RESEARCH REPORTS AND THESES:  STYLE FOR EXPERIMENTAL SECTIONS

 

                              PDF version of this guide                                  Sample Research Report (PDF)

 

Experimental Procedures Flowchart

 

(1)       GENERAL INFORMATION

 

                              You will write reports two times per year and a thesis or final report before you leave.  These reports are primarily aimed at documenting experimental data, but should also serve as the basis for your thesis when you come to write it.  These reports should cover all the significant experimentation in the same detail and EXACTLY the same style as found in experimental sections in J. Org. Chem.  Representative experimental procedures with detailed annotated comments are included in this document.

 

                              Research reports should be organized in the following way:

 

                                             Page 1    Your name, date

 

Page 2    Introduction  (WHAT are you doing?  WHY are you doing it?  WHAT has been done before?)

 

                                             Page 3    Brief Results and Discussion Section.  This section should be mainly structures, equations, yields, plots, etc., but should clearly explain the course your research has taken over the last six months.

 

                                             Page m   Detailed Experimental in correct thesis publication style

 

                                             Page n    References in J. Org. Chem. format

 

                              Reports should be electronic and drawings ChemDrawn in J. Org. Chem. style, either one column or two column format ("ACS Document 1996 1-col" or "ACS Document 1996 2-col").  For drawings containing dendrimers, it may be necessary to use the modified templates ("ACS Document 1996 1-col Dend" or "ACS Document 1996 2-col Dend").  These templates are on the Macintosh computers in the group offices. 

It is also suggested that the occasion of report writing provides an opportunity to codify and arrange spectra and non-research notebook data and to bottle and label research samples for long-range storage (please use minimum sized vials, bottle, or tubes in order to minimize storage space requirements).  Samples should be labeled clearly with notebook designation on paper tape written in either Sharpie or black ballpoint pen.  Do not store samples in round bottoms or NMR tubes for long periods of time.

 

(2)       BIANNUAL RESEARCH REPORTS

 

                              Biannual research reports are to be submitted electronically and in hard copy format promptly on the following dates:  January 31 and July 31.  These should contain a brief introduction and a detailed and duly referenced experimental section in the J. Org. Chem. style.  All new compounds must be fully characterized and this data should be included in the experimental section.  In addition, for each new compound prepared, you should submit one copy of a characterization form at the same time as your report.  Characterization forms are available on the group website.

 

(3)       ORGANIZATION AND STYLE OF RESEARCH REPORT

 

                              Good writing requires time, effort and care.  In writing theses, papers, and research reports the objective should be clarity and conciseness.  Always choose the simple expression rather than the unusual.  A reader is more favorably impressed by an easily understood report than by an exhibition of fancy literary style.  The former is the scholarly approach.

 

                              A chemical report should contain (a) an introduction, (b) results and discussion, and (c) experimental details.  The general form and style adopted by the J. Org. Chem. is to be used.

 

               A.           INTRODUCTION.            This part should include a brief and clear statement of the purpose and objectives of the work together with a concise historical background.  Remember, you are writing to inform others who may not be at all familiar with your work.

 

               B.           RESULTS AND DISCUSSION.  These sections may be written together or separately.  If many different results are needed before they can be discussed, it is better to keep these sections apart.  On the other hand, predominantly synthetic work is best written with Results and Discussion combined.  Do not be a slave to chronology, but organize the presentation for clarity.  Sentences should not be interrupted by structural formulas, which should be conveniently located between paragraphs and assigned Arabic numerals in the order of appearance.  These formulas are referred to in the text by the numerals (see J. Org. Chem. practice).  For involved syntheses, the use of Schemes is common practice.  The discussion should be self-sufficient, and should describe the reactions performed, any unusual experimental conditions, yields of products, and the melting points and any particularly significant spectral data of new products.  If you have difficulty in writing this section of your report, then you should read more literature to familiarize yourself with the style!  PAST TENSE SHOULD BE USED THROUGHOUT!!!

 

                              A scholarly report will be well documented with appropriate references to support statements and to provide precedents.  For reporting references, use the Chemical Abstracts abbreviations (see "ACS Style Guide" 1986).  As an author, you are responsible for due citation of precedent. 

