Automatic Potential Energy Surface Exploration by Accelerated Reactive Molecular Dynamics Simulations: From Pyrolysis to Oxidation Chemistry.

Automatic potential energy surface (PES) exploration is important to a better understanding of reaction mechanisms. Existing automatic PES mapping tools usually rely on predefined knowledge or computationally expensive on-the-fly quantum-chemical calculations. In this work, we have developed the PESmapping algorithm for discovering novel reaction pathways and automatically mapping out the PES using merely one starting species is present. The algorithm explores the unknown PES by iteratively spawning new reactive molecular dynamics (RMD) simulations for species that it has detected within previous RMD simulations. We have therefore extended the RMD simulation tool ChemTraYzer2.1 (Chemical Trajectory Analyzer, CTY) for this PESmapping algorithm. It can generate new seed species, automatically start replica simulations for new pathways, and stop the simulation when a reaction is found, reducing the computational cost of the algorithm. To explore PESs with low-temperature reactions, we applied the acceleration method collective variable (CV)-driven hyperdynamics. This involved the development of tailored CV templates, which are discussed in this study. We validate our approach for known pathways in various pyrolysis and oxidation systems: hydrocarbon isomerization and dissociation (C4H7 and C8H7 PES), mostly dominant at high temperatures and low-temperature oxidation of n-butane (C4H9O2 PES) and cyclohexane (C6H11O2 PES). As a result, in addition to new pathways showing up in the simulations, common isomerization and dissociation pathways were found very fast: for example, 44 reactions of butenyl radicals including major isomerizations and decompositions within about 30 min wall time and low-temperature chemistry such as the internal H-shift of RO2 → QO2H within 1 day wall time. Last, we applied PESmapping to the oxidation of the recently proposed biohybrid fuel 1,3-dioxane and validated that the tool could be used to discover new reaction pathways of larger molecules that are of practical use.

The first HyDRA challenge for computational vibrational spectroscopy.

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane-cis-1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies.

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes.

The front cover artwork is provided by Prof. K. Leonhard's group at RWTH Aachen University. The image shows ChemTraYzer, a virtual robot, while analyzing the reaction network related to the formation and oxidation of Chloro-Dibenzofuranes. Read the full text of the Research Article at 10.1002/cphc.202200783.

Improved modeling of anharmonicity for furan microsolvation.

Computational benchmark data for complexes requires accurate models of anharmonic torsional motion. State-of-the-art hindered rotor treatments come with a number of difficulties, regarding discontinuities from badly converged points or coupling, oscillations, or the consideration and correction of stationary points. Their manual handling introduces a level of arbitrariness not suitable for benchmark procedures. This study presents the TAMkinTools extension for improved modeling of one-dimensional hindered rotation which enables a more standardized workflow. We choose the structures from the Goebench challenge as test case, which comprises OH- and π-bonded complexes of methanol and furan, 2-methylfuran, and 2,5-dimethylfuran. Ahlrichs and Dunning basis sets of various sizes and their extrapolations show large differences in efficiency and accuracy for coupled-cluster energies of stationary points of these complexes. The probability density analysis of TAMkinTools provides zero-point energies for all conformations even within the same rotor profile. Zero-point energies show a large effect on the conformational order, especially for the methanol-furan complex with energy differences far below 1 kJ mol-1.

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes.

In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics - Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans.

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development.

This work presents a novel parametrization for the ReaxFF formalism as a means to investigate reaction processes of chlorinated organic compounds. Force field parameters cover the chemical elements C, H, O, Cl and were obtained using a novel optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization shows good transferability, as demonstrated on two independent ab initio validation sets. While this first part of our two-paper series focuses on force field parametrization, we apply our parameters to the simulation of chlorinated dibenzofuran formation and decomposition processes in Part II.

Completely Computational Model Setup for Spectroscopic Techniques: The Ab Initio Molecular Dynamics Indirect Hard Modeling Approach.

