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.

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.

Determination of kinetic properties in unimolecular dissociation of complex systems from graph theory based analysis of an ensemble of reactive trajectories

In this paper, we report how graph theory can be used to analyze an ensemble of independent molecular trajectories, which can react during the simulation time-length, and obtain structural and kinetic information. This method is totally general and here is applied to the prototypical case of gas phase fragmentation of protonated cyclo-di-glycine. This methodology allows us to analyze the whole set of trajectories in an automatic computer-based way without the need of visual inspection but by getting all the needed information. In particular, we not only determine the appearance of different products and intermediates but also characterize the corresponding kinetics. The use of colored graph and canonical labeling allows for the correct characterization of the chemical species involved. In the present case, the simulations consist of an ensemble of unimolecular fragmentation trajectories at constant energy such that from the rate constants at different energies, the threshold energy can also be obtained for both global and specific pathways. This approach allows for the characterization of ion-molecule complexes, likely through a roaming mechanism, by properly taking into account the elusive nature of such species. Finally, it is possible to directly obtain the theoretical mass spectrum of the fragmenting species if the reacting system is an ion as in the specific example.

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.

Photodissociation of Benzoyl Chloride: A Velocity Map Imaging Study Using VUV Detection of Chlorine Atoms

UV photodissociation of benzoyl chloride, Ph-CO-Cl, is associated with the loss of a chlorine atom. Here we excite benzoyl chloride to the S₁, S₂, and S₃ excited states at 237, 253, 265, and 279.6 nm and detect the Cl photofragment by [1 + 1'] photoionization using 118.9 nm VUV radiation. The translational energy distribution of the Cl atom is measured by velocity map ion imaging. An isotropic image and a unimodal translational energy distribution are observed at all dissociation wavelengths, and a fraction of 18-20% of the excess energy is released into translation. The results indicate a dissociation that predominately proceeds from the vibrationally hot S₀ ground state, although the observed translational energy release deviates significantly from a prior distribution. However, the impulsive model does also not represent the translational energy release. As a Cl/Cl* branching ratio of 9:1 or more is observed in one-color experiments at 235 nm, we conclude that direct dissociation from excited electronic states contributes only to a minor extent.

Spectroscopic characterization and photochemistry of the vinylsulfinyl radical

The simplest α,β-unsaturated sulfinyl radical CH2[double bond, length as m-dash]C(H)SO˙ has been generated in the gas phase by high-vacuum flash pyrolysis (HVFP) of sulfoxide CH2[double bond, length as m-dash]C(H)S(O)CF3 at ca. 800 °C. Two planar cis and trans conformers of CH2[double bond, length as m-dash]C(H)SO˙ were isolated in cryogenic matrixes (N2, Ne, and Ar) and characterized with IR and UV/Vis spectroscopy. In addition to the photo-induced cis ⇋ trans conformational interconversion, CH2[double bond, length as m-dash]C(H)SO˙ displays complex photochemistry. Upon irradiation with a purple light LED (400 nm), CH2[double bond, length as m-dash]C(H)SO˙ isomerizes to novel radicals CH3SCO˙, ˙CH2SC(O)H, and ˙CH2C(O)SH with concomitant dissociation to a caged molecular complex CH3S˙CO. Subsequent UV-laser (266 nm) irradiation causes fragmentation to ˙CH3/OCS and additional formation of an elusive carbonyl radical CH3C(O)S˙, which rearranges to ˙CH2C(O)SH upon further UV-light irradiation (365 nm). The vibrational data and bonding analysis of the two conformers of CH2[double bond, length as m-dash]C(H)SO˙ suggest that both are floppy radicals in which the unpaired electron conjugates with the vicinal π(C[double bond, length as m-dash]C) bond, leading to significant contribution of the canonical resonance form of ˙CH2-C(H)SO. The mechanism for the isomerization of CH2[double bond, length as m-dash]C(H)SO˙ is discussed based on the observed intermediates along with a computed potential energy profile at the CCSD(T)-F12a/aug-cc-pVTZ//B3LYP/6-311++G(3df,3pd) level of theory.

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.

An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis

A novel computational method is proposed in this work for use in discovering reaction mechanisms and solving the kinetics of transition metal-catalyzed reactions. The method does not rely on either chemical intuition or assumed a priori mechanisms, and it works in a fully automated fashion. Its core is a procedure, recently developed by one of the authors, that combines accelerated direct dynamics with an efficient geometry-based post-processing algorithm to find transition states (Martinez-Nunez, E., J. Comput. Chem.2015, 36, 222-234). In the present work, several auxiliary tools have been added to deal with the specific features of transition metal catalytic reactions. As a test case, we chose the cobalt-catalyzed hydroformylation of ethylene because of its well-established mechanism, and the fact that it has already been used in previous automated computational studies. Besides the generally accepted mechanism of Heck and Breslow, several side reactions, such as hydrogenation of the alkene, emerged from our calculations. Additionally, the calculated rate law for the hydroformylation reaction agrees reasonably well with those obtained in previous experimental and theoretical studies.