X Ray Crystallography
X Ray Crystallography
X Ray Crystallography
F
ifty-six years ago a new branch of summed up in a "model." I have often atoms in a crystal of sodium chloride (or
science was born with the discov been asked: "Why are you always show dinary table salt) is 2.8 1 angstrom units
ery by Max von Laue of Germany ing and talking about models? Other (an angstrom is 10-10 meter), whereas
that a beam of X rays could be diffracted, kinds of scientists do not do this." The the most commonly used wavelength in
or scattered, in an orderly way by the answer is that what the investigator has X-ray analysis is l.54 angstroms.
orderly array of atoms in a crystal. At been seeking all along is simply a struc Actually crystals came into the pic
first the main interest in von Laue's dis tural plan, a map if you will, that shows ture only because- they are a convenient
covery was focused on its bearing on the all the atoms in their relative positions means to an end. The resultant scatter
controversy about the nature of X rays; in space. No other branch of science is so ing of X rays would be hopelessly con
it proved that they were waves and not completely geographical; a list of spatial fused and impossible to interpret if the
particles. It soon became clear to some coordinates is all that is needed to tell scattering units were randomly distrib
of us, however, that this effect opened the world what has been discovered. uted in all orientations. In a crystal the
up a new way of studying matter, that in The atomic structure of a crystal is de units are all similarly oriented and hence
fact man had been presented with a duced from the way it diffracts a beam scatter the X rays in the same way; as
new form of microscope, several thou of X rays in different directions. A crys a result a total scattering measurement
sand times more powerful than any light tal is built of countless small structural made with a whole crystal leads directly
microscope, that could in principle re units, each consisting of the same ar to a determination of the amount scat
solve the structure of matter right down rangement of atoms; the units are re tered by an individual unit.
to the atomic scale. The development of peated regularly like the pattern of a
X-ray crystallography since 1912 has wallpaper, except that in a crystal the The Condition for Djffraction
more than fulfilled our early expecta pattern extends in three dimensions in
tions. It not only has revealed the way space. The directions of the diffracted The easiest way to approach the opti
atoms are arranged in many diverse beams depend on the repeat distances of cal problem of X-ray diffraction is to con
forms of matter but also has cast a flood t11e pattern. The strengths of the diA:ract sider the X-ray waves as being reflected
of light on the nature of the forces be ed beams, on the other hand, depend on by sheets of atoms in the crystal. When
tween the atoms and on the large-scale the arrangement of atoms in each unit. a beam of monochromatic (uniform
properties of matter. In many cases this The wavelets scattered by the atoms in wavelength) X rays strikes a crystal, the
new knowledge has led to a fundamental terfere to give a strong resultant in some wavelets scattered by the atoms in each
revision of ideas in other branches of sci directions and a weak resultant in others. sheet combine to form a reflected wave.
ence. A culmination of sorts has been The goal of X-ray analysis is to find the If the path difference for waves reflected
reached in the past few years with the atomic arrangement that accounts for by successive sheets is a whole number
successful structural analysis of several the observed strengths of the many dif of wavelengths, the wave trains will com
of the basic molecules of living matter fracted beams. bine to produce a strong reflected beam.
the proteins-each of which consists of This brings us to the question of why In more formal geometric terms, if the
thousands of atoms held together by an X rays, of all the available forms of elec spacing between the reflecting planes is
incredibly intricate network of chemical tromagnetic radiation, are indispensable d and the glancing angle of the incident
bonds. for this method of investigation. In or X-ray beam is B, the path difference for
The purpose of this article is to go der for the interference of the diffracted waves reflected by successive planes is
back to the beginning and broadly sum beams to produce marked changes in the 2d sin B [see upper illustration on page
marize the course of X-ray crystallog amount of scattering in different direc 60). Hence the condition for diffraction
raphy over the past half-century or so. tions, the differences in the paths taken is n'\ 2d sin B, where n is an integer
=
In so doing I shall try to answer two key by reflected beams must be on the order and ,\ is the wavelength.
