ROUTINES IN THE JEB-GROUP
GENERAL ROUTINES ....................................................................................................... 2
LAB BOOK INSTRUCTIONS ............................................................................................... 4
ANALYTICAL DATA INSTRUCTIONS ................................................................................. 6
HANDLING OF HAMILTON SYRINGES ............................................................................... 8
GUIDELINES ON HOW TO USE SENSITIVE CHEMICALS ....................................................... 9
THINGS TO DO BEFORE LEAVING THE JEB GROUP ......................................................... 12
GENERAL ROUTINES
In order for the group to be efficient and our working environment to be safe, it
is necessary to establish basic routines and it is important that everybody adopts
them. Read through the following sections carefully and make sure that you have
understood them.
As a general rule all hoods must be kept neat and clean. All used equipment should be
cleaned immediately after use and returned to its original place. Also, all chemicals
and solvent flasks must be returned to their correct shelves and not stored on the
benches.
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The person who takes the last item (septa, disposable syringes, solvents, bulk
chemicals...) in the laboratory has to make sure that it will be ordered and
replaced.
 Keep common areas clean and tidy; think of your co-workers.
 Do not leave your fume-hood door open and work with it as low as possible.
 The windows must be shut or else the ventilation will not work properly.
 When solvents and volatile chemicals are transported keep them in closed
containers. (When 7 people in a lab carry around open containers with solvent
several times a day, this means a lot of solvents in the air that we breathe.)
 If you can feel the smell of chemicals it means that somebody is not using the
hood and the rest of the equipment properly.
 Clean all balances immediately after contamination.
 If you are going to weigh something that smells and/or is toxic, use the
balance in the hood between lab 1 and 2!
 Don’t store volatile compounds outside hoods or ventilated cupboards.
 Never handle volatile compounds outside the hood.
 If you use gloves to protect your hands from chemicals, take them off when
handling stuff outside the hood. Otherwise you might contaminate things that
other people touch with their bare hands, like rotavaps, and door handles.
 All glassware except solvent bottles should be treated as hazardous waste and
treated thereafter. Dirty glassware and pipettes should be stored in the fume
hood until disposal. If you want to keep dirty glass outside the hood, first
rinse it with water and acetone.
 When evaporating something toxic or smelly use the rotavap in the hood.
 Broken glass should be placed, after cleaning, in the “broken glass box”. Write a
note if it is not obvious what is wrong.
 Glass equipment that is not clean after washing should be put in the basic or acidic
wash bath and not in the drawers.
 Waste disposal:
-Needles should be thrown away in the appropriate canister stored at ventilated
place.
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-Organic solvents waste must be stored at ventilated place in the assigned cans
(halo, non-halo and water waste).
-SiO2 and contaminated gloves, drying agents, paper etc. are thrown into waste
bags kept in fume hood. This container should be changed when it is full.
-Expensive glassware (flash columns, distillation equipment, “splash-heads” etc.)
should be cleaned ASAP by hand.
Rotavaps:
-“Splash-heads” must always be cleaned and immediately put back on the stand.
-Solvent containers on the rotavaps should always be emptied and the heating
should always be turned off directly after use.
-When evaporating high-boiling solvents (PhMe, DMF etc.)/water or acid, clean
the rotavap afterwards with acetone. Empty the solvent container on the pump.
Flasks can be used for short-time storage in the freezer. Transfer your compounds
to vials for long-time storage! Mark all stored chemicals with contents and your
name.
LAB BOOK INSTRUCTIONS
Your lab book is an important document detailing all practical aspects of your
laboratory work. It is crucial to remember that other chemists, both inside and outside
the group, must be able to read and extract the information from your lab book
necessary to repeat your experiments. If this is not the case your results will be
questioned and without much value to your project members. It is equally important
that your lab book is organized in such a way that specific experiments or compounds
can be readily identified as well as the accompanying spectroscopic data.
Because immediate observations and impressions often differ from those
remembered a week or two later, it is of crucial importance to make your notes as an
original record and not to copy them later from rough ones. It takes care and practice
to produce accurate, full and clear records directly in this way but it is essential to
acquire this skill. Occasional mistakes are inevitable and these should be clearly
crossed out. If your normal handwriting is somewhat difficult to read, make a
conscious effort to write your notes in a clear bold style.
1.
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3.
Table of contents:
Use the first pages to create a table of contents. Date, experiment number, product
number, type of reaction and page number should be included. A reaction scheme
is also very useful, although it takes up a lot of space.
Experiment number:
General form AAA-X-000, example: BMO-A-023.
