Search

Quantum chemical calculations and dynamics simulations were performed to study the reaction between methyl peroxy radical (CH 3 O 2 ) and O 2 . The reaction proceeds through three different pathways (1) H-atom abstraction, (2) O 2 addition and (3) concerted H-atom shift and O 2 addition reactions. The concerted H-atom shift and O 2 addition pathway is the most favourable reaction both kinetically and thermodynamically. The major product channel formed from these reactions is H 2 CO + OH + O 2 . Trajectory calculations also confirm that H 2 CO + OH + O 2 is the main product channel. An estimated rate constant expression for this reaction from master equation calculations is 4.20 × 10 13 e -8676/T cm 3 mole -1 s -1 .

Chemical dynamics simulations have been performed to study the energy transfer from a hot N 2 bath at 1000 K to CH 4 fuel at 300 K at different bath densities ranging from 1000 kg m -3 to 30 kg m -3 . At higher bath densities, the energy transfer from the bath to the fuel was rapid and as the density was decreased, the energy transfer rate constant decreased. The results show that in combustion systems with CH 4 as a prototype fuel, the super pressure regimes control the fuel heating and combustion processes., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

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

Direct dynamics simulations with the M06/6-311++G(d,p) level of theory were performed to study the 3 CH 2 + 3 O 2 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, CO 2 , H 2 O, OH, H 2 , 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 cm 3 molecule -1 s -1 , while the simulation rate constant at 300 K is (0.96 ± 0.28) × 10 -12 cm 3 molecule -1 s -1 . The simulated product yields show that CO is the dominant product and the CO:CO 2 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 H 2 O, the yields of the other products at 1000 K are lower at 300 K, showing a negative temperature dependence.

Thermometer ions are widely used to calibrate the internal energy of the ions produced by electrospray ionization in mass spectrometry. Typically, benzylpyridinium ions with different substituents are used. More recently, benzhydrylpyridinium ions were proposed for their lower bond dissociation energies. Direct dynamics simulations using M06-2X/6-31G(d), DFTB, and PM6-D3 are performed to characterize the activation energies of two representative systems: para -methylbenzylpyridinium ion ( p -Me-BnPy + ) and methyl,methylbenzhydrylpyridinium ion (Me,Me-BhPy + ). Simulation results are used to calculate rate constants for the two systems. These rate constants and their uncertainties are used to find the Arrhenius activation energies and RRK fitted threshold energies which give reasonable agreement with calculated bond dissociation energies at the same level of theory. There is only one fragmentation mechanism observed for both systems, which involves C-N bond dissociation via a loose transition state, to generate either benzylium or benzhydrylium ion and a neutral pyridine molecule. For p -Me-BnPy + using DFTB and PM6-D3 the formation of tropylium ion, from rearrangement of benzylium ion, was observed but only at higher excitation energies and for longer simulation times. These observations suggest that there is no competition between reaction pathways that could affect the reliability of internal energy calibrations. Finally, we suggest using DFTB with a modified-Arrhenius model in future studies.

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( 4 S)] 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.

The dynamics of the HBr + + CO 2 → 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 (S N 2) reactions of X - + CH 3 Y → CH 3 X + Y - type. In summary, this research has revealed interesting dynamics of the HBr + + CO 2 → 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.

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 Å) 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.

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/N 2 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 N 2 and 10 Bz, whereas in the other bath, 396 N 2 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, ⟨ΔE c ⟩, 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 * -N 2 collisions. The overall ⟨ΔE c ⟩, for all collisions, is found to be almost two times larger at 140 K compared to the one obtained from the 300 K bath. Such an enhancement of IET efficiency at 140 K is qualitatively consistent with the experimental observation. However, the possible reasons for not attaining a quantitative agreement are discussed. These results imply that the bath temperature and molecular composition as well as the magnitude of vibrational energy of a highly vibrationally excited molecule can shift the overall timescale of rethermalization.

Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc binding in 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-1 which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal mol-1 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.

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 -NH 3 + 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.

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.

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.

