Protein Structure Determination

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Lecture 2:

The scattering of Xrays by electrons

Wave physics and wave math
 X-rays are light

Wavelength of X-rays used in crystallography: 1 - 3

( = 10-10m) most commonly 1.54 (Cu )
Frequency of oscillation of the electric field = c/
=(3x108m/s) /(1.54x10-10m) 2x1018 s-1
Much faster than electron
motion around the nucleus.
 What happens to e- when it oscillates in
an electric field?
e- oscillation is the same frequency as the X-rays
e- oscillation is much faster that orbiting motion.
The amplitude of the e- oscillation is large because the
mass of an e- is small. Atomic nuclei dont oscillate much.

e-
E e- e-
e- e-
e- e-
e- e-

t
 An oscillating charge emits light
in all direction to the direction of oscillation.

oscillation

e-
emission
Since X-rays are not polarized...

, oscillation is not
in a line

e-
so, emission is not
polarized
 Scattering
X-rays are waves of oscillating electric field.
Charged particles are accelerated by an electric field.
Electrons have almost zero mass.
Electrons oscillate with a much higher amplitude than nuclei.
Oscillating charges emit light of the same frequency as the
oscillation.
The frequency of oscillation is roughly 2x1018 s-1, much faster
than the speed of travel of e- around the nucleus.
X-rays hit electrons like they are standing still. (No Doppler
effect!)

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 The general equation for wave

Remember:
Photons are
oscillating electric E Amplitude A
fields*. t phase
(phase)
E(t) = A cos(t + )
wavelength
The instantaneous electric field at time t
=2c/

oscillation rate in cycles/second

*also has an oscillating magnetic field of the same frequency, 90 degrees out of phase.
Wave addition by field addtion

Rule #1:
The sum of two waves with wavelength
+ always produces a wave of wavelength .

Sum the electric fields line by line.

=
Constructive interference: amplitude increases.
 Constructive interference

adding
field lines

Two electrons in the same place oscillate in phase.

 Destructive interference

adding
field lines

2 electrons separated by /2 oscillate out of phase .

 Decomposing a wave into sine and cosine

a wave 5.0
-60
=
t=0
cosine part 2.5
+
4.33
sine part
t=0
 Decomposing a wave into sine and cosine

5.0 cos(t - 1/3)

5.0
= -60
t=0
2.5 cos t 2.5
+
4.33
4.33 sin t
t=0

5.0 cos(t - 1/3) =

5.0 cos(1/3) cos t - 5.0 sin(1/3) sin t =
2.5 cos t + 4.33 sin t
 Wave math 1

All light waves are sinusoidal. (electrostatic potential vs time)

Waves consist of a wavelength, an amplitude and a phase.

Waves can be summed.

Wave summation is called interference.

Interference can be constructive or destructive.

If two waves have the same wavelength, then their sum has
that wavelength, too.

In crystallography, we only care about summing waves of the

same wavelength.

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 The sum of angles rule

cos( + ) = cos cos sin sin

 Using the sum of angles rule on the
wave equation decomposes a wave into
sine and cosine parts
The general wave equation,
E(t) = A cos(t + )
Using the sum of angles rule, becomes
A cos(t + ) = A cos cost - A sin sint

amplitude of cosine amplitude of sine

wave part wave part

A unit cosine wave. A unit sine wave.

We can call this our We can call this our
x-axis y-axis

Which corresponds to a point in a 2-D orthogonal coordinate system.

 Expressing a wave in the space of sine
and cosine reference waves

E(t) = A cos(t + )
Using the sum of angles rule:

A cos(t + ) = A cos cost - A sin sint

amplitude of amplitude of
cosine part sine part
sine part

A
cosine part
y-axis= x-axis=
Reference wave -sint
Reference wave cost
 Cosine parts and Sine parts of waves can be summed
independently, like orthogonal coordinates.
Total amplitude is Pythagorean, like orthogonal
coordinates.

Result: Waves can be expressed in orthogonal
coordinates!!

(1.
,-6
)0

(4.,
(5.
,-6

+12
0
)

0)

Conclusion:
Wave addition is vector addition!!!!
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 For mathematical convenience, a wave
can be represented as a complex number.

i
Eulers Theorem: e = cos + i sin
Proof: write cos and isin as Taylor series and sum them.
You get the Taylor series for ei.
2 4 6
cos = 1 2!+ 4! 6!!
isin = i i 3!+ i 5! i 7!+ !
3 5 7

i 2 3 4 5
e = 1+ i 2! i 3!+ 4!+ i 5!!
 Argand diagrams
(Acos, sin) Aei

sine part = imaginary part

-i
sine part

A A
cosine part r
cosine part = real part

Argand diagram

Thus we may conveniently use Argand diagrams for summing waves:

Wave addition is vector addition in Argand space

-60

A1ei1 + A2ei2
+90

B2.5 -36

Multiplying complex exponentials = phase shift

-60

A1ei1 ei2 = A1ei(1+2) +90

 Wave math 2
Wave summation is equivalent to vector summation.
Complex numbers are vectors in Argand space.
Wave summation (interference) is equivalent to
summing complex numbers in Argand space.
Eulers theorem: ei = cos + i sin
ei is mathematically equivalent to a unit wave with phase .
In other words, |ei| = 1.
Verify: |ei+ei| = 2.
Verify: |ei+ei(+)| = 0.
Verify: |ei+ei(+2/3)+ei(-2/3)| = 0.
Aei is a wave of amplitude A, phase .

