Journal Style Manuscripts

Journal Style Manuscripts

As with any other field, the practice of chemistry involves the daily use of oral and written communication skills. Like it or not, your professional success will depend very heavily on your ability to write and present papers, reports, proposals, evaluations, etc. Thinking up or carrying out a clever experiment won't bring great rewards if you cannot clearly and convincingly communicate your ideas and discuss your results.

You should be writing in a more formalized "journal" style. You are not trying to teach an undergraduate novice how to run a reaction. You can no longer "jabber" on about what went wrong and all the problems you've had scraping crystals out of a flask or having their sample blow on the floor. This is not the stuff of formal writing. You need to raise the level of presentation considerably, and at least give the appearance that you know what you are doing. With the proper writing style, one can even take a completely failed experiment and make it appear that the results have left the world a little more enlightened through a sound scientific analysis of the reaction. Before you start, write a "back-of-the-envelope" outline of how you plan to organize the manuscript, including the critical first "intro" sentence to each paragraph. For inspiration be sure to look over the original experimental background, experimental, and discussion of the experiment as provided to you originally.

Things to remember:

Try to avoid mixing completely different ideas, such as an alternate synthetic method and a mechanism discussion, in the same paragraph.

Continuous, logical flow is expected, as is a report virtually void of spelling and grammatical errors. Substantial points will be deducted for poor spelling and grammar.

Sentences in all sections should be written in a manner that is void of open-ended ideas/thoughts. If you introduce a concept, explain it completely in an intelligent, concise statement or group of statements.

The best source of format details and inspiration is the Journal of Organic

Chemistry (JOC) and the Journal of Chemical Education.

Formatting:

The reports must be produced by a word processor and include structures and reaction schemes drawn using either Chemintosh (Mac) or ChemWindow (PC) chemical structure drawing programs. These software programs are available free and may be downloaded from The password for unstuffing the Mac software is benzene. Otherwise there should be no passwords involved. Manuscripts should have a cover page of this form:

Title

Your Name or Team Member Names (Desk #s)

Date

The Formal Reports should have these seven parts:

1. Introduction

2. Experimental

3. Results & Discussion

4. Conclusions

4. References

5. Attach all spectra or chromatograms.

6. Attach the white laboratory notebook pages from each team member.

Attach the PreLab to your report (In the case of the project there will be no prelab).

INTRODUCTION

1. The Introduction demonstrates to the reader that you really know what you are talking about because of your background knowledge and reading. It does NOT contain a step-by-step description of every experimental detail, but rather talks about the chemistry in broader terms. In general, for each intermediate or product, you should cover: What class of compound you are synthesizing and isolating (for example, an alkene, organometallic compound, ester, heterocycle.etc.) and why compounds in this class are important from the commercial or biological standpoint. Give some important uses of the target substance or of compounds in its class or the reaction that led to its production. What type of reactions you are using to synthesize it (for example, elimination, oxidation, reduction, condensation, acid chloride, coordination complex formation, etc.) or methods you are using to isolate it from a natural source (for example, extraction, chromatography, etc.). Give any interesting historical information on the discovery or the development of the reaction(s) or method of isolation.

Are these methods suitable for all cases? For example, can you use chromic acid to oxidize all alcohols, 1°, 2°, and 3°, to ketones? How would results vary as the structure of the starting material changed? Would both liquid and solid starting materials be handled the same way?

What variations are available in terms of chemical reagents such as oxidizing agents or catalysts that would yield similar or improved results? For example, can both sulfuric acid and phosphoric acid be used for acid-catalyzed dehydration of an alcohol and does phosphoric acid offer some advantages over sulfuric acid?

Are there any special methods or techniques that are noteworthy? For example, the use of an acidic resin as an acid catalyst makes the isolation of the product in an ester synthesis much easier. Or the isolation of saturated fatty acids can be accomplished by using shape-excluding clathrates. Molecular Modeling - What questions might be answerable by Molecular Modeling.

