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In this Perspective, mass spectrometry experiments and chemical dynamics simulations are described that have explored the atomistic dynamics of protonated peptide ions, peptide-H(+), colliding with organic surfaces. These studies have investigated the energy transfer and fragmentation dynamics for peptide-H(+) surface-induced dissociation (SID), peptide-H(+) physisorption on the surface, soft landing (SL), and peptide-H(+) reaction with the surface, reactive landing (RL). SID provides primary structures of biological ions and information regarding their fragmentation pathways and energetics. Two SID mechanisms are found for peptide-H(+) fragmentation. A traditional mechanism in which peptide-H(+) is vibrationally excited by its collision with the surface, rebounds off the surface and then dissociates in accord with the statistical, RRKM unimolecular rate theory. The other, shattering, is a nonstatistical mechanism in which peptide-H(+) fragments as it collides with the surface, dissociating via many pathways and forming many product ions. Shattering is important for collisions with diamond and perfluorinated self-assembled monolayer (F-SAM) surfaces, increasing in importance with the peptide-H(+) collision energy. Chemical dynamics simulations also provide important mechanistic insights on SL and RL of biological ions on surfaces. The simulations indicate that SL occurs via multiple mechanisms consisting of sequences of peptide-H(+) physisorption on and penetration in the surface. SL and RL have a broad range of important applications including preparation of protein or peptide microarrays, development of biocompatible substrates and biosensors, and preparation of novel synthetic materials, including nanomaterials. An important RL mechanism is intact deposition of peptide-H(+) on the surface.

Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.

In classical and quasiclassical trajectory chemical dynamics simulations, the atomistic dynamics of collisions, chemical reactions, and energy transfer are studied by solving the classical equations of motion. These equations require the potential energy and its gradient for the chemical system under study, and they may be obtained directly from an electronic structure theory. This article reviews such direct dynamics simulations. The accuracy of classical chemical dynamics is considered, with simulations highlighted for the F− + CH3OOH reaction and of energy transfer in collisions of CO2 with a perfluorinated self-assembled monolayer (F-SAM) surface. Procedures for interfacing chemical dynamics and electronic structure theory computer codes are discussed. A Hessian-based predictor–corrector algorithm and high-accuracy Hessian updating algorithm, for enhancing the efficiency of direct dynamics simulations, are described. In these simulations, an ensemble of trajectories is calculated which represents the experimental and chemical system under study. Algorithms are described for selecting the appropriate initial conditions for bimolecular and unimolecular reactions, gas-surface collisions, and initializing trajectories at transition states and conical intersections. Illustrative direct dynamics simulations are presented for the Cl− + CH3I SN2 reaction, unimolecular decomposition of the epoxy resin constituent CH3NHCHCHCH3 versus temperature, collisions and reactions of N-protonated diglycine with a F-SAM surface that has a reactive head group, and the product energy partitioning for the post-transition state dynamics of C2H5F HF + C2H4 dissociation. © 2012 John Wiley & Sons, Ltd.

Previous experiments [J. Phys. Chem. A 116, 2833 (2012)] have studied the dissociation of 1,2-diiodoethane radical cation ( ) and found a one-dimensional distribution of translational energy, an odd finding considering most product relative translational energy distributions are two-dimensional. The goal of this study is to obtain an accurate understanding of the potential energy surface (PES) topology for the unimolecular decomposition reaction → C2H4I+ + I•. This is done through comparison of many single-reference electronic structure methods, coupled-cluster single-point (energy) calculations, and multi-reference energy calculations used to quantify spin–orbit (SO) coupling effects. We find that the structure of the reactant has a substantial effect on the role of the SO coupling on the reaction energy. Both the BHandH and MP2 theories with an ECP/6-31++G** basis set, and without SO coupling corrections, provide accurate models for the reaction energetics. MP2 theory gives an unsymmetric structure wit...

The scattering of high kinetic energy (1–6.5 eV) xenon and krypton atoms from ice was experimentally measured and theoretically modeled. The ice efficiently accommodates translational energy, but the extent to which the energy is quenched suggests the mechanism for the highest energies and near-normal incidence angles involves more than interaction with just the molecules at the ice surface. Simulations show that for these conditions the xenon penetrates into the selvedge. This penetration into the solid manifests experimentally in that the postcollision translational energy is essentially independent of the incident translational energy. This observation is in stark contrast with what is usually the situation for scattering from a surface. Finally, postexposure desorption measurements showed that some of the incident gas atoms were trapped in the bulk of the ice at temperatures well above where the absorption is thermodynamically stable. The above evidence leads to the conclusion that under conditions of...

Direct dynamics simulations at the MP2/6-31+G ∗ level of theory were performed to study the unimolecular decomposition of the epoxy resin constituent CH 3 NH CH CH CH 3 for the hyperthermal temperatures of 3500–5500 K. At these temperatures 33 different primary decomposition pathways were found, with C N bond dissociation to form CH 3 + NH CH CH CH 3 the most important path. In addition, during the 5.1 ps integration time of the simulations, an additional 15 secondary decomposition pathways were observed. The unimolecular products of the simulations are in qualitative agreement with those observed in the high temperature decomposition of a cross-linked epoxy resin for which CH 3 NH CH CH CH 3 is a constituent.

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.

