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We report here an extensive direct dynamics study on the collisions of hyperthermal (14.9 kcal mol–1) atomic oxygen with a variety of graphene surfaces to explore possible reaction channels. Severa...

Direct dynamics simulations with the M06/6-311++G(d,p) level of theory were performed to study the 3CH2 + 3O2 reaction at 1000 K temperature on the ground state singlet surface. The reaction is complex with formation of many different product channels in highly exothermic reactions. CO, CO2, H2O, OH, H2, O, H, and HCO are the products formed from the reaction. The total simulation rate constant for the reaction at 1000 K is (1.2 ± 0.3) × 10-12 cm3 molecule-1 s-1, while the simulation rate constant at 300 K is (0.96 ± 0.28) × 10-12 cm3 molecule-1 s-1. The simulated product yields show that CO is the dominant product and the CO:CO2 ratio is 5.3:1, in good comparison with the experimental ratio of 4.3:1 at 1000 K. On comparing the product yields for the 300 and 1000 K simulations, we observed that, except for CO and H2O, the yields of the other products at 1000 K are lower at 300 K, showing a negative temperature dependence.

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.

The dynamics of the HBr+ + CO2 → HOCO+ + Br reaction was recently investigated with guided ion beam experiments under various excitations (collision energy of the reactants, rotational and spin-orbital states of HBr+, etc.), and their impacts were probed through the change of the cross section of the reaction. The potential energy profile of this reaction has also been accurately characterized by high-level ab initio methods such as CCSD(T)/CBS, and the UMP2/cc-pVDZ/lanl08d has been identified as an ideal method to study its dynamics. This manuscript reports the first ab initio molecular dynamics simulations of this reaction at two different collision energies, 8.1 kcal/mol and 19.6 kcal/mol. The cross sections measured from the simulations agree very well with the experiments measured with HBr+ in the 2∏1/2 state. The simulations reveal three distinct mechanisms at both collision energies: direct rebound (DR), direct stripping (DS), and indirect (Ind) mechanisms. DS and Ind make up 97% of the total reaction. The dynamics of this reaction is also compared with nucleophilic substitution (SN2) reactions of X- + CH3Y → CH3X + Y- type. In summary, this research has revealed interesting dynamics of the HBr+ + CO2 → HOCO+ + Br reaction at different collision energies and has laid a solid foundation for using this reaction to probe the impact of rotational excitation of ion-molecule reactions in general.

Nonstatistical dynamics is important for many chemical reactions. The Rice-Ramsperger-Kassel-Marcus (RRKM) theory of unimolecular kinetics assumes a reactant molecule maintains a statistical microcanonical ensemble of vibrational states during its dissociation so that its unimolecular dynamics are time independent. Such dynamics results when the reactant's atomic motion is chaotic or irregular. Intrinsic non-RRKM dynamics occurs when part of the reactant's phase space consists of quasiperiodic/regular motion and a bottleneck exists, so that the unimolecular rate constant is time dependent. Nonrandom excitation of a molecule may result in short-time apparent non-RRKM dynamics. For rotational activation, the 2J + 1 K levels for a particular J may be highly mixed, making K an active degree of freedom, or K may be a good quantum number and an adiabatic degree of freedom. Nonstatistical dynamics is often important for bimolecular reactions and their intermediates and for product-energy partitioning of bimolecular and unimolecular reactions. Post–transition state dynamics is often highly complex and nonstatistical.

Quasi-classical direct dynamics simulations, performed with the B3LYP-D3/cc-pVDZ electronic structure theory, are reported for vibrational relaxation of the three NH stretches of the -NH3+ group of protonated tryptophan (TrpH+), excited to the n = 1 local mode states. The intramolecular vibrational energy relaxation (IVR) rates determined for these states, from the simulations, are in good agreement with the experiment. In accordance with the experiment, IVR for the free NH stretch is slowest, with faster IVR for the remaining two NH stretches which have intermolecular couplings with an O atom and a benzenoid ring. For the free NH and the NH coupled to the benzenoid ring, there are beats (i.e., recurrences) in their relaxations versus time. For the free NH stretch, 50% of the population remained in n = 1 when the trajectories were terminated at 0.4 ps. IVR for the free NH stretch is substantially slower than for the CH stretch in benzene. The agreement found in this study between quasi-classical direct dynamics simulations and experiments indicates the possible applicability of this simulation method to larger biological molecules. Because IVR can drive or inhibit reactions, calculations of IVR time scales are of interest, for example, in unimolecular reactions, mode-specific chemistry, and many photochemical processes.

The 3CH2 + 3O2 reaction has a quite complex ground state singlet potential energy surface (PES). There are multiple minima and transition states before forming the 10 possible reaction products. A ...

