Dataset Information

QSym²: A Quantum Symbolic Symmetry Analysis Program for Electronic Structure.

ABSTRACT: Symmetry provides a powerful machinery to classify, interpret, and understand quantum-mechanical theories and results. However, most contemporary quantum chemistry packages lack the ability to handle degeneracy and symmetry breaking effects, especially in non-Abelian groups, and they are not able to characterize symmetry in the presence of external magnetic or electric fields. In this article, a program written in Rust entitled QSym² that makes use of group and representation theories to provide symmetry analysis for a wide range of quantum-chemical calculations is introduced. With its ability to generate character tables symbolically on-the-fly and by making use of a generic symmetry-orbit-based representation analysis method formulated in this work, QSym² is able to address all of these shortcomings. To illustrate these capabilities of QSym², four sets of case studies are examined in detail in this article: (i) high-symmetry C₈₄H₆₄, C₆₀, and B₉^- to demonstrate the analysis of degenerate molecular orbitals (MOs); (ii) octahedral Fe(CN)₆^3- to demonstrate the analysis of symmetry-broken determinants and MOs; (iii) linear hydrogen fluoride in a magnetic field to demonstrate the analysis of magnetic symmetry; and (iv) equilateral H₃⁺ to demonstrate the analysis of density symmetries.

SUBMITTER: Huynh BC

PROVIDER: S-EPMC10782455 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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QSym<sup>2</sup>: A Quantum Symbolic Symmetry Analysis Program for Electronic Structure.

Huynh Bang C BC Wibowo-Teale Meilani M Wibowo-Teale Andrew M AM

Journal of chemical theory and computation 20231225 1

Symmetry provides a powerful machinery to classify, interpret, and understand quantum-mechanical theories and results. However, most contemporary quantum chemistry packages lack the ability to handle degeneracy and symmetry breaking effects, especially in non-Abelian groups, and they are not able to characterize symmetry in the presence of external magnetic or electric fields. In this article, a program written in Rust entitled QSym<sup>2</sup> that makes use of group and representation theories ...[more]

PMID: 38145888

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Project description:The main purpose of this study is to characterize the nature of the low-energy singlet excited states of the anthranilic acid homodimer (AA2) and their changes (symmetry breaking) caused by deformation of the centrosymmetric, ground state structure of AA2 towards the geometry of the S1 state. We employ both the correlated ab initio methods (approximate Coupled Clusters Singles and Doubles-CC2 and CASSCF/NEVPT2) as well as the DFT/TDDFT calculations with two exchange-correlation functionals, i.e., B3LYP and CAM-B3LYP. The composition of the wavefunctions is investigated using the one-electron transition density matrix and difference density maps. We demonstrate that in the case of AA2, small asymmetric distortions of geometry bring about unproportionally large changes in the excited state wavefunctions. We further provide comprehensive characterization of the AA2 electronic structure, showing that the excitation is nearly completely localized on one of the monomers, which stands in agreement with the experimental evidence. The excitation increases the π-electronic coupling of the substituents and the aromatic ring, but only in the excited monomer, while the changes in the electronic structure of the unexcited monomer are negligible (after geometry relaxation). The increased electronic density strengthens both intra- and intermolecular hydrogen bonds formed by the carbonyl oxygen atom of the excited monomer, making them significantly stronger than in the ground state. Although the overall pattern of changes remains qualitatively consistent across all methods employed, CC2 predicts more pronounced excitation-induced modifications of the electronic structure compared to the more routinely used TDDFT approach. The most important deficiency of the B3LYP functional in the present context is locating two charge-transfer states at erroneously low energies, in close proximity of the S1 and S2 states. The range-corrected CAM-B3LYP exchange-correlation functional gives a considerably improved description of the CT states at the price of overshot excitation energies.

Project description:The open-shell electronic structure of iron-sulfur clusters presents considerable challenges to quantum chemistry, with the complex iron-molybdenum cofactor (FeMoco) of nitrogenase representing perhaps the ultimate challenge for either wavefunction or density functional theory. While broken-symmetry density functional theory has seen some success in describing the electronic structure of such cofactors, there is a large exchange-correlation functional dependence in calculations that is not fully understood. In this work, we present a geometric benchmarking test set, FeMoD11, of synthetic spin-coupled Fe-Fe and Mo-Fe dimers, with relevance to the molecular and electronic structure of the Mo-nitrogenase FeMo cofactor. The reference data consists of high-resolution crystal structures of metal dimer compounds in different oxidation states. Multiple density functionals are tested on their ability to reproduce the local geometry, specifically the Fe-Fe/Mo-Fe distance, for both antiferromagnetically coupled and ferromagnetically coupled dimers via the broken-symmetry approach. The metal-metal distance is revealed not only to be highly sensitive to the amount of exact exchange in the functional but also to the specific exchange and correlation functionals. For the antiferromagnetically coupled dimers, the calculated metal-metal distance correlates well with the covalency of the bridging metal-ligand bonds, as revealed via the corresponding orbital analysis, Hirshfeld S/Fe charges, and Fe-S Mayer bond order. Superexchange via bridging ligands is expected to be the dominant interaction in these dimers, and our results suggest that functionals that predict accurate Fe-Fe and Mo-Fe distances describe the overall metal-ligand covalency more accurately and in turn the superexchange of these systems. The best performing density functionals of the 16 tested for the FeMoD11 test set are revealed to be either the nonhybrid functionals r2SCAN and B97-D3 or hybrid functionals with 10-15% exact exchange: TPSSh and B3LYP*. These same four functionals are furthermore found to reproduce the high-resolution X-ray structure of FeMoco well according to quantum mechanics/molecular mechanics (QM/MM) calculations. Almost all nonhybrid functionals systematically underestimate Fe-Fe and Mo-Fe distances (with r2SCAN and B97-D3 being the sole exceptions), while hybrid functionals with >15% exact exchange (including range-separated hybrid functionals) overestimate them. The results overall suggest r2SCAN, B97-D3, TPSSh, and B3LYP* as accurate density functionals for describing the electronic structure of iron-sulfur clusters in general, including the complex FeMoco cluster of nitrogenase.

Dataset Information

QSym²: A Quantum Symbolic Symmetry Analysis Program for Electronic Structure.

Publications

QSym<sup>2</sup>: A Quantum Symbolic Symmetry Analysis Program for Electronic Structure.

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Dataset Information

QSym2: A Quantum Symbolic Symmetry Analysis Program for Electronic Structure.

Publications

QSym<sup>2</sup>: A Quantum Symbolic Symmetry Analysis Program for Electronic Structure.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

QSym²: A Quantum Symbolic Symmetry Analysis Program for Electronic Structure.