Automatic Determination of the Non-Covalent Stable Conformations of the NO2-Pyrene Cluster in Full Dimensionality (81D) Using the vdW-TSSCDS Approach.

We present the detailed topographical characterisation (stationary points and minimum energy paths connecting them) of the full dimensional (81D) intermolecular potential energy surface associated with the non-covalent interactions between the NO2 radical and the pyrene (C16H10) molecule. The whole procedure is (quasi) fully automated. We have used our recent algorithm vdW-TSSCDS as implemented on the freely-available AutoMekin software package. To this end, a series of inexpensive classical trajectories using forces from a low-level (semi-empirical) theory are used to sample the configuration space of the system in the search for candidates to first order saddle points. These guess structures are determined by means of a graph-theory based algorithm using the concept of adjacency matrix. Low-level optimizations are followed by re-optimizations at a final high-level of theory (DFT and CCSD(T)-F12 in our case.). The resulting set of stationary points and paths connecting them constitutes the so-called reaction network. In the case of NO2-pyrene, this network exhibits four major basins which can be characterized by their point-group symmetry. A central one, of global C2 symmetry, comprises the global minimum (as well as all other permutationally related conformers) together with the corresponding C2v saddle points connecting them. This central basin is connected to three others of lower C1 symmetry. The latter can be distinguished by the projection of the position of the NO2 nitrogen atom on the pyrene plane in combination with the relative orientation of the oxygen pair pointing either inwards, outwards, upwards or downwards.

Effect of temperature on the gas-phase reaction of CH3CN with OH radicals: experimental (T = 11.7-177.5 K) and computational (T = 10-400 K) kinetic study.

Acetonitrile (CH3CN) is present in the interstellar medium (ISM) in a variety of environments. However, at the ultracold temperatures of the ISM, radical-molecule reactions are not widely investigated because of the experimental handicap of getting organic molecules in the gas phase by conventional techniques. The CRESU (French acronym for Reaction Kinetics in a Uniform Supersonic Flow) technique solves this problem. For this reason, we present in this work the kinetic study of the gas-phase reaction of CH3CN with one of the most ubiquitous radicals, the hydroxyl (OH) radical, as a function of temperature (11.7-177.5 K). The kinetic technique employed to investigate the CH3CN + OH reaction was the pulsed laser photolysis-laser induced fluorescence. The rate coefficient for this reaction k(T) has been observed to drastically increase from 177.5 K to 107.0 K (about 2 orders of magnitude), while the increase in k(T) from 107.0 K to 11.7 K was milder (around 4 times). The temperature dependent expressions for k(T) are provided in the two distinct T-ranges, excluding the upper limit obtained for k(177.5 K): In addition, the rate coefficients estimated by the canonical competitive unified statistical (CCUS) theory show a similar behaviour to the experimental results, when evaluated within the high-pressure limit. This is consistent with the experimentally observed independence of k(T) with total gas density at selected temperatures. Astrochemical networks, such as the KIDA database or UMIST, do not include the CH3CN + OH reaction as a potential depletion process for acetonitrile in the ISM because the current studies predict very low rate coefficients at IS temperatures. According to the model (T = 10 K), the impact of the titled reaction on the abundances of CH3CN appears to be negligible in dark molecular clouds of the ISM (∼1% of the total depletion reactions included in UMIST network). With respect to the potential formation of the CH2CN radical in those environments, even in the most favourable scenario, where this radical could be formed in a 100% yield from the CH3CN + OH reaction, this route would only contribute around 2% to the current assumed formation routes by the UMIST network.

New prebiotic molecules in the interstellar medium from the reaction between vinyl alcohol and CN radicals: unsupervised reaction mechanism discovery, accurate electronic structure calculations and kinetic simulations.

