Common Practices and Procedures Not Found in the Text

Experiments are reported an informal style, yet the information is complete. Organization of the data provides not only a clear but also a logical report. In the Example Tables below a format is given that is used in several of the experiments in this and future courses.

Example Reaction Table

This is a reaction with stoichiometry more complex than you will encounter in this course, but the example is instructive. The ultimate goal is to determine the theoretical yield, given the amounts of reactants. Pyridine (C₅H₅N) is converted with CrO₃ and HCl to form an intermediate compound, pyridinium chlorochromate, that is then used to oxidize 1-decanol (C₉H₁₉CH₂ OH) to decanal (C₉H₁₉CHO). The overall reaction may be written without needing to write the formula for pyridinium chlorochromate: C₅H₅N + CrO₃ + HCl + C₉H₁₉CH₂ OH --> C₉H₁₉CHO + CrCl₃ + H₂O + C₅H₅NHCl and when balanced: 2C₅H₅N + 2CrO₃ + 8HCl + 3C₉H₁₉CH₂ OH -->3C₉H₁₉CHO + 2CrCl₃ + 6H₂O + 2C₅H₅NHCl. In this example the procedure calls for 1.0 mL of pyridine, 4g of chromium trioxide, 6 mL of 6M HCl and 1.0 mL of decanol.

Densities, molecular weights are obtained from the Handbook. Note that many of the blanks are not filled in because the data is not necessary. Also the mmoles of HCl are calculated from a VxM = moles calculation since HCl is in aqueous solution. The "calculate lim. reagent" line is usually not necessary, but since the ratio of coefficients in the balanced equation is not 1:1:1 etc., another line calculation must be made; when the millimoles of decanol is divided by its coefficient the result is lower than the result for any other reactant, therefore decanol is the limiting reagent.

Note also how the calculations are made right in the table. The logic is followed with arrows so that the limiting reagent and the theoretical yield, both labeled, are easily found.

Example Table of Chemical Tests.

This table is appropriate for the identification of unknowns. Observe how the IR information is included into the line of reasoning and suggests the chemical tests. Even though the IR clearly indicates an alcohol, preliminary alkene and alkyl halide tests are run anyway, since negative tests provide confirmation. But not all chemical tests need be run, only the ones suggested by the IR and preliminary tests. The alkyl halide (Beilstein) test, like the Lucas test, was not decisive the first time, and tests were run to check the initial findings. The road to determining the functional group is often laborious. Expect conflicts and to repeat tests.

Example Table of Candidates.

This table is made to organize the selection of a single compound from a list that best fits the data. In this example the progress is followed from a Table of Tests that determined that the unknown was an alcohol having about 6 carbons and was either primary (from the IR - but note that the 1060 cm^-1 is a little high) or secondary (from the Lucas). So all candidates alcohols having boiling points 5 degrees below and 15 degrees above 159 are listed.

All candidates must have simple drawings of their structures (only some, above, could be printed in this example.) Structures are found in the Handbook in an appendix "Structural Formulas of Organic Compounds" to the list "Physical Constants of Organic Compounds"

A number of techniques are introduced in the first laboratory. Below are some more detailed instructions that will be referred to in later laboratories.

Handling of Liquids. See Mayo, et al., p.40-45 Microscale amounts of liquids are not poured but instead transferred with a pipette. In your drawer are Pasteur pipettes and rubber bulbs - which is used for most work; also in the drawer are a graduated pipette (which fits into the green pi-pump) and a syringe.

As explained in the Check-In lab, Pasteur pipettes are held in the palm of the hand with the smallest finger while the rubber bulb is squeezed with the thumb and forefinger. This technique gives the best control of the pipette tip when the other hand is holding the vessels holding the liquids.

During any transfer with a pipette some liquid may leak out. To prevent loss of this liquid it is important to bring the mouths of the dispensing and receiving vessels as close as possible together.

The Pasteur pipette holds about 2 mL and is easily cleaned for further use. If more than a few milliliters of acetone are not enough to clean the pipette it is cheaper to throw it away and replace it from the stockroom.

The 2 mL graduated pipette/pi-pump combination measures with more accuracy, but when you hold it with your thumb on the roller you will see that the pipette tip is unsteady. The other hand may need to hold the tip, but this will not allow you to hold the source or destination containers. In addition, the graduated pipettes are not so cheap to replace.

