Hamann Lab Protocols
This document is intended to serve as a guide to work in the Hamann Lab. It contains
information compiled by various members of the group regarding lab safety, standard practices
and procedures for common syntheses and experiments.
This document is in no way complete and should be used as a starting point; additional
references will be included when available. In addition, this is intended to be a working
document, thus if anyone in the group has additional comments, corrections or want to include a
new section, please send it to TWH to be added to the next version. Your contributions will be
greatly appreciated by future group members and credited in this text (furthering your legacy in
the Hamann group).
Jesse Ondersma and Kelley Hutchins are acknowledged and thanked for putting together the
initial draft of this document (July 2012).
Rule #1
If at any point while working in the lab you are unsure what to do, how to use
equipment/instruments, how to dispose of a hazardous substance, etc., please ask someone
with experience before proceeding further.
Contents:
Safety .............................................................2 – 5
Equipment ................................................... 6
Lab Notebook ...............................................7 – 8
Computers / Data .........................................9
Leave Policy ..................................................10
Conferences ..................................................10
Group Meetings ............................................11
Literature ......................................................12
Group Jobs ...................................................13
General Expectations ...................................14
1
LAB SAFETY
Good lab safety is of paramount importance while working in a chemistry lab. There are many
examples where unsafe practices in academic chemistry labs have led to serious injury, damage
and death (for one example, see article below); this risk is minimized by carefully following
established safety procedures. No behavior that compromises safety in the lab is acceptable.
Following the practices outlined here is a requirement for working in the Hamann Lab; failure to
do so may serve as cause for immediate termination.
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NEVER WORK ALONE
This is rule number one in the lab. The purpose of this rule is to ensure that you have help if
anything goes wrong in the lab; fire, injury, chemical spill, etc. This rule is potentially lifesaving
and must be adhered to.
Safety Training
All group members should complete lab safety training requirements on the ORCBS website:
Chemical Hygiene & Hazardous Waste: http://www.aware.msu.edu/TRAIN/CHI/
Lab Security: http://www.oeos.msu.edu/TRAIN/SAT/
Compressed Gas Cylinder: http://www.aware.msu.edu/TRAIN/CGC/
Safety Officer
An experienced graduate student in the group will serve as “safety officer” as their group job.
This person is responsible for ensuring proper storage and disposal of waste and to oversee
general group safety procedures. All group members are obliged to follow the suggestions of the
safety officer. If there is a difference of opinion regarding safe practices, please contact TWH as
soon as possible to help resolve the issue.
Protective Clothing
Closed toed shoes, long pants, lab coats, protective eye-wear and gloves should be used at all
times when working in the wet-lab (410).
Gloves and lab coats should not be brought into the common room (office) in order to avoid
contaminating the office area. Also gloves should not be worn when touching the doorknobs or
other surfaces that bare hands come into contact with. **Note when using lab computers gloves
should be worn.
If gloves are contaminated with oil or grease, please dispose of them immediately as to not coat
handles, keyboards, and surfaces in the lab.
When working in the lab with chemicals, eye protection must be worn, depending on chemical,
splash goggles and/or face shield should be worn.
When using acid and base baths, protective gloves, splash goggles and/or face shield, and lab
coat should be worn.
Cleaning
Except in special circumstances (NMR tubes, custom electrochemical cells), glassware is
communal. It is therefore important that glassware and other equipment be properly cleaned,
maintained, and put in its assigned place for other researcher to be able to find it. If one person in
the group is irresponsible, it can affect the entire laboratory, so it is very important that everyone
cooperates.
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All common areas, counter-tops, areas near instruments, rotovap, etc. should be left clean when
you are done working there.
All chemicals should be returned to proper storage when you are done using them. Do not leave
flammable or corrosive chemicals outside of the proper cabinet when they are not in use.
Fume hoods should be left closed when they are not actively being used.
Labeling
ALL chemicals and solutions left on benches should be labeled with your initials, date and the
full chemical name or accepted abbreviation. In addition, if the chemical is corrosive, flammable,
etc it should be labeled as so. There should be no assumptions or guesswork involved for a
knowledgeable third party to be able to independently identify the contents of any vessel. You
cannot use labels only you understand, such as “X8t4.” Think of how someone would have to
treat that chemical if there was a safety incident that required handling/disposing of it and you
were not around. Writing your initials also lets them know who to contact if there is a question;
this may save your hard made compound from being disposed of.
