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Quantum chemical calculations and dynamics simulations were performed to study the reaction between methyl peroxy radical (CH3O2) and O2. The reaction proceeds through three different pathways (1) H-atom abstraction, (2) O2 addition and (3) concerted H-atom shift and O2 addition reactions. The concerted H-atom shift and O2 addition pathway is the most favourable reaction both kinetically and thermodynamically. The major product channel formed from these reactions is H2CO + OH + O2. Trajectory calculations also confirm that H2CO + OH + O2 is the main product channel. An estimated rate constant expression for this reaction from master equation calculations is 4.20 × 1013 e−8676/T cm3 mole−1 s−1.

Gas phase intermolecular energy transfer (IET) is a fundamental component of accurately explaining the behavior of gas phase systems in which the internal energy of particular modes of molecules is greatly out of equilibrium. In this work, chemical dynamics simulations of mixed benzene/N2 baths with one highly vibrationally excited benzene molecule (Bz*) are compared to experimental results at 140 K. Two mixed bath models are considered. In one, the bath consists of 190 N2 and 10 Bz, whereas in the other bath, 396 N2 and 4 Bz are utilized. The results are compared to results from 300 K simulations and experiments, revealing that Bz*–Bz vibration–vibration IET efficiency increased at low temperatures consistent with longer lived “chattering” collisions at lower temperatures. In the simulations, at the Bz* excitation energy of 150 kcal/mol, the averaged energy transferred per collision, ⟨ΔEc⟩, for Bz*–Bz collisions is found to be ∼2.4 times larger in 140 K than in 300 K bath, whereas this value is ∼1.3 times lower for Bz*–N2 collisions. The overall ⟨ΔEc⟩, for all collisions, is found to be almost two times larger at 140 K compared to the one obtained from the 300 K bath. Such an enhancement of IET efficiency at 140 K is qualitatively consistent with the experimental observation. However, the possible reasons for not attaining a quantitative agreement are discussed. These results imply that the bath temperature and molecular composition as well as the magnitude of vibrational energy of a highly vibrationally excited molecule can shift the overall timescale of rethermalization.

Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc binding on reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal/mol which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal/mol identified previously during thermal simulations. This difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with the Ar projectile.

In a previous direct dynamics simulation of the Cl- + CH3I → ClCH3 + I- SN2 reaction, predominantly indirect and direct reaction was found at collision energies Erel of 0.20 and 0.39 eV, respectively. For the work presented here, these simulations were extended by studying the reaction dynamics from Erel of 0.15 to 0.40 eV in 0.05 eV intervals. A transition from a predominantly indirect to direct reaction is found for Erel of 0.27-0.28 eV, a finding consistent with experiment. The simulation results corroborate the understanding that in experiments indirect reaction is characterized by small product translational energies and isotropic scattering, while direct reaction has higher translational energies and anisotropic scattering. The traditional statistical theoretical model for the Cl- + CH3I SN2 reaction assumes the Cl--CH3I pre-reaction complex (A) is formed, followed by barrier crossing, and then formation of the ClCH3-I- post-reaction complex (B). This mechanism is seen in the dynamics, but the complete atomistic dynamics are much more complex. Atomistic SN2 mechanisms contain A and B, but other dynamical events consisting of barrier recrossing (br) and the roundabout (Ra), in which the CH3-moiety rotates around the heavy I-atom, are also observed. The two most important mechanisms are only formation of A and Ra + A. The simulation results are compared with simulations and experiments for Cl- + CH3Cl, Cl- + CH3Br, F- + CH3I, and OH- + CH3I.

International audience; The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

We compare algorithms to sample initial positions and momenta of a molecular system for classical trajectory simulations. We aim at reproducing the phase space quantum distribution for a vibrational eigenstate, as in Wigner theory. Moreover, we address the issue of controlling the total energy and the energy partition among the vibrational modes. In fact, Wigner's energy distributions are very broad, quite at variance with quantum eigenenergies. Many molecular processes depend sharply on the available energy, so a better energy definition is important. Two approaches are introduced and tested: the first consists in constraining the total energy of each trajectory to equal the quantum eigenenergy. The second approach modifies the phase space distribution so as to reduce the deviation of the single mode energies from the correct quantum values. A combination of the two approaches is also presented.

Direct dynamics simulations were performed to study the SN2 double inversion mechanism SN2-DI, with retention of configuration, for the F− + CH3I reaction. Previous simulations identified a transition state (TS) structure, i.e. TS0, for the SN2-DI mechanism, including a reaction path. However, intrinsic reaction coordinate (IRC) calculations from TS0 show it is a proton transfer (PT) TS connected to the F−⋯HCH2I SN2 pre-reaction complex and the FH⋯CH2I− proton transfer post-reaction complex. Inclusion of TS0 in the SN2-DI mechanism would thus involve non-IRC atomistic dynamics. Indeed, trajectories initiated at TS0, with random ensembles of energies as assumed by RRKM theory, preferentially form the SN2-DI products and ∼70% follow the proposed SN2-DI pathway from TS0 to the products. In addition, the Sudden Vector Projection (SVP) method was used to identify which CH3I vibrational mode excitations promote access to TS0 and the SN2-DI mechanism. Results of F− + CH3I simulations, with SVP specified mode excitations, are disappointing. With the CH3 deformations of CH3I excited, the SN2 single inversion mechanism is the dominant pathway. If the CH stretch modes are also excited, proton transfer dominates the reaction. SN2-DI occurs, but with a very small probability of ∼1%. The reasons behind these results are discussed.

Atomic nitrogen is formed in the high-temperature shock layer of hypersonic vehicles and contributes to the ablation of their thermal protection systems (TPSs). To gain atomic-level understanding of the ablation of carbon-based TPS, collisions of hyperthermal atomic nitrogen on representative carbon surfaces have recently be investigated using molecular beams. In this work, we report direct dynamics simulations of atomic-nitrogen [N(4S)] collisions with pristine, defected, and oxidized graphene. Apart from non-reactive scattering of nitrogen atoms, various forms of nitridation of graphene were observed in our simulations. Furthermore, a number of gaseous molecules, including the experimentally observed CN molecule, have been found to desorb as a result of N-atom bombardment. These results provide a foundation for understanding the molecular beam experiment and for modeling the ablation of carbon-based TPSs and for future improvement of their properties.

