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

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

3. HELP ! PowerPoints / Lecture Notes
Designed for Mac - Compatible with PC & viewer (please help identify problems)
OYC videos & transcripts from Fall 2008 to become available in October
in-class discussion / questions
Course Website:
assigned problems or questions
previous exams and answer keys
Course Wiki at ClassesV2
initial updates due within 36 hours of presentation
(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)
Grad Student TAs:
(Mon 7-9 pm) (Thurs 7-9 pm)
Sign up on-line (pro-forma)
Peter Jordan
(synthetic organic chemistry,
small peptide catalysts for phosphate esters)
Eugene Douglass
(chemical biology, methods for analyzing
protein - small molecule - antibody complexes)
Reed College, WPI

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

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

7. Goals of Freshman Organic Chemistry:
• Learn the crucial facts and vocabulary of Organic Chemistry
• Develop theoretical intuition about how Bonding works
, and changes
(molecular structure)
(reactivity)
• Make the scientific transition from school to university
• Learn from this model science how to be a creative scientist
Louis Pasteur
Savoir s'étonner à propos
est le premier mouvement
de l'esprit vers la découverte.
Knowing to be astonished by something is the mind’s first step toward discovery.
In a lecture to the French Chemical Society in 1883 describing his discovery of the handedness of tartrate crystals in 1848.
Oeuvres de Pasteur, I, 373.
• Learn enough about how chemistry works
so that you know when to be astonished
The characteristic comment on making a discovery is not “Eureka!” but rather “Huh, that’s funny.”
• Develop good scientific taste (sense vs. nonsense)
• Have fun

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

9. Because Lab answers the Big Question

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

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

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

13. Experimental ….Observation
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
Experimental
….Observation
From 1806 Jane Marcet’s “Conversations on Chemistry” was the most popular text in American women’s seminaries. It stressed experimental work and current theory rather than pharmacy, cooking, and other household application See M. S. Lindee, Isis, 82, 9-23 (1991)
SCL Honor Roll

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

15. Modern Science got underway in the 17th Century
Robert Hooke (Micrographia, 1665)
Modern Science got underway in the 17th Century
Luther
Reformation
Bacon
Instauration
Columbus
Navigation
1500
Copernicus
Revolution
Newton
Gravitation
1800
Lavoisier
Oxidation
1900
Planck
Quantization
2000 Us
1700
1600

16. All the philosophy of nature which is now received, is either the philosophy of the Grecians, or that other of the alchemists…
On his scholastic Cambridge tutors: "Men of sharp wits, shut up in their cells of a few authors, chiefly Aristotle, their Dictator."
Galileo
( )
Shakespeare
( )
The one is gathered out of a few vulgar observations, and the other out of a few experiments of a furnace.
from “Of Tribute: Praise of Knowledge” Works (1968) VIII p cited in Gleick, p. 206 note 10.
Utraque unum : from both one
Instauratio Magna : the great restoration
This work contained Bacon's fundamental treatise, the Novum Organum -- a new method for scientific investigation to replace the old and faulty one of Aristotle. The book was given an imposing subtitle: "True Direction Concerning the Interpretation of Nature." The ship displayed on the book's title page, is sailing through the Pillars of Hercules. Tradition had always placed these as the limits of man's possible exploration. But instead of the traditional "ne plus ultra," Bacon's title page in fact declares, as did Coronelli's, "plus ultra.”
The old oranon was Aristotle
arshtml/conclusion1.html
Elizabeth accession 1558 dies 1603
Shakespeare
Not so much that Aristotle himself was wrong as that the scholastic reverence for his authority was misplaced.
1674 BOYLE Excell. Theol. II. iv. 170 That great Restorer of Physicks, the illustrious Verulam (OED physics)
Cartoon of Bacon in lecture at Cambridge by Angus McBride
The one never faileth to multiply words, and the other ever faileth to multiply gold.
Francis Bacon ( )

17. Instauratio Magna Novum Organum ? New World Jebel al Tarik Jebel Musa
NASA/JPL/NIMA
New World
Instauratio Magna
The Great Restoration
Novum Organum
Inductive Scientific Method to
replace Aristotelian deduction ?
Jebel
al Tarik
(Gibraltar)
Jebel
Musa
(Morocco)
PLUS
ULTRA
from “Of Tribute: Praise of Knowledge” Works (1968) VIII p cited in Gleick, p. 206 note 10.
Utraque unum : from both one
Instauratio Magna : the great restoration
This work contained Bacon's fundamental treatise, the Novum Organum -- a new method for scientific investigation to replace the old and faulty one of Aristotle. The book was given an imposing subtitle: "True Direction Concerning the Interpretation of Nature." The ship displayed on the book's title page, is sailing through the Pillars of Hercules. Tradition had always placed these as the limits of man's possible exploration. But instead of the traditional "ne plus ultra," Bacon's title page in fact declares, as did Coronelli's, "plus ultra.”
The old oranon was Aristotle
arshtml/conclusion1.html
Elizabeth accession 1558 dies 1603
Shakespeare
Not so much that Aristotle himself was wrong as that the scholastic reverence for his authority was misplaced.
1674 BOYLE Excell. Theol. II. iv. 170 That great Restorer of Physicks, the illustrious Verulam (OED physics)
Cartoon of Bacon in lecture at Cambridge by Angus McBride
Pillars of Hercules
Francis Bacon ( )
Mediterranean - Classical World - Aristotle

