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.

Collisional Relaxation of Highly Vibrationally Excited Acetylene Mediated by the Vinylidene Isomer

Collisional relaxation of highly vibrationally excited acetylene, generated from the 193 nm photolysis of vinyl bromide with roughly 23,000 cm-1 of nascent vibrational energy, is studied via submicrosecond time-resolved Fourier transform infrared (FTIR) emission spectroscopy. IR emission from vibrationally hot acetylene during collisional relaxation by helium, neon, argon, and krypton rare-gas colliders is recorded and analyzed to deduce the acetylene energy content as a function of time. The average energy lost per collision, ⟨ΔE⟩, is computed using the Lennard-Jones collision frequency. Two distinct vibrational-to-translational (V-T) energy transfer regimes in terms of the acetylene energy are identified. At vibrational energies below 10,000-14,000 cm-1, energy transfer efficiency increases linearly with molecular energy content and is in line with typical V-T behavior in quantity. In contrast, above 10,000-14,000 cm-1, the V-T energy transfer efficiency displays a dramatic and rapid increase. This increase is nearly coincident with the acetylene-vinylidene isomerization limit, which occurs nearly 15,000 cm-1 above the acetylene zero-point energy. Combined quasi-classical trajectory calculations and Schwartz-Slawsky-Herzfeld-Tanczos theory point to a vinylidene contribution being responsible for the large enhancement. This observation illustrates the influence of energetically accessible structural isomers to greatly enhance the energy transfer rates of highly vibrationally excited molecules.

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.

Collisional excitation of HNC by He found to be stronger than for structural isomer HCN in experiments at the low temperatures of interstellar space

HCN and its unstable isomer HNC are widely observed throughout the interstellar medium, with the HNC/HCN abundance ratio correlating strongly with temperature. In very cold environments HNC can even appear more abundant than HCN. Here we use a chirped pulse Fourier transform spectrometer to measure the pressure broadening of HCN and HNC, simultaneously formed in situ by laser photolysis and cooled to low temperatures in uniform supersonic flows of helium. Despite the apparent similarity of these systems, we find the HNC-He cross section to be more than twice as big as the HCN-He cross section at 10 K, confirming earlier quantum calculations. Our experimental results are supported by high-level scattering calculations and are also expected to apply with para-H₂, demonstrating that HCN and HNC have different collisional excitation properties that strongly influence the derived interstellar abundances.

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.

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.

ALTRUISM: A Higher Calling

A new robust surface-walking algorithm for locating transition states is presented. By modifying the Trust-Region Image Surface Minimization method to walk to higher-order stationary points, where the Hessian has more than one negative eigenvalue, we have developed an approach that determines transition states from above, by walking downhill on the potential energy surface. We call this algorithm "ALTRUISM"-Alpine Trust-region Image Surface Method. We test the performance of the approach by applying it to a range of systems with several different quantum-chemical methods. Our results demonstrate that ALTRUISM is a systematic, robust, and unbiased method for connecting a reactant and a product via a transition state. The algorithmic combination of walking uphill (to different higher-order stationary points) and downhill to saddle points enables us to explore qualitatively distinct reaction pathways and construct a network of elementary reactions on a given potential energy surface.

Collisional Energy Transfer from Vibrationally Excited Hydrogen Isocyanide

Collisional deactivation of vibrationally excited hydrogen isocyanide (HNC) by inert gas atoms was characterized using nanosecond time-resolved Fourier transform infrared emission spectroscopy. HNC, with an average nascent internal energy of 25.9 ± 1.4 kcal mol^-1, was generated following the 193 nm photolysis of vinyl cyanide (CH₂CHCN) and collisionally deactivated with the series of inert atomic gases: He, Ar, Kr, and Xe. Time-dependent IR emission allows simultaneous experimental observation of the ν₁ NH and ν₃ NC stretch emissions from vibrationally excited HNC. Subsequent spectral fit analysis enables direct determination of the average energy of HNC in each spectrum and therefore a measure of the average energy lost per collision, ⟨ΔE⟩, as a function of internal energy. Collisional deactivation of excited HNC is shown to be relatively efficient, exhibiting ⟨ΔE⟩ values more than an order of magnitude larger than comparably sized molecules at similar internal energies. Furthermore, the lighter inert gases are shown to be more efficient quenchers. Both observations can be qualitatively explained by the momentum gap law modeled through the repulsive force dominated vibration-to-translation energy transfer mechanism. The feasibility of efficient collisional deactivation as a contributing factor to the observed overabundance of astrophysical HNC is discussed.

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.