Polyatomic Reactions Research Articles

An efficient and universal parallel algorithm for high-dimensional quantum dynamics in poly-atomic reactions.

This study presents a parallel algorithm for high-dimensional quantum dynamics simulations in poly atomic reactions, integrating distributed- and shared-memory models. The distributions of the wave function and potential energy matrix across message passing interface processes are based on bundled radial and angular dimensions, with implementations featuring either two- or one-sided communication schemes. Using realistic parameters for the H + NH3 reaction, performance assessment reveals linear scalability, exceeding 90% efficiency with up to 600 processors. In addition, owing to the universal and concise structure, the algorithm demonstrates remarkable extensibility to diverse reaction systems, as demonstrated by successes with six-atom and four-atom reactions. This work establishes a robust foundation for high-dimensional dynamics studies, showcasing the algorithm's efficiency, scalability, and adaptability. The algorithm's potential as a valuable tool for unraveling quantum dynamics complexities is underscored, paving the way for future advancements in the field.

Probing the dynamics and bottleneck of the key atmospheric SO2 oxidation reaction by the hydroxyl radical

SO2 (Sulfur dioxide) is the major precursor to the production of sulfuric acid (H2SO4), contributing to acid rain and atmospheric aerosols. Sulfuric acid formed from SO2 generates light-reflecting sulfate aerosol particles in the atmosphere. This property has prompted recent geoengineering proposals to inject sulfuric acid or its precursors into the Earth's atmosphere to increase the planetary albedo to counteract global warming. SO2 oxidation in the atmosphere by the hydroxyl radical HO to form HOSO2 is a key rate-limiting step in the mechanism for forming acid rain. However, the dynamics of the HO + SO2 → HOSO2 reaction and its slow rate in the atmosphere are poorly understood to date. Herein, we use photoelectron spectroscopy of cryogenically cooled HOSO2- anion to access the neutral HOSO2 radical near the transition state of the HO + SO2 reaction. Spectroscopic and dynamic calculations are conducted on the first ab initio-based full-dimensional potential energy surface to interpret the photoelectron spectra of HOSO2- and to probe the dynamics of the HO + SO2 reaction. In addition to the finding of a unique pre-reaction complex (HO⋯SO2) directly connected to the transition state, dynamic calculations reveal that the accessible phase space for the HO + SO2 → HOSO2 reaction is extremely narrow, forming a key reaction bottleneck and slowing the reaction rate in the atmosphere, despite the low reaction barrier. This study underlines the importance of understanding the full multidimensional potential energy surface to elucidate the dynamics of complex bimolecular reactions involving polyatomic reactants.

Construction of a Mode-Combination Hamiltonian under the Grid-Based Representation for the Quantum Dynamics of OH + HO2 → O2 + H2O.

In this work, a systematic construction framework on a mode-combination Hamiltonian operator of a typical polyatomic reaction, OH + HO2 → O2 + H2O, is developed. First, a set of Jacobi coordinates are employed to construct the kinetic energy operator (KEO) through the polyspherical approach ( Phys. Rep. 2009, 484, 169). Second, due to the multiconfigurational electronic structure of this system, a non-adiabatic potential energy surface (PES) is constructed where the first singlet and triplet states are involved with spin-orbital coupling. To improve the training database, the training set of random energy data was optimized through a popular iterative optimization approach with extensive trajectories. Here, we propose an automatic trajectory method, instead of the classical trajectory on a crude PES, where the gradients are directly computed by the present ab initio calculations. Third, on the basis of the training set, the potential function is directly constructed in the canonical polyadic decomposition (CPD) form ( J. Chem. Theory Comput. 2021, 17, 2702-2713) which is helpful in propagating the nuclear wave function under the grid-based representation. To do this, the Gaussian process regression (GPR) approach for building the CPD form, called the CPD-GPR method ( J. Phys. Chem. Lett. 2022, 13, 11128-11135) is adopted where we further revise CPD-GPR by introducing the mode-combination (mc) scheme leading to the present CPD-mc-GPR approach. Constructing the full-dimension non-adiabatic Hamiltonian operator with mode combination, as test calculations, the nuclear wave function is propagated to preliminarily compute the reactive probability of OH + HO2 → O2 + H2O where the reactants are prepared in vibrational ground states and in the first triplet electronic state.

