ABLRI: A program for calculating the long-range interaction energy between two monomers in their non-degenerate states.

An accurate description of the long-range (LR) interaction is essential for understanding the collision between cold or ultracold molecules. However, to our best knowledge, there lacks a general approach to construct the intermolecular potential energy surface (IPES) between two arbitrary molecules and/or atoms in the LR region. In this work, we derived analytical expressions of the LR interaction energy, using the multipole expansion of the electrostatic interaction Hamiltonian and the non-degenerate perturbation theory. To make these formulae practical, we also derived the independent Cartesian components of the electrostatic properties, including the multipole moments and polarizabilities, of the monomer for a given symmetry using the properties of these components and the group-theoretical methods. Based on these newly derived formulae, we developed a FORTRAN program, namely ABLRI, which is capable of calculating the interaction energy between two arbitrary monomers both in their non-degenerate electronic ground states at large separations. To test the reliability of this newly developed program, we constructed IPESs for the electronic ground state of H2O-H2 and O2-H systems in the LR region. The interaction energy computed by our program agreed well with the ab initio calculation, which shows the validity of this program.

Impact of Geometric Phase on Dynamics of Complex-Forming Reactions: H + O2 → OH + O.

Reaction dynamics on the ground electronic state might be significantly influenced by conical intersections (CIs) via the geometric phase (GP), as demonstrated for activated reactions (i.e., the H + H2 exchange reaction). However, there have been few investigations of GP effects in complex-forming reactions. Here, we report a full quantum dynamical study of an important reaction in combustion (H + O2 → OH + O), which serves as a proving ground for studying GP effects therein. The results reveal significant differences in reaction probabilities and differential cross sections (DCSs) obtained with and without GP, underscoring its strong impact. However, the GP effects are less pronounced for the reaction integral cross sections, apparently due to the integral of the DCS over the scattering angle. Further analysis indicated that the cross section has roughly the same contributions from the two topologically distinct paths around the CI, namely, the direct and looping paths.

Isotope Effects on State-to-State Photodissociation Dynamics of D2S in Its First Absorption Band.

State-to-state photodissociation dynamics of D2S in its first absorption band were explored by utilizing recently developed diabatic potential energy surfaces (PESs). Quantum dynamics calculations, involving the first two strongly coupled 1A″ states, were executed employing a Chebyshev real wavepacket method. The nonadiabatic channel via the conical intersection (CI) is facile, direct, and fast, leading to the production of rotationally and vibrationally cold SD(X̃2Π). The calculated absorption spectrum, product state distributions, and angular distributions are in reasonable agreement with the experimental results, although some discrepancies exist at 193.3 nm. Compared with H2S, there are obvious isotope effects on rotational state distributions for D2S photodissociation in its first absorption band. Moreover, we scrutinize the variation of product state distributions as a function of photon energy and the vibrational mediated photodissociation of the parent molecule. Due to the diverse shapes of the three fundamental vibrational wave functions, photoexcited wavepackets access distinct segments of the upper-state PES, resulting in a disparate absorption spectrum and ro-vibrational distributions via the nonadiabatic transition. This study provides a comprehensive figure of the isotopic effect and wavelength dependence on the photofragmentation behaviors from D2S photodissociation, which should attract more experimental and theoretical attention to this prototypical system.

Dynamics studies for the multi-well and multi-channel reaction of OH with C2H2 on a full-dimensional global potential energy surface.

The C2H2 + OH reaction is an important acetylene oxidation pathway in the combustion process, as well as a typical multi-well and multi-channel reaction. Here, we report an accurate full-dimensional machine learning-based potential energy surface (PES) for the C2H2 + OH reaction at the UCCSD(T)-F12b/cc-pVTZ-F12 level, based on about 475 000 ab initio points. Extensive quasi-classical trajectory (QCT) calculations were performed on the newly developed PES to obtain detailed dynamic data and analyze reaction mechanisms. Below 1000 K, the C2H2 + OH reaction produces H + OCCH2 and CO + CH3. With increasing temperature, the product channels H2O + C2H and H + HCCOH are accessible and the former dominates above 1900 K. It is found that the formation of H2O + C2H is dominated by a direct reaction process, while other channels belong to the indirect mechanism involving long-lived intermediates along the reaction pathways. At low temperatures, the C2H2 + OH reaction behaves like an unimolecular reaction due to the unique PES topographic features, of which the dynamic features are similar to the decomposition of energy-rich complexes formed by C2H2 + OH collision. The classification of trajectories that undergo different reaction pathways to generate each product and their product energy distributions were also reported in this work. This dynamic information may provide a deep understanding of the C2H2 + OH reaction.

