“…Sulfate ion strengthened the hydrogen-bond network and easily formed ion pairs with Li(+), showing strong kosmotropic and hard base characteristics. Our quantum mechanics/molecular mechanics (QM/MM) simulations revealed that sulfate ion paired with Li(+) helped stabilize the LCO surface and reduced the density of free water in the interface region below the point of zero charge (PZC) potential. …”
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“…[Image: see text] The initial phases of drug discovery – in silico drug design – could benefit from first principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. …”
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“…Furthermore, we show that these Schrödinger operators with oblique transmission conditions arise naturally as non-relativistic limits of Dirac operators with electrostatic and Lorentz scalar [Formula: see text] -interactions justifying their usage as models in quantum mechanics.…”
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“…In particular, we show that such better performance is rooted in key quantum mechanics concepts: i) The ground state of the Hamiltonian of a quantum system—defined from the given data—corresponds to an optimal solution for the minimization problem of the variational free energy at very low temperatures; ii) such a ground state can be achieved by a technique paralleling the quantum annealing process; and iii) starting from this ground state, the optimal solution to the VB problem can be achieved by increasing the heat bath temperature to unity, and thereby avoiding local minima introduced by spontaneous symmetry breaking observed in classical physics based VB algorithms. …”
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“…This, together with quantum mechanics:molecular mechanics (QM:MM)–based modeling for the coordination of the W-co, enables formulation of a hypothetical catalytic mechanism that paves the way to further engineering for applications in synthetic biology and biotechnology.…”
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“…Here we investigate the nature and properties of triplet states within the PSII RC using a multiscale quantum-mechanics/molecular-mechanics (QM/MM) approach. …”
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“…We also implemented in SHARC a scheme for achieving roto-translational invariance of LVC models as well as a general quantum mechanics/molecular mechanics (QM/MM) interface, an OpenMM interface, and restraining potentials for simulating liquid droplets. …”
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“…[Image: see text] In order to investigate Li(2)S as a potential protective coating for lithium anode batteries using superionic electrolytes, we need to describe reactions and transport for systems at scales of >10,000 atoms for time scales beyond nanoseconds, which is most impractical for quantum mechanics (QM) calculations. To overcome this issue, here, we first report the development of the reactive analytical force field (ReaxFF) based on density functional theory (DFT) calculations on model systems at the PBE0/TZVP and M062X/TZVP levels. …”
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“…To characterize the catalytic mechanism of glucose phosphorylation by GK, we combined molecular modeling, molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations, experimental mutagenesis and enzymatic kinetic analysis on both wild-type and mutated GK. …”
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“…In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. …”
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“…A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. …”
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“…In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). …”
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“…In this paper it is shown that it is possible to write the evolution of the probability distribution as a functional integral of the same kind introduced by Feynman in quantum mechanics, using some of the methods and results developed in statistical physics. …”
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“…In this study, we present a theoretical study on PRMT1 catalyzed arginine dimethylation by employing molecular dynamics (MD) simulation and quantum mechanics/molecular mechanics (QM/MM) calculation. …”
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“…For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. …”
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“…The ability of neutral and anionic forms of pABA to interact with TIR1 pocket was investigated by calculation of molecular electrostatic potential maps on the accessible surface area, docking experiments, Molecular Dynamics and Quantum Mechanics/Molecular Mechanics calculations. The docking study of the folate precursor pABA, its anionic form and natural auxin (indole-3-acetic acid, IAA) with the auxin receptor TIR1 revealed a similar binding mode in the active site. …”
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“…We evaluated two rotamer library development methods that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify side-chain rotamers. …”
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“…In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p) clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.…”
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“…This result demonstrates that the achievement of the ultimate bound of precision imposed by quantum mechanics is possible. Finally, we note that the same configuration is also available to the maximum of the QFI itself.…”
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“…Single-point calculations with high-level quantum mechanics (QM) methods generally lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic properties. …”
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