The traditional understanding is that the Hinshelwood-Lindemann mechanism for thermal unimolecular reactions, and the resulting unimolecular rate constant versus temperature and collision frequency ω (i.e., pressure), requires the Rice-Ramsperger-Kassel-Marcus (RRKM) rate constant k(E) to represent the unimolecular reaction of the excited molecule versus energy. RRKM theory assumes an exponential N(t)/N(0) population for the excited molecule versus time, with decay given by RRKM microcanonical k(E), and agreement between experimental and Hinshelwood-Lindemann thermal kinetics is then deemed to identify the unimolecular reactant as a RRKM molecule. However, recent calculations of the Hinshelwood-Lindemann rate constant kuni(ω,E) has brought this assumption into question. It was found that a biexponential N(t)/N(0), for intrinsic non-RRKM dynamics, gives a Hinshelwood-Lindemann kuni(ω,E) curve very similar to that of RRKM theory, which assumes exponential dynamics. The RRKM kuni(ω,E) curve was brought into agreement with the biexponential kuni(ω,E) by multiplying ω in the RRKM expression for kuni(ω,E) by an energy transfer efficiency factor βc. Such scaling is often done in fitting Hinshelwood-Lindemann-RRKM thermal kinetics to experiment. This agreement between the RRKM and non-RRKM curves for kuni(ω,E) was only obtained previously by scaling and fitting. In the work presented here, it is shown that if ω in the RRKM kuni(ω,E) is scaled by a βc factor there is analytic agreement with the non-RRKM kuni(ω,E). The expression for the value of βc is derived.

The potential energy curves (PECs) for the interaction of 3CH2 with 3O2 in singlet and triplet potential energy surfaces (PESs) leading to singlet and triplet Criegee intermediates (CH2OO) are studied using electronic structure calculations. The bonding mechanism is interpreted by analyzing the ground state multireference configuration interaction (MRCI) wave function of the reacting species and at all points along the PES. The interaction of 3CH2 with 3O2 on the singlet surface leads to a flat long-range attractive PEC lacking any maxima or minima along the curve. The triplet surface stems into a maximum along the curve resulting in a transition state with an energy barrier of 5.3 kcal/mol at CASSCF(4,4)/cc-pVTZ level. The resulting 3CH2OO is less stable than the 1CH2OO. In this study, the biradical character (β) is used as a measure to understand the difference in the topology of the singlet and triplet PECs and the relation of the biradical nature of the species with their structures. The 3CH2OO has a larger biradical character than 1CH2OO, and because of the larger bond order of 1CH2OO, the C-O covalent bond becomes harder to break, thereby stabilizing 1CH2OO. Thus, this study provides insights into the shape of the PEC obtained from the reaction between 3CH2 and 3O2 in terms of their bonding nature and from the shape of the curves, the temperature dependence or independence of the rate of the reaction is discussed.

In a previous work [ Lakshmanan , S. ; J. Phys. Chem. A 2018 , 122 , 4808 - 4818 ], direct dynamics simulations at the M06/6-311++G(d,p) level of theory were reported for 3CH2 (X3B1) + 3O2 (X3∑g-) reaction on its ground-state singlet potential energy surface (PES) at 300 K. However, further analyses revealed the simulations are unstable for the 3CH2 (X3B1) + 3O2 (X3∑g-) reactants on the ground-state singlet surface and the trajectories reverted to an excited-state singlet surface for the 1CH2 (a1A1) + 1O2 (b1∑g+) reactants. Thus, the dynamics reported previously are for this excited-state singlet PES. The PESs for the 3CH2 (X3B1) + 3O2 (X3∑g-) and 1CH2 (a1A1) + 1O2 (b1∑g+) reactants are quite similar, and this provided a means to perform simulations for the 3CH2 (X3B1) + 3O2 (X3∑g-) reactants on the ground-state singlet PES at 300 K, which are reported here. The reaction dynamics are quite complex with seven different reaction pathways and nine different products. A consistent set of product yields have not been determined experimentally, but the simulation yields for the H atom, CO, and CO2 are somewhat lower, higher, and lower respectively, than the recommended values. The yields for the remaining six products agree with experimental values. Product decomposition was included in determining the product yields. The simulation 3CH2 + 3O2 rate constant at 300 K is only 3.4 times smaller than the recommended value, which may be accommodated if the 3CH2 + 3O2 → 1CH2O2 potential energy curve is only 0.75 kcal/mol more attractive at the variational transition state for 3CH2 + 3O2 → 1CH2O2 association. The simulation kinetics and dynamics for the 3CH2 + 3O2 and 1CH2 + 1O2 reactions are quite similar. Their rate constants are statistically the same, an expected result, since their transition states leading to products have energies lower than that of the reactants and the attractive potential energy curves for 3CH2 + 3O2 → 1CH2O2 and 1CH2 + 1O2 → 1CH2O2 are nearly identical. The product yields for the 3CH2 + 3O2 and 1CH2 + 1O2 reactions are also nearly identical, only differing for the CO2 yield. The reaction dynamics on both surfaces are predominantly direct, with negligible trapping in potential energy minima, which may be an important contributor to their nearly identical product yields.