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 k uni (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 k uni (ω, E ) curve very similar to that of RRKM theory, which assumes exponential dynamics. The RRKM k uni (ω, E ) curve was brought into agreement with the biexponential k uni (ω, E ) by multiplying ω in the RRKM expression for k uni (ω, E ) by an energy transfer efficiency factor β c . Such scaling is often done in fitting Hinshelwood-Lindemann-RRKM thermal kinetics to experiment. This agreement between the RRKM and non-RRKM curves for k uni (ω, E ) was only obtained previously by scaling and fitting. In the work presented here, it is shown that if ω in the RRKM k uni (ω, E ) is scaled by a β c factor there is analytic agreement with the non-RRKM k uni (ω, E ). The expression for the value of β c is derived.

The 3 CH 2 + 3 O 2 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 previous direct chemical dynamics simulation at the UM06/6-311++G(d,p) level of theory ( J. Phys. Chem. A 2019, 123, 4360-4369) found that reaction on this PES is predominantly direct without trapping in the potential minima. The first minima 3 CH 2 + 3 O 2 encounters is that for the 1 CH 2 O 2 Criegee intermediate and statistical theory assumes the reactive system is trapped in this intermediate with a lifetime given by Rice-Ramsperger-Kassel-Marcus (RRKM) theory. In the work presented here, a direct dynamics simulation is performed with the above UM06 theory, with the trajectories initialized in the 1 CH 2 O 2 intermediate with a random distribution of vibrational energy as assumed by RRKM theory. There are substantial differences between the dynamics for 1 CH 2 O 2 dissociation and 3 CH 2 + 3 O 2 reaction. For the former there are four product channels, while for the latter there are seven in agreement with experiment. Product energy partitioning for the two simulations are in overall good agreement for the CO 2 + H 2 and CO + H 2 O product channels, but in significant disagreement for the HCO + OH product channel. Though 1 CH 2 O 2 is excited randomly in accord with RRKM theory, its dissociation probability is biexponential and not exponential as assumed by RRKM. In addition, the 1 CH 2 O 2 dissociation dynamics follow non-intrinsic reaction coordinate (non-IRC) pathways. An important finding is that the nonstatistical dynamics for the 3 CH 2 + 3 O 2 reaction give results in agreement with experiment.

Arginine has significant effects on fragmentation patterns of the protonated peptide due to its high basicity guanidine tail. In this article, thermal dissociation of the singly protonated glycine-arginine dipeptide (GR-H + ) was investigated by performing direct dynamics simulations at different vibrational temperatures of 2000-3500 K. Fourteen principal fragmentation mechanisms containing side-chain and backbone fragmentation were found and discussed in detail. The mechanism involving partial or complete loss of a guanidino group dominates side-chain fragmentation, while backbone fragmentation mainly involves the three cleavage sites of a1-x1 + , a2 + -x0, and b1-y1 + . Fragmentation patterns for primary dissociation have been compared with experimental results, and the peak that was not identified by the experiment has been assigned by our simulation. Kinetic parameters for GR-H + unimolecular dissociation may be determined by direct dynamics simulations, which are helpful in exploring the complex biomolecules., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Direct dynamics simulations, using B3LYP/6-311++G(2d,2p) theory, were used to study the unimolecular and intramolecular dynamics of vibrationally excited CH 3 NC. Microcanonical ensembles of CH 3 NC, excited with 150, 120, and 100 kcal/mol of vibrational energy, isomerized to CH 3 CN nonexponentially, indicative of intrinsic non-Rice-Ramsperger-Kassel-Marcus (RRKM) dynamics. The distribution of surviving CH 3 NC 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 CH 3 NC isomerization. Classical power spectra calculated for vibrationally excited CH 3 NC, at the experimental average energy of isomerizing molecules, show that the intramolecular dynamics of CH 3 NC are not chaotic and the C-N≡C and CH 3 units are weakly coupled. The biexponential N(t)/N(0) at 100 kcal/mol is used as a model to study CH 3 NC → CH 3 CN isomerization with biexponential dynamics. The Hinshelwood-Lindemann rate constant k uni (ω,E) found from the biexponential N(t)/N(0) agrees with the Hinshelwood-Lindemann-RRKM k uni (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 k uni (ω,E) curves may be brought into agreement by scaling ω in the Hinshelwood-Lindemann-RRKM k uni (ω,E) by a collisional energy transfer efficiency factor β c . The interplay between the value of β c , for the actual intermolecular energy transfer, and the ways the treatment of the rotational quantum number K and nonexponential unimolecular dynamics affect β c suggests that the ability to fit an experimental k uni (ω,T) with Hinshelwood-Lindemann-RRKM theory does not identify a unimolecular reactant as an intrinsic RRKM molecule.

