HIST MEDIEVAL PHILO
HIST MEDIEVAL PHILO Philos 11
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This 30 page Class Notes was uploaded by Kiarra Sipes on Saturday September 12, 2015. The Class Notes belongs to Philos 11 at University of California - Irvine taught by Staff in Fall. Since its upload, it has received 24 views. For similar materials see /class/201937/philos-11-university-of-california-irvine in PHIL-Philosophy at University of California - Irvine.
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Date Created: 09/12/15
LECTURE 11 15 Differentiability in a neighborhood of a point implies continuity at that point 5 min If f is differentiable on an interval la b and if 6 lies in that interval then f is continuous at cl Veri cation For 11 nonzero of either sign and of small magnitude consider the function 6 11 7 c 9hf c f W Note that litho gh 0 ice the limit exists and equals zero We then have limh olfch fcl EmbedWW WW limhu0hf c 7 hmhl0hgh 0 7 01imh09h 0 which shows that f is continuous at cl 16 An Alternative Form of a Limit that Gives the Derivative 5 min 7 r f a i 213 23 The connection with the above is seen by taking 1 a hr 17 Algebraic Properties of Derivatives 171 The Sum Rule for Derivatives Assume that f and g are differentiable at at Then d d d a HI 91 lza f zm g zm or in short lF 91 THEN Ma f W 9 01 This formula is derived directly by using the de nition of a derivative given in Lecture 10 an exercise which you should do 172 The Product Rule for Derivatives Assume that f and g are differentiable at at We ask fry1lza 77 or in short lF fzgz THEN 101 77 Woerpel Group Survival Manual 041 103 Notes on Personal Safety A copy of the UCI Environmental Health and Safety Chemical Hygiene Plan is located in a white binder in the clean room above the small food refrigerator Use it as a resource for speci c safety chemical storage and procedural information Everyone should peruse it at least once and a periodic refresher wouldn t hurt Although we often avoid wearing the proper protective equipment it is strongly advisable to do so The level of personal protection employed should be commensurate with the hazards involved Safety glasses with side shields are the norm but they will not adequately protect you from liquids or ying objects coming at you from an oblique angle Double or even triplegloving is common when working with particularly toxic or caustic reagents Because of the potential for situations to escape our control it is imperative that any extremely hazardous procedure be carried out with the utmost care according to well established and practiced methods For this reason one should NEVER work alone If no one is in your lab go next door or across the hall and make them aware of your presence Check up on one another periodically Exercise common sense at all times A weary or distracted mind leads to mistakes Be cognizant of the safetyrelated items in your lab and in other labs near you Familiarize yourself with the contents of our first aid kits in case you ever need to use them Replace items immediately upon usage so they may be available in the future There are eyewash stations in every sink and attached to both safety showers in our hallway located outside room 5004 and across the hall between rooms 5012 and 5024 Kits are available for common chemical spills and for mercury spills Know their location their contents and how to use them KEY Older students are ALWAYS available for consultation on any lab matter and especially with issues of safety No one is ever unapproachable Notes on Group Safety Chemical Waste 0 Proper labeling handling and storage of chemical waste is crucial Labeling has been made simpler due to recent adoption of the one label per bottle protocol Each label must list the exact date when the waste was first generated Waste carboys 5 gal must always reside in secondary containment bins and we will eventually have a large ammable cabinet explicitly for storage of these containers Small 4 L bottles of liquid waste stored in the fume hood or bench top must also have secondary containment and be capped when not in use this is the most forgotten rule Extremely hazardous waste eg chromium tin lead cannot be kept longer than 9 months Accumulation of group chemicals in fume hoods or on bench tops is discouraged Avoid pouring anything down the drain you wouldn t store in your refrigerator Polluting the environment in this fashion and likewise consciously permitting hazardous liquids to evaporate in the fume hoods is illegal Throwing chemicals or needles into the trash is strictly prohibited Utilize the solid waste and sharps containers respectively for these materials Be conscious of where waste goes when it is disposed of improperly Compressed Gas Cylinders ALL cylinders must be secured with chains in a wallmounted bracket unless they are currently being moved to a place where they eventually will be chained We are in the process of maximizing the amount of wallbracketschains in the hall closets Excess cylinders cannot merely be buttressed against chained ones or against walls If we do not have a bracket to accommodate a cylinder we should not have that cylinder Cylinders only become dangerous when they are punctured or if the top is removed These situations are most likely to occur when a cylinder falls which is most apt to happen when it is not properly chained vide supra Cleanliness Security Other Keeping personal and common work areas clean and uncluttered is bene cial to the work environment In addition general cleanliness decreases the amount of potential safety hazards We can be cited by the EPA for operating in an excessively cluttered or dirty workspace Periodically police your area and others as well It should be common sense but maintain vigilance for suspicious persons or activities operating in and around the lab and building Persons who would not ordinarily belong in a research lab should immediately identify themselves Even EPA officials cannot enter the labs without EHampS accompaniment Technically speaking bicycles are not to be kept in the research labs because they are a trip hazard and may block a potential escape route We may be cited for disregarding this minor issue As safetyrelated issues arise feel free to ask any colleague the safety coordinator who if applicable can relay a message to the pertinent party Rama Singh the PS safety coordinator rpsinghuciedu office in the stockroom or Keith How to use the solvent system ARGON A gt VACUUM closed closedlt B C v B open V open You should nd the solvent bulb in one of the two possible resting states Resting State Empty Both stopcocks on the bulb should be screwed shut Valve A is on vacuum valve B is open and valve C is closed To remove solvent when the bulb is in this resting state close valve B to place the bulb under static vacuum turn valve A to argon then follow steps 5 8 Resting State Full Both stopcocks on the bulb should be screwed shut Valve A is on argon valve B is open and valve C is closed If you want to use the solvent already in the bulb simply unscrew the top stopcock fully do not let your needle scrape against the side of the stopcock insert your needle remove solvent and put the bulb back in the appropriate resting state If you do not want to use the solvent in the bulb open the bottom stopcock and blow out the solvent into the discard bottle Close the lower stopcock and follow steps 1 8 Evacuate the solvent bulb by turning valve A to vacuum Wait until the pump stops pulling Re ll the solvent bulb with argon by turning valve A to argon Repeat the evacuation back ll procedure steps 1 2 two more times Evacuate the solvent bulb once more by turning valve A to vacuum Once the pump has stopped pulling close valve B to place the bulb under static vacuum then turn valve A to argon If using methylene chloride open the valve on the bottom of the left methylene chloride column Open valve C and pull down solvent Once enough solvent has been collected close valve C to stop solvent ow PP P Equot 0 l Open valve B to place solvent bulb under argon Unscrew the top stopcock fully do not let your needle scrape against the side of the stopcock insert your needle remove solvent and put the bulb back in the appropriate resting state 8 If using methylene chloride close valve on left methylene chloride column If you leave solvent in the bulb please record the time and date of collection on the white board to minimize waste If you need to collect a large amount of solvent you may clamp a roundbottomed ask with a 2440 joint to the groundglass joint at the bottom of the solvent bulb Open the lower stopcock and then follow steps 1 8 Notes 0 These solvents are expensive so try not to remove more than you need 0 DO NOT place valve A on vacuum while valve C is open or solvent is in the bulb 0 Please contact Sarah if septa are decomposing or if a solvent is empty or any other problems How to use the Solvent Stills Location of stills l iPrZNH and EtSN are located in 5004 2 hexanes benzene and acetonitrile are located in 5024 Before turning on the still Make sure that the stills are under a positive N2 or Ar atmosphere 2 Make sure there is an adequate enough solvent for your usage If the solvent level is low notify the stillperson to refill the still 3 So people are aware that you are using a still please place a tag or sign with your name on it on the still