Quasiclassical Trajectory Research Articles

Vibrational spectroscopy simulation of solvation effects on a G-quadruplex

It is commonly believed that solvation effects on the vibrational properties of a solute are easily accounted for by simple rules of thumbs, that is, solvating a polar molecule in a polar medium has the only effect of red shifting all its spectroscopical features and, similarly, solvating a polar molecule in a nonpolar medium has the opposite effect. In this work, we use theoretical vibrational spectroscopy at quasi-classical and quantum approximate semiclassical level to gain atomistic insights about solvent–solute interactions for 2′-deoxyguanosine and the G-quadruplex. We employ the quasi-classical trajectory method to include full anharmonicity into our calculated spectra, and then introduce quantum nuclear effects by means of divide-and-conquer semiclassical spectroscopy calculations. Solvation is treated explicitly leading to a good reproducibility of the available experimental data and reliable predictions when an experimental reference is missing.Communicated by Ramaswamy H. Sarma

Rovibrational internal energy transfer and dissociation of high-temperature oxygen mixture.

This work constructs a rovibrational state-to-state model for the O2 + O2 system leveraging high-fidelity potential energy surfaces and quasi-classical trajectory calculations. The model is used to investigate internal energy transfer and nonequilibrium reactive processes in a dissociating environment using a master equation approach, whereby the kinetics of each internal rovibrational state is explicitly computed. To cope with the exponentially large number of elementary processes that characterize reactive bimolecular collisions, the internal states of the collision partner are assumed to follow a Boltzmann distribution at a prescribed internal temperature. This procedure makes the problem tractable, reducing the computational cost to a comparable scale with the O2 + O system. The constructed rovibrational-specific kinetic database covers the temperature range of 7500-20 000K. The reaction rate coefficients included in the database are parameterized in the function of kinetic and internal temperatures. Analysis of the energy transfer and dissociation process in isochoric and isothermal conditions reveals that significant departure from the equilibrium Boltzmann distribution occurs during the energy transfer and dissociation phase. Comparing the population distribution of the O2 molecules against the O2 + O case demonstrates a more significant extent of nonequilibrium characterized by a more diffuse distribution whereby the vibrational strands are more clearly identifiable. This is partly due to less efficient mixing of the rovibrational states, which results in more diffuse rovibrational distributions in the quasi-steady-state distribution of O2 + O2. A master equation analysis for the combined O2 + O and O2 + O2 system reveals that the O2 + O2 system governs the early stage of energy transfer, whereas the O2 + O system takes control of the dissociation dynamics. The findings of the present work will provide a strong physical foundation that can be exploited to construct an improved reduced-order model for oxygen chemistry.

Analytical potential energy surface and dynamics for the OH + CH3OH reaction.

Using as functional form a combination of valence bond and mechanic molecular terms a new full-dimensional potential energy surface was developed for the title reaction, named PES-2022, which was fitted to high-level ab initio calculations at the coupled-cluster singles, doubles, and perturbative triples-F12 explicitly correlated level on a representative number of points describing the reactive system. This surface simultaneously describes the two reaction channels, hydrogen abstraction from the methyl group [(R1) path] and from the alcohol group [(R2) path] of methanol to form water. PES-2022 is a smooth and continuous surface, which reasonably describes the topology of this reactive system from reactants to products, including the intermediate complexes present in the system. Based on PES-2022 an exhaustive dynamics study was performed using quasi-classical trajectory calculations under two different initial conditions: at a fixed room temperature, for direct comparison with the experimental evidence and at different collision energies, to analyze possible mechanisms of reaction. In the first case, the available energy was mostly deposited as water vibrational energy, with the vibrational population inverted in the stretching modes and not inverted in the bending modes, reproducing the experimental evidence. In the second case, the analysis of different dynamics magnitudes (excitation functions, product energy partitioning, and product scattering distributions), allows us to suggest different mechanisms for both (R1) and (R2) paths: a direct mechanism for the (R2) path vs an indirect one, related with "nearly trapped" trajectories in the intermediate complexes, for the (R1) path.