The potential energy curves (PECs) for the interaction of 3 CH 2 with 3 O 2 in singlet and triplet potential energy surfaces (PESs) leading to singlet and triplet Criegee intermediates (CH 2 OO) 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 3 CH 2 with 3 O 2 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 3 CH 2 OO is less stable than the 1 CH 2 OO. 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 3 CH 2 OO has a larger biradical character than 1 CH 2 OO, and because of the larger bond order of 1 CH 2 OO, the C-O covalent bond becomes harder to break, thereby stabilizing 1 CH 2 OO. Thus, this study provides insights into the shape of the PEC obtained from the reaction between 3 CH 2 and 3 O 2 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.

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-His 1 -Cys 2 -Gly 3 -Pro 4 -Tyr 5 -His 6 -Cys 7 (analog methanobactin peptide-5, amb 5 ). DFT/M05-2X and B3LYP geometry optimizations of [amb 5 -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.

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 3 CH 2 (X 3 B 1 ) + 3 O 2 (X 3 ∑ g - ) reaction on its ground-state singlet potential energy surface (PES) at 300 K. However, further analyses revealed the simulations are unstable for the 3 CH 2 (X 3 B 1 ) + 3 O 2 (X 3 ∑ g - ) reactants on the ground-state singlet surface and the trajectories reverted to an excited-state singlet surface for the 1 CH 2 (ã 1 A 1 ) + 1 O 2 (b 1 ∑ g + ) reactants. Thus, the dynamics reported previously are for this excited-state singlet PES. The PESs for the 3 CH 2 (X 3 B 1 ) + 3 O 2 (X 3 ∑ g - ) and 1 CH 2 (ã 1 A 1 ) + 1 O 2 (b 1 ∑ g + ) reactants are quite similar, and this provided a means to perform simulations for the 3 CH 2 (X 3 B 1 ) + 3 O 2 (X 3 ∑ 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 CO 2 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 3 CH 2 + 3 O 2 rate constant at 300 K is only 3.4 times smaller than the recommended value, which may be accommodated if the 3 CH 2 + 3 O 2 → 1 CH 2 O 2 potential energy curve is only 0.75 kcal/mol more attractive at the variational transition state for 3 CH 2 + 3 O 2 → 1 CH 2 O 2 association. The simulation kinetics and dynamics for the 3 CH 2 + 3 O 2 and 1 CH 2 + 1 O 2 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 3 CH 2 + 3 O 2 → 1 CH 2 O 2 and 1 CH 2 + 1 O 2 → 1 CH 2 O 2 are nearly identical. The product yields for the 3 CH 2 + 3 O 2 and 1 CH 2 + 1 O 2 reactions are also nearly identical, only differing for the CO 2 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.

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.

In Density Functional Theory (DFT) direct dynamics simulations with Unrestricted Hartree Fock (UHF) theory, triplet instability often emerges when numerically integrating a classical trajectory. A broken symmetry initial guess for the wave function is often used to obtain the unrestricted DFT potential energy surface (PES), but this is found to be often insufficient for direct dynamics simulations. An algorithm is described for obtaining smooth transitions between the open-shell and the closed-shell regions of the unrestricted PES, and thus stable trajectories, for direct dynamics simulations of dioxetane and its •OCH 2 -CH 2 O• singlet diradical. © 2018 Wiley Periodicals, Inc., (© 2018 Wiley Periodicals, Inc.)