A New Full-Dimensional Ab Initio Intermolecular Potential Energy Surface and Rovibrational Energies of the H2O-H2 Complex.

H2O-H2 is a prototypical five-atom van der Waals system, and the interaction between H2O and H2 plays an important role in many physical and chemical environments. However, previous full-dimensional intermolecular potential energy surfaces (IPESs) cannot accurately describe the H2O-H2 interaction in the repulsive or van der Waals minimum region. In this work, we constructed a full-dimensional IPES for the title system with a small root-mean-square error of 0.252 cm-1 by using the permutation invariant polynomial neural network method. The ab initio calculations were performed by employing the explicitly corrected coupled cluster [CCSD(T)-F12a] method with the augmented correlation-consistent polarized valence quintuple-ζ basis set. Based on the newly developed IPES, the bound states of the H2O-H2 complex were calculated within the rigid-rotor approximation. The transition frequencies and band origins agreed well with the experimental values [Weida, M. J.; Nesbitt, D. J. J. Chem. Phys. 1999, 110, 156-167] with errors less than 0.1 cm-1 for most transitions. Those results demonstrate the high accuracy of our new IPES, which would build a solid foundation for the collisional dynamics of H2O-H2 at low temperatures.

Formation Mechanisms of Electronically Excited Nitrogen Molecules from N + N2 and N + N + N Collisions Revealed by Full-Dimensional Potential Energy Surfaces.

This work reports six new full-dimensional adiabatic potential energy surfaces (PESs) of the N3 system (four 4A″ states and two 2A″ states) at the MRCI + Q/AVQZ level of theory that correlated to N2(X1Σg+) + N(4S), N2(X1Σg+) + N(2D), N2(A3Σu+) + N(4S), N2(B3Πg) + N(4S), N2(W3Δu) + N(4S), and N(4S) + N(4S) + N(4S) channels. The neural networks with a proper account of the nuclear permutation invariant symmetry of N3 were employed to fit the PESs based on about 4000 ab initio points. The accuracy of the PESs was validated by excellent agreement on the equilibrium bond length, vertical excitation energy, and dissociation energy with experimental values. Two possible mechanisms of the formation of N2(A) were found. One is that the collision occurs between N2(X) and N(4S) in the 14A″ state, followed by a nonadiabatic transition through the conical intersection with the 24A″ PES, resulting in the formation of the N2(A) + N(4S) product. The other takes place in the collision among three N(4S) atoms in the adiabatic 24A″ state, and then, N2(A) + N(4S) is formed. This is the first systematical research of the N3 system focusing on the formation of the excited states of N2 via both adiabatic and nonadiabatic pathways.

Quantum Dynamics of Photodissociation: Recent Advances and Challenges.

Recent advances in constructing accurate potential energy surfaces and nonadiabatic couplings from high-level ab initio data have revealed detailed potential landscapes in not only the ground electronic state but also excited ones. They enabled quantitatively accurate characterization of photoexcited reactive systems using quantum mechanical methods. In this Perspective, we survey the recent progress in quantum mechanical studies of adiabatic and nonadiabatic photodissociation dynamics, focusing on initial state control and product energy disposal. These new insights helped to understand quantum effects in small prototypical systems, and the results serve as benchmarks for developing more approximate theoretical methods.

Full quantum scattering calculations of the line-shape parameters for the P and R branches of HF perturbed by Ar.

This work studied the rovibrational absorption spectral line-shape parameters of the P(1)-P(10) and R(0)-R(9) lines for Hydrogen fluoride perturbed by argon in the 0-0, 1-0, and 2-0 vibrational bands at 20-1000 K. A dataset of beyond-Voigt line-shape parameters (pressure broadening and shifting parameters, their speed dependencies, and the complex Dicke parameters) has been theoretically determined for the first time from generalized spectroscopic cross-section calculated by the full quantum scattering calculations. Then these parameters were employed to predict the line shape and asymmetry based on the partially-correlated speed-dependent hard-collision and the partially-correlated quadratic-speed-dependent hard-collision profiles. The effect of each parameter on the line shape and line asymmetry was further studied, which revealed that the beyond-Voigt effects were indispensable to accurately describe the line shape contour. Our results are in good agreement with the available experimental observations and provide a comprehensive set of theoretical references for further experimental measurements.