In a previous UB3LYP/6-31G* direct dynamics simulation, non-Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular dynamics was found for vibrationally excited 1,2-dioxetane (DO); [R. Sun et al., J. Chem. Phys. 137, 044305 (2012)]. In the work reported here, these dynamics are studied in more detail using the same direct dynamics method. Vibrational modes of DO were divided into 4 groups, based on their characteristic motions, and each group excited with the same energy. To compare with the dynamics of these groups, an additional group of trajectories comprising a microcanonical ensemble was also simulated. The results of these simulations are consistent with the previous study. The dissociation probability, N(t)/N(0), for these excitation groups were all different. Groups A, B, and C, without initial excitation in the O-O stretch reaction coordinate, had a time lag to of 0.25-1.0 ps for the first dissociation to occur. Somewhat surprisingly, the C-H stretch Group A and out-of-plane motion Group C excitations had exponential dissociation probabilities after to, with a rate constant ∼2 times smaller than the anharmonic RRKM value. Groups B and D, with excitation of the H-C-H bend and wag, and ring bend and stretch modes, respectively, had bi-exponential dissociation probabilities. For Group D, with excitation localized in the reaction coordinate, the initial rate constant is ∼7 times larger than the anharmonic RRKM value, substantial apparent non-RRKM dynamics. N(t)/N(0) for the random excitation trajectories was non-exponential, indicating intrinsic non-RRKM dynamics. For the trajectory integration time of 13.5 ps, 9% of these trajectories did not dissociate in comparison to the RRKM prediction of 0.3%. Classical power spectra for these trajectories indicate they have regular intramolecular dynamics. The N(t)/N(0) for the excitation groups are well described by a two-state coupled phase space model. From the intercept of N(t)/N(0) with random excitation, the anharmonic correction to the RRKM rate constant is approximately a factor of 1.5.

International audience; In a recent direct dynamics simulations of the collision induced dissociation (CID) of the doubly protonated tripeptide threonine–isoleucine–lysine and threonine–leucine–lysine ions, TIK(H+)2 and TLK(H+)2, a shattering fragmentation mechanism was found, in which the ion fragmented upon impact with N2 (Z. Homayoon et al., Phys. Chem. Chem. Phys., 2018, 20, 3614). In using models to interpret experiments of biological ion CID, it is important to know the collision energy threshold for the shattering mechanism. In the work presented here, direct dynamics simulations were performed to study shattering fragmentation versus the collision energy (Erel) for N2 + TIK(H+)2. From the probability of shattering fragmentation and the minimum energy transfer for fragmentation versus Erel, a threshold of ∼55 kcal mol−1 was identified for N2 + TIK(H+)2 shattering fragmentation. This threshold is substantially higher than the lowest activation energy of 14.7 kcal mol−1, found from direct dynamics simulations, for the thermal dissociation of TIK(H+)2.

Previous chemical dynamics simulations (Phys. Chem. Chem. Phys., 2014, 16, 23769-23778) were analyzed to delineate atomistic details for collision of N-protonated dialanine (ala2-H(+)) with a C8 perfluorinated self-assembled monolayer (F-SAM) surface. Initial collision energies Ei of 5-70 eV and incident angles θi of 0° and 45°, with the surface normal, were considered. Four trajectory types were identified: (1) direct scattering; (2) temporary sticking/physisorption on top of the surface; (3) temporary penetration of the surface with additional physisorption on the surface; and (4) trapping on/in the surface, by physisorption or surface penetration, when the trajectory is terminated. Direct scattering increases from 12 to 100% as Ei is increased from 5 to 70 eV. For the direct scattering at 70 eV, at least one ala2-H(+) heavy atom penetrated the surface for all of the trajectories. For ∼33% of the trajectories all eleven of the ala2-H(+) heavy atoms penetrated the F-SAM at the time of deepest penetration. The importance of trapping decreased with increase in Ei, decreasing from 84 to 0% with Ei increase from 5 to 70 eV at θi = 0°. Somewhat surprisingly, the collisional energy transfers to the F-SAM surface and ala2-H(+) are overall insensitive to the trajectory type. The energy transfer to ala2-H(+) is primarily to vibration, with the transfer to rotation ∼10% or less. Adsorption and then trapping of ala2-H(+) is primarily a multi-step process, and the following five trapping mechanisms were identified: (i) physisorption-penetration-physisorption (phys-pen-phys); (ii) penetration-physisorption-penetration (pen-phys-pen); (iii) penetration-physisorption (pen-phys); (iv) physisorption-penetration (phys-pen); and (v) only physisorption (phys). For Ei = 5 eV, the pen-phys-pen, pen-phys, phys-pen, and phys trapping mechanisms have similar probabilities. For 13.5 eV, the phys-pen mechanism, important at 5 eV, is unimportant. The radius of gyration of ala2-H(+) was calculated once it is trapped on/in the F-SAM surface and trapping decreases the ion's compactness, in part by breaking hydrogen bonds. The ala2-H(+) + F-SAM simulations are compared with the penetration and trapping dynamics found in previous simulations of projectile + organic surface collisions.

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces ‘on the fly’ has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface that accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized. Program summary Program title : VENUS/NWChem Catalogue identifier: AERS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERS_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 10,831,970 No. of bytes in distributed program, including test data, etc.: 77,141,871 Distribution format: tar.gz Programming language: Fortran 77 with some C in NWChem, MPI. Computer: All Linux based workstations and parallel supercomputers. Operating system: Linux. Has the code been vectorized or parallelized?: Venus is a sequential code; NWChem can run in parallel. Classification: 16.8. Subprograms used: Cat Id Title Reference AEGI_v1_0 NWChem CPC 181(2010)1477 Nature of problem: Direct dynamics simulations play an important role in investigating and understanding atomic-level chemical dynamics information such as atomistic reaction mechanisms, unimolecular and bimolecular rate constants, intramolecular vibrational energy redistribution rates, etc. The ability to couple direct dynamics with electronic structure methods brings a level of fidelity to the simulations that is important for complex systems. However, a tight coupling between two codes that have their own development teams and schedules can be challenging. Solution method: The VENUS/NWChem interface is designed to link the general electronic structure program (NWChem) and classical chemical dynamics simulation program (VENUS) to perform direct dynamics simulation in which the trajectories “on the fly” with the potential and its derivatives obtained directly from electronic structure theory. One of the design goals is to build interfaces that require as little interference in NWChem and VENUS as possible so that each of the code developments can continue independently. This is especially important since VENUS is currently a sequential code and NWChem is a parallel code and being able to compute the energies, gradients, and Hessian in parallel is an important aspect of making the software useful to users. In this manuscript, the tight coupling interface between the two codes is described and examples of its use are given. In the classical chemical dynamics simulation an ensemble of trajectories is calculated, and the initial sampling represents the conditions of the reactants for the chemical reaction under investigation. Each trajectory is evaluated by numerically integrating either Hamilton’s or Newton’s equations of motion. The Schrodinger equation is solved and the energy and energy gradient are calculated in the electronic structure program (NWChem), and this information is passed to the classical trajectory program (VENUS) to solve the equations of motion. Additional comments: Full documentation is provided in the distribution file. This includes a README file giving the names and brief description of all the files that make up the package and instructions on the installation and execution of the program. Sample input and output data for test run will also be provided. The software is free to download and use once a signed license agreement has been received. The agreement will be displayed when the program is requested. Running time: The running time depends on the size of the chemical system, simulation time, complexity of the ab initio method and number of CPUs. The ab initio method is the most time consuming part of each step in the calculations and scaling for different types of systems and levels of theory is available in Valiev et al. (2010). Again, there are many factors that affect the running time for the full simulation and it can range from several hours for simulations of a few atoms with DFT and a small basis set running on a single compute node to several days for the simulation of tens of heavy atoms with larger basis set running parallel.

