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Group Guide to the Practice of Chemical Research
Lectures, Seminars and Communications Work Habits When will I graduate? An efficient chemical laboratory depends on cooperation and a sense of unity. Personal
differences aside, an unwritten ethical code of the academic chemical laboratory behooves you to
work for and with all group members. This laboratory has an extended community in the
Grossman, Anthony, Daunert, Bachas, Butterfield and Meier Research groups. To a lesser
degree, you owe these people you cooperation as well. Likewise our broad sense of community
extends to the other divisions in the Chemistry Department. Undoubtedly your cooperation will
be returned when you need it the most during your time at UK.
The following is a compendium of my vision of research group leadership. I encourage
constructive expressions of opinion from you concerning all aspects of the our research
operation.
All laboratory workers must wear some form of eye protection in the laboratory at all times. The
level of protection should meet the potential (worst-case) threat. Eyeglasses are a bear minimum
at all times. Goggles are much more effective protection and should be worn whenever dealing
with materials and reactions that might splash. When you have visitors in the laboratory it is
your responsibility to make sure that they comply with the eye protection rule.
Any unlabeled "mystery" bottle may be highly dangerous. Some chemicals are dangerous only
when mixed with others or upon exposure to water. All bottles (research samples, distilled dry
solvents, stock solutions, anything you put in any container whether temporary or permanent, etc)
must be clearly labeled. All permanent or semipermanent distillation apparatus must be clearly
labeled. Acceptable labels are written in large, clearly legible letters on white paper and securely
taped/affixed (by string tag) to the container. The tape must wrap completely around the bottle or
vial. Materials that are highly dangerous (carcinogenic, pyrophoric) should be so labeled.
Glass solvent bottles can be dangerous: they can break and spill large quantities of volatile,
flammable material. These bottles should be returned to the metal solvent cabinets when not in
use. Storing these bottles on the floor where they can be kicked and broken is not acceptable.
While somewhat less convenient, the flame-resistant cabinet is the only appropriate place to store
flammable solvents in glass.
Pouring wastes down the sink is not acceptable. Solvents from
evaporators, used silica gel,
used pump oil, transition-metal-containing materials such as Cr, Hg,
and Mn salts, and unwanted
side products (DCU, Ph3P(O), etc) are to be placed in the appropriate
container, carefully labeled, and taken to the stockroom. The stockroom
sees that the waste materials are sent
to appropriate disposal facilities. The stockroom can provide you with
the required labels and
with instructions on suitable containers. BE CAREFUL! Do not mix
incompatible materials in
the same container! For example, do not mix oxidizers (HN03, CrO3) with
flammable organic
compounds. Most organic solvents can be mixed (EtOAc, ether, hexane,
etc.). Be sure to put
halogenated solvents in a separate bottle. Many reactive materials
(BuLi, SOC12, etc.) will have
to be quenched before disposal. The Aldrich catalog contains a helpful
guide to the proper
methods to dispose of materials they sell.
Organic solvents are disposed of in red 5 gallon carboys. Before you dispose of anything in these
containers estimate the volume and the content and record this data on the appropriate clipboard
above the carboys. When the carboy is about 3/4 full fill out the required data in the waste
handling sheet and transport the carboy down to the stockroom for disposal. Make sure that your
name and your advisor's name are clearly marked on the container so it finds its way back home.
In about a week the container should come back to the stockroom.
You are expected to deal with other members of this research group with respect and common
courtesy. This includes keeping your area of the lab clean enough so that others are not repulsed
from working, cleaning the balances if you spill reagents, and washing communal glassware
thoroughly and promptly returning it to the proper storage place so that others can use it.
Untidiness in common work spaces like the chromatography station is unacceptable. Use the
facility and leave the facility in a condition so someone else can work. If this cannot be done,
send the group E-mail apologizing for the mess and make clean up of this
area job one when you come to work in the morning. We all have to share the lab, and all
members of this group are expected to contribute to it's maintenance.
Literature, Seminars, and Communications Are you wondering why you are here? Well, everyone has their own reasons to go to graduate
school. Putting aside sophistries, it is the purpose of graduate study to reach the limits of
human knowledge in a chosen field, and to contribute new knowledge through research.
Most of what you will learn as a graduate student will be self-taught. It is impossible for you to
learn everything you need to know by taking classes. Reading the chemical literature is an
essential part of your graduate education, and the sooner you make a habit of reading journals,
the sooner you will be passing cumulative exams and the faster your research will progress. At a
bare minimum, you should be reading J. Am. Chem. Soc., J Org. Chem., and Angewante Chem.