New accurate diabatic potential energy surfaces for the two lowest 1A'' states of H2S and photodissociation dynamics in its first absorption band.

In this work, state-to-state photodissociation dynamics of H2S in its first absorption band has been studied quantum mechanically with a new set of coupled potential energy surfaces (PESs) for the first two 1A'' excited states, which were developed at the explicitly correlated internally contracted multi-reference configuration interaction level with the cc-pVQZ-F12 basis set and a large active space. The calculated absorption spectrum, product state distributions, and angular distributions are in excellent agreement with available experimental data, validating the accuracy of the PESs and the non-adiabatic couplings. Detailed analysis of the dynamics reveals that there are strong non-adiabatic couplings between the bound 11B1 and dissociative 11A2 states around the Franck-Condon region, leading to very fast predissociation to ro-vibrationally cold SH(X̃) fragments, during which marginal angular anisotropy of the PESs is involved. This study provides quantitatively accurate characterization of the electronic structure and detailed fragmentation dynamics of this prototypical photodissociation system, which is desirable for improving astrochemical modelling.

Computational investigation on the binding modes of PET polymer to PETase.

Poly(ethylene terephthalate) (PET) has been widely utilized in daily life, but its non-degradability has induced severe environmental and health problems. Recently, PETase, which has been isolated from bacterium Ideonella sakaiensisis, was reported to have the highest PET degradation activity and specificity under room temperature, but no crystal structure for PET in complex with PETase has been reported. To provide deep insight into the binding mode of PET polymer on PETase and the binding interactions, we employed molecular docking and molecular dynamics simulations to study the substrate binding at the atomic level. Different PET oligomers have been studied with chain lengths varying from 2 to 8. In addition, the binding energies and hot-spot residues were analyzed to gain better insights into the binding mechanism by MM/GBSA approach. The PET oligomers adopt stable and reactive conformations in a shallow cleft on a flat surface of PETase. The binding cleft can only accommodate four moieties, and others beyond the region will be stabilized by the π-stacking interactions with Trp156 at the terephthalic acid terminal. Our studies provide a clear picture of how the binding mode of PET polymer and its interactions with PETase change with the chain length. Those studies would provide useful information for the rational design of catalytically more efficient PETase variants toward plastic degradation.Communicated by Ramaswamy H. Sarma.

Accurate Full-Dimensional Global Diabatic Potential Energy Matrix for the Two Lowest-Lying Electronic States of the H + O2 ↔ HO + O Reaction.

A new and more accurate diabatic potential energy matrix (DPEM) is developed for the two lowest-lying electronic states of HO2, covering both the strong interaction region and reaction asymptotes. The ab initio calculations were performed at the Davidson corrected multireference configuration interaction level with the augmented correlation-consistent polarized valence quintuple-zeta basis set (MRCI+Q/AV5Z). The accuracy of the electronic structure calculations is validated by excellent agreement with the experimental HO2 equilibrium geometry, fundamental vibrational frequencies, and H + O2 ↔ OH + O reaction energy. Through the combination of an electronic angular momentum-method and a configuration interaction vector-based method, the mixing angle between the first two 2A″ states of HO2 was successfully determined. Elements of the 2×2 DPEM were fit to neural networks with a proper account of the complete nuclear permutation inversion symmetry of HO2. The DPEM correctly predicted the properties of conical intersection seams at linear and T-shape geometries, thus providing a reliable platform for studying both the spectroscopy of HO2 and the nonadiabatic dynamics for the H + O2 ↔ OH + O reaction.

The vibronic state dependent predissociation of H2S: determination of all fragmentation processes.

Photochemistry plays a significant role in shaping the chemical reaction network in the solar nebula and interstellar clouds. However, even in a simple triatomic molecule photodissociation, determination of all fragmentation processes is yet to be achieved. In this work, we present a comprehensive study of the photochemistry of H2S, derived from cutting-edge translational spectroscopy measurements of the H, S(1D) and S(1S) atom products formed by photolysis at wavelengths across the range 155-120 nm. The results provide detailed insights into the energy disposal in the SH(X), SH(A) and H2 co-fragments, and the atomisation routes leading to two H atoms along with S(3P) and S(1D) atoms. Theoretical calculations allow the dynamics of all fragmentation processes, especially the bimodal internal energy distributions in the diatomic products, to be rationalised in terms of non-adiabatic transitions between potential energy surfaces of both 1A' and 1A'' symmetry. The comprehensive picture of the wavelength-dependent (or vibronic state-dependent) photofragmentation behaviour of H2S will serve as a text-book example illustrating the importance of non-Born-Oppenheimer effects in molecular photochemistry, and the findings should be incorporated in future astrochemical modelling.