All of this information is available from your handout or handout references, your lecture course text, or additional books and articles in the chemical literature. Many good examples of introduction sections are to be found at the beginning of the many synthetic experiments in a lab text such as K.L. Williamson's Macroscale and Microscale Organic Experiments.

EXPERIMENTAL

The Experimental Section contains two subsections: Procedure or Methods and Instrumental:

Procedure Subsection:

-Materials: The experimental section normally starts with a brief description of the materials, their source and purity. You don't have to list the source of the common reagents like solvents and drying agents here. You can assume that the reader could easily find a source for common chemicals such as dichloromethane, sulfuric acid, ethanol, sodium hydroxide, acetic acid, etc. If any special steps were taken to test the purity of or to purify or dry starting materials or solvents, this should be stated here.

Example: Chemicals: Pyridine was obtained from J.T. Baker Chemical Co. (Phillipsburg NJ). Pyrrole, 4-anisaldehyde, and benzaldehyde were purchased from Aldrich (Milwaukee WI). All chemicals were used as supplied except for the aldehydes, which were distilled under nitrogen just prior to use. Acetaminophen, chloramphenicol, zomepirac, and probenecid (Sigma Chemical Co., St. Louis, MO), Coomassie Blue reagent (Pierce Biochemicals, Rockford, IL) were used as received, HPLC grade ammonium phosphate (monobasic), acetonitrile, and methanol were from Mallinckrodt (St. Louis, MO).

Note-

Don't capitalize chemical names.

The stockroom is not a manufacturer! - You can't write "9-anthraldehyde and TLC plates were obtained from the stockroom."

List the sources of special starting material chemicals and their purity .

-Actual Experimental Procedure: A description of the experimental procedure follows the description of the materials. The actual description of the mechanics of setting up and carrying out the experiment should follow the journal style of writing. This style is extremely concise and well organized, and it includes all the vital details of the experiment. . A complete description of the apparatus and the procedure is not necessary unless the success of the experiment depends on a specific set up or type of apparatus. This means that you don't have to put in every specific piece of glassware such as 100-mL beaker or 50-mL Erlenmeyer flask, but can assume the reader can figure out what to use. For example, don't describe glassware unless it is special (like a 250 x 20 mm test tube). It is rarely necessary to even tell the type of glassware, but if you feel it is important, just say beaker or round-bottom flask, not 30-mL beaker and 500-mL round-bottom flask. The only change I want in your experimental section is the addition of reagent amounts in moles and either mL or mg. I want to make sure you have carried out the necessary calculations, and I do not want you wasting lab time doing the calculations. If the synthesis(es) you are describing involve more than one step, you should list the preparation of each intermediate in a separate subsection.

Other comments on the Experimental Section:

Include weight and yield, mp and literature mp for all solids including isolated intermediates.

Vacuum distillations should include the distillation pressure in mm Hg.

Numbers: 0.2 g. (note zero to help reader see decimal point) can't be at start of sentence, but don't put everything in brackets.

You shouldn't start a sentence with numerical digits or a formula. Example:"1 g of NaOH is added" should be "NaOH (1.0 g, 0.025 mol) is added …

Sentences cannot start with formula, for example, Na2S04.

"The ether layer was then washed". The word then and other words such as first and finally are very often superfluous and can usually be deleted without confusing the reader.

Don't use the implied "I did something" style, i.e. don't write: "(I) Mixed aldehyde and acid, heated to boiling...... (I) cooled and extracted....." This is OK for your notebook, but not the final report.

Each synthetic step is started in a separate section headed, in bold, with the compound name (and number, if numbered anywhere in the report) at the beginning.

All quantities must be given: g& mmol for reactants, concentrations of solutions in or M. milliliter abbreviated must be mL (no period)

At the end of each synthetic procedure, a very compact list of physical properties, including melting or boiling points, and spectral data should be given. GIVE YIELDS-grams or mg, and theoretical.

