allow complete collection of the phase space in the experiments.

Journal Article↗
PubMed2004

Ab initio direct dynamics trajectory simulation of C2H5F-->C2H4 + HF product energy partitioning.

Direct dynamics classical trajectory simulations were performed to study product energy partitioning in C(2)H(5)F-->C(2)H(4)+HF dissociation. The intrinsic reaction coordinate potential energy curve, reaction energetics, and transition state (TS) properties were calculated for this reaction at different levels of electronic structure theory, and MP2/6-31G( *) was chosen as a meaningful and practical method for performing the direct dynamics. The trajectories show that the HF bond, uncoupled from the other degrees of freedom, is formed within the first 10 fs as the system moves from the TS towards products. The populations of the HF vibration states, determined from the simulations, decrease monotonically as found from experiments. However, the simulation's populations for the low and high energy vibration states are larger and smaller, respectively, than the experimental results. The HF rotational temperature found from the simulations is in agreement with experiment. Increasing the TS's excess energy gives higher rotational temperatures for both C(2)H(4) and HF. Energy is partitioned to the products from both the excess energy in the TS and the potential energy release in the exit channel. Partitioning from these two energy sources is distinguished by varying the TS's excess energy. An analysis of the simulation's energy disposal shows that the fractions of the excess energy partitioned to relative translation, C(2)H(4) vibration, C(2)H(4) rotation, HF vibration, and HF rotation, are 0.17, 0.64, 0.076, 0.067, and 0.046, respectively, and are in good agreement with previous simulations on empirical potentials and experiments. The partitioning found for the potential energy release is 81%, <0.05%, 5%, 11%, and 3% to relative translation, C(2)H(4) vibration, C(2)H(4) rotation, HF vibration, and HF rotation. This result is substantially different than the deduction from experiments, which summarizes the partitioning as 20%, 45%, 24%, and <12% to relative translation, C(2)H(4) vibration+rotation, HF vibration, and HF rotation. Possible origins of the difference between the simulations and experiments in the release of the potential energy is discussed.

Journal Article↗
PubMed2004

Modified quantum trajectory dynamics using a mixed wave function representation.

Dynamics of quantum trajectories provides an efficient framework for description of various quantum effects in large systems, but it is unstable near the wave function density nodes where the quantum potential becomes singular. A mixed coordinate space/polar representation of the wave function is used to circumvent this problem. The resulting modified trajectory dynamics associated with the polar representation is nonsingular and smooth. The interference structure and the nodes of the wave function density are described, in principle, exactly in the coordinate representation. The approximate version of this approach is consistent with the semiclassical linearized quantum force method [S. Garashchuk and V. A. Rassolov, J. Chem. Phys. 120, 1181 (2004)]. This approach is exact for general wave functions with the density nodes in a locally quadratic potential.

Journal Article↗
PubMed2005

Penning ionization electron spectroscopy of C6H6 by collision with He*(2 3 S) metastable atoms and classical trajectory calculations: optimization of ab initio model potentials.

The potential energy surface of benzene (C(6)H(6)) with a He*(2(3)S) atom was obtained by comparison of experimental data in collision-energy-resolved two-dimensional Penning ionization electron spectroscopy with classical trajectory calculations. The ab initio model interaction potentials for C(6)H(6)+He*(2(3)S) were successfully optimized by the overlap expansion method; the model potentials were effectively modified by correction terms proportional to the overlap integrals between orbitals of the interacting system, C(6)H(6) and He*(2(3)S). Classical trajectory calculations with optimized potentials gave excellent agreement with the observed collision-energy dependence of partial ionization cross sections. Important contributions to corrections were found to be due to interactions between unoccupied molecular orbitals and the He*2s orbital. A C(6)H(6) molecule attracts a He*(2(3)S) atom widely at the region where pi electrons distribute, and the interaction of -80 meV (ca. -1.8 kcal/mol) just cover the carbon hexagon. The binding energy of a C(6)H(6) molecule and a He* atom was 107 meV at a distance of 2.40 A on the sixfold axis from the center of a C(6)H(6) molecule, which is similar to that of C(6)H(6)+Li and is much larger than those of the C(6)H(6)+[He,Ne,Ar] systems.