The spectroscopic quantification of mixture compositions usually requires pure compounds and mixtures of known compositions for calibration. Since they are not always available, methods to fill such gaps have evolved, which are, however, not generally applicable. Therefore, calibration can be extremely challenging, especially when multiple unstable species, for example, intermediates, exist in a system. This study presents a new calibration approach that uses ab initio molecular dynamics (AIMD)-simulated spectra to set up and calibrate models for the physics-based spectral analysis method indirect hard modeling (IHM). To demonstrate our approach called AIMD-IHM, we analyze Raman spectra of ternary hydrogen-bonding mixtures of acetone, methanol, and ethanol. The derived AIMD-IHM pure-component models and calibration coefficients are in good agreement with conventionally generated experimental results. The method yields compositions with prediction errors of less than 5% without any experimental calibration input. Our approach can be extended, in principle, to infrared and NMR spectroscopy and allows for the analysis of systems that were hitherto inaccessible to quantitative spectroscopic analysis.

Coupled Anharmonic Thermochemistry from Stratified Monte Carlo Integration.

This study presents configuration integral Monte Carlo integration (CIMCI), a new semiclassical method for handling fully coupled anharmonicity in gas-phase thermodynamics that promises to be black boxable, to be applicable to all kinds of anharmonicity, and to scale better at higher dimensionality than other methods for handling gas-phase molecular anharmonicity. The method does so using automatically and recursively stratified, simultaneous Monte Carlo (MC) integration of multiple functions, following a modified version of the standard MISER scheme that converges at a rate of about the square of naïve MC integration. For the small systems analyzed by this study where proper reference data is available (H2O and H2O2), the method's anharmonic entropy corrections match reference data better than those of other black box anharmonic methods, e.g., vibrational perturbation theory (VPT2) and the McClurg hindered rotor model used with automatic detection of rotors; for H2O2 and NH2OH, the method is also in general agreement with one-dimensional hindered rotor treatments at low temperatures. This holds even when sampling with CIMCI is done with primitive force fields, e.g., UFF, while the competing methods are used with proper, comprehensive potentials, e.g., the M06-2X metahybrid density-functional theory (DFT) functional.

The first microsolvation step for furans: New experiments and benchmarking strategies.

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight.

Correcting Rate Constants from Anharmonic Molecular Dynamics for Quantum Effects.

Anharmonicity can greatly affect rate constants. One or even several orders of magnitude of deviation are found for obtaining rate constants using the standard rigid-rotor harmonic-oscillator model. In turn, reactive molecular dynamics (MD) simulations are a powerful way to explore chemical reaction networks and calculate rate constants from the fully anharmonic potential energy surface. However, the classical nature of the dynamics and the required numerical efficiency of the force field limit the accuracy of the resulting kinetics. We combine the best of both worlds by presenting an approximation that pairs anharmonic information intrinsic to classical MD with high-accuracy energies and frequencies from quantum-mechanical electronic structure calculations. The proposed scheme is applied to hydrogen abstractions in the methane system, which allows for the benchmarking of rate constants corrected by our approach against experimental rate constants. This comparison reveals a standard deviation of factor 2.6. Two archetypes of possible failure are identified in the course of a detailed investigation of the CH3 • + H• → CH2 2• + H2 reaction. From this follows the application range of the method, within which the method shows a standard deviation of factor 2.1. The computational efficiency and beneficial scaling of the method allow for application to larger systems, as shown for hydrogen abstraction from 2-butanone by HO2 •.

Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations.

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable, and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready to use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodological advancement of chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

The furan microsolvation blind challenge for quantum chemical methods: First steps.

Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH-O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication.

Assessing Statistical Uncertainties of Rare Events in Reactive Molecular Dynamics Simulations.

Reactive molecular dynamics (MD) simulations are a versatile tool which allow for studying reaction pathways and rates simultaneously. However, most reactions will be observed only a few times in such a simulation due to computational limitations or slow kinetics, and it is unclear how this will influence the obtained rate constants. Therefore, we propose a method based on the Poisson distribution to assess the statistical uncertainty of reaction rate constants obtained from reactive MD simulations.

Prediction of Chain Propagation Rate Constants of Polymerization Reactions in Aqueous NIPAM/BIS and VCL/BIS Systems.