Gas chromatographic data should be listed using the following example: GC: starting material 2,4.67 min; cis 3, 5.32 min; trans 3, 6.04 min. Absolute retention times in GC are not so important since they will vary from GC to GC. Defining the order of elution is more important.

Example 1:

"A solution of 9.6 g (0.1 mol) of cyclohexanone and 3.8 g (0.1 mol) of L1A1H4 in 50 mL of ether was refluxed under N2 for 30 min.

-Note that FORMULAS, i.e. LiAlH4 and N2 are used instead of the compound names.

Example 2 including compact spectral data:

Indoleamide, 2: The isatin-3-hydrazone (1, 3.0 g, 15 mmol) was dissolved and heated in 16 mL of 21 sodium ethoxide in ethanol at 60-70°C for 10 min and refluxed until the evolution of N2 stopped. After pouring the reaction mixture on ice and acidifying to pH 1 with 10 HC1, the reaction mixture is extracted with ether (2x25 mL), the combined ether extracts dried over anhydrous Na2SO4, and the ether removed under vacuum to yield a yellow solid. This was recrystallized from H20 to give 2.1 g (74%) of 2, mp 123-125°C (lit3 mp 124-126°C). 1H NMR (80 MHz, CDCl3):  2.5 (2H, d, J=7 Hz, Ar-CH2-), 7.6 (4H, m, aromatic); IR (KBr 1730 (C=0), 2880 (N-H) cm-1; MS m/z (% rel. int.) 133 (100, M+), 105 (23, M-CO), 91 (32, M-CH2CO); UV (EtOH)  max 262 nm ( 19,200).

CORRECT COMMON UNIT ABBREVIATIONS:

g - gram - no period!

mL - milliter - no period!

mol - mole(s) - no period!

mill - minute(s) - no period!

S - seconds(s) - no period!

-Note that common abbreviations do NOT have a period after them.

Instrumental Subsection: This section should include the type and manufacturer of each instrument, the sample preparation method, and calibration methods. It should also include if necessary how you carried out your chromatographic separations (the instruments used and type and supplier of GC column or LC column or TLC plate).. Information in this section should be patterned after the Experiment Section in any quality journal article.

Example: "Spectral Measurements: Infrared spectra were recorded on a Mattson Instruments (Madison, WI) model 1020 FT-IR. Ultraviolet spectra were recorded in ethanol on a Hewlett Packard 5842 Diode Array UV/Vis spectrophotometer. HPLC was carried out on a 10cm x 1.8 mm ID column packed with 10 mm silica (Keystone Scientific, Bellefonte, PA) using a Milton Roy metering pump and a GOW-MAC UV detector at 254 nm. The mobile phase was 60:40 chloroform/hexane flowing at 2 mL/min. Melting points were taken on a Thomas-Hoover melting point apparatus and are uncorrected.

GC and/or GC-MS should have column length and ID and coating and temperature program. Solvent is unimportant as is carrier gas. Example: Gas chromatography was carried out on an HP 5980 GC using a 30m x 0.25 mm i.d. capillary column with a 25 micron coating of 5phenyV95 methyl silicone which was programmed from 40 to 250°C at 10°/min.

NMR should have name of experiment performed delay between scans and sweep width.

Polarimeter should include temperature and data obtained from standard sample.

2. The Results, Discussion & References section should start with a brief summary of your results. For a synthetic experiment, this section might start like this (using the synthesis of TiC4 as an example):

RESULTS AND DISCUSSION

The results and discussion sections should not contain experimental details

described in the Experimental section. The results should be tabulated whenever possible and representative spectral data should be included in this section. Also include any calculations including %Yield, specific rotation, refractive index temperature corrections etc. The discussion should detail the success of your synthesis, giving reaction mechanisms where relevant. If your yield was low, you should explain why using sound scientific reasons (not "I dropped the flask") and give suggestions as to what could be done to improve the synthesis if you repeated it, etc. You will also include information concerning the biological transformation reaction and its success. Include any pertinent information concerning your results and the known mechanism of reaction. Are your results in line with what is known about these types of reactions or do your results contradict the current thinking. In either case discuss the relevance of your results in light of what is known about the biotransformation. If the reaction was not successful discuss what you think might have happened and suggest what can be done to alleviate this problem in the future. The discussion should also contain a detailed interpretation of all your spectral or chromatographic data. Here is where you should discuss the spectra in as much detail as required to prove unambiguously that your compound has the desired structure and purity giving specific assignments to NMR peaks, explaining mass peaks, etc. and the relation of spectra to structure or structures to GC peaks. Mass spectral fragmentations must be reasonable.

