Intermediate Laboratory 2 CHEM 373

Wednesday 1 - 4 pm

Spring 2000

Dr. Linda M. Sweeting, SM 553, ext 3113

http://www.towson.edu/~sweeting

office hours: after class or by appointment

The purpose of this laboratory is two-fold:

1. To provide theoretical and laboratory experience in the techniques of NMR, GC-MS, IR and molecular modeling sufficient for you to use them in independent investigations in the future. Such experience includes the investigation of experimental parameters and pitfalls.

2. To continue your transformation from "follower of instructions" to "creator of experimental methods" by giving you a chance to write instructions and explore instruments while providing you some instruction in scientific communication.

To achieve these goals you will be given lectures on the experimental methods (see your textbook), and divided into teams to examine a simple unknown compound by these techniques. In the process you will also complete some instructional exercises in each technique. Because almost all the instruments are new, each team will be given some responsibility for developing or improving instructions for one instrument. You will write a brief report on each technique and what you learned about parameters as well as your unknown and a final report on what you learned about the compound.

My philosophy:

Having spent much of my career doing NMR, I have a real appreciation for the importance of understanding the theory and of having practical experience with instrument maintenance, adjustment and parameter selection to obtain "good" data, i.e., data that represents reality. On the other hand, this kind of appreciation cannot be developed in a 1-credit, 3-hour course. It is my intention that with competent (not heroic) planning and effective use of time, all of the experiments can be done in the time allotted. Because the NMR and MS are delicate and require a great deal of assistance to learn, we may have to schedule some groups to start a little early and others a little late in order to provide sufficient assistance, but I promise you that this course will be manageable. The only technique that might take more time than is allotted is NMR. The teams will need to have a regular meeting time outside of class to share data and write reports; I recommend just before or just after class to ensure that any part-time students are included.

Lectures:

Text: Joseph B. Lambert, Herbert F. Shurvell, David A. Lightner, R. Graham Cooks, Organic Structural Spectroscopy, Prentice-Hall, Inc., Englewood Cliffs, NJ, 1998. This text was chosen because it is a "keeper". The instrumental methods and data interpretation you have already learned are here in greater detail, but this book discussed related techniques such as Raman spectroscopy, the "mirror image" to infrared, and a wide variety of NMR and IR methods. Because of the breadth of techniques, this book will be useful to you in Instrumental Analysis and your career beyond Towson.

The lectures will focus on how the instruments work and how instrumental parameters affect the data. You will be required to interpret the spectroscopic data in your report, but interpretation will not be discussed in the brief lectures. A level of interpretation comparable to that in your organic-chemistry text will be satisfactory; extra credit will be given for interpretation of anomalies or fine details of the spectral data using Lambert et al.

The Teams:

There are advantages and disadvantages to working in teams. It is true even in real life that not every member of the team pulls their weight. Thus students often do not like working in teams, lest their good work be diluted by a weak team-mate and their grade be reduced. Thus the student preference is to choose their own team-mates. However, this is not always fair either, because a transfer student might not be aware of who the weak team-mates are. I can tell you from experience that in the real world you do not get to choose your team-mates. However, in the real world, not all members of the team get equal credit, either. So I have concluded that the fairest and most productive way to create student teams is for me to choose them, and for the team members to provide an evaluation of each others' contribution to the finished product (reports). Members of the teams will not necessarily get the same grades. Once the teams are established, each team will be given an opportunity to put in a request for the order in which they do the experiments; the first experiment for each will involve developing instructions for the other teams.

The purpose of the course for each member of the team is the same. Thus each member of the team must participate in both data collection and report-writing, although not necessarily for each of the four experiments. At the end of the report, your acknowledgements will include an extra section stating the responsibilities of each member of the team for that part. You may wish to select a permanent team leader, or rotate the job so that each person has the experience. The team leader will be responsible for calling any meetings of the team to work on reports, share data, etc. I suggest that you give primary responsibility for each aspect of the process to one person; aspects needing a "point person" might be: laboratory record (notebook), instrument expertise, data interpretation, figure and table preparation, first draft of report, editing. Because of the possibility of illness, etc., I strongly recommend that more than one team member (perhaps all) keep electronic or paper copies of all the data and interim research reports.

Unknowns:

Each group will be given a fairly simple organic compound, one whose structure will be easy to determine (MS and NMR should tell all, and IR tell most). Your final report will give the evidence for the structure of the unknown and information (e.g. purity) you have uncovered in addition to the structure. You may use confirmatory techniques (e.g. mp) you have learned in other courses, but you are not to inconvenience other faculty members in obtaining it (by inconveniencing, I mean, asking them to let you into labs, since by so doing they must take responsibility for your safety). George Kram or I will give you the access you need if you come to us with a specific proposal, or refuse it if the experiment you plan is unsafe or not time-effective.

