Atomic structure, determination

LEED is the most powerfiil, most widely used, and most developed technique for the investigation of periodic surface structures. It is a standard tool in the surface analysis of single-crystal surfaces. It is used very commonly as a method to check surface order. The evolution of the technique is toward greater use to investigate surface disorder. Progress in atomic-structure determination is focused on improving calculations for complex molecular surface structures. 

J. B. Pendry. Low-Energy Electron Difraction. Academic Press, New York, 1974. Theoretical treatment, principally on surface atomic structure determination. 

Jiang, H., Nasibulin, A. G., Brown, D. P, 8c Kaup-pinen, E. I. (2007). Unambiguous atomic structural determination of single-walled carbon nanotubes by electron diffraction. Carbon, 45,... 

The crystal structure determines not only the arrangement of atoms in the lattice but also the external form of the crystal. 

To find appropriate empirical pair potentials from the known protein structures in the Brookhaven Protein Data Bank, it is necessary to calculate densities for the distance distribution of Ga-atoms at given bond distance d and given residue assignments ai,a2- Up to a constant factor that is immaterial for subsequent structure determination by global optimization, the potentials then ciiiergo as the negative logarithm of the densities. Since... 

Our work is targeted to biomolecular simulation applications, where the objective is to illuminate the structure and function of biological molecules (proteins, enzymes, etc) ranging in size from dozens of atoms to tens of thousands of atoms today, with the desire to increase this limit to millions of atoms in the near future. Such molecular dynamics (MD) simulations simply apply Newton s law to each atom in the system, with the force on each atom being determined by evaluating the gradient of the potential field at each atom s position. The potential includes contributions from bonding forces. 

A crystal is a solid with a periodic lattice of microscopic components. This arrangement of atoms is determined primarily by X-ray structure analysis. The smallest unit, called the unit cell, defines the complete crystal, including its symmetry. Characteristic crystallographic 3D structures are available in the fields of inorganic, organic, and organometallic compounds, macromolecules, such as proteins and nucleic adds. 

Structure determines properties and the properties of atoms depend on atomic struc ture All of an element s protons are m its nucleus but the element s electrons are dis tributed among orbitals of varying energy and distance from the nucleus More than any thing else we look at its electron configuration when we wish to understand how an element behaves The next section illustrates this with a brief review of ionic bonding... 

A representation of atomic structure. The various spheres are not drawn to scale. The lump of iron on the left would contain almost a million million million million (10 ) atoms, one of which is represented by the sphere in the top center of the page. In turn, each atom is composed of a number of electrons, protons, and neutrons. For example, an atom of the element iron contains 26 electrons, 26 protons, and 30 neutrons. The physical size of the atom is determined mainly by the number of electrons, but almost all of its mass is determined by the number of protons and neutrons in its dense core or nucleus (lower part of figure). The electrons are spread out around the nucleus, and their number determines atomic size but the protons and neutrons compose a very dense, small core, and their number determines atomic mass. 

Structure Determination from a Powder Pattern. In many cases it is possible to determine atomic positions and atomic displacement parameters from a powder pattern. The method is called the Rietveld method. Single-crystal stmcture deterrnination gives better results, but in many situations where it is impossible to obtain a suitable single crystal, the Rietveld method can produce adequate atomic and molecular stmctures from a powder pattern. 

Processes in which solids play a rate-determining role have as their principal kinetic factors the existence of chemical potential gradients, and diffusive mass and heat transfer in materials with rigid structures. The atomic structures of the phases involved in any process and their thermodynamic stabilities have important effects on drese properties, since they result from tire distribution of electrons and ions during tire process. In metallic phases it is the diffusive and thermal capacities of the ion cores which are prevalent, the electrons determining the thermal conduction, whereas it is the ionic charge and the valencies of tire species involved in iron-metallic systems which are important in the diffusive and the electronic behaviour of these solids, especially in the case of variable valency ions, while the ions determine the rate of heat conduction. 

Figure 3 Model building by Modeller [31], First, spatial restraints in the form of atomic distances and dihedral angles are extracted from the template stmcture(s). The alignment is used to determine equivalent residues between the target and the template. The restraints are combined into an objective function. Finally, the model for the target is optimized until a model that best satisfies the spatial restraints is obtained. This procedure is technically similar to the one used in structure determination by NMR.

To put the errors in comparative models into perspective, we list the differences among strucmres of the same protein that have been detennined experimentally (Fig. 9). The 1 A accuracy of main chain atom positions corresponds to X-ray structures defined at a low resolution of about 2.5 A and with an / -factor of about 25% [192], as well as to medium resolution NMR structures determined from 10 interproton distance restraints per residue [193]. Similarly, differences between the highly refined X-ray and NMR structures of the same protein also tend to be about 1 A [193]. Changes in the environment... 

The F-actin helix has 13 molecules of G-actin in six turns of the helix, repeating every 360 A. Oriented gels of actin fibers yield x-ray fiber diffraction patterns to about 6 A resolution. Knowing the atomic structure of G-actin it was possible for the group of Ken Holmes to determine its orientation in the F-actin fiber, and thus arrive at an atomic model of the actin filament that best accounted for the fiber diffraction pattern. 

A gene encoding this sequence was synthesized and the corresponding protein, called Janus, was expressed, purified, and characterized. The atomic structure of this protein has not been determined at the time of writing but circular dichroic and NMR spectra show very clear differences from B1 and equally clear similarities to Rop. The protein is a dimer in solution like Rop and thermodynamic data indicate that it is a stably folded protein and not a molten globule fold like several other designed proteins. 

The situation is different for other examples—for example, the peptide hormone glucagon and a small peptide, metallothionein, which binds seven cadmium or zinc atoms. Here large discrepancies were found between the structures determined by x-ray diffraction and NMR methods. The differences in the case of glucagon can be attributed to genuine conformational variability under different experimental conditions, whereas the disagreement in the metallothionein case was later shown to be due to an incorrectly determined x-ray structure. A re-examination of the x-ray data of metallothionein gave a structure very similar to that determined by NMR. 

Atomic structure refinements or determinations and residual stress measurements, all in bulk materials... 

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