Chemical dynamics simulations of energy transfer in CH and N collisions.

Chemical dynamics simulations have been performed to study the energy transfer from a hot N bath at 1000 K to CH fuel at 300 K at different bath densities ranging from 1000 kg m to 30 kg m. 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 as a prototype fuel, the super pressure regimes control the fuel heating and combustion processes.

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

Quantum chemical calculations and dynamics simulations were performed to study the reaction between methyl peroxy radical (CHO) and O. The reaction proceeds through three different pathways (1) H-atom abstraction, (2) O addition and (3) concerted H-atom shift and O addition reactions. The concerted H-atom shift and O addition pathway is the most favourable reaction both kinetically and thermodynamically.

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.

Direct Dynamics Simulations of the CH + O Reaction at High Temperature.

Direct dynamics simulations with the M06/6-311++G(d,p) level of theory were performed to study the CH + O 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, HO, OH, H, O, H, and HCO are the products formed from the reaction.

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.

Exploring reactivity and product formation in N(S) 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(S)] collisions with pristine, defected, and oxidized graphene.

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

The dynamics of the HBr + CO → 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 methods such as CCSD(T)/CBS, and the UMP2/cc-pVDZ/lanl08d has been identified as an ideal method to study its dynamics.

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/N baths with one highly vibrationally excited benzene molecule (Bz) are compared to experimental results at 140 K. Two mixed bath models are considered.

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 () with different collisional impact parameters (; 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 .

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.

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.

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 -NH group of protonated tryptophan (TrpH), excited to the = 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.

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.

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.

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 () to represent the unimolecular reaction of the excited molecule versus energy.

Direct Dynamics Simulations of the Unimolecular Decomposition of the Randomly Excited CHO Criegee Intermediate. Comparison with CH + O Reaction Dynamics.

The CH + O 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 ( 2019, 123, 4360-4369) found that reaction on this PES is predominantly direct without trapping in the potential minima.

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.

Is CHNC 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 CHNC. Microcanonical ensembles of CHNC, excited with 150, 120, and 100 kcal/mol of vibrational energy, isomerized to CHCN nonexponentially, indicative of intrinsic non-Rice-Ramsperger-Kassel-Marcus (RRKM) dynamics. The distribution of surviving CHNC molecules vs time, i.

Potential Energy Curves for Formation of the CHO Criegee Intermediate on the CH + O Singlet and Triplet Potential Energy Surfaces.

The potential energy curves (PECs) for the interaction of CH with O in singlet and triplet potential energy surfaces (PESs) leading to singlet and triplet Criegee intermediates (CHOO) 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 CH with O on the singlet surface leads to a flat long-range attractive PEC lacking any maxima or minima along the curve.

Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation.

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-Cys-Gly-Pro-Tyr-His-Cys (analog methanobactin peptide-5, amb). DFT/M05-2X and B3LYP geometry optimizations of [amb-3H+Zn(II)] predicted three lowest energy conformers with different chelating motifs.

Direct Dynamics Simulations of the CH + O Reaction on the Ground- and Excited-State Singlet Surfaces.

In a previous work [ Lakshmanan , S. ; J. Phys.

l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations.

Low-energy collision-induced dissociation (CID) of deprotonated l-cysteine S-sulfate, [cysS-SO], 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.

Chemical Dynamics Simulation of Energy Transfer: Propylbenzene Cation and N Collisions.

Collisional energy transfer of highly vibrationally excited propylbenzene cation in a N bath has been studied with chemical dynamics simulations. In this work, an intermolecular potential of propylbenzene cation interacting with N 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 -N, C -N, and H-N, where C is carbon on the benzene ring and C is carbon on the propyl side chain.

Unimolecular Rate Constants versus Energy and Pressure as a Convolution of Unimolecular Lifetime and Collisional Deactivation Probabilities. Analyses of Intrinsic Non-RRKM Dynamics.

Following work by Slater and Bunker, the unimolecular rate constant versus collision frequency, k(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(ω, E). Previous work using this approach is reviewed.