Two hybrid van der Waals density functionals (vdW-DFs) are developed using 25% Fock exchange with (i) the consistent-exchange vdW-DF-cx functional [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)] and (ii) with the vdW-DF2 functional [K. Lee et al., Phys. Rev. B 82, 081101 (2010)]. The ability to describe covalent and non-covalent binding properties of molecules is assessed. For properties related to covalent binding, atomization energies (G2-1 set), molecular reaction energies (G2RC set), and ionization energies (G21IP set) are benchmarked against experimental reference values. We find that hybrid-vdW-DF-cx yields results that are rather similar to those of the standard non-empirical hybrid PBE0 [C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999)], with mean average deviations (MADs) of 4.9 and 5.0 kcal/mol for the G2-1 set, respectively. In this comparison, experimental reference values are used, back corrected by wavefunction-based quantum-chemistry calculations of zero-point energies. Hybrid vdW-DF2 follows somewhat different trends, showing on average significantly larger deviations from the reference energies, with a MAD of 14.5 kcal/mol for the G2-1 set. Non-covalent binding properties of molecules are assessed using the S22 benchmark set of non-covalently bonded dimers and the X40 set of dimers of small halogenated molecules, using wavefunction-based quantum chemistry results as references. For the S22 set, hybrid-vdW-DF-cx performs better than standard vdW-DF-cx for the mostly hydrogen-bonded systems, with MAD dropping from 0.6 to 0.3 kcal/mol, but worse for purely dispersion-bonded systems, with MAD increasing from 0.2 to 0.6 kcal/mol. Hybrid-vdW-DF2 offers a slight improvement over standard vdW-DF2. Similar trends are found for the X40 set, with hybrid-vdW-DF-cx performing particularly well for binding energies involving the strongly polar hydrogen halides, but poorly for systems with tiny binding energies. Our study of the X40 set reveals the potential of mixing Fock exchange with vdW-DF, but also highlights shortcomings of the hybrids constructed here. The solid performance of hybrid-vdW-DF-cx for covalent-bonded systems, as well as the strengths and issues uncovered for non-covalently bonded systems, makes this study a good starting point for developing even more accurate hybrid vdW-DFs.
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http://dx.doi.org/10.1063/1.4986522 | DOI Listing |
Protein Sci
January 2025
Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy.
Human succinic semialdehyde dehydrogenase is a mitochondrial enzyme fundamental in the neurotransmitter γ-aminobutyric acid catabolism. It catalyzes the NAD-dependent oxidative degradation of its derivative, succinic semialdehyde, to succinic acid. Mutations in its gene lead to an inherited neurometabolic rare disease, succinic semialdehyde dehydrogenase deficiency, characterized by mental and developmental delay.
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December 2024
Laboratório de Ciências Físicas, Centro de Ciência e Tecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, Campos dos Goytacazes 28013-602, RJ, Brazil.
Phase separation is essential for membrane function, and alterations in phase coexistence by membrane-interacting molecules, such as nicotine, can impair membrane stability. With the increasing use of e-cigarettes, concerns have arisen about the impact of nicotine on pulmonary surfactants. Here, we used differential scanning calorimetry (DSC), molecular dynamics (MD) simulations, and electron spin resonance (ESR) to examine nicotine's effect on the phase coexistence of two surfactant models: pure DPPC and a DPPC/POPC/POPG mixture.
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December 2024
School of Medicine and Life Sciences, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia.
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December 2024
Grade 2022, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.
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View Article and Find Full Text PDFAngew Chem Int Ed Engl
December 2024
Goethe-Universitat Frankfurt am Main Fachbereich 14 Biochemie Chemie und Pharmazie, Institute for Pharmaceutical Chemistry, GERMANY.
Protein kinases are important drug targets, yet specific inhibitors have been developed for only a fraction of the more than 500 human kinases. A major challenge in designing inhibitors for highly related kinases is selectivity. Unlike their non-covalent counterparts, covalent inhibitors offer the advantage of selectively targeting structurally similar kinases by modifying specific protein side chains, particularly non-conserved cysteines.
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