Molecular mechanics overview

A very recent overview, including efforts to interface semi-empirical electronic structure with molecular mechanics treatments of some degrees of freedom is given by ... 

To get an overview of the currently available software for molecular mechanics calculations with their strengths, weaknesses, and application areas... 

PACKER L (1995) Antioxidant defenses in biological systems an overview. In Proceedings of The International Symposium on Natural Antioxidants - Molecular Mechanisms and Health Effects. Eds Packer, L, Traber, M G, Xin, W, Champaign, IL, USA AOCS Press 9-23. 

In this section, a group of related approaches is discussed in which the continuum dielectric description of the microscopic environment is replaced by a more detailed model in which the atomic details of the structure and the dynamics of the microscopic environment are taken into account. These models will be referred to here as coupled DFT/Molecular Mechanics (DFT/MM). For a general overview of coupled ab initio/Molecular Mechanics methods, see the recent reviews by Aquist and Warshel186 and by Gao187. 

Overview of Semi-Empirical and Ab Initio Molecular Orbital Methods. 2.2 Applications of Molecular Mechanics. 3 Experimental Structural Methods. 3.1 X-Ray Diffraction. 3.2 NMR Spectroscopy and. 3.3 Mass Spectrometry. 3.4 UV/Fluorescence. 3.5 IR Spectroscopy. 3.6 Redox Potentials. 4 Thermodynamic Aspects. 4.1 Melting Points. 5 Reactivity of Fully Conjugated Rings 6 Reactivity of Nonconjugated Rings... 

Chen H. Hirao H. Derat E. Schlichting I. Shaik S. Quantum mechanical/molecular mechanical study on the mechanisms of compound I formation in the catalytic cycle of chloroperoxidase an overview on heme enzymes. J. Phys. Chem. B 2008, 112, 9490-9500. 

A good, brief overview of the performance of MNDO, AMI and PM3 as of ca. 1999 is given by Levine [87]. Hehre has compiled a very useful book comparing AMI with molecular mechanics (Chapter 3), ab initio (Chapter 5) and DFT (Chapter 7) methods for calculating geometries and other properties [88], and an extensive collection of AMI and PM3 geometries is to be found in Stewart s second PM3 paper [70]. 

This presentation is structured in the following way. The first section outlines the procedure for the quantum mechanics and classical mechanics approach. The following two sections contain an overview of how to establish a density functional theory and molecular mechanics method along with the theoretical background for... 

This section provides an overview of several potential mechanisms involved in the development of asbestos-induced health effects (direct interaction with macromolecules, active oxygen mechanisms, and other cell-mediated mechanisms). An expert panel convened by lARC concluded in 1996, Overall, the available evidence in favor or against any of these mechanisms leading to the development of lung cancer and mesothelioma in either animals or humans is evaluated as weak (lARC Expert Panel 1996). Pulmonary inflammatory factors (a subset of other cell-mediated mechanisms) were considered by the lARC panel as having the most support among the potential mechanisms involved. For additional information on the molecular mechanisms of asbestos-induced pulmonary disease discussed below, including potential interactions between a number of the mechanisms, see recent reviews (Kamp and Weitzman 1999 Kinnula 1999 Lee and Testa 1999 Murthy and Testa 1999 Robledo and Mossman 1999). 

A few words about the basics of molecular mechanics (19,20) may provide the elements of understanding for what follows. This is not meant to be comprehensive, but rather a simple overview, to remind the reader of a few cmcial points. For a comprehensive overview of molecular modeling, the reader is referred to the excellent text by Leach (21). The interactions between atoms are divided into bonded and nonbonded classes. Nonbonded forces between atoms are based on an attractive interaction that has a firm theoretical basis and varies as the inverse of the 6th power of... 

See also Molecular modeling overview of. 919-920 plianiiaaiplioie concept in. 944 predictive ADMB in. >44- >45 quantum mechanics methods in. 923. 935-939... 

The present contribution concerns an outline of the response tlieory for the multiconfigurational self-consistent field electronic structure method coupled to molecular mechanics force fields and it gives an overview of the theoretical developments presented in the work by Poulsen et al. [7, 8, 9], The multiconfigurational self-consistent field molecular mechanics (MCSCF/MM) response method has been developed to include third order molecular properties [7, 8, 9], This contribution contains a section that describes the establisment of the energy functional for the situation where a multiconfigurational self-consistent field electronic structure method is coupled to a classical molecular mechanics field. The second section provides the necessary background for forming the fundamental equations within response theory. The third and fourth sections present the linear and quadratic, respectively, response equations for the MCSCF/MM response method. The fifth 283... 

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