questions: Why X rays? Why crystals? of a wavelength. Only X rays have wave I first stated the diffraction condi
X-ray crystallography is a strange lengths short enough to satisfy this con tion in this form in my initial adventure
branch of science. The result of an in dition. For example, the distance be into research in a paper presented to
vestigation lasting many years can be tween neighboring sodium and chlorine the Cambridge Philosophical Society in
58
1968 SCIENTIFIC AMERICAN, INC
X-RAY PHOTOGRAPH of lysozyme, the second protein and first precession photograph; it is produced by manipulating the crystal,
enzyme to have its molecular structure determined by X-ray analy the phot ographic p late and an intervening screen in such a way as
sis, symbolizes the recent achievements of the X-ray technique_ The to hold one of the three indices of the diffracted beams constant
bright spots c o rrespond to various orders of diffracted waves p ro while recording the values of the other two indices in the form of a
duced by irradiating the lysozyme crystal with a beam of monochro rectilinear pattern. The lysozyme molecule contains 1,950 atoms and
matic X rays_ This particular type of X-ray photograph is called a measures approximately 40 angstrom units in its largest dimension.
59
60
THREE POSSIBLE ARRANGEMENTS of the reflecting sheets of this case h = 2, k = 0 and I = 0.) Similarly, the initial r eflection to
atoms in a sodium chloride crystal ar e indicated by the colored appear fr om the p lanes in the diagram at center i s designated
planes. The axes o f this simple cubic crystal are denoted by the (220), whereas for the diagram at right it i s ( 1 1 1) with respect to
letters OA , OB and OC . In the diagram at left the fir st reflection to chlorine planes. I n general, order s with even indices arise fr om
appear fr om the planes p erpendicular to OA i s assigned the order sheets that are identical and hence result in strong, in.phase reflec
(200), since there is a p a th difference of two wavelengths between tions, whereas orders with odd indices arise fr om alternately oc
o and A while the reflecting planes are parallel to OB and OC . (In cupied sheets and hence result in weak, outofphase reflections.
atoms. One would expect the sequence flected from crystal faces with crystal there is a reduction in intensity owing
of successive orders to fall off regularly lographic indices (100), (1 10) and (Ill). to interference.
in intensity. As the diagram at the right As the curves show, the order (I ll) for It is important to note that F(hkl) is
on this page shows, however, the reflec sodium chloride is anomalously small, a dimensionless ratio, characteristic only
tion (Ill) comes from a more complex whereas (222) fits into the same sequence of the crystal structure. It is independent
set of planes, in that the sheets are alter with (200) and (220). For potassium of the wavelength of the X rays. If a
nately occupied by sodium and chlorine chloride, on the other hand, the scatter smaller wavelength is used, the orders
atoms. Since for (I ll) there is a path dif ing powers of the potassium atoms and appear at lower angles and path differ
ference of one wavelength for the strong the chlorine atoms are so nearly the same ences are reduced, but phase differences
ly reflecting chlorine planes, the waves that thc order (I ll) is too weak to be ob remain the same. Thus F(hkl) depends
reflected from the weaker sodium planes served. It was on the basis of such evi only on the distribution of scattering
halfway between them will be opposite dence that the sbuctural arrangement of matter in the unit cell, which it is the
in phase. The order (Ill) will be weak, both of these alkaline halides was con object of X-ray analysis to determine.
since the sodium conbibution partially firmed. The theoretical basis for measuring
offsets the chlorine contribution. On the Although the preceding analysis is values of F(hkl) was laid down by C. C.
other hand, for (222) the contributions somewhat simplified, it is a typical ex Darwin in two brilliant papers soon af
will be in phase and the order will be ample of the method used in the early ter the discovery of X-ray diffraction. In
sbong. determinations of crystal structure. A those early days the experimental obser
In this type of space lattice, as it is number of orders of diffracted waves vations were too approximate for a test of
called, there are identical pOints at the were measured, either with the ioniza his theory, and a number of years elapsed
face centers as well as at the comers of tion spectrometer or on a photographic before it could be applied.
