Structure Description Codes

We already discussed that the PPM should be structured into different layers, from application domain models to platform models (cf. Fig. 1.6). On every layer, there is a complete description of the product, i.e. the result of the design process overall configuration). Trivially, we find hierarchies on every layer. In top-down direction, from layer to layer, the number of details is growing. The model is transformed from layer to layer, from an explicit model to more implicit descriptions (code). The product is complemented by the associated design proce.s.s on every layer. Like the product, the process is hierarchically structured. An abstract process model is transformed into tool commands and corresponding code. 

In the second part (applications) we discuss some recent applications of LCAO methods to calculations of various crystalline properties. We consider, as is traditional for such books the results of some recent band-structure calculations and also the ways of local properties of electronic- structure description with the use of LCAO or Wannier-type orbitals. This approach allows chemical bonds in periodic systems to be analyzed, using the well-known concepts developed for molecules (atomic charge, bond order, atomic covalency and total valency). The analysis of models used in LCAO calculations for crystals with point defects and surfaces and illustrations of their applications for actual systems demonstrate the eflSciency of LCAO approach in the solid-state theory. A brief discussion about the existing LCAO computer codes is given in Appendix C. 

Several basic structure types often compete to determine the ground state, as illustrated for Rb Ser in Scheme 2, where we have designated the isomers using the letter coding of Table 1, along with the square-bracket descriptive coding used by the Armentrout group. These basic structure themes can be summarized as follows ... 

Hash Codes for Molecular Structure Description and Identification... 

HASH CODES FOR MOLECULAR STRUCTURE DESCRIPTION AND IDENTIFICATION... 

A special extension of SMILES is USMILES (sometimes described as Broad SMILES) [23-25]. This Unique SMILES of Daylight is a canonical representation of a structure. This means that the coding is independent of the internal atomic numbering and results always in the same canonical, unambiguous, and unique description of the compound, granted by an algorithm (see Section 2.5.2). 

WASP/TOXIWASP/WASTOX. The Water Quality Analysis Simulation Program (WASP, 3)is a generalized finite-difference code designed to accept user-specified kinetic models as subroutines. It can be applied to one, two, and three-dimensional descriptions of water bodies, and process models can be structured to include linear and non-linear kinetics. Two versions of WASP designed specifically for synthetic organic chemicals exist at this time. TOXIWASP (54) was developed at the Athens Environmental Research Laboratory of U.S. E.P.A. WASTOX (55) was developed at HydroQual, with participation from the group responsible for WASP. Both codes include process models for hydrolysis, biolysis, oxidations, volatilization, and photolysis. Both treat sorption/desorption as local equilibria. These codes allow the user to specify either constant or time-variable transport and reaction processes. 

COM interfaces are defined in an interface description language called IDL.6 These interfaces can be compiled to produce type libraries—the runtime representation of the structure of interfaces and methods—and to produce appropriate proxy, stub, and marshaling code for the case of remote object references. 

Quantum mechanics provide many approaches to the description of molecular structure, namely valence bond (VB) theory (8-10), molecular orbital (MO) theory (11,12), and density functional theory (DFT) (13). The former two theories were developed at about the same time, but diverged as competing methods for describing the electronic structure of chemical systems (14). The MO-based methods of calculation have enjoyed great popularity, mainly due to the availability of efficient computer codes. Together with geometry optimization routines for minima and transition states, the MO methods (DFT included) have become prevalent in applications to molecular structure and reactivity. 

Zeolite structures are designated by a three capital-letter code, for example, FAU stands for the faujasite structure, to which the well-known X and Y zeolites belong. A very useful short notation is used for the description of the pore system(s) each pore network is characterized by the channel directions, the number of atoms (in bold type) in the apertures, the crystallographic free diameter of the apermre (in A), asterisks (1, 2, or 3) indicating whether the systems is one-, two-, or three-dimensional. To completely specify the pore system, the eventual presence of cages (or channel intersections) should be indicated, along with their... 

Dubois et al. developed the Description, Acquisition, Retrieval, Computer-aided design-Elucidation by Progressive Intersection of Ordered Structures (DARC-EPIOS) system for structural elucidation.Their approach was based on C spectra. These were predicted using an additive method, but based on their DARC descriptor of environment, as opposed to the more common HOSE code. The EPIOS system was designed to take account of the diagnostic (or not) nature of the C spectrum with respect to environment, i.e., depending on the specific sub-structures. 

Medicinal chemists have numerous fast in sUico tools to evaluate the log Poet of NCEs prior to synthesis. These different methods can be divided in two main classes according to the level of description of molecular structure, namely 2D fragmental methods which cut the molecule in typical atomic or multiatomic fragments possessing their own lipophilicity coefficients and 3D global methods which code explicitly the principal intermolecular interactions potential of a 3D molecule. This section presents only an outline of the principal in silica methods since this subject was recently reviewed in detail [33, 34]. 

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