Quantum dynamics study of C—H stretching vibrational excitation in the F+CHD<sub>3</sub> → HF+CD<sub>3</sub> reaction

In recent decades, significant progress has been made in the precise theoretical investigation of gas-phase chemical reactions. Presently, a major challenge in the field of quantum dynamics is to develop the precise methodologies for studying chemical reactions involving more than four atoms. As a typical multi-atomic reaction system, the F+CH<sub>4</sub> reaction and its isotopic substitution reactions have attracted widespread attention from both experimental and theoretical perspectives in recent years. Experimental studies on the reaction of F+CHD<sub>3</sub> have revealed that the stretching vibration excitation of the C—H bond inhibits the bond dissociation, favoring the formation of DF+CHD<sub>2</sub> product channels. In this study, we use a seven-dimensional quantum time-dependent wave packet method to investigate the dynamics of the F+CHD<sub>3</sub> reaction in both the reactant vibrational ground state and the first stretching excited state of the C—H bond. In this work, the reaction probabilities under different vibrational conditions are analyzed, showing that when the collision energy is below 0.06 eV, the reaction probability curves exhibit numerous fast-oscillating peaks, supporting the experimentally suggested phenomena of dynamic resonance. In a collision energy range from 0.06 eV to 0.3 eV, the reaction probability for the HF product channel in the vibrational excited state is lower than that in the ground state, which is consistent with experimental observation. Through the analysis of the time-independent wave functions of product channels under low-energy collision conditions, it is found that for reactions involving vibrational ground states, the HF products in the product asymptotic region and the reaction transition state region are in the <i>v'</i> = 2 excited state and <i>v'</i> = 3 excited state of stretching vibration, respectively, which are consistent with previous experimental observations and six-dimensional quantum wave packet simulations. For reactions involving the first excited state of C—H stretching vibration, the HF products in the product asymptotic region and the reaction transition state region are both in the <i>v'</i> = 3 excited state of stretching vibration, which are consistent with the results obtained based on energy analysis. Simulation results indicate that in the case of low-energy collisions, the time-independent wave function for the C—H stretching vibrational excited state tends to be closer to the D atom side in the transition state region. This phenomenon is attributed to the more significant energy advantage of the vibrational excited state potential energy surface in the large collision angle region, explaining the inhibitory effect of stretching vibration excitation on the HF product channel. This study offers important theoretical support for explaining experimental results and contributes to a more in-depth understanding of the influence of vibrational mode excitations on the dynamical processes in poly-atomic reactions.

A quasi-classical study in a quantum spirit of mode specificity of the H + HOD abstraction reaction.

Quantum benchmark calculations of the H + HOD abstraction reaction [B. Zhao et al., Phys. Chem. Chem. Phys., 2018, 20, 17029-17037] provide an opportunity to test approximate methods, such as quasi-classical trajectories (QCTs) with Gaussian binning. However, the large mode-specific enhancements of this reaction lead to special challenges and unphysical QCT cross-section artifacts. We propose and apply a general backward-forward-backward (BFB) trajectory procedure to avoid cross-section artifacts arising from vibrational motion delocalization of the initially prepared reactants. We also develop and apply a general hybrid weighting scheme, in which vibrationally adiabatic products receive unit weights, while vibrationally non-adiabatic products are Gaussian weighted. Motivated by examination of the product vibrational actions, the hybrid weighting is necessary to avoid large cross-section errors. These QCTs with Gaussian weighting extensions are general and are recommended for future polyatomic reaction simulations.

