Radii of atoms

Figure 4.17 Schematic diagram of bound tyrosine to tyrosyl-tRNA synthetase. Colored regions correspond to van der Waals radii of atoms within a layer of the structure through the tyrosine ring. Red is bound tyrosine green is the end of P strand 2 and the beginning of the following loop region yellow is the loop region 189-192 and brown is part of the a helix in loop region 173-177.

Covalent Radii of Atoms and Interatomic Distances in Crystals containing Electron-Pair Bonds. 

The author assumed that the Born radii of atoms can be estimated from the solvent exposure factors for sampling spheres around the atoms. Two spheres were used in a five-parameter equahon to calculate the Born radii. The parameters of the equahon were eshmated using numerical calculahons from X-ray protein structures for dihydrofolate reductase. In addition to AGol the author also considered the AGJ term accounting for cavity formahon and dispersion of the solute-solvent interactions as ... 

Measuring the radii of atoms is not a walk in the park. Electrons in atoms are neither here nor there. They are merely more likely to be here than there. Measuring the size of an atom is a bit like measuring the size of a cotton ball. The answer depends on how much you decide to compress it. Similarly, the size of an atom depends on how one chooses to measure it. 

Central E14-C bonds are longer (about 0.1 A) than the E14-CMe bonds, and the E14-C-E15 angles are greater than the ideal tetrahedral angle of 109.4°, which indicates considerable steric strain due to short nonvalent contacts X---E15. For betaines of the tin series, the E14 E15 distance approaches the sum of van der Waals radii of atoms (Table XI). This regularity is distinctly seen in the experimental X-ray data (see Section 3). 

The chain lengths of different molecules were then compared with the chain lengths of hydrocarbons to calculate the carbon number which relates the elution volume of the compound to the elution volume of a real or imaginary n-hydrocarbon. The "effective" carbon number for benzene based on its elution volume was experimentally found to be 2.85 - i.e. it eluted near the elution volume for propane which has a carbon number of 3.0 while the calculations based on bond angles and radii of atoms indicated that benzene would have a carbon number of 3.55. Thus corrections to the calculations for carbon number were required. These were derived from the experimentally observed elution behavior of various molecules. 

The apparent radii of atomic states in an experimental STM image can be readily obtained from a trace. The profile of an atomic state near its peak can always be approximated as a parabola. By measuring the width 2b at a distance h from the peak, the radius at the peak is... 

An approach based on orbital radii of atoms effectively rationalizes the structures of 565 AB solids (Zunger, 1981). The orbital radii derived from hard-core pseudopotentials provide a measure of the effective size of atomic cores as felt by the valence electrons. Linear combinations of orbital radii, which correspond to the Phillips structural indices and have been used as coordinates in constructing structure maps for AB solids. 

As a result of the development of the x-ray method of studying the structure of crystals and the band-spectroscopic method and especially the electron-diffraction method of studying gas molecules, a large amount of information about interatomic distances in molecules and crystals has been collected. It has been found that the values of interatomic distances corresponding to covalent bonds can be correlated in a simple way in terms of a set of values of covalent bond radii of atoms, as described below.1... 

Other Covalent Radii.—Bipositive nickel, palladium, and platinum and tripositive gold form four coplanar dsp bonds, directed to the comers of a square, with attached atoms. Examination of the observed values of interatomic distances reveals that square dsp radii of atoms have the same values as the corresponding octahedral d sp radii, as given in Table 7-15. This is shown by the comparisons on the following page. 

Interatomic Distances Tablb 7-20.—Van dsr Waals Radii of Atoms... 

---