the cube; this implies that the indices plate, and an attempt was then made Darwin's first calculation assumed the
must be either all odd or all even. These to find an atomic arrangement that ac crystal to be "ideally perfect." Rough
observations can be generalized by stat counted for the relative intensities of the tests showed, however, that the efficien
ing that orders with even indices, such various orders. cy of reflection was many times stronger
as (200), (220) and (222), should form a than his theory indicated. Darwin cor
strong sequence, whereas those with odd The Significance of F(hkl) rectly reasoned that the cause of the dis
indices, such as (Il l), (1 13) and (333), crepancy was the departure of the crystal
should be comparatively weak. The quantity F(hkl) is the cornerstone from perfection. It is a curious paradox
This is the effect that is actually ob of X-ray analYSiS, and its determination that imperfect crystals reflect more effi
served. The illustration on page 63 shows is the final aim of all experimental meth ciently than perfect crystals. In the lat
a very early set of measurements of so ods. This quantity is a measure, for each ter case the reflection, which is almost
dium chloride and potassium chloride order (hkl), of the intensity of the beam complete over a few seconds of arc,
made with the ionization spectrometer, a scattered by the whole unit of a pattern comes from a thin superficial layer only;
device invented by my father, W. H. expressed in terms of the amount scat planes at greater depths cannot contrib
Bragg, in 19 13. The abscissas measure tered by a single electron as a unit. For ute because the uppermost layers have
the glancing angle, the ordinates the instance, the quantity F(OOO) is scattered robbed the radiation, so to speak, of the
strength of the reflection. The two peaks in the forward direction through zero component the lower layers would other
seen on each order are the Ka and Kf3 angle, so that there are no path differ wise have reflected. Actual crystals, how
"lines" in the spectrum of the palla ences to cause interference; F(OOO) is ever, are in general far from perfect.
dium anticathode, the Ka line being the therefore the total number of electrons They are like a three-dimensional crazy
stronger of the two. The orders are re- in the unit of pattern. For higher orders quilt of small blocks that differ slightly
61
LEAD SHIELD
IONIZATION CHAMBER
ANTICATHODE
('\
" j
SLIT
u
X-RAY TUBE z
<{
CATHODE :
CRYS AL TABLE /
CRYSTAL
ELECTROSCOPE
T ELESCOPE
IONIZATION SPECTROMETER was the instrument used by the the X-ray spect... a from various metallic anti cathodes and later by
author' s father, W. H . Bragg, to conduct the first investigations of the author to make the early determinations of crystal structure.
62
63
- ---
1IU.l.-.l-iL
Inorganic Compounds
MICROCRYSTALLINE POWDER
LEFT
I)) ).) I I ( (( ( (( 0 )) ) )1 I I ( (( (( 1 RIGHT
fine the positions of the atoms. In the
case of an atom at a symmetry center,
for instance, no parameters are needed;
180 90 o 90 180 it must be exactly at the center. If the
ANGLE (DEGREES) atom lies on an axis, its position along
the axis is fixed by one parameter; if on
POWDER PHOTOGRAPHS ARE MADE by aiming the X rays at a mass of tiny crystals
a reflection plane, by two; if in a position
i n all orientation s. The diffracted beams of each order (hkl) will then form a cone_ If r e
of no symmetry, by three.
cor d e d on a plate p erpendicular to the incident beam, each diffraction order will appear as
a ring surr ounding the central spot (top); the position s of the rings shown are typical o f a
The early determinations were limited
face-centered-cubic crystal lattice. It is usually more convenient to employ a cylindrical to one or two parameters; in fact, it was
photographic film whose axis is perpendicular to the incident r a diation (bottom). Arcs of doubted whether more complicated crys
the cones are intercepted at all angles up to nearly 180 degrees; the film is then unrolled. tals would ever be analyzed. The break-
64
through into much more complex struc (Be;jAI2SiG01s), for instance, is of a high ing to the negative ion from all its posi
tures was made in the early 1920's by order, with sixfoid, threefold and two tive neighbors just balances its charge.
the Manchester school, where analysis fold axes, symmetry planes and symme This might seem at first sight a simple
was extended to cases of 10 or 20 param try centers. An atom cannot overlap it rule, but it is powerful in excluding im
eters, a great advance at that time. It self, so that it must either lie exactly on probable sbuctures. Its significance is
was made possible by quantitative mea one of these symmetry elements or be that when Pauling's rule is obeyed, the
surements and increasing experience in just off it. This restriction is so demand lines of force between positive and nega
the nature of inorganic compounds. ing that the structure of beryl could be tive ions stretch only over the very short
One of the first successes of X-ray immediately deduced once the symmetry distances between nearest neighbors, so
analysis was to show that these com was determined. The top illustration on that the energy of the electric field is at a
pounds are not built of molecules. They page 67 shows the only possible way of minimum and the structure is stable.
