For the accurate computation of relative energies, domain-based local pair natural orbital coupled-cluster [DLPNO-CCSD(T)] has become increasingly popular. Even though DLPNO-CCSD(T) shows a formally linear scaling of the computational effort with the system size, accurate predictions of relative energies remain costly. Therefore, multi-level approaches are attractive that focus the available computational resources on a minor part of the molecular system, e.g., a reaction center, where changes in the correlation energy are expected to be the largest. We present a pair-selected multi-level DLPNO-CCSD(T) ansatz that automatically partitions the orbital pairs according to their contribution to the overall correlation energy change in a chemical reaction. To this end, the localized orbitals are mapped between structures in the reaction; all pair energies are approximated through computationally efficient semi-canonical second-order Møller-Plesser perturbation theory, and the orbital pairs for which the pair energies change significantly are identified. This multi-level approach is significantly more robust than our previously suggested, orbital selection-based multi-level DLPNO-CCSD(T) ansatz [M. Bensberg and J. Neugebauer, J. Chem. Phys. 155, 224102 (2021)] for reactions showing only small changes in the occupied orbitals. At the same time, it is even more efficient without added input complexity or accuracy loss compared to the full DLPNO-CCSD(T) calculation. We demonstrate the accuracy of the multi-level approach for a total of 128 chemical reactions and potential energy curves of weakly interacting complexes from the S66x8 benchmark set.
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Syst Biol
January 2025
Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.
Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils. Here, we introduce multiple new time constraints to calibrate bacterial evolution based on ancient symbiosis. This idea is implemented using a bacterial tree constructed with genes found in the mitochondrial lineages phylogenetically embedded within Proteobacteria.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
January 2025
Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, 800 Dongchuan Road, 200240, Shanghai, CHINA.
Ionogels have attracted considerable attention as versatile materials due to their unique ionic conductivity and thermal stability. However, relatively weak mechanical performance of many existing ionogels has hindered their broader application. Herein, we develop robust, tough, and impact-resistant mechanically interlocked network ionogels (IGMINs) by incorporating ion liquids with mechanical bonds that can dissipate energy while maintain structural stability.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
Chemical kinetics for second oxygen addition reactions (·QOOH + O) of long-chain alkanes are of great importance in low-temperature combustion technologies. However, kinetic data for key reactions of ·QOOH + O systems are often difficult to obtain experimentally and are primarily estimated or calculated by using theoretical methods. In this work, barrier heights (BHs), reaction energies (Δs), and relative energies (REs) of stationary points for key reactions of two representative ·QOOH + O systems in the low-temperature oxidation of -butyl as well as pressure-dependent rate constants for the involved reactions are calculated with the high-level quantum chemical method CCSD(T)-F12b/CBS.
View Article and Find Full Text PDFProteomes
December 2024
Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
Lymphatic filariasis (LF) continues to impact 657 million individuals worldwide, resulting in lifelong and chronic impairment. The prevalent anti-filarial medications-DEC, albendazole, and ivermectin-exhibit limited adulticidal efficacy. Despite ongoing LF eradication programs, novel therapeutic strategies are essential for effective control.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Institute of Nanomaterials, Faculty of Materials Science, Kim Il Sung University, Ryongnam-Dong, Taesong District, Pyongyang, Democratic People's Republic of Korea.
Significant research efforts have been devoted to improving the efficiency of catalytic carbon monoxide (CO) oxidation over α-FeO-based catalysts, but details of the underlying mechanism are still under debate. Here we apply the thermodynamic method (AITM) within the density functional theory framework to investigate the phase diagram of α-FeO(0001) surfaces with various terminations and the catalytic mechanism of CO oxidation on these surfaces. By extending the conventional AITM to consider the charge state of surface defects, we build the phase diagram of α-FeO(0001) surfaces in relation to the Fermi energy as well as the oxygen chemical potential, which makes it possible to explain the influence of point defects on the surface morphology and to predict the existence of the experimentally observed functional sites such as the ferryl group (FeO) and oxygen vacancies.
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