The Experimental section is probably the most unusual (and most useful) part of any research report. The language in the Experimental section is unusually terse, dense, and technical. At the same time, an Experimental section contains a large number of numerical parameters (including all characterization data for every new compound) and there are strict conventions for reporting each number. The only way to be certain that you have observed these conventions is to consult the rules for each number as you type it in. (Please read that last sentence again. We are saying that you must consult a rule as you type each number. You cannot guess your way through this.) Because of these challenges, we have provided this special web page of instructions to help you through this critical section of your lab report.
This page describes all of the formatting conventions that will apply to your Experimental section, but before getting buried in instructions, let’s take a look at a typical Experimental section. [NOTE]You should follow the same general stylistic principles found in this example when formatting your Experimental section, but our formatting rules are a little different so please follow the detailed formatting instructions we provide at the bottom of this page. The following paragraph describes one experiment (the synthesis of compound (7) from compound (6)) that was published in a recent research article (J. Zhou et al., J. Org. Chem., 2014, in press, DOI: 10.1021/jo501967m):
(−)-tert-Butyl (3R,4R)-4-(6-Bromo-2-pyridyl)-3,4-dihydroxypiperidine-1-carboxylate (7). AD-Mix β (33.5 g, 43.0 mmol) and methanesulfonamide (2.3 g, 23.9 mmol) were combined in a mixture of tert-butyl alcohol (150 mL) and water (150 mL). The mixture was allowed to stir for 10 min at room temperature before being cooled to 0 °C. tert-Butyl 4-(6-bromo-2-pyridyl)-3,6-dihydro-2H-pyridine-1-carboxylate (6) (8.10 g, 23.9 mmol) was added, and the reaction mixture was stirred at 0 °C for 5 h and 10 °C for 4 h and then warmed to room temperature overnight. Sodium sulfite (22 g) was added to the reaction and allowed to stir for 1 h. The reaction mixture was concentrated to half-volume under reduced pressure, and the remaining suspension was extracted with EtOAc (2× 75 mL). The organic layers were combined, washed with 1 M NaOH (1× 75 mL), dried over sodium sulfate, filtered, and concentrated under reduced pressure. The crude product was purified by silica gel column chromatography: 0−25% EtOAc/hexane to afford (−)-tert-butyl (3R,4R)-4-(6-bromo-2-pyridyl)-3,4-dihydroxy-piperidine-1-carboxylate (7) (7.72 g, 87%) as a colorless amorphous solid: 1H NMR (400 MHz, CDCl3) δ 7.62 (t, J = 7.8 Hz, 1H), 7.45 (dd, J = 10.1, 7.8 Hz, 2H), 4.22 (d, J = 12.3 Hz, 1H), 4.15−3.85 (m, 2H), 3.12 (td, J = 13.0, 2.6 Hz, 1H), 2.95 (t, J = 11.7 Hz, 1H), 1.93−1.82 (m, 1H), 1.77 (dt, J = 13.8, 2.5 Hz, 1H), 1.46 (s, 9H); 13C NMR (75 MHz, CDCl3) δ 164.5, 154.6, 140.6, 139.6, 127.0, 118.8, 79.9, 74.4, 70.0, 45.7, 39.0, 37.3, 28.4; HRMS (ESI-TOF) m/z [M + H]+ calcd for C15H22BrN2O4 373.0763, found 373.0769; [α]D = −7.8 (c 0.78, EtOH).
If you take the time to read through this paragraph carefully, you will discover that you can make fairly good sense out of the procedure, i.e., the first half. Then we get to the characterization data for compound (7) and everything seems to unravel [NOTE]The characterization data begins at “1H NMR” and is presented in four stages: 1H NMR data, 13C NMR data, high-resolution mass spectrometry or HRMS data, and finally, polarimetry or optical activity data. The authors do not report mp, bp, or IR data for compound (7), but you will need to report these data whenever you have measured them.). Unfortunately, HTML does not do complete justice to the special formatting (bold, italics, etc.) used in journal articles so you might also click this link to see a screenshot image of the experimental section in its original formatting.
Before we actually dive into the formatting instructions, we should also mention this: the Experimental section recapitulates information found elsewhere in the article (maybe in the title? abstract? results?), but only the Experimental provides 1) all of the information needed to repeat the experiment as the authors performed it, and 2) all of the characterization data needed to verify that the result of a repeat experiment is the same one observed by the authors. Therefore, there is a heavy ethical burden on authors to get the Experimental section right. There are no shortcuts here.
General formatting. Each experiment is described by a single paragraph. The first item in the paragraph is the title of the experiment in bold font. This is followed immediately (same paragraph) by a description of the experimental procedure, and then the characterization data. In general, the first characterization data reported are the mp or bp, followed by the product weight, and %theoretical yield. Spectroscopic characterization data come after that.