Int. Ed. Engi. and perhaps a few others. Try to read them as they come out. If you wait for a
month, the backlog will get to be so large you will not be able to read it all. Do not attempt to
read all of every article - read the table of contents (for awareness) and select ca. 3 articles to read
carefully/critically. Be sure to look through the experimental sections as well as the text of the
paper.
I expect all members of this group to attend all organic and departmental seminars, unless there
is a direct conflict with a class you are taking or teaching. Feeling "lost" during a seminar is
natural. Don't get discouraged: keep attending seminars, listen carefully to the speaker, ask
questions. Understanding will come with effort. Get involved; ask the speaker questions. This involvement is an important
part of your education.
The graduate and undergraduate research experience not only involves manual labor, but also
presents the opportunity for you to think and input thoughtful contributions. These span
laboratory operational innovation to starting new projects. At certain times I may even involve
you in grant-writing. You will certainly be involved in paper writing. Most of the experimental
section in the paper should be your own prose. Writing the narrative section of the paper will
involve all authors. The document will change hands multiple times until we can find enough
common ground to simply dot the i's and cross the t's. In some cases this will happen after you
have left. My arms are long. This is the nature of the game. No matter where you go, we will
find some way to communicate in order to hammer out the fine details of our communication
with the scientific community. In order for me to interact with you at this level, know the
scientific ins and outs of your project cold,
including the peripheral biological, biochemical
and/or physico-chemical arguments. The necessary knowledge cannot be
obtained by coming to
work and doing what you are told to do everyday. Coming to work and
performing
experimentation is below the minimum expectation. While experimentation
is the first thing you
should worry about, cultivation of your knowledge in your field pulls
in a close second. You are at a platinum time in your life/career at
this moment? You can choose a
sub-discipline in which to specialize. Never before or after will you
have such flexibility. Never
before, because you did not possess the knowledge to make informed
decisions regarding your scientific career. Never after, because the
pace of your schedules will accelerate to mach x. The
information in any particular field is expanding at an astounding rate.
Between these two facts
you will find it difficult to afford yourself the necessary time to
attain enough lateral mobility to
change your scientific mission.
I expect quarterly written progress reports from all members of the group (graduate students and
undergraduates). These documents fulfill a variety of functions. A progress report is a carefully
written presentation of the research plan, the approach you have used, your results (with
complete experimental), and a discussion of their impact on your project. Progress reports will
ensure that I understand what you have done and what you have left to do, and it gives you an
opportunity to collect your data and to write a section of your dissertation. It is my hope that
these reports will expedite the often painful process of writing papers and writing your
dissertation. It also gives you an opportunity to write documents required by the school. Both
undergraduate and graduate research programs have written requirements.
One of the most critical skills a Ph.D. is expected to master before graduation is efficient
problem solving. As most of you will learn, one very effective way to find a solution to a
problem is to ask other people, both in this group and in other research groups. Your interactions
with other chemists are of unparalleled importance, and it is essential that you be capable of
unfettered conversation.
It is not possible, particularly for a first year student, to predict a graduation date. However, it is
possible to list the factors that can lead to an earlier graduation. Clearly, the sooner your course
work, cumulative exams, and research projects are completed successfully, the sooner you will
be in a position to write a dissertation. Every time you complete one of these requirements, you
move closer to graduation. The largest fraction of your graduate career is spent working on your
research project. How much time should you expect to spend in the lab? A good minimum is 55
hours per week. Most students in their second through fourth years will work substantially more
than 55 hours/wk. Another factor is the "quality" of your time - do you work consistently
throughout the day, or do you spend 50% of your time talking with friends, smoking, drinking
coffee, goofing around on the web or sleeping in the library? Dedication to your project will lead
to earlier graduation, stronger letters of recommendation, and better theses, all of which are
important parts of your application for future employment.
If you have any questions concerning my expectations, feel free to come see me to discuss them.
Remember, prospective employers will have similar expectations. The more education you get
the more responsible you are expected to be in your employment. This means you work harder,
in general you have more job satisfaction and your financial rewards are greater.
The laboratory notebook plays a central role in scientific research as a faithful record of the project. Events involving falsification of laboratory records and the subsequent legal ramifications have
brought into question society's belief that all scientists faithfully report their data. Your lab
notebook cannot be considered a "diary" or a "private matter": it is a public document that must
be surrendered upon request to the agencies that fund our research. Write your notebook
knowing that your writing and your data are likely to be scrutinized by someone who is
looking for inconsistencies, omissions, and forgeries!!