Direct dynamics simulations, using B3LYP/6-311++G(2d,2p) theory, were used to study the unimolecular and intramolecular dynamics of vibrationally excited CH3NC. Microcanonical ensembles of CH3NC, excited with 150, 120, and 100 kcal/mol of vibrational energy, isomerized to CH3CN nonexponentially, indicative of intrinsic non-Rice-Ramsperger-Kassel-Marcus (RRKM) dynamics. The distribution of surviving CH3NC molecules vs time, i.e., N(t)/N(0), was described by two separate functions, valid above and below a time limit, a single exponential for the former and a biexponential for the latter. The dynamics for the short-time component are consistent with a separable phase space model. The importance of this component decreases with vibrational energy and may be unimportant for energies relevant to experimental studies of CH3NC isomerization. Classical power spectra calculated for vibrationally excited CH3NC, at the experimental average energy of isomerizing molecules, show that the intramolecular dynamics of CH3NC are not chaotic and the C-N≡C and CH3 units are weakly coupled. The biexponential N(t)/N(0) at 100 kcal/mol is used as a model to study CH3NC → CH3CN isomerization with biexponential dynamics. The Hinshelwood-Lindemann rate constant kuni(ω,E) found from the biexponential N(t)/N(0) agrees with the Hinshelwood-Lindemann-RRKM kuni(ω,E) at the high and low pressure limits, but is lower at intermediate pressures. As found from previous work [S. Malpathak and W. L. Hase, J. Phys. Chem. A 123, 1923 (2019)], the two kuni(ω,E) curves may be brought into agreement by scaling ω in the Hinshelwood-Lindemann-RRKM kuni(ω,E) by a collisional energy transfer efficiency factor βc. The interplay between the value of βc, for the actual intermolecular energy transfer, and the ways the treatment of the rotational quantum number K and nonexponential unimolecular dynamics affect βc suggests that the ability to fit an experimental kuni(ω,T) with Hinshelwood-Lindemann-RRKM theory does not identify a unimolecular reactant as an intrinsic RRKM molecule.

Chemical dynamics simulations are reported which provide atomistic details of collisions of protonated dialanine, ala2-H(+), with a perfluorinated octanethiolate self-assembled monolayer (F-SAM) surface. The simulations are performed at collision energies Ei of 5.0, 13.5, 22.5, 30.00, and 70 eV, and incident angles 0° (normal) and 45° (grazing). Excellent agreement with experiment (J. Am. Chem. Soc., 2000, 122, 9703-9714) is found for both the average fraction and distribution of the collision energy transferred to the ala2-H(+) internal degrees of freedom. The dominant pathway for this energy transfer is to ala2-H(+) vibration, but for Ei = 5.0 eV ∼20% of the energy transfer is to ala2-H(+) rotation. Energy transfer to ala2-H(+) rotation decreases with increase in Ei and becomes negligible at high Ei. Three types of collisions are observed in the simulations: i.e. those for which ala2-H(+) (1) directly scatters off the F-SAM surface; (2) sticks/physisorbs on/in the surface, but desorbs within the 10 ps numerical integration of the simulations; and (3) remains trapped (i.e. soft-landed) on/in the surface when the simulations are terminated. Penetration of the F-SAM by ala2-H(+) is important for the latter two types of events. The trapped trajectories are expected to have relatively long residence times on the surface, since a previous molecular dynamics simulation (J. Phys. Chem. B, 2014, 118, 5577-5588) shows that thermally accommodated ala2-H(+) ions have an binding energy with the F-SAM surface of at least ∼15 kcal mol(-1).

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

Analytical potential energy functions were developed for interactions of SiNCS+ and (CH3)2SiNCS+ ions with perfluorinated self-assembled monolayer (F-SAM) surfaces. Two model compounds were used to represent an F-SAM: CF4 and nine chains of perfluorobutane forming a miniSAM structure. Density functional theory plus dispersion (DFT-D) calculations were carried out to compute intermolecular potential energy curves (IPECs) for these systems. The applied DFT-D method (specifically, B97-D) was successfully tested against high-level wavefunction calculations performed on the smallest system investigated. The IPECs calculated at the B97-D level were fitted to analytical potentials of the Buckingham type. The calculations show that the parameters obtained from the fits involving CF4 are transferable to the miniSAM system, provided the fittings are conducted with caution, thus corroborating that CF4 is a good model for parameterizing intermolecular potentials for interactions of gases with F-SAM surfaces.

A chemical dynamics simulation was performed to model experiments [N. A. West et al., J. Chem. Phys. 145, 014308 (2016)] in which benzene molecules are vibrationally excited to 148.1 kcal/mol within a N2-benzene bath. A significant fraction of the benzene molecules are excited, resulting in heating of the bath, which is accurately represented by the simulation. The interesting finding from the simulations is the non-statistical collisional energy transfer from the vibrationally excited benzene C6H6* molecules to the bath. The simulations find that at ∼10-7 s and 1 atm pressure there are four different final temperatures for C6H6* and the bath. N2 vibration is not excited and remains at the original bath temperature of 300 K. Rotation and translation degrees of freedom of both N2 and C6H6 in the bath are excited to a final temperature of ∼340 K. Energy transfer from the excited C6H6* molecules is more efficient to vibration of the C6H6 bath than its rotation and translation degrees of freedom, and the final vibrational temperature of the C6H6 bath is ∼453 K, if the average energy of each C6H6 vibration mode is assumed to be RT. There is no vibrational equilibration between C6H6* and the C6H6 bath molecules. When the simulations are terminated, the vibrational temperatures of the C6H6* and C6H6 bath molecules are ∼537 K and ∼453 K, respectively. An important question is the time scale for complete energy equilibration of the C6H6* and N2 and C6H6 bath system. At 1 atm and 300 K, the experimental V-T (vibration-translation) relaxation time for N2 is ∼10-4 s. The simulation time was too short for equilibrium to be attained, and the time for complete equilibration of C6H6* vibration with translation, rotation, and vibration of the bath was not determined.