Example of an appropriate label: “TWH, 6/2/11, Co(bpy)3Cl2”
Waste
Write out full chemical name and amount AS you deposit waste into the waste container.
Waste containers are located in the farthermost SW fume hood in room 410. Please dispose of
waste in the proper containers, i.e. Organics, Aqueous, etc. If you are unsure of which container
to use ask someone. It may be necessary to begin a new container if the waste is not compatible.
Empty chemical bottles should be rinsed with appropriate solvent into waste containers and
placed in the hood to dry. Once dry, place them either in the hall to be recycled, or in the solid
hazardous waste if they remain contaminated.
The red “broken glassware” buckets are strictly for non-hazardous waste. Disposable glassware
(vials, pipettes, etc.) must be emptied of content into an appropriate waste container and rinsed
with solvent before being placed into the “broken glassware” buckets.
Dirty syringes, needles and razor blades (etc.) should be placed in a “sharps” waste container.
Needles should always be covered when not in use.
Chemical solids should be disposed of in separate containers. Silica and alumina should be
disposed of into their solid waste containers. Relatively unreactive compounds can be dumped
into the appropriate waste container.
Acid Baths and Base Baths
These should NOT be the first step to cleaning glassware. Make sure glass is free of debris and
has been cleaned with solvent or detergent beforehand. The Acid bath labeled “Clean Glassware”
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is for clean glassware only - this should be used for glassware as a final cleaning before synthesis
or analysis use.
Things that should never go in a base bath:
Anything with a fritted disk (the surface area of fritted glass the frit may have a hole in it when
you remove it, or, more likely, it will collapse the next time someone pulls a vacuum on it).
NMR tubes
Graduated cylinders
Volumetric glassware
Anything with metal components (e.g., syringes)
UV-Vis glassware
Wear the proper eyewear, gloves, and lab coat when using the baths.
Pyrophoric or Especially Reactive Chemicals
A good criterion for an ALD (atomic layer deposition) precursor, which is used extensively in
the group, is for it to be extremely reactive with water, e.g. diethyl zinc (DEZ), trimethyl
aluminum (TMA), and titanium isopropoxide (TIP). These are known as pyrophoric materials:
water reactive liquids, solids or gases which ignite spontaneously on contact with air, moisture in
the air, oxygen, or water. Many pyrophorics are also corrosive and toxic. Therefore special care
is needed when handing these chemicals. These chemicals are generally kept in their respective
ALD cylinders with the manual valve closed. If the cylinder is not attached to the ALD tool, it
should also have a sealed cap (with a new washer) to seal the cylinder. Refilling cylinders
should be done ONLY by the group member in charge of the ALD (see group jobs below) with
caution in the glovebox (DEZ and TMA) or in a fume hood (TIP).
Consult the Chemical Hygiene plan, MSDS sheets, and other pertinent information prior to
handling something with which you are unfamiliar
Aqua Regia
If necessary, Aqua Regia can be used for cleaning glassware in our lab. This may be helpful for
cleaning electrochemical cells, for example, where very small levels of contamination can
interfere and ruin an experiment.
The prep for Aqua Regia is 1 part concentrated HNO3 to 3 parts concentrated HCl by volume. It
should never be stored and should only be used in an open container in the hood. Never place
Aqua Regia in a closed container. After use, it should be carefully diluted by pouring into water
and neutralized with sodium bicarbonate. Once neutral, it can be disposed of down the sink.
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6
EQUIPMENT
In addition to general wetlab equipment (schlenk lines, sonicators, rotovap, etc) the following
equipment is available in the Hamann Lab:
2 x ALD (Cambridge Nanotech, Savanah 100 and 200)
UV-Vis spectrophotometer / integrating sphere (Perkin Elmer, Lamda 35)
Ellipsometer (Horiba Jobin Yvon, Smart-SE)
Solar Simulator / Monochrometer (Horiba Jobin Yvon)
4 x Potentiostats (Gamry reference 600, Eco Chemie Autolab, and 2 Eco Chemie Microlabs)
3 x Furnaces ()
Supercritical dryer (Tousimis, Samdri-PVT-3D)
Glovebox (MBraun, Labmaster)
Computers
Equipment and Instrument Use
Each piece of equipment has a person who is in charge of maintaining it and training additional
users. Everyone must receive proper training before using any equipment or instruments in the
lab. In addition, there is a person in charge of maintaining computers, software and backup.
