Chemistry 455: Integrated Laboratory
Fall, 2014
Meets: Tuesdays at 2:00 – 5:00 PM in Musser 232/Musser 215.
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 at 2:00 – 3:30 PM and Thursdays at 9:30 –
11:00 AM. If this is inconvenient for you, you can often catch me at a different
time or we can make a specific appointment.
Structure of the course: This is a laboratory course and its structure, therefore, is similar to that of other laboratory courses which you have taken. We will meet once
each week, either in a classroom or a laboratory (or both). There will be discussions of experimental objectives, design, and theory. We will be carrying out experiments in the laboratory which may be of a synthetic or analytical nature. We
will be analyzing and discussing the results of those experiments. We will be
drawing conclusions from what we’ve learned and then suggesting additional
work to be done.
What distinguishes this course from the others is its content. In the lower level
courses, you were presented with experimental exercises with the main purpose of
teaching you specific laboratory techniques and/or analytical tools. A variety of
these experiments gave you a well-rounded survey of these techniques. This
course is a bit different in that it will explore a single research question. You will
be expected to apply the techniques you have learned in your other courses, but
there will be new techniques as well. However, the focus of the coursework is not
learning new techniques, but rather answering the research question. Learning
new material is simply needed to make progress towards this goal.
Another distinguishing feature of this course is that it is not tied to one particular
area of chemistry. Chemistry is a vast subject and we tend to compartmentalize it
into separate areas in order to provide more easily “digested” chunks. The traditional areas are: organic chemistry, inorganic chemistry, biochemistry, analytical
chemistry, and physical chemistry. It is not difficult to find other areas as well.*
These areas are distinguished by the types of compounds that are investigated or
the specific investigational methods that are used. However, a particular chemical
system does not always fall neatly into one category or another. Iron porphyrin
can be studied in inorganic chemistry, since it contains a transition metal ion
complexed with a ligand. However, the porphyrin ring qualifies as an organic
compound and the concepts of organic chemistry are expected to apply as well.
*
Nuclear chemistry and medicinal chemistry are two particular cases. Biological chemistry is a newer field
that has become more prominent in recent years. If you think about it, though, trying to disentangle these
fields from the traditional ones is not so easy to do.
Finally, the fact that such complexes are found in hemoglobin would make this
compound an appropriate system for study in biochemistry. We cannot pigeonhole this compound into just one of the areas of chemistry. At the same time, the
techniques that are used in analytical chemistry or physical chemistry are just as
easily applied to one type of chemical system as to another. And, the concepts of
physical chemistry are often tied in closely with those of analytical chemistry.
The boundaries we place on these areas are artificial and when research is done on
chemical systems, these boundaries become blurred. Research in chemistry draws
on all areas and one purpose of this course is to illustrate this concept.
This course will focus on a particular research problem and it is our task this semester to try to probe this problem with the variety of laboratory techniques you
have already learned. As we progress, it may turn out that we will need additional
techniques and we will need to learn those as well. You will have your experiences in other courses, the literature, and the faculty in the department (and elsewhere) to draw on to help you progress on this research problem. I don’t know
where we’ll end up, but we should have fun getting there. That’s the nature of research.
Upon completion of this course, you are expected to be able to:

Integrate concepts from the various areas of chemistry to investigate a particular research problem.

Design, execute, and interpret experiments to study chemical systems.

Communicate chemical knowledge.
The project: The research problem this semester will be associated with the binding of
transition metal complexes to DNA. The project is based on a recent article in the
Journal of Chemical Education.† It is well known that certain metal complexes
have medicinal value,‡ an important class being anticancer drugs. The binding to
DNA is an important property for these drugs and the strength of the binding is
found to affect the usefulness of such drugs. The strength of binding is characterized by the binding constant, the equilibrium constant associated with the bound
and unbound complex in solution. This project will focus on measuring this
property for several metal complexes.
There are many different metal complexes possible, each presumably with its own
binding strength to DNA. One thing that is not fully understood is just what factors of the metal complex cause the complex to bind more strongly or weakly.
The charge of the ion, the ion’s size, and the size and shape of the ligand are all
factors that could affect this behavior. You will have a chance to hypothesize
which factors will have an effect and what effect they will have. And then you
can test those hypotheses.
†
A. Kulczynska, R. Johnson, T. Frost, and L. D. Margerum, How Do Structure and Charge Affect MetalComplex Binding to DNA? An Upper-Division Integrated Laboratory Project Using Cyclic Voltammetry,
J. Chem. Ed. 88, 801-805 (2011)
‡
J. Reedijk, Medicinal Applications of Metal Complexes Binding to Biological Macromolecules, Macromol. Symp. 270, 193-201 (2008).
The following is a rough schedule of the work to be done. We will start with an
overview of the research problem to be investigated. I will provide a preliminary
reference for the research topic and then it will be your job to search the literature
for related papers. We’ll get together to discuss what was found in the literature
and try to identify common themes. We can then discuss the next steps of the
project. Clearly, we will need to synthesize some metal complexes. There are
several salts and ligands available that we can use for that purpose. It will be necessary, though, to find a synthetic procedure for making the specific complexes.
A literature search would be in order here. We might also avail ourselves of a
resident expert in inorganic synthesis. We will most likely split up into groups of
2 or 3 students for this and following stages, although we will pool results in the
end.
The next step involves complexation with DNA. How to handle DNA and how to
characterize it will be important things to know here. Again, a search of the literature or consultation with a resident expert may turn up useful information. Once
we can bind the complex to DNA, we will need to measure the binding constant.
I have in mind the use of cyclic voltammetry for this purpose (as suggested in the
J. Chem. Ed. article). You may find in the literature that there are other methods
that can also measure this property and you are encouraged to try them as well. In
fact, this will provide valuable verification of the results obtained. I suspect that
you are not so familiar with cyclic voltammetry and so, another trip to the literature and/or resident expert is in order. It will be necessary to interpret our results
in order to obtain the desired binding constants. It is not straightforward and
some theory will need to be developed. As you might have guessed, another trip
to the literature and/or resident expert will need to be undertaken.
Once we have a set of results, we can get together to discuss them. Each group
will report their results and an open discussion will follow with the idea of arriving at some conclusions – and suggestions for further work. If there is sufficient
time, further experimental work may be warranted. Alternatively, this work may
continue into the spring semester. In the end, each of you will put together a research report in the form of a journal manuscript. You will need to introduce the
topic, describe what was done in sufficient detail, present your results and analysis, and discuss them. You should present justifiable conclusions and reasonable
suggestions for further work.
Grading: There are several ingredients that will go into your grade. In short, they are:

Notebook – You are expected to maintain an organized and complete
notebook.

Participation in literature/research discussions – There are several occasions where the literature is to be consulted. This may be an assignment
for everyone or a group of students may be assigned the task. You are expected to search the literature and find pertinent references for our discussions. You are also expected to participate in the discussions in class.

Your results – The quality of your results will play a role in your grade. If
an experiment does not work, you are expected to figure out why and repeat it, correcting any procedural flaws as needed.

Group report – Each group will be making a presentation of their results.
You are all expected to contribute to this effort.

Final manuscript – Your final paper will be a summary of the semester’s
efforts. It should be written as if the reader were unfamiliar with the experiments performed. Therefore, how you communicate your work will
be an important factor.
There is not a rigid point count for each contribution, but they will all contribute
to some extent. I want to see an honest effort, thoughtful analysis, true learning,
and clear communication.
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.