It is critical that everyone in this research group maintain a complete and up-to-date notebook
that contains all of the data and observations made in their project. A lab notebook must be an
accurate record of what you did and what you observed. Brief explanations of why you
performed certain experiments or procedures are also helpful, but a true discussion of the work
belongs in research reports, papers, and dissertations. The following features must appear in all
notebooks.
This will be a listing of every experiment you performed. The table of contents is extremely
handy when you are writing papers or your dissertation. The table of contents should develop
along with your notebook. Reserve the necessary amount of pages at the beginning.
Each experiment should begin on a new page and it should have a clear title: usually this is the
reaction that is described on that page, but it might be a VT NMR experiment or other
experiment. The date must also appear on the page. An experiment that involves a reaction
should begin with a clear listing of the compounds that were used and in what amounts (grams
and moles). You should also list the source of these compounds, if purchased cite the source, if
you made the material refer the reader to the synthesis of the compound in question in your
notebook or in previous notebooks. This should be followed by detailed description of the experimental procedure,
including the order and method of addition of the reagents, the temperature, inert atmospheres,
stirring, etc. It should include observations, including changes in appearance (a ppt, or a color
change), temperature, or other parameters. Use procedures from The Journal of Organic
Chemistry as models. At the end of the procedure should be recorded the details of the isolation,
purification, appearance, quantification (grams, moles, and percent yield), and should list the
methods used to characterize the sample.
page# date ------------ ------------
Graphic Depiction of the Reaction, (mechanism optional) Or title or other descriptor of the work at hand --- - ----- ------------
reference: authors J. Am. Chem. Soc. 1996, 118, 935-7 Procedure: Ethylchloroformate (5.4 g) dissolved 5 mL benzene was added to a solution of aziridine (2.3 g) and triethylamine (5.2 g) in benzene 20 mL. Work up/isolation: After slow addition and agitation at room temperature the contents of the reaction vessel were distilled. The fraction that distilled at 21 mm Hg and 60-63 °C was collected and analyzed. Purification: Describe distillations (pressure, temperature, at which fractions were collected), chromatography (scale weight of Silica gel used dimensions of column, mL/min, retention time, mass of fractions). Describe crystalization conditions in terms of solvent mixtures and temperature at which crystalization occurred. Characterization: Include nmr, IR, UV and mass spec data in text format, other procedures, titrations etc.
USER-NOTEBOOK-PAGE-NUMBER CONVENTION Every sample you synthesize and every experiment you run is to be labeled with a unique number that will be forever associated with that sample. This number will consist of your initials, the number of your lab book, and the page number in that lab book. The page number on which the sample is first isolated will identify it uniquely. Every laboratory notebook page that makes reference to the particular sample calls it by the page number and note book number on which the sample was first synthesized. For example, the preparation of some material described on page 122 of the my second notebook would be given the number ACG-II-122. If several compounds were isolated during that experiment, they would be given the numbers ACG-II-122-a, ACG-II-122-b, etc. If I isolate a benzyl derivative of ACG-II-122-b in my fourth notebook on page 3, I will refer to the starting material as ACG-II-122-a and I will refer to the product as ACG-IV-003. These numbers are to be placed on the vial that contains the sample and on all spectra of that sample. You may find me reading through your lab book for information. Be thorough, be complete, be
up-to-date, and be accurate. Keep a book that you can be proud of, one that you will not be
ashamed to show to anyone at any time. Remember it is an open document.
Characterization of New Compounds Known compounds do not have to be completely characterized. You need to be able to correlate
the spectra found in the literature (IR, NMR, chromatographic, boiling point, melting point, etc)
to your compound. To know if you have to characterize material you have synthesized, you must
go to the library and look the compound up. If you think the material should be known, you need
to find it in CAS, Beilstein, or some other reference source. If you can not find the compound,
and you or your advisor think the compound is known, a computer literature (name or structure)
search may be in order. It is extremely bad form to submit a publication or a thesis reporting a
known compound as a new compound.
New compounds need to be throughly characterized. A completely characterized new compound
effectively excludes the chance that the material could be anything else. If the compound is not
well characterized the data may not be publishable and hence might as well not have been
gathered. A new compound characterized to publishability has the following supporting
information.
FILE THE CHARACTERIZATION DATA FOR EVERY NEW COMPOUND IN A SEPARATE FOLDER AND LABEL THE FOLDER ACCORDING TO THE USER-NOTEBOOK-PAGE-NUMBER CONVENTION.
