Structure Description Methods

There are at least three methodologies for portraying crystal stmctures. Each of them has its advantages and disadvantages, but they all are based on the idea of a repeating pattern. The simplest method, the close-packed spheres description, is also the oldest. With advances in crystallography came more sophisticated descriptions, which lead to poly-hedra and, ultimately, to the crystallographic unit cell. Our discussion will follow their order of development but all of these methods still remain in use today. This is because 

Principles of Inorganic Materials Design, Second Edition. By John N. Lalena and David A. Cleary Copyright 2010 John Wiley Sons, Inc. 

---

The general name for the structural description method utilizing the adjacency relationships of molecular skeletons was selected to be molecular connectivity. The number assigned to a skeleton atom describing its adjacency relationship is called the simple connectivity value (or simple delta value) of the atom. In the development the S values were used for the first-order subgraph (or bond) between atoms i and j. The index for the entire molecule, in this case, the molecular connectivity index of the first order, is designated by the Greek letter chi, is computed as in equation 2,... 

Further improvements on the previously discussed models were proposed in the latest model for y - and e - Mn02 by Chabre and Pannetier [12, 43, 44], Starting from De Wolff s model they developed a structural description of manganese dioxides that accounts for the scattering function of all y - and e - Mn02 materials and provides a method of characterizing them quantitatively in terms of structural defects. All y — and e - Mn02 samples can be described on the basis of an ideal ramsdellite lattice affected by two kinds of defects ... 

This chapter consists of four main sections. The first provides an overall description of the process of contemporary protein structure determination by X-ray crystallography and summarizes the current computational requirements. This is followed by a summary and examples of the use of structure-based methods in drug discovery. The third section reviews the key developments in computer hardware and computational methods that have supported the development and application of X-ray crystallography over the past forty or so years. The final section outlines the areas in which improved... 

Ktihne, R., Ebert, R-U., Schtitirmann, G. Model selection based on structural similarity - method description and application to water solubility prediction. f Chem. Inf Model. 2006, 46, 636-641. 

All of the systems were initially optimized using a much higher level of theory, in order to ensure that the OM2 method provides a realistic description of the structure. The method employed was the second-order Mpller-Plesset perturbation theory (MP2) [50] using the cc-pVDZ basis set [51]. The resolution-of-identity (RI) approximation for the evaluation of the electron-repulsion integrals implemented in Turbomole was utilized [52]. 

The ISO V model for system development life cycle in computer software validation is a structured description of such a process. In this instance, the basic V model has been adapted for analytical method validation and is shown in Figure 1. 

It is clear from the foregoing discussion that the X-ray absorption and diffraction techniques to a large extent complement each other and that a much more complete structural description can be obtained by combining the two methods. Recently, a number of approaches have been developed which allow such combined measurements to be performed simultaneously on the same sample (Section V). 

From what has been shown in the preceding sections (cf. Eqs. 61 and 73, 83), it is possible to present the molecular structure resulting from both the r -fit method and any of the r()-derived methods in a convenient and easily comparable form, as a structural description in both Cartesian and internal coordinates, and with consistent errors and correlations (for small and larger molecules). A detailed comparison would require a sufficiently large SDS to determine a complete molecular structure, but the requirements are still the least restrictive of all methods presented. The input data must include the covariance matrix of the rotational constants or moments. This matrix may have to be adequately modeled to avoid grossly different weighting of isotopomers which is usually not warranted. The definition of the input data set... 

We will give further details about the periodic electronic structure calculations method as we will use results obtained with this method to support the discussion. First, we will describe how cluster approach can be used to investigate reactions catalyzed by acidic zeolites. Next, periodic electronic stmcture calculations will be used to enlighten the effects of the approximations of the cluster approach. These approximations relate mainly with the missing description of the zeolite framework contributions on the molecules involved in the reactions. Finally, by increasing the size of the aromatics involved in the isomerization reactions, we will show how steric constraints affect the course of a reaction. 

While we agree with this approach in general, the method for content description suggested by Salminen and coworkers is, in our opinion, not sufficient. The expressiveness of a structural description is rather restricted. Only the... 

The fundamental difference between the system of Locksley and the lUPAC system is the skeleton of reference. While the lUPAC system considers that most biflavonoids are derived from chromene strueture, Locksley system uses the flavonoid structure. It is important to take into accoimt that very few scientists use either system, especially since the common names, e.g., amentoflavone, cupressuflavone, and morelloflavone, are easier. These names, however, are limited because they do not contain any structural description. Locksley system is intuitive, logical, and structure-explicit, therefore, the systematic implementation of this method should be strongly encomaged. However, in order to facilitate the search for additional information regarding any of the biflavonoids presented in this review we also utilize the name most commonly used in the literature. 

---