Interatomic angles

Bond lengths Bond angles Torsional angles Interatomic distances... 

Bioisosteric replacement can be made from a position of knowledge, if the desirable properties of the substituent or substructure to be changed have been characterized. Such properties can include (with typical parameters) (a) size (volume, molar refractivity, surface area, Taft s) (b) shape (Verloop length and breadth, bond angles, interatom distances) (c) lipophilicity (log P, tt,/) (d) solubility (log S) (e) ionization state (pKg, a) ... 

Additional features determine properties such as interatomic distances, bond angles, and dihedral angles from atomic coordinates. Animations of computed vibrational modes from quantum chemistry packages arc also included. http //fiourceforge.nei/projecl /j mol/... 

You can include geometric restraints—for interatomic distances, bond angles, and torsion angles—in any molecular dynamics calculation or geometry optim i/.ation. Here are some applications of restrain ts ... 

Note You can superimpose harmonic restraining forces to interatomic distances, angles, or dihedrals that you have set up as named selections. Yon can also restrain atoms to points in space. See Using Geometric Restraints" on page SI and "Restraints" on page 105. 

Fig. Vl-4. Geometry of thiazole ring in 2-arniro-4-phenylthiazole hydrobromide. Italicized values are interatomic distances (A) other numbers are angles in degrees. From Ref. 342.

Recommended values for the force constant are 7.0 kcal/mol M for an interatomic distance, 12.5 kcal/mol degree for an angle, and 16.0 kcal/mol degree for a dihedral angle. Use the recommended values and then, if the internal coordinate is not sufficiently restrained, try a larger force constant. 

Table 1 Interatomic Distances and Bond Angles in Penicillins...

A molecular dynamics force field is a convenient compilation of these data (see Chapter 2). The data may be used in a much simplified fonn (e.g., in the case of metric matrix distance geometry, all data are converted into lower and upper bounds on interatomic distances, which all have the same weight). Similar to the use of energy parameters in X-ray crystallography, the parameters need not reflect the dynamic behavior of the molecule. The force constants are chosen to avoid distortions of the molecule when experimental restraints are applied. Thus, the force constants on bond angle and planarity are a factor of 10-100 higher than in standard molecular dynamics force fields. Likewise, a detailed description of electrostatic and van der Waals interactions is not necessary and may not even be beneficial in calculating NMR strucmres. 

Figure 11.16 Coordination geometries of the nitrate group showing typical values for the interatomic distances and angles. Further structural details are in ref. 150.

The structure is shown in Fig. 13.28a the interatomic angles and distances suggest that the bridging PhSb group is stabilized by Sb-Mn 7T interactions. A similar route leads to 3-coordinate planar organoarsinidine complexes which can also be prepared by the following reaction sequence ... 

Water is a volatile, mobile liquid with many curious properties, most of which can be ascribed to extensive H bonding (p. 52). In the gas phase the H2O molecule has a bond angle of 104.5° (close to tetrahedral) and an interatomic distance of 95.7 pm. The dipole moment is 1.84 D. Some properties of liquid water are summarized in Table 14.8 together with those of heavy water... 

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