1. Chemistry 125 - Fall 2009 Lecture 1, Sept. 2 For over 150 years Organic Chemistry courses have tended to acquire a daunting reputation. For copyright notice see final page of this file To hear the soundtrack start this ppt (browsed individual window, use timings). Then launch Lect0109.mov. Quickly click on the Powerpoint window to reactivate it, and press right arrow when the speaker finishes saying, “…daunting reputation, as I suspect many of you have heard.”

2. For copyright notice see final page of this file Chemistry 125 - Fall 2009 Lecture 1, Sept. 2 For over 150 years Organic Chemistry courses have tended to acquire a daunting reputation.

3. HELP ! PowerPoints / Lecture Notes Designed for Mac - Compatible with PC & viewer (please help identify problems) OYCOYC videos & transcripts from Fall 2008 to become available in October Course Website: https://webspace.yale.edu/chem125/https://webspace.yale.edu/chem125/ assigned problems or questions previous exams and answer keys Course Wiki at ClassesV2 initial updates due within 36 hours of presentation in-class discussion / e-mail questions (There will probably be a Text Book for the Spring semester)

4. HELP ! Instructor : Prof. J. M. McBride (Thurs 1-2:30 or by appt) Sign up on-line (pro-forma) Grad Student TAs: (Mon 7-9 pm) (Thurs 7-9 pm) Peter Jordan (synthetic organic chemistry, small peptide catalysts for phosphate esters) Eugene Douglass (chemical biology, methods for analyzing protein - small molecule - antibody complexes)

5. HELP ! Other Chem 125 students! Alumni Peer Tutors (Sunday 8-10 pm, Bass Library) Course Alumni (web advice)web advice Andrew Moir (BK’10) Terahertz Spectroscopy of Dye-Sensitized Solar Cells Hayley Israel (MC’10) Chelation of Titanium with Siderophore Models Connie Wang (BR’10) Computing Drug Targets on HIV Reverse Transcriptase

6. Exam Dates 10 lectures Fri. Sept 25 9 lect Mon. Oct 19 9 lect Wed. Nov. 11 9 lect Fri. Dec 18 100 pts 300 pts Semester grade biased by faithfulness in timely problem set submission Wiki Participation 50 pts Total 650 pts

7. The characteristic comment on making a discovery is not “Eureka!” but rather “Huh, that’s funny.” Learn enough about how chemistry works so that you know when to be astonished Goals of Freshman Organic Chemistry: Learn the crucial facts and vocabulary of Organic Chemistry Develop theoretical intuition about how Bonding works Learn from this model science how to be a creative scientist Develop good scientific taste (sense vs. nonsense) Knowing to be astonished by something is the mind’s first step toward discovery. http://www.lmcp.jussieu.fr/~soyer/cristallo/pasteur_l.html Louis Pasteur Savoir s'étonner à propos est le premier mouvement de l'esprit vers la découverte. Make the scientific transition from school to university (molecular structure)(reactivity), and changes Have fun

8. Theory & Experiment Why do we require Chem 126L?

9. Because Lab answers the Big Question Big

10. How do you know? John McBride (age 3)

11. How do you know? John McBride (age 38)

12. Four Ways of Knowing Carolingian Bookpainter ~840 A.D. (British Museum) Moses Receives the Law Tablets But Science is NOT Faith-Based! Authority 1) Divine Authority 2) Human Science Ignores: 1) Divine Authority & 2) Human Authority

13. SCL Honor Roll Do not suppose that I was a very deep thinker, or was marked as a precocious person. I was a very lively imaginative person, and could believe in the Arabian Nights as easily as in the Encyclopaedia. But facts were important to me, and saved me. I could trust a fact, and always cross- examined an assertion. So when I questioned Mrs. Marcet's book by such little experiments as I could find means to perform, and found it true to the facts as I could understand them, I felt that I had got hold of an anchor in chemical knowledge, and clung fast to it. Michael Faraday, 1858 3) Experimental ….Observation

