Molecular mechanics definition

The original molecular-mechanics force field was developed by Allinger, and is generally referred to as MM. You should read the definitive text by Burkert and Allinger (1982) for more details. This model was followed by the MM2 model (Allinger, 1977), and I thought that you might like to read the synopsis. 

There is a definite trend of bidirectional cross-talk between opioid and chemokine receptors in the central nervous system. In vitro, as well as in vivo studies, have shown desensitization of CXCR4 by MOR and thus prevent the neuroprotective action of this chemokine. Although the precise molecular mechanism underlying this cross-talk is still under investigation, based on the evidences in literature several possible pathways can be expected to act independently or in concert and lead to the deficit of CXCR4 function. Our studies have shown that p opioids can increase the brain levels of FHC which can subsequently block CXCR4 signaling. Eurther studies... 

The next section in this chapter provides a brief comparison of the dipole moment (magnitude and direction) for a set of simple alcohols. Experimental gas phase dipole moments45 are compared to ab initio and as molecular mechanics computed values. It is important to note that the direction of the vector dipole used by chemists is defined differently in classical physics. In the former definition, the vector points from the positive to the negative direction, while the latter has the orientation reversed. 

In the absence of definitive information about the structure of the active site theoretical modeling of enzyme catalyzed reactions is difficult but not impossible. These difficulties are caused by the extremely large size of the enzyme-substrate-solvent system which typically comprises thousands or tens of thousands of atoms so that direct theoretical treatment at the microscopic quantum mechanical level is not yet practical. The computational demand is simply too enormous. As a compromise, a scheme generally referred to as QM/MM (quantum mechanics/molecular mechanics) has been devised. In QM/MM calculations, the bulk of the enzyme-solvent system (i.e. most of the atoms) is treated at a low cost, usually at the molecular mechanics (MM) level, while the more nearly correct and much more expensive quantum level (QM) computation is applied only to the reaction center (active site). 

The popularity of the NASA definition among the scientists studying the origin of life reflects this obvious prejudice, that the molecular mechanism of nucleic acids is the main and only reality for defining life. This definition is particularly dear to all adherents of the RNA-world, and actually the NASA definition appears to be created to define life at the molecular level. In fact, some of the adherents to the RNA-world would probably be satisfied by the definition of minimal life summarized (Luisi, 1998) in the following terms ... 

The expression for J is derived via the general quantum mechanical definition (32), introducing the perturbation expansion for the current density and the a-state molecular wave-function (depending on n-electron space-spin coordinates ), yb—Zd e-... 

The solution structures of a number of metalloproteins with paramagnetic metal centers were determined with molecular mechanics and dynamics in combination with NMR spectroscopy (see also Chapter 9)1124-126,189]. Due to the complexity of the molecules, for metalloproteins a crystal structure of the compound or a derivative is often needed for the definition of the starting geometry. Molecular dynamics is then used to find low-eneigy conformers. The dynamics calculations also allow the visualization of areas of large flexibility, and this may lead to some understanding of the enzyme mechanism11891. 

The following definition of computational chemistry was published in 1985 (6) quantitative modeling of chemical behavior on a computer by the formalisms of theoretical chemistry. Some quantum theoreticians naturally would like to see computational chemistry as a subset of their field (7). However, today the number of scientists employed as computational chemists well exceeds the number employed as theoreticians (8). A recent textbook author (9) views computational chemistry as encompassing not only quantum mechanics, but also molecular mechanics, [energy] minimization, simulations, conformational analysis, and other computer-based methods for understanding and predicting the behavior of molecular systems. ... 

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