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To: The Group
Subject: Protocol for writing reports and manuscripts.
Below is listed a protocol that should be followed in writing manuscripts and reports. We will discuss these
items at the group meeting, and then decide on the final protocol which will be mandatory for all future
manuscripts.
Before starting a paper use the Open Header command from the Document menu. Select page, date and
time. This identifies the hard copy unambiguously.
1.
Each manuscript will be assigned a unique identification "number' from initial drafts to submitted
manuscripts to revised final submission. The "number" will be of the following type
Initials_KeyWords_Draft#_Date.
Example: MFO_Persistent_D1_070101. This would be a paper by M. Francesca Ottaviani on persistent
radicals which was written on 7-1-01 (Draft 1). Every revised draft should be saved with the date which it
was complete. Do this by using the Save As command on the Mac and then changing the date, i.e.,
MFO_Persistent_D1_070101revised on July 8, 2001 would be saved as MFO_Persistent_D1_070801. This
procedure automatically gives you a backup copy labeled the date of the penultimate version. There is a
redundancy in putting both date and draft, but it can be helpful when one is trying to figure out what version
you have.
2.
All Figures, Scheme, Tables, etc. are to have the identification number and key word when they are
saved. This is particularly important when one is dealing with more than one paper. Every paper may have a
Figure 1, but in a file of Figure 1s it will be hard to find the one that you want. It is also important to use a
footer to identify each Figure. One may have a printout of the figure but not know its ID. The footer will be
that ID. Figures and Tables should be labeled in accordance with the ID of the draft: Example:
MFO_Persistent_Fig1_D1_070101.
3.
All reference sections are to be executed in the EndNote style. A separate document titled with the
identification goes with all manuscripts. Example: MFO_Persistent_Ref_D1_070101
4.
In preparing Figures remember to always have a structure of the molecule investigated and other
pertinent conditions (solvent, temperature) on the Figure. This is also required of slides that you present for
research reviews.
5.
6.
Structure Numbering or Labeling

Every structure that is being investigated should be drawn and displayed in the paper.

The structures may be displayed as a collection in a Chart or in the vicinity of their introduction
in the text.

The proper name of each structure should be given in the Experimental Section (IUPAC), but a
common name may be used to refer to the structure in the text.
Schemes

7.
Schemes should be networks of equations, elaboration of structures, cartoons, etc.
Figures

Figures should be reserved for data display.
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Equations

Simple mathematical equations or chemical equations should be numbered (1), (2), (3) etc. to the
right of the equation and appear in the text immediately after they are introduced.

All graphics should be easy to understand and interpret. Whenever possible, figures of structures,
together with number or label, should be placed in the Figure or Scheme.

