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Schaefer, III, Henry F.

Publications and source records attributed to Schaefer, III, Henry F..

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

MolSym : A Python package for handling symmetry in molecular quantum chemistry

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Automated theoretical chemical kinetics: Predicting the kinetics for the initial stages of pyrolysis

Large scale implementation of high level computational theoretical chemical kinetics offers the prospect for dramatically improving the fidelity of combustion chemical modeling. To facilitate such efforts, we have developed a suite of codes, collectively referred to as AutoMech, that allow for the automatic prediction of the kinetics for large sets of reactions via ab initio transition-state-theory based master-equation calculations. The primary input is simply the mechanism, a dictionary relating chemically identifiable species descriptors (e.g., SMILES or InChIs) to species labels in the mechanism, and a specification of the electronic structure and transition state theory models to be implemented. Here we illustrate the current utility of AutoMech through a study of the initial stages of pyrolysis for 3 sets of fuels: sequences of alkanes, alcohols, and aldehydes. For simplicity, the analysis focuses on abstractions from the fuel by H, CH 3 , and OH, and the decomposition of the resulting radicals. Altogether, there are a total of 166 input channels in these sets (more than 363 forward reactions when expanded to the full set of elementary reactions). The code successfully produces high quality rate estimates (with apparent uncertainties less than a factor of two in limited comparisons with experiment) for > 95% of these. For the radical decomposition reactions, the analysis includes predictions for the pressure dependence of the kinetics. This wide-ranging exploration illustrates (i) the effect of different levels of prediction on the expected accuracy, (ii) the branching between abstractions at different sites for different abstractors, (iii) the dependence of the rates on the chemical structure, and (iv) the variation in radical stabilities across chemical families. These results, as well as the demonstrated feasibility of the methodology, should find further utility in the development of accurate rate expressions for arbitrary fuels. (c) 2020 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Elliott, Sarah N.↗
DOE OSTI2018

Student-Friendly Guide to Molecular Integrals

Preceding even the Hartree–Fock method, molecular integrals are the very foundation upon which quantum chemical molecular modeling depends. Discussions of molecular integrals are normally found only in advanced and technical texts or articles. The objective of the present article is to provide less experienced readers, or students in a physical/computational chemistry course, a thorough understanding of molecular integrals. Through a series of detailed Handouts, the student/reader can participate in the derivation of molecular integrals, and in turn implement them in computer code. Hartree–Fock theory is discussed in enough detail to motivate the molecular integrals and address such topics as the atomic orbital basis. An introduction to the programming language of choice, Python3, is provided, tailored toward developing the essential skills necessary for implementing molecular integrals. In conclusion, the article is intended to be useful not only to instructors of physical/computational chemistry, but also to any reader who has independently sought a primer on this elusive subject.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A remarkable case of basis set dependence: the false convergence patterns of the methyl anion

Here, the gas phase methyl anion, CH 3 ¯, has been difficult to study experimentally, and the extreme basis set dependence of its molecular properties has presented a comparable challenge to theoreticians. Reliable predictions for the electronic structure of CH 3 ¯ require the use of basis sets capable of describing both the diffuse and valence characteristics of the system. The present study examines the basis set dependence of the equilibrium geometry and harmonic vibrational frequencies of CH 3 ¯. Both Hartree–Fock and CCSD(T) levels of theories are used with cc-pVXZ (, T, Q, 5, 6) basis sets with up to triple augmentation to describe the diffuse nature of the electron distribution. We find that non-augmented basis sets systematically yield vibrational frequencies that are too high for the umbrella mode and too low for the C–H symmetric and antisymmetric stretch even when extrapolated to the complete basis set limit, displaying false convergence patterns. The inclusion of one set of augmented functions significantly improves the convergence of these properties, but again yields false convergence patterns. Only with the doubly augmented basis set do we approach the basis set limit for the CH 3 ¯ vibrational frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

High-level theoretical characterization of the vinoxy radical ( • CH 2 CHO) + O 2 reaction