Quasi-Classical Trajectory Dynamics Study of the Reaction OH + H2S→H2O + SH and Its Isotopic Variants: Comparison with Experiment

The hydrogen abstraction reaction OH + H2S→H2O + SH plays an important role in acid rain formation, air pollution and climate change. In this work, the product energy disposals of the reaction and its isotopic variants OD + H2S and OD + D2S are calculated on a new ab-initio-based ground electronic state potential energy surface (PES) using the quasi-classical trajectory method. The PES is developed by fitting a total of 72,113 points calculated at the level of UCCSD(T)-F12a/aug-cc-pVTZ and using the fundamental invariant-neural network method, resulting in a total RMSE of 4.14 meV. The product H2O formed in the OH + H2S reaction at 298 K is found to be largely populated in the first overtone states of its symmetric and asymmetric stretching modes, while the vibrational distributions of the products HOD and D2O in the isotopically substituted reactions are visibly different. The computed product vibrational state distributions agree reasonably well with experimental results and are rationalized by the sudden vector projection model.

Dynamics study of the post-transition-state-bifurcation process of the (HCOOH)H+ → CO + H3O+/HCO+ + H2O dissociation: application of machine-learning techniques.

The process of protonated formic acid dissociating from the transition state was studied using ring-polymer molecular dynamics (RPMD), classical MD, and quasi-classical trajectory (QCT) simulations. Temperature had a strong influence on the branching fractions for the HCO+ + H2O and CO + H3O+ dissociation channels. The RPMD and classical MD simulations showed similar behavior, but the QCT dynamics were significantly different owing to the excess energies in the quasi-classical trajectories. Machine-learning analysis identified several key features in the phase information of the vibrational motions at the transition state. We found that the initial configuration and momentum of a hydrogen atom connected to a carbon atom and the shrinking coordinate of the CO bond at the transition state play a role in the dynamics of HCO+ + H2O production.

Quasi-classical trajectory study of the OH- + CH3I reaction: theory meets experiment.

Regarding OH- + CH3I, several studies have focused on the dynamics of the reaction. Here, high-level quasi-classical trajectory simulations are carried out at four different collision energies on our recently developed potential energy surface. In all, more than half a million trajectories are performed, and for the first time, the detailed quasi-classical trajectory results are compared with the reanalysed crossed-beam ion imaging experiments. Concerning the previously reported direct dynamics study of OH- + CH3I, a better agreement can be obtained between the revised experiment and our novel theoretical results. Furthermore, in the present work, the benchmark geometries, frequencies and relative energies of the stationary points are also determined for the OH- + CH3I proton-abstraction channel along with the earlier characterized SN2 channel.

Imaging rotational energy transfer: comparative stereodynamics in CO + N2 and CO + CO inelastic scattering.

State-to-state rotational energy transfer in collisions of ground ro-vibrational state 13CO molecules with N2 molecules has been studied using the crossed molecular beam method under kinematically equivalent conditions used for 13CO + CO rotationally inelastic scattering described in a previously published report (Sun et al., Science, 2020, 369, 307-309). The collisionally excited 13CO molecule products are detected by the same (1 + 1' + 1'') VUV (Vacuum Ultra-Violet) resonance enhanced multiphoton ionization scheme coupled with velocity map ion imaging. We present differential cross sections and scattering angle resolved rotational angular momentum alignment moments extracted from experimentally measured 13CO + N2 scattering images and compare them with theoretical predictions from quasi-classical trajectories (QCT) on a newly calculated 13CO-N2 potential energy surface (PES). Good agreement between experiment and theory is found, which confirms the accuracy of the 13CO-N2 potential energy surface for the 1460 cm-1 collision energy studied by experiment. Experimental results for 13CO + N2 are compared with those for 13CO + CO collisions. The angle-resolved product rotational angular momentum alignment moments for the two scattering systems are very similar, which indicates that the collision induced alignment dynamics observed for both systems are dominated by a hard-shell nature. However, compared to the 13CO + CO measurements, the primary rainbow maximum in the DCSs for 13CO + N2 is peaked consistently at more backward scattering angles and the secondary maximum becomes much less obvious, implying that the 13CO-N2 PES is less anisotropic. In addition, a forward scattering component with high rotational excitation seen for 13CO + CO does not appear for 13CO-N2 in the experiment and is not predicted by QCT theory. Some of these differences in collision dynamics behaviour can be predicted by a comparison between the properties of the PESs for the two systems. More specific behaviour is also predicted from analysis of the dependence on the relative collision geometry of 13CO + N2 trajectories compared to 13CO + CO trajectories, which shows the special 'do-si-do' pathway invoked for 13CO + CO is not effective for 13CO + N2 collisions.