International audience; In the present work we have investigated the gas phase reactivity of protonated urea after collision with the diatomic inert gas N2, by studying the energy transfer and fragmentation induced by collisions. We first developed an analytical pair potential to describe the interaction between the projectile and the ion, and then performed QM/MM direct chemical dynamics simulations of the collision between the projectile and protonated urea in its two most stable isomers. In particular, the effect of the diatomic projectile, and the role of its initial rotational state, were compared with the fragmentation and energy transfer obtained previously (J. Phys. Chem. A 2009, 113, 13853) for the monoatomic projectile Ar. The diatomic projectile was found to be less efficient in energy transfer compared to the monoatomic projectile. In addition, rotational activation of UreaH+ is dependent on the initial rotational quantum number of N2. Finally, we investigated the UreaH+ gas phase reactivity as a function of its rovibrational activation by means of chemical dynamics simulations where the initial structure for the simulations is the transition state (TS) that the system can reach after collisional activation of the most stable isomer. The simulation time-length is not able to directly access this TS from the most stable isomer since its lifetime is notably longer, of about two order of magnitude in time.

In a previous study (J. Chem. Phys.2008, 129, 094701) it was shown that for a large molecule, with a total energy much greater than its barrier for decomposition and whose vibrational modes are harmonic oscillators, the expressions for the classical Rice-Ramsperger-Kassel-Marcus (RRKM) (i.e., RRK) and classical transition-state theory (TST) rate constants become equivalent. Using this relationship, a molecule's unimolecular rate constants versus temperature may be determined from chemical dynamics simulations of microcanonical ensembles for the molecule at different total energies. The simulation identifies the molecule's unimolecular pathways and their Arrhenius parameters. In the work presented here, this approach is used to study the thermal decomposition of CH3-NH-CH═CH-CH3, an important constituent in the polymer of cross-linked epoxy resins. Direct dynamics simulations, at the MP2/6-31+G* level of theory, were used to investigate the decomposition of microcanonical ensembles for this molecule. The Arrhenius A and Ea parameters determined from the direct dynamics simulation are in very good agreement with the TST Arrhenius parameters for the MP2/6-31+G* potential energy surface. The simulation method applied here may be particularly useful for large molecules with a multitude of decomposition pathways and whose transition states may be difficult to determine and have structures that are not readily obvious.

A hierarchy of electronic structure calculations, scalings, and fittings were used to develop an analytic intermolecular potential for dimethyl methylphosphonate (DMMP) interacting with the TiO2 rutile (110) surface. The MP2/aug-cc-pVDZ (6-311+G** for Ti) level of theory, with basis set superposition error (BSSE) corrections, was used to calculate multiple intermolecular potential curves between TiO5H6 as a model for the Ti and O atoms of the TiO2 surface, and CH3OH and O═P(CH3)(OH)2 as models for different types of atoms comprising DMMP. Each intermolecular potential energy emphasized a particular atom–atom interaction, and the curves were fit simultaneously by a sum of two-body potentials between the atoms of the two interacting molecules. The resulting analytic intermolecular potential gives DMMP/TiO5H6 potential curves in excellent agreement with those calculated using MP2/aug-cc-pVDZ (6-311+G** for Ti) theory. MP2 theory with the smaller basis set, 6-31++G** (6-31G** for Ti), gives DMMP/TiO5H6 potent...

Algorithms are presented for sampling quantum microcanonical ensembles for a potential energy minimum and for the conical intersection at the minimum energy crossing point of two coupled electronic states. These ensembles may be used to initialize trajectories for chemical dynamics simulations. The unimolecular dynamics of a microcanonical ensemble about a potential energy minimum may be compared with the dynamics predicted by quantum Rice-Ramsperger-Kassel-Marcus (RRKM) theory. If the dynamics is non-RRKM, it will be of particular interest to determine which states have particularly long lifetimes. Initializing a microcanonical ensemble for the electronically excited state at a conical intersection is a model for electronic nonadiabatic dynamics. The trajectory surface-hopping approach may be used to study the ensuing chemical dynamics. A strength of the model is that zero-point energy conditions are included for the initial nonadiabatic dynamics at the conical intersection.

In a previous article (Phys. Chem. Chem. Phys.2010, 12, 4435), nonequilibrium molecular dynamics (MD) simulations of heat transfer from a hot Au{111} substrate to an alkylthiolate self-assembled mo...

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.

Ion imaging experiments and direct chemical dynamics simulations were performed to study the atomic-level dynamics for the F− + CH3I → FCH3 + I− SN2 nucleophilic substitution reaction at 0.32 eV collision energy. The simulations reproduce the product energy partitionings and the velocity scattering angle distribution measured in the experiments. The simulations reveal that the substitution reaction occurs by two direct atomic-level mechanisms, that is, rebound and stripping, and an indirect mechanism. Approximately 90% of the indirect events occur via a prereaction F−···HCH2I hydrogen-bonded complex. This mechanism may play an important role for other F− SN2 reactions due to the strong electronegativity of fluorine. The average product energy partitioning for the F− + CH3I indirect mechanism agrees with the prediction of PST, even though a FCH3···I− postreaction complex is not formed.

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.