Numerous processes in atmospheric and combustion chemistry produce the vinoxy radical ( • CH 2 CHO). To understand the fate of this radical and to provide reliable energies needed for kinetic modeling of such processes, we have examined its reaction with O 2 using highly reliable theoretical methods. Utilizing the focal point approach, the energetics of this reaction and subsequent reactions were obtained using coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] extrapolated to the complete basis set limit. These extrapolated energies were appended with several corrections including a treatment of full triples and connected quadruple excitations, i.e., CCSDT(Q). In addition, this study models the initial vinoxy radical + O 2 reaction for the first time with multireference methods. We predict a barrier for this reaction of approximately 0.4 kcal mol –1 . This result agrees with experimental findings but is in disagreement with previous theoretical studies. The vinoxy radical + O 2 reaction produces a 2-oxoethylperoxy radical which can undergo a number of unimolecular reactions. Abstraction of a β-hydrogen (a 1,4-hydrogen shift) and dissociation back to reactants are predicted to be competitive to each other due to their similar barriers of 21.2 and 22.3 kcal mol –1 , respectively. The minimum-energy β-hydrogen abstraction pathway produces a hydroperoxy radical (QOOH) that eventually decomposes to formaldehyde, CO, and • OH. Two other unimolecular reactions of the peroxy radical are α-hydrogen abstraction (38.7 kcal mol –1 barrier) and HO 2 • elimination (43.5 kcal mol –1 barrier). Furthermore, these pathways lead to glyoxal + • OH and ketene + HO 2 • formation, respectively, but they are expected to be uncompetitive due to their high barriers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde

Here, geometric energy derivatives which rely on core-corrected focal-point energies extrapolated to the complete basis set (CBS) limit of coupled cluster theory with iterative and noniterative quadruple excitations, CCSDTQ and CCSDT(Q), are used as elements of molecular gradients and, in the case of CCSDT(Q), expansion coefficients of an anharmonic force field. These gradients are used to determine the CCSDTQ/CBS and CCSDT(Q)/CBS equilibrium structure of the S 0 ground state of H 2 CO where excellent agreement is observed with previous work and experimentally derived results. A fourth-order expansion about this CCSDT(Q)/CBS reference geometry using the same level of theory produces an exceptional level of agreement to spectroscopically observed vibrational band origins with a MAE of 0.57 cm –1 . Second-order vibrational perturbation theory (VPT2) and variational discrete variable representation (DVR) results are contrasted and discussed. Vibration–rotation, anharmonicity, and centrifugal distortion constants from the VPT2 analysis are reported and compared to previous work. Additionally, an initial application of a sum-over-states fourth-order vibrational perturbation theory (VPT4) formalism is employed herein, utilizing quintic and sextic derivatives obtained with a recursive algorithmic approach for response theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Spin–Orbit Coupling via Four-Component Multireference Methods: Benchmarking on p-Block Elements and Tentative Recommendations

Within current electronic structure theory methods, fully relativistic four-component (4c) approaches based on the Dirac Hamiltonian treat spin–orbit coupling with the most rigor. The spin treatment arises naturally from the formulation and does not need to be included ad hoc. Spin–orbit splittings can provide insightful benchmark criteria for the assessment of 4c methods; however, there have not been extensive studies in this respect. Spin–orbit splittings of the p-block elements B–I were computed using the 4c-CASSCF, 4c-CASPT2, and 4c-MR-CISD+Q methods, as recently implemented in BAGEL, with uncontracted Dunning basis sets. Comparison with experiment reveals that the four-component methods yield good results, with most of the computed splittings falling within 15% of the experimental values. A large basis set is needed to obtain accurate splittings of the light elements B–F, while splittings of heavier elements show little basis dependence. The 4c-MR-CISD+Q method gave the best splittings for light elements, while 4c-CASSCF showed the best splittings for elements beyond fluorine. In conclusion, the 4c-CASPT2 method gave the best splittings for group 13 atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Re-examining ammonia addition to the Criegee intermediate: converging to chemical accuracy

Here stabilized Criegee intermediates (SCI) are formed during the ozonolysis of unsaturated hydrocarbons and have been implicated in the formation of hydroxyl radicals and aerosols. Previous theoretical research computed the rate constants for addition of ammonia to simple SCIs, but reported a wide distribution of quantum chemical energies, depending on the basis set used. We report optimized geometries for these reactions at the CCSD(T)/ANO2 and CCSD(T)/ANO1 levels, and CCSD(T)/CBS energies with perturbative quadruples corrections. We find the inclusion of perturbative quadruples corrections elevates the energy of the transition state by 0.76–0.88 kcal mol –1 relative to the reactants, which qualitatively changes the reaction surface. We calculate rate constants and find that Jørgenson and Gross previously overestimated the rate constants for ammonia addition to SCIs, but were within an order of magnitude.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