In previous research, direct dynamics simulations have been used to provide atomistic information for the Cl− + CH3I, F− + CH3I, and OH− + CH3I SN2 and proton transfer (PT) reactions. An important component of these simulations is comparison with molecular beam, ion imaging experiments. From the simulations, comparisons may be made with the product translational energy distributions determined from the experiments and the simulations give quite good agreement with these distributions. Though the experiments provide the in-plane angular distribution for a reaction’s product translational energy distribution, the number of direct dynamics trajectories for a simulation is not sufficient to compare with this angular distribution. In the work presented here, the average percentage product translational energy partitioning for forward scattered events with scattering angle θ = 0–90° and for backward scattered events with θ = 90–180° are compared for the experiments and simulations. Overall good agreement is found, with a maximum difference as high as 5–10%. Additional atomistic details, regarding the dynamics of these reactions, are provided by scatter plots of their product relative translational energy versus the scattering angle θ.

Collisional energy transfer of highly vibrationally excited propylbenzene cation in a N2 bath has been studied with chemical dynamics simulations. In this work, an intermolecular potential of propylbenzene cation interacting with N2 was developed from SCS-MP2/6-311++G** ab initio calculations. Using a particle swarm optimization algorithm, the ab initio results were simultaneously fit to a sum of three two-body potentials, consisting of Ca–N, Cb–N, and H–N, where Ca is carbon on the benzene ring and Cb is carbon on the propyl side chain. Using the developed intermolecular potential, classical trajectory calculations were performed with a 100.1 kcal/mol excitation energy at 473 K to compare with experiment. Varying the density of the N2 bath, the single collision limit of propylbenzene cation with the N2 bath was obtained at a density of 20 kg/m3 (28 atm). For the experimental excitation energy and in the single collision limit, the average energy transferred per collision, ⟨ΔEc⟩, is 1.04 ± 0.04 kcal/mol a...

Following work by Slater and Bunker, the unimolecular rate constant versus collision frequency, kuni(ω,E), is expressed as a convolution of unimolecular lifetime and collisional deactivation probabilities. This allows incorporation of nonexponential, intrinsically non-RRKM, populations of dissociating molecules versus time, N(t)/N(0), in the expression for kuni(ω,E). Previous work using this approach is reviewed. In the work presented here, the biexponential f1 exp(−k1t) + f2 exp(−k2t) is used to represent N(t)/N(0), where f1k1 + f2k2 equals the RRKM rate constant k(E) and f1 + f2 = 1. With these two constraints, there are two adjustable parameters in the biexponential N(t)/N(0) to represent intrinsic non-RRKM dynamics. The rate constant k1 is larger than k(E) and k2 is smaller. This biexponential gives kuni(ω,E) rate constants that are lower than the RRKM prediction, except at the high and low pressure limits. The deviation from the RRKM prediction increases as f1 is made smaller and k1 made larger. Of c...

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.

To address the possible role of pyrene dimers in soot, chemical dynamics simulations are reported to provide atomistic details for the process of collisional association of pyrene dimers and ensuing decomposition of pyrene dimers. The simulations are performed at 600, 900, 1200, 1600, and 2000 K temperatures (T) with different collisional impact parameters (b; 0-18 A) using the all-atom optimized potentials for liquid simulations intermolecular force field. Corresponding to each b, ensembles of 1000 trajectories are computed up to a maximum time of 110 ps at each T. Microcanonical association rate constants for the pyrene-dimerization processes decrease with an increase in T. The ensuing dissociation of the pyrene dimers is statistical and could be well represented by the Rice-Ramsperger-Kassel-Marcus theory of unimolecular dissociation. Fits of the dissociation rate constants versus the harmonic Rice-Ramsperger-Kassel equation revealed that partial energy randomization occurs among the inter- and intramolecular vibrational modes during the dissociation of pyrene dimers, whereas rotational and translational modes play a significant role. Based on the low probability of association and short lifetime at 1600 (∼13.3 ps) and 2000 (∼12.8 ps) K, it is concluded that pyrene dimers are unlikely to play any major role in soot nucleation processes.

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.

Direct chemical dynamics simulations at high temperatures of reaction between 3O2 and graphene containing varied number of defects were performed using the VENUS-MOPAC code. Graphene was modeled using (5a,6z)-periacene, a poly aromatic hydrocarbon with 5 and 6 benzene rings in the armchair and zigzag directions, respectively. Up to six defects were introduced by removing carbon atoms from the basal plane. Usage of the PM7/unrestricted Hartree–Fock (UHF) method, for the simulations, was validated by benchmarking singlet-triplet gaps of n-acenes and (5a,nz) periacenes with high-level theoretical calculations. PM7/UHF calculations showed that graphene with different number of vacancies has different ground electronic states. Dynamics simulations were performed for two 3O2 collision energies Ei of 0.4 and 0.7 eV, with the incident angle normal to the graphene plane at 1375 K. Collisions on graphene with one, two, three, and four vacancies (1C-, 2C-, 3C-, and 4C-vacant graphene) showed no reactive trajectories...

