Extended atom

Force fields split naturally into two main classes all-atom force fields and united atom force fields. In the former, each atom in the system is represented explicitly by potential functions. In the latter, hydrogens attached to heavy atoms (such as carbon) are removed. In their place single united (or extended) atom potentials are used. In this type of force field a CH2 group would appear as a single spherical atom. United atom sites have the advantage of greatly reducing the number of interaction sites in the molecule, but in certain cases can seriously limit the accuracy of the force field. United atom force fields are most usually required for the most computationally expensive tasks, such as the simulation of bulk liquid crystal phases via molecular dynamics or Monte Carlo methods (see Sect. 5.1). 

The GRID energy is usually computed pairwise between the probe at its grid point and each extended atom of the target, one by one. First versions of the programme used only three energy components for each pairwise energy ( ) ... 

Molecular calculations provide approaches to supramolecular structure and to the dynamics of self-assembly by extending atomic-molecular physics. Alternatively, the tools of finite element analysis can be used to approach the simulation of self-assembled film properties. The voxel4 size in finite element analysis needs be small compared to significant variation in structure-property relationships for self-assembled structures, this implies use of voxels of nanometer dimensions. However, the continuum constitutive relationships utilized for macroscopic-system calculations will be difficult to extend at this scale because nanostructure properties are expected to differ from microstructural properties. In addition, in structures with a high density of boundaries (such as thin multilayer films), poorly understood boundary conditions may contribute to inaccuracies. 

About 80% of the elements are solid metals in their standard states at 298 K. Of the metallic elements, only mercury is a liquid at 298 K and at 1 atmosphere pressure (caesium melts at 302 K, gallium at 302.9 K). The non-metallic elements exist as either discrete small molecules, in the solid (S8), liquid (Br2) or gaseous (H2) states, or as extended atomic arrays in the solid state (C as graphite or diamond). The elements of Group 18 are monatomic gases at 298 K. 

The present reduced density operator treatment allows for a general description of fluctuation and dissipation phenomena in an extended atomic system displaying both fast and slow motions, for a general case where the medium is evolving over time. It involves transient time-correlation functions of an active medium where its density operator depends on time. The treatment is based on a partition of the total system into coupled primary and secondary regions each with both electronic and atomic degrees of freedom, and can therefore be applied to many-atom systems as they arise in adsorbates or biomolecular systems. 

The Coulomb term of the Klopman relationship (Equation 6.50) is based on a point charge model. It does not consider potential differences in the geometric availability of the spatially extended atomic sites for polar intermolecular interactions (which holds true in particular when employing the site-specific net atomic charge, QA [Equation 6.57], as a simple descriptor for the... 

In order to perform a qualitative analysis of the /1-decay-induced redistribution of electron density it is sufficient to calculate the molecular electron states in the MO LCAO approximation, i.e., not taking into account the correlation of electrons. Below we present the calculation data for a number of molecules, which we have obtained using the Gaussian-70 program with the basis of s and p functions. We have used the extended atomic basis 4-31G, which contains about twice as many atomic functions as the minimal one (Ditchfield et al, 1971). 

Carbohydrates (extended atom) Grootenhuis 1993 Carborane Holbrey 1993 COCO, CCCO, cocc Veal 1993... 

In contrast with the short-lived MLCT-excited states [Ru(bpy)3] [74], the electrogenerated [Ru(bpy)3]"+ can be conveniently studied by temperature-dependent ESR [42, 50a, b. Analysis of the broad unresolved lines of this and related species reveals electron hopping between the three equivalent ligand sites with activation energies of approximately 10 kJ mol . Similar slow vs. fast exchange phenomena were reported for the extended atom [75] species 17 which contains an encapsulated Na+ ion and mobile spins in the bpy-containing periphery. 

P.D.J. Grootenhuis and C.A.G. Haasnoot, A charmm based force-field for carbohydrates using the cheat approach -carbohydrate hydroxyl-groups represented by extended atoms Mol. Simul., 10 (1993)75. 

M.L.C.E. Kouwijzer and P.D.J. Grootenhuis, The CHEAT95 force field a carbohydrate force field in which the Carbohydrate Hydroxyls are represented by Extended Atoms. J. Phys. Chem., 99 (1995) 13426. 

Carbohydrates (extended atom) Crootenhuis 1993 Carbohydrates (CHEAT95) Kouwijzer 1995 Carbohydrates (glycol, glycerol, dimethoxymethanol, etc.) Reiling 1996 Carborane Holbrey 1993 Dimethylorthoacetate... 

In addition to flame annealing methods for the preparation of single crystal faces of metals with extended atomically smooth terraces [5.10-5.13], the already traditional technique of electrolytic growth of single crystals [5.6-S.9] has remained unrivaled for the preparation of perfect, screw dislocation-free faces or faces with single, isolated screw dislocations. ... 

A perfect crystal face should be completely free of any surface defects. In view of its further application for crystal growth studies, however, a face not intersected by screw dislocations can be considered conditionally as perfect. All other defects have either little or no effect on the growth behavior of the face. To meet this situation, the term quasi-ideal or quasi-perfect" has been introduced for the description of faces free of screw dislocations [5.14]. A quasi-perfect face is characterized by extended atomically smooth terraces separated by monatomic steps and absence of emergence points of screw dislocations. A smooth quasi-perfect face without steps can be described as an intact quasi-perfect face". 

Dipeptides are useful models for conformational transitions of proteins. They form minimal models on which protein backbone conformational changes can be investigated. A schematic picture of valine dipeptide is shown in Fig. 6. An extended atom model (CH groups are treated as a point mass) is used. 

Glycine dipeptide has 11 extended atoms and valine dipeptide, with its larger side chain, has 14 atoms. Nevertheless the backbone of the two peptides is essentially identical. It includes only two soft degrees of freedom, the... 

The most simple filters are calculated directly from the molecular formula, from the element composition, or from an extended description of the atom types of a molecule. Extended atom types are notations of atoms that include more information than just the element name (e.g., level of hybridization, membership in a certain functional group, etc.). Many molecular properties are usable as filter descriptors [24-27]. 

Extended atom types contain information about the element and the neighborhood of the atom. Examples are carbon in a methyl group , carbon bonded to oxygen , etc. The neighborhood can include atoms at a distance of one, two, or more chemical bonds. Depending on the distance analyzed, the number of extended atom type descriptors is between 100 and 200. 

Most of the methods that are used to predict logP values of molecules depend on fragmental codes or lipophilicity increments based on extended atom types. Obviously, it is possible to assign lipophilicity increments directly to every atom of a structure as an atomic property. The distribution of lipophilic and hydrophilic properties in a molecule can be described in this way [53]. 

The first 133 descriptors refer to extended atom types [27]. 

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