Physical Measurements and Analysis

PHYSICAL MEASUREMENTS AND ANALYSIS CHEMISTRY 160a,b

GENERAL INSTRUCTIONS

The purpose of this laboratory is twofold. First, it is designed to introduce you to the experimental techniques currently used in research in many fields in which the measurement of physico-chemical properties or the qualitative and quantitative analysis of samples is important. Second, it will enable you to obtain a better understanding of some of the principles discussed in the physical chemistry and analytical chemistry lecture courses. In addition, you will obtain valuable experience in the use of a computer for data processing, statistical analysis, and laboratory automation. Finally, you will begin to learn how one transmits research findings in science in the form of a journal article.

COURSE REQUIREMENTS: Chemistry 160 is normally taken in half-course increments, Chemistry 160a and Chemistry 160b. Chemistry 160a is offered in the fall and 160b in the spring. Since Chemistry 158a or the equivalent in physics is a prerequisite for Chemistry 160b, Chemistry 160a would normally be taken first. However, provided that the prerequisites are satisfied, the two modules can be taken in any order. Starting with the 2006-2007 academic year, Chemistry 160a and 183 will be merged into Chemistry 161, a full course offered in the fall with lecture and laboratory components. Similarly, Chemistry 160b will morph into Chemistry 162. This spring course will have the laboratory material presently in Chemistry 160b. Its lecture material will include statistical mechanics, group theory, and crystallography. A list of available experiments is provided separately; the requirements are as follows:

a) Chemistry 160a, Instrumental Analysis: At the beginning of the semester a series of two lectures on hypothesis testing and ANOVA will be given. An exercise dealing with these topics is assigned and is due two weeks after the completion of the lectures. The six required experiments for the course primarily focus on instrumental analysis and are listed on the sheet entitled “Chemistry 160a, Instrumental Analysis”. The order in which the experiments will be carried out will be different for each student. A schedule for each student will be set at the beginning of the semester. All experiments require a short report and two of these experiments are written up as full reports (see below).

b) Second 1/2 Course (Chemistry 160b): Two lectures on regression techniques are given at the start of the semester. However, in the fall of 2002, the final semester of a transition period, all students enrolled in 160 will cover the material in Chemistry 160a. A statistics exercise is assigned and is due two weeks after the completion of the lectures. The six required experiments for the course primarily focus on experimental physical chemistry and are listed on the sheet entitled “Chemistry 160b, Experimental Physical Chemistry”. The order in which the experiments will be carried out will be different for each student. A schedule for each student will be set at the beginning of the semester. All experiments require a short report and two of these experiments are written up as full reports (see below). The laboratory will be open Tuesday and Thursday from 9:00 to 17:00. Every one must be out of the lab by 17:00 unless permission is granted. Variances on the operating rules are ordinarily granted only when it is impossible to complete the work in the allotted time. When the size of the class exceeds 5-6, students will work in pairs. In either case, students are asked to choose a group from the schedule. Each student should inform the instructor of his/her choice one full week in advance of the scheduled time period. At that time arrange with the instructor a time prior to running the experiment for instruction on the use of the equipment in that experiment.

SAFETY: Walking barefoot or wearing sandals is absolutely forbidden. It is assumed that you are familiar with standard laboratory safety practices. Particular attention must be given to the need for eye protection when handling hazardous chemicals or when working in the vicinity of the vacuum line even is you are not actually working on the vacuum experiment). Do not bring any magnetic materials into the room containing the 400 MHz NMR spectrometer. Failure to treat this rule may result in physical injury to the magnet and the transgressor. If any accident occurs (even a minor one) report this fact to the instructor as soon as possible.

TEXT: The required texts are the ACS Style Guide by Janet S. Dodd and Chemometrics for Analytical Chemistry by James and Jane Miller. A recommended text for 160b is Experiments in Physical Chemistry by Shoemaker et al. Some experiments make page references to this text. The text is organized into two sections. The first part of the book contains the various experiments for the laboratory. The second part contains discussion on the apparatus and methods of the experimental chemistry. Helpful comments about the instruments and techniques used in the laboratory will be found here. This section should be examined even though specific references may not be made to it. (A copy of Experimental Physical Chemistry, Seventh Edition, by Daniels, et al., is available in the library and also provides useful reference material.) A recommended text for 160a that should be in every chemist’s personal library is Principles of Instrumental Analysis by D. Skoog.