Monte Carlo sampling calculations were performed to determine the anharmonic sum of states, Nanh(E), for I–(H2O), (H2O)2, and I–(H2O)2 versus internal energy up to their dissociation energies. The anharmonic density of states, ρanh(E), is found from the energy derivative of Nanh(E). Analytic potential energy functions are used for the calculations, consisting of TIP4P for H2O···H2O interactions and an accurate two-body potential for the I–···H2O fit to quantum chemical calculations. The extensive Monte Carlo samplings are computationally demanding, and the use of computationally efficient potentials was essential for the calculations. Particular emphasis is directed toward I–(H2O)2, and distributions of its structures versus internal energy are consistent with experimental studies of the temperature-dependent vibrational spectra. At their dissociation thresholds, the anharmonic to harmonic density of states ratio, ρanh(E)/ρh(E), is ∼2, ∼ 3, and ∼260 for I–(H2O), (H2O)2, and I–(H2O)2, respectively. The lar...

Energy transfer in collisions of O2 with a graphite surface was studied by chemical dynamics simulations. The simulations were performed for three collision energies Ei of 2.1, 7.4, and 15 kcal/mol, with the initial incident angle fixed at θi = 45°. Simulations were performed for each Ei at a surface temperature Tsurf = 300 K. For the higher surface temperature of 1177 K, a simulation was only performed for Ei = 15 kcal/mol. The following properties were determined and analyzed for the O2 + graphite collisions: (1) translational energy distributions of the scattered O2; (2) distribution of the final polar and azimuthal angle for the scattered O2; and (3) number of bounces of O2 on the surface before scattering. The average energy transferred to the graphite surface and that remaining in O2 translation, i.e., ⟨ΔEsurf⟩ and ⟨Ef⟩, exhibit a linear dependence with the initial translational energy. For the O2 + graphite scattering, the physisorption/desorption residence time distribution decays exponentially, w...

Direct dynamics simulations were performed to investigate unimolecular dynamics of the F − ⋯HCH 2 I pre-reaction complex for the F − + CH 3 I S N 2 reaction. The simulations were performed for a total energy commensurate with the 0.32 eV collision energy considered in previous experiments and simulations of this reaction. Two excitation patterns of the complex were considered for the simulations: one with the excitation energy primarily in vibration and the other with the energy primarily in rotation. For the latter equal amounts of energy were added about the three external rotation axes of the complex, giving rise to J and K rotation quantum numbers of 357 and 66 for the initial excitation. For the vibrational excitation the unimolecular dynamics agrees with RRKM theory and dissociation of the complex to the F − + CH 3 I reactants is negligible, since the barrier for this reaction is 20.2 kcal/mol in contrast to the 2.4 kcal/mol barrier for accessing the S N 2 transition state (TS). The unimolecular dynamics are much different for the rotational excitation simulation. They are non-RRKM and the instantaneous unimolecular rate constant for F − ⋯HCH 2 I decomposition increases with time. Apparently, this arises from K -mixing and vibration/rotation energy redistribution. At the end of the 10 ps simulation, the instantaneous simulation rate constant for accessing the S N 2 transition state is an order of magnitude smaller than the harmonic RRKM rate constant with the K quantum number treated as an active degree of freedom, indicating that K -mixing and vibration/rotation energy redistribution are not complete on this time scale. For rotational excitation, dissociation to the F − + CH 3 I reactants is the dominant unimolecular pathway, instead of forming the S N 2 products. This is a result of a much higher rotational barrier at the S N 2 TS than for the TS leading to F − + CH 3 I.

The reaction of 3CH2 with 3O2 is of fundamental importance in combustion, and the reaction is complex as a result of multiple extremely exothermic product channels. In the present study, direct dynamics simulations were performed to study the reaction on both the singlet and triplet potential energy surfaces (PESs). The simulations were performed at the UM06/6-311++G(d,p) level of theory. Trajectories were calculated at a temperature of 300 K, and all reactive trajectories proceeded through the carbonyl oxide Criegee intermediate, CH2OO, on both the singlet and triplet PESs. The triplet surface leads to only one product channel, H2CO + O(3P), while the singlet surface leads to eight product channels with their relative importance as CO + H2O > CO + OH + H ∼ H2CO + O(1D) > HCO + OH ∼ CO2 + H2 ∼ CO + H2 + O(1D) > CO2 + H + H > HCO + O(1D) + H. The reaction on the singlet PES is barrierless, consistent with experiment, and the total rate constant on the singlet surface is (0.93 ± 0.22) × 10–12 cm3 molecule–1...

International audience; Dissociation chemistry of the diproline anion [Pro2-H]− is studied using chemical dynamics simulations coupled with quantum-chemical calculations and RRKM analysis. Pro2– is chosen due to its reduced size and the small number of sites where deprotonation can take place. The mechanisms leading to the two dominant collision-induced dissociation (CID) product ions are elucidated. Trajectories from a variety of isomers of [Pro2-H]− were followed in order to sample a larger range of possible reactivity. While different mechanisms yielding y1– product ions are proposed, there is only one mechanism yielding the b2– ion. This mechanism leads to formation of a b2– fragment with a diketopiperazine structure. The sole formation of a diketopiperazine b2 sequence ion is experimentally confirmed by infrared ion spectroscopy of the fragment anion. Furthermore, collisional and internal energy activation simulations are used in parallel to identify the different dynamical aspects of the observed reactivity.