MP2 and DFT electronic structure theories, with the functionals OPBE, OLYP, HCTH407, BhandH, and B97-1 for the latter, were used to investigate stationary point properties on the F(-) + CH(3)I → FCH(3) + I(-) potential energy surface (PES). The aug-cc-pVDZ and aug-cc-pVTZ basis sets for C, H, and F, with Wadt and Hay's 3s3p valence basis and an effective core potential (ECP) for iodine, were employed for both MP2 and DFT. Single-point CCSD(T) calculations were also performed to obtain the complete basis set (CBS) limit for the stationary point energies. The CCSD(T)/CBS reaction exothermicity is only 5.0 kJ/mol different than the experimental value. MP2 and DFT do not predict the same stationary points on the PES. MP2 predicts the C(3v) F(-)-CH(3)I and FCH(3)-I(-) ion-dipole complexes and traditional [F-CH(3)-I](-) central barrier as stationary points, as well as a C(s) hydrogen-bonded F(-)-HCH(2)I complex and a [F-HCH(2)-I](-) transition state connecting this latter complex to the F(-)-CH(3)I complex. A CCSD(T)/CBS relaxed potential energy curve, calculated for the MP2 structures, shows that going from the F(-)-CH(3)I complex to the [F-CH(3)-I](-) TS is a barrierless process, indicating these two structures are not stationary points. This is also suggested by the DFT calculations. The structures and frequencies for CH(3)I and CH(3)Cl given by MP2 and DFT are in overall good agreement with experiment. The calculations reported here indicate that the DFT/B97-1 functional gives the overall best agreement with the CCSD(T) energies, with a largest difference of only 7.5 kJ/mol for the FCH(3)-I(-) complex.

Results are reported for PM3 and RM1 QM+MM direct dynamics simulations of collisions of N-protonated octaglycine (gly(8)-H(+)) with an octanethiol self-assembled monolayer (H-SAM) surface. Detailed analyses of the energy transfer, fragmentation, and conformational changes induced by the collisions are described. Extensive comparisons are made between the simulations and previously reported experimental studies. Good agreement between the two semiempirical methods is found regarding energy transfer, while differences are seen for their fragmentation time scales. Trajectories were calculated for 8 ps with collision energies from 5 to 110 eV and incident angles of 0 degrees and 45 degrees. A linear relationship is found between the collision energy and key parameters of the final internal energy distributions of both gly(8)-H(+) and the H-SAM. In general wider distributions are seen for the H-SAM than for the peptide ion. An incident angle of 45 degrees leads to more energy transfer to the peptide, with wider distributions. The average percentage energy transfer to gly(8)-H(+) is nearly independent of the collision energy, while the average percentage transfer to the surface increases with collision energy. For normal incidence, we find an average percentage energy transfer to gly(8)-H(+) which is in excellent agreement with the experimentally measured value 10.1 +/- 0.8% for the octapeptide des-Arg(1)-bradykinin [J. Chem. Phys. 2003, 119, 3414]. At each collision energy dramatic conformational changes of gly(8)-H(+) are seen. The initial folded structure rearranges to form a beta-sheet like structure showing that the collision induces peptide unfolding. This process is more pronounced at an incident angle of 45 degrees. Following the conformation change, nonshattering fragmentation, promoted by proton transfer, is observed at the highest collision energies. Substantially more fragmentation occurs for the RM1 simulations.

International audience; Quantum mechanical plus molecular mechanical direct chemical dynamics were used, with electrospray tandem mass spectrometry experiments, potential energy surface calculations, and RRKM analyses, to study the gas-phase collision-induced dissociation (CID) of protonated urea. The direct dynamics were able to reproduce some of the experimental observations, in particular the presence of two fragmentation pathways, and, thus, to explain the dynamical origin of the two fragmentation ions observed in the CID spectra. A shattering dissociation mechanism takes place during the collision, and it becomes more important as the collision energy increases, thus explaining the linear increase of the high-energy reaction path (loss of ammonia) versus collision energy. By combining the different theoretical and experimental findings, a complete dynamical picture leading to the fragmentation was identified: (i) Oxygen-protonated urea, the most stable structure in the gas phase, must first isomerize to the nitrogen-protonated form. This can happen by multiple CID collisions or in the electrospray ionization process. (ii) Once the nitrogen-protonated isomer is formed, it can dissociate via two mechanisms: i.e, a slow, almost statistical, process forming a NH4+--NHCO intermediate that rapidly dissociates or a fast nonstatistical process which may lead to the high-energy products.

Results are reported for a direct dynamics simulation of NH(4)(+) + CH(4) gas phase collisions. We interpret the results with protonated peptide/hydrogenated alkanethiolate self-assembled monolayer (H-SAM) surface collisions in mind. Previous theoretical studies of such systems have made use of nonreactive surfaces, and therefore, our goal is to investigate the types and likelihood of peptide/H-SAM reactions. In that vein, the NH(4)(+) + CH(4) reaction represents a simple gas phase system which includes many of the important interactions present in protonated peptide/H-SAM surfaces. Thirty-seven open pathways are seen in the 5-35 eV collision energy range. An energy dependence on the likelihood of forming CN bonds is found. This type of bonding could deposit both the peptide and its molecular fragments on the H-SAM surface. For our gas phase collision system, around 50% of the trajectories result in the formation of CN bonds. For all collision energies in which reactive scattering occurs, CN bond formation is an important reaction pathway.