CONCLUSIONS:

Restate the focus of the experiment and in the case of a project your hypothesis and how the experimental plan was used to investigate the problem. Summarize the results of the experiments and make connections to the hypothesis. Did your results confirm or dispute your hypothesis and use a logical series of sentences to make your case. Evaluate your synthetic and biotransformation methods and discuss whether or not they should be improved. Discuss any future experiments on this topic that are necessary to advance the knowledge of these reactions and the chemistry.

REFERENCES:

In the reference section use the citation style found in the Journal of Chemical Education. Number your references in endnote style and be consistent. Make sure you have references wherever necessary including your introduction and conclusion when you are discussing previous work in this area of chemistry.

Emphasizing the Right Thing at the Right Time:

Higher-Order and Lower-Order Concerns in Writing

Brad Hughes, English Department, University of Wisconsin-Madison

It is especially helpful in a discussion of good writing to differentiate between higher- and lower-order writing concerns. You should focus on conceptual-level planning and revisions before lexical-level revisions.

Higher-Order Concerns - Generic whole-text issues such as ideas or content, focus, genre, argument, thesis, development, organization, clarity of purpose, awareness of audience.

Does your draft respond specifically and appropriately to the demands of the assignment? (Read the Lab Guide!)

Do you understand the readings (data, field observations, lab experiment) that you’re writing about?

Do you have something worth saying? Does the draft make points. appropriately sophisticated (original, interesting, provocative...) for the assignment, the level of the course, etc.?

Does the draft have clear main points?

Does the draft match or fulfill your intentions? Does the draft do justice to your ideas?

Is the draft effectively organized? Does it follow a logical sequence of points?

Are points adequately developed and explained?

Is there appropriate and sufficient evidence to support the main points?

Does the introduction effectively signal the topic, scope, and organization of the paper?

Are paragraphs unified and well-developed?

Lower-Order Concerns – Generic lexical issues at the paragraph, sentence and word levels ...

Are there effective transitions between sections?

How can the style be improved?

Are there muddy or confusing sentences?

Where do sentence or word problems interfere with your communicating clearly with readers?

Are there any grammatical errors?

How can the word choice be improved?

Are there punctuation errors?

Have you carefully proofread your draft to make sure you caught all obvious mistakes?

Writing Style and Manuscript Organization

Adapted from "Writing a Scientific Manuscript: Highlights for Success", T. Spector (1994) J. Chem. Ed, 71, 47-50.

(Division of Experimental Therapy, Burroughs Welicome Co., Research Triangle Park, NC 27709)

Many scientists are far more comfortable performing scientific experiments than they are reporting their findings. Although they could benefit from the excellent books available on scientific writing, they may not have time to read these comprehensive articles. As a result, considerable data either are not reported or are published in ways that inadequately express their significance.

This article was written to complement the extensive reviews. It presents techniques for optimally relaying the content and meaning of scientific studies and for avoiding common problems. It begins with simple strategies to construct succinct sentences that are easy to read and understand. It then discusses key features of the standard journal sections, tables, and figures and suggests strategies for their effective construction.

Writing Style

Succinct Sentences

Well-constructed sentences are succinct. They are easy to read and understand. Succinct sentences unambiguously relay content and meaning. The five topics of this section describe methods for writing succinct sentences. You should try to construct the major part of manuscripts with succinct sentences. Less succinct sentences may be used for emphasis or to break up a string of succinct sentences that have become monotonous.