Dynamics Trajectory Calculations Research Articles

How do the structures of polyatomic molecules affect their reaction dynamics?

The reactions of Cl atoms with three organic ethers, dimethyl ether (CH3OCH3), oxirane (c-C2H2O) and oxetane (c-C3H6O) provide an opportunity to study the effects of different molecular structural motifs on the chemical dynamics. The rotational excitation of the nascent HCl reaction product has been measured for all three reactions, and the results are compared with direct dynamics trajectory calculations that allow mechanisms to be visualized with the aid of trajectory animations. Reaction of oxirane, a strained, three-membered ring compound, gives rise to HCl that is markedly rotationally cooler (Trot = 168 ± 7 K) than the products of the two other reactions (Trot = 418 ± 25 K for Cl + dimethyl ether and 399 ± 23 K for Cl + oxetane). Possible reasons are discussed in terms of the reorientational dynamics of the polar HCl and organic radical products in the post-transition state regions of the reaction potential energy surfaces.

The extratropical transition of Hurricane Erin (2001): a potential vorticity perspective

The Ertel potential vorticity (PV) is a powerful tool that provides insight into the development and evolution of weather systems. In this study the extratropical transition of Hurricane Erin (2001) is investigated from a PV perspective using operational analyses along with best track data and satellite imagery. Insight is gained from dynamic tropopause maps, on which potential temperature and wind are plotted on a constant PV surface - denoted an isertelic surface in deference to Ertel. The addition of low-level PV to the dynamic tropopause maps gives a clear overview of extratropical transition. On dynamic tropopause maps an upper-level trough appears as a region of low isertelic potential temperature, i.e. a tropopause depression. Two tropopause depressions interacted with Hurricane Erin. During the first interaction the hurricane recurved, but the tropopause depression passed to the north of the hurricane. At this time the circulation of Erin was impinging on the low-level baroclinic zone. During the interaction with the second tropopause depression the hurricane accelerated northeastwards and reintensified rapidly as an extratropical cyclone. The reintensification began when Erin moved into a favourable location for cyclogenesis both from a PV perspective, since Erin was located directly to the east of the tropopause depression, and from quasigeostrophic dynamics, since Erin was located between the entry region of a downstream jet and the exit region of an upstream jet streak. Subsequently, the tropopause depression wrapped up cyclonically and the low-level PV remnants of Hurricane Erin moved into the centre of the extratropical cyclone, thus enhancing the surface winds. Vertical cross sections through the tropical and midlatitude PV anomalies illustrate their approach and interaction. Both PV diagnostics and trajectory calculations indicate that the outflow of a second tropical cyclone, Gabrielle, steepened the tropopause in the region of the upstream jet streak, thus strengthening the upstream jet streak and contributing to Erin's reintensification. Time series of dynamic tropopause maps and trajectory calculations suggest that the pronounced ridging downstream of Erin can be attributed to the outflow of Erin. The downstream impact of the outflow extended across the Atlantic basin and influenced western Europe.

Rotational effects in dissociation of H2 on Pd(111): Quantum and classical study

We study rotational effects in dissociation of H2 on Pd(111) through six-dimensional quantum dynamical and classical trajectory calculations. The potential energy surface was obtained from density functional theory. Quantum dissociative adsorption and rotational excitation probabilities are compared with initial-rotational-state-selective measurements. At low energies, dynamic trapping plays an important role, promoting reaction. For low values of the rotational quantum number J, the trapping is mainly due to translation to rotation energy transfer. The decreasing role of trapping when J increases contributes to the decrease of the dissociation probability. For larger values of J trapping is the result of energy transfer to parallel translational motion. Because trapping due to energy transfer to parallel translational motion is only effective at very low energies, the change in trapping mechanism with J causes the minimum of the reaction probability versus collision energy curve to shift to lower energies with increasing J, as previously observed in experiments. Together with dynamic trapping, rotational hindering (for small values of J) and an adiabatic energy transfer from rotation to translation (for high values of J) produce the nonmonotonous dependence of Pdiss on J that is observed in our calculations and experiments at low energies. Finally, we predict a nonmonotonous dependence of the quadrupole alignment A0(2) on J as observed in associative desorption experiments on H2/Pd(100). It is due to rotational hindering for small J and adiabatic energy transfer from rotation to translation for large J.

