Chemistry 343: Atomic and Molecular
Structure
Fall, 2015
Meets: Lecture – Mondays, Wednesdays, and Fridays at 9:30 – 10:30 AM in Musser
232.
Laboratory – Tuesdays at 8:00 – 11:00 PM in Musser 232/Musser 215.
Text: A. Cooksy, Physical Chemistry, Quantum Chemistry and Molecular Interactions,
(Pearson, Boston, 2014).
Instructor: Gary G. Hoffman, Musser 224, 361-1241, hoffmang@etown.edu.
Web Page: http://users.etown.edu/h/hoffmang
Office Hours: I am available much of the time during the week, but I will make a point
of being in my office on Mondays and Wednesdays at 2:00 – 3:30 PM. If this is
inconvenient for you, we can make an appointment for a different time.
Exams: There will be two in-class exams during the semester. They are planned for
1. Friday, Oct. 2, 2015
2. Friday, Nov. 13, 2015
These dates assume a certain rate of coverage of the material. If this rate is different than expected, these dates may change. I will provide at least a week’s notice if this happens.
Final exam: Monday, Dec. 7, 2015 at 2:30 – 5:30 PM. This will be a comprehensive
exam.
Problem assignments: Problems will be assigned as we go along. Often, problems will
be assigned at the end of one class to be turned in at the next class, although some
assignments may be given extra time for completion.
Laboratory component: This course includes a laboratory component, which consists of
both a lecture and an in-lab portion. Handouts will be provided for the lab exercises and I will cover background material in the lecture portion. Assignments
earlier in the semester will be in the form of specific tasks, the results of which
you are to submit. Later in the semester, experiments will be performed in which
data are collected, analyzed, and interpreted. Formal lab reports are to be submitted for these exercises.
Grading: Towards the final grade, the problem sets will contribute 200 points total (the
actual grades received may have to be renormalized to achieve this), each in-class
exam will contribute 100 points, the laboratory component will contribute 200
points, and the final exam will contribute 200 points. The key ingredient for a
passing grade is a demonstrated understanding of the concepts. This will be taken
into account when arriving at the final grade. Qualitatively, a grade of “A” indi-
cates work that is outstanding, showing a complete understanding of the material
and the ability to synthesize it in creative ways. A grade of “B” indicates an understanding of the material and a demonstrated competence in solving problems
based on it. A grade of “C” indicates an understanding of the material, although
there are some difficulties in applying it. A grade of “D” shows an incomplete
understanding of the material, never mind problem solving abilities. A grade of
“F” indicates someone who lacks any understanding.
Prerequisites: Physics 201, College Physics II, Mathematics 122, Calculus II.
Structure of the course: This course and its partner, Ch 344, Physical Chemistry of
Matter, present the fundamental laws that govern chemical phenomena. Instead
of being content with a catalog of what happens in a chemical system or how it
happens, physical chemistry focuses on why it happens.

Ethene and tetrafluoroethene have very similar structures; their Lewis structures are very nearly the same. Yet, tetrafluoroethene reacts explosively when
exposed to oxygen, while ethene remains unaffected without some kind of
spark. Why?

Sodium chloride and silver chloride have the same crystal structure with very
similar cell dimensions. Sodium ions and silver ions have very nearly the
same ionic radius. Yet, as we learn in general chemistry, sodium chloride is
very soluble, but silver chloride is not. Why?

The protein, hemoglobin, will pick up four oxygen molecules when it is in the
lungs, but then give them up when in the vicinity of cells which need the molecules. Why?

Metalloporphyrins found in the geological setting (in petroleum and shale
samples, in particular) contain exclusively nickel and vanadium. However,
other metals can form more stable complexes, complexes with other metals
are more easily formed, and some other metals are more abundant in the geosphere. Why are only nickel and vanadium found in these geological samples?