Vibrational mode-specific quasi-classical trajectory studies for the two-channel HI + C2H5 reaction.

We report a detailed dynamics study on the mode-specificity of the HI + C2H5 two-channel reaction (H-abstraction and I-abstraction), through performing quasi-classical trajectory computations on a recently developed high-level ab initio full-dimensional spin-orbit-corrected potential energy surface, by exciting four different vibrational modes of reactants at five collision energies. The effect of the normal-mode excitations on the reactivity, the mechanism, and the post-reaction energy flow is investigated. Both reaction pathways are intensely promoted when the HI-stretching mode is excited while the excitations imposed on C2H5 somewhat surprisingly inhibit the dominant H-abstraction reaction pathway. The enhancement effect of the excitation in the HI vibrational mode is found to be much more effective than increasing the translational energy, similar to the HBr + C2H5 reaction. Not like the Br-abstraction pathway, however, the I-abstraction reaction pathway could be comparable to the dominant H-abstraction reaction pathway. The dominance of the direct stripping mechanism is indicated in H-abstraction while the direct rebound mechanism is observed in I-abstraction. The H-abstraction is much pickier about the initial attack angle distributions for HI than I-abstraction is, which leads to a decrease in reactivity in the H-abstraction reaction pathway. The dominance of side-on CH3CH2 attack in I-abstraction is more obvious than in the case of H-abstraction. In the case of the H-abstraction reaction pathway, the major part of the initial translational energy ends up in translational recoil, while for I-abstraction most energy excites the product C2H5I.

Potential energy surfaces for singlet and triplet states of the LiH2+ system and quasi-classical trajectory cross sections for H + LiH+ and H+ + LiH.

A new set of six accurate ab initio potential energy surfaces (PESs) is presented for the first three singlet and triplet states of LiH2+ (1,21A', 11A'', 1,23A', and 13A'' states, where four of them are investigated for the first time), which have allowed new detailed studies gaining a global view on this interesting system. These states are relevant for the study of the most important reactions of lithium chemistry in the early universe. More than 45 000 energy points were calculated using the multi-reference configuration interaction level of theory using explicitly correlated methods (ic-MRCI-F12), and the results obtained for each individual electronic state were fitted to an analytical function. Using quasiclassical trajectories and considering the initial diatomic fragment in the ground rovibrational state, we have determined the integral cross sections for the H + LiH+(X2Σ+, C2Π) and H+ + LiH(X1Σ+, B1Π) reactions. In these calculations all available reaction channels were considered: the chemically most important H or H+ transfer/abstraction as well as atom exchange and collision induced dissociation for up to 1.0 eV of collision energy.

Dissociation cross sections and rates in O2 + N collisions: molecular dynamics simulations combined with machine learning.

The collision-induced dissociation reaction of O2 (v, j) + N, a fundamental process in nonequilibrium air flows around reentry vehicles, has been studied systematically by applying molecular dynamics simulations on the 2A', 4A' and 6A' potential energy surfaces of NO2 in a wide temperature range. In particular, we have directly investigated the role of the 6A' surface in this process and discussed the applicability of the simplified approximate rate models proposed by Esposito et al. and Andrienko et al. based on the lowest two surfaces. The present work indicates that the state-selected dissociation of O2 + N is dominated by the 6A' surface for all except for the low-lying O2 states. Furthermore, a complete database of rovibrationally detailed cross sections and rate coefficients is a prerequisite for modeling the relevant nonequilibrium air flows in spacecraft reentry. Here, the combination of the quasi-classical trajectory (QCT) and the neural network (NN) has been proposed to predict all state-selected dissociation cross sections and further construct dissociation parameter sets. All NN-based models established in this work accurately reproduce the results calculated from QCT simulations over a wide range of rovibrational quantum numbers with R2 > 0.99. Compared with the explicit QCT simulations, the computational requirement for predicting cross sections and rates based on the NN models significantly reduces. Finally, thermal equilibrium rate coefficients computed from NN models match remarkably well the available theoretical and experimental results in the whole temperature range explored.

