1.6.6.1 X-Ray Crystallography
When it comes to determining the geometry of a drug molecule, X-ray crystallography
remains “the gold standard.” It is used extensively to study the structure of molecules and
is the most powerful method available for the determination of molecular structure. To
apply X-ray crystallography to drug molecules, the compound must first be crystallized
into a solid form; within this crystalline solid, many drug molecules lie stacked together.
X-rays have wavelengths of approximately 1 nm, a scale of atomic dimensions. When
X-rays strike a crystalline solid, the X-rays interact with electrons in the atoms and are
scattered in different directions, with varying intensities due to interference effects. When
this interference is constructive, in-phase waves combine to produce a wave of greater
amplitude that can be indirectly detected by exposing a spot on a photographic film. When
the interference is destructive, the waves cancel each other such that a decreased X-ray
intensity is recorded. These interference effects arise because the different atoms within
the molecule of the crystalline solid scatter the X-rays in different directions. This scat-
tered radiation produces maxima and minima in various directions, generating a diffrac-
tion pattern. The quantitative aspects of the diffraction pattern are dependent on the
distances between planes of atoms within the crystal and on the X-ray wavelength; these
relationships may be mathematically analyzed by means of the Bragg equation
wherenis an integer,λis the X-ray wavelength,dis the spacing between atomic
layers, and θis the angle of scattering. By analyzing the angles of reflection and the
intensities of diffracted X-ray beams, it is possible to determine the location of atoms
within the molecule. Thus, determining the molecular structure of a crystalline solid is
equivalent to determining the structure of one molecule. This in turn provides detailed
information about the structure of the drug molecule (i.e., bond lengths, bond angles,
interatomic distances, molecular dimensions).
X-ray crystallography has a long history of contributions to medicinal chemistry.
Perhaps first and foremost is the work of Dorothy Hodgkin who transformed X-ray
crystallography into an indispensable scientific method. Her first major achievement
was the crystallographic determination of the structure of penicillin in 1945; in 1964
she received the Nobel Prize in Chemistry for determining the structure of Vitamin B12.
Myoglobin and hemoglobin were the first proteins (in 1957 and 1959) to be subjected
to a successful X-ray analysis. This was achieved by J. C. Kendrew and Max Perutz at
Cambridge University; they received the 1962 Nobel Prize. In what is perhaps the most
famous application of X-ray crystallography, James Watson and Francis Crick in 1953
used X-ray data from Rosalind Franklin and Maurice Wilkins to deduce the double-
helix structure of DNA. Watson, Crick, and Wilkins received the 1962 Nobel Prize in
Medicine for this work; Franklin was already deceased.
Clearly, in its infancy X-ray crystallographic determination of molecular structure
was a challenging task. Nowadays, this is no longer the case. Automated X-ray diffrac-
tometers, direct methods for structure determination, and increasingly sophisticated
computers and more efficient software have permitted X-ray crystallography of small
drug molecules to become almost routine. Rather than solving single molecule structures,
DRUG MOLECULES: STRUCTURE AND PROPERTIES 57nλ= 2 dsinθ (1.15)