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c–C2H4O3, the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H2COO) and formaldehyde (H2CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on new high-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 ± 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (∼30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum.

Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH(-)(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I(-), and to a lesser extent CH2I(-) (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH](-). In contrast, for the unsolvated OH(-) + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH(-)(H2O) + CH3I SN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I(-) post-reaction complex for the SN2 reaction is negligible.

Chemical dynamics simulations were performed to study the unimolecular dissociation of randomly excited Na(+)(Bz) and Na(+)(Bz)2 clusters; Bz = benzene. The simulations were performed at constant energy, and temperatures in the range of 1200-2200 K relevant to combustion, using an analytic potential energy surface (PES) derived in part from MP2/6-311+G* calculations. The clusters decompose with exponential probabilities, consistent with RRKM unimolecular rate theory. Analyses show that intramolecular vibrational energy redistribution is sufficiently rapid within the clusters that their unimolecular dynamics is intrinsically RRKM. Arrhenius parameters, determined from the simulations of the clusters, are unusual in that Ea is ∼10 kcal/mol lower the Na(+)(Bz) → Na(+) + Bz dissociation energy and the A-factor is approximately two orders-of-magnitude too small. Analyses indicate that temperature dependent anharmonicity is important for the Na(+)(Bz) cluster's unimolecular rate constants k(T). This is consistent with the temperature dependent anharmonicity found for the Na(+)(Bz) cluster from a Monte Carlo calculation based on the analytic PES used for the simulations. Apparently temperature dependent anharmonicity is quite important for unimolecular dissociation of the Na(+)(Bz)1,2 clusters.

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar-CH(3)OH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH(3)OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar-C, Ar-O, Ar-H(C), and Ar-H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol(-1), and adding an additional r(-n) term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar-CH(3)OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol(-1) with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol(-1) smaller than this value. The well depths of the other two minima are within 0.16 kcal mol(-1) of the global minimum. The analytic Ar-CH(3)OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol(-1) of the ab initio values. Combining this Ar-CH(3)OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

Electronic structure calculations based on multiconfiguration wave functions are used to investigate a set of archetypal reactions relevant to O(3P) processing of hydrocarbon molecules and surfaces. These include O(3P) reactions with methane and ethane to give OH plus methyl or ethyl radicals, O(3P) + ethane to give CH3O + CH3, and secondary reactions of the OH product radical with ethane and the ethyl radical. Geometry optimization is carried out with CASSCF/cc-pVTZ for all reactions, and with CASPT2/cc-pVTZ for O(3P) + methane/ethane. Single-point energy corrections are applied with CASPT2, CASPT3, and MRCI + Q with the cc-pVTZ and cc-pVQZ basis sets, and the energies extrapolated to the complete basis set limit (CBL). Where comparison of computed barriers and energies of reaction with experiment is possible, the agreement is good to excellent. The best agreement (within experimental error) is found for MRCI + Q/CBL applied to O(3P) + methane. For the other reactions, CASPT2/CBL and MRCI + Q/CBL predictions differ from experiment by 1-5 kcal/mol for 0 K enthalpies of reaction, and are within 1 kcal/mol of the best-estimate experimental range of 0 K barriers for O(3P) + ethane and OH + ethane. The accuracy of MRCI + Q/CBL is limited mainly by the quality of the active space. CASPT2/CBL barriers are consistently lower than MRCI + Q/CBL barriers with identical reference spaces.

A study of the energy accommodation of neon colliding with a crystalline self-assembled 1-decanethiol monolayer adsorbed on Au(111) is presented. The intensity and velocity dependencies of the scattered neon as a function of incident angle and energy were experimentally measured. Scattering calculations show good agreement with these results, which allows us to examine the detailed dynamics of the energy and momentum exchange at the surface. Simulation results show that interaction times are, at most, a few picoseconds. Even for these short times, energy exchange with the surface, both normal and in-plane, is very rapid. An important factor in determining the efficiency of energy exchange is the location at which the neon collides with the highly corrugated and structurally dynamic unit cell. Moreover, our combined experimental and theoretical results confirm that these are truly surface collisions in that neon penetration into the organic boundary layer does not occur, even for the highest incident energies explored, 560 meV.

A washboard with moment of inertia (WBMI) model for gas atom scattering from a flexible surface is proposed and applied. This model is a direct extension of the washboard model [J. Chem. Phys. 92, 680 (1990)] proposed for gas atom scattering from relatively rigid, corrugated surfaces. In addition, a moment of inertia is incorporated in the original washboard model to describe the flexibility of softer, more highly corrugated surfaces such as polymer or liquid surfaces. The moment of inertia of the effective surface object introduces a dependence of the efficiency of energy transfer on the position and direction of impact, a feature that has been shown to be critical by molecular dynamics simulations. The WBMI model is solved numerically by Monte Carlo integration, which makes the implementation of multiple impacts between a colliding atom and the surface very efficient. The model is applied to Ne and Ar atoms scattering from an alkylthiolate self-assembled monolayer surface and reproduces the major results obtained by classical trajectory simulation of the same system, i.e., a bimodal translation energy distribution P(E(f)) with the low-energy component well-fit with a Boltzmann distribution, but with a temperature that may (Ar) or may not (Ne) be the same as the surface temperature. This indicates that the WBMI model, with well-motivated physical assumptions and simplified interaction, reveals many of the major aspects of the gas-surface collision dynamics, though it does not take into account the real-time dynamics explicitly.

Quasiclassical, direct dynamics trajectories, calculated at the B3LYP/6-31G** level of the theory, have been used to study the energy transfer dynamics and collision-induced dissociation (CID) of formaldehyde cation in collisions with Ne. Effects of varying collision energy were probed for ground state H2CO+, and H2CO+ with excitation in three different vibrational modes: ν6+ (in-plane CH2 rock), ν4+ (out-of-plane bend), and ν5+ (asym. CH stretch). The trajectories are in excellent agreement with an earlier detailed experimental study of state-selected H2CO+ CID. Energy disposal branching between product recoil, vibrational energy, and rotational excitation is found to vary with collision energy, vibrational state, impact parameter, and orientation. An analysis of the trajectories illustrates how mode-specific vibrational excitation effects the efficiency of translational-to-vibrational (T→V) energy transfer to promote CID.