are ionic in character, with a regular al packing the atoms of the beryl formula The study of inorganic compounds
ternation of positive and negative ions into the network of symmetry elements. culminated in the determination of all
held together by electrical attraction. For The laws governing the structure of in thc common mineral forms, in particular
instance, in the sodium chloride structure organic compounds, established by Linus the silicates. These compounds obey
there are no sodium chloride groups but Pauling in 1929, afford another guide Pauling's rule rigorously, because they
rather a chessboard pattern of positive in seeking a solution. They also explain must be very stable in order to exist as
sodium ions and negative chlorine ions. why some compounds are stable, where minerals. The explanation of their com
It was difficult in the early days to rec as others that seem equally plausible position proved to be very interesting.
oncile the new view of ionic compounds from a chemical point of view do not Their nature is determined by the silicon
with classical chemical ideas, but once actually exist. Pauling's rule is based on to-oxygen ratio, ranging from Si04 in the
accepted the ionic view afforded a much the requirement that for stability the en basic rocks to SiO in quartz. Although
fuller understanding of the construction ergy of the compound must be as low the ratio varies widely, the silicon ion
of such compounds. as possible. Each small positive ion lies is always surrounded by four oxygen
In an ionic compound the ions pack inside a cluster of larger negative ions; atoms; the silicon-oxygen tetrahedrons
together as if they had characteristic for instance, very small positive ions such may, however, share no corners, one cor
sizes. Their dimensions are not complete as beryllium or boron are each surround ner, two corners, three corners or four
ly fixed, but they vary only over a small ed by three oxygen atoms; silicon is corners by having an oxygen atom in
range. On the whole the negative ions surrounded by four oxygens, magnesium common. In the Si03 silicates, for exam
are by far the largest, because their elec and iron by six oxygens and still larger ple, there are long strings of Si04 groups
trons are more loosely held. ions by eight or more oxygens. If we pic that run endlessly through the structure,
The packing of ions of characteristic ture electric fields in terms of lines of representing infinite linear negative ions
size is a very useful concept when postu force, suppose the number of lines repre bound laterally by the positive ions. The
lating various atomic arrangements, par senting the charge on the positive ion silicate groups occur as sheet ions in the
ticularly when combined with a knowl is divided equally between the negative micas and clays, and as three-dimension
edge of the symmetry elements. The ions coordinated around it. Pauling's rule al-network ions with metals in their
hexagonal symmetry of the crystal beryl states that the total number of lines com- iuterstices in the feldspars. This unex-
65
66
1968 SCIENTIFIC AMERICAN, INC
O X Y G E N ----i
B E RY L L I U M --='.It-,
A L U M I N U M --+----i
V E RT I C A L - R OTAT I O N A X E S
o TWO-FOLD A X I S
S I L I C O N ----.zr=.=-i.
L T H R E E - FO L D A X I S
o S I X - FO L D A X I S
STRUCTURE OF BERYL ( right ) , a complex inorganic compound fraction. Since an atom must l i e exactly on o n e of the symmetry
with the formula Be H AI:!Si 6 0 1 8 , was deduced from a knowledge elements or be just off it, there could be only one way of packing
of the packi n g of the constituent ions ( le/t ) as soon as the basic the atoms of the beryl formula into the network o f symmetry ele
hexa gonal symmetry of the crystal was determined by X.ray dif ments. A key to the symmetry axes of the crystal is given at bottom.
FOURIER REPRESENTATION o f the e lectron.density distribu pable o f scattering X rays. The density distribution of the molecule
tion in a molecule of phthalocyanine ( le/t ) was used to construct as a whole is obtained by adding together the terms of a Fourier
the atomic model of the molecule (right ) . The Fourier "density series, a mathematical expression that can be used to represent the
map" i s arrived at by treating a molecular structure not as a cluster periodic variation o f sets of electron.density sheets in all direc
of individual atoms but as a continuous electron distribution ca tions. The Fourier method i s ideal for analyzing organic molecules.
67
CARBON
N IT R O G E N
0 OXYG E N
0 PHOSPHORUS
e C O B A LT
STRUCTURE OF VITAMIN B.12, solved by D orothy Crowfoot ments o f what might be called the classical methods of Xray analy.
Hod gkin in 1955, represented one of the outstanding achieve. sis. The formula o f vitamin B -12 molecule is C63H S 4 N 1 4 0 14PCo.
68
O rganic Molecules
69
70
s h o u l d m u n ch e rs 1
M a n y food processors a re u t i l i z i n g f l a v o r fo r
m u l a t i o n s f r o m U O P t o e n h a n c e t h e s u cc u
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t ec h n o l o g i sts w i t h c o n c e n trated s a u c e b a ses,
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