 

               C.           EXPERIMENTAL PART.  This section should contain complete details of the laboratory operations, should be written in the past tense, passive voice (e.g. "the crude product was distilled") and should be consistent in style throughout.  It is usually convenient to specify some general practices in a footnote at the beginning of this section.  Study the sample Experimental Procedures and Annotated Comments provided in this packet for details.

 

(4)       EXPERIMENTAL STYLE (with Annotated Comments)

 

                              (E-4-Bromo-4-(trimethylsilyl)-3-buten-1-yl p-Toluenesulfonate (12).1,2  A solution of 11 (6.67 g, 29.9 mmol), p-toluenesulfonyl chloride (6.56 g, 34.4 mmol), and dry pyridine (60 mL)4,5 was stirred at 0 ¡C5 until all the sulfonyl chloride had dissolved and the resulting solution6 was stored in a -20 ¡C refrigerator for 24 h.7  The reaction mixture was then poured onto ice (ca. 100 g) and extracted with Et2O8 (2 x 100 mL).  The organic extracts were washed with saturated aq Cu(NO)3 solution until no further color change was observed and then with H2O, 1 M HCl and brine (ca. 25 mL of each).  After drying (MgSO4), concentration gave crude 11 (9.4 g, 83%)9 as a pale yellow solid.10  Recrystallation from hexane gave analytically pure colorless crystals:11  mp 59-60 ¡C; IR (KBr) 3029, 2971, 2858, 1609, 1355, 1178, 939, 850 cm-1; 1H NMR (300 MHz, CDCl3) d 7.33 (d, J =12 7.2 Hz, 2H), 6.94 (d, J = 7.2 Hz, 2H12), 6.17 (t, J = 7.1 Hz, 1H), 3.85 (t, J = 7.2 Hz, 2H,), 2.3-2.5 (m,13 5H), 0.33 (s, 9H); 13C NMR (75 MHz, CDCl3) d 138.6,14 128.2, 110.3, 108.6, 97.3, 95.2, 64.5, 28.6, -0.8; MS (CI) m/z 379 (M+H+), 377 (M+H+), 207, 205, 110; MS (EI) m/z 379.1346 (10%,15 379.1352 calcd for C14H21BrO3SSi), 263 (47%),16 211 (100%), 153 (57%).  Anal. calcd17 for C14H21BrO3SSi:  C, 44.56; H, 5.57.  Found:  C, 44.63; H. 5.58%

 

                              (1S,8S,9S)18-2-Carboethoxy-8,9-dimethoxy-2-azabicyclo[4.3.0]non-5-en-7-one (22).  Carbamate 20 (103 mg, 0.260 mmol) was dissolved (3x) in dry benzene (ca. 5 mL) and19 the resulting solution was concentrated to azeotropically dry the sample.  Dry THF (3 mL) then was added, the resulting solution was cooled to -78 ¡C and stirred rapidly while s-BuLi20 in hexane (1.4 M; 0.22 mL,21 0.31 mmol) was added slowly (ca. one drop per second).  After an additional 30 min at -78 ¡C, the reaction mixture was stirred rapidly and quenched by adding HOAc (0.2 mL).  Aqueous 3 M HCI (0.5 mL) was added, the reaction mixture was allowed to warm22 to 23 ¡C and poured into CH2Cl2 (ca. 100 mL).  The organic layer was separated, washed with brine (10 mL), dried (MgSO4) and concentrated.  Chromatography23 of the residue on silica gel (3:2 hexane-Et2O) gave enone 22 (44 mg, 66%) (92% pure by GLC24 analysis) as a yellow oil:  [a]-80.0¡ (c 1.1, CHCl3);25 IR (film) 2952, 2904, 2831, 1731, 1705, 1660, 1449, 1103 cm-1; 1H NMR (300 MHz, C6D6, 85 ¡C) d 6.7-6.8 (m, 1H), 4.80 (broad26 s, 1H), 3.9-4.2 (m, 4H), 3.32 (s, 1H), 3.30 (s, 3H), 3.05 (s, 3H), 2.05-2.15 (m, 1H), 1.6-1.7 (m, 1H), 1.05 (t, J = 7.0 Hz, 3H); MS (CI) m/z 270 (M+H+), 238; MS (EI) m/z 269.1269 (3%, 269.1263 calcd for C13H19NO5), 178 (100%), 133, 111.