Bringing up the stills 1 Turn up the variac to the setting indicated on it for filling the stills 2 Allow the solvent to re ux and rinse down the sides of the receiving bulb 3 Once the bulb has been completely rinsed close the valve and begin to collect solvent DO NOT REFLUX TO DRYNESS 4 Upon collection of the desired amount of solvent turn down the variac to the resting setting indicated on it 5 Allow the solvent to cool before taking it up in a syringe Use proper syringe tech niquel l l 6 Once complete drop the solvent Operating Instructions to the IIP6850 GC and autosampler Resting state All gases turned off at tank valve with Shutdown method chosen The last person to leave at night is responsible for shutting down the GC if samples are not currently running Ready State All gases hydrogen helium and air turned on at tank valve with the appropriate method chosen Green box at the lefthand side of the screen will indicate ready Sign Up Sign up for use in GC logbook record samples and any problems encountered Communicate with previous user to ensure availability of GC Sample preparation Use vials made available for the GC The vials from the stockroom do not fit Filter your material lmgmL through a silica plug celite or basic alumina also ok eluting with EtOAc or diethyl ether Column fractions can be used as samples as long as the solvent is appropriate NO HALOGENATED SOLVENTS ARE TO BE INJECTED IN THE GC Select Appropriate Method click on OVEN Edit times and temperature Please do not edit other parts of the method without consulting the GC manager For single sample 1 choose single sample button 2 Run control gt sample info 3 Enter Operator name keith Subdirectory KAW File Name kawII36D Location Vial 9 Sample Name kawII36 Comment reaction at 2h 4 When information is lled in click Run Method or OK then Start For sequence of samples 1 choose sequence button 2 Sequence gt Load Sequence Choose appropriate sequence EX KAWiGCS 3 Sequence gt Sequence Parameters 4 Enter Operator Name keith Subdirectory KAW 5 Sequence gt Sequence Table 6 Enter Information I Location I Sample Name I Method Name I InjLocation I Sample Type I I Vial 8 I KawII36frl I Kwoerpel I l I sample I 7 To enter more samples click Append Line to create new line Fill in information as described in 6 8 When table is complete click Run Sequence or OK then Start Old GC HP5890 Operating Instructions 0 Why use the HP5890 It contains a column more suited for more polar compounds If non adequate separation is seen with the HP 6850 try the HP5890 NO HALOGENATED SOLVENTS ARE TO BE INJECTED IN THE GC This means you must rotavap your NMR samples and redissolve if necessary This will contribute to longer detector life and better performance from the ignitor coil RESTING STATE Injector ON 250 OC Detector ON 200 OC Oven ON 100 OC Gases ALL OFF on GC panel H2 and Air are OFF at tank He is ON at tank This allows the column to be ushed with a continuous yet minute ow of He to keep the column clean STARTUP 1 Turn on H2 and Air at tank valves and on GC panel 2 Turn detector temperature up to 275 OC and let gases ow through the column 5710 minutes 3 Ignite detector a get signal reading Push SIGl A ENTER SIGl on GC panel should read zero or nearly so b push ignite button and hold ame above the detector A pop should be heard followed by an increase in the signal Check ignition by holding a pipette or Vial above detector 7 condensation should be observed If GC does not light after a few attempts ask the GC manager to adjust the ow rates andor clean the detector 4 Turn AUX GAS on at GC panel 5 Turn oven up to 250 0C at GC panel for 20730 minutes Signal should read N 3 but less than 5 without uctuation Then turn the oven down to your desired temperature at GC panel METHOD On GC panel 1 Push INIT TEMP button type in starting temperature then ENTER 2 Push INIT TIME type in holding time at starting temperature then ENTER 3 For a ramp push RATE enter for degrees per minute then ENTER Otherwise type in 0 degmin then ENTER 4 Push FINAL TEMP type in ending temperature then ENTER 5 Push FINAL TIME type in holding time at final temperature then ENTER INJECTION 1 Zero detector by pressing ZERO and ENTER 2 Flush syringe with your sample three times 3 Use syringe to inject roughly 10 ML of sample and simultaneously press START button Be careful to not bend needle 4 Flush syringe with EtOAc three times SHUTDOWN Return GC to resting state described above and sign the LOGBOOK Remember to report any GAS CYLINDER SHORTAGES to the GC manager Glovebox Standard Operating Procedure General Use 1 Antechamber Normal Materials glassware plastic metals To bring items into the box be sure inner door is closed 1 Fill the antechamber with N2 by changing the black valve from evacuate to N2 ll 2 Remove the outer door by unscrewing the door Place your materials into the antechamber and replace the outer door 3 Place the valve to evacuate and allow the pump to pull the antechamber down to lt100 mTorr Partially re ll the antechamber with N2 Repeat the process 45 times 4 Re ll the antechamber with N2 and the materials can be brought into the box using the inner door of the antechamber 5 After you are done place the materials in the antechamber if it was never open to outside close inner door open outer door and remove items Replace door and always leave the valve on evacuate 2 Antechamber Other Materials solids liquids With solids and liquids a closed system under ambient pressure must never be used when pumping something into the box through the antechamber 2 The system must either be vented ie vial containing solid has septa with a needle in it or a round bottom tted with a frit or completely under vacuum ie a liquid that has undergone three freeze pump thaw cycles 3 Paper products are porous and require special handling such as being pumped on in the antechamber overnight prior to use never bring in cork rings paper towels or other paper products 3 Use of Gloves 1 Never use gloves with bare hands if a ring watch or bracelet is worn Cotton gloves can be used to cover rings 2 When using liquids it is recommended that secondary gloves are worn over the box gloves 3 Take extreme caution when handling sharp objects 4 Common Protocols 1 When using solids always clean the area with tape Kim Wipes will only push the solids around 2 V Any trash that is generated should be placed in the ziplock bag or in the glasswaste can unless a volatile liquid is on the item then it must be brought out of the glove box 3 Leave the glove box the way in which you found it 5 Precautions taken with volatile bp lt 200 C liquids 1 Prior to using volatile liquids the circulator must be turned off be sure red light on the control panel is not lit 2 When nished with the box purge the system by turning the yellow handle at the top ofthe box to a 45 angle 3 Allow the box to purge at least 5 minutes if volatile liquids were used for a short time and typically 10 15 minutes if the circulator was off for 30 120 minutes 4 After purging is complete press the circulation button a question on the screen will tell you to continue with ins you must press the ins button to turn the circulator on If there are any problems please notify Tim or Tom immediately Instructions to use PerkinElmer 1600 FTIR To turn on the IR simply turn the knob that is located behind the IR counterclockwise Press Enter Press Backg followed by Scan to identify background scanning From the screen press 4 initiate background scanning Once background scanning has completed at the bottom right of the screen under scan it should read Ready 6 Lift the lid to the left of the IR screen and place your sample in the slot 7 Press Scan 8 From the screen press 1 6 to initiate scanning of your sample 9 Once the scanning is complete the bottom right hand comer of the screen under scan should read Ready 10 Your spectra will come up on the screen 11 To mark peaks 959 Press Shift and Peaks simultaneously to introduce cursor onto the screen Using the arrows will allow you to move around Stop at the peak that you wish to label and press Shift and Mark simultaneously Repeat steps 2 and 3 as many times as necessary Press Shift and Peaks to remove the cursor from the screen 959 12 Turn on plotter and follow the directions to the right on the plotter Replace step 5 with Press Plot 13 Once done plotting remove the pen from the carousel of the plotter and CAP IT 14 Turn off plotter remove your sample and dim the monitor screen by turning the knob on the back of the IR counterclockwise 15 Finally sign your name PI date and the of samples you took an IR of on the notebook right next to the plotter HPLC Varian Prostar instructions Before use all solvents must be ltered and sonicated Use solvents for HPLC only Make sure that there is enough solvent in both bottles before pumping so that no air gets into the pumps Injection is manual Before injecting the sample the injector should be in the LOAD position Flush it with solvent several times before and after injecting Before exposing the column to the solvent you need to make sure that there is no air coming out of the pumps Depending on the column and solvent used the instrument can serve as both normal and reverse phase HPLC However some of the columns tolerate only certain solvents and can be destroyed by even very small amounts of other ones It is therefore imperative that you know what solvent