10 Reaction mechanisms : Part (iii) Pericyclic reactions

Computational studies of pericyclic reaction mechanisms have greatly enhanced our understanding of, and predictions regarding, reaction mechanisms. In recent years, the importance of non-statistical effects in pericyclic reactions, as studied using dynamics trajectory calculations, has been recognized. Some examples are the electrocyclic ring opening of the cyclopropyl radical, the Cope rearrangement of hepta-1,2,6-triene, and the rearrangement of bicyclo[n.1.0]polyenes. High quality mechanistic studies, though becoming less common, were also carried out. For example, two studies were published on vinylcyclobutane derivatives, one focusing on the thermal stereomutations and cycloreversions, and the other on the [1,3] sigmatropic reactions. The strength of the interplay between experiment and theory is demonstrated in studies of the intramolecular [4+2] cycloaddition of cyclobutadiene with tethered alkenes, in the use of isotope effects to determine the mechanism of an electron-transfer catalyzed Diels–Alder reaction, and in the degenerate interconversions of bicyclo[3.1.0]hex-2-ene.

The iconoclastic dynamics of the 1,2,6-heptatriene rearrangement.

CASSCF(8,8)/6-31G* and AM1-SRP direct dynamics trajectory calculations have been run on the rearrangement of 1,2,6-heptatriene to 3-methylene-1,5-hexadiene. They show that the experimental results of Roth et al. on this reaction can be explained without the need to invoke a concerted, pericyclic mechanism. Instead, bifurcation occurs at the transition state for conversion of the reactant to 2-methylenecyclohexane-1,4-diyl. Some trajectories leaving the transition state do enter the PES local minimum for the intermediate, but others, differing only in the phases of the real-frequency vibrational modes, bypass the intermediate and proceed over a second transition state to the product. A significant fraction of the trajectories that do enter the biradical local minimum proceed on to the product in <500 fs, despite the fact that the minimum is some 12 kcal/mol deep at the CASSCF level. This nonstatistical behavior seems to be due in part to a resonance between key C-H bending and C-C stretching vibrations in the intermediate.

Carbene formation in its lower singlet state from photoexcited 3H-diazirine or diazomethane. A combined CASPT2 and ab initio direct dynamics trajectory study.

The potential energy surfaces of the ground and valence excited states of both 3H-diazirine and diazomethane have been studied computationally by mean of the CASSCF method in conjunction with the cc-pVTZ basis set. The energies of the critical points found on such surfaces have been recomputed at the CASPT2/cc-pVTZ level. Additionally, ab initio direct dynamic trajectory calculations have been carried out on the S(1) and S(2) surfaces, starting each trajectory run at the region dominated by the conformational molecular rearrangement of diazomethane. It is found that both isomers are interconnected along a C(s)() reaction coordinate on each potential surface. Radiationless deactivation of the corresponding S(1) state of each isomer occurs through the same point on the surface, an S(1)/S(0) conical intersection. Thereafter, the system has enough energy to surmount the barrier which leads to dissociation products (CH(2) + N(2)) on S(0) state. Therefore, photoexcitation to S(1) state of either diazirine of diazomethane produces methylene in its lower singlet state on a very short time scale (ca. 100 fs). Furthermore, both isomers can generate excited singlet carbene when they are excited onto the S(2) surface; in this case, they lose the activation energy passing through another common S(2)/S(1) conical intersection and then proceed to dissociation into carbene and N(2) on the S(1) surface. For the special case of methylene, it rapidly experiences deexcitation to S(0) state.