A previous direct dynamics trajectory study of the thermal vinylcyclopropane–cyclopentene rearrangement [C. Doubleday, J. Phys. Chem. A, 2001, 105, 6333], based on an AM1-SRP potential energy surface (PES), is extended to study details of the intramolecular and unimolecular dynamics in the biradical region of the PES. The branching ratio of the 4 diastereomeric products and the time dependence of their formation depend on the transition state at which the trajectories are initialized and its vibrational temperature or mode specific excitation. For the small amount of reaction occurring after ∼600 fs, there is considerable stereorandomness in the product yield, which contrasts with the short-time nonstatistical and mode specific reaction. Varying the initial amount of energy in reaction coordinate translation has only a minor effect on the biradical lifetime, but may have an appreciable effect on the relative product yield. Changing the rotational temperature has a negligible effect on the reaction dynamics. This study illustrates the utility of the quasiclassical trajectory method for studying short-time unimolecular dynamics and the importance of including zero-point energy motion in the trajectory initial conditions.

The dynamics of friction and energy dissipation of a small nanoscale hydroxylated alumina surface sliding across a large identical surface were investigated by molecular dynamics (MD) simulations. The energy released into both the sliding and stationary surfaces and the energy transfer from the sliding interface to the bulk were investigated by monitoring the temperature of the surfaces and their sublayers. Steady state temperature gradients are found for the sublayers of each surface as a result of the balance between the heat released from the sliding friction and heat transfer to the bulk. The MD simulations show periodic friction energy release from the interface to the surfaces, giving rise to periodic changes in the temperature of the surface sublayers. This temperature depends on the sliding velocity. The periodicity in the friction energy release arises from the periodic unit cell structures of the surfaces. Atomic-level vibrational motions and interdigitation of the surface atoms give rise to the frictional energy of the sliding surfaces. Velocity distributions are determined for atoms within different surface layers and they become more Boltzmann-like the further the layers are from the interface and if the sliding is fast and not in the stick–slip regime. Tribological properties for continuous sliding across the same regime of the bottom surface, by using periodic boundary conditions, differ from those for sliding across a large bottom surface.

Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH3CN → HF + CH2CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. The experiments were performed at 300 K, and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F⋯HCH2CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation. The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH2CN and then trapping in the CH2CN⋯HF post-reaction potential energy well of ∼10 kcal/mol with respect to the HF + CH2CN products. In contrast to this IRC, five different trajectory types were observed: the majority proceeded by direct H-atom transfer and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH2CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. Simulations with an anharmonic zero-point energy constraint gave product distributions for relative translation, HF rotation, HF vibration, CH2CN rotation, and CH2CN vibration as 5%, 11%, 60%, 7%, and 16%, respectively. In contrast, the experimental energy partitioning percentages to HF rotation and vibration are 6% and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational population for F + CH3CN → HF + CH2CN resemble those for other reactions. A detailed discussion is given of possible origins of the difference between the simulation and experimental energy partitioning dynamics for F + CH3CN → HF + CH2CN. The F + CH3CN reaction also forms the CH3C(F)N intermediate, in which the F-atom adds to the C≡N bond. However, this intermediate and F⋯CH3CN and CH3CN⋯F van der Waals complexes are not expected to affect the F + CH3CN → HF + CH2CN product energy partitioning.

In previous work, ion imaging experiments and direct chemical dynamics simulations with DFT/B97-1 were performed to study the atomic-level dynamics of the F(-) + CH3I → FCH3 + I(-) SN2 nucleophilic substitution reaction at different collision energies. Overall, the simulations are in quite good agreement with experiment at the low collision energy of 0.32 eV, however there are differences between experiment and simulation at the high collision energy of 1.53 eV. A recent CCSD(T) study of the potential energy surface for the F(-) + CH3I → FCH3 + I(-) SN2 reaction shows that it has both a traditional C3v and a hydrogen-bond entrance channel. They are represented by MP2 but not by B97-1, which has only the latter channel. On the other hand, B97-1 gives a reaction exothermicity in excellent agreement with experiment, while MP2 is in error by 24.3 kJ mol(-1). In the work presented here, direct dynamics simulations using MP2/aug-cc-pvdz/ECP/d were performed for the F(-) + CH3I → FCH3 + I(-) reaction at a 1.53 eV collision energy. The same direct rebound and stripping and indirect atomistic reaction mechanisms are found in the B97-1 and MP2 simulations. Both the B97-1 and MP2 simulations agree with the experimental fraction of the available product energy partitioned to CH3F internal energy, i.e. fint = 0.59 ± 0.08. However, the MP2 fint distribution is broader and in better agreement with experiment than B97-1. The two simulations methods give the same product energy partitioning for the stripping mechanism, but different partitionings for the rebound and indirect mechanisms. Compared to experiment, the principal difference between the B97-1 and MP2 results is the differential cross section which is nearly isotropic for B97-1. For MP2 backward scattering is more important than forward, as found in the experiments. Though there is no overall barrier for the reaction, B97-1 gives a reaction cross section appreciably larger than that for MP2, i.e. 8.6 ± 2.2 Å(2)versus 1.8 ± 0.3 Å(2). For B97-1 59% of the reaction consists of indirect mechanisms, while for MP2 the indirect mechanisms only comprise 11% of the reaction. The experimental differential cross section is more consistent with the atomistic mechanisms for MP2 than for B97-1.

Classical dynamics simulations, coupled directly with semiempirical molecular orbital theory, reveal some of the important oxidation chemistry occurring in single wall carbon nanotubes. Two chemisorption reactions, 1,2 and 1,4-cycloaddition with 1O2, are observed from the simulations, the latter determined as the kinetically favored adsorption pathway and confirmed with ab initio HF/6-31g total energy calculations. Opening of the nanotube is found to occur by the decomposition of a cyclic 1,2-peroxide-like addition product, which can be formed directly through a symmetric concerted addition reaction or by diffusion of the O2 moiety from the 1,4-addition product. The oxygen induced degradation of the nanotube is initiated by tube opening followed by a two-step mechanism involving desorption of CO. The presence of a highly strained four-membered ring in the cap, following elimination of CO, is observed in the simulations. Consistent with experimental observation, the nanotube cap is oxidized substantially faster than is the cylindrical base of the tube. This suggests, as has previous work, that oxidation will initially occur preferentially at the cap and selectively with the pentagons. A likely product of cap removal consists of an open end oxygen-terminated nanotube.

