Radical Stereochemistry: Accounting for Diastereomers in Kinetic Mechanism Development.

Recent work in combustion and atmospheric chemistry has revealed cases in which diastereomers must be distinguished to accurately model a reacting flow. This paper presents an open-source framework for introducing such stereoisomer resolution into a kinetic mechanism. We detail our definitions and algorithms for labeling and enumerating the stereoisomers of a molecule and then generalize our system to describe the transition state (TS) of a reaction. This allows for the stereospecific enumeration of reactants and products while accounting for "fleeting" stereochemistry that is unique to the TS. We also present the AutoMech Chemical Identifier (AMChI), an InChI-like string identifier that accounts for stereocenters omitted by InChI. This identifier is extended to describe the TSs of reactions, providing a universal lookup key for specific reaction channels. The final piece of our methodology is an analytic formula to remove redundancy from a stereoresolved mechanism when its enantiomers exist as a racemic mixture, making it as compact as possible while fully accounting for the differences between diastereomers. In applying our methodology to two subsets of the NUIGMech1.1 mechanism, we find that our approach reduces the extra species added for large-fuel oxidation from 2231 (133%, full expansion) to 694 (41%, nonredundant expansion). We also find that for pyrolysis more than a quarter of the species in the expanded mechanism cannot be properly described by an InChI string, requiring an AMChI string to communicate their identity. Finally, we find that roughly one-quarter of the large-fuel oxidation reactions and one-third of the pyrolysis reactions include fleeting TS stereochemistry, which may have relevant effects on their kinetics.

Substitution Reactions in the Pyrolysis of Acetone Revealed through a Modeling, Experiment, Theory Paradigm.

The development of high-fidelity mechanisms for chemically reactive systems is a challenging process that requires the compilation of rate descriptions for a large and somewhat ill-defined set of reactions. The present unified combination of modeling, experiment, and theory provides a paradigm for improving such mechanism development efforts. Here we combine broadband rotational spectroscopy with detailed chemical modeling based on rate constants obtained from automated ab initio transition state theory-based master equation calculations and high-level thermochemical parametrizations. Broadband rotational spectroscopy offers quantitative and isomer-specific detection by which branching ratios of polar reaction products may be obtained. Using this technique, we observe and characterize products arising from H atom substitution reactions in the flash pyrolysis of acetone (CH3C(O)CH3) at a nominal temperature of 1800 K. The major product observed is ketene (CH2CO). Minor products identified include acetaldehyde (CH3CHO), propyne (CH3CCH), propene (CH2CHCH3), and water (HDO). Literature mechanisms for the pyrolysis of acetone do not adequately describe the minor products. The inclusion of a variety of substitution reactions, with rate constants and thermochemistry obtained from automated ab initio kinetics predictions and Active Thermochemical Tables analyses, demonstrates an important role for such processes. The pathway to acetaldehyde is shown to be a direct result of substitution of acetone's methyl group by a free H atom, while propene formation arises from OH substitution in the enol form of acetone by a free H atom.

Simulating X-ray Absorption Spectra with Linear-Response Density Cumulant Theory.

We present a new approach for simulating X-ray absorption spectra based on linear-response density cumulant theory (LR-DCT) [ Copan , A. V. ; Sokolov , A. Yu. J. Chem. Theory Comput. 2018 , 14 , 4097 - 4108 ]. Our new method combines the LR-ODC-12 formulation of LR-DCT with core-valence separation approximation (CVS) that allows us to efficiently access high-energy core-excited states. We describe our computer implementation of the CVS-approximated LR-ODC-12 method (CVS-ODC-12) and benchmark its performance by comparing simulated X-ray absorption spectra to those obtained from experiment for several small molecules. Our results demonstrate that the CVS-ODC-12 method shows good agreement with experiment for relative spacings between transitions and their intensities, but the excitation energies are systematically overestimated. When compared to results from excited-state coupled cluster methods with single and double excitations, the CVS-ODC-12 method shows a similar performance for intensities and peak separations, while coupled cluster spectra are less shifted, relative to experiment. An important advantage of CVS-ODC-12 is that its excitation energies are computed by diagonalizing a Hermitian matrix, which enables efficient computation of transition intensities.

Reinterpreting the infrared spectrum of H + HCN: Methylene amidogen radical and its coproducts.

The methylene amidogen radical (H2CN) plays a role in high-energy material combustion and extraterresterial atmospheres. Recent theoretical work has struggled to match experimental assignments for its CN and antisymmetric CH2 stretching frequencies (ν2 and ν5), which were reported to occur at 1725 and 3103 cm-1. Herein, we compute the vibrational energy levels of this molecule by extrapolating quadruples-level coupled-cluster theory to the complete basis limit and adding corrections for vibrational anharmonicity. This level of theory predicts that ν2 and ν5 should occur at 1646 and 2892 cm-1, at odds with the experimental assignments. To investigate the possibility of defects in our theoretical treatment, we analyze the sensitivity of our approach to each of its contributing approximations. Our analysis suggests that the observed deviation from experiment is too large to be explained as an accumulation of errors, leading us to conclude that these transitions were misassigned. To help resolve this discrepancy, we investigate possible byproducts of the H + HCN reaction, which was the source of H2CN in the original experiment. In particular, we predict vibrational spectra for cis-HCNH, trans-HCNH, and H2CNH using high-level coupled-cluster computations. Based on these results, we reassign the transition at 1725 cm-1 to ν3 of trans-HCNH, yielding excellent agreement. Supporting this identification, we assign a known contaminant peak at 886 cm-1 to ν5 of the same conformer. Our computations suggest that the peak observed at 3103 cm-1, however, does not belong to any of the aforementioned species. To facilitate further investigation, we use structure and bonding arguments to narrow the range of possible candidates. These arguments lead us to tentatively put forth formaldazine [(H2CN)2] as a suggestion for further study, which we support with additional computations.

