The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods hasbecome alternative tool for many applications that pure QM and MM could not be suitable.The QM/MM method has been used for different type of problems, for example: structuralbiology, surface phenomena, and liquid phase. In this paper we have performed these methods forsome antibiotics and vitamins and then we comp...

Steiner 3-wise balanced designs are constructed for parameters 3-(3n − 1, {4, 8}, 1), 3(qnm− qm, {q− 1, q, q+ 1}, 1), 3-(qnm− 2qm− 1, {qm− 3, qm− 2, qm− 1, qm, qm+ 1}, 1), 3-(qnm − 2qm, {qm − 3, qm − 2, qm − 1, qm, qm + 1}, 1), 3-(qnm − 2qm + 1, {qm − 3, qm − 2, qm−1, qm, qm+1}, 1), where q is a prime power and n ≥ 2, m ≥ 1 are integers. Further designs are obtained from these. © 2008 Elsevier ...

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)...

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...