Reporting numerical data. The sample lab reports will help you master the language and formatting of experimental procedures. However, it is quite common for students to get confused about how to report quantitative measurements inside the procedure. Here are some useful guidelines [NOTE]Additional tips specific to the reporting of spectroscopic parameters are listed in the next section:
- The amount of a compound that participates in the reaction, i.e., appears in the chemical equation as a reactant or catalyst, must be reported in two ways: 1) the amount you actually used (mass or volume) in the units that you relied on for your measurement (g or mL) and 2) the number of moles (mol or mmol) that this represents. Report both quantities in parentheses after the reagent’s name. An example from the journal sample, “methanesulfonamide (2.3 g, 23.9 mmol)”.
- The amounts of solvents and neutralization reagents also must be reported, but just the volume (or maybe mass) of solvent/reagent, and not the number of moles. An example from the journal sample, “tert-butyl alcohol (150 mL) and water (150 mL)”.
- Always report the mass or volume in the units you actually used in the lab for your measurement. Do not convert ‘mL’ to ‘g’ or vice versa.
- Always report an appropriate number of significant figures. ‘2.3 g’ contains two significant figures, so the authors of the journal sample should have reported the number of moles as ’24 mmol.’
- Yields depend on fundamental factors like Keq, rate constants, and the importance of competing reactions, but they also depend on experimental technique. As a result, yields are rarely reproducible. Always round %yields off to the closest 1%, i.e., report just two significant figures. In the journal sample, the authors report the product weight (7.72 g) with three significant figures, yet realistically round off the yield to the closest 1% (87%).
- Research articles, like the sample provided above, do not routinely report E-factors. Instructions for calculating E-yields can be found in the Calculations appendix.
- Melting and boiling temperatures, mp and bp, should be reported to the closest 0.5 oC and should be reported as ranges [NOTE]An exception can be made if the range is narrower than 0.5 oC. In this case report a single temperature.
Reporting spectroscopic data. These data will generally appear last (exceptions: some experiments include GC or GC-MS data; these will follow your spectroscopic data). The spectroscopic data will appear in the order IR, 1H NMR, and 13C NMR. The general formatting principle is to provide 1) the name of the spectroscopy, 2) information about the instrument and/or sample type, 3) the units of measurement, followed by 4) a list of signals. A full set of characterization data might look like this:
IR (sample type, cm-1): absorption (intensity, functional group/bond assignment), absorption (intensity, functional group/bond assignment); 1H NMR (xx MHz, solvent): δ chemical shift (coupling pattern, nH, J = xx Hz, assignment), chemical shift (coupling pattern, nH, J = xx Hz, assignment); 13C NMR (xx MHz, solvent): δ chemical shift (assignment), chemical shift (assignment); GC (oven temperature): retention time (peak assignment), retention time (peak assignment) min; GC-MS m/z (% relative intensity, ion): retention time, m/z = value (% relative intensity by peak height, fragment assignment), value (% relative intensity by peak height, fragment assignment).
The items in black should always appear exactly as shown above, while the red-colored items must be replaced with appropriate entries as described below. It should almost go without saying that sometimes these data might not be available in which case certain items will be omitted, and sometimes a data list will be longer than what is shown here in which case the corresponding items will be repeated additional times.
Here are two examples of properly formatted observations [NOTE]These examples follow the formatting instructions provided here. The journal sample does not and should be ignored when preparing your reports.:
Blah-blah yielded methyl benzoate (3.0 g, 72% from benzoic acid): bp 210-214 oC (lit. 213 oC ); IR (neat, cm-1) 1735 (vs, C=O); 1H NMR (400 MHz, CCl4): δ 7.30 (d, 2H, J =8.0 Hz, ortho CH), 7.10 (m, 3H, meta and para CH), 4.30 (s, CH3); GC-MS m/z (% relative intensity, ion): 3.4 min, m/z = 150 (30, M), 122 (40, M-CO), 105 (100, PhCO), 77 (50, Ph).
Blah-blah yielded styrene (3.0 g, 72% from benzaldehyde): 1H NMR (400 MHz, CDCl3): δ 7.35 (m, 5H, phenyl), 6.70 (dd, 1H, J = 8.0, 14.0 Hz, =CH), 5.75 (d, 1H, J = 14.0 Hz, =CHHtrans), 5.25 (d, 1H, J = 8.0 Hz, =CHHcis); 13C NMR (100 MHz, CDCl3): δ 137.6 (C-1), 136.9 (C-2), 128.5 (C-3), 127.8 (C-4), 126.2 (C-5), 113.7 (C6); GC (90 oC): 1.1 (styrene), 1.4 (benzaldehyde) min.
