Hybrid quantum mechanics/molecular mechanics (QM/MM) is one of the most reliable approaches for accurately modeling and studying the complex pharmaceutical discovery system. Classical mechanics has significantly accelerated the drug discovery process in the past decade. However, the current challenge is the large pool of false positives, which require extensive validation. Hybrid QM/MM is an effective solution for accurately studying ligand binding, structural mechanisms, free energy evaluation, and spectroscopic characterization. This article highlights the methodological details relevant to cost-effective hybrid QM/MM methods. This approach, combined with traditional pharmacoinformatics methods, could be a reliable strategy to balance the cost and accuracy of the calculations.
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http://dx.doi.org/10.1016/j.drudis.2022.103374 | DOI Listing |
J Phys Chem A
January 2025
Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan 250014, China.
Organic room-temperature phosphorescence (RTP) emitters with long lifetimes, high exciton utilizations, and tunable emission properties show promising applications in organic light-emitting diodes (OLEDs) and biomedical fields. Their excited-state properties are highly related to single molecular structure, aggregation morphology, and external stimulus (such as hydrostatic pressure effect). To gain a deeper understanding and effectively regulate the key factors of luminescent efficiency and lifetime for RTP emitters, we employ the thermal vibration correlation function (TVCF) theory coupled with quantum mechanics/molecular mechanics (QM/MM) calculations to investigate the photophysical properties of three reported RTP crystals (Bp-OEt, Xan-OEt, and Xan-OMe) with elastic/plastic deformation.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
December 2024
Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden.
Photosystem II (PSII) catalyzes light-driven water oxidation that releases dioxygen into our atmosphere and provides the electrons needed for the synthesis of biomass. The catalysis occurs in the oxygen-evolving oxo-manganese-calcium (MnOCa) cluster that drives the oxidation and deprotonation of substrate water molecules leading to the O formation. However, despite recent advances, the mechanism of these reactions remains unclear and much debated.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
The effect of conformational dynamics and solvent interactions on the second-order nonlinear optical (NLO) responses of the open and closed forms of a donor-acceptor Stenhouse adduct (DASA) are investigated by a mixed quantum/classical computational approach, which couples molecular dynamics (MD) simulations and time-dependent density functional theory (TD-DFT) calculations. The latter are further combined with various solvation schemes, including polarizable continuum models, hybrid QM/MM approaches using either non polarizable or polarizable electrostatic embedding, and QM/QM' schemes with explicit treatment of a few molecules of the first solvation shell. The performances of the different solvation models are discussed in the context of comparisons with experimental data obtained from hyper-Rayleigh scattering measurements.
View Article and Find Full Text PDFJ Phys Chem B
December 2024
Aix Marseille Univ, CNRS, ICR, 13013 Marseille, France.
The automatic rhodopsin modeling (ARM) approach is a computational workflow devised for the automatic buildup of hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild-type rhodopsins and mutants, with the purpose of establishing trends in their photophysical and photochemical properties. Despite the success of ARM in accurately describing the visible light absorption maxima of many rhodopsins, for a few cases, called outliers, it might lead to large deviations with respect to experiments. Applying ARM to rhodopsin (GR), a microbial rhodopsin with important applications in optogenetics, we analyze the origin of such outliers in the absorption energies obtained for GR wild-type and mutants at neutral pH, with a total root-mean-square deviation (RMSD) of 0.
View Article and Find Full Text PDFACS Phys Chem Au
November 2024
Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan.
OaPAC is a photoactivated enzyme that forms a homodimer. The two blue-light using flavin (BLUF) photoreceptor domains are connected to the catalytic domains with long coiled-coil C-terminal helices. Upon photoreception, reorganization of the hydrogen bonding network between Tyr6, Gln48, and the chromophore in the BLUF domain and keto-enol tautomerization of Gln48 are thought to occur.
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