Home About us Contact
|
Home About us Contact | ||
|
|
||
Quantum Mechanical (quantum + mechanical)
Terms modified by Quantum Mechanical Selected AbstractsModeling dioxygen binding to the non-heme iron-containing enzymesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2006A. V. Nemukhin Abstract The structures and properties of the complexes formed upon binding the oxygen molecule to the iron sites in non-heme 2-oxoglutarate-dependent enzymes are characterized by QM(CASSCF)/MM and density functional theory (DFT) calculations. Molecular models for the calculations are constructed following the crystal structure of hypoxia-inducible factor asparaginyl hydroxylase (FIH-1). DFT calculations for the 37-atomic cluster have been carried out at the B3LYP(LANL2DZdp) level. The flexible effective fragment potential method is used as a combined quantum mechanical,molecular mechanical (QM/MM) technique to characterize the fragment of the enzymatic system, including 1,758 atoms in the MM part and 27 atoms in the QM part. In these calculations, the CASSCF(LANL2DZdp) approach is applied in the QM subsystem, and AMBER force field parameters are used in the MM subsystem. With both approaches, equilibrium geometry configurations have been located for different spin states of the system. In DFT calculations, the order of the states is as follows: septet, triplet (+7.7 kcal/mol), quintet (+10.7 kcal/mol). Geometry configurations correspond to the end-on structures with no evidences of electron transfer from Fe(II) to molecular oxygen. In contrast, QM(CASSCF)/MM calculations predict the quintet state as the lowest one, while the septet structure has slightly (<2 kcal/mol) higher energy, and the triplet state is considerably more energetic. In QM/MM calculations, in both quintet and septet states, the electronic configurations show considerable electron charge transfer from iron to oxygen, and the oxidation state of iron in the metal binding site can be characterized as Fe(III). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Energy decomposition scheme for combined ab initio quantum mechanical / molecular mechanical methodsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2005Imre Berente Abstract A new energy decomposition scheme is presented which paves the way toward the accurate and simple treatment of boundary atoms in combined ab initio quantum mechanical / molecular mechanical methods. We extend the wave function beyond the quantum region to a few atoms of the molecular mechanical region, which are linked directly to boundary atoms. Furthermore, we apply an approximate decomposition scheme, which allows calculating the total energy in terms of one-center atomic contributions. Comparisons with reference ab initio calculations are made, and good agreement is obtained for geometry parameters referring to CC, CC, and CX (XO, S, N) bonds at the boundary, as well as for the rotational energy curve of n -butane. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Application of QM simulations and multivariate analysis in the study of alkene reactivity in the zeolite H-ZSM5JOURNAL OF CHEMOMETRICS, Issue 6 2008Duangkamol Gleeson Abstract Reported herein are the results of an investigation into the effect of the extended framework of the zeolite ZSM-5 on the reaction energetics and structures of (a) the physisorbed complex formed between the zeolite and six alkenes, (b) the corresponding chemisorbed alkoxide intermediate and (c) the transition states (TS) connecting the two. For this, quantum mechanical (QM) simulations of ZSM-5 in the presence and absence of the zeolite framework have been employed. A 46T density functional theory (DFT) cluster model and a 3T:46T DFT:UFF ONIOM model are used to represent the former scenario and a simple 3T DFT cluster model for the latter. The structural implications of neglecting the zeolite framework have been rigorously compared using the multivariate statistical method principal components analysis (PCA). This method allows one to assess the correlated nature of the changes in structure along the reaction coordinate, for multiple different alkenes, in a facile, reliable way. Copyright © 2008 John Wiley & Sons, Ltd. [source] Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum modelJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2006Carles Curutchet Abstract We report a systematic comparison of the dispersion and repulsion contributions to the free energy of solvation determined using quantum mechanical self-consistent reaction field (QM-SCRF) and classical methods. In particular, QM-SCRF computations have been performed using the dispersion and repulsion expressions developed in the framework of the integral equation formalism of the polarizable continuum model, whereas classical methods involve both empirical pairwise potential and surface-dependent approaches. Calculations have been performed for a series of aliphatic and aromatic compounds containing prototypical functional groups in four solvents: water, octanol, chloroform, and carbon tetrachloride. The analysis is focused on the dependence of the dispersion and repulsion components on the level of theory used in QM-SCRF computations, the contribution of those terms in different solvents, and the magnitude of the coupling between electrostatic and dispersion,repulsion components. Finally, comparison is made between the dispersion,repulsion contributions obtained from QM-SCRF calculations and the results determined from classical approaches. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source] Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solutionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2003Ramkumar Rajamani Abstract We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H3N,H,NH3]+ using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1775,1781, 2003 [source] Continuum and discrete calculation of fractional contributions to solvation free energyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2003Antonio Morreale Abstract Approaches to compute fractional contributions to the solvation free energy are developed in the context of continuum self consistent reaction field calculations (both classical and quantum mechanical), as well as in the framework of discrete molecular dynamics simulations. It is found that for a series of typical pharmacological drugs there is a good agreement between the different fractional descriptions. Algorithms reported here can be easily applied as molecular descriptors in the context of quantitative structure-activity relationships. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1610,1623, 2003 [source] An analysis of all the relevant facts and arguments indicates that enzyme catalysis does not involve large contributions from nuclear tunnelingJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7 2010Shina C. L. Kamerlin Abstract Enzymatic reactions are crucial toward controlling and performing most life processes, and, as such, understanding how they really work has both fundamental and practical importance. Thus, one of the major current challenges of biophysics involves understanding the origin of the enormous catalytic power of enzymes, an issue that is still not widely understood and remains controversial within the scientific community. Several proposals have been put forth to try to explain the origin of enzyme catalysis, one of which is the idea that enzyme catalysis involves special factors such as nuclear quantum mechanical (NQM) effects, and, in particular, nuclear tunneling. Here, we will discuss both the factors for and against this proposition, and demonstrate that an analysis of all the relevant facts and arguments seems to establish that enzyme catalysis does not involve large contributions from nuclear tunneling. Copyright © 2010 John Wiley & Sons, Ltd. [source] Study of the vibrational spectra of (CH3)3GeCl from experimental and DFT calculationsJOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2009María Lorena Roldán Abstract New infrared (for gas and liquid phase) and Raman (for liquid) spectra were measured for the chlorotrimethylgermane to obtain a complete assignment of its fundamental modes. The measurement of the low-temperature infrared spectrum together with the application of Fourier self-deconvolution to the Raman spectra resolves the CH vibrational modes into their components. The Rauhut and Pulay scaled quantum mechanical (SQM) force field methodology and the wavenumber-linear scaling (WLS) method were used to predict the vibrational spectra as a guide to the assignment of the fundamental bands. A quantum mechanical analysis was carried out to obtain the harmonic force field. Copyright © 2009 John Wiley & Sons, Ltd. [source] Today's challenges in quantum dot materials research for tomorrow's quantum functional devicesPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 8 2007Richard Nötzel Abstract Size, shape, position control, and self-organized lateral ordering of epitaxial semiconductor quantum dot (QD) arrays are demonstrated. This constitutes the prerequisite for the ultimate control of the electronic and optical properties of man-made semiconductor heterostructures at the single and multiple charge, spin, and photon level, including their quantum mechanical and electromagnetic interactions in view of applications such as quantum information processing and computing. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] | ||||||||||