Collisional energy transfer of highly vibrationally excited propylbenzene cation in a N 2 bath has been studied with chemical dynamics simulations. In this work, an intermolecular potential of propylbenzene cation interacting with N 2 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 C a -N, C b -N, and H-N, where C a is carbon on the benzene ring and C b 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 N 2 bath, the single collision limit of propylbenzene cation with the N 2 bath was obtained at a density of 20 kg/m 3 (28 atm). For the experimental excitation energy and in the single collision limit, the average energy transferred per collision, ⟨Δ E c ⟩, is 1.04 ± 0.04 kcal/mol and in good agreement with the experimental value of 0.82 kcal/mol.

Following work by Slater and Bunker, the unimolecular rate constant versus collision frequency, k uni (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 k uni (ω, E). Previous work using this approach is reviewed. In the work presented here, the biexponential f 1  exp(- k 1 t) + f 2  exp(- k 2 t) is used to represent N( t)/ N(0), where f 1 k 1 + f 2 k 2 equals the RRKM rate constant k( E) and f 1 + f 2 = 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 k 1 is larger than k( E) and k 2 is smaller. This biexponential gives k uni (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 f 1 is made smaller and k 1 made larger. Of considerable interest is the finding that, if the collision frequency ω for the RRKM plot of k uni (ω, E) versus ω is multiplied by an energy transfer efficiency factor β c , the RRKM k uni (ω, E) versus ω plot may be scaled to match those for the intrinsic non-RRKM, biexponential N( t)/ N(0), plots. This analysis identifies the importance of determining accurate collisional intermolecular energy transfer (IET) efficiencies.

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.

The role of vibrational excitation of reactants in driving reactions involving polyatomic species has been often studied by means of classical or quasi-classical trajectory simulations. We propose a different approach based on investigation of vibrational features of the Cl - ⋯CH 3 Cl pre-reaction complex for the Cl - + CH 3 Cl S N 2 reaction. We present vibrational power spectra and frequency estimates for the title pre-reaction complex calculated at the level of classical, semiclassical, and second-order vibrational perturbation theory on a pre-existing analytical potential energy surface. The main goals of the paper are the study of anharmonic effects and understanding of vibrational couplings that permit energy transfer between the collisional kinetic energy and the internal vibrations of the reactants. We provide both classical and quantum pictures of intermode couplings and show that the S N 2 mechanism is favored by the coupling of a C-Cl bend involving the Cl - projectile with the CH 3 rocking motion of the target molecule. We also illustrate how the routines needed for semiclassical vibrational spectroscopy simulations can be interfaced in a user-friendly way to pre-existing molecular dynamics software. In particular, we present an implementation of semiclassical spectroscopy into the VENUS suite of codes, thus providing a useful computational tool for users who are not experts of semiclassical dynamics.

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 N 2 -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 C 6 H 6 * molecules to the bath. The simulations find that at ∼10 -7 s and 1 atm pressure there are four different final temperatures for C 6 H 6 * and the bath. N 2 vibration is not excited and remains at the original bath temperature of 300 K. Rotation and translation degrees of freedom of both N 2 and C 6 H 6 in the bath are excited to a final temperature of ∼340 K. Energy transfer from the excited C 6 H 6 * molecules is more efficient to vibration of the C 6 H 6 bath than its rotation and translation degrees of freedom, and the final vibrational temperature of the C 6 H 6 bath is ∼453 K, if the average energy of each C 6 H 6 vibration mode is assumed to be RT . There is no vibrational equilibration between C 6 H 6 * and the C 6 H 6 bath molecules. When the simulations are terminated, the vibrational temperatures of the C 6 H 6 * and C 6 H 6 bath molecules are ∼537 K and ∼453 K, respectively. An important question is the time scale for complete energy equilibration of the C 6 H 6 * and N 2 and C 6 H 6 bath system. At 1 atm and 300 K, the experimental V-T (vibration-translation) relaxation time for N 2 is ∼10 -4 s. The simulation time was too short for equilibrium to be attained, and the time for complete equilibration of C 6 H 6 * vibration with translation, rotation, and vibration of the bath was not determined.