Classical trajectory simulations are performed to study the energy transfer and unimolecular dynamics associated with collisions of Cr(CO)6+ ions with n-hexyl thiolate self-assembled monolayer (SAM) and diamond{111} surfaces at a collision energy and angle of 30 eV and 45°. The trajectories are calculated with an analytic potential energy function fit to high-level ab initio calculations and experimental data. The “soft ” SAM and “hard” diamond surfaces have highly different collision dynamics. The average percent energy transfer to Cr(CO)6+ internal degrees of freedom, the surface, and Cr(CO)6+ translation are 10, 60 and 21% respectively, for the SAM surface and 30, 14 and 56% for the diamond surface. The Cr(CO)6+ ions, which collide with the SAM surface, dissociate by intramolecular vibrational energy redistribution (IVR) and lifetimes in accord with RRKM theory. In contrast, Cr(CO)6+ ions, activated by collision with the diamond surface, dissociate ia direct translation to vibration (T–V) energy transfer and a shattering mechanism.

Classical trajectory simulations are used to determine the energy transfer distribution function P ( E f ) for Ne-atoms scattering off the n -hexylthiolate self-assembled monolayer (SAM)/Au{1 1 1} surface. The form of P ( E f ) depends on the angles at which it is measured. Though trapping desorption is insignificant for this system, backward scattering and scattering normal to the surface give rise to a unimodal P ( E f ) in excellent agreement with the Boltzmann distribution. Forward scattering at large polar angles is bimodal with a Boltzmann-like component. These simulation results show that a Boltzmann component in P ( E f ) does not necessarily correspond to a trapping desorption intermediate.

In this paper we describe a practical implementation of parallel computation for the molecular dynamics (MD) simulation of an alkane/aluminum oxide interface. A serial MD program was converted into a parallel code utilizing the message passing interface (MPI). This code was evaluated on a twelve processor symmetrical multiprocessor as well as on a cluster of four processor SMPs. A maximum speedup of 5.25 was achieved with twelve processors on the large shared memory machine. The cluster performance saturated at a speedup of 4.5 with two nodes. High communication costs and considerable load imbalance in the system were identified as areas that need further investigation for obtaining better performance.

A classical trajectory simulation is performed to study the dynamics of Ne-atom scattering off an n-hexyl thiolate self-assembled monolayer (SAM). The energy distribution of the scattered Ne-atoms may be deconvoluted into a Boltzmann component based on the surface temperature and a remaining non-Boltzmann high energy component. The former component becomes as large as 100% at low Ne-atom incident energies and appears to assume a high incident energy asymptotic value of ∽0.2–0.3 for incident angles less than 50°. This Boltzmann component does not arise from a Ne–SAM intermediate, since the vast majority of the collisions are direct with only one inner turning point in the Ne+SAM motion. Instead, it has varying contributions from trajectories which directly scatter from and those that penetrate the SAM. The translation (T)→vibration (V) energy transfer mechanism for the former class of trajectories may have similarities to exit-channel T→V coupling in models of unimolecular dissociation. SAM penetration becomes more important as the initial translational energy Ei is increased, resulting in both efficient and inefficient energy transfer. The latter results from repulsive forces as the Ne-atom is ‘‘ expelled’’ from the SAM. For incident angles less than 50° the size of the Boltzmann component scales with the total incident energy Ei reflecting equivalent energy transfer probabilities from the normal and parallel components of Ei. Such a result is consistent with the corrugated SAM surface. Penetration of the SAM scales with the normal component of Ei for small incident angles θi and Ei . Both the Boltzmann component to the transitional energy distribution of the scattered Ne atom, P(Ei) and SAM penetration become negligible for an increase in θi from 45° to 60°, suggesting an abrupt transition in the collision dynamics. The angular distributions for the scattered Ne-atoms are random for low initial energies Ei and θi, reflecting the surface corrugation and not the presence of an actual Ne–SAM intermediate. At high Ei and θi the scattering is non-random, preferring to remain in the incident plane with the parallel component of Ei conserved. This study shows there are ambiguities in associating a trapping desorption intermediate with statistical gas–surface scattering attributes, such as a Boltzmann component, in the translational energy distribution and a random angular distribution.

Classical trajectories can be computed directly from electronic structure calculations without constructing a global potential-energy surface. When the potential energy and its derivatives are needed during the integration of the classical equations of motion, they are calculated by electronic structure methods. In the Born–Oppenheimer approach the wave function is converged rather than propagated to generate a more accurate potential-energy surface. If analytic second derivatives (Hessians) can be computed, steps of moderate size can be taken by integrating the equations of motion on a local quadratic approximation to the surface (a second-order algorithm). A more accurate integration method is described that uses a second-order predictor step on a local quadratic surface, followed by a corrector step on a better local surface fitted to the energies, gradients, and Hessians computed at the beginning and end points of the predictor step. The electronic structure work per step is the same as the second-ord...

Classical RRKM (i.e., microcanonical) rate constants are often calculated for analytic potential energy surfaces (PESs) developed to represent unimolecular decomposition reactions. The values for these rate constants reflect the complete anharmonicities of the PESs. A common procedure is to fit these rate constants with the expression of RRK theory, which is the harmonic limit of classical RRKM theory. These RRK fits often give values for s significantly less than 3n−6(5), which are not meaningful, since anharmonic rate constants are represented with a harmonic model. In this work different schemes are proposed for introducing anharmonic and also variational transition state effects into the RRK expression. These modified RRK schemes allow one to fit classical anharmonic RRKM rate constants with s=3n−6(5). The fits give information about the importance of anharmonicity in the unimolecular reactant’s density of states and the transition state’s sum of states.

A direct dynamics technique, using energies, forces and second derivatives calculated at the UHF/6–31G* level of theory, was used to investigate product energy distributions of the F+C2H4→C2H3F+H collision reaction. The shifting and broadening of the product translational energy distribution as the system moves from the exit-channel barrier to the products was studied. Since properties associated with the rupturing C···H bond are similar for the C2H5‡ and C2H4F‡ exit-channel barriers, and integration of the C2H5‡→C2H4+H reaction is approximately 2.5 times faster than the C2H4F‡→C2H3F+H reaction, trajectories of the former reaction were propagated to gain insight into the exit-channel dynamics. Ensemble averaged results for C2H5‡ dissociation are well described by a model based on isotropic exit-channel dynamics which assumes that the product relative translational distribution arises from the centrifugal potential and relative translational energy distributions at the exit-channel barrier plus the exit-channel potential release. The width of the product translational energy distribution is sensitive to overall rotational angular momentum and its partitioning between C2H4···H‡ orbital angular momentum and C2H4‡ rotational angular momentum. The simulated product translational energy distribution for the C2H4F‡→C2H3F+H reaction is broadened by relative translation–vibrational couplings in the exit-channel and is similar to the distribution used to fit crossed molecular beam data. Approximately 50% of the available energy is in product relative translation, which also agrees with experiment. RRKM calculations indicate that a second reaction mechanism, involving 1–2 hydrogen migration prior to C···H bond fission, does not significantly contribute to C2H3F+H product formation.