Exercises and Experiments:

1. Writing.

Go to the library and find a full paper in the Journal of the American Chemical Society (affectionately known as JACS). Choose one that has an Experimental Section with spectroscopic data so you can use it as a model for this course. Make a copy and read the paper as best you can, trying to understand the organization. How does it differ from the description attached? Use it as a model for your References and Experimental Section. Now find a full article in Science, copy it and mark the hidden sections.

The verbs in each section should be characteristic of the content of each section. For example, the expermental section might contain the verbs "analyzed" or "measured" and the results section the verbs "found" or "observed". Identify the verbs that are indicative of the section they are in and any that seem to belong elsewhere (mark them differently).

2. IR, NMR, MS.

For each, you will be given a draft of instructions. The first group to work on each instrument will have the primary responsibility of (re)writing the instructions for the subsequent groups. This will be your first research report and must be turned in early enough to be useful to the next group. The NMR instructions are the most complete, and may not need much modification, but they will need checking. For all others, instructions must be submitted on disk. You will be given instruction on varying the instrumental conditions to explore how they affect the appearance of the spectrum. For instruments after the first, the focus of your report will be the effect of instrumental conditions on the data, plus the information you collected on the unknown.

3. Molecular modelling.

The instructions for this are fairly complete but any corrections or improvements will be welcome (and receive appropriate credit). The initial exercises are designed to illustrate how molecular computations are done and how they can lead you astray. The computations on your unknown cannot be done until you have a good idea what it is.

The basic program used is called HyperChem, which does both molecular mechanics and quantum mechanics; we will do only molecular mechanics. It has an add-on called HyperNMR which will calculate the NMR spectrum of the calculated conformation. In addition, once you have the chemical shifts and coupling constants, you can also use Acorn Nuts to simulate an NMR spectrometer and calculate the spectrum using a different algorithm.

These experiments are not scheduled into a time slot. You will have time to work on them after the lecture classes; if you wish, you may work on them outside of class time, but most of the other experiments will not consume the 3 weeks allotted and thus will give you a chance to work on the modelling. Don't forget that each of you needs to learn how to do the computations, so do it together.

4. Other

You may collect other information about the unknowns such as mp or bp. You must go to the library or other sources and find further information about the material, e.g. a literature mp or bp for comparison. In particular, you must find the Material Safety Data Sheet for your unknown and comment in your final report on safe handling of the material.

Reports and Other Paperwork

Each team will have at least one laboratory notebook. One person will be responsible for this notebook at all times, and the other members of the team will know where the notebook is. All entries made in the notebook must have a clear identification of the person who made the entry. Buy a notebook like the ones we use for Organic Chemistry which allows copies to be made and make sure the copies are in the hands of a different member of the team. Never leave the building without ensuring that copies of the notebook are in the hands of at least two members of the team. Alternatively, you may leave the notebook in a secure but accessible location in the building that each of you has access to.

Please refer to the attached description of a scientific paper. For each assigned technique, you will generate a Research Report which discusses both what you learned about the instrumental method and what you learned about the unknown; attach to this report a copy of your notebook pages. Please note that spectral data without the acquisition parameters are unacceptable (see description of paper below). When you have completed all the experiments, you will turn in a final report in the style of a Full Paper just on the unknown itself. In preparation for the final report, I suggest that each of you keep a copy of the data and the Research Reports. Don't forget the safety assignment. Report writing MUST be rotated among the members of the group. In fact, I strongly suggest that one person draft the report and others provide editorial suggestions for improvement in each case. I will give you sufficient time to do this, except for the instructions, for which the needs of the next group create an inflexible deadline.

Schedule CHEM 373 Spring 2000

The first few assignments are reading assignments in your text. I have assigned only the sections of the book on the theory and practical aspects of the techniques. You will no doubt need to read parts of the rest of the book to analyze the spectrum of your unknown; the text thus also serves as a reference book on spectral interpretation.

The three weeks assigned for each experiment should be more than enough time to complete each; the NMR experiment will take a little longer because of the complexity of the instrument -- it just takes time to learn how to use it. Use the intervening time to work on the modelling and on the reports. Note that Research Reports are due ONE WEEK after the experiment is complete; in all cases you can begin the report before you complete the experiment, since the discussion section is fairly small.

During the first class, you will submit requests for the order in which you do the experiments. I will compare the requests and give every team the clsoest I can to their first choice. I will announce the order of experiments at the second class. Fill in your group's assigned experiments 1 - 3 in the boxes provided.


