Chemistry with a Twist

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Transcript Chemistry with a Twist

Bryn Mawr College
was founded in 1885
with a mission to
provide graduate
education to women.
This is not your father’s (or
my mother’s) physical
chemistry course….
Michelle Francl
Bryn Mawr College
Course Goals
Oure termes so lerned
and queynte
Whan we be ther where we shul
Oure elvish craft, we seme
wondrous wyse,
Oure termes be so lerned and so
Yet wil I telle them, as they
come to mynde,
Though I can not them set right
in their kind;
As sal armoniak, verdegres,
Geoffrey Chaucer
Traditionally, the earliest
known production of what
Chaucer calls “sal
armoniak”, or ammonium
chloride, was from the
burning of camel dung in
the temple of Jupiter
Ammon in what is now
Libya – hence “sal
ammoniac” or salt of
Ammon. This term is the
root for “amine” and
eventually “amino acid”.
• Use quantitative, mathematical approach to the
description and analysis of the structure and
behavior of matter
• Apply these methods to other fields
• Appreciate the strength and limitations of the
• Take and succeed in a next course in physical
chemistry or subfield
• Read the literature as a novice
• Retain student interest in the field
Calculus of Hours
“The Curta is a precision
calculating machine for all
arithmetical operations.
Curta adds, subtracts,
multiplies, divides, square
and cube roots... and every
other computation arising
in science and
commerce... Available on
a trial basis. Price $125”
From an advertisement in
the back pages of
Scientific American in the
1960s. This is about $700
in 2002 dollars – about the
same price as
• There is not as much time as you
– Less than 40 hours/semester in the
– Read 180,000 words
– Do 150-200 problems
• 150 to 200 hours total/semester
Qu i c k T i m e ™ a n d a
T I F F (Un c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c tu re .
Authority vs. Activity
Life is good for
only two things,
mathematics and
Siméon Poisson
Act ive
Act ive
Strategies should be
Josiah Willard Gibbs
was not paid a salary
for the first 9 years of
his job at Yale. Once
he had a job offer from
Johns Hopkins
University in
Maryland, Yale began
to pay him. He gained
little recognition for
his work during his
lifetime mainly
because of his
inability to
communicate his ideas
so that others could
understand the
concepts he was
“Let us learn to dream,
gentlemen: then
perhaps we will find the
truth. But let us beware
of publishing our
dreams until they have
been tested by the
waking understanding.”
– August Kekule von
Stradonitz (taken from
The Scientific Attitude,
2nd Edn by Frederic
Talk less, they learn more
Using the pause procedure to enhance lecture recall. [Ruhl, K. L., Hughes, C.
A., & Schloss, P. J. (1987, Winter). Teacher Education and Special Education,
10, 14-18]
The importance of lecture in general-chemistry course performance [Birk,
J.P., Foster, J. (1993) J Chem Ed 70 179]
Departing from Lectures: An Evaluation of a Peer-Led Guided Inquiry
Alternative [Lewis, S.E., Lewis, J.E. (2005) J Chem Ed 82 135]
Do less, they learn more
Effects of lecture information density on medical student
achievement [Russell. I.J., Hendricson, W.D., & Herbert, R.J.
(November, 1984).. Journal of Medical Education, 59, 881-889]
Active Materials
Materials they can talk about
Physical Chemistry: A Guided Inquiry Atoms, Molecules and
Spectroscopy. R. S. Moog, J. N. Spencer, J. J. Farrell;
Houghton Mifflin: Boston, 2004. )POGIL/NSF
Physical Chemistry Online (PCOL) NSF
Culture of Chemistry: Physical Chemistry in Context NSF
Materials they can use
Science: (n.) The
attempt by subroutines
in an operating system
to deduce the source
code, and write the
instruction manual.
Dave Logan
SymMath collection at JCE
Katharine Blodgett was
the first woman to earn
a Ph.D. in physics from
Cambridge under
Ernest Rutherford after
Irving Langmuir
intervened on her
behalf. She earned her
A.B. from Bryn Mawr
College early in the
last century. She is best
known for her work on
Context rich materials
• Who, what, where, when, why?
As such, physical chemistry underlies much of modern science and is a
motor driving advances in a very wide range of fields. Building on
information and concepts from chemistry, physics, mathematics, physical
chemistry contributes to and is stimulated by areas as diverse as
medicine, molecular biology, biochemistry, molecular engineering,
chemical engineering, materials science and earth sciences.
