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Chemical Biology
Jeff Landry

First class ch 1April20121035 PMThe teamInstructor Jeff Landry room ABB121He is synthetic chemist does moleculesHas taken multiple organic chemistryHe has a phd thesis on carbon carbon double bondCourse administrationGreg laboratory Coordinator instructional assistantAny issues with the course hes your manHe knows a lot about this course so go to his office hours and ask him questionsRoom ABB 301Dr HarrisonWill be teaching the 2nd orgoDo not doDo not email them on avenue they HATE ITEmails are on the course outline sheet so use that one they will respond to that oneEmail through your McMaster address especially if your talking about marks etcTextbookKlein Organic Chemistry 1st edition95 of txtbook on a subject contains 95 of the same information so if you want to go through another text book then you can get the same information from there so it doesnt matter what textbook you useUse any one of them they all have the same information but the one above is what will be used in the class ie Figure numbers and page numbersModelsuse them Jillian They will help YOUR LIFE LOLUsed mostly in the stereochemistry unitLabsBegin next week and not this weekFor anybody thats in Mondays lab at 230That lab will be pushed to the last Monday of the termALL THIS INFO IS POSTED ON AVENUE REGARDING LABSLabs take place 3rd floor on ABBWhat do you needGet a lab manual they are having a bit of a delay in printing right now and if its not there by next week there will be some paper you can print outLaboratory notebook HaydenMcNeil carbon copy book dont need to buy another one if you have oneGoggles worn at all timesProper attire shoes that are covered no sandalsCover from wrist to your neck all the down to your toesThey do let shorts slide but after your kneebut dont just encaseSaplingIts a very similar system to mastering chemistry Its optional and you dont have to use itGo to saplinglearningcait cost money 29 per semester3 assignments in itFirst due next FridayThey are tutorial based assignmentsTheres questions hints you get unlimited tries its designed to get you to the correct answer just like mastering in chemistry wasGo in sign up pick university then course chem 2ao3 and then your inImportantWhen you sign up for this you need to go to avenue and see how to enter your IDHe needs to know who we are so he needs our student numberSo go in the website and edit your profile and theres a section for your id number and you can put your ID there that way you can get the marksAssignments2 written assignments due Thursday may 17th and June 7thDrop boxes hard to find they are in the back hallway in chemistry buildingView instructions to know how to get to the drop boxesThey will be posted up1 TA will mark every single question for every single 450 student be very very very careful and dont copy other people its soo easy to get charged with academic dishonesty in this chem course i have seen about 2 ppl get in trouble bc of that Write individually talk with ppl but things go down on paperBY YOURSELFBe careful giving your assignment to someone else to hand in if you are then make sure you really trust themorgo Page 1 Test and exam1 term test Thursday may 24th in classExam June 14th in class timeStructureMultiple choice and long answerslearn to draw neatly and properly so the TAs can understand itHelpTheres tutorials that start next weekEvaluation for courseAssignments 5 25 eachLab 20Sapling 50all sapling counts nothing gets droppedIf you choose not to do sapling then that 5 is redistributed everywhere else in the courseTerm test 20 0Final exam 5070They will calculate our grades in different ways and see which one is higherWe set up course for lecture capturePodcast basically to watch class notes and listen to class11 Organic Chemistrysome examples of where you see organic chemistryie Nylons kevlar some drugsWe are going to do ch110 and then talk about ch 15 and 1616 spectroscopy which are tools chemists useCh 14 are review from chem 1AA3 he will go quickly through it and everything in those chapters are testable material they are just basic chemistry stuffHe will remind us of stuff but wont reteach it we must already know itSlide 2Why do we distinguish between organic and inorganic compoundsHe doesnt knowOrganic carbonated primarily carbon basedInorganic noncarbonWhy are organic compounds importantBecause they are involved in all the biological systems that we look at so its important to know how carbon behaveThe stuff organic chemist design and synthesis is CRAYZAYY And make really complex things and a hugely complex moleculeSlide 313 covalent bondinglewis structureREVIEWGo back to 1st year text book because there is overlap 2535 so its an extremely valuable resourceSlide 414 formal chargeIts important to know formal chargesThe formal charge dictates the activity that happens so you need to be able to identify the formal charges very quickly Example is on the slideTake methanol move a proton methoxideYou will get things wrong if you do not put formal chargeHow to identify formal charge in a moleculeDo that by knowing how many electrons the atom has and wantsThey want 8 electrons always To be stableThe carbon ring in example is giving electrons to hydrogen