Journal Article↗
PubMed2005

Quasiclassical trajectory calculations on the photodissociation of CF2CHCl at 193 nm: product energy distributions for the HF and HCl eliminations.

Quasiclassical trajectory calculations were carried out to determine product energy distributions for the HCl and HF eliminations that take place in the photodissociation of 2-chloro-1,1-difluoroethylene at 193 nm. The trajectories were initiated at the transition states of the HCl and HF elimination channels under microcanonical, quasiclassical conditions, and were propagated with the energies and gradients taken directly from density functional theory calculations. Good agreement with experiment is found, except for the translational energy distribution of the HF elimination channel and the average vibrational energy of the HCl fragment. Possible sources of disagreement are discussed.

Journal Article↗
PubMed2005

Electronic energy levels with the help of trajectory-guided random grid of coupled wave packets. I. Six-dimensional simulation of H2.

As a preliminary to future work on the behavior of atoms and molecules in strong time-dependent fields, we apply the coupled coherent-states (CCS) technique of multidimensional phase-space quantum dynamics to obtain Born-Oppenheimer energy levels of electrons in molecules. Unlike traditional approaches based on atomic and molecular-orbital basis sets and time-independent Schrodinger equation the CCS method exploits the solution of the time-dependent Schrodinger equation in the basis of Monte Carlo-selected trajectory-guided coherent states, which treat classical electron correlations exactly. In addition the CCS trajectories move over averaged potentials, which remove the Coulombic singularities.

Journal Article↗
PubMed2005

Ab initio and direct quasiclassical-trajectory study of the F+CH4-->HF+CH3 reaction.

We present an electronic structure and dynamics study of the F+CH4-->HF+CH3 reaction. CCSD(T)/aug-cc-pVDZ geometry optimizations, harmonic-frequency, and energy calculations indicate that the potential-energy surface is remarkably isotropic near the transition state. In addition, while the saddle-point F-H-C angle is 180 degrees using MP2 methods, CCSD(T) geometry optimizations predict a bent transition state, with a 153 degrees F-H-C angle. We use these high-quality ab initio data to reparametrize the parameter-model 3 (PM3) semiempirical Hamiltonian so that calculations with the improved Hamiltonian and employing restricted open-shell wave functions agree with the higher accuracy data. Using this specific-reaction-parameter PM3 semiempirical Hamiltonian (SRP-PM3), we investigate the reaction dynamics by propagating quasiclassical trajectories. The results of our calculations using the SRP-PM3 Hamiltonian are compared with experiments and with the estimates of two recently reported potential-energy surfaces. The trajectory calculations using the SRP-PM3 Hamiltonian reproduce quantitatively the measured HF vibrational distributions. The calculations also agree with the experimental HF rotational distributions and capture the essential features of the excitation function. The results of the SRP semiempirical Hamiltonian developed here clearly improve over those using the two prior potential-energy surfaces and suggest that reparametrization of semiempirical Hamiltonians is a promising strategy to develop accurate potential-energy surfaces for reaction dynamics studies of polyatomic systems.

Journal Article↗
PubMed2006

Quasiclassical trajectory calculations comparing the reactivity and dynamics of symmetric and asymmetric stretch and the role of the bending mode excitations of methane in the Cl + CH4 reaction.

To analyze the effects of the symmetric (nu(1)) and asymmetric (nu(3)) stretch mode excitations and the role played by the "umbrella" bending (nu(4)) mode excitation in the reactivity and the dynamics of the gas-phase Cl+CH(4) reaction, an exhaustive dynamics study was performed. Quasiclassical trajectory (QCT) calculations, including corrections to avoid zero-point energy leakage along the trajectories, were used in this work on an analytical potential energy surface previously developed by Espinosa-Garcia et al. [J. Chem. Phys. (to be published)]. First, with respect to the reactivity, we found that the nu(1) mode excitation is more reactive than the nu(3) mode by a factor of 1.20, in agreement with the experimental tendency between these modes. The inclusion of the nu(4) bending mode practically does not affect this relative reactivity, (nu(1+)nu(4))(nu(3+)nu(4)) = 1.16. Second, with respect to the dynamics (rotovibrational and angular distributions of the products), the two stretch modes, nu(1) and nu(3), give very similar pictures, reproducing the experimental behavior, and the nu(4) "umbrella" mode does not affect the dynamics. The satisfactory reproduction (always qualitatively acceptable and sometimes even quantitatively) of a great variety of experimental data by the QCT study presented here lends confidence to the potential energy surface constructed by Espinosa-Garcia et al. [J. Chem. Phys. (to be published)].