Computational investigation of chemical and non-equilibrium effects on the Richtmyer–Meshkov instability

In order to study the reactive Richtmyer–Meshkov instability (RMI) at a microscale, we have implemented a direct simulation Monte Carlo (DSMC) method which is recently developed for resolving thermal–chemical processes at the scale of molecular motions. The method allows efficient simulations of polyatomic reactions and non-equilibrium processes without violation of the detailed balance which is generically suffered by the conventional algorithms and leads to failure of local thermal equilibrium eventually. With attainment of essential accuracy, the effects of nonequilibrium and chemical reactions on the evolution of two-dimensional (2D) RMI at the microscale are investigated. The results show that the nonequilibrium effect slows down the heat release of chemical reactions and strengthens the viscous and diffusive effects for the mixture and shock conditions tested, which inhibit the growth of the RM instability. The heat release via combustion, however, can substantially increase the RMI growth due to induced baroclinic torque. Consequently, the intricate coupling of these effects nonlinearly dominates the development of RMI at the microscale. Therefore, the influence of nonequilibrium conditions where the translational energy is higher than that of the internal modes of polyatomic molecules, specifically the vibrational energy, in the post-shock region should be considered. The procedure provides a paradigm for further research in pursuit of accurate evaluation of microscopic processes and the resulted performance in supersonic combustion that plays a key role in the development of hypersonic vehicles.

State-to-State Dynamics in Mode-Selective Polyatomic Reactions.

Chemical reactions are intrinsically quantum mechanical transformations of reactants to products. Recent experimental and theoretical advances have enabled the exploration of reaction dynamics with a quantum state resolution for both reactants and products. To this end, reactions involving more than three atoms are of particular interest, because they exhibit rich dynamics concerning the role of different reactant modes in controlling reactivity and product energy disposal. A clear understanding of the state-to-state dynamics requires new paradigms. In this Perspective, we examine some new concepts that have emerged from recent state-to-state studies of polyatomic reactions and illustrate the key role played by the transition state.

Accurate fundamental invariant-neural network representation of ab initio potential energy surfaces.

Highly accurate potential energy surfaces are critically important for chemical reaction dynamics. The large number of degrees of freedom and the intricate symmetry adaption pose a big challenge to accurately representing potential energy surfaces (PESs) for polyatomic reactions. Recently, our group has made substantial progress in this direction by developing the fundamental invariant-neural network (FI-NN) approach. Here, we review these advances, demonstrating that the FI-NN approach can represent highly accurate, global, full-dimensional PESs for reactive systems with even more than 10 atoms. These multi-channel reactions typically involve many intermediates, transition states, and products. The complexity and ruggedness of this potential energy landscape present even greater challenges for full-dimensional PES representation. These PESs exhibit a high level of complexity, molecular size, and accuracy of fit. Dynamics simulations based on these PESs have unveiled intriguing and novel reaction mechanisms, providing deep insights into the intricate dynamics involved in combustion, atmospheric, and organic chemistry.

The direct and steady state rate constants of C2H6+X (X=H, Cl, OH): Influence of van der Waals well

The reaction of ethane with atom or radical is the benchmark system to study the kinetics and dynamics of polyatomic chemical reaction. The rate constants and kinetic isotope effects for...

Unconventional SN2 retention pathways induced by complex formation: High-level dynamics investigation of the NH2 - + CH3I polyatomic reaction.

Investigations on the dynamics of chemical reactions have been a hot topic for experimental and theoretical studies over the last few decades. Here, we carry out the first high-level dynamical characterization for the polyatom-polyatom reaction between NH2 - and CH3I. A global analytical potential energy surface is developed to describe the possible pathways with the quasi-classical trajectory method at several collision energies. In addition to SN2 and proton abstraction, a significant iodine abstraction is identified, leading to the CH3 + [NH2⋯I]- products. For SN2, our computations reveal an indirect character as well, promoting the formation of [CH3⋯NH2] complexes. Two novel dominant SN2 retention pathways are uncovered induced by the rotation of the CH3 fragment in these latter [CH3⋯NH2] complexes. Moreover, these uncommon routes turn out to be the most dominant retention paths for the NH2 - + CH3I SN2 reaction.