ABC+D: A time-independent coupled-channel quantum dynamics program for elastic and ro-vibrational inelastic scattering between atoms and triatomic molecules in full dimensionality.

We discuss the details of a time-independent quantum mechanical method and its implementation for full-dimensional non-reactive scattering between a closed-shell triatomic molecule and a closed-shell atom. By solving the time-independent Schrödinger equation within the coupled-channel framework using a log-derivative method, the state-to-state scattering matrix (S-matrix) can be determined for inelastic scattering involving both the rotational and vibrational modes of the molecule. Various approximations are also implemented. The ABC+D code provides an important platform for understanding an array of physical phenomena involving collisions between atoms and molecules.

Accelerated Quantum Mechanics/Molecular Mechanics Simulations via Neural Networks Incorporated with Mechanical Embedding Scheme.

A powerful tool to study the mechanism of reactions in solutions or enzymes is to perform the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. However, the computational cost is too high due to the explicit electronic structure calculations at every time step of the simulation. A neural network (NN) method can accelerate the QM/MM-MD simulations, but it has long been a problem to accurately describe the QM/MM electrostatic coupling by NN in the electrostatic embedding (EE) scheme. In this work, we developed a new method to accelerate QM/MM calculations in the mechanic embedding (ME) scheme. The potentials and partial point charges of QM atoms are first learned in vacuo by the embedded atom neural networks (EANN) approach. MD simulations are then performed on this EANN/MM potential energy surface (PES) to obtain free energy (FE) profiles for reactions, in which the QM/MM electrostatic coupling is treated in the mechanic embedding (ME) scheme. Finally, a weighted thermodynamic perturbation (wTP) corrects the FE profiles in the ME scheme to the EE scheme. For two reactions in water and one in methanol, our simulations reproduced the B3LYP/MM free energy profiles within 0.5 kcal/mol with a speed-up of 30-60-fold. The results show that the strategy of combining EANN potential in the ME scheme with the wTP correction is efficient and reliable for chemical reaction simulations in liquid. Another advantage of our method is that the QM PES is independent of the MM subsystem, so it can be applied to various MM environments as demonstrated by an SN2 reaction studied in water and methanol individually, which used the same EANN PES. The free energy profiles are in excellent accordance with the results obtained from B3LYP/MM-MD simulations. In future, this method will be applied to the reactions of enzymes and their variants.

Recent advances in quantum theory on ro-vibrationally inelastic scattering.

Molecular collisions are of fundamental importance in understanding intermolecular interaction and dynamics. Its importance is accentuated in cold and ultra-cold collisions because of the dominant quantum mechanical nature of the scattering. We review recent advances in the time-independent approach to quantum mechanical characterization of non-reactive scattering in tetratomic systems, which is ideally suited for large collisional de Broglie wavelengths characteristic in cold and ultracold conditions. We discuss quantum scattering algorithms between two diatoms and between a triatom and an atom and their implementation, as well as various approximate schemes. They not only enable the characterization of collision dynamics in realistic systems but also serve as benchmarks for developing more approximate methods.

Full-Dimensional Quantum Dynamics Studies of Ro-vibrationally Inelastic Scattering of H2O with Ar: A Benchmark Test of the Rigid-Rotor Approximation.

While the rigid-rotor (RR) approximation is usually considered to be accurate for describing pure rotationally inelastic scattering involving diatoms in their ground or low-lying vibrational states, its validity in scattering involving polyatomic molecules has not been fully examined. The existence of soft/anharmonic vibrational modes in polyatomic molecules could make rotational-vibrational energy transfer rather efficient, thus undermining the premise of the RR approximation. In this work, we conduct a benchmark test of the RR approximation in the rotationally inelastic scattering of the H2O(v2 = 0, 1) + Ar system by comparing with full-dimensional quantum scattering calculations. We demonstrate that the error in the RR rate coefficient for v2 = 0 is less than 5%, while it can reach up to 20% for some initial states within the v2 = 1 manifold. These results indicate that the RR approximation gradually deteriorates with increasing quantum number v2. Vibrational relaxation dynamics of this system was also studied, and it is found that transitions from initial states with a large rotational quantum number of projection on the a principal axis are more efficient. These results shed valuable light on ro-vibrationally inelastic scattering involving polyatomic molecules.