Formation and fragmentation of 2-hydroxyethylhydrazinium nitrate (HEHN) cluster ions: a combined electrospray ionization mass spectrometry, molecular dynamics and reaction potential surface study.

The 2-hydroxyethylhydrazinium nitrate ([HOCH2CH2NH2NH2]+NO3-, HEHN) ionic liquid has the potential to power both electric and chemical thrusters and provide a wider range of specific impulse needs. To characterize its capabilities as an electrospray propellant, we report the formation of HEHN cluster ions in positive electrospray ionization (ESI) and their collision-induced dissociation. The experiment was carried out using ESI guided-ion beam mass spectrometry which mimics an electrospray thruster in terms of ion emission, injection into a vacuum and fragmentation in space. Measurements include compositions of primary ions in the electrospray plume and their individual dissociation product ion cross sections and threshold energies. The results were interpreted in light of theoretical modeling. To determine cluster structures that are comprised of [HE + H]+ and NO3- constituents, classical mechanics simulations were used to create initial guesses; and for clusters that are formed by reactions between ionic constituents, quasi-classical direct dynamics trajectory simulations were used to mimic covalent bond formation and structures. All candidate structures were subject to density functional theory optimization, from which global minimum structures were identified and used for construction of reaction potential energy surface. The comparison between experimental values and calculated dissociation thermodynamics was used to verify the structures for the emitted species [(HEHN)nHE + H]+, [(HEHN)n(HE)2 + H]+, [(HE)n+1 + H]+ and [(HE)nC2H4OH]+ (n = 0-2), of which [(HE)1-2 + H]+ dominates. Due to the protic nature of HEHN, cluster fragmentation can be rationalized by proton transfer-mediated elimination of HNO3, HE and HE·HNO3, and the latter two become dominant in larger clusters. [(HE)2 + H]+ and [(HE)nC2H4OH]+ contain H-bonded water and consequently are featured by water elimination in fragmentation. These findings help to evaluate ion formation and fragmentation efficiencies and their impacts on electrospray propulsion.

Efficient quasi-classical trajectory calculations by means of neural operator architectures.

An accurate description of non-equilibrium chemistry relies on rovibrational state-to-state (StS) kinetics data, which can be obtained through the quasi-classical trajectory (QCT) method for high-energy collisions. However, these calculations still represent one of the major computational bottlenecks in predictive simulations of non-equilibrium reacting gases. This work addresses this limitation by proposing SurQCT, a novel machine learning-based surrogate for efficiently and accurately predicting StS chemical reaction rate coefficients. The QCT emulator is constructed using three independent components: two deep operator networks (DeepONets) for inelastic and exchange processes and a feed-forward neural network (FNN) for the dissociation reactions. SurQCT is tested on the O2 + O system, showing a computational speed-up of 85%. Furthermore, we carry out a StS master equation analysis of an isochoric, isothermal heat bath simulation at various temperatures to study how the predicted rate coefficients impact the accuracy of multiple quantities of interest (QoIs) at the kinetics level (e.g., global quasi-steady state (QSS) dissociation rate coefficients and energy relaxation times). For all these QoIs, the master equation analysis relying on SurQCT data shows an accuracy within 15% across the entire temperature regime.

Competition between the H-abstraction and the X-abstraction pathways in the HX (X = Br, I) + C2H5 reactions.

