The atomic dipole polarizability α and the van der Waals (vdW) radius R_{vdW} are two key quantities to describe vdW interactions between atoms in molecules and materials. Until now, they have been determined independently and separately from each other. Here, we derive the quantum-mechanical relation R_{vdW}=const×α^{1/7}, which is markedly different from the common assumption R_{vdW}∝α^{1/3} based on a classical picture of hard-sphere atoms. As shown for 72 chemical elements between hydrogen and uranium, the obtained formula can be used as a unified definition of the vdW radius solely in terms of the atomic polarizability. For vdW-bonded heteronuclear dimers consisting of atoms A and B, the combination rule α=(α_{A}+α_{B})/2 provides a remarkably accurate way to calculate their equilibrium interatomic distance. The revealed scaling law allows us to reduce the empiricism and improve the accuracy of interatomic vdW potentials, at the same time suggesting the existence of a nontrivial relation between length and volume in quantum systems.
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http://dx.doi.org/10.1103/PhysRevLett.121.183401 | DOI Listing |
Mar Drugs
December 2024
Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, China.
Two new cembrane-derived tricyclic diterpenes belonging to the sarcophytin family, namely 4-hydroxy-chatancin () and sarcotoroid (), together with two known related ones ( and ), were isolated from the soft coral collected off Ximao Island in the South China Sea. The structures of the new compounds were elucidated by extensive spectroscopic analysis, a quantum mechanical nuclear magnetic resonance (QM-NMR) method, a time-dependent density functional theory electronic circular dichroism (TDDFT-ECD) calculation, X-ray diffraction analysis, and comparison with the reported data in the literature. A plausible biosynthetic pathway of compounds - was proposed, involving undergoing a transannular Diels-Alder cycloaddition.
View Article and Find Full Text PDFMar Drugs
November 2024
Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
Cembranoid diterpenes are characteristic compounds of soft corals with diverse structures and significant activities, making them an important source of drug lead compounds. In this paper, five new cembranoid diterpenes, meijicrassolins A-E (-), were isolated from the soft coral , along with five previously reported compounds (-). The structures and absolute configuration for new compounds - were assigned by extensive spectroscopic analysis, single-crystal X-ray crystallography, quantum mechanical nuclear magnetic resonance (QM-NMR), and time-dependent density functional theory/electronic circular dichroism (TDDFT/ECD) calculations.
View Article and Find Full Text PDFJ Phys Chem B
December 2024
Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147001, Punjab, India.
This study presents a detailed density functional theory (DFT) investigation into the mechanism and energetics of C-H activations catalyzed by bioinspired Fe(IV)O complexes, particularly in the presence of -hydroxy mediators. The findings show that these mediators significantly enhance the reactivity of the iron-oxo complex. The study examines three substrates with varying bond dissociation energies─ethylbenzene, cyclohexane, and cyclohexadiene─alongside the [Fe(IV)O(N4Py)] complex.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA.
Machine learning interatomic potentials (MLIPs) are rapidly gaining interest for molecular modeling, as they provide a balance between quantum-mechanical level descriptions of atomic interactions and reasonable computational efficiency. However, questions remain regarding the stability of simulations using these potentials, as well as the extent to which the learned potential energy function can be extrapolated safely. Past studies have encountered challenges when MLIPs are applied to classical benchmark systems.
View Article and Find Full Text PDFJ Am Chem Soc
December 2024
Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
Non-heme iron (Fe), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of Fe/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others.
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