Fully quantum calculations of the line shape parameters for 1-0 P(22) and P(31) lines of CO perturbed by He or Ar.

This work reports the full quantum calculations of the spectral line shape parameters for the P(22) line of 13CO and the P(31) line of 12CO in the fundamental band perturbed by He or Ar from 20 to 1000 K for the first time. The generalized spectroscopic cross sections of CO-He/Ar indicate that the Dicke narrowing effect competes with the pressure broadening effect. The pressure broadening can be explained by the dynamic behaviors of intermolecular collisions. The intermolecular inelastic collisions contribute more than 95% to the pressure broadening in both CO-He and CO-Ar systems at high temperatures. Regarding the state-to-state inelastic contributions to pressure broadening, the maximum contribution out of the final state of a given line is close to that out of the initial state. The Dicke narrowing effect influences the line shape profile significantly at high temperatures, which suggests that it is indispensable for reproducing the spectral line profile. With the Dicke narrowing effect, the calculated pressure-broadening coefficients and spectral intensity distribution are in good agreement with the available experimental observations.

Extended coupled-states approximation for full-dimensional quantum treatments of rovibrationally inelastic scattering between atoms and triatomic molecules.

While the rigorous time-independent close-coupling approach is ideally suited for cold and ultracold rovibrationally inelastic collision, its application beyond atom-diatom systems in full dimensionality is numerically expensive. Coupled-states (CS) approximation and its extensions are good choices to reduce the computational cost and have been successfully applied to diatom-diatom systems. In this work, we introduce the extended CS (ECS) approximation, in which one or a few nearest Coriolis coupled helicity channels are included. Its usefulness in atom-triatom systems is demonstrated for scattering of H2O with rare gas atoms. The results show that the ECS approximation, even when only the nearest neighbors are included, is generally much better than the CS approximation in describing scattering. At low collision energies, the ECS gradually converges to the exact results with the increasing number of Coriolis coupled helicity blocks. We further discuss three major factors that may lead to the failure of the CS approximation, namely, the reduced mass, collision energy, and triatomic rotational quantum number. It is illustrated that these factors could impact the relative importance of off-diagonal matrix elements in the Hamiltonian, thus influencing the coupling between different helicity channels.

Global Full-Dimensional Potential Energy Surface for the Reaction 23Na87Rb + 23Na87Rb → 23Na2 + 87Rb2 and the Formation Rate and Lifetime of the 23Na287Rb2 Collision Complex.

A full-dimensional global potential energy surface (PES) for the reaction 23Na87Rb + 23Na87Rb → 23Na2 + 87Rb2 was constructed based on high-level ab initio calculations. The short-range part was expressed as a permutation invariant polynomial-neural network (PIP-NN) fit of 22 003 ab initio points calculated using a coupled cluster method with the one-electron basis 5s5p5d2f plus effective core potentials and core polarizability potentials, while the long-range part was represented in an asymptotically correct form based on multipole expansion. The formation rate of the 23Na287Rb2 complex calculated using a quantum statistical method is in good agreement with experiment, while the estimated 19.20 µs lifetime of the complex from Rice-Ramsperger-Kassel-Marcus (RRKM) theory is significantly shorter than the measured millisecond decay rate, signaling either the inadequacy of RRKM theory or a yet unresolved loss mechanism.

Photodissociation of H2S: A New Pathway for the Production of Vibrationally Excited Molecular Hydrogen in the Interstellar Medium.

Hydrogen sulfide (H2S) is the most abundant S-bearing molecule in the solar nebula. Although its photochemistry has been studied for decades, the H2 fragment channel is still not well-understood. Herein, we describe the photodissociation dynamics of H2S + hv → S(1S) + H2(X1Σg+) with the excitation wavelength of 122 nm ≤ λ ≤ 136 nm. The results reveal that the H2(X) fragments formed are significantly vibrationally excited, with the quantum yields of ∼87% of H2(X) fragments populated in vibrational levels v″ = 3, 4, 5, and 6. Theoretical analysis suggest that these H2 products are formed on the H2S 41A' state surface following a nonadiabatic transition via an avoided crossing from the 31A' to 41A' state. The estimated quantum yield of the S(1S) + H2 channel is ∼0.05, implying this channel should be incorporated into the appropriate interstellar chemistry models.