Electron diffraction code

D Molecule Representation of Structures Based on Electron Diffraction Code (3D MoRSE Code)... 

Gasteiger et al. returned to the initial I s) curve and maintained the explicit form of the curve [36]. For A they substituted various physicochemical properties such as atomic mass, partial atomic charges, and atomic polarizability. To obtain uniform length descriptors, the intensity distribution I s) is made discrete, calculating its value at a sequence of evenly distributed values of, for example, 32 or 64 values in the range of 0 - 3lA. The resolution of the molecule representation increases with higher number of values. The resulting descriptor is the 3D MoRSE (Molecular Representation of Structures based on Electron diffraction) Code. 

D molecule representation of structures based on electron diffraction code (3D MoRSE code)... 

The 3D MoRSE code is closely related to the molecular transform. The molecular transform is a generalized scattering function. It can be used to predict the intensity of the scattered radiation i for a known molecular structure in X-ray and electron diffraction experiments. The general molecular transform is given by Eq. (22), where i(s) is the intensity of the scattered radiation caused by a collection of N atoms located at points r. ... 

Preliminary models of the surface topography, for example, can be determined by atomic-probe methods, ion-scattering, electron diffraction, or Auger spectroscopy. The chemical bonds of adsorbates can be estimated from infrared spectroscopy. The surface electronic structure is accessible by photoelectron emission techniques. In case the surface structure is known, its electronic structure has to be computed with sophisticated methods, where existing codes more and more rely on first principles density functional theory (DFT) [16-18], or, in case of tight-binding models [19], they obtain their parameters from a fit to DFT data [20]. The fit is not without ambiguities, since it is unknown whether the density of states used for the fit is really unique. 

Figure 1. The electron diffraction structure of bacteriorhodopsin (pdb code IBRD) at 3.5 resolution as reported by Henderson et af. The structure is viewed from the extracellular side with helix 1 shown at the top. The ligand, retinal, is located between helices 3, 5, and 6 forming a Schiff base with Lys 216 on helix 7.

Another code for representation of the 3D structure of a molecule with a fixed number of variables irrespective of the number of atoms in the molecule (3D MoRSE code) has been proposed by Soltzberg and Wilkins. This molecular description is based on methods used in the interpretation of electron diffraction data. The approach has been used successfully for both the simulation of infrared spectra... 

Many years later, it was found that this characteristic of the descriptor could be used for the correlation of biological activity and three-dimensional structure of molecules. The activity of a compound also depends on the distances between atoms (such as H-bond donors or acceptors) in the molecular structure [91]. Adaptation of the RBF function to biological activity led to the so-called 3D-MoRSE code (3D-Molecule Representation of Structures based on Electron diffraction) [92]. The method of RBF calculation can be simplified in order to derive a descriptor that includes significant information and that can be calculated rapidly ... 

RDFs have certain characteristics in common with the 3D Molecular Representation of Strnctnres Based on Electron Diffraction (MoRSE) code. In fact, the theory of RDF is related to the theoretical basis of 3D MoRSE functions. In 1937, Degard nsed the exponential term in the RDE to account for the experimental angular limitations in electron diffraction experiments [2]. 

In electron diffraction experiments, the intensity is the Eourier transform of dnr j gif) and is related to the electron distribution in the molecule [3]. The Eourier transform of a 3D MoRSE code leads to a frequency pattern, but lacks a most important feature of RDF descriptors the frequency distribution. In contrast to the corresponding RDF descriptors 3D MoRSE codes can be hardly interpreted directly. Nevertheless, 3D MoRSE codes lead to similar results when they are used with methods where direct interpretability is not required. 

The two techniques for gas phase structure determination are spectroscopy and electron diffraction. The following codes are used to indicate the method used for each set of data ... 

Fig. 10.5 In the vapour state, formic acid exists as both (a) a monomer and (b) a dimer, the structures of which have been determined by electron diffraction, (c) In the solid state, a more complex assembly is formed as revealed in a neutron diffraction study of deuterated formic acid, DCO2D the figure shows part of the packing diagram for the unit cell. [A. Albinati et al. (1978) Acta Crystallogr., Sect. B, vol. 34, p. 2188.] Distances are in pm. Colour code C, grey O, red H, white D, yellow.

In the three-dimensional (3D) approach the 3D structure (see Structure Generators) of a molecule is transformed into a structure code. This is performed by regarding every atom pair in the molecule as a point scatterer and calculating the center symmetric diffraction pattern of the molecule as it would be obtained from an electron diffraction experiment. Based on these equations the 3D molecular representation of structures based on electron diffraction (3D-MoRSE) code has been developed. The 3D-MoRSE code is calculated using the equation... 

The Protein Data Bank (PDB) was established as a service to international science at the Brookhaven National Laboratory in the United States in 1971 to store and curate the atomic coordinates of macromo-lecular stmctures. Original versions of the whole data bank were distributed on magnetic tape to scientists, then on compact discs, and now they are freely available via the Internet (http //www.rcsb.org/). The PDB is part of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniformly coded data. Other related sites are located in Japan (PDBj, http //www.pdbj.org/) and in Europe (MSD-EBI, http //www.ebi.ac.uk/msd/). In addition to coordinates, the PDB stores experimental diffraction data, and it provides many tools for analyzing and displaying structures. As of April 15, 2008, the PDB held 50,277 sets of atomic coordinates from proteins, nucleic acids, and carbohydrates determined by X-ray diffraction, NMR spectroscopy, and electron microscopy. About 5000 new stmctures are released each year, and the database is expected to treble to 150,000 by 2014. 

---