Molecular mechanics potential

Takada T et al (2002) Fas ligand exists on intervertebral disc cells a potential molecular mechanism for immune privilege of the disc. Spine (Phila Pa 1976) 27(14) 1526-1530... 

The work of Devi and associates [22] provided a potential molecular mechanism for mu-delta interactions and a physical basis to explain biochemical observations of a mu-delta opioid receptor complex [23,24]. Their work and the efforts of others [25] have clearly demonstrated that mu and delta receptors can form heterodimers, leading to synergistic interactions and the generation of novel signaling units. This work, in other words, provides a molecular mechanism to explain how it is possible for three basic types of opioid receptors to form a greater number of pharmacologically defined opioid receptor subtypes. 

Moghaddam A, Olszewska W, Wang B, Tregoning JS, Helson R, Sattentau QJ, Openshaw PJ. A potential molecular mechanism for hypersensitivity caused by formalin-inactivated vaccines. Nat Med. 2006,12(8) 905-907. 

In the remainder of this chapter it is the second alternative, that of hybrid potentials, which is discussed in detail. The union of the two types of potential, molecular mechanical (MM) and quantum mechanical (QM), is crucial to the success of hybrid potentials and will be discussed in de-... 

Structure Simulation Using Interatomic Potentials Molecular Mechanics... 

Titushkin, 1., Shin, J., Sun, S., Cho, M. Physicochemical control of adult stem cell differentiation shedding light on potential molecular mechanisms. J. Biomed. Biotechnol. (2010). doi 10.1155/2010/743476... 

To distinguish a force field like the one in Eq. [23] from ion pair potentials, we shall call the former a molecular mechanics force field, a notation adopted in Allinger s pioneering work on predicting structures of hydrocar-bons and used for his series of force fields. > > 77 In contrast to ion pair potentials, molecular mechanics force fields include higher order terms from Eq. [14], usually up to fourth order for torsions. 

Characteristics Ion Pair and Shell Model Potentials Molecular Mechanics Potentials... 

Hwang et al. (2011) described the cross-linking of CL hydrogels with GP. The reaction between GP and CL induces the formation of cyclic structures, which serve as the intramolecular and intermolecular cross-links between CL molecules within fibers. Two potential molecular mechanisms for GP modification of biopolymers containing primary amine groups are described in literature and for CL, they are reported in Fig. 16.15. 

For this reason, there has been much work on empirical potentials suitable for use on a wide range of systems. These take a sensible functional form with parameters fitted to reproduce available data. Many different potentials, known as molecular mechanics (MM) potentials, have been developed for ground-state organic and biochemical systems [58-60], They have the advantages of simplicity, and are transferable between systems, but do suffer firom inaccuracies and rigidity—no reactions are possible. Schemes have been developed to correct for these deficiencies. The empirical valence bond (EVB) method of Warshel [61,62], and the molecular mechanics-valence bond (MMVB) of Bemardi et al. [63,64] try to extend MM to include excited-state effects and reactions. The MMVB Hamiltonian is parameterized against CASSCF calculations, and is thus particularly suited to photochemistry. 

Field, M.J., Bash, P.A., Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11 (1990) 700-733. 

Stanton, R.V., Heutsough, D.S., Merz, K.M. Jr An Examination of a Density Functional-Molecular Mechanical Coupled Potential. J. Comput. Chem. 16 (1995) 113-128. 

Additionally, as in all Tl-based approaches, the free energy differences are linear functions of the potential. Thus non-rigorous decompositions may be made into contributions from the different potential energy terms, parts of system and individual coordinates, providing valuable insight into the molecular mechanisms of studied processes [8, 9, 10). 

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

To see the contributions to the molecular mechanics potential energy function and their mathematical representation... 

Why "force field . In many situations it is necessary to know about the forces between atoms. This is the case for molecular dynamics, but also for many molecular mechanics applications. According to Eq. (17), the forces F are calculated as the negative derivative of the potential energy E with respect to the coordinates r ... 

Figure 7-8. Bonded (upper row) and non-bonded (lower row) contributions to a typioal molecular mechanics force field potential energy function. The latter two types of Interactions can also occur within the same molecule.

The mathematical formulation of a typical molecular mechanics force field, which is also called the potential energy function (PEF), is shown in Eq. (18). Do not wony yet about the necessary mathematical expressions - they will be explained in detail in the following sections ... 

A Fortran90 library for the simulation of molecular systems using molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM)/ MM) potential energy functions. http //www.ibs.fr/ext/labos/LDM/projet6/... 

Generating the potential energy surface (PCS) using this equation requires solutions for many configurations ofnnclei. In molecular mechanics, the electronic energy is not evaluated explicitly. 

Molecular Mechanic use an aiialyLical, dil fereiiliable, aiui relatively simple potential energy function, -(R). for describing the inieraciions between a set of atoms specified by their Cartesian coordinates R. 

Many molecular mechanics potentials were developed at a time when it was computationally impractical to add large numbers of discrete water m olecules to ih e calcu la Lion to sim ulate th e effect of ac ueous media. As such, tech n iq ties cam e into place that were intended to Lake into account the effect of solvent in some fashion. These tech niqiieswcre difficult to justify physically but they were used n cvcrth eless. 

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