• Advantages
Context Rich
The famous Boltzmann
equation, S=k ln , is
inscribed on Boltzmann’s
tombstone in Vienna,
Austria. Boltzmann did
not write it in this form,
however, Planck did.
Boltzmann also has two
other equations named for
him, the first is a diffusion
equation used in neutron
transport theory and the
second describes particles
in a gravitational field.
Qu i c k T i m e ™ a n d a
T I F F (U n c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c tu re .
Context Free:
Find an expression for the half-life of the third-order reaction 3A  B.
The gas-phase formation of phosgene, CO + Cl2  COCl2 is 3/2 order with respect to CO. Derive the integrated
rate equation for a 3/2 order reaction. Derive the expression for the half-life.
Context rich:
In a paper by Bada, Protsch and Schroeder [Nature 241, 394 (1973)], the rate of isomerization of isoleucine in
fossilized bone is used as an indication of the average temperature of the sample since it was deposited.
The reaction
L-isoleucine  D-alloisoleucine
produces a nonbiological amino acid, D-alloisoleucine, that can be measured using an automatic amino acid
analyzer. At 200C, this first order reaction has a half-life of 125,000 years and its activation energy is 139.7
kJ mol-1. After a very long time, the ratio allo/iso reaches an equilibrium value of 1.38. You may assume
that this equilibrium constant is temperature independent.
For a hippopotamus mandible found near a warm spring in South Africa, the allo/iso ration was found to be 0.42.
Assuming that no allo was present initially, calculate the ratio of the concentration of allo now present to the
concentration of allo after a very long time (Note: the correct answer is between 0.40 and0.60)….
Radiocarbon dating, which is temperature independent, indicated an age of 38,600 years for the hippo tooth….
Nano comes from the
Greek for dwarf:
Develop materials keyed to primary
scientific literature
• Proof of concept: NSF CCLI-EMD
• Early adopter cadre
• Development of materials
• Assessment
What they are not…
Does anyone actually
use nanowires? Well,
Dr. Ock in Spiderman
2 claimed to use
“nanowires” to
connect his neural
circuitry to a machine
circuit. In fact, silicon
nanowires have
recently been used to
build sensors for
DNA. The sensors are
designed to detect the
presence of mutations
in a cystic fibrosis
gene. [Nano Letters
2004, 4, 51 -54]
• Not to teach library or literature skills
• Not to replace texts
• Not to add new topics
What they are…
Engineers think that
equations approximate
the real world.
Scientists think that
the real world
Mathematicians are
unable to make the
Stand alone
Design of Materials
Cross disciplinary
A Case of Mistaken
Fischer of Fischer
projections is not the
Fischer of Fischer
carbenes, and yet
another Fischer lends
his name to the FischerTropsch reaction All,
however, were German.
Critical reading
Basic concepts
Faces of chemistry
First order kinetics
and ostrich eggs
• Kinetics
• Archeology
• Biochemistry
Chaos is a name for
produces confusion in
our minds.
George Santayana
Prof. Francisco received
his Ph.D. in 1983 from
MIT, then spent time as a
post-doctoral fellow at
Cambridge. Prof.
Francisco’s group blends
high resolution laser
spectroscopy and
sophisticated electronic
structure theory to tease
out the connections
between reaction rates and
chemical structure in free
radical chemistries. His
research has been key to
showing that some
refrigerants, such as
HFC’s may not pose the
same hazards to the ozone
layer as CFCs.
How many millions of years ago were these sediments
deposited? Were the colors in this folio applied when it
was printed, or sometime later? Is this a modern hippo
bone, or a fossil of some similar, earlier species? Just
how old is it? The determination of the age of an artifact
or sample is a crucial question in many fields, including
geology, paleontology, archaeology, anthropology and
history. Context often provides a clue to the age of an
object. For example, the style of decoration of a vase or
the types of pigments applied to a fresco can be used to
narrow the time period in which a particular artifact was
produced. How deeply something is buried is yet another
source of information about an item’s age. Provenance,
or the written record of an object’s history, is another
source from which the age of an object can be
determined. These approaches obviously cannot be
applied to find an age for every object or specimen.
Chronometric methods, such as the familiar 14C dating,
can be brought to bear when the relative dates derived
from contextual information are inadequate, or when
forgery is suspected.
Amino acids are nearly always found in the L-form in natural
products, such as proteins. Uncatalyzed epimerization at
the chiral carbon is, not surprisingly, an exceedingly
Qu i c k T i m e ™ a n d a
T I F F (Un c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c t u re .
