Todd:Guidelines

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Reaction Numbering Reactions need to be given a unique identifier. The number takes the following form: Your Initials X-Y-Z where X is the reaction type, Y is the attempt number and Z is the page of your lab book where the reaction appears. A reaction type means ‘starting material-arrow-product.’ If you are attempting a certain transformation of a particular starting material to a particular product, then any attempt at that reaction has the same reaction number, regardless of reagents. The reaction also has this number regardless of the outcome. It is the intention that counts. Stereochemistry of products is also important – if the intended stereochemical outcome is different, the reaction has a different number. The numbering of reactions is unique to you, you do not use the same numbers as previous people in the group even if you are repeating their work. Attempt number just increases by 1 each time you do the reaction. Screening several different reaction conditions on small scale on the same page of your lab book can be named with ‘A’ ‘B’ ‘C’ after the full name if so desired, rather than exhaustively giving each reaction a different Y, so e.g. MHT 1-2-3A, MHT 1-2-3B etc. Z is the page number of your lab book where the reaction diagram appears. This number stays the same if the reaction write-up extends over more than one page. In fact it is a good idea to begin each new reaction on the right hand-facing page of the book, allowing overspill at a later date. Example. The first three reactions in MHT’s lab book are shown below. The first reaction here is the first in the lab book. This transformation is given the number ‘1.’ It is the first attempt at this reaction, and appears on page 1, hence it is called ‘MHT 1-1-1.’ The second reaction is the same transformation (remember, regardless of reagents), so also has X = 1. It is the second attempt, and appears on page 3 of the lab book, so has the identifier MHT 1-2-3. The third reaction is a different transformation, so has a different X, and this is the first time it has been done, so Y = 1, and has been entered on page 5 of the lab book, giving MHT 2-1-5. Examples of Reaction Numbering It is a very good idea to keep a tally at the end of your book where you list each transformation separately together with the identifiers of all the attempts along with the yields in each case. Remember the identifier stays the same even if the yield is 0%. For reactions that produce multiple products, and where those products are isolated e.g. by column chromatography, additional numbers may be needed, MHT 1-1-1/1, MHT 1-1-1/2 etc, and the relevant spectra and vials should be labelled as such. Lab Book Write-up DO NOT WRITE NOTES ABOUT WHAT YOU HAVE DONE ON LITTLE BITS OF PAPER When writing your lab book, you should include all details, but in a concise manner. The reason for keeping a lab book is so that the people who come after you can understand and replicate what you have done. You are writing it for them, not for me. Your lab book must be written in pen, not pencil. You must never remove or add pages. Mistakes must be crossed out lightly, so that they may still be read. Do not use white-out/Tippex. All lab book pages must be dated somewhere, and when complete, should be signed. Ideally periodically you should get another member of the group to sign and date your lab book pages. All relevant TLC’s must also be drawn in pen, and RF values given to two decimal places, as well as the solvent system used for each. (Drawing TLC’s allows you to throw away your TLC plates) The first line of the write up for each reaction can have a brief remark about the reason for doing the reaction, to aid your memory when you come to write up your work, e.g. ‘Scale-up of MHT 5-4-36’ or ‘MHT 7-4-98 at increased temp.’ The write up should look something like this: Examples of Lab Book Write-up Points to note here: Some information about where the chemicals have come from is given Some incidental detail about what happened is given, and you have to judge what is useful and what is not. Unexpected things should always be included (e.g. ‘now-yellow’ above) ‘Benzaldehyde’ is listed in the text with no quantities, because these have already been given in the reaction scheme above References are given for the reaction. Here they are literature papers, but if the reaction has relevance to a previous reaction you have done (which is most of the time) then that unique identifier should be given here Try to minimise use of the word ‘then.’ This word is often redundant ‘Concentrated in vacuo’ implies hivac. ‘Concentrated under reduced pressure’ implies rotavap When typing this up, the formatting has to be exactly right. There are spaces between quantities and units for everything except % and degrees C. So we write ‘3 h’ and ‘1 M’ but ‘49%.’ Remember also that millilitres are abbreviated ‘mL’ not ‘ml’ Sample Characterization If you want to make a molecule, the first thing to do is check whether it’s been made before. Use SciFinder frequently (often you'll need to use it daily). You can access previously-used methods, characterization data etc. It’s the most important resource we have. Besides being able to search for literature examples of reactions you may be attempting, it's also a very rapid way to find characterization data for compounds you're making (from the "experimental properties" link). If you want to know how to handle a reagent, check e-EROS online. All of the Chemistry databases are here When you use a starting material for the first time, acquire a 1H spectrum of it to check its purity and to compare with your reaction product. In general there are two kinds of characterization required for molecules before we can publish the work. The first is for known compounds, i.e. compounds previously synthesized either in the group or by others in the chemical community. For these compounds we require three pieces of characterization that match the literature (usually a 1H NMR, IR and low resolution mass spectrum). For crystalline solids we need a melting point and a comparison with the literature value, which can count as one of the three pieces of data. For enantiopure or scalemic compounds