“…From a combination of (1)H, (29)Si and (2)H magic-angle-spinning (MAS) NMR results and quantum mechanical (29)Si chemical shift calculations, silicon atoms on the surface of “as-received” np-Si were found to exist in a variety of chemical structures, with apparent populations in the order (a) (Si–O–)(3)Si–H > (b) (Si–O–)(3)SiOH > (c) (HO–)(n)Si(Si)(m)(–OSi)(4−m−n) ≈ (d) (Si–O–)(2)Si(H)OH > (e) (Si–O–)(2)Si(–OH)(2) > (f) (Si–O–)(4)Si, where Si stands for a surface silicon atom and Si represents another silicon atom that is attached to Si by either a Si–Si bond or a Si–O–Si linkage. …”
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“…Second, their reaction paths were investigated in detail by a range of quantum mechanical calculations. Single-configuration theoretical methods, like various DFT and a range of MP2-based methods, typically overestimate this barrier by 3–8 kcal/mol (after inclusion of zero-point energy, thermal, and solvation corrections), whereas MP2 itself underestimates the barrier significantly. …”
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“…In this paper, the spin state of the FeS clusters and the reaction mechanism is investigated by the combined quantum mechanical and molecular mechanics approach. The calculations show that the ground state of the two FeS clusters, both in the [4Fe4S](2+) oxidation state, is a singlet state with antiferromagnetically coupled high-spin Fe ions and that there is quite a large variation of the energies of the various broken-symmetry states, up to 40 kJ/mol. …”
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“…We explore the structural dynamics in the early photocycle leading to channel opening by classical (MM) and quantum mechanical (QM) molecular simulations. With QM/MM simulations, we generated a protein-adapted force field for the retinal chromophore, which we validated against absorption spectra. …”
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“…These are likely to proceed via the formation of a dimeric B–X–B motif (X = O, NR), which is uniquely able to provide activation of the carboxylic acid, whilst orchestrating the delivery of the amine nucleophile to the carbonyl group. Quantum mechanical calculations of catalytic cycles at the B3LYP+D3/Def2-TZVPP level (solvent = CH(2)Cl(2)) support the proposal of several closely related potential pathways for amidation, all of which are likely to be lower in energy than the currently accepted mechanism.…”
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“…When biochemical activity is strictly controlled by the quantum-mechanical super-orbital of the cell, this orbital can deliver energetic quanta as biological information, distributed through many fractal levels of the cell to guide form and behavior of an individual single or a multi-cellular organism. …”
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“…The UV–vis, resonance Raman, and electron paramagnetic resonance spectroscopies clearly show that the ferric form of the WT protein is a pentacoordinate quantum mechanically mixed-spin state, which is very unusual in biological systems. …”
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“…Furthermore, they review the various in silico studies reported against various targets in neurodegenerative diseases, including homology modeling, molecular docking, virtual high-throughput screening, quantitative structure activity relationship (QSAR), hologram quantitative structure activity relationship (HQSAR), 3D pharmacophore mapping, proteochemometrics modeling (PCM), fingerprints, fragment-based drug discovery, Monte Carlo simulation, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design, support vector machines, and machine learning approaches. …”
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“…To begin to overcome these challenges, we trained artificial neural networks (ANNs) to predict quantum-mechanically-derived properties, including spin-state ordering, sensitivity to Hartree–Fock exchange, and spin-state specific bond lengths in transition metal complexes. …”
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“…Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. …”
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“…These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). …”
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“…The resistance profile of two AHAS-inhibiting herbicides, tribenuron methyl and thifensulfuron methyl, was obtained by estimating their binding affinity with 29 KsAHAS (1 WT and 28 mutated) using 6 molecular mechanical (MM) and 18 hybrid quantum mechanical/molecular mechanical (QM/MM) methods in combination with three structure sampling strategies. …”
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“…We have performed quantum-mechanical calculations to examine the impact of disorder on thermodynamic, structural and electronic (magnetic) properties of Fe-Al systems with vacancies. …”
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“…These electrochemically-based results were reinforced by computational quantum mechanical modeling. DFT calculations indicated that both the C9-NO(2) and C10-NO(2) positional isomers of NO(2)-OA occurred in two conformers with different internal angles (69° and 110°) between the methyl- and carboxylate termini. …”
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“…[Image: see text] We address the double hydrogen transfer (DHT) dynamics of the porphycene molecule, a complex paradigmatic system in which the making and breaking of H-bonds in a highly anharmonic potential energy surface require a quantum mechanical treatment not only of the electrons but also of the nuclei. …”
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“…Here we present detailed structural models of Y(D) and its environment using large-scale quantum mechanical models and all-atom molecular dynamics of a complete PSII monomer. …”
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“…This not only provides a detailed description of anharmonic effects but also an accurate inclusion of the coupling between the investigated vibrational states on a quantum mechanical level. All results obtained for the constructed normal modes are benchmarked against their analytical counterparts obtained from the diagonalization of the total Hessian of the entire system. …”
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“…Finally, combined quantum mechanical/molecular mechanical (QM/MM) modelling of the IdmH reaction shows that the active site of the enzyme provides an appropriate environment to promote indane-ring formation, supporting the assignment of IdmH as the key Diels–Alderase catalysing the final step in the biosynthesis of indanomycin through a similar mechanism to other recently characterized Diels–Alderases involved in polyketide-tailoring reactions. …”
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“…In silico loop structure sampling and semiempirical quantum mechanical calculations identified a 3L2 loop conformation that enabled the Fe(2+) cofactor to interact with the double bond of the allyl side chain. …”
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“…Both the conducted quantum-mechanical [TD]DFT–Time-Dependent Density Functional Theory) calculations and excited state dipole moment change calculations for the analyzed molecule in solvents with varying pH confirmed the association between the observed fluorescence phenomena and the two aforementioned effects.…”
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