MSE 6412

Core Structure
Homework 4
Due Monday December 11 Noonish

nswers

Sureyou didnt even win your conference division, let alone the conference
championship. But we think you should play for a national title anyway.
Merry Christmas from the BCS Selection Committee
 Answer: Reflections
Inspect these pictures of powder snow. Make an analogy between the interaction of the light with the
snowflakes and x-ray powder diffraction.

Whether its powder diffraction or

sunlight/moonlight glinting off powder
snow, only those specks of crystal that are
oriented properly result in light going to
the detector (or eye).

http://static.panoramio.com/photos/large/38667049.jpg https://mindfulwalksbelfast.wordpress.com/

Grading Rubric:
APTEC Workbook Copyright APTEC 2017 Keywords: Scattering, powder diffraction
Virtual Book Chapters: Ch14, Scattering
 Answer: Gauss parameters
We considered the probability density for chain end-to-end distancese.g., P(r) = A exp(-Br2/nl2)which is a
simple Gaussian. Derive the coefficients A and B.

The equation has unknowns, A and B, so we

need two conditions. The first will be set by
normalizing the distribution, the second will
be set by demanding the mean squared
distance be nl2 because thats what we got
for our freely jointed calculation. We also
assume the chain end can be found with
equal probability in any direction. So that
means we can use spherical polar
coordinates and just write 4p for the angular
dependence. Then the differential volume
element in which chains of length r are found
is 4pr2dr.

Grading Rubric:
APTEC Workbook Copyright APTEC 2017 Keywords: Gaussian probability distribution
Virtual Book Ch: 6 Doi Ch 3 Rubinstein Ch. 7
 Answer: Bi-Gauss, by golly!
Think of some polymers that would have a P(r ) distribution that is bi-Gaussian.
Simply mixing two polymers with different masses does not count.
One possibility: polymers made of macromonomers. That is,
polymers made from polymers, connected by flexible links,
but with some monomer still present.

Probably better: polymers that fold back on themselves, or

form helical zones, but exist in equilibrium with their
random coil form.

Grading Rubric:

APTEC Workbook Copyright APTEC 2017 Keywords: Gaussian probability distribution

Virtual Book Ch: 6 Doi Ch 3 Rubinstein Ch. 7
http://kitchingroup.cheme.cmu.edu/blog/2013/01/29/Curve-fitting-to-get-overlapping-peak-areas/
 Answer: Self-avoiding walk: use existing program.
Working with a team of 5 to 8 others, use the existing SAW program on
the website to estimate the molecular weight dependence of a2 (in two
dimensions).
Conclusions:
1) The data trend upward, as expected, but even at just 10 bonds
we required 712 attempts to find conformations that did not
crash. This grows to 5407 attempts by 15 bonds! So.we need
far more bonds and that means much more computer speed.
2) Excel is massively slowand in this case we are asking it to
plot the graph at each try. (It would speed up enormously
without that.)
3) As I recall, the right answer is nFlory ~ 3/(D + 2) where D is the
dimension of the SAW simulation (you should check this claim
before using it). For D = 3 (three-dimensions) that gives us
nFlory ~ 3/5 = 0.60. In two dimensions we expect nFlory ~3/4 =
0.75 which would imply a Log10(r2) vs Log10(n) slope of 1.5.
Instead we get 1.375not bad for such a short calculation of
short polymers.

Grading Rubric:
APTEC Workbook Copyright APTEC 2017 Keywords: Self-avoiding walk, dimensions, excluded volume
Virtual Book Ch: 6 Doi Ch 3 Rubinstein Ch. 7
 Answer: W
To a good approximation, there are p x 107 seconds per year. What is
the molecular weight of a polyethylene that has that many bond
configurations? Assume equal potential energies for trans, gauche plus
and gauche minus conformations.

Let n + 1 = # of beads (methylene groups, CH2, Mo=14).