Formatting instructions for each type of spectroscopic measurement are provided separately:
sample type: neat, Nujol, ATR (whichever applies; ATR or ‘attenuated total reflectance’ accessory is usually the correct choice)
absorption: vibration frequency; report this value to the closest 1 cm-1
intensity: s (strong), m (medium), w (weak). v(very) can be used to modify the intensity as in: vs or vw. sh (shoulder) and bd (broad) can also be appropriate as in: bd vs.
assignment: list atoms in functional group responsible for absorption, e.g., C=O or NH2.
Do not list all of the bands in your IR spectrum. List bands that 1) correspond to significant functional groups, or 2) are strong and can be used as defining characteristics of your compound’s IR spectrum. If you list more than one band, list them in order of increasing frequency.
solvent: CDCl3, acetone-d6, D2O (whichever applies, CDCl3 is usually the correct choice)
xx MHz: 400 MHz is the correct (and only choice) for Reed 1H NMR
chemical shift: report this value to the closest 0.01 ppm
nH: report integrals only if they have been measured; these values are frequently off (from the desired integer) by 10-15% when an FT-NMR instrument like Reed’s is used to measure the integral; it is permissible, therefore, to “re-interpret” integral values by adding or subtracting 1H when needed to bring the measured integral in line with the structural formula (example: suppose your measured integration is 2.2H : 6H while the structure requires 3H : 6H; it is ok to report this as 3H : 6H)
coupling pattern: s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet). Use ‘m’ when a pattern is uninterpretable. Write out the names of larger patterns: quintet, sextet, septet, octet, 9 lines, 10 lines.
Multiple couplings result in combination patterns, such as doublet of triplets, or triplet of doublets. Since these patterns are due to several independent spin-spin couplings, you must report a separate coupling constant (J) for each type of coupling. For example, a six-line pattern that can be interpreted as a doublet of triplets with coupling constants of 8 Hz (doublet) and 5 Hz (triplet) would be reported in the Experimental as (dt, nH, J = 8.0, 5.0 Hz, assignment).
Note: combination patterns are always named according to the strengths of the coupling patterns with the strongest coupling (largest J) first. For example, the six-line pattern described above is named a ‘doublet of triplets’ (dt) because the doublet coupling is stronger (J = 8.0 Hz). It would not be named a ‘triplet of doublets’ (td) because the triplet coupling is weaker (J = 5.0 Hz).
J = xx Hz: report this value to the closest 0.1 Hz. Include this information only when a pattern displays coupling that is interpretable. Singlets (s) show no coupling so no J can be reported. Multiplets (m) are uninterpretable patterns so J should not be reported for them either.
assignment: In general, give a condensed formula fragment that unambiguously defines the hydrogens (or carbons) responsible for the signal. If your compound is CH3-O-CH2CH3 then “CH2” is an unambiguous fragment and can be entered as the assignment for the 1H or 13C NMR. However,”CH3” does not identify a unique set of hydrogens (or carbon). The signals created by the nuclei in the two methyl groups should be assigned as “OCH3” and “CH2CH3“. Since the latter formula contains two kinds of hydrogens (and carbons), use special fonts (bold or italic) or underlining to identify the hydrogens (or carbons) that produce the NMR signal. For example, you might write: CH2CH3 or CH2CH3or CH2CH3 to identify the methyl hydrogens as the source of the NMR signal.
There are many cases when convenient formula fragments cannot be constructed. When this happens, draw a structural formula of your compound, label each hydrogen (or carbon) in the formula (Ha, Hb, and so on), and label the drawing as a figure. You can then use the labels in this figure wherever assignments are needed.
You must list all of the signals in your NMR spectrum that are created by your compound. Do not list signals created by the NMR solvent (CHCl3, HCl), the internal standard (TMS), or by other impurities, such as residual chromatographic solvent.
GC & GC-MS
GC only oven temperature: Give the oven temperature in oC
GC and GC-MS retention time: Give the time that elapsed between the injection of your sample and its emergence from the GC. If you identify several components of the mixture, list the retention time for each.
GC-MS only m/z = value: Give m/z ratio of peak as an integer.
GC-MS only % relative intensity by peak height: The “base” peak is defined as the tallest peak in the spectrum and its height is defined as “100 %.” All other peak heights are necessarily between 0 and 100. Round peak heights to closest integer unless height is less than one.
GC-MS only fragment assignment: The molecular ion is assigned by showing the symbol “M” or “M+”. Larger fragment ions are usually assigned according to what has been lost from the molecular ion, e.g., loss of a methyl group would be represented by“M-CH3”. Smaller fragment ions are usually assigned according to what they contain, e.g., an acetyl ion would be “CH3CO”.
GC-MS only etc.: Always list peaks in decreasing m/z order, i.e., largest m/z first and smallest m/z last.
Do not list all of the peaks in your GC-MS mass spectrum. List the most intense peaks and list the ones that help you identify your compound (the latter might be very weak). The peak produced by the molecular ions should always be listed if it is observed.