 

ANNOTATED COMMENTS

 

(1)          Title of the experimental is indented with the first letter capitalized.  Compounds are named by IUPAC (or CA) conventions.  Note that substituents are organized alphabetically.  If the experimental reports a reaction that is more important than the final compound, an experiment could be entitled, e.g. "Stability of Diene 3 in Trifluoracetic Acid," etc.  Fonts:  _ implies typeset in italics, ~ implies typeset boldbut since modern word processors support these fonts, they are not necessary in your document.  Hence, use them instead of these markings: E, Z, cis, trans, meta, para.  Rather, use italics.

 

(2)          Parentheses are used for 12 since it follows a complete name.  In all other cases, no parentheses is used (e.g. see "Carbamate 20" not "Carbamate (20)" in the second line of second experimental.)

 

(3)          Weights are typically reported to 3 significant figures (never 4).  If a weight is accurate to only 2 figures (e.g. weighing NaH, KH, etc.) use 2 significant figures.  Volumes are typically accurate to only two significant figures.  Mmols must be reported with the same number of significant figures as the weights or volumes to which they apply.  Note that periods are not used for most abbreviations.  Weights of less than 0.10 g should be given in mg; for less than 0.5 mol use mmol. 

 

(4)          Any solvents are listed the same as reagents.  Although they are typically listed last, they are NEVER preceded by "in," but rather "and" as a standard part of a list.

 

(5)          The degree sign is a special character, NOT a superscript lowercase o.  On Macs this character is Shift-Option-8.  Note the format: space between the temperature and degree sign, NOT between degree sign and Celsius abbreviation:  "27 ¡C" NOT "27¡C" NOT "27¡ C."

 

(6)          Be careful with the distinction between solution (something that is homogeneous and cannot be qualified, i.e. never say a complete solution) and a mixture which is heterogeneous.  Since solutions are homogeneous, their properties cannot be affected by stirring.  We should, therefore, not write experimentals that suggest that stirring a solution is important for our chemistry!  Say instead that a solution was maintained at 30 ¡C for 10 h.  However, if something (solid or solution) is added to a solution, it is generally done while stirring and this should be indicated!  E.g. "To a stirred solution of ... was added ..."

 

(7)          Note in the sentence that ends on this line, that the order of mixing the reagents was not specified.  Experimentals should be written this way unless the order of mixing is obviously important.  To specify the order of mixing when it makes no difference is confusing to the reader since it implies that this is an important detail.

 

(8)          Chemical formulas or accepted abbreviations for functional groups can be used instead of names to save space.

 

(9)          Yields should be reported to two significant figures and also typically the weight of the final product.

 

(10)        The physical state of a new material should be specified.

 

(11)        Note that the characterization data for a compound follows a colon and that individual parts of the characterization data are separated by semicolons.  Infrared data should be specified either as (KBr), (film), or (CHCl3) and film is not capitalized.  Note that cm-1 comes at the end of the infrared absorptions.

 

(12)        Spaces should be used on either side of equal signs.  Note that ASSIGNMENTS ARE NOT MADE for NMR spectra except in the case of definitive identification with an advanced technique such as COSY or NOESY spectra.

 

(13)        Indicate the number of hydrogens, i.e. 2H.  Coupling constants should be reported to a tenth of Hz, peak positions to a hundredth of a part per million, multiplets should be specified as a range starting from low field and going to high field. 

 

(14)        13C NMR data should be reported to a tenth of a part per million unless two peaks are not resolved at that level.

 

(15)        For mass spec data, the intensities of peaks in chemical ionization mass spec is not a useful characteristic of a chemical structure because peak intensities depend on the concentration of the reagent gas.  Consequently, we will not specify peak intensities in CI mass spec, but only in EI mass spec.

 

(16)        Note in the EI mass spec that I have combined high resolution and low resolution data.  This is done to save journal or thesis space.  Typically we will report high resolution data only on the molecular ion or the highest molecular weight fragment of a compound.  Note also the form for reporting the calculated molecular weight.

 

(17)        Analytical data should be reported in exactly this format.  Note punctuation!  It is a separate sentence!  Found should typically agree with calcd to ± 0.25% (± 0.4% is allowed in tough cases).

 

(18)        This is the best way to specify stereochemistry.  If relative stereochemistry was implied, one would use the S*, R* convention, starting with R* for the lowest numbered carbon.

 

(19)        Note that in the sentence starting on this line that the order of adding the reagents is important and consequently is clearly specified.