A survey is presented of theoretical models and computational studies for unimolecular reaction dynamics. Intrinsic RRKM and non-RRKM dynamics are described, and properties of the unimolecular reactant's classical phase space giving rise to these dynamics are discussed. Quantum dynamical calculations of isolated resonances and state-specific decomposition are reviewed, and the resulting possible mode-specific or statistical state-specific decomposition is delineated. The relationship between the latter and RRKM theory is described. Computational studies give the probability that a molecule dissociates in a time interval of t --t + dt, that is, the lifetime distribution P(t), and determining unimolecular rate constants versus pressure, energy, and temperature from P(t) is outlined. Non-RRKM behavior evident in P(t) is not always present in the rate constants. The need to include anharmonicity and the proper treatment of the K quantum number, in calculating the RRKM unimolecular rate constant, is explained. The possibility of observing "steps" in unimolecular rate constants is considered. The extensive experimental non-RRKM dynamics found for several classes of chemical reactions are surveyed. The direct coupling of chemical dynamics with electronic structure theory, that is, direct dynamics, has allowed one to study the atomic-level dynamics for numerous unimolecular reactions, and extensive non-RRKM and nonintrinsic reaction coordinate (IRC) dynamics have been discovered. These dynamics for OH(-) + CH(3)F and F(-) + CH(3)OOH are reviewed.

A chemical dynamics simulation was performed to study collisions between neon (Ne) atoms and a liquid squalane (2,6,10,15,19,23-hexamethyltetracosane) surface. Ten thousand trajectories were calculated, with an incident energy of 10 kcal/mol, incident polar angle 45° with respect to the surface normal, and random azimuthal angle. The final energy distribution, angular distribution, and impact sites were determined and analyzed. The incident Ne atoms have short residence times on the surface with most atoms successfully scattering within 3−7 ps. Due to thermal fluctuations of the surface, the incident energy is dissipated efficiently, and more than 60% of the initial energy of the Ne atoms is transferred with three or more “kicks” on the surface. For in-plane scattered Ne atoms with a final polar angle of 45°, the energy transfer is 58% ± 8%, which is in good agreement with the experimental value of 60% (J. Chem. Phys. 1993, 99, 7056). A bimodal energy distribution is observed for both in-plane and out-of-...

Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl− ··· CH3Br → ClCH3 + Br− and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl− ··· CH3Cl complexes mediating the Cl− + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH− + CH3F and F− + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.

Classical trajectory simulations are performed to study energy transfer in collisions of protonated diglycine, gly2-H+, and dialanine, ala2-H+, ions with a fluorinated octanethiol self-assembled monolayer (F-SAM) surface for collision energies Ei in the range of 5−70 eV and incident angles θi of 0 and 45° with respect to the surface normal. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface. The simulations show the distribution of energy transfer to the peptide−ion’s internal degrees of freedom, ΔEint, to the surface, ΔEsurf, and in peptide−ion translation, Ef, are very similar for gly2-H+, and ala2-H+. The average percentage energy transferred to ΔEsurf and Ef increases and decreases, respectively, with an increase in Ei, while the average percentage energy transfer to ΔEint is nearly independent of Ei. Changing θi from 0 to 45° decreases and increases the percentage of energy transfer to ΔEsurf and Ef, respectively, but has little change in the transfer to ΔEin...

Nonequilibrium molecular dynamics simulations were performed to study the kinetics of heat transfer across the interface of a hot diamond {111} nanoparticle and a diamond {111} surface whose bulk temperature was maintained at 300 K. The heat transfer depends on the nanoparticle’s interfacial energy and not its total energy. Thus, there is a linear relationship between the heat transfer rate constant, k, and the inverse of the hot nanoparticle’s thickness. However, k does not depend on the nanoparticle’s interfacial energy density, which decreases during its cooling, and the heat transfer occurs exponentially. For nanoparticles of fixed thickness, increasing the nanoparticle−surface interfacial contact area increases the rate for heat transfer but does not change the rate constant. The atomic-level dynamics found here, for the dependence of the heat transfer rate constant on the nanoparticle’s interfacial area, thickness, and energy content, agree with Fourier’s macroscopic law of heat conduction. However,...

Microsolvation offers a bottom-up approach to investigate details of how solute-solvent interactions affect chemical reaction dynamics. The dynamics of the microsolvated S(N)2 reaction F(-)(H2O) + CH3I are uncovered in detail by using direct chemical dynamics simulations. Direct rebound and stripping and indirect atomic-level mechanisms are observed. The indirect events comprise ∼70% of the solvated reaction and occur predominantly via a hydrogen-bonded F(-)(H2O)···HCH2I prereaction complex. The reaction dynamics show propensity for the direct three-body dissociation channel F(-)(H2O) + CH3I → CH3F + I(-) + H2O after passing the reaction's dynamical bottleneck. The water molecule leaves the reactive system before traversing the postreaction region of the PES, where water transfer toward the product species occurs. This provides an insight into the very interesting finding of strongly suppressed formation of energetically favored solvated products for almost all SN2 reactions under microsolvation.

International audience; Beyond the established use of thermodynamic vs kinetic control to explain chemical reaction selectivity, the concept of bifurcations on a potential energy surface (PES) is proving to be of pivotal importance with regard to selectivity. In this article, we studied by means of post-transition state (TS) direct dynamics simulations the effect that vibrational and rotational excitation at the TS may have on selectivity on a bifurcating PES. With this aim, we studied the post-TS unimolecular reactivity of the [Ca(formamide)]2+ ion, for which Coulomb explosion and neutral loss reactions compete. The PES exhibits different kinds of nonintrinsic reaction coordinate (IRC) dynamics, among them PES bifurcations, which direct the trajectories to multiple reaction paths after passing the TS. Direct dynamics simulations were used to distinguish between the bifurcation non-IRC dynamics and non-IRC dynamics arising from atomistic motions directing the trajectories away from the IRC. Overall, we corroborated the idea that kinetic selectivity often does not reduce to a simple choice between paths with different barrier heights and instead dynamical behavior after passing the TS may be crucial. Importantly, rotational excitation may play a pivotal role on the reaction selectivity favoring nonthermodynamic products.