Peroxyacetyl radical: electronic excitation energies, fundamental vibrational frequencies, and symmetry breaking in the first excited state.

Peroxyacetyl radical [CH3C(O)O2] is among the most abundant peroxy radicals in the atmosphere and is involved in OH-radical recycling along with peroxyacetyl nitrate formation. Herein, the ground (X̃) and first (Ã) excited state surfaces of cis and trans peroxyacetyl radical are characterized using high-level ab initio methods. Geometries, anharmonic vibrational frequencies, and adiabatic excitation energies extrapolated to the complete basis-set limit are reported from computations with coupled-cluster theory. Excitation of the trans conformer is found to induce a symmetry-breaking conformational change due to second-order Jahn-Teller interactions with higher-lying excited states. Additional benchmark computations are provided to aid future theoretical work on peroxy radicals.

Linear-Response Density Cumulant Theory for Excited Electronic States.

We present a linear-response formulation of density cumulant theory (DCT) that provides a balanced and accurate description of many electronic states simultaneously. In the original DCT formulation, only information about a single electronic state (usually, the ground state) is obtained. We discuss the derivation of linear-response DCT, present its implementation for the ODC-12 method (LR-ODC-12), and benchmark its performance for excitation energies in small molecules (N2, CO, HCN, HNC, C2H2, and H2CO), as well as challenging excited states in ethylene, butadiene, and hexatriene. For small molecules, LR-ODC-12 shows smaller mean absolute errors in excitation energies than equation-of-motion coupled cluster theory with single and double excitations (EOM-CCSD), relative to the reference data from EOM-CCSDT. In a study of butadiene and hexatriene, LR-ODC-12 correctly describes the relative energies of the singly excited 11Bu and the doubly excited 21Ag states, in excellent agreement with highly accurate semistochastic heat-bath configuration interaction results, while EOM-CCSD overestimates the energy of the 21Ag state by almost 1 eV. Our results demonstrate that linear-response DCT is a promising theoretical approach for excited states of molecules.

Benchmark Study of Density Cumulant Functional Theory: Thermochemistry and Kinetics.

We present an extensive benchmark study of density cumulant functional theory (DCFT) for thermochemistry and kinetics of closed- and open-shell molecules. The performance of DCFT methods (DC-06, DC-12, ODC-06, and ODC-12) is compared to that of coupled-electron pair methods (CEPA0 and OCEPA0) and coupled-cluster theory (CCSD and CCSD(T)) for the description of noncovalent interactions (A24 database), barrier heights of hydrogen-transfer reactions (HTBH38), radical stabilization energies (RSE30), adiabatic ionization energies (AIE), and covalent bond stretching in diatomic molecules. Our results indicate that out of four DCFT methods the ODC-12 method is the most reliable and accurate DCFT formulation to date. Compared to CCSD, ODC-12 shows superior results for all benchmark tests employed in our study. With respect to coupled-pair theories, ODC-12 outperforms CEPA0 and shows similar accuracy to the orbital-optimized CEPA0 variant (OCEPA0) for systems at equilibrium geometries. For covalent bond stretching, ODC-12 is found to be more reliable than OCEPA0. For the RSE30 and AIE data sets, ODC-12 shows competitive performance with CCSD(T). In addition to benchmark results, we report new reference values for the RSE30 data set computed using coupled cluster theory with up to perturbative quadruple excitations.

Investigating the Effects of Basis Set on Metal-Metal and Metal-Ligand Bond Distances in Stable Transition Metal Carbonyls: Performance of Correlation Consistent Basis Sets with 35 Density Functionals.

Density functional theory (DFT) is a widely used method for predicting equilibrium geometries of organometallic compounds involving transition metals, with a wide choice of functional and basis set combinations. A study of the role of basis set size in predicting the structural parameters can be insightful with respect to the effectiveness of using small basis sets to optimize larger molecular systems. For many organometallic systems, the metal-metal and metal-carbon distances are the most important structural features. In this study, we compare the equilibrium metal-ligand and metal-metal distances of six transition metal carbonyl compounds predicted by the Hood-Pitzer double-ζ polarization (DZP) basis set, against those predicted employing the standard correlation consistent cc-pVXZ (X = D,T,Q) basis sets, for 35 different DFT methods. The effects of systematically increasing the basis set size on the structural parameters are carefully investigated. The Mn-Mn bond distance in Mn2(CO)10 shows a greater dependence on basis set size compared to the other M-M bonds. However, the DZP predictions for re(Mn-Mn) are closer to experiment than those obtained with the much larger cc-pVQZ basis set. Our results show that, in general, DZP basis sets predict structural parameters with an accuracy comparable to the triple and quadruple-ζ basis sets. This finding is very significant, because the quadruple-ζ basis set for Mn2(CO)10 includes 1308 basis functions, while the equally effective double-ζ set (DZP) includes only 366 basis functions. Overall, the DZP M06-L method predicts structures that are very consistent with experiment.