the person before you used and if necessary to ush the pumps for extended periods of time Pumps are labeled A and B If you are changing the solvents make sure that the more polar one goes to pump A To turn on the HPLC 1 Turn on the detector and both pumps on the instrument itself 2 Attach the column you wish to use 3 Choose HPLCdata acquisition on apple menu 4 Under DATA select SHOW DATA TRACE window shows up 5 Under CONTROL select SELECT PUMPS window shows up 6 Under CONTROL select MANUAL CONTROL window shows up Here you can set the wavelength ow and solvent ratio 7 Under SYSTEM select SYSTEM STATUS This will allow you see the actuals during the run 8 On MANUAL CONTROL window set the solvent ratio only pump B is shown 9 Type in the ow warning by setting the ow you are setting the pressure too Make sure that the pressure ow you use is in the allowed range of the column otherwise both pumps and the column can be destroyed 10 To start the pumps press START RAMP button Before than make sure that the solvent is not going through the column but through the outside loop That is achieved by loosening the black knob on the side of the instrument the first time you use the HPLC ask somebody who knows how to use it to show you 11 Let solvents ow until there are no more air bubbles coming out of the pumps Then you can tighten the black knob mentioned in 9 so that the solvents go through the column Again make sure that the pressure you are using is ok 12 Press START ACQUISITION on the MANUAL CONTROL window 13 Let solvents ow for 30 min or until the base line on the data trace window is at Then hit STOP ACQUISITION in the manual control window 14 Injection Use the at needle syringes provided Make a solution of your sample for analytical columns optimal concentration is 1 mgml for preparative it depends on the column and it can be a lot higher Inject your sample into the injection loop Then turn the loop into the INJECT position and hit START ACQUISITION 15 When your run is done hit STOP ACQUISITION and then print your chromatograph Monitor the pressure during the run and write it down in the log book 16 You may want to let the solvents go for additional time to rinse the column 17 Sign the log book and rinse the injection loop 9 8 How to Perform Routine Computer tasks on the Apple G4 Computer Burning a CDRCDRW Put a blank CD IUCD RW in the CD RW drive of Woerpel G4 Type in a name for the disk Select the format type Use the default setting The other settings are for audio CD s or MP3 s Drag the desired les onto the CD IUCD RW disk Be careful not to exceed the storage space on the disk From the Finder click on the Special drop down window Click on Burn CD Click Burn Make certain that you have copied all of the desired files to the disk This IS the point of no return When you are nished the disk should eject Label the disk and case Congratulations you have successfully backed up your information Using the HP Precision Scan Pro When Scanning from the Platen Glass 1 2 3 4 Place document on the platen glass Use the updown arrow key on the scanner to select the le typelocation to which you would like to scan Microsoft Word Adobe Photoshop Acrobat Reader printer etc Hit the scan button picture of the scanner Ignore the other buttons Remove your document from the glass Using this method you can only scan one document per file I believe If you have multiple documents per le use the following When Scanning from the Automatic Document Feeder 1 Place your documents text up with the top of the document heading into the document feeder 25 page limit 2 Open up HP Precisionscan Pro software from the Apple MenuScanning dropdown window Select the desired output type from the drop down window grayscale black and white etc DO NOT ADJUST THE RECOMMENDED OUTPUT RESOLUTION Select the Scan To tab Select the Image type you wish to scan to Word Photoshop Acrobat Reader etc Click Scan When the last page in the feeder has run through reload the feeder to scan more images into the current document and press Scan or press Done 8 Your file will be in Macintosh HDHP Scanning SoftwareScanner Output E 8094 Alternatively you can carry out steps 13 and then select the Save option Select the file type you wish to save as typically PDF and you can then select the desired saving location Steps 67 are the same Printing Transparencies from the IIP4100dtn Printer You can print your group meeting transparencies directly from the printer in the clean room HOWEVER you must follow the following guidelines Use only the HP LaserJet monocrome transparencies 92296T Print only from the manual feed tray Tray 1 Print only 13 transparencies at one time and then allow the printer to rest a minute Printing too many transparencies at one time can cause the printer to heat up and MELT THE TRANSPARENCIES ONTO THE ROLLERS Make sure you TURN OFF the dupleXing option when you print transparencies DO NOT have the printer set to print on both sides This probably won t be a problem for ChemDraw but it will be for PowerPoint Transparencies can be found in the bottom drawer of the large filing cabinet in the clean room The Complete Notebook 597 These policies are adapted from are adapted from Organic Synthesis and from Professor James Nowick s instructions to students The following is a description of the information that should be included in experimental procedures describing the synthesis of compounds These guidelines are adapted from Organic Synthesis and are to be followed in writing notebook entries quarterly reports written reports for the advancement to candidacy quotoralsquot doctoral dissertations and experimental procedures for publication The objective in writing preparative procedures is to provide a quotrecipequot by which others who are less experienced than yourself eg students with a good laboratory course backgrounds who are just beginning research could reproduce your synthesis Use abbreviations that can be deciphered easily The following details should be included 1 Quantities of reagents and solvents used How quickly key reactants was added Times and temperatures used How the crude product was isolated Include the mass of the material To write an experimental you will need to include volumes of solventssolutions used in workup How the product was purified The yield both mass and percent A description of the purified material color phase oil solid etc Characterization of the material that is what spectral and analytical data did you acquire 9 any unusual apparatus apparatus For this information to be included in written reports it must be included in your notebook In addition to all of the details described above a good notebook entry should include 1 a heading eg an equation 2 the date 3 a table of reagents MW mass equivalents density volume and sourcesample number as well as purification drying etc relevant references to other notebook pages and the published literature detailed observations drawings of TLC plates GC traces should be photoreduced and taped into the notebook 1H NMR spectra of crude products numbers should be assigned to spectra Your designation should include your initials notebook number page number and some indication whether the spectrum is the first second etc on the page I designated my data as KAWHI38A for 1H NMR s 13CKAWIH38B for the 13C NMR etc the A and B indicating that something was the first or second spectrum for that page I must confess I never took more than 26 spectra per page 10 concise description of spectra e g 1H NMR shows desired product contaminated with 5 starting material 11 conclusions and suggestions for future experiments eg rerun at lower temperature or the more informal went to tar Heww 9 89 908994 50 12 elemental analysis forms should be taped into the notebook with relevant page references General Procedure for Performing 3 Reaction When carrying out an experiment the following should be performed except for special circumstances CI 1 Literature or personal precedent should be considered For example if you figured out that the ethyl derivative was hydrolyzed at 22 C try the methyl case at 22 C 2 Make sure you have all the reagents before you get too far DD Decide on a reasonable scale for the experiment For most reactions about 1 mmol i 01 mmol is good for a first try if you have enough material Otherwise decide scale accordingly If the starting materials are cheap lt050 g and the reaction seems sure to work consider running the reaction on a few grams 4 Make the time to set it up and to work it up You can purify the product later if the reaction works Don t let reactions sit around they aren t wine V39 Distill reagents and solvents 0 Get the reaction going gt1 Make sure you have an NMR and a TLC of your starting material you will have to know how it changed during the course of the reaction Save a TLC sample 8 TLC reaction right after you get it started Maybe it is already done 50 Write the reaction up in your notebook with the weights you actually used 10 Monitor the reaction by TLC The only exception is when starting materials or products decompose in air or on TLC When reaction is over by TLC work it up Again consider literature or personal precedent 12 GET A CRUDE 1H NMR Assign peaks to starting materials products reagents etc No exceptions How else do you know what happened 13 Purify by ash chromatography recrystallization distillation sublimation etc 14 