we require an optical rotation and a comparison with the literature value. For novel compounds, we require the full level of characterization. This includes 1H and 13C NMR and IR spectra. We also need a low-resolution mass spectrum. For crystalline solids we require a melting point. If you have distilled a liquid, we require the boiling point. The ‘killer’ bit of characterization that finishes off the data is either a high-resolution mass spectrum or (better) an elemental (CHN) analysis (not both). For enantiopure or scalemic compounds we require an optical rotation and some indication of the level of enantiopurity - this must come from chiral HPLC or NMR shift reagent analysis. For any compounds that undergo some form of further evaluation (e.g. biological evaluation) we need some assessment of purity, which is usually gained from comparison of melting points (for known compounds) or analytical HPLC analysis (for novel compounds). RF values are important for internal purposes, but have questionable reproducibility between labs. Thus while we need these values in lab books and internal reports, we do not generally report them in publications. Spectra should be kept in order of their unique identifier in folders. The identifier and structure should be written clearly so that someone browsing the file can locate the appropriate spectrum quickly. Think about the people who will come after you. Generally if you're asked to produce a spectrum, you should be able to find it in a few seconds. For NMR spectra, expand regions of interest - typically maybe 3-4 expansions for a 1H, one aromatic and one alkyl for a 13C. For writing up the data you will need the exact J values for each well-defined peak, and an accurate J needs ppm values for the relevant peaks to an accuracy greater than 2 decimal places. You must make sure the integrals for peaks have horizontal start and end lines, so that the values are real. Draw the structure of the molecule on the front page of the spectrum. Assign the peaks. If the spectrum shows a byproduct, draw this structure also. If the spectrum shows an unidentified product, draw the intended reaction and product on the front page, and indicate that the spectrum does not show this product. (It’s all about putting yourself in somebody else’s shoes and asking yourself whether your spectra would be clear to them – no mental notes) For publication purposes, we almost always require scanned copies of 1H and 13C NMR spectra for the supporting information. Thus you must examine and assign spectra very carefully to ensure that there are no ‘rogue’ peaks and no large solvent peaks. Obtaining clean NMR spectra and assigning them is the most important skill of the synthetic chemist. Once you've done all the above with your spectrum, you can show it to Mat. Instructions for producing jcamp.dx files coming... Experimental Write-up Progress reports are due on the last days of March, June, September and December. Put these dates in your diary and plan ahead to get them in on time. If your report’s late, you will owe Mat one pint of Coopers Red. For each further 12-hour period that elapses, you owe Mat a further pint. That could get very expensive for you, and really great for Mat, but reports still need to be in on time. Initially paper copies are required, Times New Roman, double-spaced, unstapled. Reports should be double line-spaced and double-sided, ideally with the facing page devoted to schemes. Mat does not want to correct English language mistakes. If you feel you might make such mistakes, ensure you have your report read by someone else before you give it to Mat. Obviously no part of your report should be copied/plagiarised from any source. Everything needs to be in your own words. Once you've been through the report with Mat, and you've corrected the report, you should provide a corrected electronic copy that will be archived. The main purpose of the report is to summarize what you have achieved. However, these reports should contain everything that has gone through your chemical mind in the previous three months, and are useful places to record references and project ideas for the future. Time and effort spent on this is very helpful in minimizing the work involved in submitting publications. This is particularly the case for your descriptions of experimental work, and the documentation of spectra. Use the group characterization form to keep track of what characterization you have for a compound, and which experiments you did which generated a given compound. Experimental procedure write-up check-list: * Spaces between numbers and their units except for percentages and degrees C * NMR spectroscopy, mass spectrometry; spectrum vs. spectra * Compound numbers in bold * Minimisation of the use of the word ‘it’; don't start sentences with the word 'this' * The words Figure, Scheme and Table capitalized in main body of text Examples of experimental data Novel compound: How to write up a novel compound Known compound: How to write up a known compound It’s important you check write-ups against these examples. Things to note here: NMR spectra peaks listed in increasing value and must be assigned. 1H values given to two d.p., 13C to one. J is italicized; when two couplings, use ‘&’ and give largest first. No space between value and H for integrals, i.e. ‘1H’ not ‘1 H’ Only give the large, important peaks for MS, and give % height for them. HRMS should be correct to within 0.0008 for small molecules. CHN should be correct to within 0.4% Reference given after the name of the compound is for the procedure followed (if any) not necessarily for that particular compound. Thus a novel compound can have a reference for a general procedure that was followed. Known compounds require a final "Spectroscopic data matched those in the literature." and a reference. Molecular formula for HRMS includes extra H for MH+. When you leave the group, all your lab books and spectra remain in the department and all reports/write-ups need to be handed in digitally. Formatting of references Reference markers go after punctuation, and references are listed as endnotes, not footnotes. You will learn how to use references if you read research papers. Use the following style, exactly as shown: