Atomic Structure and Interatomic Bonding

One of the lasting practical results of treating metals in this model has been the tabulation of atomic radii and interatomic distances in metals [39-42]. Another interesting application of the unsynchronized-resonating-covalent-bond-theory of metal is its use in the elucidation of the to the structure and properties of elemental boron and the boranes [43]. 

Fig. 2.8 Structural phase transftnmation in clathrate cP124 BaeGe25 (top) crystal structure with the atomic arrangement relevant for the structural transformation (middle) atomic arrangements and interatomic distances in the vicinity of the Ge4-Ge6 bond above (left) and below (right) the transformation temperature (bottom) changes in the coordination sphere of the Ba2 atoms caused by the transformation [67]...

This chapter starts with a short explanation of the basic principles of atomic structure and the nature of the chemical bond. Afterwards, the three main groups of materials, metals, ceramics, and polymers, are discussed. The most important characteristics of their interatomic bonds are covered, and the microscopic structure of the different groups is also treated. 

Figure 13.14. The structure of the neutral bases in the pyrimidine class. The black circles represent C atoms, the gray circles are N atoms and the white circles are O atoms. The smaller circles are the H atoms. Single and double bonds are indicated by lines joining the circles. The interatomic distances for the bases uracil ([/), cytosine (C) and thymine (J) which take part in DNA and RNA formation are shown in angstroms. All atoms lie on the same plane, except for the two H atoms in the NH2 unit bonded to C4 in cytosine and the three H atoms in the CH3 unit bonded to C5 in thymine. All distances are indicative of typical bond lengths which vary somewhat depending on the environment the C-H bond distance is 1.10 A and the N-H bond distance is 1.00 A. In the case of U, C and T the H atom normally attached to N1 is replaced by the symbol 0, denoting the C atom that connects the base to the sugar-phosphate backbone the distance indicated in these cases corresponds to the Nl-C bond.

EXAFS is a nondestructive, element-specific spectroscopic technique with application to all elements from lithium to uranium. It is employed as a direct probe of the atomic environment of an X-ray absorbing element and provides chemical bonding information. Although EXAFS is primarily used to determine the local structure of bulk solids (e.g., crystalline and amorphous materials), solid surfaces, and interfaces, its use is not limited to the solid state. As a structural tool, EXAFS complements the familiar X-ray diffraction technique, which is applicable only to crystalline solids. EXAFS provides an atomic-scale perspective about the X-ray absorbing element in terms of the numbers, types, and interatomic distances of neighboring atoms. 

Figure 3-4. Dimensions of a fully extended polypeptide chain. The four atoms of the peptide bond (colored blue) are coplanar. The unshaded atoms are the a-carbon atom, the a-hydrogen atom, and the a-R group of the particular amino acid. Free rotation can occur about the bonds that connect the a-carbon with the a-nitrogen and with the a-carbonyl carbon (blue arrows). The extended polypeptide chain is thus a semirigid structure with two-thirds of the atoms of the backbone held in a fixed planar relationship one to another. The distance between adjacent a-carbon atoms is 0.36 nm (3.6 A). The interatomic distances and bond angles, which are not equivalent, are also shown. (Redrawn and reproduced, with permission, from Pauling L, Corey LP, Branson PIR The structure of proteins Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 1951 37 205.)...

The crystal structures of two compounds are isotypic if their atoms are distributed in a like manner and if they have the same symmetry. One of them can be generated from the other if atoms of an element are substituted by atoms of another element without changing their positions in the crystal structure. The absolute values of the lattice dimensions and the interatomic distances may differ, and small variations are permitted for the atomic coordinates. The angles between the crystallographic axes and the relative lattice dimensions (axes ratios) must be similar. Two isotypic structures exhibit a one-to-one relation for all atomic positions and have coincident geometric conditions. If, in addition, the chemical bonding conditions are also similar, then the structures also are crystal-chemical isotypic. 

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