Then n = # of bonds
W = 3n = 3(M/Mo)
M=MoLog10(W) /Log103 = 14Log10(p x 107) /Log103 = 220
This is a small chain!

Grading Rubric:
APTEC Workbook Copyright APTEC 2017 Keywords: Dimensions
Virtual Book Ch: 6 Doi Ch 3 Rubinstein Ch. 7
 Answer: Trans vs gauche
At room temperature, how much more likely is a C-C bond to be trans
http://images.slideplayer.com/26/8630088/slides/slide_33.jpg
than to be in either of the gauche states?
Ntrans
= e ( E / k BT )
Ngauche
[ 12000 J /( 298 K *8.314 J .mol 1K 1 )] 125
e

Grading Rubric:
APTEC Workbook Copyright APTEC 2017 Keywords: Dimensions, rotational isomeric state
Virtual Book Ch: 6 Doi Ch 3 Rubinstein Ch. 7
 Answer: Flory/deGennes errors
Genius is often about making the right mistakes. Both the Flory and de
Gennes treatments of excluded volume make mistakes that cancel out.
What are the two mistakes?
Best to look it up in in de Gennes book. As I recall, using the concentration to
compute the probability of collisions between different beads on the chain
overcounts because the chain does have some persistence, however small.
That means close-by beads are not likely to collide. Opposing that is
computing the free energy spring as though its expanded up from nl2 when
the equilibrium size is really nl2 a2 . So, we overestimate the stretch due to
collisions and the restore force due to extending the chain, both. Cancels. Like
most deGennes theories, its a sorta theory. Full of insight, not
quantitatively correct.

Grading Rubric:
APTEC Workbook Copyright APTEC 2017 Keywords: Gaussian probability distribution
Virtual Book Ch: 6 Rubinstein Ch. 7 deGennes
 Answer: Guinier
The picture shows noisy (red) and clean (black) data from
some particles dispersed in solution.
2.0
Obtain the size of the particles with uncertainty estimate.
Rg = sqrt[-3 x Slope] = sqrt[-3 (-5.3 2.0)/(0.04 0)]
= 23.4
Get uncertainty from different estimates of slope. Will be
only modest because error down-propagates in this square-
root calculation. Example: using -5 instead of -5.3 only
changes the answer to 22.9 which is only 0.4% different. about -5.3

Why is there more noise at high angles than low?

The intensity is actually whats left after subtracting the
solvent signal. That difference approaches zero at high q, and
the logarithm of zero goes off to wildly negative values. Also,
there is a less signal at high q.
What is the structure factor S(q) for this solution?
Adaoted from: http://journals.iucr.org/s/issues/2013/02/00/co5027/co5027fig2.html
Unity. One. 1.0 no evidence of any bumps.

Grading Rubric:
APTEC Workbook Copyright APTEC 2017 Keywords: Guinier, scattering, radius of gyration
Virtual Book Ch: 14
Answer: Plot form factor, SAXS
a. Sometimes it is a good idea to make plots of what we anticipate seeing in an experiment. Make a plot of the form factor for a solid sphere of radius R against
scattering angle (not q). Assume R = 500.0 nm, lo = 1.5 (CuKa radiation), n = unusual for X-rays (look it up) It is up to you to find the interesting angular range
to plot. As before, you will use the usual equation,
P(q)=(3/x3)2[sin(x)-xcos(x)]2
where x = qR and q is the scattering vector magnitude.
b. Repeat the plot for R = 100.0 nm and put the result on the same graph.
c. Repeat the plot for R = 10.0 nm and put the result on the same graph.
The P(q) vs q plots will look exactly as they did before. What we want is the angular range.
Lets set the limit of the Guinier range as our arbitrary value:
qR = 1 q = 1/5000 = 0.0002 -1 = 4pnsin(q/2)/lo .
20 cm
The refractive index of x-rays is ~1.0 (slightly less than 1.0) and lo = 1.5.