The recently-developed high-level full-dimensional spin-orbit-corrected potential energy surfaces based on ManyHF-UCCSD(T)-F12a/cc-pVDZ-F12 + SOcorr(MRCI-F12+Q(5,3)/cc-pVDZ-F12) (cc-pVDZ-PP-F12 for the Br and I atoms) energy points for the reactions of HX (X = Br, I) with C2H5 are improved by adding three to four thousand new geometries with higher energies at the same ab initio level to cover a higher-energy range. Quasi-classical trajectory simulations in the 30-80 kcal mol-1 collision energy range on the new surfaces are performed and show that as collision energy increases, the reaction probability of the submerged-barrier H-abstraction reaction pathway decreases a bit but the reactivity of the X-abstraction reaction, which has an apparent barrier, increases significantly, which leads to the co-domination of the two reaction pathways at high collision energies. The excitation in HX vibrational mode helps both reaction pathways, but more for X-abstraction. The mode-specific excitations in C2H5 inhibit the H-abstraction, especially for CH2 wagging mode, but almost no effect is found for X-abstraction. The deuterium effect is similar for both pathways. The sudden vector projection model can only predict the HX-stretching vibrational enhancements in X-abstraction. Forward/backward scattering is favored for H/X-abstraction, indicating the dominance of the direct stripping/rebound mechanism. The decrease of reactivity for the H-abstraction reaction pathway partly comes from the fact that the H-abstraction is much pickier about the initial attack angle. The reactivity of both reaction pathways increases when side-on CH3CH2 attack happens. The major part of the initial translational energy is preserved as translational energy in the products in H-abstraction, while for X-abstraction a large amount of it is transferred into the internal energy of C2H5X.

Theoretical studies on the kinetics and dynamics of the BeH+ + H2O reaction: comparison with the experiment.

The reaction of BeH+ with background gaseous H2O may play a role in qubit loss for quantum information processing with Be+ as trapped ions, and yet its reaction mechanism has not been well understood until now. In this work, a globally accurate, full-dimensional ground-state potential energy surface (PES) for the BeH+ + H2O reaction was constructed by fitting a total of 170 438 ab initio energy points at the level of RCCSD(T)-F12/aug-cc-pVTZ using the fundamental invariant-neural network method. The total root-mean-square error of the final PES was 0.178 kcal mol-1. For comparison, quasi-classical trajectory calculations were carried out on the PES at an experimental temperature of 150 K. The obtained thermal rate constant and product branching ratio of the BeD+ + H2O reaction agreed quite well with experimental results. In addition, the vibrational state distributions and energy disposals of the products were calculated and rationalized using the sudden vector projection model.

Effect of reactant’s rotational excitation on stereodynamic properties of C + SH($$v = 0, j =0{-}40$$) → H + CS reaction investigated with quasi-classical trajectory method

Effect of reactant’s rotational excitation on stereodynamic properties of C + SH($$v = 0, j =0{-}40$$) → H + CS reaction investigated with quasi-classical trajectory method

Low-temperature kinetics for the N + NO reaction: experiment guides the way.

The reaction N(4S) + NO(X2Π) → O(3P) + N2(X1Σ+g) plays a pivotal role in the conversion of atomic to molecular nitrogen in dense interstellar clouds and in the atmosphere. Here we report a joint experimental and computational investigation of the N + NO reaction with the aim of providing improved constraints on its low temperature reactivity. Thermal rates were measured over the 50 to 296 K range in a continuous supersonic flow reactor coupled with pulsed laser photolysis and laser induced fluorescence for the production and detection of N(4S) atoms, respectively. With decreasing temperature, the experimentally measured reaction rate was found to monotonously increase up to a value of (6.6 ± 1.3) × 10-11 cm3 s-1 at 50 K. To confirm this finding, quasi-classical trajectory simulations were carried out on a previously validated, full-dimensional potential energy surface (PES). However, around 50 K the computed rates decreased which required re-evaluation of the reactive PES in the long-range part due to a small spurious barrier with a height of ∼40 K in the entrance channel. By exploring different correction schemes the measured thermal rates can be adequately reproduced, displaying a clear negative temperature dependence over the entire temperature range. The possible astrochemical implications of an increased reaction rate at low temperature are also discussed.

Full-dimensional potential energy surface for the photodissociation of HNCO via its S1 band.

