“…Post-MD simulation analyses such as PCA, DCCM, and free energy landscape were also evaluated. The quantum mechanical and electronic properties of the potential bioactive compounds were assessed using the density functional theory (DFT) study. …”
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“…A molecular dynamics study at 200 ns was also carried out for the most promising anticoagulants to provide insights into the dynamic and thermodynamic properties of promising compounds. Moreover, a quantum mechanical study was also conducted which helped us to attest to some of the molecular docking and dynamics findings. …”
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“…Here, a comprehensive computational investigation is performed to explore the nature of interactions in the formation of phytosomes between phosphatidylcholine (PC) and a series of polyphenols (PP), including epigallocatechin-3-gallate (Eg), luteolin (Lu), quercetin (Qu), and resveratrol (Re). Our quantum mechanical calculation revealed that the intermolecular hydrogen bonds (HBs) of phosphate and glycerol parts of PC with the polyphenol compounds are the main driving force in the formation of phytosomes. …”
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“…Transmission coefficients were calculated by applying a quantum-mechanical approach based on reflection factor [3,4]. …”
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“…The mechanism for the reaction is the formation of a weakly-bound complex followed by quantum mechanical tunnelling through the small barrier to form HCN + HCO products. …”
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“…Starting with the theozyme constructed using a quantum-mechanical approach, the theoretical enzyme-skeleton combinations were assembled and optimized via the Rosetta “inside-out” protocol. …”
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“…They include MM-PBSA and thermodynamic integration, which are based on classical force fields, and a recently developed approach to computing binding free energies from large-scale quantum mechanical first principles calculations with the linear-scaling density functional code onetep. …”
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“…In order to analyze the possible quantitative structure-activity relationships (QSARs) of the enzymatic reactivity of the compounds, their electron-accepting potency and other reactivity indices were assessed by quantum mechanical methods. In P-450R-catalyzed reactions, both BFXs and NACs showed the same reactivity dependence on their electron-accepting potency which might be consistent with an “outer sphere” electron transfer mechanism. …”
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“…Complementary molecular dynamics simulations in conjunction with mixed quantum mechanical/molecular mechanical calculations accurately reproduced the vibrational frequency shifts in these probes and provided atomic-level insight into the residues influencing these changes. …”
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“…In conclusion, it is a challenge to calculate binding affinities for this octa-acid system with quantum–mechanical methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10822-016-9957-5) contains supplementary material, which is available to authorized users.…”
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“…These 1° DKIEs are much smaller than those observed for enzyme-catalyzed hydrogen transfer that occurs mainly by quantum mechanical tunneling. These results support the conclusion that the rate acceleration for GPDH-catalyzed reactions is due to the stabilization of the transition state for hydride transfer by interactions with the protein catalyst. …”
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“…Small-molecule X-ray crystallography, NMR spectroscopy, and quantum mechanical calculations are consistent with fluorination at C(3) having negligible effects on the hydrogen bond donor capacity of the C(4) hydroxyl, but inverting the natural preference of Hyp from C(4)-exo to C(4)-endo pucker. …”
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“…First-principles quantum mechanical calculations based on density functional theory (DFT) have been conducted to understand the electronic structures and properties of the interface between Co, Ni, and graphene. …”
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“…It has become recognized that the topological properties of the quantum-mechanical electronic structures of certain materials can give them unusual and perhaps useful properties. …”
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“…In this work we investigate quantum mechanically the interaction of an intense ultrashort laser pulse with the graphene monolayer as well as with the armchair graphene ribbons of different widths. …”
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“…Full Marcus-like model fits of the rate and KIE profiles provided evidence for a high-temperature reaction via low-frequency conformational sampling associated with a broad distribution of hydride donor–acceptor distances (long-distance population centered at 3.31 ± 0.02 Å), only poorly suitable for quantum mechanical tunneling. Collectively, dynamical characteristics of TaCPa2E-catalyzed hydride transfer during transient oxidation of CDP-glucose reveal important analogies to mechanistically simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase. …”
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“…The function of the recently isolated sulerythrin (SulE) has been investigated using a combination of structural and electronic analyses based on quantum mechanical calculations. In the SulE structure of Fushinobu et al. (2003), isolated from a strictly aerobic archaeon, Sulfolobus tokadaii, a dioxygen-containing species was tentatively included at the active site during crystallographic refinement although the substrate specificity of SulE remains unclear. …”
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“…Therefore, using classical methods such as the protein bank database and quantum mechanical calculations are insufficient owing to the dimensionality of search spaces. …”
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“…The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. …”
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“…In particular, the study of quantum batteries, small quantum mechanical systems able to temporarily store energy and further release it on-demand, recently emerged as a fast-growing subject in this context.…”
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