Page 13 - Color Atlas of Biochemistry

P. 13

4 Basics

Bonds tatable, since rotation would distort the π-
molecular orbital. This is why all of the atoms
lie in one plane (2c); in addition, cis–trans
A. Orbital hybridization and chemical
isomerism arises in such cases (see p. 8).
bonding
Double bonds that are common in biomole-
Stable, covalent bonds between nonmetal cules are C=C and C=O. C=N double bonds are
atoms are produced when orbitals (see p. 2) found in aldimines (Schiff bases, see p.178).
of the two atoms form molecular orbitals that
are occupied by one electron from each of the
atoms. Thus, the four bonding electrons of the B. Resonance
carbon atom occupy 2s and 2p atomic orbitals Many molecules that have several double
(1a). The 2s orbital is spherical in shape, while bonds are much less reactive than might be
thethree 2p orbitals areshapedlikedumb- expected. The reason for this is that the
bells arranged along the x, y, and z axes. It double bonds in these structures cannot be
might therefore be assumed that carbon localized unequivocally. Their π orbitals are
atoms should form at least two different types not confined to the space between the dou-
of molecular orbital. However, this is not nor- ble-bonded atoms, but form a shared,
mally the case. The reason is an effect known extended S-molecular orbital. Structures
as orbital hybridization. Combination of the s with this property are referred to as reso-
orbital and the three p orbitals of carbon gives nance hybrids, because it is impossible to de-
rise to four equivalent, tetrahedrally arranged scribe their actual bonding structure using
3
3
sp atomic orbitals (sp hybridization). When standard formulas. One can either use what
these overlap with the 1s orbitals of H atoms, are known as resonance structures—i. e.,
four equivalent σ-molecular orbitals (1b)are idealized configurations in which π electrons
formed. For this reason, carbon is capable of are assigned to specific atoms (cf. pp. 32 and
forming four bonds—i. e., it has a valency of 66, for example)—or one can use dashed lines
four. Single bonds between nonmetal atoms as in Fig. B to suggest the extent of the delo-
arise in the same way as the four σ or single calized orbitals. (Details are discussed in
bonds in methane (CH 4 ). For example, the chemistry textbooks.)
2–
hydrogen phosphate ion (HPO 4 )and the Resonance-stabilized systems include car-
+
ammonium ion (NH 4 ) are also tetrahedral boxylate groups, as in formate;aliphatic hy-
in structure (1c). drocarbons with conjugated double bonds,
A second common type of orbital hybrid- such as 1,3-butadiene; and the systems known
ization involves the 2s orbital and only two of as aromatic ring systems. The best-known
the three 2p orbitals (2a). This process is aromatic compound is benzene, which has
therefore referred to as sp 2 hybridization. six delocalized π electrons in its ring. Ex-
2
The result is three equivalent sp hybrid orbi- tended resonance systems with 10 or more
tals lying in one plane at an angle of 120° to π electrons absorb light within the visible
one another. The remaining 2p x orbital is ori- spectrum and are therefore colored. This
ented perpendicular to this plane. In contrast group includes the aliphatic carotenoids (see
2
to their sp 3 counterparts, sp -hybridized p.132), for example, as well as the heme
atoms form two different types of bond group, in which 18 π electrons occupy an ex-
when they combine into molecular orbitals tended molecular orbital (see p.106).
2
(2b). The three sp orbitals enter into σ bonds,
as described above. In addition, the electrons
in the two 2p x orbitals, known as S electrons,
combine to give an additional, elongated π
molecular orbital, which is located above
and below the plane of the σ bonds. Bonds
of this type are called double bonds.They
consist of a σ bond and a π bond, and arise
only when both of the atoms involved are
2
capable of sp hybridization. In contrast to
single bonds, double bonds are not freely ro-

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