International audience; In the present work we have investigated mechanisms of gas phase unimolecular dissociation of a relatively simple dipeptide, the di-proline anion, by means of chemical dynamics simulations, using the PM3 semi-empirical Hamiltonian. In particular, we have considered two activation processes that are representative limits of what occurs in collision induced dissociation experiments: (i) thermal activation, corresponding to several low energy collisions, in which the system is prepared with a microcanonical distribution of energy; (ii) collisional activation where a single shock of hundreds of kcal mol−1 (300 kcal mol−1 in the present case) can transfer sufficient energy to allow dissociation. From these two activation processes we obtained different product abundances, and for one particular fragmentation pathway a clear mechanistic difference for the two activation processes. This mechanism corresponds to the leaving of an OH− group and subsequent formation of water by taking a proton from the remaining molecule. This last reaction is always observed in thermal activation while in collisional activation it is less favoured and the formation of OH− as a final product is observed. More importantly, we show that while in thermal activation unimolecular dissociation follows exponential decay, in collision activation the initial population decays with non-exponential behaviour. Finally, from the thermal activation simulations it was possible to obtain rate constants as a function of temperature that show Arrhenius behaviour. Thus activation energies have also been extracted from these simulations.

Producción Científica, We show, by means of direct dynamics simulations, how it is possible to define possible reactants and mechanisms leading to the formation of formamide in the interstellar medium. In particular, different ion-molecule reactions in the gas phase were considered: NH3OH+, NH2OH{}2+, H2COH+, and NH4 + for the ions and NH2OH, H2CO, and NH3 for the partner neutrals. These calculations were combined with high level ab initio calculations to investigate possible further evolution of the products observed. In particular, for formamide, we propose that the NH2OH{}2+ + H2CO reaction can produce an isomer, NH2OCH{}2+, that, after dissociative recombination, can produce neutral formamide, which was observed in space. The direct dynamics do not pre-impose any reaction pathways and in other reactions, we did not observe the formation of formamide or any possible precursor. On the other hand, we obtained other interesting reactions, like the formation of NH2CH{}2+. Finally, some radiative association processes are proposed. All of the results obtained are discussed in light of the species observed in radioastronomy., Junta de Castilla y León (programa de apoyo a proyectos de investigación – Ref. VA330U13)

Dynamics of Ar atom collisions with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) surface on gold were investigated by classical trajectory simulations and atomic beam scattering techniques. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface; in the UA model, the CF3 and CF2 units are represented as single pseudoatoms. Additionally the nonbonded interactions in both models are different. The simulations show the three limiting mechanisms expected for collisions of rare gas atoms (or small molecules) with SAMs, that is, direct scattering, physisorption, and penetration. Surface penetration results in a translational energy distribution, P(Ef), that can be approximately fit to the Boltzmann for thermal desorption, suggesting that surface accommodation is attained to a large extent. Fluorination of the alkanethiol monolayer leads to less energy transfer in Ar collisions. This results from a denser and stiffer surface structure in comparison with that of the alkanethiol SAM, which introduces constraints for conformational changes which play a significant role in the energy-transfer process. The trajectory simulations predict P(Ef) distributions in quite good agreement with those observed in the experiments. The results obtained with the EA and UA models are in reasonably good agreement, although there are some differences.

Linear molecules with degenerate bending modes have states, which may be represented by the quantum numbers N and L. The former gives the total energy for these modes and the latter identifies their vibrational angular momentum jz. In this work, the classical mechanical analog of the N,L-quantum states is reviewed, and an algorithm is presented for selecting initial conditions for these states in quasiclassical trajectory chemical dynamics simulations. The algorithm is illustrated by choosing initial conditions for the N = 3 and L = 3 and 1 states of CO2. Applications of this algorithm are considered for initial conditions without and with zero-point energy (zpe) included in the vibrational angular momentum states and the C-O stretching modes. The O-atom motions in the x,y-plane are determined for these states from classical trajectories in Cartesian coordinates and are compared with the motion predicted by the normal-mode model. They are only in agreement for the N = L = 3 state without vibrational angular momentum zpe. For the remaining states, the Cartesian O-atom motions are considerably different from the elliptical motion predicted by the normal-mode model. This arises from bend-stretch coupling, including centrifugal distortion, in the Cartesian trajectories, which results in tubular instead of elliptical motion. Including zpe in the C-O stretch modes introduces considerable complexity into the O-atom motions for the vibrational angular momentum states. The short-time O-atom motions for these trajectories are highly irregular and do not appear to have any identifiable characteristics. However, the O-atom motions for trajectories integrated for substantially longer period of times acquire unique properties. With C-O stretch zpe included, the long-time O-atom motion becomes tubular for trajectories integrated to approximately 14 ps for the L = 3 states and to approximately 44 ps for the L = 1 states.