Competiting S N 2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying S N 2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over S N 2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the S N 2 reaction, a feature which attributes to a differential solute-solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the S N 2 mechanism becomes more pronounced, concomitant with drastic suppression of the E2 route. This work highlights the interplay between energetics and dynamics in determining mechanistic selectivity and provides insight into the impact of solvent molecules on a general transition from elimination to substitution for chemical reactions proceeding from gas- to solution-phase environments.

Monte Carlo sampling calculations were performed to determine the anharmonic sum of states, N anh ( E), for I - (H 2 O), (H 2 O) 2 , and I - (H 2 O) 2 versus internal energy up to their dissociation energies. The anharmonic density of states, ρ anh ( E), is found from the energy derivative of N anh ( E). Analytic potential energy functions are used for the calculations, consisting of TIP4P for H 2 O···H 2 O interactions and an accurate two-body potential for the I - ···H 2 O 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 - (H 2 O) 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, ρ anh ( E)/ρ h ( E), is ∼2, ∼ 3, and ∼260 for I - (H 2 O), (H 2 O) 2 , and I - (H 2 O) 2 , respectively. The large ratio for I - (H 2 O) 2 results from the I - (H 2 O) 2 → I - (H 2 O) + H 2 O dissociation energy being more than 2 times larger than the (H 2 O) 2 → 2H 2 O dissociation energy, giving rise to highly mobile H 2 O molecules near the I - (H 2 O) 2 dissociation threshold. This work illustrates the importance of treating anharmonicity correctly in unimolecular rate constant calculations.

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.

The reaction of 3 CH 2 with 3 O 2 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, CH 2 OO, on both the singlet and triplet PESs. The triplet surface leads to only one product channel, H 2 CO + O( 3 P), while the singlet surface leads to eight product channels with their relative importance as CO + H 2 O > CO + OH + H ∼ H 2 CO + O( 1 D) > HCO + OH ∼ CO 2 + H 2 ∼ CO + H 2 + O( 1 D) > CO 2 + H + H > HCO + O( 1 D) + 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 cm 3 molecule -1 s -1 in comparison to the recommended experimental rate constant of 3.3 × 10 -12 cm 3 molecule -1 s -1 . The simulation product yields for the singlet PES are compared with experiment, and the most significant differences are for H, CO 2 , and H 2 O. The reaction on the triplet surface is also barrierless, inconsistent with experiment. A discussion is given of the need for future calculations to address (1) the barrier on the triplet PES for 3 CH 2 + 3 O 2 → 3 CH 2 OO, (2) the temperature dependence of the 3 CH 2 + 3 O 2 reaction rate constant and product branching ratios, and (3) the possible non-RRKM dynamics of the 1 CH 2 OO Criegee intermediate.

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-C 2 H 4 O 3 , 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 (H 2 COO) and formaldehyde (H 2 CO). 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.

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 t o 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 t o , 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 (ala 2 -H + ) physisorbed on/in a perfluorinated self-assembled monolayer (F-SAM) surface. Previously developed analytic potentials were used for the F-SAM and the ala 2 -H + /F-SAM intermolecular interaction, and the AMBER valence force field was used for ala 2 -H + . The activation energy, E a = 13.2 kcal/mol, determined from the simulations is consistent with previous simulations of the ala 2 -H + /F-SAM binding energy. The A-factor, 7.8 × 10 11 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 ala 2 -H + and the F-SAM upon desorption. Using the Arrhenius parameters for ala 2 -H + desorption from the F-SAM, the lifetime of ala 2 -H + adsorbed on the F-SAM at 300 K is 5 × 10 -3 s. Larger peptide ions are expected to have longer adsorption lifetimes.