Handling of Solids. Microscale quantities of solids are weighed on ordinary pieces of paper; but these can be folded to channel the solids as they are then poured into the test tube, flask, etc. containers. Because small amounts are used it is advantageous to precut the paper so the solid runs along a fold directly to the bottom of the vessel without touching its neck. For emptying vessels use of the microspatula requires practice and patience.

Boiling Point. The micro technique will be described in a future procedure.

Recrystallization. This is a technique for purification of solids, Generally, a solvent is selected that, when boiling, will dissolve the solid. When the solution is then cooled, the solvent will not be able to dissolve the solid as well. As a consequence, purified solid will precipitate out of solution as crystals. These crystals are recovered by filtering them from the solvent; the separated solvent carries the impurities with it. Specific instructions will be given in procedures.

Routine use of the Gas Chromatograph. Text p. 66-70. Instrument is a Gow-Mac with a Carbowax 20 M (polar) column and a DC-200 (non - polar) column. Setting up an instrument such as the gas chromatograph is a skill learned in an advanced course, but the parameters of the analysis must be measured and written right on the chart: The carrier gas, helium, with a back pressure at about 18 pounds per square inch read at the gauge and a flow about 20-25 ml/min read at the flowmeter. The column used, the oven temperature, the attenuation, the nature of the sample and the amount injected, the attenuation (i.e. the sensitivity of the detector) and the chart speed. (about 1 inch per minute; this should be verified with a ruler and a clock.). The instrument will be set up for your work; make sure that the detector power is on only when helium is flowing.

Prior to your injection, adjust the pen, with the chromatograph zero knob, to the right side of the main chart (the small chart on the right side of the recorder is not used.)

To inject, take the automatic syringe and clean it several times by filling and emptying it several times with your sample; discharge the syringe into the air. Adjust the barrel of the syringe to the microliter (µL = 0.001 L) capacity desired. For normal runs 3 µL is typical. Take up the sample into the syringe, and inject it into the injector port corresponding to the desired column. Make a mark with a pen on the chart at the point of injection. While you await peaks, make sure you have documented the parameters underlined above on the chart.

The first injection may cause the chromatogram to be too big or too small. To make the peaks larger, increase the sensitivity by lowering the attenuation. If your peaks of interest are too large, turn up the attenuator. Often large peaks which are not of interest, are allowed to pin the pen so that smaller peaks can be seen and measured. This will be the case with the free radical chlorination experiment.

If another student is about to inject, permit him/her to inject and wait until your chromatogram has passed the sprocket. Now tear off your chart, take it to your bench and staple it to an empty page in your notebook. Identify as many of the peaks as possible by marking them. The instructions for measuring the retention time and integrating each peak are given in the "check-in" lab.

Calculations of the retention times for the peaks of interest must be put on the chromatogram or on the same notebook page that the chromatogram is attached to. Since the chart speed is 1 inch per minute, it is easiest to measure (in millimeters) the horizontal distance between the injection point and the point when the peak has reached its maximum. Multiply this distance by (minute/25.4 mm) to obtain the retention time. Repeat this for all peaks needing to be measured.

Calculations for the areas for each peak to be measured - also written on the chromatogram - are done by the height times width-at-half-height method: 1) draw a baseline that would have resulted if the peak had not appeared; 2) from the baseline measure and record the height, the vertical distance in millimeters from the baseline to the top of the peak; 3) mark the midpoint of this line; 4) measure the width of the peak, through the midpoint mark (i.e. the width-at-half-height). Multiply the height by the width-at-half-height and record the result. The area of each measured peak is then calculated as a percent of the total measured peaks.

Preparation and Analysis of Samples for an Infrared (IR) Spectrum . McM sections 12.5-12.9. (the Mayo, et al. treatment in Ch. 6 need only be scanned since it is overly detailed for an introduction). The procedure the preparation and measurement of a liquid (neat) sample is found in the "check-in…" lab file.

The instrument is a Perkin Elmer Model Spectrum One infrared spectrometer.

For liquid samples disk shaped NaCl plates are used to place the sample in the beam.

Prepare the spectrum for interpretation by inserting and identifying a vertical line in your spectrum that marks 3000 cm^-1. This line will be helpful in identifying your unknown since any sharp peaks to the left of this line (between 3020-3100 cm^-1 - see McM Table 12.1) represent C-H bonds in which the C is sp² hybridized. Absorptions to the right of this line, 2960-2850 cm^-1 represent C-H bonds in which the C is sp³ hybridized.

Solids melting below 80 ^oC are run as "melts": a clean salt plate is loaded with 3-5 mg of the solid and the plate is carefully warmed on a clean, dry surface (aluminum foil on a warm hot plate) until the solid is melted. The sample is mounted and run as usual.

