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.

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.

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.

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.

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.

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.

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.

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.

Effect of the Metal Ion on the Enantioselectivity and Linkage Isomerization of Thiosemicarbazone Helicates.

The effect of the metal ion and ligand design on the enantioselectivity and linkage isomerization of neutral cobalt and zinc bisthiosemicarbazone metallohelicates has been investigated in this work. The electrochemical synthesis has afforded the enantioselective formation of chirally pure cobalt helicates, and the ΛΛ isomer of a single enantiomer has been crystallized as only product for the cobalt methyl-substituted thiosemicarbazone helicate. Interestingly linkage isomers have been formed from zinc ethyl-substituted thiosemicarbazone helicate enantiomers for the first time. The co-existence of these isomers has been evaluated from the point of view of both experimental results and computational calculations.

Photodissociation of acryloyl chloride at 193 nm: interpretation of the product energy distributions, and new elimination pathways.

The ground electronic state potential energy surface of acryloyl chloride, CH2CHC(O)Cl, has been mapped using an automated transition state search procedure. A total of 174 minima, 527 TSs, and 20 different dissociation channels have been found. Among others, three novel HCl elimination pathways, namely, a five-center mechanism and two three-body dissociations (leading to CO + HCl + HCCH) have been discovered. While the bimodal character of the experimental HCl rotational distributions was previously attributed to the presence of two competing channels, our dynamics simulations show that a single channel, the four-center HCl elimination of CH2ClCHCO following a 1,3-Cl-shift of CH2CHC(O)Cl, displays a bimodal distribution in nearly prefect agreement with the experiment. Overall, our simulation results suggest that, as far as molecular elimination is concerned, this channel dominates in the 193 nm photodissociation of the molecule. The simulations also show evidence of non-IRC dynamics for this channel.

Methanol dimer formation drastically enhances hydrogen abstraction from methanol by OH at low temperature.

The kinetics of the reaction of methanol with hydroxyl radicals is revisited in light of the reported new kinetic data, measured in cold expansion beams. The rate constants exhibit an approximately 10(2)-fold increase when the temperature decreases from 200 to 50 K, a result that cannot be fully explained by tunneling, as we confirm by new calculations. These calculations also show that methanol dimers are much more reactive to hydroxyl than monomers and imply that a dimer concentration of about 30% of the equilibrium concentration can account quantitatively for the observed rates. The assumed presence of dimers is supported by the observation of cluster formation in these and other cold beams of molecules subject to hydrogen bonding. The calculations imply an important caveat with respect to the use of cold expansion beams for the study of interstellar chemistry.

On the gas phase fragmentation of protonated uracil: a statistical perspective.

The potential energy surface of protonated uracil has been explored by an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory and Kinetic Monte Carlo (KMC) simulations allowed us to determine the relative abundances of each fragmentation channel as a function of the ion's internal energy. The KMC/RRKM product abundances are compared with novel mass spectrometry (MS) experiments in the collision energy range 1-6 eV. To facilitate the comparison between theory and experiments, further dynamics simulations are carried out to determine the fraction of collision energy converted into the ion's internal energy. The KMC simulations show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments, although the abundance obtained in the KMC simulations is very low, suggesting that non-statistical dynamics might play an important role in this channel. Isocyanic acid (HNCOH(+)) is also an important product in the KMC simulations, although its abundance is only significant at internal energies not accessible in the MS experiments.

An automated method to find transition states using chemical dynamics simulations.

A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high-energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) is used to integrate the trajectories and also to optimize the TSs, and a higher level (HL) is used to reoptimize the structures. The method has been tested in three MSs: formaldehyde, formic acid (FA), and vinyl cyanide (VC), using MOPAC2012 and Gaussian09 to run the LL and HL calculations, respectively. Both the efficacy and efficiency of the method are very good, with around 15 TS structures optimized every 10 trajectories, which gives a total of 7, 12, and 83 TSs for formaldehyde, FA, and VC, respectively. The use of CDS makes it a powerful tool to unveil possible nonstatistical behavior of the system under study.

An automated transition state search using classical trajectories initialized at multiple minima.

Very recently, we proposed an automated method for finding transition states of chemical reactions using dynamics simulations; the method has been termed Transition State Search using Chemical Dynamics Simulations (TSSCDS) (E. Martínez-Núñez, J. Comput. Chem., 2015, 36, 222-234). In the present work, an improved automated search procedure is developed, which consists of iteratively running different ensembles of trajectories initialized at different minima. The iterative TSSCDS method is applied to the complex C3H4O system, obtaining a total of 66 different minima and 276 transition states. With the obtained transition states and paths, statistical RRKM calculations and Kinetic Monte Carlo simulations are carried out to study the fragmentation dynamics of propenal, which is the global minimum of the system. The kinetic simulations provide a (three-body dissociation)/(CO elimination) ratio of 1.49 for an excitation energy of 148 kcal mol(-1), which agrees well with the corresponding value obtained in the photolysis of propenal at 193 nm (1.1), suggesting that at least these two channels: three-body dissociation (to give H2 + CO + C2H2) and CO elimination occur on the ground electronic state.

HCN elimination from vinyl cyanide: product energy partitioning, the role of hydrogen-deuterium exchange reactions and a new pathway.

The different HCN elimination pathways from vinyl cyanide (VCN) are studied in this paper using RRKM, Kinetic Monte Carlo (KMC), and quasi-classical trajectory (QCT) calculations. A new HCN elimination pathway proves to be very competitive with the traditional 3-center and 4-center mechanisms, particularly at low excitation energies. However, low excitation energies have never been experimentally explored, and the high and low excitation regions are dynamically different. The KMC simulations carried out using singly deuterated VCN (CH2=CD-CN) at 148 kcal mol(-1) show the importance of hydrogen-deuterium exchange reactions: both DCN and HCN will be produced in any of the 1,1 and 1,2 elimination pathways. The QCT simulation results obtained for the 3-center pathway are in agreement with the available experimental results, with the 4-center results showing much more excitation of the products. In general, our results seem to be consistent with a photodissociation mechanism at 193 nm, where the molecule dissociates (at least the HCN elimination pathways) in the ground electronic state. However, our simulations assume that internal conversion is a fully statistical process, i.e., the HCN elimination channels proceed on the ground electronic state according to RRKM theory, which might not be the case. In future studies it would be of interest to include the photo-prepared electronically excited state(s) in the dynamics simulations.