“…However, recent quantum mechanical calculations and experimental data show that persulfides are not “super” nucleophiles, but rather potent electrophiles in cellular biology. …”
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“…We present in this review the most interesting results of the molecular modeling of the structural parameters and optical and vibrational spectra of the chromophorecontaining domains of fluorescent proteins by methods of quantum chemistry, molecular dynamics, and combined quantum-mechanical-molecular-mechanical approaches. The main emphasis is on the correlation of theoretical and experimental data and on the predictive power of modeling, which may be useful for creating new, efficient biomarkers.…”
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“…The experimental studies on the hydrolysis reaction mechanism were supplemented by calculations using quantum mechanical (QM) models employing density functional theory. …”
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“…[Image: see text] Neglect of diatomic differential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models commonly employed in combined quantum mechanical/molecular mechanical simulations fail to adequately describe the deoxyribose and ribose sugar ring puckers. …”
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“…However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB(12)-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. …”
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“…The entanglement entropy is a fundamental quantity, which characterizes the correlations between sub-systems in a larger quantum-mechanical system. For two sub-systems separated by a surface the entanglement entropy is proportional to the area of the surface and depends on the UV cutoff, which regulates the short-distance correlations. …”
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“…Theoretical methods were used for further study. Quantum mechanical calculations indicated the binding mode of Cl(−) with Arg113. …”
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“…By further demanding time reversibility of the drift, the Langevin equation can also describe equivalent quantum-mechanical systems in a path-wise manner. The resulting statistical description obeys the Fokker–Planck equation of the probability density of the differential system, which can be readily estimated from simulations of the random paths. …”
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“…The ideal spatial conformation of the serine catalytic triad and the oxygen anion hole at the substrate-binding site was constructed by quantum mechanical calculation. The catalytic triad and oxygen anion holes were then embedded in the protein scaffold using the new enzyme protocol in Rosetta 3. …”
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“…The steric and electronic contributions of all chemical reagents and solvents were quantified by quantum mechanical calculations. The trained model accurately predicts stereoselectivities for unseen nucleophiles, electrophiles, acid catalyst, and solvents across a wide temperature range (overall root mean square error 6.8%). …”
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“…We discuss an iterative high-throughput workflow for connectivity preserving geometry optimizations exploiting the nearness between quantum mechanical models. The methodology is benchmarked on the QM9 dataset comprising DFT-level properties of 133 885 small molecules, wherein 3054 have questionable geometric stability. …”
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“…The role of quantum-mechanical coherences in the elementary photophysics of functional optoelectronic molecular materials is currently under active study. …”
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“…We find that quantum mechanical calculations using B3LYP/aug-cc-pVTZ model chemistry involving anharmonic correction on simple conjugated organic compounds without rotating moieties provide the dipole moment values and molecular geometries with high accuracy. …”
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“…By introducing the amidoxime functional group into the glucose unit at the C-6 position, highly effective reactive sorbent was prepared and used to destroy priority hazardous substances such as organophosphate pesticides or nerve-paralytic chemical warfare agents (CWAs). Quantum mechanical (QM) calculations were performed to study the interactions of organophosphates with amidoxime functional groups at the molecular level. …”
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“…The experimental results are supported by quantum mechanical calculations. This work has proven that co-delivery with POSS offers a potentially advantageous and simple approach for improved efficacy in chemotherapy, avoiding often complicated synthesis of conjugates, involving covalent bonding between drug, nanocarrier and targeting agents.…”
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“…Magnetism in low-dimensional materials has been of sustained interest due to its intriguing quantum mechanical origin and promising device applications. …”
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“…The analysis of the spectral and kinetic features of t-DZH and t-DZ has been supported by quantum-mechanical DFT calculations, the maximum entropy method, and the determination of their colourability ([Formula: see text]). …”
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“…The synthetic utility of this method was readily elaborated by a gram-scale reaction, and synthetic transformations to other important chiral indolizine derivatives. Quantum mechanical explorations constructed a plausible synergetic catalytic cycle, revealed the origins of stereodivergence, and rationalized the protonation-stimulated stereoselective Friedel–Crafts type cyclization to form the indolizine products.…”
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“…To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. …”
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“…However, selecting the active space alone is not enough to accurately describe quantum mechanical effects such as correlation. This study emphasizes the importance of optimizing the active space orbitals to describe correlation and improve the basis-dependent Hartree–Fock energies. …”
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