“…Active site residues central to the hydrolytic mechanism include a novel catalytic triad Asp-His-His supported by structural comparison and hybrid quantum mechanics/classical mechanics simulations. A hydrolytic mechanism for a Mn(2+) dependent amidohydrolases that disfavour Zn(2+) as the primary catalytically active site metal proposed here is supported by these likely cases of convergent evolution. …”
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“…In this study, we shed light on the mechanism through which AdiC distinguishes Arg(+) from Arg(2+) of arginine by investigating the binding of both forms in addition to that of divalent agmatine, using a combination of molecular dynamics simulations with molecular and quantum mechanics calculations. We show that AdiC indeed preferentially binds Arg(+). …”
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“…We investigated the ionization profiles for open-ring (OR) and closed-ring (CR) forms of midazolam and drug-binding modes with heptakis-(2,3,6-tri-O-methyl)-β-cyclodextrin (trimethyl-β-cyclodextrin; TRIMEB) using molecular modeling techniques and quantum mechanics methods. The results indicated that the total net charges for different molecular forms of midazolam tend to be cationic for OR and neutral for CR at physiological pH levels. …”
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“…Using the principles of quantum mechanics, quantum communication offers provable security of communication and is a promising solution to counter such threats. …”
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“…The emerging quantum cryptography, harnessing the random nature of quantum mechanics, may also enable unconditionally secure control network, beyond the applications in secure communications. …”
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“…From a theoretical point of view, these materials turn out to be excellent systems for testing quantum mechanics-based computational methods for strongly correlated electronic systems. …”
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“…Here we combine ambient pressure X-ray photoelectron spectroscopy with quantum mechanics to examine the processes as Ag is exposed to CO(2) both alone and in the presence of H(2)O at 298 K. …”
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“…The full enzymatic molecular mechanisms, starting from the initial electron transfer from a reductant to oxygen activation and hydrogen peroxide formation, are not yet understood. Using quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, we have uncovered the oxygen activation mechanisms by LPMO in the presence of ascorbic acid, one of the most-used reductants in LPMOs assays. …”
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“…Mixed ab initio quantum mechanics and molecular mechanics (QM/MM) calculations coupled to free energy perturbation and Monte Carlo sampling (FEP/MC) that utilized M06-2X/6-31G(d) and OPLS-VSIL gave activation free energy barriers of 14.9 and 16.0 kcal/mol for the endo-cis and exo-cis Diels-Alder reaction pathways, respectively (exptl. …”
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“…Output from these sources can be transformed into large numbers of elements of knowledge in a Knowledge Representation Store (KRS), here using the notation and to some extent the algebraic principles of the Q-UEL Web-based universal exchange and inference language described previously, rooted in Dirac notation from quantum mechanics and linguistic theory. In a KRS, semantic structures or statements about the world of interest to medicine are analogous to natural language sentences seen as formed from noun phrases separated by verbs, prepositions and other descriptions of relationships. …”
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“…We used molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate how structural dynamics influences the selectivity and mechanisms of the AlkB- and AlkBH2-catalyzed demethylation of 3-methylcytosine (m(3)C) in single (ssDNA) and double (dsDNA) stranded DNA. …”
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“…A lattice distortion theory for promotor containing clathrate hydrates is formulated using the statistical thermodynamics based model of van der Waals and Platteeuw in association with the ab initio quantum mechanics to compute the cavity potentials. Despite of high degree of lattice distortion anticipated for large and polar molecules of liquid promotors, their variable lattice energy concept is unreported. …”
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“…For a Clauser–Horne–Shimony–Holt inequality, it emulates the CHSH violation predicted by quantum mechanics up to [Formula: see text] . For the Garg–Mermin inequality—re-calibrated by incorporating non-detection events—our method emulates its exact local bound at any efficiency above the threshold. …”
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“…However, it is less clear how equilibrium thermodynamics emerges through the dynamics that follows the principle of quantum mechanics. In this paper, we develop a theory of quantum thermodynamics that is applicable for arbitrary small systems, even for single particle systems coupled with a reservoir. …”
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“…Heat is detrimental for the operation of quantum systems, yet it fundamentally behaves according to quantum mechanics, being phase coherent and universally quantum-limited regardless of its carriers. …”
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“…Given the existing similarities between these two processes in macromolecules, in this work, we suggest using Quantum Mechanics (QM) to study allostery.…”
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“…Molecular docking and quantum mechanics calculations are carried out to probe the interaction of phenol with the peroxidase site of COXs and the reactivation mechanism. …”
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“…Here, we present a combined molecular dynamics/quantum mechanics protocol that accurately predicts experimental NN ΔG°(37) parameters for modified nucleotides with neighboring Watson–Crick base pairs. …”
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“…Since NPRF is also responsible for the postulates of special relativity, and therefore its counterintuitive aspects of time dilation and length contraction, we see that the symmetry group relating non-relativistic quantum mechanics and special relativity via their “mysteries” is the restricted Lorentz group.…”
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“…In this study, sequential absorption, distribution, metabolism, and excretion (ADME) profiling, quantum mechanics calculations, and molecular docking simulations by extra precision Glide protocol predicted the drug-likeness of (-)-epicatechin (−7.862 kcal/mol) and proanthocyanidin B2 (−8.145 kcal/mol) with the least reactivity and substantial binding affinity in the catalytic pocket of human MMP-1 by comparison to reference bioactive compound epigallocatechin gallate (−6.488 kcal/mol). …”
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