In addition, everyone has their own lab space (hood, bench, drawers) that they are responsible for
maintaining. This includes changing oil in the pumps for schlenk lines and maintaining a clean /
safe space.
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LAB NOTEBOOK
One of the most important things you need to do is accurately write down what you did, what
happened, the final result and note all relevant data collected. If you do experiments and don’t
write everything down, then you are wasting time and materials. We cannot publish or patent
anything that was not documented thoroughly in your lab notebook to prove what was done.
In practice, there are numerous ways that you could organize your notebooks and data. It will
sometimes be necessary for TWH or other group members (including future group members who
need to reproduce your results) to be able to access your notebook data easily. Therefore,
everyone should organize their notebooks similarly.
You should label your Notebooks with Roman numerals (I, II, III, IV, …).
You should skip the first 6 pages of your notebook and use these to generate a Table of Contents
for that notebook. This greatly speeds up finding data in Notebook I when you need it to
compare with some data you just wrote in Notebook VI.
Here is an example entry for what your notebook should look like:





Date (M/D/Y)
What you are doing, e.g. “A + B → Expected Product” or “MS measurement of n-Si”
Any reference on related synthesis / experiment
Conditions: Solvent, temperature, formula weights, instrument, etc.
Narrative on how the reaction was done and any observations, or how the experiment
turned out. When applicable, discuss any conclusions you made from the experiment.
In addition, it is very helpful to have a hard copy of the data you collect. One option is to print
the relevant spectrum/graph and paste it directly into your lab notebook; in this case all the
information is in the same place. Alternatively you can make a separate “Data Notebook”
consisting of all print outs of data that you collect. In this case it is important to clearly crossreference your Notebook and Data Notebooks accurately and consistently.
For example, you can label an individual piece of data that corresponds to the experimental
description in your Lab Notebook (see example above) with a number or symbol for the specific
piece of data (in case there are multiple measurements for that set). Thus, you would label the
data with your Initials, Notebook#, date, and data#. Then all your data is in your Data Notebook
where you can find it, but also allows you to find the experimental details for a plot by directing
you to the date in your Notebook.
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COMPUTERS / DATA
The Network
Important group papers, presentations, lab information, chemical inventory, connecting to
printer, etc. can be found on the network. Connect to the network on your control panel and then
to TOMHAMANN-LAB.
When new chemicals are ordered and received, the chemical inventory list on the network should
be updated.
Back up
It is important that all of your data be saved often and backed up. Make sure to have a back up
of all your data on the server. Ben recommends using a program called SyncToy in which you
can backup your data to the network easily.
Analogous to labeling plots of your data, and chemicals, your raw data should be labeled in a
way to correlate it to your lab notebook (and thus your hard copy of worked up plots, etc.).
Therefore, a label such as TWH_IV_071712_7.XYZ would allow any of us to know that data
corresponds to TWH’s seventh measurement described in his fourth notebook on July 17, 2012.
Again, it is important to be consistent with your lab notebook and data notebook.
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LEAVE
The Hamann group policy for leave is basically the same as the departmental policy which is
stated in the The Chemistry Graduate Program Guide: “During the course of the calendar year,
graduate assistants are allowed a total of two weeks of paid vacation time. A period of absence
beyond two weeks MUST have the approval of the student’s research advisor. Additional
absences for vacation purposes may not be granted with pay. An absence beyond a period of
three weeks will be treated as a Leave of Absence.”
If you want to take a vacation for a consecutive two weeks, it would be appreciated to give three
month notice, and one month notice is mandatory. If you are traveling overseas and want to stay
longer than two weeks, you will not be paid for that additional time off: it is an unpaid leave of
absence at that point, not a paid vacation.
CONFERENCES
Going to a conference to present your research and hear about what is happening in your (and
other) field(s) is a valuable experience as part of your graduate training. My expectation is
therefore to support each group member to attend a couple of national/international conferences
during their PhD work. Note that time and money is limited, however. In addition, you should
understand that when you are attending a conference (or any professional activity) you are
representing me and the entire group as well as yourself. With this in mind, I have the following
guidelines for attending meetings.