Vinyl alcohol (VyA) and cyanide (CN) radicals are relatively abundant in the interstellar medium (ISM). VyA is the enolic tautomer of acetaldehyde and has two low-lying conformers, characterized by the syn or anti placement of hydroxyl hydrogen with respect to the double bond. In this paper, we present a gas-phase model of the barrierless reactions of both VyA's conformers with CN employing accurate quantum chemical computations in the framework of a master equation approach based on the transition state theory. Our results indicate that both VyA conformers feature a similar reactivity with CN, starting with a barrierless addition to the double bond and followed by different isomerization, dissociation, and/or hydrogen elimination steps. The rate constants computed for temperatures up to 600 K show that several reaction channels are open even under the harsh conditions of the ISM, with the favoured one providing the first feasible formation route of a prebiotic molecule not yet detected in the ISM, namely cyanoacetaldehyde. This finding suggests looking for cyanoacetaldehyde in regions where both VyA and CN have already been detected, like, e.g., Sagittarius B2N or G+0.693-0.027.

Gas-phase formation of glycolonitrile in the interstellar medium.

Our automated reaction discovery program, AutoMeKin, has been utilized to investigate the formation of glycolonitrile (HOCH2CN) in the gas phase under the low temperatures of the interstellar medium (ISM). The feasibility of a proposed pathway depends on the absence of barriers above the energy of reactants and the availability of the suggested precursors in the ISM. Based on these criteria, several radical-radical reactions and a radical-molecule reaction have been identified as viable formation routes in the ISM. Among the radical-radical reactions, OH + CH2CN appears to be the most relevant, considering the energy of the radicals and its ability to produce glycolonitrile in a single step. However, our analysis reveals that this reaction produces hydrogen isocyanide (HNC) and formaldehyde (CH2O), with rate coefficients ranging from (7.3-11.5) × 10-10 cm3 molecule-1 s-1 across the temperature range of 10-150 K. Furthermore, the identification of this remarkably efficient pathway for HNC elimination from glycolonitrile significantly broadens the possibilities for any radical-radical mechanism proposed in our research to be considered as a feasible pathway for the formation of HNC in the ISM. This finding is particularly interesing given the persistently unexplained overabundance of hydrogen isocyanide in the ISM. Among the radical-molecule reactions investigated, the most promising one is OH + CH2CHNH, which forms glycolonitrile and atomic hydrogen with rate coefficients in the range (0.3-6.6) × 10-10 cm3 molecule-1 s-1 within the 10-150 K temperature range. Our calculations indicate that the formation of both hydrogen isocyanide and glycolonitrile is efficient under the harsh conditions of the ISM.

Barrier Height Prediction by Machine Learning Correction of Semiempirical Calculations.

Different machine learning (ML) models are proposed in the present work to predict density functional theory-quality barrier heights (BHs) from semiempirical quantum mechanical (SQM) calculations. The ML models include a multitask deep neural network, gradient-boosted trees by means of the XGBoost interface, and Gaussian process regression. The obtained mean absolute errors are similar to those of previous models considering the same number of data points. The ML corrections proposed in this paper could be useful for rapid screening of the large reaction networks that appear in combustion chemistry or in astrochemistry. Finally, our results show that 70% of the features with the highest impact on model output are bespoke predictors. This custom-made set of predictors could be employed by future Δ-ML models to improve the quantitative prediction of other reaction properties.

Reaction of OH radicals with CH3NH2 in the gas phase: experimental (11.7-177.5 K) and computed rate coefficients (10-1000 K).

