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Chemistry 343: Atomic and Molecular
Structure
Fall, 2016
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 100A, 361-1241, [email protected].
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. Monday, Oct. 10, 2016
2. Friday, Nov. 18, 2016
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: Friday, Dec. 16, 2016 at 7:30 – 10:30 AM. 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” indicates 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.
Statement on school closure: In the event that the college closes or is delayed such that
class is cancelled, the instructor will notify you by e-mail with details of an assignment to be performed for the following class.
Attendance Policy: Attendance will not be taken, so there is no direct penalty for missing
class. However, classes are beneficial for you in that the course material is presented in a logical format, emphasizing those concepts that are important. You
would be only hurting yourself by not attending class.
Make-up policy: In general, if you miss an exam, the consequence is a zero on that exam.
It is recognized that occasions arise where attending an exam is not possible. In
such a situation, it is your responsibility to demonstrate this. You must first contact
me before the exam, letting me know that you will not be attending and providing
the reason. Afterward, you are expected to provide documentation (doctor’s note,
accident report, arrest warrant, etc.). This must be done as soon as possible, before
the next class. With an acceptable excuse, I may give an excused absence – the
other exam scores will be used to obtain an average. Alternatively, I will write a
different exam and you will have to take that – before the next class.
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 direct 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.
If there is time, 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 [email protected]. 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.
COURSE SYLLABUS STATEMENT ON RELIGIOUS OBSERVANCES
The College is willing to accommodate individual religious beliefs and practices. It is your responsibility to meet with the class instructor in advance to request accommodation related to
your religious observances that may conflict with this class, and to make appropriate plans to
make up any missed work.
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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
Exam 1
••••••••••••••••••••••••
Many-electron atoms
4
Molecules
5
Symmetry
6
••••••••••••••••••••••••
Exam 2
••••••••••••••••••••••••
Spectroscopy
••••••••••••••••••••••
7-9
Final Exam
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