A paper is an organized description of hypotheses, data, and conclusions, intended to instruct the
reader. Papers are a central part of research. If your research does not generate papers, it might
just as well not been done. "Interesting and unpublished" is equivalent to "non-existent."
Realize that your objective in research is to formulate and test hypotheses, to draw conclusions
from those tests, and to teach these conclusions to others. Your objective is not "to collect data."
A paper is not just an archival device for storing a completed research program, it is also a
structure for planning your research in progress. If you clearly understand the purpose and form
of a paper, it can be immensely useful to you in organizing and conducting your research. A
good outline for the paper is also a good plan for the research program. You should write and
rewrite these plans/outlines throughout the course of the research. At the beginning, you will
have mostly plan; at the end, mostly outline. The continuous effort to understand, analyze,
summarize, and reformulate hypotheses on paper will be immensely more efficient for you than a
process in which you collect data and only start to organize them when their collection is
"complete." Formulation of the communication while the work is in progress allows for an
interactive relationship between what is said and what is done.
An outline occupies a central place in the writing of papers, preparing seminars, and planning
research. An outline organizes a paper, including the data which supports the text. You should,
in fact, think of an outline as a carefully organized and presented set of data, with attendant
objectives, hypotheses, and conclusions, rather than an outline of text. An outline sketches a
statement about which multiple authors can come to consensus.
An outline contains little text. If you and I can agree on the details of the outline (that is, on the data and organization), the supporting text can be assembled fairly easily. If we do not agree on the outline, any text is useless. Much of the time in writing a paper goes into the text; most of the thought goes into the organization of the data and into the analysis. It can be relatively efficient in time to go through several (even many) cycles of an outline before beginning to write text; writing many versions of the text of a paper is slow. All the writing that I do --- papers, reports, (and, of course, slides for seminars) -- I do from
outlines. I urge you to learn how to use them as well.
The classical approach is to start with a blank piece of paper, and write down, in order, all
important ideas that occur to you concerning the paper. Ask yourself the obvious questions:
"Why did I do this work?" "What does it mean?" "What hypotheses did I mean to test?" "What
ones did I actually test?" "What were the results?" Did the work yield a new method or
compound? What?" "What measurements did I make?" "What compounds?" "How were they
characterized?" Sketch possible equations, figures, and schemes. It is essential to try to get the
major ideas. If you start the research to test one hypothesis, and decided, when you see what you
have, the data really seem to test some other hypothesis better, don't worry. Write them both
down, and pick the best combinations of hypotheses, objectives and data. Often the objectives of
a paper when it is finished are different from those used to justify starting the work. Much of
good science is opportunistic and revisionist.
When you have written down what you can, start with another piece of paper and try to organize
the jumble of the first one. Sort all of your ideas into three major heaps (A - C)
A) Introduction Why did I do the work? What were the central motivations and hypotheses? B) Results and Discussion What were the results? How were compounds made and characterized? What was measured? C) Conclusions You might want to make a third list based on which topics open natural segues to other topic. Which transitions are made in which order optimizes the flow of the prose? What does it all mean? What hypotheses were disproved (hypotheses are never proved)? Which
hypotheses are still possible? Which hypotheses are definitely non-viable due to this work? What
did I learn? Why does it make a difference?
Next, take each of these sections and organize it on yet a finer scale. Concentrate on organizing
the data. Construct figures, tables, and schemes to present the data as clearly and compactly as
possible. This process can be slow, I may sketch a figure 5-10 times in different ways trying to
decide how it is most clear (and looks best aesthetically).
Finally, put everything outline of sections, tables, sketches of figures, equations-in good order. When you are satisfied that you have included all the data (or that you know what additional data you intend to collect), and have a plausible organization, give the outline to me. Simply indicate where missing data go, how you think (hypothesize) they will look, and how you will interpret them if your hypothesis is correct. I will take this outline, add my options, suggest changes, and return it to you. It usually takes 4-5 iterations (often with additional experiments) to agree on an outline. When we have agreed, the data are usually in (or close to) final form (that is, the tables, figures, etc., in the outline will be the tables, figures, ... in the paper.) You can then start writing, with some assurance that much of your prose will be used. The key to efficient use of your and my time is that we start exchanging outlines as early as
possible in a project. Do not, under any circumstances, wait until the collection of data is
"complete" before starting to write an outline. No project is ever complete, and it saves
enormous effort and much time to propose a plausible paper and outline as soon as you see the
basic structure of a project. Even if we decide to do substantial additional work before seriously
organizing a paper, the effort of writing an outline will have helped to guide the research.
