physical organic

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physical organic
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physical organic
synthetic organic
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physical organic
synthetic organic
total synthesis
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physical organic
synthetic organic
total synthesis
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physical organic
synthetic organic
total synthesis
synthetic methodology
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physical organic
synthetic organic
total synthesis
synthetic methodology
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physical organic
synthetic organic
synthetic methodology
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physical organic
synthetic organic
synthetic methodology
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organic fields
industrial chemistry
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organic fields
industrial chemistry
natural products chemistry
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organic fields
industrial chemistry
natural products chemistry
medicinal chemistry
many others...
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job functions
research development
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job functions
research development
production management
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job functions
research development
production management
marketing and sales
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job functions
research development
production management
marketing and sales
patent law
many others...
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1997 chemical and drug company funds for RD
18.6 billion Source National Science
Foundation 1999
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The quadrilateral principle of synthesis
Technique
Documentation
Literature
Ideas
Each is dependent upon the other
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The importance of the lab notebook

• It is an organizational tool
• It is a tool for communication
• It is a link from present to future
• It is the only way to reproduce your experiment
• It is the only way to document discovery
• It is a legal document
• It is a way of life

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The importance of the lab notebook
Put a title on the page which is descriptive and
straightforward
Each new chemical reaction should start on a new
page and include a reaction equation (graphical)
A sketch of your apparatus will help future
readers repeat your experiment
Use this space to note information you will need
for calculations, etc.
Jot down various important figures IN YOUR LAB
BOOK! Never use scrap paper
Its generally a good idea to set reagent
additions apart, so you can spot them easily for
write-ups
It is a very good habit to record not only the
amount of reagent as added (i.e., mL), but
also in terms of grams, moles, and
equivalents Not only will you need this data
for the write-up, but doing it as you work can
help you spot-- and prevent--mistakes from
calculations
Always include a description of any reagents and
starting materials--this is a way to
establish tracability for your products
Use the left 1/3 of the page for scratch use the
remainder to record your data in some readable
flow
Sign and date each page as you finish it
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The importance of the lab notebook
Make sure you leave a page trail throughout the
experiment for future reference
Remember--one fundamental aspect of an experiment
is OBSERVATION. Make sure you record things
that may be important. However, dont get bogged
down in minutiae. For example, it is probably not
that critical to know that the heating mantle had
a grey cord. On the other hand, the fact that a
yellow color developed in the reaction
flask might be an important clue.
If timing something, note the clock when you
start and finish, and jot this in your scratch
section
Seems pretty obvious, but always jot down a
mnemonic word for your scratch data. Its easy to
grab the wrong item from a jumble of numbers
Behold!--the ONLY acceptable way to correct an
error in a lab notebook. Draw one line
through the error and write the correct data
as closely as possible. It is interesting
to note that this error arose from making the
false assumption that the cyclohexanone was 100
pure. Had I not gone back to record the label
info, this error would have gone uncorrected.
It is supremely important that your lab book
be legible and logical. Write it not
for yourself, but for the one who
comes afterwards.
If there is space left on a page at the end of
the day, draw a line through the blank space,
then sign and date page
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The importance of the lab notebook
Headings make it easy to follow the flow and also
help later in finding things quickly
Indispensable Habit No. 425 ALWAYS take a TLC of
your reaction mixture before you work up!
Sketch TLC data into your notebook. Make sure
you record all pertinent details, like
what solvent system was used, and how
you visualized the spots
Its a good idea to calculate your yield on the
fly-- that way you can see if there are
any issues you need to address. This particular
case is also a good illustration of why you NEVER
discard the aqueous layer until you have
the product in hand.
Dont forget to tare your Rotavap flask!--and
make sure you record this data directly IN YOUR
LAB NOTEBOOK!
Behold!--the sample number. This is
dash
your initials
consecutive no.
volume no. (usually 01)
THIS page no.
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Other elements of documentation

• Remember to affix important TLCs
• Spectra and analysis (NMR, IR, C,H,N)
• Organization is absolutely essential
• Be legible!
• Dont write a travelogue!
• Make good use of visual organization
• Get into the habit of signing and dating!

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Who needs the literature anyway?
What do I use it for?
Thorough background search for a research
project - what has been done? - where does my
work fit in? - has anyone else had my idea?
How do I - synthesize a particular compound? -
purify a particular compound? - carry out a
certain technique?
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Background Search Strategy
Chemical Abstracts (CA)
Science Citation Index (SCI)
STN Online
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Background Search Strategy
now
1900
1950
Awareness
high
low
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Background Search Strategy
now
1900
1950
Awareness
high
low
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Search Strategies Mechanics
Compound
Keyword
carbapenem antibiotics
chiral oxazolidinones asymmetric Diels-Alder
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STN Database Structure
Registry
CA
WPI
ChemCats
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STN Database Structure
Registry File
CA File
- Structure - Chemical Name(s) - CAS RN No. -
Molecular Formula
- Keywords - Bibliographic Info - Abstracts -
Registry No.
A file of compounds
A file of words
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Registry File
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CA File
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Search Strategies Compound
REG
CA
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Search Strategies Substructure
Substructure
collection of compounds
REG
CA
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Search Strategies Text-based
CA
- Truncation with ? - Boolean operators
L1 and (synth? or prepar?)
L4 not L3
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STN Command Language A Primer
d scan allows you to see certain fields of the
hit list at no charge.
Navigation gt file reg opens the registry file gt
file ca opens the abstracts file
e expand. This function shows you how many
hits a search term would be, free of charge.
Your term will always show up as E3.
Display gt d scan gt d cbib abs 1-
Search gt e C6H12O6/mf gt s E3
recommended format for display
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Some handy search terms
s bivens/au author s C6H12O6/mf molecular
formula s aniline/cn chemical name s
1745-12-2/rn registry number s novel/ti title s
1998/py publication year s L1/p preparation
What about substructure?
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In thinking about your project

• Remember the basics
• Always know whats going on
• Think mechanistically
• Read the current literature
• Always have an eye toward the project goal
• Dont be afraid to explore, but
• Beware of old shoes
• Always know why you want to try something

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An important philosophical aspect
BOSS
Research Advisor
Student Researcher
Student Researcher
Student Researcher
TECHNICIANS
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An important philosophical aspect
A community of scientists
Student Researcher
Student Researcher
Research Advisor
Consultant
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Important considerations of technique

• Keep safety first and foremost
• Never construct a closed system!
• How can I prevent contamination?
• What do I need to exclude (water, etc.)?
• How do I avoid any physical loss?
• What are the properties of my product?

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Even more important considerations

• Remember were all learning technique
• Be diligent--dont get discouraged
• If possible, find someone who has done it
• Dont confuse issues of technique with
  issues of project design

If we knew what we were doing it wouldnt be
called research