A QM + MM direct dynamics simulation, using MP2/6-31G* theory as a model for the intramolecular potential of protonated glycine (gly-H+), is used to study gly-H+ + diamond {1 1 1} SID. The simulations are performed for collisions normal (θi = 0°) and oblique (θi = 45°) to the surface and at a collision energy of 70 eV (1614 kcal/mol). The gly-H+ energy-transfer dynamics, observed in this study, are in accord with previous studies in which AMBER and AM1 were used for the ion's intramolecular potential [S.O. Meroueh, Y. Wang, W.L. Hase, J. Phys. Chem. A 106 (2002) 9983]. A particularly important finding is that a significant fraction of the gly-H+ ions fragment by a shattering mechanism as they collide with the surface. This result supports earlier studies in which shattering fragmentation was also observed for both gly-H+ and gly2-H+, in QM + MM direct dynamics simulations in which the AM1 semiempirical QM model was used for the ion's intramolecular potential, instead of the MP2/6-31G* model. Using MP2/6-31G* the predominant shattering fragmentation channels, in decreasing order of importance, are NH3 + CH2COOH+, NH3 + CO + CH2OH+, H2 + NH2CHCOOH+, and NH2CH2+ + C(OH)2 for θi = 0°, and NH3 + CH2COOH+, NH2CH2+ + C(OH)2, NH2CH2+ + HCOOH, and NH + C(OH)2CH3+ for θi = 45°. SID at θi = 45° was studied previously with AM1 and the percentage of gly-H+ trajectories which shatter with MP2/6-31G* is the same as found for AM1.

Nonequilibrium molecular dynamics simulations were performed to study the dynamics of heat transfer across the interface of two H-terminated diamond {111} nanosurfaces. It was found that when the surfaces are brought into contact, a coherent low-frequency oscillatory motion, normal to the interface, is initiated for the atomic layers of each surface. This motion lasts more than 50 ps, significantly longer than the relaxation of the interfacial force which occurs on a subpicosecond time scale. Amplitudes of these coherent oscillations gradually increase from the outer atomic layers to the interfacial layer. The temperature of the hot surface does not have a significant effect on the nature of oscillations. Thicker nanosurfaces have oscillations of lower frequency. This coherent oscillation of the surfaces' atomic layers creates beats in the potential energy of the surface and, thus, in the total energy content of the surface. The amplitude of the energy beat increases as the distance between the interfacial H-atom layers decreases. Thus, the atomic-level energy transfer dynamics from the hot surface to the cold surface is more complex than the exponential dynamics observed for overall heat transfer between the surfaces.

The biosynthesis of abietadiene is the first biosynthetically relevant process shown to involve a potential energy surface with a bifurcating reaction pathway. Herein, we use gas-phase, enzyme-free direct dynamics simulations to study the behavior of the key reaction (bifurcating) step, which is conversion of the C20 pimaradienyl cation to the abietadienyl cation. In a previous study (J. Am. Chem. Soc.2011, 133, 8335), a truncated C10 model was used to investigate this reaction. The current work finds that the complete C20 pimaradienyl cation gives reaction dynamics similar to that reported for the truncated C10 model. We find that in the absence of the enzyme, the C20 abietadienyl cation is generated in almost equal quantity (1.3:1) as an unobserved (in nature) seven-membered ring product. These simulations allude to a need for abietadiene synthase to steer the reaction to avoid generation of the seven-membered ring product. The methodology of post-transition state chemical dynamics simulations is also considered. The trajectories are initiated at the rate-controlling transition state (TS) separating the pimaradienyl and abietadienyl cations. Accurate results are expected for the short-time direct motion from this TS toward the abietadienyl cation. However, the dynamics may be less accurate for describing the unimolecular reactions that occur in moving toward the pimaradienyl cation, due to the unphysical flow of zero-point energy.

Direct dynamics simulations are a very useful and general approach for studying the atomistic properties of complex chemical systems, since an electronic structure theory representation of a system's potential energy surface is possible without the need for fitting an analytic potential energy function. In this paper, recently introduced compact finite difference (CFD) schemes for approximating the Hessian [J. Chem. Phys.2010, 133, 074101] are tested by employing the monodromy matrix equations of motion. Several systems, including carbon dioxide and benzene, are simulated, using both analytic potential energy surfaces and on-the-fly direct dynamics. The results show, depending on the molecular system, that electronic structure theory Hessian direct dynamics can be accelerated up to 2 orders of magnitude. The CFD approximation is found to be robust enough to deal with chaotic motion, concomitant with floppy and stiff mode dynamics, Fermi resonances, and other kinds of molecular couplings. Finally, the CFD approximations allow parametrical tuning of different CFD parameters to attain the best possible accuracy for different molecular systems. Thus, a direct dynamics simulation requiring the Hessian at every integration step may be replaced with an approximate Hessian updating by tuning the appropriate accuracy.

There are two components to the review presented here regarding simulations of collisions of protonated peptide ions peptide-H(+) with organic surfaces. One is a detailed description of the classical trajectory chemical dynamics simulation methodology. Different simulation approaches are used, and identified as MM, QM + MM, and QM/MM dependent on the potential energy surface used to represent the peptide-H(+) + surface collision. The second are representative examples of the information that may be obtained from the simulations regarding energy transfer and peptide-H(+) surface-induced dissociation, soft-landing, and reactive-landing for the peptide-H(+) + surface collisions. Good agreement with experiment is obtained for each of these four collision properties. The simulations provide atomistic interpretations of the peptide-H(+) + surface collision dynamics.