14. When someone says science teaches such and such, he is using the word incorrectly. Science doesn't teach it; experience teaches it. If they say to you science has shown such and such, you might ask, "How does science show it - how did the scientists find out - how, what, where?" Not science has shown, but this experiment, this effect has shown. Learn from science that you must doubt the experts… Science is the belief in the ignorance of experts. (to Nat’l Science Teachers Assn. 1966) Why quote Feynman? Because he is an expert? Though literally “expert” means someone who has done experiments. Because what he says makes sense. 4) Logic

15. Modern Science got underway in the 17 th Century 1800 Lavoisier Oxidation 1900 Planck Quantization Newton Gravitation Luther Reformation Columbus Navigation 2000 Us 17001600 1500 Copernicus Revolution Robert Hooke (Micrographia, 1665) Bacon Instauration

16. Shakespeare (1564-1616) Galileo (1564-1642) On his scholastic Cambridge tutors: "Men of sharp wits, shut up in their cells of a few authors, chiefly Aristotle, their Dictator." All the philosophy of nature which is now received, is either the philosophy of the Grecians, or that other of the alchemists … The one is gathered out of a few vulgar observations, and the other out of a few experiments of a furnace. The one never faileth to multiply words, and the other ever faileth to multiply gold. Francis Bacon (1561-1626)

17. Instauratio Magna The Great Restoration Novum Organum Inductive Scientific Method to replace Aristotelian deduction ? NASA/JPL/NIMA Jebel Musa (Morocco) Jebel al Tarik (Gibraltar) PLUS ULTRA Pillars of Hercules Mediterranean - Classical World - Aristotle

18. "Many will pass through and knowledge will be increased. ” Daniel 12:4

19. Instauratio Magna (1620) “…that wisdom which we have derived principally from the Greeks is but like the boyhood of knowledge, and has the characteristic property of boys: “…it is but a device for exempting ignorance from ignominy.” “…the end which this science of mine proposes is the invention not of arguments but of arts.” “…not so much by instruments as by experiments …skilfully and artificially devised for the express purpose of determining the point in question.” “restoration of learning and knowledge” it can talk, but it cannot generate;” Cf. “Correlation Energy” (Lect 11), “Strain Energy” (Lect 32)

20. Astronomy Horology Meteorology Cartography Chemistry Royal Society 1662 Ac ne forte roges, quo me..duce, quo lare tuter, Nullius addictus jurare in....verba magistri Quo me cumque rapit........tempestas, deferor hospes............. Horace (15 B.C.) Lest you ask who leads.... me, in what household.. I lodge, There is no master in...... whose words I am........ bound to take an oath, Wherever the storm........ forces me, there I put in.. as a guest. “The Royal Society for the Improving of Natural Knowledge by Experiments” (the late) Francis Bacon Viscount Brouncker (President) Navigation

21. Crucial www.bluestreetjazzband.com “finally decides between two rival hypotheses, proving the one and disproving the other” cross = crux Bacon’s most important kind of experiment: Chapel Trinity College, Cambridge

22. Experimentum Crucis Newton’s “Experimentum Crucis” (1666 -1672) Proved (to Newton) that Light is a Substance, not Hooke’s pulses. “Nec variat lux fracta colorem.” “The broken light does not change its color.” How does the prism make color? by altering pulses (à la Hooke & Descartes) or by separating existing colors?

23. Experiments are indispensable in organic chemistry (an empirical science) but so is logic. Believe what I say only when it makes sense to you. What if it doesn’t?