The first three letters are your initials. If you don’t have a middle name, use the
first two letters of your family name.
The second part is the numbering of you lab book, where the first book is A, the
next is B...
The numbers should be in consecutive order, starting with 001, 002, 003...NB:
The next lab book starts from -001 again (e.g. BMO-B-001).
Product number:
It is useful to have a unique number for each product that you make, especially when
storing analysis data (see the analytical data instructions). This means that every time
you repeat a reaction, the product gets the same number, although the experiment
number is different.
 General form AAA-000, example: BMO-038.
 The letters are your initials as described above.
 The numbers should be in consecutive order, starting with 001, 002, 003..., for
each new product. A racemic product gets a different number than the
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4.
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enantiomerically enriched product. NB: These numbers are not the same as the
experiment number. Do not start from 001 again when you start with a new lab
book, just continue the consecutive order.
If you get several products (or byproducts) in a reaction, each product gets a
unique number.
Discuss special cases with project members, in order to get a common,
satisfactory routine (e. g. if many reactions in your project will lead to the same
product but in various es/ds).
Experimental part:
Write experiment title, date and experiment number on the headline.
Make a reaction scheme with product numbers.
Tabulate all reagents with molecular weight, density, moles, equiv., weight /
volume used. Specify source / purity when appropriate (distilled, recrystallized,
columned…)
Include relevant literature references or references to your own previous
experiments.
Write the experimental clearly enough for someone else to follow! Include
workup procedure too. If you run parallell reactions, you can refer to the first
reaction in the set for all the details that are common for all the reactions.
Include TLC information (copy or make a drawing of the TLC plate) with eluation
system.
Purification method should be mentioned detailed enough for someone else to
repeat. For column chromatography, the amount of silica can practically be noted
by noting the diameter and height of the column. Also write the eluation
system(s). Distillation should be indicated with temperature and pressure.
If several fractions are collected from the column or distillation, the fractions can
be numbered I, II, III… or A, B, C… to make them easily distinguishable in
analysis data.
Analysis data: write if you have run an NMR (and if it was OK!), mp, HRMS etc,
so any person looking can easily identify if there is a point in searching for these
data in you analysis files. Mark your analysis data with the experiment number
and product structure!
Write in English and use an ink pen!
ANALYTICAL DATA INSTRUCTIONS
All the analytical data that you collect should be organized so that other people in the
group can easily find them.
1.
Storing of data:
 Mark your analysis data with the experiment number (see lab book instructions for
numbering information) and product structure. Distinguish between crude spectra
and purified compounds by adding an appropriate suffix (e.g. crude/flashed). If
you get several products in a reaction, clearly mark which fraction that is
analyzed, by adding the fraction number/letter to the experiment number (e.g.
BMO-A-023 II).
 Collect all the data belonging to the same experiment in a plastic wallet (plastficka)
with the experiment number on. Collect the plastic wallets in number order in a
file.
 Write the experiment number range and your name on the back of the files.
 Keep backup files of the NMRs, so you can leave a CD with all your files in the
group.
2.
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3.
Structure you data:
Keep a ChemDraw file with the structures of all the compounds you have made,
sorted in product number order. It is a good idea to use the automatic molecular
weight calculation at the same time! With this list, it is easy to find the product
number (and MW) for each compound, and thus find the reactions of interest in
your lab book.
Fill out an “Analysis data” list (see next page) with all your compounds. It should
contain product #, experiment # (the experiment that has the best data for this
compound), structure and specifications on what analyses have been run.
Published compounds:
It is especially important that data of published compunds can be found easily, as
someone might contact JEB about those data long after you have left the group.
So before leaving the group, sort out the data of published (=novel) compounds into a
separate file - you might have >600 experiments and <50 novel compounds, so this
helps a lot!
N.B. Keep reference samples of all new (stable) compounds, marked with product #,
structure and your name!
Analysis data: Project name
Prod. #
Exp. #
Structure
1H
13C
MS = high resolution mass (HRMS) or elementary analysis
IR
ee
[]D
MS
mp
HANDLING OF HAMILTON SYRINGES
Microlitre syringes are very expensive and need to be handled carefully. Correctly
handled they last a lifetime and since somebody else will inherit the syringes you have
when you leave this department, it is important both to make sure that they don’t get
stuck and start leaking.
1.
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2.
Cleaning
Always clean the syringe immediately after use, as this greatly reduces the risk
of it getting stuck. See to that you have a flask with cleaning solvent within
reach before you use the syringe!