Direct chemical dynamics simulations, at collision energies Erel of 0.32 and 1.53 eV, were performed to obtain an atomistic understanding of the F(-) + CH3I reaction dynamics. There is only the F(-) + CH3I → CH3F + I(-) bimolecular nucleophilic substitution SN2 product channel at 0.32 eV. Increasing Erel to 1.53 eV opens the endothermic F(-) + CH3I → HF + CH2I(-) proton transfer reaction, which is less competitive than the SN2 reaction. The simulations reveal proton transfer occurs by two direct atomic-level mechanisms, rebound and stripping, and indirect mechanisms, involving formation of the F(-)···HCH2I complex and the roundabout. For the indirect trajectories all of the CH2I(-) is formed with zero-point energy (ZPE), while for the direct trajectories 50% form CH2I(-) without ZPE. Without a ZPE constraint for CH2I(-), the reaction cross sections for the rebound, stripping, and indirect mechanisms are 0.2 ± 0.1, 1.2 ± 0.4, and 0.7 ± 0.2 A(2), respectively. Discarding trajectories that do not form CH2I(-) with ZPE reduces the rebound and stripping cross sections to 0.1 ± 0.1 and 0.7 ± 0.5 A(2). The HF product is formed rotationally and vibrationally unexcited. The average value of J is 2.6 and with histogram binning n = 0. CH2I(-) is formed rotationally excited. The partitioning between CH2I(-) vibration and HF + CH2I(-) relative translation energy depends on the treatment of CH2I(-) ZPE. Without a CH2I(-) ZPE constraint the energy partitioning is primarily to relative translation with little CH2I(-) vibration. With a ZPE constraint, energy partitioning to CH2I(-) rotation, CH2I(-) vibration, and relative translation are statistically the same. The overall F(-) + CH3I rate constant at Erel of both 0.32 and 1.53 eV is in good agreement with experiment and negligibly affected by the treatment of CH2I(-) ZPE, since the SN2 reaction is the major contributor to the total reaction rate constant. The potential energy surface and reaction dynamics for F(-) + CH3I proton transfer are compared with those reported previously (J. Phys. Chem. A 2013, 117, 7162-7178) for the isoelectronic OH(-) + CH3I reaction.

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 used to study Bz + Na(+)(Bz) → Na(+)(Bz)2* association and the ensuing dissociation of the Na(+)(Bz)2* cluster (Bz = benzene). An interesting and unexpected reaction found from the simulations is direct displacement, for which the colliding Bz molecule displaces the Bz molecule attached to Na(+), forming Na(+)(Bz). The rate constant for Bz + Na(+)(Bz) association was calculated at 750 and 1000 K, and found to decrease with increase in temperature. By contrast, the direct displacement rate constant increases with temperature. The cross section and rate constant for direct displacement are approximately an order of magnitude lower than those for association. The Na(+)(Bz)2* cluster, formed by association, dissociates with a biexponential probability, with the rate constant for the short-time component approximately an order of magnitude larger than that for the longer time component. The latter rate constant agrees with that of Rice-Ramsperger-Kassel-Marcus (RRKM) theory, consistent with rapid intramolecular vibrational energy redistribution (IVR) and intrinsic RRKM dynamics for the Na(+)(Bz)2* cluster. A coupled phase space model was used to analyze the biexponential dissociation probability.

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.

Chemical dynamics simulations at collision energies of 3.0, 10.6, and 20.0 kcal/mol were performed to study energy transfer in perpendicular (θi = 0°) collisions of carbon dioxide with a perfluorinated octanethiol self-assembled monolayer (F-SAM) surface. An accurate carbon dioxide + F-SAM intermolecular potential was developed from ab initio calculations extrapolated to the complete basis set limit. Three types of collision events are observed in the trajectories: direct scattering, physisorption on the top of the surface, and penetration of the surface. Energy transfer to carbon dioxide rotation and the final translational energy of carbon dioxide are both analyzed for each of these trajectory types. Penetration leads to near complete thermal accommodation with the F-SAM, whereas accommodation is not reached for either the direct or physisorption trajectories. The distributions of the translational energy and rotational angular momentum, P(Ef) and P(J), of the scattered CO2 molecules and for the differ...

A direct dynamics simulation, at the MP2/6-31G* level of theory, was performed for the Cl − +CD 3 Cl S N 2 reaction. An ensemble of 88 trajectories was initiated at the [Cl– –CD 3 – –Cl] − central barrier, in accord with a 300 K Boltzmann distribution, and integrated in both the forward and reverse directions off the barrier. The dynamics of these trajectories are inconsistent with both RRKM theory and transition state theory (TST). Only 1% of the trajectories dissociate to Cl − +CD 3 Cl products in comparison to the RRKM prediction of greater than 50%. Also, in contrast to the assumption of TST and prediction of RRKM theory, recrossings of the central barrier are observed in the trajectories, giving rise to an upper limit of 0.7 for the correction factor to the 300 K TST rate constant. The results of this study are compared with a previous direct dynamics simulation, also at the MP2/6-31G* level of theory, of the central barrier dynamics for the Cl − +CH 3 Cl S N 2 reaction. Both reactions exhibit extensive non-RRKM dynamics. However, central barrier recrossings are more important for the Cl − +CH 3 Cl reaction and the upper limit to its TST correction factor is 0.2.

We have used molecular dynamics simulations to investigate the in situ self-assembly of modified hydrocarbon nanoparticles (mean diameter of 1.2 nm) at a water-trichloroethylene (TCE) interface. The nanoparticles were first distributed randomly in the water phase. The MD simulation shows the in situ formation of nanoparticle clusters and the migration of both single particles and clusters from the water phase to the trichloroethylene phase, possibly due to the hydrophobic nature of the nanoparticles. Eventually, the single nanoparticles or clusters equilibrate at the water-TCE interface, and the surrounding liquid molecules pack randomly when in contact with the nanoparticle surfaces. In addition, the simulations show that the water-TCE interfacial thickness analyzed from density profiles is influenced by the presence of nanoparticles either near or in contact with the interface but is independent of the number of nanoparticles present. The nanoparticles, water molecules, and TCE molecules all exhibit diffusion anisotropy.