A long chain of amino acids can orient itself in a huge number of different,
stable ways, yet in a biological system, only one structure is normally found.
Why? Further, can we predict what that one structure is?
We can be confident in the observations given, but we still do not have answers to
why they occur. Such an answer requires a fundamental understanding of the system on which the observation is made. These are chemical systems, built up from
molecules. So, to understand them requires understanding what goes on at the
molecular level. In addition, we must understand how the behavior at the molecular level translates to behavior at the bulk level. This two-semester physical
chemistry sequence follows this chain of reasoning, starting with an understanding of the behavior of individual molecules and then putting them together to
form a bulk chemical system.
The first semester focuses on the atomic and molecular level, for which quantum
mechanics must be applied. The fundamental theory will be briefly presented and
we will go on right away to practical applications of the theory. After attaining an
understanding of the general characteristics of the results of quantum theory, the
application to atoms and then molecules will be presented in some detail. Computational methods used and general consequences of the theory will be emphasized. The most obvious consequence for the chemist is the nature of spectroscopic measurements. A study of the different forms of spectroscopy and their
analysis with the tools of quantum mechanics will be presented towards the end of
the semester. We will finish the semester with an investigation of the interactions
that occur between molecules. An understanding of these interactions will be important for understanding the properties of bulk chemical systems which we will
take up in Ch 344.
The laboratory component of this course will give you a chance to see the consequences of quantum mechanics first-hand. Early in the semester, time will be
spent on the proper treatment of data and its presentation. You have seen much of
this already in other courses, but we will explore these topics in greater depth, at a
level appropriate for work which would be submitted to a scientific publication.
Later in the semester, experiments will be performed that involve the application
of quantum mechanics. Electronic structure calculations will be performed on a
number of systems, giving the student enough experience to be able to apply these
methods to general systems of interest. The student may wish to use these methods to study the molecules that they will encounter in research they perform subsequently. We will also begin to perform experiments involving spectroscopy.
Additional spectroscopic experiments will be performed in the second semester
course, Ch 344L.
After taking this course, the student is expected to be able to:

Explain chemical phenomena on the basis of quantum mechanics.

Perform electronic structure calculations on atoms or molecules of interest.
This involves both submitting a job and interpreting the results.

Interpret spectra from a quantum mechanical perspective.
I intend to present much of the course material in the form of lectures. These lectures will not necessarily be exhaustive, though. It is expected that you will have
read the necessary material before coming to class and I expect you to have at
least a rough familiarity with what is to be covered. My job is to help you master
the material, putting things in their proper perspective and suggesting alternative
viewpoints that might help you make sense of some of the more subtle ideas. For
everyone to benefit, it is imperative for both the teacher and students to come to
class prepared.
At the same time, I expect some participation in the classroom. Some (or much)
of what you read may not make sense at first. Write down questions as they come
to you during your reading and bring them to class with you. If we engage in
some dialog during class, we can make sure that we focus attention on just those
points that are causing confusion. I also welcome philosophical comments and
questions. Quantum theory can be bizarre and counter-intuitive at times! Trying
to interpret it on a philosophical basis has been an active pursuit of scientists ever
since it was first formulated in the 1920’s. In fact, no one has really come up with
a philosophical interpretation that is universally accepted. Discussions at this level can be fascinating.
I will also ask you questions during class. Much of what is covered will build on
what we’ve done previously (or what you’ve seen in other courses). I expect you
to be able to perform some analysis of the course material without my having to
simply present it to you. Responding to such questions will get you thinking
about what is being presented, placing it in proper context, and will help you understand it better.
Much of your time in this course will be spent on the assigned problems. The
concepts are presented in the readings and in class but they don’t really sink in
until you actually use them. The problems are intended to give you the chance to
do that. It is therefore important for you to put some effort into solving them.
Remember: the point of an assigned problem is not just to come up with the correct answer, but for you to able to figure out how to get the answer. The better
able you are to work out the solutions yourself, the better prepared you will be for
the exams and the better able you will be to apply the concepts of this course to
future scientific endeavors. Sometimes you will be stumped and some discussion
with others will help get you on the right track. This is fine. I think that discussion of ideas among classmates is a beneficial thing. However, make sure that
such exchanges really are discussions. Don’t simply ask for or give answers.
This does not provide any help in the long run. Further, the solutions to the problems must be written up independently and in your own words. If I see identical
solutions to a problem, I will assume it to have been written up collaboratively. I
view this as academic dishonesty and will treat it accordingly. I expect all students to be familiar with the College’s policy on academic integrity and to agree
“to be honest and to uphold integrity” with respect to all submitted work in this
course.
COURSE SYLLABUS STATEMENT ON DISABILITY
Elizabethtown College welcomes otherwise qualified students with disabilities to
participate in all of its courses, programs, services, and activities. If you have a
documented disability and would like to request accommodations in order to access course material, activities, or requirements, please contact the Director of
Disability Services, Lynne Davies, by phone (361-1227) or e-mail daviesl@etown.edu. If your documentation meets the college’s documentation
guidelines, you will be given a letter from Disability Services for each of your
professors. Students experiencing certain documented temporary conditions, such
as post-concussive symptoms, may also qualify for temporary academic accommodations and adjustments. As early as possible in the semester, set up an appointment to meet with me, the instructor, to discuss the academic adjustments
specified in your accommodations letter as they pertain to my class.
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A rough outline of what is to be covered is given below. Also indicated are the
associated chapters in the textbook and the placement of the exams.
Rough Outline
Topic
Chapter
Review of mathematics and physics
A
Quantum mechanics and the wave equation
1-2
One-electron atoms
3
Many-electron atoms
4
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Exam 1
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Molecules
5
Symmetry
6
Spectroscopy
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7-9
Exam 2
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Intermolecular forces
10
Bulk systems
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11-13
Final Exam
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