Biochemistry - The Chemical Reactions of Living Cells Volume 1 - D. Metzler 1980

The Molecules We Are Made Of
Principles of Small Molecule Architecture
Bond Angles

The integrity of stable organic molecules is due to The formation of covalent bonds. As a rule, these are very strong bonds: their Standard Free energy of formation (∆Gf) is about —400 kJ∙mol^-1. They have a specific directionality (determined by bond angle values) and a definite length.

Single bonds formed by carbon atoms, as well as by most phosphorus atoms, typically exhibit a tetrahedral configuration. In such carbon atoms, all 6 bond angles are approximately equal and correspond to the tetrahedral angle of 109.5°. This angle is worth keeping in mind. In Organic compounds along the carbon atom chain, bond angles differ very little from this value. Similar values are typically characteristic even of atoms bonded to fewer than four other atoms; for instance, the H—O—H angle in a Water molecule is 105°, and in an ammonia molecule, the H—N—H angles are 107°. Ethers are characterized by a C—O—C angle of 111°. At the same time, some simple compounds feature bond angles close to 90° (for example, 92° in H₂S and PH₃ molecules, and 101° in the H₂O₂ molecule).

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The presence of double bonds results in a planar configuration, with bond angles approaching ~ 120° (the vertex angle of a regular hexagon). In many cases, groups that at first glance should not be planar are planar due to Resonance: for example, all atoms involved in the Formation of the peptide group (Fig. 2-4) lie practically in the same plane, with bond angles deviating from 120° by no more than 4°.

Table 2-1 Dimensions of certain atoms^a_'^б

^а Pauling L., The Nature of the Chemical Bond, 3rd ed., pp. 224—227 and 260. Cornell Univ. Press, Ithaca, New York, 1960.

^б The interatomic distance is determined by adding two covalent radii. Van der Waals radii indicate how tightly molecules can be packed. Thus, the shortest distance between atoms in macromolecules is approximately 0.02 nm less than the sum of their van der Waals radii. [Sasisekharian V., Lakshminarayanan А. V., Ramachandran G. N., in: Conformation of Biopolymers (G. N. Ramachandran, ed.), Vol. 2, p. 641, Academic Press, New York, 1967.]