Ab initio direct dynamics was used to calculate product energy distributions for the F + C 2 H 4 → C 2 H 3 F + H reaction. A broad product translational energy distribution, similar to that observed experimentally, is found when the trajectories are initialized with a statistical vibrational energy distribution at the exit channel barrier. The trajectories show that, on average, orbital angular momentum is conserved in going from the exit channel barrier to products, and a model which incorporates this dynamical constraint reproduces the ensemble averaged trajectory results.

A molecular dynamics simulation is presented of a beam of neon atoms scattering off a n-hexyl thiolate self-assembled monolayer adsorbed on a Au {111} surface. Ab initio QCISD(T)/6-311++G** calculations, for a model system consisting of a neon atom and a methane molecule, were used to derive an accurate interaction potential between the neon projectile and the monolayer. Four initial translational energies of 1.2, 5, 20, and 40 kcal/mol and five incident angles (with respect to the surface normal) of 10, 30, 45, 60, and 80 degrees were investigated in the simulations. Both trapping desorption and direct inelastic scattering collisional events were observed. The fraction of trapping desorption decreases as the initial translational energy and/or the angle of incidence increases. For high initial translational energy, trapping desorption may involve penetration of the monolayer. The overall energy transfer probability and the fraction of trapping desorption are in good agreement with previous experiments [J. Chem. Phys. 99, 7056 (1993)] and computational studies [J. Chem. Phys. 100, 8408, 6500 (1994)] of neon atom beams colliding with liquid squalane surfaces. There is a small but measurable change in the energy transfer efficiency for neon atoms colliding parallel versus perpendicular to the “tilt angle” of the SAM. The distributions of the change in the azimuthal angle and the scattering angle between the neon final velocity vector and surface normal provide additional information about the collision dynamics. A general discussion of these simulation results is given, in the context of existing models and theories for gas/surface collisions, to achieve a more fundamental understanding of the dynamics of interfaces.

This paper shows how a compact finite difference Hessian approximation scheme can be proficiently implemented into semiclassical initial value representation molecular dynamics. Effects of the approximation on the monodromy matrix calculation are tested by propagating initial sampling distributions to determine power spectra for analytic potential energy surfaces and for “on the fly” carbon dioxide direct dynamics. With the approximation scheme the computational cost is significantly reduced, making ab initio direct semiclassical dynamics computationally more feasible and, at the same time, properly reproducing important quantum effects inherent in the monodromy matrix and the pre-exponential factor of the semiclassical propagator.

The quasiclassical trajectory (QCT) method was used to study the dynamics of the OH(X 2Π) and OD(X 2Π)+HBr chemical reactions on an empirical potential energy surface (PES). The main emphasis in the calculation was the vibrational energy distributions of H2O (and HDO) and the magnitude and temperature dependence of the rate constant. However, this PES also serves as a generic model for the dynamics of direct H atom abstraction by OH radicals. Since this PES has no formal potential energy barrier, variational transition‐state theory was used to obtain rate constants for comparison with the QCT calculations and experimental results. The parameters of the potential energy surface were adjusted to obtain better agreement with the experimentally measured fraction of H2O vibrational energy, 〈fV(H2O)〉=0.6, without significantly changing the entrance channel. No isotope effect for the partition of energy to H2O vs HOD was found. Analysis of the trajectories indicates that the reactant OH(OD) bond is a spectator, ...

Coupling terms in the reaction path Hamiltonian (RPH) provide a qualitative interpretation of the non-statistical effects observed in classical trajectory simulations and experiments for the Cl− + CH3Br → ClCH3 + Br− SN2 nucleophilic substitution reaction. The small couplings between the Cl− + CH3Br relative translational, which is the reaction coordinate as the reactants collide, and the CH3Br vibrational modes explain why translation to vibration (T → V) energy transfer is unimportant for Cl− ⋯CH3Br complex formation and, instead, the complex is formed by T → R energy transfer. A large coupling term between the ClCBr symmetric stretch and the reaction coordinate leads to a large reaction path curvature at regions along the reaction path separating the central barrier and the pre- and post-reaction complexes. Such sharp values for the curvature can trap trajectories in the vicinity of the central barrier, which is consistent with the central barrier recrossings observed in classical trajectory simulations. Because of singularities in the RPH it is difficult to use it in classical trajectory simulations. Numerical difficulties in evaluating the long-time flux-flux autocorrelation function for the RPH precludes using this approach for calculating the quantum mechanical rate constant for Cl− + CH3Br SN2 nucleophilic substitution. Also, since the RPH does not include overall rotation and rotational/vibrational coupling and assumes a quadratic expansion for displacements away from the reaction path, this Hamiltonian may not give an accurate quantum mechanical rate constant even if a converged flux-flux autocorrelation function could be evaluated.