Alan Turing is perhaps
best known for his
work on codes in
World War II,
particularly with the
Enigma machines. He
is also often called the
father of computer
science. Turing also
had a long standing
interest in chemistry,
and was a long
distance running of
near Olympic caliber.
Qu i c k T i m e ™ a n d a
T I F F (Un c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c t u re .
• In an early paper describing this method [Science, 1970, 170,
730-732], there is a note that at equilibrium a small excess of Dalloisoleucine is present (at 140oC they report the ratio of
alloisoleucine to isoleucine is 1.25), but that for most amino
acids the equilibrium constant between the L and D forms is 1.
Why should that be? Why do you suppose it is different for
• Using the expression in question 5 and the parameters given in
the paper, compute the forward rate constant at 144oC. What is
the value of the rate constant for the reverse reaction at this
Winning the Prize
wasn’t half as
exciting as doing the
Maria Goeppert
Nobel Prize winner in
physics (1963)
How old is a whale?
Humans are among the longest-living mammals, with a life-span
on the order of 100 years. Human ages can be verified by
consulting birth and census records. Whales are also
apparently very long-lived, but discovering the age of a
whale is a somewhat more daunting task and the lifespans of most whale species have not been established.
The ages of some whales, such as blue whales and fin
whales can be determined by counting the layers of ear
wax in their inner ears. ….. The degree of racemization
of aspartic acid in the lens of the eye has been used to find
the ages in 20 different species, including humans. Ages
were obtained for 48 different whales, one which had an
apparent age of 211 years [Can. J. Zool. 1999, 77, 571–
580], making the bowheads the longest living mammals
What can you do with an M.D./Ph.D.?
(Bio)chemical kinetics, of course.
Maude Menten (1879-1960) was an early M.D./Ph.D.,
and one of the first women to become a
physician in Canada. …….
Unnatural Amino Acids
Thirty years ago, it was assumed that all amino acid
residues in naturally occurring polypeptides
were in the L-form. We now know there are a
few exceptions. For example, some polypeptide
antibiotics found in fungi incorporate D-amino
acids. It is thought that in most cases the
peptide is synthesized with all L-amino acids,
subsequently individual amino acids undergo
enzymatically catalyzed epimerization. Only
one such epimerase has been identified to date.
The serine epimerase found in the venom of the
funnel spider, Agelenopsis aperta…
Qu i c k T i m e ™ a n d a
T I F F (U n c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c tu re .
Qu i c k T i m e ™ a n d a
T I F F (U n c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c tu re .
Further Reading
There was a time when
the newspapers said that
only twelve men
understood the theory of
relativity. I do not
believe that there ever
was such a time. There
might have been a time
when only one man did,
because he was the only
guy who caught on,
before he wrote his
paper. But after people
read the paper a lot of
people understood the
theory of relativity in
some way or other,
certainly more than
twelve. On the other
hand, I think I can
safely say that nobody
understands quantum
R. Feynman in The
Character of Physical
Law. 1965
• “Reliability of Amino Acid Racemization Dating and
Paleotemperature Analysis on Bones”, M. L. Bender, Nature,
1974, 252, 378-379. “Dr. Bada Replies”, J.L. Bada, ibid.
1974, 252, 379-381. An early controversy over the accuracy
of the dates obtained from amino acid racemization.
• See the whole Chaucerian litany in either Middle English or
Modern English at Want the full
medieval experience? Images of the full text of two 15th
century versions can be found at You
can read the Canon’s Yeoman’s Tale in (almost) its original
form thanks to the British Library.
Further information
E-mail [email protected]
Physics is very
muddled again at
the moment; it is
much too hard for
me anyway, and I
wish I were a
movie comedian or
something like that
and had never heard
anything about
Wolfgang Pauli (19001958) From a letter to
R. Kronig, 25 May
• Marginalia
• Topics
• Solicit and post student
Activation Energy:
The useful quantity of
energy available in
one cup of
Joseph Alia
Swarna Basu
Joseph Brom
Jeanne Bundens
Franklin Chen
Lisa Chirlian
Paul Davis
Raymond Esquerra
Brian Gilbert
Rainer Glaser
Sam Glazier
Alan Goren
Steve Gravelle
Barry Hicks
David Horner
Jerry Jasinski
Kristin Krantzman
Patti Lang
Anne McCoy
Michael Moore
Lynn Melton
Maria Pacheco
Carol Parish
Virginia Pett
Ray Rataiczak
Tracy Schoolcraft
Marcy Towns
Matt Tuchler
Jane Van Doren
John Wheeler
Stephanie Schaertel
Kathleen Howard
Bryn Mawr College
Which picture is of Gibbs?