Journal Article↗
PubMed2006

Exact quantum dynamics study of the O(+)+H2(v=0,j=0)-->OH(+)+H ion-molecule reaction and comparison with quasiclassical trajectory calculations.

The close-coupling hyperspherical (CCH) exact quantum method was used to study the title barrierless reaction up to a collision energy (E(T)) of 0.75 eV, and the results compared with quasiclassical trajectory (QCT) calculations to determine the importance of quantum effects. The CCH integral cross section decreased with E(T) and, although the QCT results were in general quite similar to the CCH ones, they presented a significant deviation from the CCH data within the 0.2-0.6 eV collision energy range, where the QCT method did not correctly describe the reaction probability. A very good accord between both methods was obtained for the OH(+) vibrational distribution, where no inversion of population was found. For the OH(+) rotational distributions, the agreement between the CCH and QCT results was not as good as in the vibrational case, but it was satisfactory in many conditions. The kk(') angular distribution showed a preferential forward character, and the CCH method produced higher forward peaks than the QCT one. All the results were interpreted considering the potential energy surface and plots of a representative sampling of reactive trajectories.

Journal Article↗
PubMed2006

Multidimensional reactive scattering with quantum trajectories: dynamics with 50-200 vibrational modes.

The dynamics of ensembles containing thousands of quantum trajectories are studied for multidimensional systems undergoing reactive scattering. The Hamiltonian and equations of motion are formulated in curvilinear reaction path coordinates, for the case of a planar (zero-torsion) reaction path. In order to enhance the computational efficiency, an improved least squares fitting procedure is introduced. This scheme involves contracted basis sets and the use of inner and outer stencils around points where fitting is performed. This method is applied to reactive systems with 50-200 harmonic vibrational modes which are coupled to motion along the reaction coordinate. Dynamical results, including trajectory evolution and time-dependent reaction probabilities, are presented and power law scaling of computation time with the number of vibrational modes is described.

Journal Article↗
PubMed2006

Multidimensional reactive scattering with quantum trajectories: dynamics with Morse vibrational modes.

The reactive scattering of a wave packet is studied by the quantum trajectory method for a model system with up to 25 Morse vibrational modes. The equations of motion are formulated in curvilinear reaction path coordinates with the restriction to a planar reaction path. Spatial derivatives are evaluated by the least squares method using contracted basis sets. Dynamical results, including trajectory evolution and time-dependent reaction probabilities, are presented and analyzed. For the case of one Morse vibrational mode, the results are in good agreement with those derived through direct numerical integration of the time-dependent Schrodinger equation.

Journal Article↗
PubMed2006

The effects of collision energy, vibrational mode, and vibrational angular momentum on energy transfer and dissociation in NO2+-rare gas collisions: an experimental and trajectory study.

A combined experimental and trajectory study of vibrationally state-selected NO2+ collisions with Ne, Ar, Kr, and Xe is presented. Ne, Ar, and Kr are similar in that only dissociation to the excited singlet oxygen channel is observed; however, the appearance energies vary by approximately 4 eV between the three rare gases, and the variation is nonmonotonic in rare gas mass. Xe behaves quite differently, allowing efficient access to the ground triplet state dissociation channel. For all four rare gases there are strong effects of NO2+ vibrational excitation that extend over the entire collision energy range, implying that vibration influences the efficiency of collision to internal energy conversion. Bending excitation is more efficient than stretching; however, bending angular momentum partially counters the enhancement. Direct dynamics trajectories for NO2+ + Kr reproduce both the collision energy and vibrational state effects observed experimentally and reveal that intracomplex charge transfer is critical for the efficient energy transfer needed to drive dissociation. The strong vibrational effects can be rationalized in terms of bending, and to a lesser extent, stretching distortion enhancing transition to the Kr+ -NO2 charge state.