Dissociation chemistry of the diproline anion [Pro 2 -H] - is studied using chemical dynamics simulations coupled with quantum-chemical calculations and RRKM analysis. Pro 2 - 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 [Pro 2 -H] - were followed in order to sample a larger range of possible reactivity. While different mechanisms yielding y 1 - product ions are proposed, there is only one mechanism yielding the b 2 - ion. This mechanism leads to formation of a b 2 - fragment with a diketopiperazine structure. The sole formation of a diketopiperazine b 2 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 - (H 2 O) 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 H 2 O: a three-site model H 2 O 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 - ---H 2 O 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 the four-site model is quite adequate for determining densities of states and partition functions for I - (H 2 O) n clusters at high energies and temperatures, respectively. The PSO algorithm was also applied to the eight potential energy curves, with the four-site model, for a short time ∼8 min fitting. The RMSE was small, only 0.37 kcal/mol, showing the high efficiency of the PSO algorithm with retention of a good fitting accuracy. The PSO algorithm is a good choice for fitting analytic potential energy functions, and for the work presented here was able to find an adequate fit to an I - (H 2 O) analytic intermolecular potential with a small number of parameters.

Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N 2 , and previous thermal activation simulation results; Z. Homayoon, S. Pratihar, E. Dratz, R. Snider, R. Spezia, G. L. Barnes, V. Macaluso, A. Martin-Somer and W. L. Hase, J. Phys. Chem. A, 2016, 120, 8211-8227. Upon thermal activation unimolecular fragmentation is statistical and in accord with RRKM unimolecular rate theory. Simulations show that in collisional activation some non-statistical fragmentation occurs, including shattering, which is not present when the ions dissociate statistically. Products formed by non-statistical shattering mechanisms may be related to characteristic mass spectrometry peaks which distinguish the two isomers I and L.

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: NH 3 OH + + CH 3 COOH and NH 2 OH 2 + + CH 3 COOH 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.

Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH 3 CN → HF + CH 2 CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. The experiments were performed at 300 K, and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F⋯HCH 2 CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation. The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH 2 CN and then trapping in the CH 2 CN⋯HF post-reaction potential energy well of ∼10 kcal/mol with respect to the HF + CH 2 CN products. In contrast to this IRC, five different trajectory types were observed: the majority proceeded by direct H-atom transfer and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH 2 CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. Simulations with an anharmonic zero-point energy constraint gave product distributions for relative translation, HF rotation, HF vibration, CH 2 CN rotation, and CH 2 CN vibration as 5%, 11%, 60%, 7%, and 16%, respectively. In contrast, the experimental energy partitioning percentages to HF rotation and vibration are 6% and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational population for F + CH 3 CN → HF + CH 2 CN resemble those for other reactions. A detailed discussion is given of possible origins of the difference between the simulation and experimental energy partitioning dynamics for F + CH 3 CN → HF + CH 2 CN. The F + CH 3 CN reaction also forms the CH 3 C(F)N intermediate, in which the F-atom adds to the C≡N bond. However, this intermediate and F⋯CH 3 CN and CH 3 CN⋯F van der Waals complexes are not expected to affect the F + CH 3 CN → HF + CH 2 CN product energy partitioning.

Intermolecular energy transfer for the vibrationally excited propylbenzene cation (C 9 H 12 + ) 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 C 9 H 12 + . Spin component scaled MP2/6-311++G** calculations were used to develop an intermolecular potential for He + C 9 H 12 + . The He + He intermolecular potential was determined from a previous explicitly correlated Gaussian electronic structure calculation. For the simulations, C 9 H 12 + was prepared with a 100.1 kcal/mol excitation energy to compare with experiment. The average energy transfer from C 9 H 12 + , ⟨ΔE c ⟩, decreased as C 9 H 12 + was vibrationally relaxed and for the initial excitation energy ⟨ΔE c ⟩ = 0.64 kcal/mol. This result agrees well with the experimental ⟨ΔE c ⟩ value of 0.51 ± 0.26 kcal/mol for collisions of He with the ethylbenzene cation. The ⟨ΔE c ⟩ value found for He + C 9 H 12 + collisions is compared with reported values of ⟨ΔE c ⟩ for He colliding with other molecules.