LABORATORY WRITE-UPS AND REFERENCE MATERIAL: Write-ups on each experiment including short report forms (see below) are now provided with the lab manual. Read through the procedure thoroughly and be prepared with questions prior to the briefing given by the instructor (see above). For the convenience of the class, several useful reference books have been provided in the laboratory and the student lounge, Seaver North l06. If they are to be equally available to everyone, they must not be removed from the building.

NOTEBOOKS: No laboratory experiment is of much value unless the results are communicated to others. The first part of this communication process in the laboratory notebook. A reprint which discusses the proper use of a notebook is included with the lab manual. All data should be entered in indelible ink directly into a bound notebook in a fairly neat fashion at the time that the experiment is performed. Date the experiment and include any observations and comments which might be helpful in interpreting the data at a later time, i.e., leave nothing to your memory when they time comes to write your report and to interpret your results. Collection of literature data and notes from the references should also be included in your notebook. Carbon copies of all notebook pages as well as all supporting material such as spectra, graphs, sample calculations, and computer printouts must be submitted with each report; the bookstore has a supply of laboratory notebooks which have a convenient arrangement for making carbon copies

2 and should therefore be purchased for this course. Anyone, including the instructor, should be able to make sense out of your notebook entries provided he or she were familiar with the experiment.

COMPUTATIONS: We have standardized on NCSS which is available via the campus network and is installed on PC’s in Seaver North. If the software is not permanently installed on the PC, the user must access NCSS or any other utility, e.g. Maple, via the Novell Applications Launcher. This approach is subject to change; the instructor will make every effort to provide the current protocol as part of the orientation with each experiment.

NCSS has an excellent multiple regression routine that handles well the requirements for I2, MRI, gas adsorption, stopped-flow and AA. NCSS’s non-linear regression routine is needed for the NMR barrier experiment. A spreadsheet approach such as Excel is suitable for the X-ray experiment. In some cases, a hand calculator is the most appropriate technology.

DEADLINES: The schedule for experiments provided with the lab manual is designed so that all experimental work will be completed well before the last week of classes. The exact dates for deadlines are provided on the schedule. Short reports are due two weeks after completion of the experimental work. However, no written work may be submitted after Friday of the last week of classes. In order to receive a passing ground in each module of Chemistry 160, a student must complete all 6 experiments and submit the statistics exercise, all 6 short reports, and both long reports.

REPORTS: Two types of reports will be utilized in this course. One type which we call a "short report" consists of the data sheet supplied with the experimental write-up (in duplicate), the carbon copies of your laboratory notebook pages, any supporting materials, and an experiment evaluation sheet (if you wish to submit one). Be sure to be complete on your short report and give careful attention to reporting values with units to the correct number of significant digits. Also include statistics whenever possible. Literature values are not required as part of the short report.

Short reports are due at 17:00 two weeks after the experiment is finished. Late reports will be penalized a fraction of a letter grade unless the lateness is excused beforehand by the instructor. Unless and excuse is granted, reports handed in 4 weeks after the experiment is completed will not be accepted. A variance will be granted only in cases of instrument or computer failure or personal illness. Experiments will be graded for accuracy, precision, general technique, and quality of the report.

The other is a full report as described below. A long report can be written on any experiment although some experiments, e.g. the vacuum line experiment, are less appropriate for this purpose. To allow time for revisions, follow the deadlines on the schedule. To discourage late papers, the grade on a paper will be reduced one full letter grade for each day that the paper is late. Although a long report can be written on any experiment, the long paper on an experiment should be completed after the instructor has graded your short report so that any errors in theory shown on the short report can be corrected. Consequently, students cannot write a long report on the last experiment. Furthermore, consult the instructor if you wish to write a long report on his/her experiment. The instructor for that experiment will make every effort to grade the short report within a week's time so that you can use the comments in writing your long report. If there is a

3 difficulty in getting the short report back to you in time, an extension of the long report will be given. The grade on the long report will reflect not only an evaluation of the content, including thoroughness and correct interpretation, but also organization, clarity, and writing mechanics. When the paper has stylistic flaws, it will be returned for revision. In that case, the grade for the paper is that assigned to the revised paper. In some cases a revision may be required to receive a grade. To repeat, the long reports must be submitted in time to allow for grading and revision.