Get 1H NMR s of major fractions from your purification and assign peaks 15 Get yields 16 Write up notebook 17 Catalogue NMR s 000000 I I3 DUI DUI I 18 Wash your glassware Clean up CI 19 Ifthe product is a new compound get mp IR 1H and 13C NMR DEPT or HMQC if compound is structurally complex or assignment isn t clear MS low res high res a if optically active and elemental analysis CI 20 If compound isn t fully characterized with yield and full experimental it cannot be reported in a thesis or in the literature Silica Gel Chromatography Information Copyright E Vedejs U of Michigan This material summarizes the most important preparative separation methods preparative layer chromatography PLC and ash chromatography FC It is important to learn both of these techniques Neither one is well suited for all of the following tasks 1 isolation of pure samples 2 determination of material balance 3 determination of yield 4 product recovery of several gram scale FC requires less preparative time PLC plates require 23 days to dry It is often a very useful way to obtain at least some pure material in cases where the total yield is not critical FC also has the advantage to remove the worst polar contaminants from a mixture by plug ltration through a layer of cheaper silica gel prior to using the good column However FC demands constant attention during the separation and it is seldom done with sufficient care to achieve total separations Although there is no inherent reason why total separations could not be achieved by FC the amount of time and level of skill required to do this on a column is higher For difficult separations each repeat separation requires the same constant monitoring and many fractions have to be collected to minimize the risk of overlapping sections The PLC technique requires the same skill level for any separation and total separation ie no overlapping fractions is achieved by reducing plate loading This advantage is especially important when it is necessary to establish the upper limit for isolated yield from a given reaction Although there are a few tricks that must be learned to achieved maximum resolution there are some major advantages 1 whenever two components are separated by 01 Rf or more they can be completely separated by PLC 2 the Rf values will translate directly from an analytical plate to a wellmade prep plate there is no guess work regarding fractions if the zones can be visualized 3 separations require minimum monitoring once the optimum solvent system is known no further optimization is necessary for subsequent repeat separations Using FC a similar level of control is possible if 1 the column is uniform 2 the solvent system has been optimized to give Rf 03 for the desired zone 3 the column is adjusted for different loading by changing the diameter not length If these precautions are taken and the instructions provided by Still et al attached are followed carefully the desired material will elute predictably Successful FC requires high quality solvents because more solvent is needed to elute a column than to develop a plate and to extract individual zones We have experienced few if any problems using the solvents at UM but technical grade solvents cannot be trusted They usually contain nonvolatile residues due to polymerization of unsaturated impurities air oxidation and other contaminants If high purity solvents are stored for a long time after air exposure they too can become contaminated Puri ed samples from FC that show extraneous NMR signals due to solvent residues are not adequate for characterization purposes or for the calculation of yield unless the contamination can be determined and reported Unless such samples can be recrystallized distilled or carefully PLC d or HPLC d after FC the data will not be acceptable for publication or for thesis purposes especially in cases where the exact mass sill be used to establish the molecular formula MS data can be misleading for a variety of reasons a tiny impurity can produce the molecular ion so sample quality is especially important and the same level of purity is needed as for samples that give satisfactory elemental analyses Samples that show ANY extra unknown peaks in the NMR spectrum are automatically suspect PLC also has inherent limitations The technique is laborious than FC if material has to be purified on several gram scale No more than ca 200 mg Rf difference gt 025 or 50 mg Rf difference ca 01 can be separated on one 8 X 2 mm plate PLC can also be difficult if the mixture is not UV active However PLC is superior for sample characterization and for the determination of yield because it minimizes solvent use and routinely allows for total separation of the mixture It is important to learn both techniques and to know when each one is appropriate FC can be used whenever fast access to reasonable pure material is desired especially for reactions done on a gram scale or larger PLC can be used to obtain a reliable optimum yield of a reaction that is being optimized For this purpose the reaction can be done on ca 100 mg scale or less depending on the difficulty of separation If the best yields require working on a larger scale then the reaction is diluted to a known volume and an appropriate aliquot is taken for PLC separation The overall isolated yield is then calculated Remember that the isolated yield is the recovery of 1 material or an estimate based on recovery adjusted for the of a known impurity There is no deception involved if you separate 110 of the reaction by PLC and report the overall yield based on 10x the recovery from one PLC plate because the procedure will report isolation by PLC Anyone who wants to use 10 plates will be able to reproduce the reported result Yields based on FC or PLC can be deceptive unless there is a way to assay solvent residues Another misleading practice is to determine product ration by NMR and then to calculate the yield from the weight of mixed fractions or crude product This is unacceptable because there is no way to isolate this yield and often there is no information about what impurities really are It would be misleading to report the yield of a mixture without reporting the yield of the separated material that was used for characterization Yield results for FC must identify the weight and purity of all fractions that are used in the yield calculation Furthermore the experimental procedure MUST identify the number and volume of all fractions and must indicate which fractions contain which products Otherwise there is no way for someone to reproduce the isolation method unless you use the same conditions each time optimized Rf value column height use of solvent combination for elution Gradient chromatography is notoriously difficult to reproduce because it is seldom described with sufficient detail DO NOT use gradient unless you have to it will be easier to write up your results if you stick to the recommended procedure below and separations will be easily predictable PLC is superior to FC for the purification of samples for characterization but analytically pure samples may require a second small scale ca 1020 mg separation using the minimum of silica gel and reliable solvents Semiprep HPLC can also be used Regardless of the separation method solids must always be recrystallized to a good melting point from a specified solvent and distillable liquids should always be distilled prior to HRMS analysis Analytical TLC DIMENSIONS Recommended plate size 25 67 cm vertical horizontal depends on the number of spots l4 per spot is ample room Shorter plates will not do well with difficult mixtures longer ones are OK for really tough separations but after ca 6 they begin to suffer from diffusion because of the excessive development time SOLVENT SYSTEM AND TRICKS Most common for neutral organics 525 etherhexanes 525 acetonehexanes helps sharpen up OH or amide NH containing spots The three component system l5ll hexaneetherdichloromethane can have remarkable properties sometimes resulting in inverted relative Rf values compared to the simpler two component systems especially with multifunctional molecules Many poly functional unsaturated compounds can also benefit from benzene or halocarbon based systems Always optimize the solvent system for a difficult separations The differences can be amazing and they are in no way predictable or rationable Avoid methanol or ethanol These solvents will extract binder from the silica gel Depending on the cosolvent and the care taken to equilibrate the devolping chamber with the phase polar solvents such as the alcohols may create an arti cial solvent front where the polar solvent stops climbing the plate with unpredictable consequences for the separation IF you need a polar solvent try isopropanol or THF Basic amines do not run well on silica gel a weak acid unless they are sterically hindered Buffering the silica gel with NHAOH during plate preparation or addition of a drop of aqueous NHAOH to the developing chamber can help minimize the tailing of amines Aqueous NHAOH can be used in the homogeneous system with isopropanol as cosolvent for polar amines If an organic solvent has to be used to achieve Rf 03 then separation of an aqueous phase can be controlled by adding anhydrous sodium sulfate to the solventammonia mixture Enough ammonia will remain dissolved in the organic phase to help improve spot shape Tailing