Direct dynamics simulations were performed to study the S N 2 double inversion mechanism S N 2-DI, with retention of configuration, for the F - + CH 3 I reaction. Previous simulations identified a transition state (TS) structure, i.e. TS0, for the S N 2-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 - HCH 2 I S N 2 pre-reaction complex and the FHCH 2 I - proton transfer post-reaction complex. Inclusion of TS0 in the S N 2-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 S N 2-DI products and ∼70% follow the proposed S N 2-DI pathway from TS0 to the products. In addition, the Sudden Vector Projection (SVP) method was used to identify which CH 3 I vibrational mode excitations promote access to TS0 and the S N 2-DI mechanism. Results of F - + CH 3 I simulations, with SVP specified mode excitations, are disappointing. With the CH 3 deformations of CH 3 I excited, the S N 2 single inversion mechanism is the dominant pathway. If the CH stretch modes are also excited, proton transfer dominates the reaction. S N 2-DI occurs, but with a very small probability of ∼1%. The reasons behind these results are discussed.

The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X -  + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity. This characteristic fingerprint is also confirmed by direct dynamics simulations for ethyl as residue and attributed to the dynamics of elimination reactions. This work opens the door to a detailed atomistic understanding of transformation reactions in even larger systems.The competition between chemical reactions critically affects our natural environment and the synthesis of new materials. Here, the authors present an approach to directly image distinct fingerprints of essential organic reactions and monitor their competition as a function of steric substitution.

Chemical dynamics simulations were performed to study collisional intermolecular energy transfer from a thermalized N 2 bath at 300 K to vibrationally "cold" C 6 F 6 . The vibrational temperature of C 6 F 6 is taken as 50 K, which corresponds to a classical vibrational energy of 2.98 kcal/mol. The temperature ratio between C 6 F 6 and the bath is 1/6, the reciprocal of the same ratio for previous "hot" C 6 F 6 simulations (J. Chem. Phys. 2014, 140, 194103). Simulations were also done for a C 6 F 6 vibrational temperature of 0 K. The average energy of C 6 F 6 versus time is well fit by a biexponential function which gives a slightly larger short time rate component, k 1 , but a four times smaller long time rate component, k 2 , compared to those obtained from the "hot" C 6 F 6 simulations. The average energy transferred per collision depends on the difference between the average energy of C 6 F 6 and the final C 6 F 6 energy after equilibration with the bath, but not on the temperature ratio of C 6 F 6 and the bath. The translational and rotational degrees of freedom of the N 2 bath transfer their energies to the vibrational degrees of freedom of C 6 F 6 . The energies of the N 2 vibrational mode and translational and rotational modes of C 6 F 6 remain unchanged during the energy transfer. It is also found that the energy distribution of C 6 F 6 broadens as energy is transferred from the bath, with an almost linear increase in the deviation of the C 6 F 6 energies from the average C 6 F 6 energy as the average energy of C 6 F 6 increases.

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'., (© 2017 The Author(s).)

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'., (© 2017 The Author(s).)

Influences of solvent molecules on S N 2 reaction dynamics of microsolvated F - (H 2 O) n with CH 3 I, 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 - (H 2 O), 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 influences microsolvated S N 2 dynamics.

In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular S N 2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.

Anti-E2, syn-E2, inv-, and ret-S N 2 reaction channels for the gas-phase reaction of F - + CH 3 CH 2 I 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-S N 2 paths has been clarified in the present work. A positive barrier of +19.2 kcal/mol for ret-S N 2 shows the least feasibility to occur at room temperature. Negative activation energies (-16.9, -16.0, and -4.9 kcal/mol, respectively) for inv-S N 2, anti-E2, and syn-E2 indicate that inv-S N 2 and anti-E2 mechanisms significantly prevail over the eclipsed elimination. Varying the leaving group for a series of reactions F - + CH 3 CH 2 Y (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 > I. The reactivity of each channel nearly holds unchanged except for the perturbation between anti-E2 and inv-S N 2. RRKM calculation reveals that the reaction of the fluorine ion with ethyl iodide occurs predominately via anti-E2 elimination, and the inv-S N 2 pathway is suppressed, although it is energetically favored. This phenomenon indicates that, in evaluating the competition between E2 and S N 2 processes, the kinetic or dynamical factors may play a significant role. By comparison with benchmark CCSD(T) energies, MP2, CAM-B3LYP, and M06 methods are recommended to perform dynamics simulations of the title reaction.