In this work a particle swarm optimization (PSO) algorithm was used to fit an analytic potential energy function to I–(H2O) intermolecular potential energy curves calculated with DFT/B97-1 theory. The analytic function is a sum of two-body terms, each written as a generalized sum of Buckingham and Lennard-Jones terms with only six parameters. Two models were used to describe the two-body terms between I– and H2O: a three-site model H2O and a four-site model including a ghost atom. The fits are compared with those obtained with a genetic/nonlinear least-squares algorithm. The ghost atom model significantly improves the fitting accuracy for both algorithms. The PSO fits are significantly more accurate and much less time-consuming than those obtained with the genetic/nonlinear least-squares algorithm. Eight I–---H2O potential energy curves, fit with the PSO algorithm for the three- and four-site models, have RMSE of 1.37 and 0.22 kcal/mol and compute times of ∼20 and ∼68 min, respectively. The PSO fit for th...

A chemical dynamics simulation was performed to study low energy collisions between N2 and a graphite surface. The simulations were performed as a function of collision energy (6.34 and 14.41 kcal/mol), incident polar angle (20–70°) and random azimuthal angle. The following properties were determined and analyzed for the N2 + graphite collisions: (1) translational and rotational energy distributions of the scattered N2; (2) distribution of the final polar angle for the scattered N2; (3) number of bounces of N2 on the surface before scattering. Direct scattering with only a single bounce is dominant for all incident angles. Scattering with multiple collisions with the surface becomes important for incident angles far from the surface normal. For trajectories that desorb, the parallel component of the N2 incident energy is conserved due to the extremely short residence times of N2 on the surface. For scattering with an incident energy of 6.34 kcal/mol, incident polar angle of 40°, and final polar angle of 5...

The rate constant for OH − (H 2 O) 2 + CH 3 I reaction was determined by selected ion flow tube (SIFT) experiments for temperatures in the range of 298–398 K. It is found to be an order of magnitude smaller than the collision capture rate constant, a result substantially different than found previously for the OH − + CH 3 I and OH − (H 2 O) + CH 3 I reactions. The rate constants for these reactions are only ∼25% and ∼two times smaller, respectively, than their collision capture rate constants. Only two product ions are observed experimentally, i.e. I − and I − (H 2 O), and their respective percentage yields are 90:10 and 83:17 at 298 and 348 K. The kinetics for the OH − (H 2 O) 2 + CH 3 I reaction were also studied by direct dynamics simulations using the DFT/B97-1/ECP/d electronic structure theory, the same theory used in previous direct dynamics simulations of the OH − + CH 3 I and OH − (H 2 O) + CH 3 I reactions. Simulations for OH − (H 2 O) 2 + CH 3 I at 387 K give respective percentage yields of 91:9 for I − and I − (H 2 O), in good agreement with the experimental results. For both the experiments and simulations, the microsolvated ion I − (H 2 O) 2 is not formed and the formation of I − dominates I − (H 2 O). For the OH − + CH 3 I and OH − (H 2 O) + CH 3 I reactions the experimental and direct dynamics simulation rate constants agree. However, this is not the case for OH − (H 2 O) 2 + CH 3 I, for which the simulation rate constant is 8–9 times larger than the experimental value. Comparisons of the experimental, simulation, and collision capture rate constants for the OH − (H 2 O) 2 + CH 3 I reaction indicate the height of the submerged S N 2 barrier for the reaction is an important feature of its potential energy surface. The actual barrier is expected to be higher than the value given by the DFT/B97-1 calculations. In future work it will be important to perform higher level electronic structure calculations and establish an accurate value for this barrier. Preliminary calculations reported here indicate the barrier height is sensitive to the electronic structure method.

Chemical dynamics simulations were performed to study collisional intermolecular energy transfer from a thermalized N2 bath at 300 K to vibrationally “cold” C6F6. The vibrational temperature of C6F6 is taken as 50 K, which corresponds to a classical vibrational energy of 2.98 kcal/mol. The temperature ratio between C6F6 and the bath is 1/6, the reciprocal of the same ratio for previous “hot” C6F6 simulations (J. Chem. Phys. 2014, 140, 194103). Simulations were also done for a C6F6 vibrational temperature of 0 K. The average energy of C6F6 versus time is well fit by a biexponential function which gives a slightly larger short time rate component, k1, but a four times smaller long time rate component, k2, compared to those obtained from the “hot” C6F6 simulations. The average energy transferred per collision depends on the difference between the average energy of C6F6 and the final C6F6 energy after equilibration with the bath, but not on the temperature ratio of C6F6 and the bath. The translational and rot...