FORM FOR LONG REPORTS: Our desire in this course is for you to begin to learn how to write in a manner acceptable for the scientific literature. As such, your long reports are to be in the form of a journal article in the field appropriate for the experiment concerned. For a general discussion on report writing, consult the ACS Style Guide. More specific information is found in the manuscript requirements for the journals Analytical Chemistry and the Journal of Physical Chemistry which are provided to you for guidance. Refer to the appropriate description of requirements for the type of experiment about which you are writing. It is a good idea to read a few articles in these two journals to get an idea of the proper form we expect in these papers. The reports should be typewritten, and as brief as possible, but should contain in a clear and meaningful form the following items:

1. Title Page. This should include the title of the paper and your name. You are the co-author of the paper but assistance from others may be recognized in the Acknowledgements section at the close.

2. Abstract. Prepare a one-paragraph statement of the goals of your study and the most important results. This is often called an Executive Summary.

3. Introduction: This section should state the purpose of the experiment. State what you measured and what the measurement allowed you to determine. An encyclopedic review of the literature is not recommended.

4. Theoretical principles involved in the experiment. Indicate limitations and assumptions, but do not give a textbook description of theory. Be brief.

5. Procedure and Apparatus: State the equipment used and conditions you used when running the experiment. There should be enough detail to allow another researcher to duplicate your results. Omit details of procedures that are inconsequential or common knowledge. If this detail is commonly known, cite it, but do not describe it in detail. Give references to the procedure followed and to a discussion and description of the apparatus used.

6. Experimental Data. Tabulate experimental data and calculated results in a concise and clearly labeled form. The print-out sheets from the computer, with appropriate additions and editing, can be transformed into acceptable tables. A cut-and-paste operation, if performed neatly, is acceptable; submission of unedited printouts is not. If a graph is used to present data do not list the values for the points on the graph, but do indicate the points plainly. Put only related curves on the same graph. Choose your coordinates in such a way that the curve will fill out the graph but at the same time avoid expansion of the coordinates beyond the

4 significance of the data and avoid the use of inconvenient divisions of the printed grid. Do not extrapolate your curve indefinitely to regions of unknown experimental response, but do extrapolate to zero when significant. Normally use the computer to generate your graphs. Graphs which must be done by hand should be made on mm graph paper. Use log-log or semi-log paper when it is more convenient. Graph paper is available at the stockroom.

5. Statistics. The statistical analysis of your data will be discussed in class. Experimental results are practically meaningless without this analysis.

6. Source and direction of experimental errors. Do not merely put down two or three of the more obvious errors and feel that you have done a good job. If an error can be plus or minus, state it as such but specifically state the direction of error for either plus or minus. A propagation-of-errors analysis can be quite informative. A thorough discussion of experimental uncertainty generally shows an understanding of the chemical principles and the experimental method.

7. Interpretation of the results. This is the heart of the paper. In some experiments, especially the spectroscopic experiments, one can discuss the significance of the results. Are the data self consistent? What does it allow one to conclude about the universe?

8. Comparison of data with the primary literature. Whenever possible compare your results with data given in the primary literature. The papers provide the opportunity to employ serious search engines such as SciFinder Scholar and Web of Science. The instructors take a very dim view of papers that substitute URL’s for full citations to journal articles. References to secondary sources such as Beilstein, Gemelin or a CRC Handbook are not acceptable. These secondary sources can be helpful in tracking down a primary source. Secondary sources are acceptable only if the issuing agency has critically analyzed the assembled data. Compilations of the National Institute of Standards and Technology (formerly the U.S. National Bureau of Standards)are acceptable in this respect. Be sure to indicate in your report both the literature data and the source.

9. References. Each citation should include the following information: names of the authors, full title of the paper, abbreviation of the journal, year of publication, full page range, and volume number. Include the names of all the authors; et al. is not acceptable in the bibliography of a formal paper although some respectable journals have been reduced to this barbarism in order to save space. Give the first and middle (if available) initials of each author. Scientific papers combine the footnote and bibliographic sections of a paper. If a paper is referenced more than once, do not use Ibid. but simply repeat the citation number used the first time. That is, if 7 papers are referenced, only the numbers 1-7 are used to cite the references. Refer to the manuscript requirements for the proper form of the reference. c160syl.doc, 1 August 2002