“…These descriptors were paired with the relative energy gradient method, which solidifies the connection between quantum mechanical properties and chemical interpretation. …”
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“…Molecular dynamics simulations provide insights into the dynamics and roles of active site components as well as the interactions between substrate and enzymes. Hybrid quantum mechanical/molecular mechanical (QM/MM) can model reactions in active sites while considering steric and electrostatic contributions provided by the surrounding environment. …”
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“…In this work, we have filled this gap by employing a state-of-the-art computational approach, Born–Oppenheimer molecular dynamics simulations with ab initio quantum mechanical/molecular mechanical potential and umbrella sampling. …”
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“…The elongation of the O…O distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP.…”
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“…Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. …”
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“…A new γ-lactone that is capable of inhibiting the LasI/R QS system, plakofuranolactone (1), was discovered in the extract of the marine sponge Plakortis cf. lita, and its structure, including absolute configuration, was determined by NMR spectroscopy, MS spectrometry, and quantum-mechanical prediction of optical rotation. The quorum quenching activity of plakofuranolactone was evaluated using reporter gene assays for long- and short-chain signals (E. coli pSB1075, E. coli pSB401, and C. violeaceum CV026) and was confirmed by measuring the total protease activity (a virulence factor which is under control of the LasI/R system) of the wild-type P. aeruginosa PAO1. …”
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“…We describe this effect both with exact classical electrodynamic modeling and qualitative quantum-mechanical calculations. We identify the formation of strong hot spots between all particles as the main mechanism for the loss-less coupling and thus coherent ultra-fast energy transfer between the remote partners. …”
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“…The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. …”
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“…In this article, we present a simple method to calculate a quantum analog of this correlation, a generalized deflection function that can shed light onto the reaction mechanism using just quantum mechanical results. Our results show that there is a very good agreement between the quantum and classical correlation functions as long as quantum effects are not all relevant. …”
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“…We also investigated this size dependent magnetic behavior using Heisenberg model. Taking some quantum mechanical approximations in to consideration, we determined magnetic behavior of the clusters. …”
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“…Here, the influence of the adenine and thymidine (AT) interstrand linkage, the covalent bond between the adenine N6 and thymidine C5 methylene group, on the isolated base pair as well as double-stranded DNA (dsDNA) was taken into quantum mechanical/molecular mechanical (QM/MM) consideration at the m062x/6-31+G*:UFF level of theory in the aqueous phase. …”
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“…For contact with the lipid phase, the lipid/water partition coefficient is of importance as a macroscopic property for the flavonoids, while intramolecular rotation towards coplanarity upon oxidation by the carotenoid radical cation has been identified by quantum mechanical calculations to be an important microscopic property. …”
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“…Factors affecting the kinetic isotope effects (KIEs) of the gas-phase S(N)2 reactions and their temperature dependence have been analyzed using the ion-molecule collision theory and the transition state theory (TST). The quantum-mechanical tunneling effects were also considered using the canonical variational theory with small curvature tunneling (CVT/SCT). …”
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“…For tentative rationalization of the reaction processes, the global and local reactivity indices of certain compounds, taking part in the reaction pathway, were assessed by means of quantum mechanical calculations using the conceptual density functional theory (DFT) approach. …”
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“…The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. …”
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“…The force field used in this paper has been validated by comparing adsorption energy results with quantum mechanical (QM) calculations. All simulations were performed under the canonical (NVT) ensemble. …”
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“…Finally, by considering the Butler–Volmer (B–V) equation for the cathodic reaction (HER) in the MPM, and assuming the quantum mechanical tunneling of the charge carriers across the barrier layer of the passive film, it was shown that the HER was primarily controlled by the slow electrochemical discharge of protons at the barrier layer/solution (outer layer) interface.…”
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“…Based on this finding, we could identify artefacts that arose from quantum mechanical calculations in the Harvard Clean Energy Project dataset. …”
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“…[Image: see text] Molecular simulations based on classical force fields are computationally efficient but lack accuracy due to the empirical formulation of non-bonded interactions. Quantum mechanical (QM) methods, albeit accurate, have inhibitory computational costs for large molecules and clusters. …”
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“…Using QM/MM calculations in conjunction with the utilization of parameters such as quantum mechanically derived atomic charges, we have examined the chemical foundation for the altered equilibrium with this central biological reaction. …”
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