Nitrogen-bearing molecules, like methylamine (CH3NH2), can be the building blocks of amino acids in the interstellar medium (ISM). At the ultralow temperatures of the ISM, it is important to know its gas-phase reactivity towards interstellar radicals and the products formed. In this work, the kinetics of the OH + CH3NH2 reaction was experimentally and theoretically investigated at low- and high-pressure limits (LPL and HPL) between 10 and 1000 K. Moreover, the CH2NH2 and CH3NH yields were computed in the same temperature range for both pressure regimes. A pulsed CRESU (French acronym for Reaction Kinetics in a Uniform Supersonic Flow) apparatus was employed to determine the rate coefficient, k(T), in the 11.7-177.5 K range. A drastic increase of k(T) when the temperature is lowered was observed in agreement with theoretical calculations, evaluated by the competitive canonical unified statistical (CCUS) theory, below 300 K in the LPL regime. The same trend was observed in the HPL regime below 350 K, but the theoretical k(T) values were higher than the experimental ones. Above 200 K, the calculated rate coefficients are improved with respect to previous computational studies and are in excellent agreement with the experimental literature data. In the LPL, the formation of CH3NH becomes largely dominant below ca. 100 K. Conversely, in the HPL regime, CH2NH2 is the only product below 100 K, whereas CH3NH becomes dominant at 298 K with a branching ratio similar to the one found in the LPL regime (≈70%). At T > 300 K, both reaction channels are competitive independently of the pressure regime.

New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited.

The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH3 (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.

Photoisomerization of Linear and Stacked Isomers of a Charged Styryl Dye: A Tandem Ion Mobility Study.

The photoisomerization behavior of styryl 9M, a common dye used in material sciences, is investigated using tandem ion mobility spectrometry (IMS) coupled with laser spectroscopy. Styryl 9M has two alkene linkages, potentially allowing for four geometric isomers. IMS measurements demonstrate that at least three geometric isomers are generated using electrospray ionization with the most abundant forms assigned to a combination of EE (major) and ZE (minor) geometric isomers, which are difficult to distinguish using IMS as they have similar collision cross sections. Two additional but minor isomers are generated by collisional excitation of the electrosprayed styryl 9M ions and are assigned to the EZ and ZZ geometric isomers, with the latter predicted to have a π-stacked configuration. The isomer assignments are supported through calculations of equilibrium structures, collision cross sections, and statistical isomerization rates. Photoexcitation of selected isomers using an IMS-photo-IMS strategy shows that each geometric isomer photoisomerizes following absorption of near-infrared and visible light, with the EE isomer possessing a S1 ← S0 electronic transition with a band maximum near 680 nm and shorter wavelength S2 ← S0 electronic transition with a band maximum near 430 nm. The study demonstrates the utility of the IMS-photo-IMS strategy for providing fundamental gas-phase photochemical information on molecular systems with multiple isomerizable bonds.

AutoMeKin2021: An open-source program for automated reaction discovery.

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling.

A new approach is presented to improve the performance of semiempirical quantum mechanical (SQM) methods in the description of noncovalent interactions. To show the strategy, the PM6 Hamiltonian was selected, although, in general, the procedure can be applied to other semiempirical Hamiltonians and to different methodologies. A set of small molecules were selected as representative of various functional groups, and intermolecular potential energy curves (IPECs) were evaluated for the most relevant orientations of interacting molecular pairs. Then, analytical corrections to PM6 were derived from fits to B3LYP-D3/def2-TZVP reference-PM6 interaction energy differences. IPECs provided by the B3LYP-D3/def2-TZVP combination of the electronic structure method and basis set were chosen as the reference because they are in excellent agreement with CCSD(T)/aug-cc-pVTZ curves for the studied systems. The resulting method, called PM6-FGC (from functional group corrections), significantly improves the performance of PM6 and shows the importance of including a sufficient number of orientations of the interacting molecules in the reference data set in order to obtain well-balanced descriptions.

ChemDyME: Kinetically Steered, Automated Mechanism Generation through Combined Molecular Dynamics and Master Equation Calculations.

In many scientific fields, there is an interest in understanding the way in which chemical networks evolve. The chemical networks which researchers focus upon have become increasingly complex, and this has motivated the development of automated methods for exploring chemical reactivity or conformational change in a "black-box" manner, harnessing modern computing resources to automate mechanism discovery. In this work, we present a new approach to automated mechanism generation which couples molecular dynamics and statistical rate theory to automatically find kinetically important reactions and then solve the time evolution of the species in the evolving network. The key to this chemical network mapping through combined dynamics and ME simulation approach is the concept of "kinetic convergence", whereby the search for new reactions is constrained to those species which are kinetically favorable at the conditions of interest. We demonstrate the capability of the new approach for two systems, a well-studied combustion system and a multiple oxygen addition system relevant to atmospheric aerosol formation.