Journal Article↗
PubMed2006

Quasiclassical trajectory study of the reaction H+CH4(nu3 = 0,1)-->CH3+H2 using a new ab initio potential energy surface.

Detailed quasiclassical trajectory calculations of the reaction H+CH4(nu3 = 0,1)-->CH3 + H2 using a slightly updated version of a recent ab initio-based CH5 potential energy surface [X. Zhang et al., J. Chem. Phys. 124, 021104 (2006)] are reported. The reaction cross sections are calculated at initial relative translational energies of 1.52, 1.85, and 2.20 eV in order to make direct comparison with experiment. The relative reaction cross section enhancement ratio due to the excitation of the C-H antisymmetric stretch varies from 2.2 to 3.0 over this energy range, in good agreement with the experimental result of 3.0 +/- 1.5 [J. P. Camden et al., J. Chem. Phys. 123, 134301 (2005)]. The laboratory-frame speed and center-of-mass angular distributions of CH3 are calculated as are the vibrational and rotational distributions of H2 and CH3. We confirm that this reaction occurs with a combination of stripping and rebound mechanisms by presenting the impact parameter dependence of these distributions and also by direct examination of trajectories.

Journal Article↗
PubMed2006

Classical line shapes based on analytical solutions of bimolecular trajectories in collision induced emission.

The classical theory of collision induced emission (CIE) from pairs of dissimilar atoms is studied. This radiation emitted by accelerating dipoles is produced essentially by their overlap and exchange interaction at short range. This classical calculation is based on exact collinear solutions of the trajectories of two spherical particles in a head-on collision under the influence of a Morse potential with a well of arbitrary depth. Without too restrictive conditions a variety of simple solutions in closed form is obtained that illustrates the connection between collision dynamics and CIE. Depending on the well depth and energy of the particles, they may radiate in the far infrared to infrared or visible and shorter wavelength regions. The results are characterized by a fixed total energy. Nevertheless, a connection is demonstrated between the line shape in CIE computed through the trajectory and that based on the emission of a thermally equilibrated system.

Energy Transfer↗
PubMedDate not supplied

Family interventions during the trajectory of recovery from cardiac event: an integrative literature review.

The experience of a cardiac event is a source of stress for both patients and their family members that may be viewed as a family crisis. The trajectory of cardiovascular disease, including both the acute and recovery phases, involves continuous adjustment by patients and family members as they attempt to reconcile the impact of the event and adapt to the uncertainties associated with the chronicity of coronary heart disease. This article reviews empirical intervention research available to practitioners and researchers that may guide the use of family centered cardiovascular nursing interventions. Although a significant amount of research has been conducted in this area, conclusions regarding patient and family interventions are varied. Directions for future research focus on the need for family centered interventions that address the needs of patients with cardiovascular disease that are specific to phases in the trajectory of illness.

Acute Disease↗
PubMed1992

Visible persistence is reduced by fixed-trajectory motion but not by random motion.

Despite the sluggish temporal response of the human visual system, moving objects appear clear and without blur, which suggests that visible persistence is reduced when objects move. It has been argued that spatiotemporal proximity alone can account for this modulation of visible persistence and that activation of a motion mechanism per se is not necessary. Experiments are reported which demonstrate that there is a motion-specific influence on visible persistence. Specifically, points moving in constant directions, or fixed trajectories, show less persistence than points moving with the same spatial and temporal displacements but taking random walks, randomly changing direction each frame. Subjects estimated the number of points present in the display for these two types of motion conditions. Under conditions chosen to produce 'good' apparent motion, ie small temporal and spatial increments, the apparent number of points for the fixed-trajectory condition was significantly lower than the apparent number in the random-walk condition. The traditional explanation of the suppression of persistence based on the spatiotemporal proximity of objects cannot account for these results. The enhanced suppression of persistence observed for a target moving in a consistent direction depends upon the activation of a directionally tuned motion mechanism extended over space and time.

Female↗