Mechanism and Kinetics of Methane Combustion. Part II: Potential Energy Surface for Hydrogen-Abstraction Reaction of CH4 + O(3P).

Methane combustion plays an important role in various fields such as combustion chemistry and atmospheric chemistry of the stratosphere. Highly accurate study of its initial reaction remains a key challenge. Here, through extensive studies with a state-of-the-art ab initio and neural network method, we present a potential energy surface of the O(3P) + CH4 → OH + CH3 reaction on the ground state 13A and the first excited state 23A. In this work, the energies of 10 167 points covering all important regions are obtained with state-averaged complete active space self-consistent field calculations and then fitted using the Levenberg-Marquardt algorithm with a root-mean-square error of 0.391 and 0.442 kcal/mol for the 13A and 23A states, respectively. This study explores the characteristics of the radical van der Waals (VdW) complex and reveals a detailed mechanism of the methane combustion initial reaction. Within the scope of this mechanism, this surface gives a fairly accurate description of the regions around the saddle point, conical intersection, and vdW wells in the entrance for efficient computational simulations. As a theoretical study on a prototypical polyatomic reaction, it is hopeful that this work will modify our understanding of the primary process in hydrocarbon combustion.

Toward a Comprehensive Understanding of Mode-Specific Dynamics of Polyatomic Reactions: A Full-Dimensional Quantum Dynamics Study of the H + NH3 Reaction.

Mode specificity not only sheds light on reaction dynamics but also opens the door for chemical reaction control. This work reports a state-of-the-art full-dimensional quantum dynamics study on the prototypical hydrogen abstraction reaction of hydrogen with ammonia, which serves as a benchmark for advancing our fundamental understanding of polyatomic reaction dynamics. By taking advantage of the (3 + 1) Radau-Jacobi coordinates, the bond-specific probabilities are resolved with the reactant NH3 initiated from either a non-degenerate or degenerate stretching vibrational state. The observed different atom-specific abstraction probabilities from individual states of the degenerate pair are rationalized in the local mode representation according to the different vibrational energy deposited in each N-H bond. It is verified that the three H atoms in NH3 have the same abstraction probability as that from the degenerate pair and the linear combination of the degenerate pair gives the same reaction probability. In addition, the symmetric and asymmetric stretching modes of the reactant NH3 have comparable efficacies on driving the reaction.

A chemical dynamics study of the reaction of the methylidyne radical (CH, X2Π) with dimethylacetylene (CH3CCCH3, X1A1g).

The gas-phase reaction of the methylidyne (CH; X2Π) radical with dimethylacetylene (CH3CCCH3; X1A1g) was studied at a collision energy of 20.6 kJ mol-1 under single collision conditions with experimental results merged with ab initio calculations of the potential energy surface (PES) and ab initio molecule dynamics (AIMD) simulations. The crossed molecular beam experiment reveals that the reaction proceeds barrierless via indirect scattering dynamics through long-lived C5H7 reaction intermediate(s) ultimately dissociating to C5H6 isomers along with atomic hydrogen with atomic hydrogen predominantly released from the methyl groups as verified by replacing the methylidyne with the D1-methylidyne reactant. AIMD simulations reveal that the reaction dynamics are statistical leading predominantly to p28 (1-methyl-3-methylenecyclopropene, 13%) and p8 (1-penten-3-yne, 81%) plus atomic hydrogen with a significant amount of available energy being channeled into the internal excitation of the polyatomic reaction products. The dynamics are controlled by addition to the carbon-carbon triple bond with the reaction intermediates eventually eliminating a hydrogen atom from the methyl groups of the dimethylacetylene reactant forming 1-methyl-3-methylenecyclopropene (p28). The dominating pathways reveal an unexpected insertion of methylidyne into one of the six carbon-hydrogen single bonds of the methyl groups of dimethylacetylene leading to the acyclic intermediate, which then decomposes to 1-penten-3-yne (p8). Therefore, the methyl groups of dimethylacetylene effectively 'screen' the carbon-carbon triple bond from being attacked by addition thus directing the dynamics to an insertion process as seen exclusively in the reaction of methylidyne with ethane (C2H6) forming propylene (CH3C2H3). Therefore, driven by the screening of the triple bond, one propynyl moiety (CH3CC) acts in four out of five trajectories as a spectator thus driving an unexpected, but dominating chemistry in analogy to the methylidyne - ethane system.