Influences of solvent molecules on SN2 reaction dynamics of microsolvated F–(H2O)n with CH3I, for n = 0–3, are uncovered by direct chemical dynamics simulations. The direct substitution mechanism, which is important without microsolvation, is quenched dramatically upon increasing hydration. The water molecules tend to force reactive encounters to proceed through the prereaction collision complex leading to indirect reaction. In contrast to F–(H2O), reaction with higher hydrated ions shows a strong propensity for ion desolvation in the entrance channel, diminishing steric hindrance for nucleophilic attack. Thus, nucleophilic substitution avoids the potential energy barrier with all of the solvent molecules intact and instead occurs through the less solvated barrier, which is energetically unexpected because the former barrier has a lower energy. The work presented here reveals a trade-off between reaction energetics and steric effects, with the latter found to be crucial in understanding how hydration infl...

Abnormalities in zinc metabolism have been linked to many diseases, including different kinds of cancers and neurological diseases. The present study investigates the fragmentation pathways of a zinc chaperon using a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analog methanobactin peptide-5, amb5). DFT/M05-2X and B3LYP geometry optimizations of [amb5-3H+Zn(II)]- predicted three lowest energy conformers with different chelating motifs. Direct dynamics simulations, using the PM7 semiempirical electronic structure method, were performed for these conformers, labeled a, b, and c, to obtain their fragmentation pathways at different temperatures in the range 1600-2250 K. The simulation results were compared with negative ion mode mass spectrometry experiments. For conformer a, the number of primary dissociation pathways are 11, 14, 24, 70, and 71 at 1600, 1750, 1875, 2000, and 2250 K, respectively. However, there are only 6, 10, 13, 14, and 19 pathways corresponding to these temperatures that have a probability of 2% or more. For conformer b, there are 67 pathways at 2000 K and 71 pathways at 2250 K. For conformer c, 17 pathways were observed at 2000 K. For conformer a, for two of the most common pathways involving C-C bond dissociation, Arrhenius parameters were calculated. The frequency factors and activation energies are smaller than those for C-C homolytic dissociation in alkanes due to increased stability of the product ions as a result of hydrogen bonding. The activation energies agree with the PM7 barriers for the C-C dissociations. Comparison of the simulation and experimental fragmentation ion yields shows the simulations predict double or triple cleavages of the backbone with Zn(II) retaining its binding sites, whereas the experiment exhibits single cleavages of the backbone accompanied by cleavage of two of the Zn(II) binding sites, resulting in b- and y-type ions.

Low-energy collision-induced dissociation (CID) of deprotonated l-cysteine S-sulfate, [cysS-SO 3 ] - , delivered in the gas phase by electrospray ionization, has been found to provide a means to form deprotonated l-cysteine sulfenic acid, which is a fleeting intermediate in biological media. The reaction mechanism underlying this process is the focus of the present contribution. At the same time, other novel species are formed, which were not observed in previous experiments. To understand fragmentation pathways of [cysS-SO 3 ] - , reactive chemical dynamics simulations coupled with a novel algorithm for automatic determination of intermediates and transition states were performed. This approach has allowed the identification of the mechanisms involved and explained the experimental fragmentation pathways. Chemical dynamics simulations have shown that a roaming-like mechanism can be at the origin of l-cysteine sulfenic acid.

A recent guided ion beam study of the HCl + HCl+ reaction has revealed two different products [Phys. Chem. Chem. Phys. 2015, 17 (25), 16454–16461]. The first is the proton transfer product, H2Cl+ + Cl, where the cross section of the reactions associated with this product, as predicted, monotonically decreases as the collision energy between the product increases. The second is the product HCl+ + HCl, where the cross section of the reaction shows a local maximum at the collision energy of 0.5 eV. The nature of this unusual behavior of the cross section is not clear. In this manuscript, state of the art ab initio molecular dynamics (AIMD) simulation is performed to study this bimolecular collision of HCl+ + HCl. The potential energy of profile of this system is first characterized with high-level ab initio methods, and then a computationally efficient method is selected for AIMD simulation. The cross sections from AIMD agree well with those from the experiments for both products. The AIMD trajectories reveal the complexity of this seemingly-simple reaction – a total of five different pathways that result in the aforementioned two products. The simulation also sheds light on the mystery of the local maximum of the cross section regarding the HCl+ + HCl product.

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.

Anti-E2, syn-E2, inv-, and ret-SN2 reaction channels for the gas-phase reaction of F– + CH3CH2I were characterized with a variety of electronic structure calculations. Geometrical analysis confirmed synchronous E2-type transition states for the elimination of the current reaction, instead of nonconcerted processes through E1cb-like and E1-like mechanisms. Importantly, the controversy concerning the reactant complex for anti-E2 and inv-SN2 paths has been clarified in the present work. A positive barrier of +19.2 kcal/mol for ret-SN2 shows the least feasibility to occur at room temperature. Negative activation energies (−16.9, −16.0, and −4.9 kcal/mol, respectively) for inv-SN2, anti-E2, and syn-E2 indicate that inv-SN2 and anti-E2 mechanisms significantly prevail over the eclipsed elimination. Varying the leaving group for a series of reactions F– + CH3CH2Y (Y = F, Cl, Br, and I) leads to monotonically decreasing barriers, which relates to the gradually looser TS structures following the order F > Cl > Br ...