Gas-surface scattering models for particle fluid dynamics: a comparison between analytical approximate models and molecular dynamics calculations

A parametric study is performed to test the validity of some of the most common models of gas-surface scattering used in particle simulations of rarefied flows. The simplified models are compared with results of semiclassical molecular dynamics trajectory calculations for inelastic scattering of Xe atoms on GaSe. The simple models are shown to be inadequate to accommodate all the features of the real dynamics. Sample calculations of oxygen heterogeneous recombination on silica are also provided to emphasise the importance of vibrationally state-resolved models.

Ion pairing and dissociation at liquid/liquid interfaces: Molecular dynamics and continuum models

The thermodynamics and dynamics of NaCl ion-pair dissociation at the water/1,2-dichloroethane liquid/liquid interface are examined using a continuum electrostatic model, molecular dynamics free energy calculations, and nonequilibrium dynamic trajectory calculations. The continuum model shows increased stability of the ion pair relative to that in bulk water and strong dependence of the potential of mean force on the orientation and location of the ion pair relative to the interface. These are in qualitative agreement with the molecular dynamics results. In particular, the equilibrium free energy calculations show that the ion pair is locally stable at the interface and that the dissociation must involve ion transfer and considerable change in the interface structure. These are also confirmed by the nonequilibrium dynamics calculations: Dissociation of the ion pair at the interface involves a simultaneous transfer of both ions into the aqueous side of the interface. The faster transfer of the sodium than the chloride ion influences the lifetime of the ion pair at the interface. In particular, a strong dependence of the ion pair’s stability on its orientation is found.

Combined Monte Carlo and Molecular Dynamics Simulation of Fully Hydrated Dioleyl and Palmitoyl-oleyl Phosphatidylcholine Lipid Bilayers

We have applied a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer to hydrated bilayers of dioleyl-phosphatidylcholine (DOPC) and palmitoyl-oleyl phosphatidylcholine (POPC). The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer in a constant volume and temperature ensemble. The procedure is applied to bilayers of 128 molecules of POPC with 4628 water molecules, and 128 molecules of DOPC with 4825 water molecules. Progress toward equilibration is almost three times as fast in central processing unit (CPU) time compared with a purely molecular dynamics (MD) simulation. Equilibration is complete, as judged by the lack of energy drift in 200-ps runs of continuous MD. After the equilibrium state was reached, as determined by agreement between the simulation volume per lipid molecule with experiment, continuous MD was run in an ensemble in which the lateral area was restrained to fluctuate about a mean value and a pressure of 1 atm applied normal to the bilayer surface. Three separate continuous MD runs, 200 ps in duration each, separated by 10,000 CBMC steps, were carried out for each system. Properties of the systems were calculated and averaged over the three separate runs. Results of the simulations are presented and compared with experimental data and with other recent simulations of POPC and DOPC. Analysis of the hydration environment in the headgroups supports a mechanism by which unsaturation contributes to reduced transition temperatures. In this view, the relatively horizontal orientation of the unsaturated bond increases the area per lipid, resulting in increased water penetration between the headgroups. As a result the headgroup-headgroup interactions are attenuated and shielded, and this contributes to the lowered transition temperature.

Molecular dynamics computation of gas-phase nanoparticle sintering: a comparison with phenomenological models

The mechanism and kinetics of the growth of silicon nanoparticles via particle–particle interactions has been investigated through the use of classical molecular dynamics (MD) trajectory calculations. Computations over a broad range of temperatures and particle sizes have shown that particle sintering is very dependent on size and temperature when solid-like, and considerably less sensitive when liquid-like. These atomistic computations have been used for the first time to validate previously postulated phenomenological mechanisms/models for both solid and liquid particle coalescence. The results have shown that solid-like particles sinter by a solid-state diffusion mechanism while liquid-like particles sinter by a viscous flow mechanism.

Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer

We describe a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer. The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer, in a constant volume and temperature ensemble. The procedure is described in detail and is applied to a bilayer of 100 molecules of dipalmitoyl phosphatidylcholine (DPPC) and 3205 water molecules. We find that the hybrid simulation procedure enhances the equilibration of the bilayer as measured by the convergence of the area per molecule and the segmental order parameters, as compared with a simulation using only molecular dynamics (MD). Progress toward equilibration is almost three times as fast in CPU time, compared with a purely MD simulation. Equilibration is complete, as judged by the lack of energy drift in three separate 200-ps runs of continuous MD started from different initial states. Results of the simulation are presented and compared with experimental data and with other recent simulations of DPPC. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1153–1164, 1999

Dynamics of Electron Attachment and Ionization Processes in the CCl4 Molecule: An ab Initio MO and Direct Dynamics Study

Electron attachment and ionization processes in the CCl4 molecule to form CCl4 radical anion and cation, CCl4 + e- (hole) → CCl4- (CCl4+), have been studied by means of both ab initio MO and direct dynamics calculations. The ab initio calculations of CCl4- show that two conformers of the radical anion CCl4- are obtained for the stable structures: the elongated and compressed structures distorted from Td symmetry of neutral CCl4 due to the Jahn−Teller effect. The elongated structure is more stable by 11.8 kcal/mol relative to the compressed structure at the MP4SDQ/6-31G(d) level. The CCl4+ is unstable relative to its dissociation limit (CCl3+ and Cl atom). The direct dynamics trajectory calculations show that the radical anion CCl4-, formed by a vertical electron attachment of the CCl4 molecule, leads directly to the elongated form of CCl4-. On the other hand, CCl4+ formed by a vertical ionization directly dissociates to CCl3+ + Cl without an activation barrier. The reaction mechanisms of electron attachment and ionization processes are discussed on the basis of theoretical results.

Correlations between angular momentum orientation and exit velocity in gas–surface scattering: A probe of the dependence of collision dynamics on the position of impact

The scattering of rotationally cold N2 from Ag(111) results in angular momentum alignment and orientation of the scattered molecules; measurement of the angular momentum polarization as a function of exit angle, final J state, and exit translation energy provides direct information on the dynamics of the collisions. In this paper, the orientation of the angular momentum vector of the scattered N2 molecules, A{1}1−(J) has been measured for slow, medium, and fast groups of molecules in single rotational states at fixed exit angles. With normal incidence scattering (θi=0°) and off-normal detection, for a given final J state, the ‘‘slow’’ molecules have a higher probability of tumbling backwards (‘‘back spin’’) than the ‘‘fast’’ molecules. Conversely, for glancing incidence scattering (θi=30°) with quasi-specular detection, the opposite trend is observed: the slow molecules have a higher probability of tumbling forwards (‘‘top spin’’) than the fast molecules. These experiments were simulated and analyzed using molecular dynamics trajectory calculations. The calculations show that the amount of gas kinetic energy transferred to the surface is sensitive to the narrow dispersion of impact sites and molecular orientations that lead to scattering into a given final rotational state at a given exit angle. The calculations demonstrate that for both incident angles, collisions near the top of a surface atom lead to slower final velocities than collisions with the hollow sites in analogy with the simple case of two colliding spheres. Therefore, the experimentally observed dependence of the angular momentum orientation on the exit velocity results from the correlation between the initial molecular bond angle and the impact site for scattering into a given J state and at a fixed exit angle.

Mass asymmetry dependence of fusion time-scales in11B+237Np and12C,16O,19F+232Th reactions in a dynamical trajectory model

Dynamical trajectory calculations were carried out for the reactions of11B+237Np and12C,16O and19F+232Th, having mass asymmetries on either side of the Businaro-Gallone critical mass asymmetry αBG, in order to examine the mass asymmetry dependence of fusion reactions in these systems. The compound nucleus formation times were calculated as a function of the partial wave of the reaction for all the systems. This study brings out that for systems with α αBG, which is caused by the dynamical effects involved in the large scale shape changes taking place in the fusion process as well as due to the interplay between the thermal and the collective motion during the collision process. The calculated time scales are comparable to the experimental values derived from the pre-fission neutron multiplicity measurements.

