Atom specification

Figure 10.3-38. An Indication of other speclRcatlon elements for a substructure query, For both the atom specifications and the bond specifications a vast list of attributes can be set (aromatic/ not aromatic, member of ring with n atoms, substituted, etc.).

In these simplified representations called bond line formulas or carbon skeleton dia grams, the only atoms specifically written m are those that are neither carbon nor hydro gen bound to carbon Hydrogens bound to these heteroatoms are shown however... 

Since X-ray absorption is an atom-specific process, any atoms known to be, or deliberately placed, on a solid consisting of different atoms can be studied with high sensitivity. 

Table 8.53 shows the main features of XAS. The advantages of EXAFS over diffraction methods are that the technique does not depend on long-range order, hence it can always be used to study local environments in amorphous (and crystalline) solids and liquids it is atom specific and can be sensitive to low concentrations of the target atom (about 100 ppm). XAS provides information on interatomic distances, coordination numbers, atom types and structural disorder and oxidation state by inference. Accuracy is 1-2% for interatomic distances, and 10-25 % for coordination numbers. 

Perhaps the most important conclusion to be drawn from results for metal atoms in groups such as 7SiL3 or -PL3+ is undetectably small (70,71). Indeed, the R2C- moiety displays hyperfine interaction with H and 13C that suggest normal planarity at carbon with essentially unit spin-density thereon, and coupling to the metal atom (specifically, 31P) is small and probably negative. This implies that spin-density is acquired by spin-polarisation of the C-M o-electrons and not by p -d delocalisation, as is so often... 

Konishi, J. Ishii, Y. Onaka, T., and Maruhashi, K., Purification and Characterization of the Monooxygenase Catalyzing Sulfur-Atom Specific Oxidation of Dibenzothiophene and Benzothiophene From the Thermophilic Bacterium Paenibacillus Sp Strain All-2. Applied Microbiology and Biotechnology, 2002. 60(1-2) pp. 128-133. 

Benzodiazepines are very important drugs from a turnover point of view. A large number of these compounds has been synthesized, developed and marketed (about thirty have been launched), a dozen of which contain fluorine atoms. Specific clinical indications for each compound do not result from a difference in the mechanism but from the pharmacokinetic and pharmacodynamic behavior of each one. 

From a theoretical point of view XES furthermore provides a very strong basis for the evaluation of methods for population analysis, i.e., the decomposition of the molecular orbitals into atomic contributions [10]. Many different schemes subdividing the charge density into contributions assigned to respective atoms have been proposed, but the lack of means to directly measure the atomic populations in different orbitals has made all techniques somewhat arbitrary and a matter of taste. Due to the strongly localized character of the intermediate core-excited state, however, in combination with the direct dependence of the XES transition probability on the amount of local -population (assuming a Is core hole), XES provides a very sensitive tool to directly measure this atomic population. In all, we have an atom-specific tool, which can be used to address important questions regarding... 

Figure 2.2. Comparison between atom-specific and symmetry-resolved XE spectra [6,10] with an UPS spectrum of N2 adsorbed on Ni(100) measured at a photon energy of 35 eV [9]. From Ref. [3].

Although the occupied orbitals are of main importance, since they are directly involved in the formation of the chemical bond, the unoccupied states also provide complementary information. In X-ray absorption spectroscopy (XAS), often denoted Near Edge X-ray Absorption Fine Structure (NEXAFS), we excite a core electron to the empty states above the Fermi level [3,4,13]. There is a close connection between XES and XAS where the former gives information on the occupied orbitals while the latter relates to the character and symmetry of the unoccupied levels. Both are governed by the dipole selection rule and the localized character of the core orbitals allows a simple atom-specific projection of the electronic structure the major difference is in the final states. In XAS the empty electronic states are probed... 

In the future, we need to develop ways to apply novel and more sophisticated surface science techniques, such as the soft X-ray spectroscopies outlined in Chapter 2, to electrified interfaces under realistic conditions. For example, atom-specific probing of the occupied and unoccupied electronic states of electrochemical surface intermediates during the electrocatalytic reactions described in the present chapter has not been achieved to date. Modern synchrotron-based soft X-ray methods will aid these efforts to obtain more insight into the bonding of electrochemical intermediates. 

So, what steps can be taken to decrease the scope of the problem One approach is to make certain parameters that depend on more than one atom themselves functions of single-atom-specific parameters. For instance, for use in Eq. (2.16), one usually defines... 

Numbers of Neighbor Atoms, Specific Surface Energies, and Work Functions of Different Planes of a Tungsten Crystal (4S)... 

In an effort to extend the applicability of NOE matching to the larger proteins of pharmaceutical interest, for example kinases and phosphatases, we have adapted NOE matching to be able to utilize data from any residue (and atom)-specific labeling scheme. An illustrative example is provided below. 

John Dalton surmised that each element is made of atoms specific to that element. This theory led to the modern understanding of atomic mass Each element has a different mass because of its unique atomic composition. 

The atoms, specifically their nuclei, that comprise the solar system were made in a variety of environments (cf. Woolum, 1988). H and most of the He were made in the Big Bang. The He/H ratio, and the isotope ratios D/H and 3He/4He, are adequately accounted for in Big Bang models perhaps a better statement is that these ratios provide important constraints on such models. The Big Bang made just a little heavier... 

Atom specification Elemental identity is represented by a standard atomic symbol without explicit hydrogen if the number of attached hydrogens... 

The most precise approximations are given by eqs. (3.16) and (3.17) yielding results which perfectly coincide with the exact (SLG-MINDO/3) ones even for very polar O-H and F-H bonds. This may be qualified as using estimates of the second order in /r, provided the bond polarity (or equivalently (r2TO)) are linear in /. if the orders up to the second are considered. Estimates obtained in the limit Cm > 1 by the formulae eq. (3.12) give reasonable results for the ESVs of the bonds in not too polar molecules at their equilibrium geometries. The bond- and atom-specific corrections of the first and second order in Cm1 and //,m acquire the form ... 

---