is often seen with other polar compounds such as phenols or carboxylic acids This problem can usually be controlled by tinkering with solvent systems add Hbond acceptors like acetone but buffering with acids may be necessary in extreme cases Whatever you do remember that TLC depends on multiple equilibration events The solvent reservoir silica gel and air space in the developing chamber must all be in equilibrium and this will take time for nonvolatile solvents such as alcohols or acetonitrile If you don t allow enough time for the chamber to equilibrate the less volatile solvents will not be distributed evenly on the plate due to differences in the extent of evaporation and the results will be unpredictable Mixtures containing highly polar components may also produce false solvent fronts resulting for what amounts to chromatographic separation of the solvent mixture OPTIMUM TECHNIQUE Until you are experienced spot 23 concentrations of each sample to find the one that does not tail due to overloading A good solvent system will give nearly a circular zone from a spot if the plate is not overloaded Always spot knowns along with the mixture being assayed Include starting material expected products and a sample of the crude product from various attempts or from parallel experiments Sidebyside comparisons are always important for revealing subtle differences Never trust Rf values alone to identify spots When optimizing a reaction do several reactions at the same time so that sidebyside comparisons are easier Place a strip of filter paper along the wall of the developing chamber to help speed up equilibration of liquid and vapor phases For difficult separations optimize the solvent system and adjust polarity ie vary hexane until the Rf of the most important zones is gt0l and lt04 if possible This will permit multiple up to three developments to maximize separation if necessary VISUALIZATION Always check for UVvisible and for iodineabsorbing spots Place enough iodine in a covered beaker to produce visible vapors a thin layer of crystals is all it takes Nearly all organics absorb more I2 than silica gel alone resulting in a brown spot Some halides amides and certain very polar compounds will resist the iodine These show up as white spots against a pale brown background Other more specialized developing methods are available in the form of spray reagents Many of these are speci c for functional groups Check any chromatography book for recipes For preparative work UVinvisible zones can also be detected by dusting the plate with IZsaturated silica gel to mark the surface of the plate UV markers can also be added to provide reference points for scraping zones Aromatics sucha s ourenone chalcone anthracene benzil etc are convenient additives because they are easily visible in milligram quantities Choose one that has a convenient Rf value to run ahead or behind the zone of interest TLC MONITORING OF REACTION MIXTURES The ideal conditions for typical reactions will usually result in detectable changes in the starting material vs product ratios over a time scale of tens of minutes to several hours Always monitor reactions by TLC as often as necessary to determine how fast the reaction is under a given set of conditions This is an important part of the optimization process Avoid overnight reactions unless you know that they really need that much time Frequent TLC monitoring early in the optimization process ensures that transient intermediates or sensitive products will not be missed If you monitor low temperature reactions remember that the act of spotting will warm up the reactants and will accelerate the reaction Unless you can first quench the reaction this type of monitoring may be misleading and could lead to a dangerous situation premature warming of an incomplete reaction can result in an exotherm P1 1 H La er C111 A a 139 TLC AS A STARTING POINT FOR PLC Any mixture that can be separated on a 34 analytical plate can be separated on a preparative plate The solvent system for typical preparative separations can be the same as for the analytical plate if the separation is easy Rf differences of 015 or more provided that the zone of interest has polarity perhaps from 10 etherhexane to 5 etherhexane so that multiple developments are possible In this situation the plate is developed once to resolve the least polar zones These are scraped off using careful razor blade technique The remaining undamaged silica layer is dried with a gentle stream of air until the back of the plate appears dry ca 2 min is enough and the remaining zones are developed again this time only as far as the scraped zone This technique will maximize the separation of the nonpolar as well as polar zones and can be repeated as many as three times for tough mixtures The only difference between analytical and preparative work is that equilibration of the solvent chamber takes more time for the preparative work It is best to avoid relatively polar nonvolatile solvents in PLC to minimize the equilibration problem SAMPLE APPLICATION Use the prepTLC applicator first time ask someone to demonstrate dissolve your sample in 05lmL of CHZClz transfer the solution with a pipette into the apparatus CAREFUL After the application rinse your ask and using the same pipette transfer the solution to the application apparatus and apply it to the plate Things to look out for Do not tilt the apparatus too much otherwise your solution might sill out or the needle can come out making the application zone too wide Manual application using a supported straight edge guide and a pipette drawn out to a capillary is also possible with practice use a nonvolatile solvent like CCl4 for this very fast and easy once you learn DEVELOPMENT If the application was perfect you may want to predevelop the plate 23 times to sha1pen the origin zone Extreme problems can be handled by developing the plate just past the applied zone using a more polar solvent system than you plan for chromatography drying the plate gentle air hose ow and repeating the process until the zone looks uniform This sha1pens the zone because the lower edge will run longer than the front of the zone If the application was successful and the separation is expected to be easy Rf differences of gt02 then the predevelopment is not necessary For difficult separations difference in Rf values of 005 to 015 12 predevelopments using the same solvent system as for the optimum separation is recommended to sharpen zones The ultimate separations may require predevelopment as well as one or two redevelopments Each time the plate must be taken out of the developing chamber and dried before the next development can be performed As already mentioned the optimized solvent system will be the one that moves the desired zone at Rf 0203 and that produces round spots on the TLC with no tailing or streaking Since prep plates run longer than analytical plates somewhat more diffusion of zones will occur There will be also more time for the decomposition of sensitive compounds It is a good idea to check the stability of your mixture using the twodimensional TLC test spot mixture at the corner of a square analytical plate and develop in one direction dry and store for an arbitrary decomposition time then develop the plate at a direction perpendicular to the original direction if the sample is stable on silica gel there will be no streaking in the second development no residue at the second origin and spots will fall along a diagonal of the plate If the stability of your compound is in question try to minimize the development time Remember that a 4 x 8 analytical plate can hold ca 510 mg of mixture These can be developed in 10 minutes minimizing contact time Samples that decompose of prep plates sensitive acetals TMS ethers etc can often be purified this way for characterization purposes VISUALIZATION See comments under TLC for the most important methods For prep work it is often possible to see zones of UVinvisible compounds by watching from behind the plate as the solvent dries Zones that contain significant amounts of organics absorbed on the silica gel will stay wet longer than areas that contain no absorbed material and the front of the zone will be most distinct This will not work for small quantities and the zone will not be visible for more than a few seconds as the solvent evaporates Be ready with a sharpie to mark the outline of the zone on the back of the plate EXTRACTION ZONES Use a safety razor to scrape the silica gel onto glassine weighing paper or a smooth piece of aluminum foil Crush lumps with a spatula and place the powder in a COARSE POROSITY sintered glass filter funnel that contains a layer of ca 3 mm MgSO4 and tap it into a uniform column Pressed into place with a glass rod or filter packed as a slurry under aspirator vacuum The filter should be ca 1cm in diameter for PLC Zones for a 8 plate and the filter should be connected to ca 510 cm of 1 cm tubing to allow ample room for the silica gel and solvent Pour the powder into the filter on top of the MgSO4 and tap it into a uniform column For 90 of typical organic mixtures ether is the ideal extraction solvent Add ether slowly enough to be continuously absorbed by the silica gel Once the silica gel is wetted through apply a little more ether at the top and gently apply air pressure or gentle aspirator vacuum A typical