 

(20)        Note in this line the abbreviations for butyl and also for milliliter.

 

(21)        Note that fractional numbers are all given as decimals preceeded by a zero.  Also note that in the next line that one uses decimal numbers rather than numerical ones, i.e. one would never say 1/2 mL.

 

(22)        Use "allowed to warm" if you let the reaction warm up itself.  Use "warm" if you warmed up the reaction mixture.

 

(23)        Note in the sentence that starts here that what is being purified is specified - i.e. a residue.  One could also say purification of the residue by flash chromatography or chromatographic purification of the residue -- these are all acceptable.  Note in this sentence also the form I specify for reporting solvent mixtures used in chromatographic separations.  Use abbreviations for solvents to save space, i.e. ethyl acetate should be abbreviated EtOAc.

 

(24)        For solids, we typically report mp as a measure of their purity.  For liquids, this is replaced by a bp or GLC analysis of purity (if we have one) or some comment on its TLC purity.  Note here that one cannot say "92% by GC" (which is lab slang).  One can say homogeneous by TLC analysis.

 

(25)        Note the form for reporting optical rotations.  The degree sign here and with temperatures is a special character, NOT a superscript lowercase o.  On Macs this character is Shift-Option-8.

 

(26)        Note that broad has to be spelled out.  Quintet must be spelled out.  We also use apparent (abbreviated app) when a signal appears simpler than it really should be.  For example, if an ABq appears as only three lines, we would report it as an apparent triplet and then report a single coupling constant.

 

           Miscellaneous Notes:

 

(a)           If several reactions were conducted the same way, you need to describe the general details only once.  Thereafter, write the experimental in the following form:  "Following the procedure described for the preparation of 10, alcohol 36 (1.32 g, 0.113 mol) was silylated with Me3SiCl (2.3 g, 0.16 mmol) to give, after purification on silica gel (4:1 hexane-Et2O), the silyl ether 15 (2.10 g, 89%):  etc."  For more details on this see the Experimental Procedures Flowchart document. 

 

               Note that the purification process is described in detail.

 

(b)          Include experimental observations in your experimentals - colors, gas evolution, etc.  This is very important for new (non-routine) procedures.

 

(c)           If a compound was never fully purified (typically because we couldn't do it) and was therefore used in a crude state for the next reaction, the experimental procedure will likely be nested with another and should read something like the following:

 

               "... followed by removal of the volatiles in vacuo (20 mm/1 h) to provide the crude a-chloroether 40 (1.36 g).  The 1H NMR spectrum showed that 40 contained no starting materials using the acetal proton at 4.68 pm as a probe:  1H NMR (300 MHz, CDCl3) 5.75 (m, 1H, ROCHCl), 4.10-3.25 (m, 5H), 2.30-2.00 (m, 2H), 1.14-1.10 (m, OH).

 

               A solution of crude 40 (1.16 g., 3.68 mmol), alcohol 8 (1.25 g, 3.88 mmol ..."

 

               Note only diagnostic spectral data are reported for 40 and that the second step (i.e. the use of 40) begins a new paragraph.

 

(5)       FREQUENTLY MISSPELLED OR MISUSED WORDS

 

                              The verb to react is intransitive and therefore cannot take an object.  Wrong:  "Robinson reacted the ketone and semi-carbazide."  Nor can it be used in the passive voice.  Wrong:  "The ketone was reacted with..."  Right:  "Upon reaction with semi-carbazide, the ketone was converted..." or "The ketone was allowed to react with..."

 

                              Data and spectra are plural nouns.  It is wrong to say, "the spectra of the compound was determined"  or the data shows that..."  Instead, say "The spectrum was determined."

 

                              Avoid the use of such laboratory jargon as filter off, suck dry and separate out.

 

                              Others commonly misused words and phrases include:

 

                                             a number of experiments were carried out

                                             a column of 150 g of Florisil (capital F)

                                             affect (to act, or produce and effect on)

                                             effect (to bring about or accomplish)

                                             absorption (not absorbtion)

                                             acknowledgment (not ackowledgement)

                                             can (denotes power or ability)

                                             may (denotes possibility, permission, or opportunity)

                                             data (plural), datum (singular)

                                             ensure, insure

                                             distill, distills, distilled, distillation

                                             expel (not expell), expels, expelled

                                             forerun

                                             gauge or gage (not guage)

                                             hypodermic (not hyperdermic)

                                             infrared (not infra red)

                                             judgment (not judgement)

                                             precede (step 1 precedes step 2

                                             proceed (when you have finished step 1, proceed to step 2)

                                             procedure( follow the procedure used in step 2)

                                             wavelength

                                             regardless (not irregardless)

                                             Spell out numbers when in a formal statement:  "It was four times as..."