and hydrogen is giving electrons to carbon so normally carbon has4 valence electrons 4 that it owns and have 8 total around it so it has a formal charge of zeroOxygen in general in atomic state normally has 6 electronsIn this example the carbon is giving one electron to oxygen and in total there are 8 electrons around oxygen but of those 8 electrons oxygen owns 7 and one of those 8 are from carbon and it doesnt own itIt gained an extra electron from somewhere from hydrogen and carries a formal charge of negative one because it gained an electron If you dont draw that negative charge you dont realize that methoxide has a negative charge and acts as a base and you wont know that its a good nucleophile and your not going to be able to predict any of the activities of the methoxideThat formal charge tells you exactly whats happeningSlide 5polar covalent bondIf you have disparity between 2 atoms you get apolar covalent bondProperties of a carbon oxygen bond dictates crazy chemistry that we must know and it all comes to the fact that oxygen is more electronegative than carbonThus the carbon is a good electrophilemeaning its very susceptable to getting electrons from somewhere else bc oxygen isa bully and its taking all the electronsmore electronegativeSolvent polarity orgo Page 2 and its taking all the electronsmore electronegativeSolvent polarityDo organic reaction put it in a nonplar reaction nothing will happenIf change solvent and make it more polar something will happen bc it loosens up the hydrogen so polar bonds are very very importantReview polar and nonpolar covalent bondsSlide 7 and 8Atomic OrbitalsWhen chemical reaction happens bonds breakWhen any chemical reactions happen you go from bonds that are less stable to bonds that are more stableWave functions are orbits so electrons are waves and occupy a space around a nucleus and take form of orbits and then we get these shapesIts these shapes and properties that tell us a lot about the bonding and we can then know what molecule is more or less stable Pictures on slide are of the orbitals When you talk about p orbital its red up top and blue in bottom so its wave functionn2 l1 and theres 2 phases the red positive phase and blue negative phaseThis is important property of p orbitalthe fact that it has 2 phasesSlide 9S orbitals are complex outside surface is that its all one phaseSo it can be either one phase or the other positive or a negative phase its random one or the other probability is the sameWont talk about d orbitalsSlide 10P orbitals make 4 bonds and never 5Slide 11Valence bond theoryTo understand how bonds are made we do this by overlapping 2 orbitalsOne from one atom and another atom both have 1 electron and they overlapThey are wave functionsSo if 2 s orbitals have positive phase then they amplify each other and we get a stronger wave out of it constructive interferenceOpposite way too if theres 2 s orbitals together in opposite negative phase you get destructive interferencea positive and a negative and you get an antibondSlide 12Valence bond theoryExample is shown in slideTheres 50 percent probability of getting bonding orbital or antibonding orbital because s orbit can be positive or negativeSlide 13Molecular orbital theoryNeed to know how to draw molecular orbit diagrams bc he will test you in the assignmentH atom represents atomic atoms and in centre it represents our molecular species H2 so what happens when we bring a 1s and another 1s together when they are in same phase we get constructive interference and energy goes down and we make a bonding molecular orbital Theres 50 probability where theres one in positive and one in negative and it destabilizes it and thats when we get deconstructive interferenceNo differenceMolecular orbitalAntibonding molecular orbitalHydrogen in right hand side and left hand side have one electron and they go to the lowest energy orbital and then we make a bond thats a brief molecular orbital theory Imagine you want to me He2This molecule doesnt exist helium doesnt make a bondIts molecular orbital diagram is the same as hydrogen so whats the differenceWe have a couple extra electrons because each helium atom has 2 electrons in its 1s orbitalWe make bonding molecular orbital and antibonding molecular orbitalProblem is we end up putting 2 electrons in bonding and antibonding orbital what happens2 electrons in bonding orbital you make a bond and 2 electrons in antibonding orbital make antibond and 1 10so there is no bonding going on in heliumParamagnetic means its a really magnetic speciesHow do you get that You need to have unpaired electronsHighly magnetic species have a lot of unpaired electrons ie Liquid oxygenif poor liquid oxygen and poor it onto magnet you can influence the stream of liquid oxygenSlide 14Molecular orbital theoryWe wont do anything with the big atoms and moleculesPplpeople do a lot of this to see which molecular orbital has the highest number of electronsOrbital has to have the same symmetry to react with each other ie D orbital wont react with s orbital unless things look similar and if they dont react with each other then you will have a really hard time interacting with each otherSlide 1719 hybridized atomic orbitals orgo Page 3
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