“…These results, together with molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations, indicate that electron transfer from [Formula: see text] to O(2) occurs when the O(2) is bound to the empty bicarbonate site on Fe(2+). …”
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“…[Image: see text] Quantum mechanics/molecular mechanics (QM/MM) calculations are applied for anharmonic vibrational analyses of biomolecules and solvated molecules. …”
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“…Based on theories of theoretical mechanics, modern quantum mechanics, thermodynamics, and other disciplines, first, this paper explained the causes of infrared radiation energy in the process of coal-rock fracture by using the microanalysis method. …”
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“…AsHS2 mutants with a substitution at site 410 could synthesize hopenol B alone or mixed with a side product isomotiol. The combined quantum mechanics and molecular mechanics calculation demonstrated that the side chain size of the residue at site 410 regulated the relative orientations between the hopyl C22 cation and Phe257, leading to a difference in deprotonation positions through providing or not providing cation–π interaction between the aromatic ring of F257 and the carbocation intermediate. …”
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“…The present study deals with finding a formula of the molar specific heat capacity using the theory of the integral equations for Morse interaction which is a very important potential for the study of the general oscillations in the quantum mechanics. We use the approximation (Mean-Spherical) for finding the total energy of the compositions described by Morse interaction. …”
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“…OBJECTIVE: To study structure-specific solubilization effect of Sulfobutyl ether-β-cyclodextrin (SBE-β-CD) on Remdesivir (RDV) and to understand the experimental clathration with the aid of quantum mechanics (QM), molecular docking and molecular dynamics (MD) calculations. …”
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“…A combination of quantum mechanics/molecular mechanics calculations and ultrafast visible and infrared spectroscopies demonstrates how proton-coupled dynamics in the excited state of Pfr leads to a restructured hydrogen-bond environment of early Lumi-F, which is interpreted as a trigger for downstream protein structural changes. …”
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“…Hydrogen–deuterium exchange mass spectrometry analysis, quantum mechanics/molecular mechanics calculations, together with site-directed mutagenesis indicated the antiviral activities of schaftoside were related with non-covalent interactions with H41, G143 and R188 of 3CL(pro), and K157, E167 and A246 of PL(pro). …”
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“…However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). …”
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“…Our experimental results, coupled with quantum-mechanics/molecular-mechanics calculations, reveal that the monophenol substrate docks in the active-site pocket of oxy-Ty fully protonated, without coordination to a copper or cleavage of the μ:η(2):η(2)-peroxide O-O bond. …”
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“…The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. …”
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“…The combinatorial use of quantum mechanics studies and molecular dynamic simulation has enabled us to precisely predict the inhibition mechanism of the newly designed structure, which is based on carbohydrates and amino acids, and compare it with that of the traditional chemotherapeutic drugs such as Cytarabine. …”
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“…A minimum length scale of the order of Planck length is a feature of many models of quantum gravity that seek to unify quantum mechanics and gravitation. Recently, Perivolaropoulos in his seminal work (Perivolaropoulos in Phys. …”
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“…Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. …”
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“…I further explore how these ideas might relate to the “Bayesian blur problem,” or how it is that a seemingly discrete experience can be generated from probabilistic modeling, with some consideration of analogies from quantum mechanics as potentially revealing different varieties of inferential dynamics. …”
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“…Starting from four distinct enzyme:substrate complexes, umbrella sampling quantum mechanics/molecular mechanics simulations (converged within less than 1 kcal·mol(–1) within a total simulation time of 1.6 ns) indicated that the reaction occurrs with a Gibbs barrier of 13.9 kcal·mol (–1), in one asynchronous concerted step encompassing an acid–base reaction with Glu233 followed by a loose S(N)2-like nucleophilic substitution by the Asp197. …”
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“…Intriguingly, in the early part of 20th century, the concept of the “morphogenetic field” was proposed by Gurwitsch to explain how the shape of an organism was determined, while a role for quantum mechanics in biology was suggested by Bohr and Schrödinger, among others. …”
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“…MBAR is also useful to estimate reliable free-energy differences using MD trajectories based on a semi-empirical quantum mechanics/molecular mechanics (QM/MM) model and ab initio QM/MM energy calculations on the MD snapshots. …”
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“…For example, in their adaptation of the classic double-slit experiment in quantum mechanics to develop a quantum eraser, Scully and his colleagues relied on entanglement between: 1) an atom’s emitting a photon in one of two micromaser cavities as the atom passes through the cavity system and 2) the atom’s subsequent passage through the fixed double-slit screen. …”
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“…Quantum field theory, which started with Paul Dirac’s work shortly after the discovery of quantum mechanics, has produced an impressive and important array of results. …”
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