24. How to Succeed in Chem 125 Samuel Pepys as a Model Science Student

25. Samuel Pepys (1633-1703) Diary 1660-1669 Saw Charles I beheaded 1649 B.A. Cantab. 1654 “Clerk of the Acts” Navy Board 1660

26. Samuel Pepys (1633-1703) July 4, 1662 …By and by comes Mr. Cooper, mate of the Royall Charles, of whom I intend to learn mathe- matiques, and do begin with him to-day, he being a very able man... After an hour's being with him at arithmetique (my first attempt being to learn the multiplication- table); then we parted till to- morrow. Diary 1660-1669

27. Samuel Pepys (1633-1703) July 9, 1662 Up by four o'clock, and at my multiplicacion-table hard, which is all the trouble I meet withal in my arithmetique. July 11, 1662 Up by four o'clock, and hard at my multiplicacion-table, which I am now almost master of… December 25, 1662 …so to my office, practising arithmetique alone and making an end of last night's book with great content till eleven at night, and so home to supper and to bed Motivated, Diligent

28. Samuel Pepys (1633-1703) December 6, 1663 [Sunday] …I below by myself looking over my arithmetique books and timber rule. So my wife rose anon, and she and I all the afternoon at arithmetique, and she is come to do Addition, Subtraction, and Multiplicacion very well, and so I purpose not to trouble her yet with Division... Worked with study partner

29. Isaac Newton (1643-1727)

30. Six years later Pepys encountered a “problem” with Dice.

31. Pepys’s Problem (11/22/1692) A - has 6 dice in a Box, wth wch he is to fling a 6. B - has in another Box 12 Dice, wth wch he is to fling 2 Sixes. C - has in another Box 18 Dice, wth wch he is to fling 3 Sixes. Q. whether B & C have not as easy a Taske as A, at even luck? If the Question be thus stated, it appears by an easy computation that the expectation of A is greater then that of B or C, that is, the task of A is the easiest. What is ye expectation or hope of A to throw every time one six at least wth six dyes? [etc.] Newton’s Reply (11/26/1692)

32. But yet I must not pretend to soe much Conversation wth Numbers, as presently to comprehend as I ought to doe, all ye force of that wch you are pleas'd to assigne for ye Reason of it, relating to their having or not having ye Benefit of all their Chances Pepys’s Reply (12/6/1692)...You give it in favour of ye Expectations of A, & this (as you say) by an easy Computation.. ; and therefore were it not for ye trouble it must have cost you; I could have wish'd for a sight of ye very Computation. Not ashamed to admit when he didn’t really understand Insisted on proof

33. 31031 46656 A 0.6651 = 1346704211 2176782336 B 0.6187 = 

34. Pepys “WHY?” "I cannot bear the Thought of being made Master of a Jewell I know not how to wear." “I never went to his office hours for help because I felt like he would make me feel stupid, because he is superior to me in chemistry.” (from an anonymous end-of-semester course evaluation - Jan 2007) Contrast with: Willing to swallow his pride in the search for solid understanding

35. Read Pepys & Newton and get together to do Problems for Monday.Pepys & Newton Contribute to Wiki when asked.

36. Problems For Friday (optional): 1)What are the three most common items of advice from course veterans?advice For Monday: Isotope problems (from Pepys & Newton )Pepys & Newton For Wednesday: Two Coulomb Problems For Friday (Sept. 11): 1) Draw Lewis Structures for Functional GroupsFunctional Groups 2) Are Lewis Structures correct? 3) What do Lewis Structures show? Collaborative Group Submissions form two groups of 4 (or 5) students from each of the following sets of residential colleges: BK (BR+CC) (DC+ES) (JE+MC) (PC+SM) (SY+TC+TD)

37. Isotope Ratio Mass Spectrometry

38. Wiki Assignments

39. End of Lecture 1 Sept. 2, 2009 Copyright © J. M. McBride 2009. Some rights reserved. Except for cited third-party materials, and those used by visiting speakers, all content is licensed under a Creative Commons License (Attribution-NonCommercial-ShareAlike 3.0).Creative Commons License (Attribution-NonCommercial-ShareAlike 3.0) Use of this content constitutes your acceptance of the noted license and the terms and conditions of use. Materials from Wikimedia Commons are denoted by the symbol. Third party materials may be subject to additional intellectual property notices, information, or restrictions. The following attribution may be used when reusing material that is not identified as third-party content: J. M. McBride, Chem 125. License: Creative Commons BY-NC-SA 3.0