Molecular structure, COSMOS

Many problems in force field investigations arise from the calculation of Coulomb interactions with fixed charges, thereby neglecting possible mutual polarization. With that obvious drawback in mind, Ulrich Sternberg developed the COSMOS (Computer Simulation of Molecular Structures) force field [30], which extends a classical molecular mechanics force field by serai-empirical charge calculation based on bond polarization theory [31, 32]. This approach has the advantage that the atomic charges depend on the three-dimensional structure of the molecule. Parts of the functional form of COSMOS were taken from the PIMM force field of Lindner et al., which combines self-consistent field theory for r-orbitals ( nr-SCF) with molecular mechanics [33, 34]. 

COSMO/rag makes use of these similarity indices in two ways. First, it calculates the sum of the similarity indices of order 7 for all atoms of a molecule. The resulting molecular similarity index is essentially an identity index, because to our best knowledge identical indices imply identity of the molecular structures, apart from stereochemical differences. This can be used to detect the identity of molecular structures in the database. Much more... 

Julg, A. 1988a. From atom to cosmos. Journal of Molecular Structure TJIEOCHEM 166 33-38. 

By determining the most stable conformation of 13 imidazole derivatives, their structure was approximated to the molecular form present in vivo (biomimetic). The most stable structure was next determined by CAChe Worksystem 4.9 MOPAC (PM3) (Fig. 2). The CC50 value (determined by experiments) against HL-60 and HSC-3 cells, and chemical descriptors (determined by calculations) such as heat of formation (COSMO), stability of... 

Solvation behavior can be effectively predicted using electronic structure methods coupled with solvation methods, for example, the combination of continuum solvation methods such as COSMO with DFT as implemented in DMoF of Accelrys Materials Studio. An attractive alternative is statistical-mechanical 3D-RISM-KH molecular theory of solvation that predicts, from the first principles, the solvation structure and thermodynamics of solvated macromolecules with full molecular detail at the level of molecular simulation. In particular, this is illustrated here on the adsorption of bitumen fragments on zeolite nanoparticles. Furthermore, we have shown that the self-consistent field combinations of the KS-DFT and the OFE method with 3D-RISM-KH can predict electronic and solvation structure, and properties of various macromolecules in solution in a wide range of solvent composition and thermodynamic conditions. This includes the electronic structure, geometry optimization, reaction modeling with transition states, spectroscopic properties, adsorption strength and arrangement, supramolecular self-assembly,"and other effects for macromolecular systems in pure solvents, solvent mixtures, electrolyte solutions, " ionic liquids, and simple and complex solvents confined in nanoporous materials. Currently, the self-consistent field KS-DFT/3D-RISM-KH multiscale method is available only in the ADF software. 

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