A full-dimensional potential energy surface (PES) for the first excited state S1(1A'') of HNCO has been built up by the neural network method based on more than 36 000 ab initio points, which were calculated at the multireference configuration interaction level with Davidson correction using the augmented correlation consistent polarized valence triple zeta basis set. It was found that two minima, namely, trans and cis isomers of HNCO, and another seven stationary points exist on the S1 PES for the two dissociation pathways: HNCO(S1) → H + NCO/NH + CO. Particularly, a new out-of-plane transition state between the two minima was found in this work, thanks to including all the degree of freedoms for this system. The adiabatic excitation energy of the S1(1A'') ← S0(1A') transition and dissociation energies D0(HNCO → H + NCO) and D0((HNCO →NH(a1Δ) + CO) calculated on the PES are in good agreement with experimental results. In addition, based on the newly constructed S1 PES, the percentage of products H + NCO in the photodissociation of HNCO(S1) was obtained by a quasi-classical trajectory method at the photon wavelengths ranging from 190 to 225 nm, which is in reasonably good agreement with earlier theoretical and experimental results. For the dissociation lifetimes of the trajectories, they were calculated to be less than 5 ps, which is also consistent with experimental observations.

Dynamic-dependent selectivity in a bisphosphine iron spin crossover C-H insertion/π-coordination reaction.

Reaction pathway selectivity is generally controlled by competitive transition states. Organometallic reactions are complicated by the possibility that electronic spin state changes rather than transition states can control the relative rates of pathways, which can be modeled as minimum energy crossing points (MECPs). Here we show that in the reaction between bisphosphine Fe and ethylene involving spin state crossover (singlet and triplet spin states) that neither transition states nor MECPs model pathway selectivity consistent with experiment. Instead, single spin state and mixed spin state quasiclassical trajectories demonstrate nonstatistical intermediates and that C-H insertion versus π-coordination pathway selectivity is determined by the dynamic motion during reactive collisions. This example of dynamic-dependent product outcome provides a new selectivity model for organometallic reactions with spin crossover.

Theoretical vibrational mode-specific dynamics studies for the HBr + C2H5 reaction.

A quasi-classical trajectory (QCT) study is performed for the HBr + C2H5 multi-channel reaction using a recently-developed high-level ab initio full-dimensional spin-orbit-corrected potential energy surface (PES) by exciting five different vibrational modes of reactants at five collision energies. The effect of the normal-mode excitations on the reactivity, the mechanism, and the post-reaction energy flow is followed. A significant decrease of the reactivity caused by the longer initial distances of the reactants for the vHBr = 1 reaction at low collision energy (Ecoll) is observed due to the intramolecular vibrational-energy redistribution and the classical nature of the QCT method. All of the three reaction pathways (H-abstraction, Br-abstraction, and H-exchange) are intensely promoted when the HBr-stretching mode is excited. No clear promotion is observed when excitation is imposed to C2H5 except that asymmetric CH-stretching helps the H-exchange process. The enhancement effect of the excitation in the HBr vibrational mode is found to be much more effective than increasing the translational energy, in contrast to the HBr + CH3 reaction. The forward scattering mechanism can be clearly promoted by the excitation of the HBr-stretching mode, or by the high collision energy, indicating the dominance of the direct stripping mechanism in these cases. At low collision energy with no excitation or excitation of any vibrational mode of C2H5, the forward scattering feature is less obvious. At Ecoll = 1 kcal mol-1, when HBr-stretching is excited, the product clearly gains more relative translational energy. However, it is interesting to see that when the excitation is in C2H5, the effect is the opposite, i.e., the product gains less relative translational energy compared to the ground-state reaction.

Full-dimensional automated potential energy surface development and detailed dynamics for the CH2OO + NH3 reaction.

With the help of the ROBOSURFER program package, a global full-dimensional potential energy surface (PES) for the reaction of the Criegee intermediate, CH2OO, with the NH3 molecule is developed iteratively using different ab initio methods and the monomial symmetrization fitting approach. The final permutationally-invariant analytical PES is constructed based on 23447 geometries and the corresponding ManyHF-based CCSD(T)-F12b/cc-pVTZ-F12 energies. The accuracy of the PES is confirmed by the excellent agreement of its stationary-point properties and one-dimensional potential energy curves compared with the corresponding ab initio data. The reaction probabilities and integral cross sections are calculated for the ground-state and several vibrationally excited-state reactions by quasi-classical trajectory simulations. Remarkable is that the maximum impact parameter b where reactivity vanishes is almost independent of collision energy ranging from 1 to 40 kcal mol-1, and the reaction probability increases with increasing collision energy for this negative-barrier reaction. At the same time, a slight mode-specificity effect is observed. In addition, the deuterium effect is investigated and the sudden vector projection is discussed.