Chemistry Reference
In-Depth Information
The analysis of protein structure at the molecular level tells us that structural
features sufficient to characterise and distinguish the kinds of organic compounds
studied in the nineteenth century, such as the topological ordering of bonded
atoms and the geometric orientation of bonded atoms about a given atom, would
seem insufficient to characterise proteins. When denatured, by gentle heating or
subjecting to low pH conditions, proteins loose their biologically relevant chemical
properties and become biologically inert, although the underlying pattern of cova-
lent bonding—the so-called primary structure—that would serve to characterise
many organic compounds is preserved. What is lost is their secondary and tertiary
structure, characteristic of the way long chains fold back on themselves and are
held in place by weak hydrogen bonds, which is correlated with chemical reac-
tivity of the kind traditionally taken to be characteristic of a substance. It seems
that the loss of chemical reactivity compels us to take secondary and tertiary
structure to be essential features of the characteristic molecular structure. Merely
considering which atoms are covalently bonded to which and how the bonds are
oriented in space would count proteins in the natural and denatured states at the
same temperature and pressure as the same substance, despite a considerable
difference in chemical reactivity. But taking similar account of hydrogen bonding
in water would lead us to consider it a mixture with continually varying
composition.
Intermolecular interactions are always present, raising the question of when they
contribute to determining the structure of the substance-determining microentity in
accordance with the molecular structure thesis and when not. Equimolar mixtures
of stereo enantiomers are racemic, with zero net optical rotation. Some form
separate (+)- and (-)-rotatory crystals when they crystallise, in which case the
mixture is a mechanical mixture displaying a melting-point diagram (plotting
melting temperature against composition) typical of mixtures. The melting point
of either pure form is lowered by addition of the other, reaching a minimum
(eutectic point) at the 50:50 % composition. But some racemates crystallise as a
single racemic compound, acting as a compound distinct from either enantiomer
and displaying a peak in the melting point diagram at the 50:50 % composition
point. Addition of the (+) form lowers its melting point until a eutectic point is
reached, and addition of the (-) form similarly lowers its melting point until
another eutectic point is reached. The IR spectrum of solid racemic compounds
also differ from the enantiomers (Eliel
1962
, pp. 43-7). The presence of two distinct
molecular structures is therefore not sufficient to determine whether there are one
or two substances present. A thermodynamic criterion determines whether the
50:50 % composition point corresponds to a single substance, a racemic compound,
or a mixture.
Questions about the individuation of the relevant molecular entity also arise
because molecular structure is not a static feature. Molecular geometry is in reality
constantly changing within certain limits as bond angles and lengths change in
vibrational modes and because of distortion due to rotation. The threat of a single
molecular structure giving way to an indefinite number of varieties is avoided, it
seems, by resorting to tabulated values of bond angles and lengths understood as