zone from one plate can easily be extracted with 45 mL ether if the silica gel is crushed to a powder and forced into the filter air pressore or glass rod to avoid channels Use a tared 10 mL or 25 mL ask as the receiver so that recording the weight after evaporation is easy Evaporate the ether In case any microdroplets of water always present in the silica gel made it through the MgSOA azeotropic removal of the water will occur when the residue is freed of ether residues by evaporation of 12 mL CCl4 or CDCl3 prior to NMR analysis However you should be careful to weigh the sample before this is done An accurate weight will be more difficult after NMR analysis since NMR solvents are nonvolatile Most plates can be used twice if the mixture being developed is not too messy Plan to develop the plate 23 of the way if the separation is not too difficult The top can then be used for a second separation NonPolar material that climbs with the solvent front will run faster than your mixture when the plate is inverted and used a second time GENERAL COMMENTS ABOUT SILICA GEL SEPARATIONS The size of a zone on a column or plate is limited by the amount of silica gel needed to absorb the organic material A zone containing ca 3040 mg of material on a well made 15 mm plate can be as narrow as 05 The width of the zone will increase in proportion to weight and a 100 mg zone will take up ll5 If the silica layer is uneven there will be variations in zone width This will also happen for overloaded plates 150250 mg per 8 plate is the limit Dark streaks that slowly fade in the course of development indicate initial overloading The same factors apply to columns and zone dimensions are sensitive to column packing Uneven packing causes channels in the column and a nonuniform front As with plates the volume and polarity of the solvent used to apply the mixture to the silica column will also in uence zone width Beginners often become convinced that their product is absorbed tightly on the silica gel and use huge amounts of solvent trying to extract or elute the missing material Most of the time the problem is that crude reaction mixtures contain residual solvent that disappears during the separation process Highly polar sideproducts also tend to disappear because they stick to the origin However there is no way that a zone will migrate with 20 etherhexane but will refuse to extract with straight ether Probably 95 of typical organic materials will do nothing irreversible with silica gel If a spot migrates on an analytical plate but seems to disappear on a column or a prep plate try the twodimensional test for decomposition If that isn t the problem then the next most likely source is pilot error All silica based separation methods are fundamentally the same Claims of large differences and advantages for specific devices and techniques can usually be traced back to individuals who learn one method well and don t look carefully at the alternatives Particle size is important for resolution and convenient speed of elution Best results require using silica gel of uniform size optimized by the manufacturers specifically for FC controlled to avoid fine particles that cause too much back pressure or for PLC inorganic binder added for mechanical stability of the dried silica layer Characterization of New Compounds August 2001 These policies are adapted from the Journal of Organic Chemistry and from Professor James Nowick s instructions to students Full characterization of new compounds those not previously reported in the published literature is required for publication in journals such as the Journal of the American Chemical Society and the Journal of Organic Chemistry You will need this data as well for the second year written exam the advancement to candidacy exam quotoralsquot and your dissertation The goal of characterization is to establish both the structure and the degree of purity of a compound One piece of advice characterize compounds as soon as you rst prepare and purify them Delaying characterization can lead to unsatisfying months of simply running ash columns and getting combustion analyses Since the requirements for characterization will affect your advancement to candidacy doctoral dissertation publication of papers and timely departure from the group you cannot get around characterization The following is taken from the Journal of Organic Chemistry Instructions to Authors regarding characterization they chose to bold certain sentences which has been preserved Characterization For all known compounds the source of the material or references to the utilized literature preparation method and published characterization data must be provided Spectral data should be presented only if it augments or updates the previously published data For all new compounds that appear as title compounds in the Experimental Section of Articles and Notes adequate evidence to establish identity AND degree of purity see below must be provided This can be presented in the body of the manuscript in which case it will appear in the printed version of the Journal Alternatively it can appear as Supporting Information For Articles that report the preparation of large numbers of new compounds authors should be selective in presenting spectral data for the printed version of the Journal In most cases a listing of l H and 13 C NMR resonances will suffice NMR peak assignments should not be given in the printed version of the Journal unless they are derived from definitive experiments such as isotopic labeling DEPT or twodimensional NMR experiments If desired a full listing of NMR data accompanied by subjective peak assignments may be included in the Supporting Information Full lists of infrared absorptions and mass spectral fragrnentations should not be presented in the printed version of the Journal List only those infrared absorptions that are diagnostic for important functional groups and only those mass spectral fragments that are diagnostic for a particular skeleton Authors may supply high resolution mass spectral HRMS data as an additional criterion of compound identity Additional spectral and characterization data may be published as Supporting Information In general evidence of the degree of purity of each new compound should include elemental analyses for carbon and hydrogen and nitrogen if present Acceptable error limits for combustion analytical data are 04 For some compounds combustion analysis is not feasible At the author s discretion an 85 x 11 in photocopy of the proton or carbon NMR spectrum will fulfill the requirement Photocopied spectra should be of sufficient contrast that they will in turn photograph well and must each be labeled with the compound number and structure They will be published as Supporting Information See Supporting Information below for requirements For some kinds of work indicators of purity other than NMR spectra and elemental analysis are more appropriate Distillation followed by gas chromatography column chromatography followed by HPLC and gel electrophoresis are acceptable as evidence of purity in these cases The purpose of this requirement is to allow a reader who repeats a preparation to determine that the procedure has resulted in the expected product of the expected purity Note that HRMS data cannot serve as a criterion of compound purity in lieu of elemental analysis The characterization of any compound will include the following Melting Point solids only Provides evidence of purity Melting points are required for all solids Infrared Spectroscopy IR Critical to establishing functional groups present in your compounds Make sure to record the state of the sample eg thin film solution in CHCl3 KBr pellet nujol mull etc List major peaks particularly ones of characteristic functional groups For publication most lists are about a halfdozen or so peaks 1H NMR Spectroscopy 1H NMR Critical to establishing both structure and purity of compounds Make sure to record the solvent and field strength eg 300 MHz CDCl3 Chemical shifts should be reported to hundredths of a ppm Integrals should be calculated and rounded to the nearest integer Most integrals are accurate to within 5 10 If the integral is particularly important such as a ratio of compounds you will need to obtain integrals from a onepulse spectrum Peak printouts should be obtained to facilitate calculation of coupling constants Coupling constants are reported in Hz and should be rounded to the nearest tenth of a Hz A photocopy of the 1H NMR spectrum of each new compound must be included in second year written exams the advancement to candidacy exam quotoralsquot and your dissertation Never alter the spectrum or integrals with pen or white out as this constitutes an act of scientific fraud 13C NMR Spectroscopy 13C NMR Make sure to record the solvent analfielal strength eg 75 MHz CDCl3 Remember the field strength for 13C NMR is approximately one quarter that of 1H NMR Chemical shifts should be reported to tenths of a ppm and any coupling data say to a heteroatom such as 2H or 31P must be noted All signals should be present if you have overlapping signals you must take the spectrum in a different solvent High Resolution Mass Spectrometry HRMS Provides evidence for the molecular weight and 39 t 39 r quot39 of a F but provides no indication of purity Calculated and observed weights should be reported to four decimal