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.

Classical chemical dynamics simulation results are presented for the thermal desorption kinetics and energetics of protonated dialanine ions (ala2-H+) physisorbed on/in a perfluorinated self-assembled monolayer (F-SAM) surface. Previously developed analytic potentials were used for the F-SAM and the ala2-H+/F-SAM intermolecular interaction, and the AMBER valence force field was used for ala2-H+. The activation energy, Ea = 13.2 kcal/mol, determined from the simulations is consistent with previous simulations of the ala2-H+/F-SAM binding energy. The A-factor, 7.8 × 1011 s–1, is about an order of magnitude lower than those representative of small molecule desorption from metal and semiconductor surfaces. This finding is consistent with the decreased entropies of ala2-H+ and the F-SAM upon desorption. Using the Arrhenius parameters for ala2-H+ desorption from the F-SAM, the lifetime of ala2-H+ adsorbed on the F-SAM at 300 K is 5 × 10–3 s. Larger peptide ions are expected to have longer adsorption lifetimes.

A zero-point energy (ZPE) constraint model is proposed for classical trajectory simulations of unimolecular decomposition and applied to CH4* → H + CH3 decomposition. With this model trajectories are not allowed to dissociate unless they have ZPE in the CH3 product. If not, they are returned to the CH4* region of phase space and, if necessary, given additional opportunities to dissociate with ZPE. The lifetime for dissociation of an individual trajectory is the time it takes to dissociate with ZPE in CH3, including multiple possible returns to CH4*. With this ZPE constraint the dissociation of CH4* is exponential in time as expected for intrinsic RRKM dynamics and the resulting rate constant is in good agreement with the harmonic quantum value of RRKM theory. In contrast, a model that discards trajectories without ZPE in the reaction products gives a CH4* → H + CH3 rate constant that agrees with the classical and not quantum RRKM value. The rate constant for the purely classical simulation indicates that anharmonicity may be important and the rate constant from the ZPE constrained classical trajectory simulation may not represent the complete anharmonicity of the RRKM quantum dynamics. The ZPE constraint model proposed here is compared with previous models for restricting ZPE flow in intramolecular dynamics, and connecting product and reactant/product quantum energy levels in chemical dynamics simulations.

Experimental and simulation studies of the OH – (H2O) + CH3I reaction give temperature dependent rate constants which are in excellent agreement. Though there are statistical uncertainties, there is an apparent small decrease in the rate constant as the temperature is increased from − 60 to 125 ℃, and for this temperature range the rate constant is ∼ 1.6 times smaller than that for the unsolvated reactants OH – + CH3I. Previous work [J. Phys. Chem. A 117 (2013) 14019] for the unsolvated reaction found that the S N 2 and proton transfer pathways, forming CH3OH + I – and CH2I – + H2O, have nearly equal probabilities. However, for the microsolvated OH – (H2O) + CH3I reaction the S N 2 pathways dominate. An important contributor to this effect is the stronger binding of H2O to the OH – reactant than to the proton transfer product CH2I – , increasing the barrier for the proton transfer pathway. The effect of microsolvation on the rate constant for the OH – (H2O)0,1 + CH3I reactions agrees with previous experimental studies for X – (H2O)0,1 + CH3Y reactions. The simulations show that there are important non-statistical attributes to the entrance- and exit-channel dynamics for the OH – (H2O) + CH3I reaction.

Classical chemical dynamics simulations were performed to study the intramolecular and unimolecular dissociation dynamics of the benzene dimer, Bz2 → 2 Bz. The dissociation of microcanonical ensembles of Bz2 vibrational states, at energies E corresponding to temperatures T of 700-1500 K, were simulated. For the large Bz2 energies and large number of Bz2 vibrational degrees of freedom, s, the classical microcanonical (RRKM) and canonical (TST) rate constant expressions become identical. The dissociation rate constant for each T is determined from the initial rate dN(t)/dt of Bz2 dissociation, and the k(T) are well-represented by the Arrhenius eq k(T) = A exp(-E(a)/RT). The E(a) of 2.02 kcal/mol agrees well with the Bz2 dissociation energy of 2.32 kcal/mol, and the A-factor of 2.43 × 10(12) s(-1) is of the expected order-of-magnitude. The form of N(t) is nonexponential, resulting from weak coupling between the Bz2 intramolecular and intermolecular modes. With this weak coupling, large Bz2 vibrational excitation, and low Bz2 dissociation energy, most of the trajectories dissociate directly. Simulations, with only the Bz2 intramolecular modes excited at 1000 K, were also performed to study intramolecular vibrational energy redistribution (IVR) between the intramolecular and intermolecular modes. Because of restricted IVR, the initial dissociation is quite slow, but N(t) ultimately becomes exponential, suggesting an IVR time of 20.7 ps.