General cleaning order: acetone*3, water*3, acetone*3. NB: If you’ve used
something that will react with acetone (e.g. BuLi) you need to start with an
inert solvent, e.g. pentane.
The plunger should not be removed from the syringe, as this is bad for the
Teflon part of the plunger. Only do this if you’re trying to fix a clogged
needle.
Do not leave the syringes by the sink, as they easily break.
If a syringe needle gets stuck, try the ultrasonic bath or vacuum. If it doesn’t
help, replacement needles can be ordered for the “removable needle syringes”.
Storage
After cleaning, the syringes need to be dried under vacuum for a few hours before you
can use them for any sensitive chemicals. A good routine is to store the syringes in a
desiccator or a drying tube. Used syringes don’t get put back in the desiccator until
the end of the day, when the desiccator is put under vacuum over night (or a few
hours). This makes sure that all the syringes in the desiccator are always dry.
Do not put the syringes in the oven!!! Neither the Teflon parts nor the glassware can
stand heat, and the syringes will start leaking and/or loose precision.
Do not remove the plunger for faster drying!
The choice of syringe storage depends on whether you need them to be dry, or
whether you just need them for exact measurements. In the latter case the desiccator
routine might be unnecessary.
3.
When you leave this place
Hand in the syringes to the person who’s responsible for the ordering and handling of
syringes. He/she will then make sure the next new person in the group gets them.
GUIDELINES ON HOW TO USE SENSITIVE CHEMICALS
Sensitive chemicals are usually delivered in “sure seal” bottles which allow using
them without contamination by oxygen and moisture. However, frequent use of these
bottles damages the septa which can result in decomposition of the compound. We
have therefore started to use Aldrich SureSeal bottles with extra storage caps.
Compounds which should be handled in this way are for example:
• Organometallics, such as methyl lithium, diethylzinc, trimethyl aluminium.
• Compounds very sensitive to hydrolysis, such as titanium tetrachloride.
• Anhdrous solvents (CHCl3, Dioxane, DMF, DMSO, MeOH, Pyridine, Et3N).
Some information on the handling of Aldrich SureSeal bottles with extra storage caps:
• If the compound is stored in the fridge, the argon inlet of the SureSeal bottle should
always be fitted with a septum/pipette “napp” to prevent water from being condensed
into it. Allow the flask to warm to room temperature (this may take several minutes –
have patience!) before removing the septum. Please note that the concentration given
on the label of standardised solutions refers to room temperature unless otherwise
indicated (Concentration is temperature-dependent!). If you nevertheless see some
water, remove it with a piece of paper towel before you connect the flask to your
manifold. In such a case it is of particular importance to thoroughly evacuate the tube
before opening the Young’s tap.
• Fix the bottle carefully with a clamp when using them. Then attach the argon inlet to
a
tube of your manifold, evacuate the tube for 1 – 2 minutes and charge it with argon.
Repeat this process two more times. This is important to remove air and moisture
from the tube. Open the cap of the SureSeal bottles under a sufficient flow of argon
and replace it by a septum. Once the flask is fitted with a septum, the argon flow
should be reduced (But not completely shut down – check your bubbler!) to avoid
solvent from being evaporated. Please note that evaporation of solvent from
standardised solutions of, e. g., organolithiums, increases the concentration! Always
make sure that the syringe and needle you use to take out the chemical are dry and
that the syringe was flushed with argon/nitrogen several times immediately prior to
use. Disposable plastic syringes and needles are sufficiently dry, provided that they
are only unwrapped immediately prior to use.
• Never store sensitive solids or neat high-boiling liquids in flasks fitted with septa for
a prolonged period of time. A dry septum is not really air tight (a rubber septum on a
reaction flask soaks up the solvent fumes and this provides a good seal). Always use a
glass or PTFE stopper for long-term storage.
Butyl lithium titration methods
1) The GILMAN Double Titration i
The most reliable method to determine the concentration of an organolithium is still
the double titration procedure described by Gilman 40 years ago. It is preferred over
single titration methods because it not only gives the concentration of the solution but
also provides an indication of the quality of the organolithium.