places Make sure to use quotexact massesquot atomic masses of main isotopes in calculating molecular weights Experimental and calculated masses must match within 5 ppm 00015 amu on a compound with molecular weight 300 Elemental Analysis A timehonored technique that provides evidence for both purity and molecular formula Samples should be sent to Atlantic Microlabs as soon as materials of high purity are obtained In general it is a good idea to place samples under high vacuum overnight prior to submission to ensure that samples contain no traces of solvent Special care should be taken with viscous oils as it is difficult to remove all traces of solvent from these samples Note that small traces of chlorinated solvents generally will introduce larger deviations in analyses than small traces of nonchlorinated solvents Acceptable error limits for elemental analyses are i04 The analytical labs39 results are generally precise to within about i01 so if your sample does not give an acceptable analysis further purification is probably required 1 Optical Rotation enantiomerically enriched compounds only This technique provides evidence of purity All enantiomerically enriched compounds should be analyzed by optical rotation This technique is easy and quick Gas Chromatography Data Periodically you will wish to report GC data for product ratios such as diastereomer ratios The GC provides response ratios between peaks as determined by the detector in our case ame ionization it does not provide product ratios If you know that two peaks have the same molecular formula then the response ratios correlate quite well with actual product ratios If the compounds have different formulas the ratio is irrelevant and will need to be calibrated calibration is relatively easy if you have clean samples of both materials Ratios obtained by GC must be in agreement with ratios obtained by NMR methods In order to call a minor peak in the GC trace a minor isomer either an authentic sample of that isomer must be made or GCMS will be required to assign that peak s structure Keep copies of GC traces from which product ratios are determined the dynamic range should be such that small amounts of minor products under 23 are registered by the detector and integrator All traces used to obtain product ratios will be submitted with manuscripts Yields You will need yields on all reactions for which you wish to write an experimental These yields should be on preparative scale gt100 mg in most cases and must be for pure materials as determined by 1H and 13C NMR spectroscopies GC etc Regarding Unstable and Known Compounds Unstable intermediates may be characterized less rigorously eg crude 1H NMR IR provided that a subsequent product is isolated purified and fully characterized Compounds that are observed in small quantities as interesting sideproducts may also be characterized less rigorously e g 1H NMR IR HRMS but if you are going to spend much time discussing a compound it should be fully characterized In some cases it may be appropriate to purify only a small portion of an intermediate to a high level of purity eg an intermediate in a largescale multistep synthesis In such cases you should indicate this in the experimental procedure and provide characterization data for the analytical sample eg quotAn analytical sample was purified by column chromatography on silica gel to afford a colorless oil IR 1H NMR 13C NMR HRMS Analquot Compounds that are known and fully characterized in the literature may also be characterized less rigorously 1H NMR and 13C NMR are sufficient but IR and MS can be obtained easily so should be performed elemental analysis is not required Some Tips for Writing Manuscripts A worthwhile guide to writing would take about 100 pages Mercifully Strunk and White have written just such a guide Elements of Style an outstanding investment if you happen to be at a bookstore Believe it or not computer grammar checkers are quite good so I would try that first They are imperfect however so I have compiled a few reminders for you These topics tend to be the same ones I notice with every paper or grant I read 1 Paragraphs and Thesis statements Paragraphs are units that include related sentences Paragraphs have thesis statements that indicate how the sentences are related These sentences are the rst sentence of every paragraph For example you might have a series of sentences that describe important NMR data such as hydrogen bonding or a variable temperature NMR experiment These sentences should ow logically from one to the next N L 4 V39 0 gt1 9 0 O and not jump around One might use the following thesis sentence Variable temperature NMR experiments provided important information about the hydrogen bonding pattern of compound 11 Verb tense You should not switch verb tense in the middle of a paper Usually past tense is preferred although sometimes present is more appropriate Subjectverb agreement Check to make sure subjects and verbs are either both singular Amide 6 crystallized or both plural Amides 6 and 8 m crystallized Be aware that sometimes the subject defines a collection but is itself singular A mixture of amides 6 and 8 E crystallized with mixture as the subject Extraneous words Words such as surprisingly interestingly much to our delight and in the event add little to text Very also adds little to a qualifier just think would you trump very with oh so very or more simply very very Colloquial expressions The above words are colloquial as well but some other colloquial expressions are better rendered more formal For example The ester was reacted with the amine sounds fine in the laboratory but this level of informality is not appropriate for a report The word treated can often be substituted for reacted and therefore papers can be made more formal rather easily Be aware though that sometimes you can overuse the same sentence structure so change it up a bit Contractions Contractions aren t I mean are not appropriate for formal writing Imprecise subjects of sentences This cannot serve as the subject of a sentence Although it can serve as a noun it is not a precise one Specifying what this is can be much better the expressions this phenomenon this compound or this experiment can serve as subjects of sentences Weak sentence constructions A few common sentence constructions are believed to be weak because the infinitive to be must be employed as the verb For example sentences starting with There is or There are need no other verbs Consider the following gt7 4 There are no examples of silacyclopropanes used as synthetic intermediates compared with Silacyclopropanes have not been employed as synthetic intermediates The second sentence has a more active verb and is thus a stronger sentence Quali cation Do not have gradations of yield like high A quot f A J PUUI Calling quot 39 high yield or poor yield is descriptive but one person s modest is another s poor The same idea applies to selectivities etc Numbers Numbers less than or equal to twelve are normally written out whereas 13 and higher are not Experimental data In figures put only the most imp01tant experimental details Too much information will only serve to hide key data You will find that a description of reagents is sufficient and the details of solvent and temperature are not critical Do not include too much experimental detail in the text of a paper either Save the details like how much solvent etc for the experimental section Tips for simplifying the writing process 1 Make a full sentence outline For an example please see the attached outline A full sentence outline will force you to see the big picture and make decisions about your material What you will see emerge is the thesis statements for the paragraphs of your paper 2 Draw the equations figures and schemes They should follow from the outline If you wanted to draw it but it is not in the outline either put it in the outline because it is important or do not draw a gure for it Between the gures and the outline your point should come across clearly 3 Go ahead and write a rst draft Pay particular attention to what you want to say not how you say it That will come later Try and get everything into the paper that must be there Extraneous material can be edited out later Do not feel bad if the rst draft is not Shakespeare 4 Now give the manuscript a rst edit Think about every paragraph Does it have a thesis statement Does each paragraph follow a theme Is the ow logical if you only read the first sentence of each paragraph At this stage you should be focusing in on content and whether the overall ow of the paragraph is good Wording comes later 5 When you are happy that the paper ows properly go through each sentence First x the spelling Second try the grammar checker It will ag gross mistakes so you do not have to parade your Neanderthal writing in front of others Does each sentence hold together by itself Does it t within the paragraph following the previous sentence leading into the next one 6 Give your paper to a colleague preferably one who is not too knowledgeable about their work Have them read it critically both noting its good parts and its bad ones Take their comments into consideration when you revise By the way pride of authorship is an ugly thing So is a vindictive reader 7 A nal note Someone once told me There is no paper that does not improve upon shortening We have all