Femtochemistry under scrutiny: Clocking state-resolved channels in the photodissociation of CH3I in the A-band.

Clocking of electronically and vibrationally state-resolved channels of the fast photodissociation of CH3I in the A-band is re-examined in a combined experimental and theoretical study. Experimentally, a femtosecond pump-probe scheme is employed in the modality of resonant probing by resonance enhanced multiphoton ionization (REMPI) of the methyl fragment in different vibrational states and detection through fragment velocity map ion (VMI) imaging as a function of the time delay. We revisit excitation to the center of the A-band at 268 nm and report new results for excitation to the blue of the band center at 243 nm. Theoretically, two approaches have been employed to shed light into the observations: first, a reduced dimensionality 4D nonadiabatic wavepacket calculation using the potential energy surfaces by Xie et al. [J. Phys. Chem. A 104, 1009 (2000)]; and second, a full dimension 9D trajectory surface-hopping calculation on the same potential energy surfaces, including the quantization of vibrational states of the methyl product. In addition, high level ab initio electronic structure calculations have been carried out to describe the CH3 3pz Rydberg state involved in the (2 + 1) REMPI probing process, as a function of the carbon-iodine (C-I) distance. A general qualitative agreement is obtained between experiment and theory, but the effect of methyl vibrational excitation in the umbrella mode on the clocking times is not well reproduced. The theoretical results reveal that no significant effect on the state-resolved appearance times is exerted by the nonadiabatic crossing through the conical intersection present in the first absorption band. The vibrationally state resolved clocking times observed experimentally can be rationalized when the (2 + 1) REMPI probing process is considered. None of the other probing methods applied thus far, i.e., multiphoton ionization photoelectron spectroscopy, soft X-ray inner-shell photoelectron spectroscopy, VUV single-photon ionization, and XUV core-to-valence transient absorption spectroscopy, have been able to provide quantum state-resolved (vibrational) clocking times. More experiments would be needed to disentangle the fine details in the clocking times and dissociation dynamics arising from the detection of specific quantum-states of the molecular fragments.

Specific Reaction Parameter Multigrid POTFIT (SRP-MGPF): Automatic Generation of Sum-of-Products Form Potential Energy Surfaces for Quantum Dynamical Calculations.

We present Specific Reaction Parameter Multigrid POTFIT (SRP-MGPF), an automated methodology for the generation of global potential energy surfaces (PES), molecular properties surfaces, e.g., dipole, polarizabilities, etc. using a single random geometry as input. The SRP-MGPF workflow integrates: (i) a fully automated procedure for the global topographical characterization of a (intermolecular) PES based on the Transition State Search Using Chemical Dynamical Simulations (TSSCDS) family of methods;i (ii) the global optimization of the parameters of a semiempirical Hamiltonian in order to reproduce a given level of electronic structure theory; and (iii) a tensor decomposition algorithm which turns the resulting SRP-PES into sum of products (Tucker) form with the Multigrid POTFIT algorithm. The latter is necessary for quantum dynamical studies within the Multiconfiguration Time-Dependent Hartree (MCTDH) quantum dynamics method. To demonstrate our approach, we have applied our methodology to the cis-trans isomerization reaction in HONO in full dimensionality (6D). The resulting SRP-PES has been validated through the computation of classical on-the-fly dynamical calculations as well as calculations of the lowest vibrational eigenstates of HONO as well as high-energy wavepacket propagations.