When applying several spectra or fits to a Figure, be sure that each is clearly distinguishable from
the other. When you run out of different notations for a data set, you probably have too many items
in the Figure.
Data Presentation
1.
If you are going to make a mechanistic conclusion in comparing two sets of data, you must indicate
error limits in some manner, i.e., a minimum of two experiments or the use of computer statistical
analysis of spectral data.
2.
Spectra presentation should be consistent throughout the paper and similar to prior publications of
the Group.
Mechanical Items
1.
For proofing purposes, print a double spaced copy (not space and a half!).
2.
References should appear immediately after the Conclusion (and Acknowledgements) of the text.
3.
Tables, Charts, Schemes, Figures should appear immediately after the References. Legends for each
should appear before they are presented. Captions need not appear on Graphics, but are o.k., too.
Place a page break to separate each Legend.
Below are some details that should be helpful in preparing a manuscript or report.
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I.
General comments
All papers and reports should be set up in the following manner:
A. General introduction and background
1. What are the general issues being investigated?
2. What are the classic experiments that precede your work?
3. What is the paradigm that you are going to use to determine your experimental
approach, techniques, parameters, and interpretations?
B. Purpose and motivation
1. You should indicate in the introduction the purpose and motivation of your report. For
a manuscript you should indicate the motivation for the research. There is no single
motivation, but you should give the reader some idea of the context that is driving the
research. This would be different if the paper were dealing mainly with synthesis or with a
detailed analysis of spectroscopy for example. The group is supported by agencies that are
promoting research in biochemistry, environment, materials science, among other topics.
You should have some familiarity of the issues that are relevant to the field of your topic.
C. Receiver (reader). What to keep in mind. These ideas are valid for writing and for giving oral
presentations.
1. Classic receiver mindsets
a) Apathy
(1) He's not interested to begin with
(2) Your job is to get his/her interest aroused
b) Skeptic
(1) Not against your message, he's above it
(2) He's had trouble with similar systems
(3) Your job is to show him ideas in a new light
c) Opponent
(1) He's hostile to your message
(2) Your point of view may be threatening
(3) Your job is to eliminate the threat and get him to join you
d) Believer
(1) He's on your side to begin with. Don't lose him!
(2) Your job is to strengthen his belief in you
e) Rationalist
(1) He's willing to listen and to be convinced
(2) He's inclined to believe a message with sound reasoning
(3) He's inclined not to believe sloppy or non-existent reasoning
(4) Your job is to present a good argument backed by good data
2. You must understand the mindset and paradigms of the receiver
3. You must be explicit about your assumptions
4. You must have a series of logical, self-consistent statements
D. Impact
1. To achieve purpose and impact, you must form a picture
2. What picture do you want in the receiver's mind?
3. If there is picture in your mind, don't expect one in his
E. Design
1. The specific design: based on desired purpose/receiver/impact
F. Execution
1. The physical appearance of the executed report is important
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2. A sloppy appearance suggests sloppy scholarship
3. Anticipate using the report or its parts in the future
a) The report should be produced so as to be reusable
b) Artwork and Tables are especially reusable
c) Proper artwork can be used for slides/transparencies
II. General approach
A. Observations
1. Usually this means techniques. What techniques are you using?
B. Data
1. Usually you don’t report observations, but data which is the observation transformed
into a number or structure through a formula or algorithm.
C. Parameters
1. Usually the data, it numbers is relatively meaningless until you transform it into a
parameter through the use of some paradigm or assumed mechanism.
D. Variables
1. Variables are usually thermodynamic in nature (temperature, pressure, concentration,
applied fields, etc.) or structural in nature (composition, constitution, configuration,
conformation, isotopic, etc.)
E. Parables
1. This is the story you’re going to tell about the observables, in terms of the variation of
parameters.
III. Working draft
General comments: Precision in language is crucial in successful writing. Precision means not being
ambiguous or vague. Since it is impossible to define everything from scratch it is of utmost
importance to decide on your audience's paradigm when you begin.
Each paragraph should communicate a single idea. You should be able to express the elements of
the idea in a single sentence.
1.
2.
3.
4.
5.
Decide at the beginning the information you wish to communicate in the report.
Define your purpose in writing the report.
Gear your report to the proper reader mindset
Use a proper format
Differentiate observations, data and interpretations.
a) Observations can be described in such a manner that they can be reproduced at
any time.
b) Data are observations translated into scientific notation. No one has ever
observed a rate constant, or a quantum yield or an aggregation number.
c) Interpretations result from translating data into ideas based on conventional
paradigms. Paradigms change, so do interpretations. Observations and data do not.
A. Logistics
1. Figures
a) General format: Structure on Figure, other data
2. Tables
a) Use Table format in word or spread sheet
3. Scientific processes
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Keep clear in mind the differences between observables, data, parameters, variables, interpretations
and conclusions. Observables are what you see. Data are observables processes through a model.
Parameters are mechanistic forms of the data that can be related to variables by a theoretical or
empirical model. Interpretations are the picture we deduce about the molecules from the behavior of
parameters as a function of variables. Conclusions are the interpretations we believe are most likely
to be correct.
The Final Draft
I. Title, Abstract
A. Don’t agonize about the title and abstract at the beginning of the paper. It can be done quickly at
first and then redone after the paper is finished.
II. Introduction
A. Open with a summary of important points you intend to make
1. Short statement of purpose and scope
2. What are the basic issues?
3. What are the likely forces of significant findings?
B. Brief review of specific related systems
1. What are the closely related recent publications?
2. How does the current study fit with respect to these and the field in general?
3. What are the goals of the reported investigation?
C. Brief review of your approach
1. Use the general approach described above
2. Methods and procedures
3. Paradigms to be assumed
4. Criteria for evaluation
III. Results
A. Describe the results in the results section. Save the interpretation for the Discussion section.
B. Substrates
1. What are the chemical substrates being studied?
a) What are their topological, geometrical and chemical variations?
2. What are the reactive intermediates involved?
3. What are the environments for the systems studied?
C. Receptors (environments)
1. What are the chemical receptor systems being studied?
2. What are their topological, geometrical and chemical variations?
D. Chemical methodology
1. How are the chemical substrates synthesized?
2. How are the reactive intermediates being characterized?
3. How are the stable isolable products characterized?
4. How are the environments being characterized?
E. Techniques
1. What are the analytical methods being employed?
2. Why are you using these techniques compared to other possibilities?
3. How are observations being taken into data?
4. How good is the data?
a) Mass balance
b) Statistical analysis
c) Reproducibility
IV. Discussion
A. Review the paradigm discussed in the introduction.
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B. Use the paradigm to check the consistency of the results and to cross check
C. Does the paradigm survive or is a paradigm shift needed?
V. Conclusions
A. Conclusions are evaluations of results in light of current paradigms
B. What do you know now that was not known before?
C. What recommendations can be made for future research?
D. Did the paradigm hold? Does it have to be modified?
E. Remember that paradigm shifts are strongly resisted by the community and must be strongly
supported by the results.
VI. Experimental
For physical type papers, use the format of J. Phys. Chem.
For organic type papers, use the format of J. Org. Chem.
A. This section can come earlier or at the end
B. The interested reader should be able to trace your methods
C. The source of all chemicals should be identified
D. A competent chemist should be able to repeat your results
E. Use ACS journal styles (JACS, JOC or JPC) in writing up the experimental. Do not be inventive
here! Use the conventional methods.
X. Acknowledgements
A.
B.
C.
D.
Who helped you with the experiments?
Who helped you with the ideas?
Who read the manuscript for you?
Be sure to include information on the grant that supported the research.
XI. References
References are one of the most important parts of a manuscript. Readers are pleased when they can
document or review material as the result of your citations.
A.
B.
C.
D.
E.
F.
All references must be dumped into EndNote for future reference
Always be careful to properly cite and reference
Acknowledge the prior work by reviews or key papers
Acknowledge the most recent how stuff
Remember the authors in the field get your stuff to review
Remember these authors will be upset if you
1. Fail to spell their names correctly
2. Fail to properly acknowledge their work
3. Remember: These may be the same authors who will be refereeing your future papers
and proposals.
XII. Further readings
A. T. Spector, “Writing a Scientific Manuscript”, J. Chem. Ed., 71, 47 (1994).
B. “Ethical Guidelines to Publication of Chemical Research”, Acc. Chem. Res. 26, 75 (1993).
C. Waldemar Adam’s ppt on writing a scientific paper.
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