A Perfect Reaction: You are about to write a paper. You have fully characterized your compound, so you do not need to rerun any experiments before submission. Also, you have written an exact description of your experiment in your notebook, which another chemist can reproduce without further consultation, on the first try.
A Nightmare Scenario: It's time to write your thesis. You find that characterization data is missing, and need to repeat some experiments you ran earlier. Your notebook is not very detailed, and you have trouble reproducing the results, and have to work out the experimental conditions and a purification protocol all over again.
Designate a notebook for literature search information. Record the date, the search parameters, what references were found, and which ones you looked up.
Develop a filing system for literature/ experimental procedures that is consistent and allows you to find things easily. Everyone has different methods that make sense to them.
Ask your advisor how to organize your notebook entries- each group has different standards.
Leave space for an index at the beginning of the notebook, and record each experiment and the results by page number.
Write a complete experimental procedure.
Write in your notebook the complete reference for the literature source you are using.
Record the date you start an experiment.
Do NOT write down a complete equation (Reactants --> products) until after you have run the experiment and identified the products. Instead, start with "Reactants --> <blank>". Sometimes you don't get what you expected, and sometimes the experiment doesn't work. It is nice to be able to see what happened from the equation in the notebook.This way you can record what actually happened during the experiment.
Calculate and write down the theoretical yield of the process.
Write the concentration of the reagents in solvent (see Rule of thumb).
If you've run the experiment before, reference the earlier page for procedure. You should still record times, yield, and anything you do differently from the referenced page.
Write down the time (o'clock) you start the reaction, times of temperature changes, and the time you quench it. Sometimes recording TLC data at an intermediate time is also informative.
Record observations like color, clarity of solution, appearance of precipitate, etc.
Include all TLC plate data, including type of stain, solvent system, and any colors or UV activity. Drawing a picture of the plate or even Xeroxing it is a good idea.
Describe the workup and purification method in detail, noting any problems that occur along the way. This is very helpful when repeating the experiment.
Calculate and record yield, and describe the appearance of the isolated product.
If you have ideas for changes to improve the process, WRITE the suggestions in your notebook. These notes will be helpful for reference, the next time you run the experiment.
Develop a consistent labeling system for experiments that produce more than one product.
Starting with the most nonpolar compound, label the first product (notebook #)-A, the second (notebook #)-B, etc.
Develop a method for organizing your spectra.
Write your notebook page number on your spectrum.
Write the structure of the suspected product on the spectrum, as well as isomer ratios, if applicable.
Keep routine spectra in notebook number sequence. For example, I-10 (crude), I-10A, I-10B, I-11, etc.
Keep all good-quality spectra (1H and 13C NMR, IR, etc.) for important compounds together in their own files.
Develop a method for organizing storage of your synthetic samples
Keep everything that is an unsolved mystery.
Keep small samples of synthetic intermediates for TLC comparison.
Keep samples well sealed, well-labeled and in the freezer.
Keep any sample intermediate or reagent you made that is greater than or equal to 0.5 grams - someone might find it useful!