Accurate thermochemistry computations often require proper treatment of torsional modes. The one-dimensional hindered rotor model has proven to be a computationally efficient solution, given a sufficiently accurate potential energy surface. Methods that provide potential energies at various compromises of uncertainty and computational time demand can be optimally combined within a multifidelity treatment. In this study, we demonstrate how multifidelity modeling leads to (1) smooth interpolation along low-fidelity scan points with uncertainty estimates, (2) inclusion of high-fidelity data that change the energetic order of conformations, and (3) predicting best next-point calculations to extend an initial coarse grid. Our diverse application set comprises molecules, clusters, and transition states of alcohols, ethers, and rings. We discuss limitations for cases in which the low-fidelity computation is highly unreliable. Different features of the potential energy curve affect different quantities. To obtain "optimal" fits, we apply strategies ranging from simple minimization of deviations to developing an acquisition function tailored for statistical thermodynamics. Bayesian prediction of best next calculations can save a substantial amount of computation time for one- and multidimensional hindered rotors.
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http://dx.doi.org/10.1021/acs.jctc.4c00475 | DOI Listing |
J Biomol Struct Dyn
December 2024
Amity Institute of Biotechnology, Amity University, Kolkata, India.
The first FDA approved, MDR-TB inhibitory drug bedaquiline (BDQ), entraps the c-ring of the proton-translocating F region of enzyme ATP synthase of , thus obstructing successive ATP production. Present-day BDQ-resistance has been associated with cardiotoxicity and mutation(s) in the atpE gene encoding the c subunit of ATP synthase (ATPc) generating five distinct ATPc mutants: Ala63→Pro, Ile66→Met, Asp28→Gly, Asp28→Val and Glu61→Asp. We created three discrete libraries, first by repurposing bedaquiline via scaffold hopping approach, second one having natural plant compounds and the third being experimentally derived analogues of BDQ to identify one drug candidate that can inhibit ATPc activity more efficiently with less toxic properties.
View Article and Find Full Text PDFJ Phys Chem Lett
December 2024
Univ Paris Est Creteil and Université Paris Cité, CNRS, LISA, F-94010 Créteil, France.
Large amplitude motions (LAMs), most notably represented by proton tunneling, mark a significant departure from small amplitude vibrations where protons merely oscillate around their equilibrium positions. These substantial displacements require tunneling through potential energy barriers, leading to splittings in, e.g.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Chemistry, University of Graz, Heinrichstraße 28/IV, 8010 Graz, Austria.
Intermolecular vibrations are extremely challenging to describe but are the most crucial part for determining entropy and hence free energies and enable, for instance, the distinction between different crystal-packing arrangements of the same molecule via THz spectroscopy. Herein, we introduce a benchmark dataset-V30-containing 30 small molecular dimers with intermolecular interactions ranging from exclusively van der Waals dispersion to systems with hydrogen bonds. All the calculations are performed with the gold standard of quantum chemistry CCSD(T).
View Article and Find Full Text PDFAdv Mater
November 2024
School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen, Guangdong, 518172, China.
Phototheranositcs has recently aroused extreme attention due to its exceptional advantages. However, the poor photothernostic efficiency, limited penetration depth, strong oxygen-dependence, and inevitable damage to normal tissue of conventional photothernostic materials severely hindered their total theranostic efficacy. Herein, a series of near-infrared second (NIR-II) photosensitizers (PSs) featuring aggregation-induced emission (AIE), NIR-II fluorescence imaging (FLI), type I photodynamic therapy (PDT) and mild-temperature photothermal therapy (PTT) are constructed through dual-strategy methods combining donor group engineering and fluorination engineering.
View Article and Find Full Text PDFJ Chem Theory Comput
November 2024
Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Km. 6 Antigua carretera a Progreso Apdo. Postal 73, Cordemex, 97310 Mérida, Mexico.
The recrossing effect and hindered rotations can lead to significant inaccuracies in rate constant calculations using transition state theory and the harmonic oscillator approximation. To address these issues, we enhanced , a -based computational tool, by integrating the canonical variational transition state theory (CVT) and the hindered rotor model, effectively mitigating the limitations of traditional methods. CVT rate constants are calculated using electronic structure data from nonstationary points along the minimum-energy path.
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