In subsystem density functional theory (DFT), the bottom-up strategy to approximate the multivariable functional of the non-additive kinetic energy (NAKE) makes it possible to impose exact properties on the corresponding NAKE potential (NAKEP). Such a construction might lead to a non-symmetric and non-homogeneous functional, which excludes the use of such approximations for the evaluation of the total energy. We propose a general formalism to construct a symmetric version based on a perturbation theory approach of the energy expression for the asymmetric part. This strategy is then applied to construct a symmetrized NAKE corresponding to the NAKEP developed recently [Polak et al., J. Chem. Phys. 156, 044103 (2022)], making it possible to evaluate consistently the energy. These functionals were used to evaluate the interaction energy in several model intermolecular complexes using the formal framework of subsystem DFT. The new symmetrized energy expression shows a superior qualitative performance over common decomposable models.
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http://dx.doi.org/10.1063/5.0143602 | DOI Listing |
ACS Chem Biol
September 2024
Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada.
The equilibrium dissociation constant () is a major characteristic of affinity complexes and one of the most frequently determined physicochemical parameters. Despite its significance, the values of obtained for the same complex under similar conditions often exhibit considerable discrepancies and sometimes vary by orders of magnitude. These inconsistencies highlight the susceptibility of determination to large systematic errors, even when random errors are small.
View Article and Find Full Text PDFNat Catal
February 2024
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia Canada.
Epistasis, the non-additive effect of mutations, can provide combinatorial improvements to enzyme activity that substantially exceed the gains from individual mutations. Yet the molecular mechanisms of epistasis remain elusive, undermining our ability to predict pathogen evolution and engineer biocatalysts. Here we reveal how directed evolution of a β-lactamase yielded highly epistatic activity enhancements.
View Article and Find Full Text PDFJ Chem Theory Comput
March 2024
Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, University of Münster, Corrensstraße 36, Münster 48149, Germany.
J Chem Phys
May 2023
Department of Physical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Genève 4, Switzerland.
In subsystem density functional theory (DFT), the bottom-up strategy to approximate the multivariable functional of the non-additive kinetic energy (NAKE) makes it possible to impose exact properties on the corresponding NAKE potential (NAKEP). Such a construction might lead to a non-symmetric and non-homogeneous functional, which excludes the use of such approximations for the evaluation of the total energy. We propose a general formalism to construct a symmetric version based on a perturbation theory approach of the energy expression for the asymmetric part.
View Article and Find Full Text PDFJ Chem Theory Comput
November 2022
Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Löbdergraben 32, 07743Jena, Germany.
A practical and effective implementation of density functional theory based embedding is reported, which allows us to treat both periodic and aperiodic systems on an equal footing. Its essence is the expansion of orbitals and electron density of the periodic system using Gaussian basis functions, rather than plane-waves, which provides a unique all-electron direct-space representation, thus avoiding the need for pseudopotentials. This makes the construction of embedding potential for a molecular active subsystem due to a periodic environment quite convenient, as transformation between representations is far from trivial.
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