Solids melting above 80 ^oC are run as KBr pellets: 1) obtain a small agate mortar and pestle from the stockroom, and grind 3-6 mg of sample and about 50 mg of KBr until the solid is caked and glassy. 2) With a spatula, transfer the mixture to a cup provided for reflectance sampling. The instructor will then press the sample into a window that will be mounted in the spectrophotometer and the sample is run as usual.

Interpreting an IR Spectrum. In the "check-in" lab, identification of the unknown substance only requires comparison of the spectrum obtained with 25 spectra in chapter 6 of Mayo, et al.. All future spectra must be interpreted and annotated even if a match happens to be found. In McM, section 12.5 you will find a quick introduction to IR theory: vibrations of the bonds within molecules give rise to the various peaks in IR spectra, and therefore analysis of the spectra will give information on the bond sequences or functional groups within the compound being scanned.. Mayo, et al., p. 231, gives a good strategy on organizing this information.

1. Measure and mark the wavenumber values (corrected, if necessary, after calibration) for all significant peaks between 4000 and 1350 cm^-1. Remember that the wavenumber values, not so much the intensities, of these peaks is important. Also note the shapes (rounded, sharp, wide, narrow) of the peaks.

2. If solvents or Nujol were used to mount the sample, they must be marked out. Spectra for these substances are found in the Aldrich IR Library

3. Interpretation of the spectrum itself is best done by first checking major features for fundamental functional groups. There are 3 regions to scan initially. These are best followed from McM Figure 12.14 and the figures in Mayo, et al., Chapter 6:

4. The Handbook has "Infrared Correlation Charts" which are helpful. In the Aldrich IR Library the spectra are organized by functional group (alkenes, alcohols, etc.); each section begins with a general discussion of the characteristic peaks that are present in the functional group.

5. Remember to look first at the most outstanding aspects of the spectrum, not get into minor details. Do not try to interpret every peak in the spectrum.

6. Also remember that the absence of a peak is often just as important as finding one, for it will narrow the list of possibilities for your compound.

7. Now that the major peaks have been identified, further confirming and sub-classifying peaks can be located. The best strategy for this is to refer to the appropriate section in McM. Always check example spectra in McM and in Mayo, et al. Details of groups that may be encountered in this course:

In general, once a functional group is identified, specifics on its IR characteristics can be confirmed and sub-classified by looking up the group's IR data in the "spectroscopic analysis" section of the appropriate chapter of McM.

8. A match can be sought from an on-line reference: http://www.aist.go.jp/RIODB/SDBS/menu-e.html or The Aldrich Library of FT-IR Spectra by C.J. Pouchert, Aldrich Chemical Publishing Co. Milwaukee, WI. For an exact match there should be a peak for peak correspondence between your spectrum and the library entry. Note, however, that the intensities will differ if the amounts sampled are  not the same. Also the wavenumber values should match even though scaling is different; the spectrum you obtain is linear in wavenumbers (cm^-1 values) while the Aldrich Library spectra are linear in microns, so each major peak should be measured separately. A handy conversion: wavenumbers = 10,000/microns.

9. Mark your spectrum liberally. Make notations on each diagnostic peak (see McM Figure 12.13 for example) and for each peak that you used to arrive the structure of your unknown.

10. If two candidate compounds you found in the Aldrich Library are both almost identical to your spectrum, make a peak-for peak comparison. To do this mark off two 0.5-1 cm-wide bands along the length of your spectrum. Label each band is labeled with a candidate's name and insert small vertical lines in the positions corresponding to that candidate's peaks (heavy lines for strong peaks, etc.) All the information is now on your spectrum and you should be able to determine the best fit for your unknown.

References:

Text, frequently "Mayo" in the procedures: Mayo, D.W., Pike, R.M., Butcher, S.S. and Trumper, P.K. Microscale Techniques for the Organic Laboratory; Wiley: New York, 1991

Text for the Lecture, frequently "McM" in the procedures: McMurry, J. Organic Chemistry, 5th ed., Brooks/Cole Publishing Company, Pacific Grove, CA. 1999

The "Handbook" refers to any of the recent editions of: Weast, R.D. Handbook of Chemistry and Physics; The Chemical Rubber Co.: Cleveland, 1960-present.

The "Aldrich IR Library" refers to any edition of: Pouchert, C.J. The Aldrich Library of Infrared Spectra; Aldrich Chemical Co. Milwaukee, 1970-present.

Rev. January, 2001