Relaxation of vibrationally excited C6F6* in a thermalized bath of N2 molecules is studied by condensed-phase chemical dynamics simulations. The average energy of C6F6 as a function of time, ⟨E(t)⟩, was determined using two different models for the N2–C6F6 intermolecular potential, and both gave statistically the same result. A simulation with a N2 bath density of 20 kg/m3 was performed to check the convergence and validate the results obtained previously with a higher bath density of 40 kg/m3. The initial ensemble of C6F6 is nearly monoenergetically excited, but the ensemble acquires as energy distribution P(E) as it is collisionally relaxed. An evaluation of P(E) and the root-mean-square deviation ⟨ΔE2⟩1/2 of P(E), versus time, shows that P(E) first broadens and then narrows. Simulations with the C6F6 vibrational excitation energy of 85.8 kcal/mol, studied experimentally, show that the width of P(E) does not affect the average collisional deactivation rate. The role of the intramolecular vibrational fre...

For some gas-phase X − + CH 3 Y → XCH 3 + Y − S N 2 nucleophilic substitution reactions a pre-reaction complex is formed in which the attacking anion binds to a H-atom to form X − ⋯HCH 2 Y. In this work properties of this complex are investigated, for the OH − + CH 3 I and F − + CH 3 I reactions, to determine whether the HO − ⋯HCH 2 I and F − ⋯HCH 2 I complexes should be considered hydrogen-bonded complexes. Properties considered for these complexes are their structures, vibrational frequencies, well depths, and partial atomic charges. Also considered is the role of the HO − ⋯HCH 2 I complex in proton transfer for both the proton transfer and S N 2 reaction pathways. The results of these analyses indicate that these X − ⋯HCH 2 Y complexes are hydrogen bonding complexes.

The potential energy surface (PES) of the F − + CH 3 I → FCH 3 + I − S N 2 nucleophilic substitution reaction has been studied previously using MP2 and DFT levels of theory ( J. Phys. Chem. A 2010, 114 , 9635–9643). This work indicated that DFT gives a better representation of the PES which has only an hydrogen-bonded entrance channel reaction path, with a hydrogen-bonded transition state [F··HCH 2 ··I] − connecting the hydrogen-bonded pre-reaction complex F − ⋯HCH 2 I and C 3v post-reaction complex FCH 3 ⋯I − . For the work presented here, CCSD(T) with three different basis set and two effective core potentials (i.e. PP/d, PP/t and ECP/d) was employed to investigate stationary point properties for this reaction. Besides the hydrogen-bonded entrance channel stationary points, CCSD(T) also predicts a traditional C 3v transition state [F··CH 3 ··I] − connecting a C 3v pre-reaction complex F − ⋯CH 3 I with the C 3v post-reaction complex FCH 3 ⋯I − . Though CCSD(T) gives a CH 3 F⋯I − binding energy and CH 3 F and CH 3 I geometries in almost exact agreement with experiment, it gives a heat of reaction ∼20 kJ/mol less exothermic than experiment. The MP2 PES for this reaction, determined in the previous study, is very similar to the CCSD(T), but obtained with a much smaller computational cost. Direct dynamics simulations for the F − + CH 3 I → FCH 3 + I − reaction are feasible with MP2.

International audience; In the present work, we investigated the reaction dynamics that will possibly lead to the formation of protonated glycine by an ion–molecule collision. In particular, two analogous reactions were studied: NH3OH+ + CH3COOH and NH2OH2+ + CH3COOH that were suggested by previous experiments to be able to form protonated glycine loosing a neutral water molecule. Chemical dynamics simulations show that both reactants can form a molecule with the mass of the protonated glycine but with different structures, if some translational energy is given to the system. The reaction mechanisms for the most relevant product isomers are discussed as well as the role of collision energy in determining reaction products. Finally, in comparing collision dynamics at room and at very low initial internal temperature of the reactants, the same behavior was obtained for forming the protonated glycine isomers products. This supports the use of standard gas phase ion-chemistry setups to study collision-induced reactivity as a model for astrophysical cold conditions, when some relative translation energy is given to the system.

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.

Intermolecular energy transfer for the vibrationally excited propylbenzene cation (C9H12+) in a helium bath was studied with chemical dynamics simulations. The bond energy bond order relationship and electronic structure calculations were used to develop an intramolecular potential for C9H12+. Spin component scaled MP2/6-311++G** calculations were used to develop an intermolecular potential for He + C9H12+. The He + He intermolecular potential was determined from a previous explicitly correlated Gaussian electronic structure calculation. For the simulations, C9H12+ was prepared with a 100.1 kcal/mol excitation energy to compare with experiment. The average energy transfer from C9H12+, ⟨ΔEc⟩, decreased as C9H12+ was vibrationally relaxed and for the initial excitation energy ⟨ΔEc⟩ = 0.64 kcal/mol. This result agrees well with the experimental ⟨ΔEc⟩ value of 0.51 ± 0.26 kcal/mol for collisions of He with the ethylbenzene cation. The ⟨ΔEc⟩ value found for He + C9H12+ collisions is compared with reported values of ⟨ΔEc⟩ for He colliding with other molecules.

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.