The ZPE constrained trajectory model is found to retain the ergodicity and intrinsic Rice–Ramsperger–Kassel–Marcus (RRKM) behavior observed previously [J. Chem. Phys. 101, 8535 (1994)] in unconstrained trajectories of Al3 decomposition. Microcanonical unimolecular rate constants for Al3 decomposition are calculated from the ZPE constrained trajectories and compared with the predictions of the vibrator and flexible transition state models of RRKM theory, phase space theory, and the orbiting transition state model of phase space theory (OTS/PST). Quantum anharmonic Al3 vibrational densities of state, determined by a semiclassical approach, are used to calculate these statistical rate constants. Anharmonicity increases the density of states threefold for total energies 1–2 kcal/mol above the classical product asymptotic limit, but has a negligible effect on the Al2‐‐‐Al transition state sum of states. The ZPE constrained trajectory unimolecular rate constants are in poor agreement with the quantum anharmonic OTS/PST and flexible RRKM rate constants. This is because the ZPE constraint is too restrictive and some of the ZPE constrained trajectories are temporarily trapped in the ZPE forbidden region of phase space. The ZPE constrained trajectory rate constants are smaller than their purely classical counterparts, since Al2 is not formed without its ZPE and thus the effective dissociation threshold is larger for the ZPE constrained trajectories. ZPE constrained sums and densities are calculated by including the ZPE constraint when solving the classical phase integral. RRKM rate constants calculated from these ZPE constrained sums and densities are in much better agreement with the quantum anharmonic OTS/PST and flexible RRKM rate constants, than are those calculated from the ZPE constrained trajectories. The difference between the ZPE constrained RRKM and quantum flexible RRKM rate constants becomes small and much less than the anharmonic correction, for energies slightly in excess of the Al2+Al classical asymptotic limit. This is because the number of real frequencies in the instantaneous normal mode analysis decreases as the total energy is increased, which makes the ZPE constrained RRKM rate constant more accurate. Product energy partitioning from the ZPE constrained trajectories is in good agreement with the predictions of quantum phase space theories, except that the product diatom is formed too rotationally excited. The ZPE constraint scheme retains a spurious frequency and zero‐point energy for the Al2‐‐‐Al bending motion at large separations, which increases the Al2 product rotational energy. The work reported here supports the proposal that a ZPE constraint model, based on an instantaneous normal mode analysis, may be a valid approach for including zero‐point energy effects in trajectory simulations of ergodic anharmonic coupled systems. However, additional work needs to be done to remove some of the numerical problems with the current ZPE constraint model and to make the model less restrictive.

Direct dynamics calculations are performed, using the semiempirical neglect of diatomic differential overlap (NDDO) molecular orbital theory, to explore the level of electronic structure theory required to accurately describe the product energy partitioning when formaldehyde dissociates into hydrogen and carbon monoxide. Trajectories are initiated at the saddlepoint and are propagated for the short time needed to form products, by obtaining the energy and gradient directly from the NDDO theory. The resulting product energy partitioning is compared to available experimental data and the findings of two previous trajectory studies, including one ab initio trajectory study at the HF/6‐31G** level of theory [Chem. Phys. Lett. 228, 436 (1994)]. The MNDO, AM1, and PM3 semiempirical Hamiltonians are studied, as well as Hamiltonians based on specific reaction parameters (SRP). For the latter, the original PM3 and AM1 parameters are adjusted to reproduce some ab initio potential energy surface properties, such as stationary points and part of the reaction path. A series of NDDO‐SRP Hamiltonians are chosen by fitting different features of a HF/6‐31G** potential energy surface. Only qualitative agreement is found between the product energy distributions of the NDDO‐SRP Hamiltonians and that of the HF/6‐31G** Hamiltonian. This result is consistent with the well known difficulty of reproducing a HF/6‐31G** Hamiltonian with a NDDO‐SRP model, since dynamic correlation is not treated in ab initio SCF, but is incorporated into semiempirical methods. Trajectory results with NDDO‐SRP Hamiltonians, which reproduce a few experimental and/or high‐level ab initio stationary points, are in poor agreement with the experimental product energy partitioning. Reparameterizing the NDDO Hamiltonian is laborious, and only a few properties of the potential energy surface can be reproduced at the same time. This indicates the limitations of the NDDO‐SRP approach, which might be well suited for locally interpolating ab initio data, but not for quantitatively describing global potential energy surfaces.

Comparisons, for J=0, are made between HO2→H+O2 reaction path anharmonic energy levels, variational transition states, and unimolecular rate constants determined by three different semiclassical models and a quantum mechanical model. The semiclassical models are based on the reaction path Hamiltonian. However, to determine anharmonic energy levels, the harmonic potential of this Hamiltonian is replaced by the actual anharmonic DMBE IV potential for the HO2 system. Two of the semiclassical models use Einstein–Brillouin–Keller (EBK) quantization to determine energy levels for motion orthogonal to the reaction path; i.e., one model neglects anharmonic coupling between modes, while the other retains all the coupling. The third semiclassical model is based on a quartic expansion of the potential and second‐order perturbation theory to determine the energy levels. A comparison of the results of these three semiclassical models shows that anharmonic coupling between modes orthogonal to the reaction path is unimp...

A previous trajectory study of the dissociation of Cl−...CH3Cl complexes formed by Cl−+CH3Cl association is further analyzed to determine (1) the relationship between classical and quantum Rice–Ramsperger–Kassel–Marcus (RRKM) rate constants for Cl−...CH3Cl→Cl−+CH3Cl dissociation; (2) the importance of anharmonicity in calculating the RRKM dissociation rate constant; (3) the role of angular momentum in interpreting the trajectory distribution N(t)/N(0) of Cl−...CH3Cl complexes versus time; and (4) the pressure‐dependent collision‐averaged rate constant k(ω,E) for Cl−...CH3Cl dissociation. It is found that only the low‐frequency intermolecular modes of Cl−...CH3Cl are initially excited by Cl−+CH3Cl association. Classical and quantum RRKM rate constants for dissociation of this intermolecular complex are in excellent agreement. Anharmonicity lowers the rate constant by a factor of 4–8 from its harmonic value. The dissociation rate for the long‐time tail of the trajectory N(t)/N(0) distribution is much smaller than predicted by a RRKM model, which accurately treats angular momentum. It is suggested that the long‐lived trajectories may arise from motion on vague tori. The trajectory collision‐averaged rate constant k(ω,E) is in agreement with an experimental study at 300 K.

Three‐dimensional quantum mechanical calculations are carried out, in a time‐independent scattering approach, to study the unimolecular dissociation HO2→H+O2. The dissociation cross section is governed by narrow resonances with widths that vary over five orders of magnitude. The unimolecular dissociation rates strongly fluctuate about an average which agrees surprisingly well with the Rampsberger–Rice–Kassel–Marcus (RRKM) theory.

Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for (1)O(2) + C(2)H(4), the singlet ·O-O-CH(2)-CH(2)· biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche ·O-CH(2)-CH(2)-O· biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G∗ method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP∕6-31G∗ direct dynamics trajectories were initiated at the TS connecting the ·O-O-CH(2)-CH(2)· biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed (1)O(2) + C(2)H(4) and of these ∼ 40% went directly from the TS to (1)O(2) + C(2)H(4) without getting trapped and forming an intermediate in the ·O-O-CH(2)-CH(2)· biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice-Ramsperger-Kassel-Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche ·O-CH(2)-CH(2)-O· biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.

International audience; In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)]2+, in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational–vibrational energy transfer for Ar + [Ca(urea)]2+ collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational–rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.