Solving, we get q = 0.003 degrees. Which is small! To put this in context, a typical SAXS detector is about 10
cm radius (4 inches). Such a detector must be placed a sample-detector distance xSD = 10 cm/tan(q) = 2
kilometers away (!). Butthat is if we want the scattered light to hit the outside of the detector. If we use
pixels nearer the center of the cameralet us say the first 0.5 cmmaybe we can hit the Guinier range
using at least a few pixels if the camera is at 100 meters. Sogetting the Guinier range requires a BIG
instrument for this big particle. At some point, visible scattering is just easier. For the particles at 1000 of xSD
course, the Guinier range can be captured at shorter sample-to-detector distances. Often, we just skip the
Guinier range and fir the whole structure factorcomplete with its little bumps. There is a lot of progress in
making miniature SAXS detectors. Also, there are clever geometries (Google Bonse-Hart camera) to make
very low angle instruments more compact.

Grading Rubric:
a. Easy to follow proof, stating any assumptions. (6 points) Keywords: Scattering, interference
b. Plot (4 points) APTEC Workbook Copyright APTEC 2015
Virtual Book Chapters: Ch14, Scattering
 Answer: Problem: Blowing leaves
Blowing Leaves
In the United States (the real one, as seen on TV) there is a season known as fall. It's called that because the beautifully colored leaves of deciduous trees decide
it is time to fall. Happy, plaid-clad families gather on weekends to rake the leaves into a pile. Just as often, the wind will blow the leaves out of the pile after the
families go inside to warm up with some hot chocolate and cinnamon toast. Obtain a scaling law for the distance r traveled by the average leaf as a function of
time on a blustery day with erratically shifting winds (here, we imagine they can go in any direction at any instant in time).
Just by analogy to random walk process, if the number of steps is
proportional to the time elapsed, we get: <r2> ~ t or <r2> = tl2 where l
is some average step size.

How is your answer modified if the winds were to only blow from those mythical four corners, but changes in steps, one compass point at a timee.g., West can change
to North or South but not to East.

This is similar to the freely rotating (not freely jointed) problem, as

discussed in the notes on polymer size. The result is that squared
distance is expanded by (1 + cosq)/(1-cosq) where q is the bond angle
supplement for chains or the change in direction for polymers. We get:
<r2> = tl2[(1 + cosq)/(1-cosq)]. As the problem is written, q = 90o.so
the effect is nil.

q
Freely rotating model

What if winds blow from the points of an 8-point compass (N, NE, E, ES, S, etc.) with winds switching from N to NE or NW (but not from N to S)?

Now the problem has q = 45o.so the result is

<r2> = tl2[(1 + cos45)/(1-cos45)] = tl2(1.707/.293) = 5.8tl2

Grading Rubric:
a) Right equation: 6 points Keywords: Flory-Huggins, Phase
b) Valid development and explanation: 2 pts APTEC Workbook Copyright APTEC 2015
c) The two compass questions: 2 pts Virtual Book Chapters: Ch11, Thermodynamics
 Answer: David Brant Persistence (Ref WB110) (Ref WB110)

1. The figure below was scanned from an article by Burton and Brant (Biopolymers, 22, 1769-92 (1983)).
It represents a computer simulation of a polysaccharide. The scales are marked in Angstroms. Assuming
this particular conformation to be average, estimate the persistence length of the chain being
simulated.

<r2> = 2a[L - a + aexp(-L/a)]

Results vary
Method: dental floss to get L (about 7 cm), ruler to get r (about 5, so rsq = 25).
Solve using solver: 2.84 cm.
Apply scale from ruler to this plot: 3.8 mm = 200 units
Answer = 2.84 x 100/3.7 = 76 Angstroms

The necessary equation is in the Virtual Books chapter on polymer dimensions. You may need some string, or at least a ruler.

Keywords: Polymer dimensions

Tell how you did it /2
Virtual Book Chapters: Ch6, Dimensions
Reasonable answer /8
12
APTEC Workbook Copyright APTEC 2017