1. You must tell me what conference you want to attend and justify why you chose that
meeting.
2. You must have a project on your research progressed sufficiently enough that it is ready
to be shared with the scientific community. This means that before applying to a
conference, you should be ready to write your results up for a publication. This can be
demonstrated in a group meeting or to me separately. If the latter, you need to be able to
show me an outline of a paper that is supported by figures and clearly explain the story of
the paper to me. You cannot present the same topic (paper) at more than one conference.
3. You must actively help support your trip financially. There are several avenues for
graduate students to get funding to support attending professional meetings including the
graduate school (http://grad.msu.edu/fellowships/travel.aspx) the local ACS section if
attending an ACS meeting (http://www2.chemistry.msu.edu/msuacs/) travel grants from
the conference you are attending.
4. You must be prepared to present before going to the meeting. This means you need to
present a very polished practice talk (or poster) to the group before you leave. You should
also have a draft of the paper that you are presenting completed; there is usually at least 3
months time between submitting an abstract for a meeting and the start date of the
meeting which leaves plenty of time to write up your results.
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MEETINGS
Group Meeting:
The primary function of a group meeting is for students/postdocs to give a relatively formal
presentation of the recent progress of their research. Ideally the presentation should take the
format of a talk at a conference, and translate to the framework of a paper. This will help you
organize your research results, allow everyone to understand what each other is working on, and
facilitate questions. The additional benefits are practice in organizing and communicating your
research; the ability to clearly explain a scientific idea critical for a PhD scientist. A good group
meeting will also open up room for discussion and critical remarks about the scientific problems
by group members, which will help identify problems - and solutions – about your research.
Suggestions by the group often lead to new ideas for further experiments and research directions.
Creativity is valued, and it is up to each person to structure and present their work as they see fit.
However, as a general rule, a group meeting presentation should start with an introduction which
gives a background to the project. It should give clear idea about the necessity and importance of
the problem to be investigated so that everybody can follow the results to come. It should also
include the current status about the knowledge of the problem from the scientific literature. The
results should be presented in a professional manner in the form of tables and graphs with
complete titles and legends. This should be followed by a concise conclusion that can be drawn
from each result. All the data and plots should be comparable to publishable data as it will be
good practice of communicating your results to a scientific community. A details description of
how to make figures and PowerPoint slides is already in our group guides.
Everyone presents approximately every 4 months (3 times a year) so you can tell a more
complete story. It is very important that everyone understands each other’s research and have a
clear idea about the progress of the overall project.
Sub-group Meetings:
Subgroup meetings are generally scheduled every other week. The purpose is to give a short,
informal presentation of your resent research results. This is also a good forum to discuss any
problems you are facing. All members of a subgroup should actively participate in this meeting
with their own research as well as during the presentations of other members. High-quality
figures and slides are also expected here since the purpose is to clearly, and efficiently,
communicate your results. In addition, this is a good forum to discuss experimental procedures
and calculations to inform other members of the subgroup about the method, as well as get
valuable suggestions from others on how to modify and improve your experimental procedures.
Though it may not be possible to finish all the experiments related to a project in two weeks, it is
possible to describe what you have learnt in this duration and the other experiments you want to
perform to get further information.
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LITERATURE
It is always a good idea to keep up with the literature. This often proves difficult since we work
in a competitive field that publishes frequently in a large (and increasing) number of journals. To
help stay aware of what is being published in a timely fashion, we work together on this.
Everyone is assigned to keep up with a subset of journals and look for potentially interesting
articles that relate to someone in the groups research. You then email abstracts and links to the
webpage to a literature coordinator who compiles these for everyone to see. Thus, we all get a
glimpse of important papers from 20 different journals every week.
Journals we need to keep up with are:
Science
Nature
Energy & Environmental Science
Journal of the American Chemical Society
Chemical Science
Journal of Physical Chemistry A
Journal of Physical Chemistry B
Journal of Physical Chemistry C
Journal of Physical Chemistry Letters
Journal of Inorganic Chemistry
Langmuir
Nano Letters
Chemical Reviews
Accounts of Chemical Research
References
Something about endnote databases
Should we compile pdf’s of papers together or just individually?
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