Atomic environment definition

Atomic environment definition (and symbols) and corresponding coordination numbers andpolyhedra... 

The concept of electronegativity is easy to visualize but difficult to apply quantitatively. Muffiken s definition, based on free-atomic properties, does not account for the influence of the local atomic environment on the ionic state that is reflected, for example, in the fact that the degree of ionicity... 

Having resolved the molecular perception problem and achieved a unique representation of all atoms, bonds, and rings in the molecule, the second major step is the definition of the most useful measure for local similarity of atoms and atomic environment. For the purpose of COSMO/rag, we need to achieve the state that atoms are considered as most similar, if their partial molecular surfaces and surface polarities, i.e., polarization charge densities, are most similar. But since the latter is not known, at least for the new molecule under consideration, we have to ensure that the local geometries and the electronic effects of the surrounding atoms are most similar. Obviously, two similar atoms should at legist be identical with respect to their element and their hybridization. Turning this information into a unique real number, a similarity index of the lowest order (zeroth order) can be defined for each atom from the atom element numbers and... 

R. Davis, Recent advances regarding the definition of the atomic environment, film growth and microelectronic device development in SiC, in The Physics and Chemistry of Carbides, Nitrides and Borides, R. Freer (Ed.), Kluwer, Dordrecht, 1990, pp. 589-623. 

Clearly, the LL- and SL-environment components of a-Si presented above are a direct parallel of the 5-7-sided and 6 6-sided polyhedra in the 2D simulation of a sub-cooled metallic liquid and glass discussed in Section 1.7 and the examples shown in Figs. 1.1 l(a)-(c). Both types of these representations of LL and SL atom environments are in full conformity with the definition introduced by Cohen and Grest (1979). The direct role of these special environments, their formation, and alterations during plastic flow are the subject of Chapter 7. 

Several physical properties, including density, melting point, and boiling point, are related to the sizes of atoms, but atomic size is difficult to define. As we saw in Section 2.2, the electron density in an atom extends far beyond the nucleus, but we normally think of atonfic size as the volume containing about 90 percent of the total electron density around the nucleus. When we must be more specific, we define the size of an atom in terms of its atomic radius. Definitions for atonfic radius depend upon the identity and environment of the element in question ... 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

Atom types represen t the chemical environment of an atom. The atom types associated with a given force field could be hard-wired to have specific vahiesand meaning. llyperChem also allows flexible definitions of the atom types and the associated chemical en vironmen Is. Th e ch em ical en viron men t of an atom (a set of rules for defining a type) and the default rules are in a standard ASCII text file, chem.nil. included with llyperChem. You can modify this file and compile it m a binary form that llyperChem... 

The low Ti content (up to 3 wt % in Ti02) makes the extraction of vibrational, energetic, and geometric features specific to Ti04 moieties a difficult task as the experimental data are dominated by the features of the siliceous matrix. This is the reason why the structure of the local environment around Ti(IV) species inside TS-1 was only definitively assessed more than 10 years after the discovery of the material, when the atomic selectivity of X-ray absorption spectroscopies (both XANES and EXAFS) were used [58-60]. 

These definitions are interpreted as follows environment atoms recognize the average weighted states of the ligands each ligand recognizes only the environment atoms and itself with the full scale for estimation of its effective Bom radius. Alternate definitions of the electrostatic solvation energy and the effective Bom radius at the intermediate states are also possible.81... 

The definition of stability of an oxidation state of a given atom is meaningless without referring to its immediate environment. Any ligated metal atom which undergoes a redox process with its ligands at a measurable rate is here defined as being in an unstable state of oxidation. This is somewhat broader than the con-... 

EXAFS has provided detailed information about the local environment of the active Co and Ni sites and the Mo atoms to which they are attached in terms of the types of atoms within two atomic shells away from the atom being characterized. Cobalt and nickel were shown to be definitely bonded to the surfaces of small MoS2 crystallites. Representative structures for the environments of Mo and Co are illustrated in the following diagram. In such structures, Mo has a coordination number (CN) of 6, with six nearneighbor sulfur atoms, three nearby Mo atoms, and one nearby Co or Ni atom. Co-S configurations were either CN = 5 (square pyramidal) or CN = 6 (octahedral), with either one nearby Mo atom (low HDS activity) or two nearby Mo atoms (high HDS activity) (62). 

---