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-SO3]-, 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. To understand fragmentation pathways of [cysS-SO3]-, reactive chemical dynamics simulations coupled with a novel algorithm for automatic determination of intermediates and transition states were performed. This approach has allowed the identification of the mechanisms involved and explained the experimental fragmentation pathways. Chemical dynamics simulations have shown that a roaming-like mechanism can be at the origin of l-cysteine sulfenic acid.

A Trajectory-Based Method to Explore Reaction Mechanisms.

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics.

A new software, called tsscds2018, has been developed to discover reaction mechanisms and solve the kinetics in a fully automated fashion. The program employs algorithms based on Graph Theory to find transition state (TS) geometries from accelerated semiempirical dynamics simulations carried out with MOPAC2016. Then, the TSs are connected to the corresponding minima and the reaction network is obtained. Kinetic data like populations vs time or the abundancies of each product can also be obtained with our program thanks to a Kinetic Monte Carlo routine. Highly accurate ab initio potential energy diagrams and kinetics can also be obtained using an interface with Gaussian09. The source code is available on the following site: http://forge.cesga.es/wiki/g/tsscds/HomePage © 2018 Wiley Periodicals, Inc.

Influence of Multiple Conformations and Paths on Rate Constants and Product Branching Ratios. Thermal Decomposition of 1-Propanol Radicals.

The potential energy surface involved in the thermal decomposition of 1-propanol radicals was investigated in detail using automated codes (tsscds2018 and Q2DTor). From the predicted elementary reactions, a relevant reaction network was constructed to study the decomposition at temperatures in the range 1000-2000 K. Specifically, this relevant network comprises 18 conformational reaction channels (CRCs), which in general exhibit a large wealth of conformers of reactants and transition states. Rate constants for all the CRCs were calculated using two approaches within the formulation of variational transition-state theory (VTST), as incorporated in the TheRa program. The simplest, one-well (1W) approach considers only the most stable conformer of the reactant and that of the transition state. In the second, more accurate approach, contributions from all the reactant and transition-state conformers are taken into account using the multipath (MP) formulation of VTST. In addition, kinetic Monte Carlo (KMC) simulations were performed to compute product branching ratios. The results show significant differences between the values of the rate constants calculated with the two VTST approaches. In addition, the KMC simulations carried out with the two sets of rate constants indicate that, depending on the radical considered as reactant, the 1W and the MP approaches may display different qualitative pictures of the whole decomposition process.

Quasi-Classical Trajectory Dynamics Study of the Cl(2P) + C2H6 → HCl(v,j) + C2H5 Reaction. Comparison with Experiment.

To understand and simulate the dynamics behavior of the title reaction, QCT calculations were performed on a recently developed global analytical potential energy surface, PES-2017. These calculations combine the classical description of the dynamics with pseudoquantization in the reactants and products to perform a theoretical/experimental comparison on the same footing. Thus, in the products a series of constraints are included to analyze the HCl(v = 0,j) product, which is experimentally detected. At collision energies of 5.5 and 6.7 kcal mol-1 the largest fraction of available energy is deposited as translation, 67%, while the ethyl radical shows significant internal energy, 27%, and so it does not act as a spectator of the reaction, thus reproducing recent experimental evidence. The HCl(v=0, j) rotational distribution is cold, peaking at j = 2, only one unit hotter than experiment, which represents an error of 0.12 kcal mol-1. At a collision energy of 5.5 kcal mol-1 product translational distribution is slightly hotter than experiment, but at 6.7 kcal mol-1 agreement with recent experiments is practically quantitative, suggesting that the first experiments should be revised. In addition, we observe that the HCl(v=0, j) scattering distribution shifts from isotropic at low values of j to backward at high values of j, which is in agreement with experimental data. Finally, no evidence was found for the "chattering" mechanism suggested to explain the low translational energy of the HCl product in the backward scattering region. In sum, agreement with experiments of a series of sensible dynamic properties permits us to be optimistic on the quality and accuracy of the theoretical tools used in the present work, QCT and PES-2017.

Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces.

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.