We report a comparison of QM-only and QM/MM approaches for the modeling of enzymatic reactions. For this purpose, we present a QM/MM case study on the formation of vinyl alcohol in the catalytic cycle of tungsten-dependent acetylene hydratase. Three different QM regions ranging from 32 to 157 atoms are designed for the reinvestigation of the previously suggested one-water attack mechanism. The ...

The previously laboratory-evolved cytochrome P450 2B1 quadruple mutant V183L/F202L/L209A/S334P (QM), which showed enhanced H(2)O(2)-mediated substrate oxidation, has now been shown to exhibit a >3.0-fold decrease in K(m,HOOH) for 7-ethoxy-4-trifluoromethylcoumarin (7-EFC) O-deethylation compared with the parental enzyme L209A. Subsequently, a streamlined random mutagenesis and a high-throughput...

The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential ene...

QM/MM hybrid methods employ accurate quantum (QM) models only in regions of interest (defects) and switch to computationally cheaper interatomic potential (MM) models to describe the crystalline bulk. We develop two QM/MM hybrid methods for crystalline defect simulations, an energy-based and a force-based formulation, employing a tight binding QM model. Both methods build on two principles: (i)...

شاخص‌های مؤثر بر ادراک کیفیت بازیابی در فضاهای شهری مورد علاقه شهروندان مشهدی (با تأکید کاهش فشار روانی افراد)

To evaluate the associated factors for quality measurement (QM) on shear wave speed (SWS) imaging and the additional value of QM for differentiation of thyroid nodules. A consecutive series of 238 patients with 254 thyroid nodules were enrolled. They were all evaluated by conventional ultrasound and SWS imaging and were finally proven pathologically. QM was used to assess whether SWS propagatio...

We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. In...

The Einstein, Podolski and Rosen (EPR) argument aiming to prove the incompleteness of quantum mechanics (QM) was opposed by most EPR’s contemporary physicists and is not accepted within the standard interpretation of QM, which maintains that QM is a complete theory. An analysis of the semantic implications of the opponent positions shows that they imply different notions of truth. The introduct...

Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transf...