4. The Outline What should an outline contain? Title: Authors: Abstract: Do not write an abstract. That can be done when the paper is complete.
Introduction: The first paragraph or two should be written out completely. Pay particular attention to the opening sentence. Ideally, it should state concisely the objective of the work, and indicate why this objective is important. In general, the Introduction should have these elements: The objectives of the work. The justification for these objectives: Why is the work important? Background.- Who else has
done what? How? What have we done previously?
Guidance to the reader: What should the reader watch for in the paper? What are the interesting
high points? What strategy did we use?
Summary Conclusion: What should the reader expect as conclusions?
Results and Discussion. The results and discussion are usually combined. This section should
be organized according to major topics. The separate parts should have subheadings in boldface
to make this organization clear, and to help the reader scan through the final text to find the parts
of interest. The following list includes examples of phrases that might plausibly serve as section
headings:
Synthesis of Alkane Thiols Characterization of Monolayers Absolute Configuration of the Vicinal Diol Unit Hysteresis Correlates with Roughness of the Surface Dependence of the Rate Constant on Temperature The Rate of Self-Exchange Decreases with the Polarity of the Solvent
Try to make these section headings as specific and information-rich as possible. For example,
the phrase "The Rate of Self-Exchange Decreases with the Polarity of the Solvent" is obviously
longer than "Measurement of Rates," but much more useful to the reader. In general, try to cover
the major common points:
synthesis of starting materials characterization of products methods of characterization methods of measurement results (rate constants, contact angles, whatever)
In the outline, do not write any significant amount of text, but get all the data in their proper place: Any text should simply indicate what will go in that section. Examples of this text are as follows. Section Headings Figures (with captions) Schemes (with captions and footnotes) Equations Tables (correctly formatted)
Remember to think of a paper as a collection of experimental results, summarized as clearly and
economically as possible in figures, table, equations, and schemes. The text in the paper serves
just to explain the data and is secondary. The more information can be compressed into tables,
equations, etc., the shorter and more readable the paper will be.
Conclusions. In the outline, summarize the conclusions of the paper as a list of short phrases or sentences. Do
not repeat what is in the Results section, unless special emphasis is needed. The Conclusions
section should bejust that, not a summary. It should add a new, higher level of analysis, and
should indicate explicitly the significance of the work.
Experimental. Include, in the correct order to correspond to the order in the Results section' all of the paragraph
subheadings of the Experimental section. In advanced versions of the outline you can also
indicate what information will go in the Microfilm section.
Start writing possible outlines for papers early in a project. Do not wait until the "end".
Organize the outline and the paper around easily assimilated data -- tables, equations, figures,
schemes -- rather than around text.
Organize in order of importance, not in chronological order. An important detail in writing papers concerns the weight to be given to topics. Neophytes often organize a paper in terms of chronology: that is, they give a recitation of their experimental program, starting with their cherished initial failures and leading up to a climactic finale. This approach is completely wrong. Start with the important results, and put the secondary results later, if at all. The reader does not care how you arrived at your big results, only what they are. Shorter papers are easier to Type all papers double-spaced (not single or one-and-a-half spaced), and leave two spaces after colons and after periods at the end of sentences. Leave generous margins.
Assume that we will write all papers using the style of the American Chemical Society. You can
get a good idea of this style from three sources:
1) The journals. Simply look at articles in the journals and copy the organization (J. Am. Chem. Soc., J Org. Chem., Biochemistry, Nature, Science) you see there. 2) The ACS Handbook for Authors. Useful detail, especially the section on references, pp
106-114.
1) Do not use nouns as adjectives: ATP formation reaction product Use formation of ATP product of the reaction
2) The word "this" must always be followed by a noun, so that its reference is explicit.
Do not use this is a fast reaction this leads us to conclude use this reaction is fast this observation leads us to conclude
3) Describe experimental results uniformly in the past tense. Do not use Addition of water gives product use Addition of water gave product
4) Use the active voice whenever possible. Do not use It was observed that the solution turned red. Use The solution turned red. or We observed that the solution turned red. Usually the active voice abbreviates sentences. Parsimony in sentence structure is best.
5)Complete all comparisons. Do not use The yield was higher using bromine. Use The yields obtained with bromine were higher than yields obtained with chlorine. Substitution of chlorine with bromine typically resulted in higher yield of product A.
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