The effects of temperature on energy transfer during collisions of protonated diglycine ions, Gly(2)-H(+), with a diamond {111} surface were investigated by chemical dynamics simulations. The simulations were performed for a collision energy of 70 eV and angle of 0 degrees with respect to the surface normal. In one set of simulations the initial surface temperature, T(surf), was varied from 300 to 2000 K, while the Gly(2)-H(+) vibrational and rotational temperatures were maintained at 300 K. For the second set of simulations the Gly(2)-H(+) vibrational temperature, T(vib), was varied from 300 to 2000 K, keeping both the Gly(2)-H(+) rotational and surface temperatures at 300 K. Increasing either the surface temperature or Gly(2)-H(+) vibrational temperature to values as high as 2000 K has, at most, only a negligible effect on the partitioning of the incident collision energy to the surface and to the vibrational and rotational modes of Gly(2)-H(+). To a good approximation, the initial surface and peptide ion energies are nearly adiabatic during the collisional energy transfer. This adiabaticity of the initial peptide ion energy agrees with experiments (J. Phys. Chem. A 2004, 108, 1). A more quantitative analysis of the effects of T(vib) and T(surf) shows there are small, but noticeable, effects on the energy transfer efficiencies. Namely, increasing the vibrational or surface temperature results in a near-linear decrease in the energy transfer to the degrees of freedom associated with this temperature.

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.

A molecular dynamics simulation was performed to study the effect of an applied force on heat transfer at the interface of model diamond [111] nanosurfaces. The force was applied to a small, hot nanosurface at 800, 1000, or 1200 K brought into contact with a larger, colder nanosurface at 300 K. The relaxation of the initial nonequilibrium interfacial force occurs on a subpicosecond time scale, much shorter than that required for heat transfer. Heat transfer occurs with exponential kinetics and a rate constant that increases linearly with the interfacial force according to 7 x 10(-4) ps(-1)/nN. This rate constant only increases by at most 10% as the temperature of the hot surface is increased from 800 to 1200 K. Replacing the interfacial H-atoms on both surfaces by D atoms also has a very small effect on the heat transfer. However, if one nanosurface has H atoms on its interface and the other nanosurface's interface has D atoms, then there is a marked 25% decrease in the rate constant for heat transfer. Increasing the size of the hot surface, and, thus, the interfacial contact area, increases the rate of heat transfer but not the rate constant. For the same interfacial force, different anharmonic models for the nanosurfaces' potential energy function give the same heat transfer rate constant. The possibility of quantum effects for heat transfer across the diamond interface is considered.

Quasiclassical, direct dynamics trajectories have been used to study the reaction of formaldehyde cation with molecular hydrogen, simulating the conditions in an experimental study of H2CO+ vibrational effects on this reaction. Effects of five different H2CO+ modes were probed, and we also examined different approaches to treating zero-point energy in quasiclassical trajectories. The calculated absolute cross-sections are in excellent agreement with experiments, and the results provide insight into the reaction mechanism, product scattering behavior, and energy disposal, and how they vary with impact parameter and reactant state. The reaction is sharply orientation-dependent, even at high collision energies, and both trajectories and experiment find that H2CO+ vibration inhibits reaction. On the other hand, the trajectories do not reproduce the anomalously strong effect of nu2(+) (the CO stretch). The origin of the discrepancy and approaches for minimizing such problems in quasiclassical trajectories are discussed.

The PM3 semiempirical electronic structure theory is reparametrized with specific reaction parameters (SRPs) to develop a potential energy surface (PES) for O(3P) processing of alkanes. The results of high-level ab initio calculations for the O(3P) + C2H6 primary reactions, yielding OH + C2H5, C2H5O + H, and CH3O + CH3, 11 ensuing secondary and unimolecular dissociation reactions involving products of these primary reactions, and additional reactions were used to develop two PM3-SRP models for the PES. The ab initio results used for this fitting were taken from previous multiconfiguration calculations and additional PMP2/cc-pVTZ calculations reported here. Even though these two PM3-SRP models are unable to quantitatively represent the many reactions that occur in high-energy collisions of O(3P) with alkanes, they are vast improvements over the PES of PM3 theory. These models are used in direct dynamics classical trajectory simulations of the O(3P) + C2H6 reaction at a 5 eV collision energy. The results of...

A MP2/6-31G* direct dynamics simulation is used to study the dynamics of the central barrier [Cl-C2H5-Cl]– for the Cl– + C2H5 SN2 reaction. The majority of the trajectories move off the central barrier to form the Cl––C2H5Cl complex and appear to undergo efficient IVR as assumed by RRKM theory. However, some of the trajectories move directly to products without forming the complex, a non-RRKM result. A hydrogen atom link-atom QM/MM model is described for studying the dynamics of [X-CH2R-Y]– central barriers with the -R substituent. The model is used to calculate vibrational frequencies for the [Cl-C2H5-Cl]– central barrier.Key words: SN2 reaction dynamics, RRKM theory, QM/MM model, central barrier dynamics, direct dynamics classical trajectories.