18. "Many will pass through and knowledge will be increased.” Daniel 12:4
In The Advancement of Learning Bacon makes this analogy explicit. Speaking to James I, to whom the book is dedicated, he writes: "For why should a few received authors stand up like Hercules columns, beyond which there should be no sailing or discovering, since we have so bright and benign a star as your Majesty to conduct and prosper us."
"Many will pass through and knowledge will be increased.” Daniel 12:4

19. Instauratio Magna (1620) “restoration of learning and knowledge”
“…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 can talk, but it cannot generate;”
“…it is but a device for exempting ignorance from ignominy.”
Cf. “Correlation Energy” (Lect 11) , “Strain Energy” (Lect 32)
“…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”

20. Astronomy Horology Navigation Meteorology Cartography
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.)
Chemistry
Astronomy
Horology
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.
Navigation
Meteorology
Cartography
John Evelyn (Silva 1664 was RS first book). He apparently designed this fronticepiece to Prat’s History of the RS (1667) which was engraved by Wenceslaus Hollar ( )
Viscount Brouncker
(President)
(the late)
Francis Bacon
“The Royal Society for the Improving of Natural Knowledge by Experiments”
Royal Society 1662

21. Crucial Bacon’s most important kind of experiment: ?
“finally decides between two rival hypotheses, proving the one and disproving the other”
cross = crux ?
OED Crucial 2. That finally decides between two rival hypotheses, proving the one and disproving the other; more loosely, relating to, or adapted to lead to such decision; decisive, critical. Freq. in trivial use = ‘very important’. 
This sense is taken from Bacon's phrase instantia crucis, explained by him as a metaphor from a crux or finger-post at a bivium or bifurcation of a road. Boyle and Newton used the phrase experimentum crucis. These give ‘crucial instance’, ‘crucial experiment’, whence the usage has been extended.
Chapel
Trinity College, Cambridge

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

23. Believe what I say only when it makes sense to you.
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. Samuel Pepys as a Model Science Student
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
mi from lecture room.
John Hayls (1600?-1679).
In his diary, Pepys records on 17 March 1666: 'I sit to have it full of shadows and so almost break my neck looking over my shoulders to make the posture for him to work by'. There were more sittings on 20, 23, 28 and 30 March, when he sat 'till almost quite darke upon working my gowne which I hired to be drawne in; an Indian gowne'. Pepys paid Hayls ｣14 for the picture and 25s for the frame on 16 May, commenting that he was 'well satisfied' with it. The music he holds is his own setting of a lyric by Sir William Davenant, 'Beauty, retire'.
B.A. Cantab. 1654
“Clerk of the Acts”
Navy Board 1660

26. Samuel Pepys (1633-1703) Diary 1660-1669 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.

27. Motivated, Diligent 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.
Motivated,
Diligent
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

28. Worked with study partner Samuel Pepys (1633-1703)
December 6, [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 ( )

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

31. Pepys’s Problem (11/22/1692) Newton’s Reply (11/26/1692)
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. Not ashamed to admit when he didn’t really understand
Pepys’s Reply (12/6/1692)
...You give it in favour of ye Expectations of A, & this (as you say) by an easy Computation.
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
; 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 = B
0.6187 =

34. for solid understanding
Pepys “WHY?”
"I cannot bear the Thought of being made Master of a Jewell I know not how to wear."
Contrast with:
Willing to swallow
his pride in the search
for solid understanding
“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)

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

36. Problems For Friday (optional): What are the three most common items
of advice from course veterans?
For Monday:
Isotope problems
(from Pepys & Newton )
For Wednesday:
Two Coulomb Problems
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)
For Friday (Sept. 11):
1) Draw Lewis Structures for Functional Groups
2) Are Lewis Structures correct?
3) What do Lewis Structures show?

37. Isotope Ratio Mass Spectrometry

38. Wiki Assignments

39. End of Lecture 1 Sept. 2, 2009
Copyright © J. M. McBride 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).
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