heard Brevity is the soul of wit and A picture is worth a thousand words I KAW take these comments to heart when I write Finally Itry desperately to avoid R B Woodward s blistering criticism You write like a truck driver talks Sample Fullsentence Outline for W S Palmer K A Woerpel Organometallics 1997 16 10971099 I Introduction A Metalmediated reactions of silirenesSeyferth 1977 64 Seyferth 1984 60 Seyferth 1985 24 and alkylidenesiliranesAndo 1986 85 Saso 1989 16 Saso 1988 58 with alkynes result in extrusion of a silylene unit or an insertion reaction Although mechanisms have been postulated which explain these products little experimental support has been reported No applications of these reactions to siliranes have been reported and no stereochemical information has been obtained to date largely because of dif culties in making siliranes B We reasoned that the mechanisms of these reactions of threemembered silanes could be evaluated if they could be extended to siliranes bearing stereochemical markers In this way the stereochemical outcome of the reactions could be determined and the mechanisms either supported or refuted We have used Boudjouk s stable siliranes llditertbutyl23 dimethylsilirane 1 to address similar issues regarding insertion reactions of carbonyl compoundsBodnar 1995 2 We have discovered that stable siliranes llditert butyl23dimethylsilirane 1 in fact undergo insertion reactions and silole synthesis with stereospecific retention of con guration at the carbon atom We can also comment on oxidative addition reactions of metals into CSi bonds as well as on the speci c reactions of siliranes Silylene intermediates may be implicated but are not required II Reaction with a variety of alkynes A Reactions with a variety of terminal alkynes provides silole products The product is obtained with high regioselectivity favoring materials with the alkene substituent away from the bulky silyl group In some cases particularly with the cis silirane insertion products are sometimes obtained as well With diynes we observe formation of oligosiloles as well as macrotetrasiloles The regiochemistry of the insertion product is also high Control experiments indicate that palladium is necessary Modification of reaction conditions does not lead to more insertion product B The stereochemical course of these reactions is worthy of note The insertion reaction proceeds stereospecifically with retention of configuration although the low extent of insertion with trans 1 does not allow for a more detailed analysis than presented here The stereochemistry with respect to liberated alkene is also stereospecific retention Both processes have the same stereochemical outcome C The regiochemistry with respect to substituents on the silirane ring is interesting It gives the product of addition at the least hindered position in contrast to our observations of reactions with aldehydes and alcohols D When no alkyne was added we see slow conversion to the rearranged product III Mechanism analysis The proposed mechanisms for these transformations involves oxidative addition Our data indicates it proceeds with stereospecific retention of configuration of stereochemistry at the carbon atom This intermediate can partition in one of three ways leading to silole silacyclopentene and silane Considering the interest in the stereochemical aspects of extrusion from other small heterocycles such as epoxides aziridines and episulfides carbenes we can contribute that silylene extrusion proceeds with retention of configuration The mechanism supported by our data is shown in the scheme This logical proposal was suggested by other authors many years ago but the stereochemical experiments reported provide additional support IV Conclusion In conclusion palladiummediated reactions of siliranes have been demonstrated to proceed with stereospecific retention of configuration Our data points at the formation of palladasilacyclobutanes Further experiments will be directed at transferring silylene units to other functionalaties Writing Experimentals Symbols Punctuation and Formating for Experimental Data This section has been adapted from a handout by Professor Scott Rychnovsky Note The key strokes involve an older version of Microsoft Word for Macintosh so if your symbols do not look ideal you will need to gure out which are the best keystrokes for your word processing program Temperature 65 OC Temperature 778 OC Selectivity 982 Yield 95 Joining names HorneriEmmons reaction A melting point mp 65767 0C A weight 73 mg or 0073 g A volume 35 mL of water Hours 7 h Micromoles 132 pmol Compound Formulas BF3OEt2 NMR Format 5 725 s 1H Coupling dd J 67 100 1H 17714m 3 H degree sign SHIFTOPTION8 minus en dash OPTIONhyphen without space no space before and after normalized to 100 use spaces in ChemDraw gures though because the 75 reduction makes the numbers microscopic no space between number and no decimals en dash OPTIONhyphen use en dash and degree sign Add spaces around 39 and after the number but not around the en dash Space after number use small In capital L then of before the solvent space before h same symbol for singular and plural u OPTIONm u m in Symbol font 3939 character SHIFTOPTION9 or 5 d in Symbol font Italicize J Spaces around E no space in the integration Hz does not need to be written as the general experimental has this in it Use en dash for a range of values 1H NMR Data 1H NMR 300 MHz CDC13 5 720435 m 5H 505 d 1 29 1H 424 dq 1 64 20 1H If overlapping data use the following 108 s 9H and m 1H 13C NMR Data 13C NMR 125 MHz CDC13 5 1433 1280 1269 Rotation oc24D 121quot 0 091 CHCl3 MS Analysis or a in Symbol font 0 italicized space after it HRMS CIisobutane m z calcd for C19H33OZSi M HJr 3212250 found 3212249 Space around or Space after italic m and before italic z not italicized 394 is superscript If the ion is an M then use Ml with the as superscript in the parentheses Also if you have lost a tBu group for example use M 7 C4H9Jr with the fragment listed as its molecular formula Note punctuation Calcd has no period Anal Calcd for C19H32028i C 7118 H 1008 Found C 7097 H 998 Naming 2R3SDimethyl Volumes 3 X 10 mL 39R39 and 39S are italicized and always put in parentheses Use no spaces in a name Only numbers and italicized words have dashes around them X is X in Helvetica font 7Roxaticin Use en dash for minus sign separate name fragments with a hyphen no line break Nmethylmorpholine Noxide Italicize atom symbols in a chemical name E2butene Italicize 39E39 and 39Z tertbutyl alcohol italicize tert sec 1585 7 2080 EtOAchexanes Spaces around L en dash but not gt94 ee No space between gt or and number Space between and ee39 References A space but no punctuation before J and 1969 example Dale J A Dull D L Mosher H S J Org Chem 1969 34 254372549 Tetrahedron Lett 1980 21 1007104 Tetrahedron Lett 1979 1007104 No volume number before 1980 The formatting of references may be handled by EndNote a commonly used program for managing bibliographic information Miscellaneous Symbols hyphen hyphen en dash 397 39739 OPTIONhyphen em dash 7 397 SHIFTOPTIONhyphen Line return not a new paragraph SHIFTRETURN heat A A OPTIONj Triple bond 539 39E OPTIONb in Symbol font Words that should not be abbreviated saturated quantitative aqueous powdered Nouns that take singular verbs grams milligrams equivalents number mixture Useful abbreviations h hours min minutes equiv equivalents eq equation mmol millimoles calcd calculated Numbering Scheme 1 2 3 Figure l 2 3 eq 1 2 3 Table l 2 3 Abbreviations For a complete list of standard abbreviations see J Org Chem 2001 66 24A Miscellaneous Words to describe rotovapping Celite capitalized onepot overalkylate transmetalation re ux is not a verb heated at re ux is the more accurate description 1 4 concentrated in vacuo The following text is a sample experimental in JOC format we thank Dr J H Smitrovich for assembling this experimental Please note the grammar used to describe the procedure and the format for reporting characterization data 1R2S3R 1 Phenyl 2 methyl 13 butanediol 2 To a cooled 0 OC solution of tert butylhydroperoxide 0207 g 230 mmol 90 in 13 mL of DMF was added CsOHHZO 0331 g 197 mmol After the mixture was allowed to warm to 25 0C a solution of oxasilacyclopentane 1 0050 g 0164 mmol in 08 mL of DMF was added dropwise by syringe After 10 min nBu4NF 0214 g 082 mmol hydrate lyophilized from benzene was added The reaction mixture was heated at 75 0C for 8 h After the mixture was cooled to 25 OC Na28203 was added and the solvent was removed in vacuo The resultant oily solid was partitioned between 5 mL of H20 and 10 mL of Et20 The layers were separated and the aqueous layer was extracted with 2 X 10 mL of Et20 The combined organic layers were washed with 10 X 1 mL of H20 and 5 mL of brine dried MgSO4 and concentrated in vacuo to afford 0057 g of a yellow oil The oil was puri ed by ash chromatography 2575 7 3565 EtOAchexanes to yield the product as a colorless oil 0019 g 64 1H NMR 300 MHz CDC13 8 720735 m 5H 505 d J 29 1H 424 dq J 64 20 1H 385 br s 1H 34 hr s1H 171 m 1H 123 d J 65 3H 083 dJ 72 3H 13C NMR 125 MHz CDC13 8 1433 1280 1269 1256 784 720 449 214 40 IR thin lm 3355 2975 1380 1199 974 742 cm39l HRMS CIisobutane m z calcd for C19H33OZSi M HJr 3212250 found 3212249 Anal Calcd for C19H32028i C 7118 H 1008 Found C 7097 H 998
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