Vibrational and Rotational Gaussian Binning selections on QCT calculations for the OH + D2 → HOD((vHO’, vHOD’, vOD’), J’) + D reaction

Abstract A large sample has been employed to obtain total reaction cross sections and product state distributions (translational, vibrational and rotational) for the title reaction. Quasi-Classical Trajectory (QCT) calculations and the Gaussian Binning (GB) methodology have been used on Wu-Schatz-Lendvay-Fang-Harding (WSLFH) and Neural Networks (NN) potential energy surfaces. After a first selection, Vibrational-Gaussian Binning (V-GB), (vHO’, vHOD’, vOD’), and a second selection, Rotational-Gaussian Binning (R-GB), although the preference observed (odd or even J') is not exactly followed by each vibrational excitation of HOD, there is a similar behavior to the physical laser phenomenon observed in another triatomic molecule utilized in the gas laser of CO2. The dynamics of polyatomic chemical reactions (e.g., OH + D2 → HOD* + D and its isotopic variants), of relevance in the excitation/emission processes of current and future chemical lasers, could be studied theoretically from the results obtained in this article.

About Chemical Modifications of Finite Dimensional QED Models

Suggestion of modifications of finite-dimensional quantum-electrodynamic (QED) models are proposed for interpreting chemical reactions in terms of artificial atoms and molecules on quantum dots placed in optical cavities. Moving both photons and atoms is possible between the cavities. Super dark states of diatomic systems are described, in which the motion of atoms between cavities is impossible due to quantum interference. Chemical processes with two level atoms and three level atoms with lambda spectrum are schematically modeled by solving the single quantum master equation with the Lindblad operators of photon leakage from the cavity and influx into it; association and dissociation reactions then differ only in the initial states. An example is given of the optical interpretation of the transition of an electron from atom to atom in terms of the multilevel Tavis-Cummings-Hubbard model with an estimate of the accuracy. Polyatomic chemical reactions are too complex for accurate modeling. Our method of rough interpretation helps to obtain their long-term results, for example, the form of stationary states of reagents, such as dark and super dark states.

Atomistic dynamics of elimination and nucleophilic substitution disentangled for the F- + CH3CH2Cl reaction.

Chemical reaction dynamics are studied to follow and understand the concerted motion of several atoms while they rearrange from reactants to products. With the number of atoms growing, the number of pathways, transition states, and product channels also increases and rapidly presents a challenge to experiment and theory. Here, we disentangle the competition between bimolecular nucleophilic substitution (SN2) and base-induced elimination (E2) in the polyatomic reaction F- + CH3 CH2 Cl. We find quantitative agreement for the energy- and angle-differential reactive scattering cross sections between ion imaging experiments and quasi-classical trajectory simulations on a 21-dimensional potential energy hypersurface. The anti-E2 pathway is most important, but the SN2 pathway becomes more relevant as the collision energy is increased. In both cases the reaction is dominated by direct dynamics. Our study presents atomic level dynamics of a major benchmark reaction in physical organic chemistry, thereby pushing the number of atoms for detailed reaction dynamics studies to a size that allows applications in many areas of complex chemical networks and environments.

Fifty years of nucleophilic substitution in the gas phase.

Bimolecular nucleophilic substitution (SN2) reactions have become a model system for the investigation of structure–reactivity relationships, stereochemistry, solvent influences, and detailed atomistic dynamics. In this review, the progress during five decades of experimental and theoretical research on gas phase SN2 reactions is discussed. Many advancements of the employed methods have led to a tremendous increase in our understanding of the properties and the dynamics of these reactions. For reactions involving six atoms a quantitative agreement of the differential reactive scattering cross sections has already been achieved, in the future it is expected that even larger polyatomic reactions systems become tractable. Furthermore, studies with higher precision, improved reactant control, and a more accurate theoretical treatment of quantum effects are envisioned.