Date: Experiment Scheduled / Assignments Due

Feb 2: Introduction, Library, Molecular Modelling, the Fourier Transform

Feb 9: FT NMR / Read LSLC 1, 2, 5.1 - 5.6

Feb 16: MS, FTIR / Read LSLC 13.1 - 13.4, 7.1 - 7.6, 7.9

Feb 23 expt 1 / Library exercise due

Mar 1: expt 1

Mar 8: expt 1 / instructions for first instrument due

Mar 15: expt 2 / expt 1 Research Report due

Mar 22: Spring Break

Mar 29: expt 2

Apr 5: expt 2

Apr 12: expt 3 / expt 2 Research Report due

Apr 19: expt 3 / Mol. Model Research Report due

Apr 26: expt 3

May 3: disaster buffer, makeups / expt 3 Research Report due

May 10: disaster buffer, makeups / Full Paper on all experiments due


Components of a Full Research Paper in Science

First some comments. Most of the papers in the scientific literature are not read in great detail by very many people. One of your most important tasks in writing a paper is to provide enough information in the Title, Abstract, Figures and Tables to give people an overview so that they can decide whether the want to or need to read it. Ideally, these parts of your paper will attract readers.

1. Title

It should describe the study and may even be in the form of a sentence.

2. Authors

All those making substantive contribution to the planning, execution, analysis and writing of the project should be listed, in order of decreasing contribution, with their work addresses. Usually the person who did the writing had to do most of the analysis and thus is listed first.

3. Abstract

This is a brief summary of the entire paper, ideally in about three sentences: purpose, methods and results. A fourth might describe what you think it means. The abstract is very important, since on-line searches use title and abstract for keywords (some journals ask for other keywords as well).

4. Introduction

Here you describe the background of the project, previous work and the problem you are trying to solve. This section is likely to have the most references, because it puts the paper in the context of related work. Usually, the introduction ends with a brief summary of what you did ("In this paper we report the results of ... and propose a new theory to explain... "). Once again, you are trying to keep the person reading.

5. Experimental Section

This part of the paper is often divided into Materials and Methods subsections, which may be further subdivided as needed. This section contains everything a reader would need to know to replicate the experiment. Materials should be identified by source (and lot number), instruments by brand and model and all relevant conditions for the experiments should be described. For each instrument used, all the settings needed to replicate the spectrum must be given. Synthetic apparatus need not be described in detail if it is standard (e.g. reflux) but the temperature, solvent, time and neutralization and purification must be described. Spectroscopic (e.g. NMR spectrum) and physical characteristics (e.g. MP) of new compounds are also described in this section.

6. Results

This part of the paper is often very short, and consists of a brief description of the outcome of the experiments, augmented by the judicious choice of tables and figures (graphs) to present the results in the most efficient way. If necessary, it maybe divided into sections. It is always necessary to say something about what experiments were done in this section, because most people will not read the Experimental Section unless they are really interested or want to repeat the experiments.

All Figures and Tables should be numbered in the order in which they appear in the paper, one set of sequence numbers for each. Each must have a caption at the top, e.g. "Figure 1. Title 1"; an excellent figure or table makes it unnecessary to read the text to understand its content. Use a table when you can to replace narrative, and use a figure when you can to replace a table; pictures communicate more effectively than words, especially to the busy people reading your work.

7. Discussion

Tell the reader what you think the Results mean. To do so, you will refer to the Figures and Tables and compare your results with information already in the literature. If you have complex computations applied to the data, the methods are described here. This is one of the most difficult parts to write, because you are often figuring out what the data means while you are writing it. This part is usually the longest, although the length varies with the type of study. It too may be divided into sections, and it would help the reader if the sections paralleled any you created in the Results

You may need to introduce additional Tables and Figures in this part which provide analysis of the results. Say as much as you need to make sense of the results, but don't try to make it long to impress people. What impresses reviewers and editors is the ability to tell your story clearly and succinctly.

8. Conclusions

This part of the paper is optional. It is only used if the results and discussion have a lot of sections, to summarize the overall discussion and tie everything together.

9. Acknowledgements

While you were doing these experiments, people helped you with instruments, laboratory techniques, and discussion of principles. Their contribution may not merit authorship, but certainly merits recognition. Do it here.

10. References

This is the section where you effectively thank the people whose written work helped you to devise your experiments and understand your results by citing their work. All written sources should be here, not as a random or alphabetical list but linked to the paper by a proper citation. There are two common styles (detail in each journal): 1) numbers, both in text and in this list, and in order of appearance in the text (ACS journals) or 2) name of author and year in text and alphabetical order in this list (most biochemistry journals). Page numbers are usually needed for books, but not for journal articles.

Other Types of Paperwork Styles

For More Detailed Information:

  1. Howard M. Kanare, Writing the Laboratory Notebook, American Chemical Society, Washington, DC, 1985. An excellent guide for chemists.

  2. David Porush, A Brief Guide to Writing about Science, HarperCollins College Publishers, New York, 1996. Writing for scientific and non-scientific audiences. TU bookstore.

  3. Janet S. Dodd, Ed. The ACS Style Guide, A Manual for Authors and Editors, American Chemical Society, Washington, DC, 1986. All the formatting rules.

  4. Edward R. Tufte, The Visual Display of Quantitative Information, Graphics Press, Cheshire, CT, 1983. An art and science book about how to tell the truth and lies effectively with figures.

LMS January 2000