Mechanism, energetics, kinetics and dynamics of the reaction C2H6+˙ → C2H4+˙ + H2

AbstractThe distributiosn of relative translational energy released during (i) loss of H2 from metastable CH3CH3+˙ ions, (ii) loss of HD from metastable CH3CD3+˙ ions and (iii) loss of D2 from metastable CD3CD3+˙ ions were measured. The relevant parts of the potential energy surface of the reaction C2H6+˙ → C2H4+˙ + H2 (including isotopic variants) were investigated using various theoretical methods (high‐level ab initio quantum chemistry, RRKM calculations, dynamic reaction trajectory calculations). A consistent reaction model is presented which reproduces available experimental data. Quantum mechanical barrier tunnelling is found to be important, leading to an activation energy (on the microsecond time‐scale) which is approximately 0.1 eV below the critical energy.

Ultrafast photodissociation of I3− in ethanol: A molecular dynamics study

A detailed molecular model of I3− photodissociation in liquid ethanol is developed. Extensive molecular dynamics trajectory calculations are used to determine product energy distribution, time-dependent spectra, and reorientation dynamics in semiquantitative agreement with experimental data.

Dynamics of ion transfer across a liquid–liquid interface: A comparison between molecular dynamics and a diffusion model

Most theoretical approaches to ion transfer dynamics across a liquid–liquid interface describe the process as a stochastic crossing of a one-dimensional barrier whose shape is a priori unknown. We describe a molecular model of the ion transfer dynamics across an interface between two immiscible polar and nonpolar liquids. The results of extensive molecular dynamics trajectory calculations for the ion transfer are compared with the solution of a diffusion equation for an ion moving in an external field. The external field used in the equation is obtained from an independent free energy calculation using non-Boltzmann sampling. Near quantitative agreement is found, with discrepancies that may be attributed to solvent–shell exchange dynamics.

Spectral shifts and structural classes in microsolutions of rare gas clusters containing a molecular chromophore

We present the results of a series of molecular dynamics (MD) trajectory calculations of the structural, spectral, and dynamical properties of model clusters consisting of one impurity particle interacting with a pure host cluster. Our initial focus is on SF6Arn and SiF4Arn clusters in order to compare MD predictions of structure with the results of the IR studies of these systems performed by the Scoles group. We then show, more generally, how the preferred structural class (matrix or surface) of the heterogeneous cluster system depends on the interaction potential between guest and host molecules. The temperature dependence of the mobility of the impurity within the cluster is also investigated. Finally, the way in which our results can be adapted to interpret and predict solvation behavior for a wide variety of heterogeneous cluster systems is discussed.

Compound nucleus formation, fast fission phenomena and deep inelastic reactions: (I). Dynamical trajectory calculations

In a statistical theory based on semi-classical approximations, we show that the fast fission phenomena (FF) can appear as the natural link between the deep inelastic reactions (DIR) and the compound nucleus formation (CN), depending on the initial conditions of energy and mass asymmetry. The DIR deal essentially with the energy and the angular momentum dissipation, the FF with the mass asymmetry relaxation. By the analysis of the dynamical trajectories and of the mean values of the physical observables E, θ, Δl, ΔA, we show how to separate the ranges of l 0 waves in the entrance channel which specifically contribute to each process. The calculations are performed for the systems Ar on Ho and Mg on Ta at several identical c.m. energies.

Quasi-classical kinetics on the ground-state potential-energy surface of CH 2

Quasi-classical dynamical trajectory calculations have been carried out for the triplet ground-state surface of CH 2. The calculated rate constant for CH( 2Π) + H( 2S) → C( 3P) + H 2( 1Σ g +) at 2000 K is 0.4 × 10 −10 cm 3 molecule −1 s −1 which is a factor of four lower than an order-of- magnitude experimental estimate for this reaction in hydrocarbon flames.