                                             Use figures with abbreviated units:  5 g, 7 h

                                             Use zero to introduce a decimal fraction:  0.36, 0.5%

                                             Dry Ice

 

               COMMON ABBREVIATIONS

 

                              The following symbols can be used without identification:  (Note:  periods are typically not used)

 

                                             g for grams

                                             mL for milliliters

                                             L for liters

                                             mp for melting point

                                             mmp for mixture melting point

                                             bp for boiling point

                                             % for percent

                                             mm for millimeters

                                             h for hours

                                             min for minutes

                                             1H NMR for proton NMR

                                             13C NMR for carbon NMR

                                             IR for infrared

                                             TLC for thin layer chromatograph

                                             HPLC for high performance liquid chromatography

                                             GC for gas chromatography

                                             mmol for millimoles

                                             mol for moles

                                             ca. (about)

                                             cf. (compare)

                                             e.g. (for example)

                                             et al. (and others, no period after et)

                                             i.e. (that is/in other words)

                                             M (moles/liter)

                                             mol % (moles percent)

                                             vol (volume)

                                             in vacuo

                                             vide supra (see above)

                                             vide infra (see below)

 

                              Symbols for radicals or groups:

 

                                             Ac (Acetyl)

                                             Bn

                                             Bu (n-Bu, sec-Bu, i-Bu, t-Bu)

                                             butyl (n-butyl, sec-butyl, isobutyl, tert-butyl)

                                             Bz (benzoyl) ** not benzyl!

                                             Et (ethyl)

                                             Me (methyl)

                                             Ph (phenyl)

                                             Pr (i-Pr, c-Pr) [propyl (isopropyl, cyclopropyl)]

 

 

 

               WORD VARIATION AND CONCISE PHRASES

 

               Word Variation:

 

                              ¡        Add, introduce, mix with, pour into, quench, combine with, add portionwise, add dropwise, add by drops

                              ¡        Yields, gives, gives rise to, results in, forms, generates, produces, furnishes, leads to, is transformed into, develops, acquires, obtains, precipitates, deposits, evolves

                              ¡        Observations, results, data, readings, measurements, points, values, estimates

                              ¡        To carry out, perform, try, conduct an experiment

 

               Phrases (be as concise as possible):

 

                              ¡        after (not subsequent to)

                              ¡        because or since (not due to circumstances that)

                              ¡        butadiene was treated with, butadiene was allowed to react with, or butadiene reacted with (not butadiene was reacted with bromine)

                              ¡        carefully (not in a careful manner)

                              ¡        clearly (not it is clear that)

                              ¡        concluded (not arrived at the conclusion that)

                              ¡        cools (not cools off)

                              ¡        if (not in the event that; not if conditions are such that)

                              ¡        not (not at the present time)

                              ¡        outcome (not final outcome)

                              ¡        precipitates (not precipitates out)

                              ¡        the reaction gave the ketone in 60% yield (not the reaction gave a 60% yield of the ketone)

                              ¡        undoubtedly (not there is no doubt that; not it is undoubtedly true that)

                              ¡        we do not doubt that (not we do not doubt whether)

                              ¡        product was isolated from the reaction mixture (not worked up the reaction mixture)

                              ¡        in the usual manner (not by the usual manner)

 

(6)       SUPPLEMENTS FOR THESES AND FINAL REPORTS

 

                              When you submit a final copy of your thesis (or for postdoctorals, the final report), it will be necessary to also provide a bound copy of the thesis or report supplement.  This supplement will contain appropriately photoreduced xerox copies of all the spectra, HPLC characteristics and microanalytical data for all the compounds referred to in the experimental section of your thesis or final report.  The supplement of a thesis will be available to the examiners during your defense and will subsequently be retained by me.  In addition, of course, it will be necessary for you to provide all the original spectra duly labeled, your notebooks, electronic copies of spectra obtained from the NMR facility and clearly labelled samples of all your synthetic intermediates and final products.