Microgels have a wide range of possible applications and are therefore studied with increasing interest. Nonetheless, the microgel synthesis process and some of the resulting properties of the microgels, such as the cross-linker distribution within the microgels, are not yet fully understood. An in-depth understanding of the synthesis process is crucial for designing tailored microgels with desired properties. In this work, rate constants and reaction enthalpies of chain propagation reactions in aqueous N-isopropylacrylamide/N,N'-methylenebisacrylamide and aqueous N-vinylcaprolactam/N,N'-methylenebisacrylamide systems are calculated to identify the possible sources of an inhomogeneous cross-linker distribution in the resulting microgels. Gas-phase reaction rate constants are calculated from B2PLYPD3/aug-cc-pVTZ energies and B3LYPD3/tzvp geometries and frequencies. Then, solvation effects based on COSMO-RS are incorporated into the rate constants to obtain the desired liquid-phase reaction rate constants. The rate constants agree with experiments within a factor of 2-10, and the reaction enthalpies deviate less than 5 kJ/mol. Further, the effect of rate constants on the microgel growth process is analyzed, and it is shown that differences in the magnitude of the reaction rate constants are a source of an inhomogeneous cross-linker distribution within the resulting microgel.

General formulation of rovibrational kinetic energy operators and matrix elements in internal bond-angle coordinates using factorized Jacobians.

We show how inverse metric tensors and rovibrational kinetic energy operators in terms of internal bond-angle coordinates can be obtained analytically following a factorization of the Jacobian worked out by Frederick and Woywod. The structure of these Jacobians is exploited in two ways: On one hand, the elements of the metric tensor as well as its determinant all have the form ∑rmsin(αn)cos(ßo). This form can be preserved by working with the adjugate metric tensor that can be obtained without divisions. On the other hand, the adjugate can be obtained with less effort by exploiting the lower triangular structure of the Jacobians. Together with a suitable choice of the wavefunction, we avoid singularities and show how to obtain analytical expressions for the rovibrational kinetic energy matrix elements.

Efficient yet accurate approximations for ab initio calculations of alcohol cluster thermochemistry.

We have calculated the binding enthalpies and entropies of gas phase alcohol clusters from ethanol to 1-decanol. In addition to the monomers, we have investigated dimers, tetramers, and pentamers. Geometries have been obtained at the B3LYP/TZVP level and single point energy calculations have been performed with the Resolution of the Identity-MP2 (RIMP2) method and basis set limit extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Thermochemistry is calculated with decoupled hindered rotor treatment for large amplitude motions. The results show three points: First, it is more accurate to transfer the rigid-rotor harmonic oscillator entropies from propanol to longer alcohols than to compute them with an ultra-fine grid and tight geometry convergence criteria. Second, the computational effort can be reduced considerably by using dimerization energies of longer alcohols at density functional theory (B3LYP) level plus a RIMP2 correction obtained from 1-propanol. This approximation yields results almost with the same accuracy as RIMP2 - both methods differ for 1-decanol only 0.4 kJ/mol. Third, the entropy of dimerization including the hindered rotation contribution is converged at 1-propanol with respect to chain length. This allows for a transfer of hindered rotation contributions from smaller alcohols to longer ones which reduces the required computational and man power considerably.

Automated discovery of reaction pathways, rate constants, and transition states using reactive molecular dynamics simulations.

We provide a methodology for deducing quantitative reaction models from reactive molecular dynamics simulations by identifying, quantifying, and evaluating elementary reactions of classical trajectories. Simulations of the inception stage of methane oxidation are used to demonstrate our methodology. The agreement of pathways and rates with available literature data reveals the potential of reactive molecular dynamics studies for developing quantitative reaction models.

Hydrogen abstraction from n-butyl formate by H˙ and HO2˙.

The combustion chemistry of esters has been elucidated in the past through the study of smaller formates and acetates. Hydrogen abstraction from the fuel as an initiation step is mostly modeled based on estimations for similar abstractions from nonoxygenated hydrocarbons. This study reports computed ab initio rates for abstractions by H˙ and HO2˙ radicals from the recently proposed biofuel candidate n-butyl formate. The energies are evaluated with a double hybrid density functional that performs especially well for barrier heights (B2KPLYP/aug-cc-pvtz). Hindered rotation of HO2˙ with respect to n-butyl formate is treated using accurate eigenvalue summation and shows large influence on the rates. Transition states at the γ and δ positions are still influenced by the formate group. The abstraction from the γ carbon by HO2˙ is slowest, although proceeding over the lowest barriers, due to the important influence of transition state entropies. A comparison with smaller esters and n-butanol shows that estimated rates deviate within 1 order of magnitude from the ab initio computations for similar groups in n-butyl formate.