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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.

Chemical dynamics simulations have been performed to study the energy transfer from a hot N2 bath at 1000 K to CH4 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 CH4 as a prototype fuel, the super pressure regimes control the fuel heating and combustion processes.

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 ...

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.

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...

International audience; 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-methyl-benzylpyridinium ion (p-Me-BnPy +) and methyl,methyl-benzhydrylpyridinium 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 modified-Arrhenius model in future studies.

The dynamics of the HBr

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.

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.

The

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.

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...

International audience; 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.

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.

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 ...

Zwitterionic group 14 complexes of the alkali metals of formula [E(SiMe2OCH2CH2OMe)3M], where E = C, Si or Ge and M = Li, Na or K, have been prepared, structurally characterized and their electronic nature was investigated by computational methods., Zwitterionic group 14 complexes of the alkali metals of formula [C(SiMe2OCH2CH2OMe)3M], (M-1), [Si(SiMe2OCH2CH2OMe)3M], (M-2), [Ge(SiMe2OCH2CH2OMe)3M], (M-3), where M = Li, Na or K, have been prepared, structurally characterized and their electronic nature was investigated by computational methods. Zwitterions M-2 and M-3 were synthesized via reactions of [Si(SiMe2OCH2CH2OMe)4] (2) and [Ge(SiMe2OCH2CH2OMe)4] (3) with MOBut (M = Li, Na or K), resp., in almost quantitative yields, while M-1 were prepared from deprotonation of [HC(SiMe2OCH2CH2OMe)3] (1) with LiBut, NaCH2Ph and KCH2Ph, resp. X-ray crystallographic studies and DFT calculations in the gas-phase, including calculations of the NPA charges confirm the zwitterionic nature of these compounds, with the alkali metal cations being rigidly locked and charge separated from the anion by the internal OCH2CH2OMe donor groups. Natural bond orbital (NBO) analysis and the second order perturbation theory analysis of the NBOs reveal significant hyperconjugative interactions in M-1–M-3, primarily between the lone pair and the antibonding Si–O orbitals, the extent of which decreases in the order M-1 > M-2 > M-3. The experimental basicities and the calculated gas-phase basicities of M-1–M-3 reveal the zwitterionic alkali metal methanides M-1 to be significantly stronger bases than the analogous silanides M-2 and germanium M-3.

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 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CH2 -CH2 O• singlet diradical. © 2018 Wiley Periodicals, Inc.

The reaction of

Dissociation chemistry of the diproline anion [Pro

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.

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.

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.

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.

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’.

Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of OH(-) rotational excitation on the OH(-) + CH3I reaction dynamics. The overall reaction probability and the probabilities for the SN2 and proton-transfer pathways have little dependence on J. Possible effects on the atomistic mechanisms were investigated for the SN2 pathway and the probability of the direct rebound mechanism increased with J. However, the other atomistic mechanisms were not appreciably affected by J.

Anti-E2, syn-E2, inv-, and ret-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’.