A chemical dynamics study on the gas-phase formation of triplet and singlet C5H2 carbenes

Since the postulation of carbenes by Buchner (1903) and Staudinger (1912) as electron-deficient transient species carrying a divalent carbon atom, carbenes have emerged as key reactive intermediates in organic synthesis and in molecular mass growth processes leading eventually to carbonaceous nanostructures in the interstellar medium and in combustion systems. Contemplating the short lifetimes of these transient molecules and their tendency for dimerization, free carbenes represent one of the foremost obscured classes of organic reactive intermediates. Here, we afford an exceptional glance into the fundamentally unknown gas-phase chemistry of preparing two prototype carbenes with distinct multiplicities-triplet pentadiynylidene (HCCCCCH) and singlet ethynylcyclopropenylidene (c-C5H2) carbene-via the elementary reaction of the simplest organic radical-methylidyne (CH)-with diacetylene (HCCCCH) under single-collision conditions. Our combination of crossed molecular beam data with electronic structure calculations and quasi-classical trajectory simulations reveals fundamental reaction mechanisms and facilitates an intimate understanding of bond-breaking processes and isomerization processes of highly reactive hydrocarbon intermediates. The agreement between experimental chemical dynamics studies under single-collision conditions and the outcome of trajectory simulations discloses that molecular beam studies merged with dynamics simulations have advanced to such a level that polyatomic reactions with relevance to extreme astrochemical and combustion chemistry conditions can be elucidated at the molecular level and expanded to higher-order homolog carbenes such as butadiynylcyclopropenylidene and triplet heptatriynylidene, thus offering a versatile strategy to explore the exotic chemistry of novel higher-order carbenes in the gas phase.

Measurement of rate constants for ion-ion reactions – O+ and N+ with the atomic halide anions Cl−, Br−, and I− at thermal energies

We present 300 K rate constants for the ion-ion reactions of O+andN+ with the atomic halide anions: Cl-,Br-,andI- measured using a flowing afterglow – Langmuir probe apparatus. All six rate constants were >1×10-8cm3s-1, larger than those typical for atomic ion – atomic ion reactions, approaching the rate constants of more complex ion-ion systems. Evaluation of literature atomic ion – atomic ion rate constants shows variation over orders of magnitude, but limited to below the expected value for a polyatomic ion-ion reaction of the same reduced mass, fitting into an expected physical picture. Unlike for polyatomic systems, estimation of rate constant for atomic ion – atomic ion reaction rates by simple means does not seem effective.

Mode specificity of a multi-channel reaction prototype: F + CH3OH → HF + CH3O/CH2OH

Mode-specific chemistry has been a hot research topic in the field of molecular reaction dynamics since different degrees of freedom play potentially divergent effects on the reactivity of different channels and the associated product branching ratios. In this work, we examine the mode specificity effect in the reaction F + CH3OH → HF + CH3O (R1)/CH2OH (R2), a prototypical polyatomic reaction with multiple channels and submerged barriers, by extensive vibrational state-specific molecular dynamical calculations with the quasi-classical trajectory approach on a globally accurate full-dimensional potential energy surface. Complicated mode specificity effects are revealed. In particular, the vibrational excitations of the O–H stretching motion and the torsional motion with respect to the C–O axis can enhance the reactivity of R1 significantly. The excitations of the C–H stretching vibrational motions do not influence R1. For another channel, R2, the C–H stretching vibrational excitation shows some weak enhancement effect, while the O–H stretching vibrational excitation shows no effect on the reactivity. Then, the sudden vector projection model is employed to rationalize the mode specificity effects and understand the product energy partitioning in the two channels. The ro-vibrational state distributions of the nascent product HF/DF from F + CH3OH/CH3OD/CD3OH/CD3OD are also in good agreement with available experiments.