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 Try it: Add these waves using a protractor and ruler
Start at the origin. Add head to tail.

3.0, -30
2.0, 180
0.5, +90
2.0, +45
1.0, +135
2.0, +120
0.5
0.5, -120 1.0
2.0
3.0
Use these bars to calibrate a makeshift ruler, if necessary.
Every electron has a location in
the crystal relative to the origin.
The location determines the
phase of scatter.
proof to follow...

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 Rayleigh Scatter: Light turns a corner at
the crystal

X- tor
de
ray
tec

X-ray
source e-

length/ = the number of oscillations completed when

hitting the plane of the detector
The phase is the non-integer part times 2
Exactly where the light turns the corner determines
the phase.
Phase depends on the distance traveled

Phase = D/ nearest integer(D/)

Same for scattered path

 Reminder: The Dot Product
two definitions:
ab = |a||b|cos()

ab = axbx+ayby+azbz

a
b

b

If a is a unit vector, then ab is the length of the projection of b on a.

If a and b are both unit vectors, then ab equals cos().
 Scattering by 2e-
rs0
s0 s
e-

r
e- rs
Difference in pathlength = rs - rs0
Relative phase: = 2(rs - rs0)/

If e-(1) scatters with amplitude A1, and e-(2) scatters with

amplitude A2, then the sum of their scattered waves is
i
A1 + A2ei A2

R
A1
 Phase equals additional distance traveled...
...divided by the wavelength
Distance from source to origin = a
Distance from origin to detector = b
Distance from source to e- = a + rs0
Distance from e- to detector = b - rs

phase = = total distance / wavelength

det
= [a+rs0+b-rs - (a+b)]2/ = 2(rs0 - rs)/

ect
or
rs0
e- s
source

s0 r

a
-rs b
origin
 Definition of scattering vector S
phase of a point in space r:
r = 2(rs - rs0)/
simplifying...
(r1s - r1s0)/ = r1(s - s0)/ -s0/

So we define the scattering vector S as

S s/
S (s - s0)/ s0 s

Substituting S into expressions for phase:

1 = 2(r1s - r1s0)/ = 2 Sr1
Note the reciprocal units.
2 = 2(r2s - r2s0)/ = 2 Sr2 S is reciprocal space!
 Scattering factor for two or more regions
of e- density.
Pick any two locations in space, r1 and r2, and a direction of
scatter s (a unit vector). What is the amplitude and phase The exponent must
of the scattered X-rays? be unit-less. Lets
check:
r2s0 r is in .
s S is in 1/.
e-
So units cancel!
s0 e - r2
r1

1 = 2 Sr1
r2s
origin of unit cell 2 = 2 Sr2

F(s,s0)=A1ei1+A2ei2 = k Akei
k

where Ak is the electron density at rk. If we sum over all points k,

F(S)= Akei2Srk
k
 Amplitude of scatter from a point is
proportional to its electron density.

F(S)= Akei2Srk
k

i 2 S r1 i2 S r2
( r1 )e Ak=+ (r2 )e
dr k
dr + ...
=electron density

where the subscript k corresponds to a location in the unit cell, rk.

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 Wave math 3
When a wave turns a corner (scatters from), its phase
depends on where it turned the corner.
We arbitrarily choose the origin (scatter from the origin) to have
phase = 0.
The phase for a wave scattered from incident unit vector s0 to
scattered unit vector s, turning at r is
r = 2(rs - rs0)/
The Scattering vector S (capital S) is defined as
(s - s0)/
S is a vector in reciprocal space the inverse of real space
where the units are reciprocal distances.
The amplitude of scatter from point r is proportional to the
number of electrons at r.

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 Fourier transform is the sum waves from
all points in the crystal
The amplitude of scatter from each volume unit dr is proportional
to the electron density at the point, (r), times the volume unit
dr, and the phase is 2Sr. This is summed over all dr, so the
total wave summation can be written as

limit
dr->0
[ ( r )e
1
i 2 S r1
dr + (r2 )e i2 S r2
dr + ... ]
i2 S r
=
(r )e dr

Please note: this is really a triple integral: dr is equivalent to dx dy dz

 Review
How are protein crystals grown?
What is symmetry?
What are X-rays?
Why do electrons scatter X-rays?
What is the phase of a wave?
Why can waves be expressed as vectors?
How does the position of an electron relative to the
origin determine its phase?
In what units is the Fourier transform of 3D space in
?
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 Physics of Xray versus NMR
In NMR long-wavelength light interacts with the nuclei.
In Xray, short wavelength light interacts with the electrons.
In NMR, light is an oscillating magnetic field.
In Xray, light is an oscillating electric field.
In NMR we Fourier transform from the time domain to the
frequency domain (reciprocal time).
In Xray we Fourier transform from the space domain to the
reciprocal space domain.
In NMR we solve a protein structure by determining the
internal coordinates (pairwise distances).
In Xray we solve a structure by determining the Cartesian
coordinates.

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