To determine the total content of base, an aliquot (usually 0.50 to 1.5 ml, depending
on the expected concentration) of the solution of the organolithium is quenched with
20 ml of water. The resulting solution of LiOH is titrated with a solution of
standardised hydrochloric acid using phenolphthalein as the indicator. To determine
the residual content of base of the organolithium, an aliquot (preferably the same
amount as before) of the organolithium is reacted with 1,2-dibromoethane as follows:
0.20 ml of dry 1,2-dibromoethane (BE CAREFUL: CARCENOGENIC) are dissolved
in 3 ml of dry DEE in an inert atmosphere. The organolithium is added dropwise with
vigorous stirring. After 5 min of stirring, the solution is diliuted with 20 ml of water
and then titrated as described above. 1,2-Dibromethane reacts with organolithiums as
follows:
R Li
Br
Br
R H
Br
LiBr
This procedure destroys the organolithium without producing LiOH, so that the
difference of the two titrations gives the exact concentration of the organolithium. A
typicale example is given below:
I. A 0.50 ml aliquot of a solution of n-BuLi in hexanes was quenched with water,
treated with a few drops of a phenolphthalein solution in water/methanol and titrated
with standardised hydrochloric acid unitil complete disappereance of the pink colour.
When titrating highly flammable organometallics such as t-BuLi, step I should be
carried out with degassed water under nitrogen.
II. A second 0.50 ml aliquot was quenchend with dibromoethane as described above.
After 5 min of stirring, the mixture was diluted with water and after addition of the
indicater titrated (with vigorous stirring – it is a biphasic system).
c(HCl) = 0.1034 N; V(HCl)I = 7.90 ml; V(HCl)II = 0.25 ml.
V(HCl)eff = V(HCl)I – V(HCl)II = 7.90 ml – 0.25 ml = 7.65 ml
c(n-BuLi) = [V(HCl)eff x c(HCl)] / V(aliquot) = [7.65 ml x 0.1034 mmol ml-1] / 0.50
ml =
1.58 M
Residual base = [0.25 ml / 7.90 ml] x 100 % = 3.2 %. This value is typical for a high
quality organolithium. If the content of residual base is higher than ~ 10 % of the total
content of base, the quality of the organolithium is poor, which may be detrimental to
very sensitive reactions.
2) Single Titration Method
This titration method widely used and is perhaps more rapid than the Gilman method
described above, but has the disadvantage that it is a measure only of the total base
concentration. You may also find that it is difficult to see the end point of the titration
as you are looking for a colour change from dark yellow to orange-red. In order to
obtain an accurate titre, it is necessary to carry out the titration at least three times and
calculate an average of the results obtained.
Li
H
N
Ts
N
BuLi
H
N
Ts
N
Li
red-orange
1,3-diphenyl-2-propane p-toluenesulfonylhydrazide (approx. 200 mg) is placed into a
dry 10 mL, round-bottomed flask equipped with a magnetic stirrer bar and septum.
The system should then be purged with argon or nitrogen and kept under a positive
pressure of inert gas.
Dry THF is then added (4 mL) via syringe and the reaction mixture stirred rapidly to
dissolve the hydrazone. The butyl lithium solution should then be added dropwise
from an acurate 1 mL syringe until the yellow solution reaches the orange-red end
point. The volume of butyl lithium required should then be noted and the following
equation used to determine the molarity of the solution.
Molarity of BuLi = [(1000 x no moles hydrazone)/volume butyl lithium]
For a discussion of other titration methods see: J. Suffert, J. Org. Chem. 1989, 54,
509.
i.
H. Gilman, F. K. Cartledge, J. Organomet. Chem. 1964, 2, 447 – 454.
THINGS TO DO BEFORE LEAVING THE JEB GROUP
Tidying up chemicals
Clean out fridge, freezer & cupboard below fume hood.
Destroy any unusable or old reagents.
Arrange others in appropriate location.
If any chemicals are not labeled with location; give to Micke.
Organize compounds that have been synthesized
Throw away tlc, gc, hplc samples.
Pass on any compounds needed in the project to the appropriate person.
Give any large quantity compounds to Micke for registration in database.
Label other compounds with structure and compound number; put in box in
the freezer at level 2.
Cleaning of lab & desk areas
Clean and tidy lab bench and cupboard above.
Clean and tidy fume hood and cupboard below.
Clean and sort glassware into general drawers / cupboards.
Clean and tidy desk and bookshelf.
Documents for storage
Lab books: Label with name and give to Robin for making of copies & PDF
file. Then pass on to the appropriate person in the project or to JEB for
storage.
Burn a CD of NMR, HPLC, GCMS data.
Burn a CD of thesis / report, publications and other documents of interest.
Analysis files should be labeled and given to Robin for storage in the
basement.
Pass on relevant literature to the appropriate person. Dispose of remainder.
Clean up the Q and C drives.
Signatures:
___________________________
_____________________________
(Leaving person)
(Lab boss)