Mechanism and kinetics for the reaction of methyl peroxy radical with O2.

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

Sampling initial positions and momenta for nuclear trajectories from quantum mechanical distributions.

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 of the 3CH2 + 3O2 Reaction at High Temperature.

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 of energy transfer in CH4 and N2 collisions.

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.

Unimolecular Fragmentation Properties of Thermometer Ions from Chemical Dynamics Simulations.

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.

Exploring reactivity and product formation in N(4S) collisions with pristine and defected graphene with direct dynamics simulations.

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.

Dynamics of Pyrene-Dimer Association and Ensuing Pyrene-Dimer Dissociation.

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.

Theoretical Study of the Dynamics of the HBr+ + CO2 → HOCO+ + Br Reaction.

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.

Comparison of intermolecular energy transfer from vibrationally excited benzene in mixed nitrogen-benzene baths at 140 K and 300 K.

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.

Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces.

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.

Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide.

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.

Time-Dependent Perspective for the Intramolecular Couplings of the N-H Stretches of Protonated Tryptophan.

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.

Nonstatistical Reaction Dynamics.

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 generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry.

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.

Comparison of Exponential and Biexponential Models of the Unimolecular Decomposition Probability for the Hinshelwood-Lindemann Mechanism.

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

Direct Dynamics Simulations of the Unimolecular Decomposition of the Randomly Excited 1CH2O2 Criegee Intermediate. Comparison with 3CH2 + 3O2 Reaction Dynamics.

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 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 3CH2 + 3O2 encounters is that for the 1CH2O2 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 1CH2O2 intermediate with a random distribution of vibrational energy as assumed by RRKM theory. There are substantial differences between the dynamics for 1CH2O2 dissociation and 3CH2 + 3O2 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 CO2 + H2 and CO + H2O product channels, but in significant disagreement for the HCO + OH product channel. Though 1CH2O2 is excited randomly in accord with RRKM theory, its dissociation probability is biexponential and not exponential as assumed by RRKM. In addition, the 1CH2O2 dissociation dynamics follow non-intrinsic reaction coordinate (non-IRC) pathways. An important finding is that the nonstatistical dynamics for the 3CH2 + 3O2 reaction give results in agreement with experiment.

Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine.

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.

Is CH3NC isomerization an intrinsic non-RRKM unimolecular reaction?

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

Potential Energy Curves for Formation of the CH2O2 Criegee Intermediate on the 3CH2 + 3O2 Singlet and Triplet Potential Energy Surfaces.

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 (ß) 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.