1. Chemistry 125: Lecture 18 October 11, 2010 Amide, Carboxylic Acid, and Alkyl Lithium; Oxygen and the Chemical Revolution (Beginning to 1789) For copyright notice see final page of this file Key properties of biological polypeptides derive from the mixing of localized orbitals that we associate with “resonance” of the amide group. The acidity of carboxylic acids and the aggregation of methyl lithium into solvated tetramers can be understood in analogous terms. More amazing than the power of modern experimental and theoretical tools is that their results did not surprise traditional organic chemists, who already had developed an understanding of organic structure with much cruder tools. The next quarter of the semester is aimed at understanding how our scientific predecessors developed the structural model and nomenclature of organic chemistry that we still use. Studying the logic of the development of modern theory, technique and nomenclature helps to use them more effectively. Chronological treatments of organic chemistry often begin with Lavoisier, the father of modern chemistry. But his “Chemical Revolution” depended upon the practices of ancient technology and alchemy and discoveries like those of Scheele, the Swedish apothecary who discovered oxygen and prepared the first pure samples of organic acids. Lavoisier’s “Traité Elémentaire de Chimie” launched modern chemistry with its focus on facts, ideas, and words. Lavoisier weighed gases and measured heat with a calorimeter, as well as clarifying chemical language and thought. Preliminary

2. Resonance: Intramolecular HOMO/LUMO Mixing Why the Amide Functional Group is not an Amine and a Ketone C N O

3. vs. Amide Pyramidal NPlanar N Easy N-C RotationBarrier to Rotation Amine Carbonyl StableMore Stable Naïve PredictionExperimental Observation by 16 kcal/mole (1/4 C-N) 16 kcal/mole by 0.14Å by 0.03Å HOMO LUMO Long N-CShorter N-C … Short C=OLonger C=O … (mostly) Opposing Dipoles net Strongly Dipolar (in  direction) ~1/3 e - transfer N  O Crucial for Structural Biology Basic and AcidicRelatively Unreactive Skin works ! (best overlap)

4. formamide HOMO :  electron pair “from” N shared with C=O creates electric dipole

5. -- ++ Repeating Unit in Protein  -Helix Stabilized by electrostatic “Hydrogen Bonding” (reducing backbone “floppiness” by 1/3) and by local planarity of C-N = C-C groups O = -- ++ ++

6. Four Functional Groups: Carbonyl Amide Carboxylic Acid Alkyl Lithium  

7. Acidity of Carboxylic Acids R-OH 10 11  stronger! R-C O OH pK a ~5 + H + R-C O O pK a ~16 R-O + H + HOMO-LUMO REALLY stabilizes carboxylate anion. R-C O O HOMO-LUMO mixing stabilizes neutral acid compared to ROH. R-C O OH + higher (Less “Uphill”) Predicts more uphill?

8. LUMO+1 (  ) Aggregation of CH 3 Li HOMO (  ) LUMO (  )

9. Aggregation of CH 3 Li HOMO (  ) LUMO+1 (  ) 2HOMO (  ) 2LUMO+1 (  ) Dimerization

10. Aggregation of CH 3 Li 3-Center 2-Electron Bonds use only 2 of the 4 valence AOs of each Li LUMO (  ) in Li-C-Li-C plane LUMO+1 (  ) out of plane Dimerization Rotate to superimpose the red lobes. BH 2 H H H2BH2B Vacant Li + AOs stabilize unshared pairs of CH 3

11. Aggregation of CH 3 Li HOMO (  ) LUMO+1 (  ) rotated 90° LUMO+1 (  ) HOMO (  )

12. Aggregation of (CH 3 Li) 4 HOMO (1 of 4) LUMO (1 of 4) Distorted Cubic Tetramer 4-Center 2-Electron Bond H3CH3CCH 3 O : 4 CH 3 OCH 3 Last Valence AO of each Li (vacant) 3 vacant Li + AOs stabilize unshared pair of C. (CH 3 ) 2 OO(CH 3 ) 2 CH 3 OCH 3 This is as baroque as we will get in this course.

13. Aggregation of (CH 3 Li) 4 Excess Ether Rips Aggregates Apart by bonding with Li-AOs to form CH 3 Li 3 O(CH 3 ) 2 4 CH 3 OCH 3 HOMO “NON-BONDED” INTERACTIONS & SOLVENT EFFECTS ARE A VITAL PART OF LORE. (e.g. facilitating ionization)

14. But organic chemists were not at all surprised by what they showed! We have seen amazing modern tools for revealing the Å / psec world of molecules: SPM X-ray Diffraction Spectroscopy: IR, ESR, (NMR, etc.) Quantum Mechanics (computer "experiments")

15. How Did They Know?

16. 17th Century 1800 Lavoisier Oxidation 1900 Planck Quantization Newton Gravitation Bacon Instauration Luther Reformation Columbus Navigation 2000 Us 17001600 1500 Copernicus Revolution Hooke (1665) The Organic Structural Model & Chemistry Science & Force Laws HookeCoulomb Electron Bonds: Observation & Quantum Mechanics Schrödinger

17. Yale Chemistry 1901S Greek symbols denote substituent positions.  Cf. Clairvoyant Benzene

18. Sheffield Chemistry Lab (SSS) (only quantitative tool)

19. Yale Chemistry 1901S Balance Burettes The precious Analytical Balances were key, but were not portable Quantitative Tools? C. Mahlon Kline (1901S)

20. Kline Chemistry Laboratory (1964) Kline Biology Tower (1965) #4 in Big Pharma (2010)

21. Quartz Crystals for Purity and Quantitation (face angles)

22. Silliman Crystal

24. Boyle Lavoisier

25. Berzelius etc.

26. Wöhler/Liebig

27. Genealogy

28. GenealogyBottom YOU resonance, x-ray, proteins

29. Genealogy Top

30. Background in Ancient Arts and Lore Noah Mosaic 12 th Century ) Sicily (Monreale) “Florence” Flask

31. Roman Glass Perfume Vial ~2000 years old Class of 1954 Chemical Research Building -5 days old

32. 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)

33. Bega Alchemist 1663 e.g. Newton OCCULT Title of Exhibition on Alchemy at the Beinecke Library 2009 “The Book of Secrets”

34. Mellon ms 41 Elements ~1570 Beinecke Library, Yale Visio mystica Arnold of Villanova 13 th Century (England ~1570)

35. On the Philosopher’s Stone (13 th Cent; Basel, 1571) Beinecke Library, Yale

36. alchemist Paracelsus (early 1500s) Poison Ivy Doctrine of Sympathies In nature antidotes are to be found near the source of illness. ©2006 Derek Ramsey Jewel Weed Double-blind Clinical Test (1997) No better than water OH

37. Salicilic Acid Willow (Salix) found in malarial swamps Salicin (from bark) hydrolyze oxidize

38. “Vade mecum” Alchemical Lab Manual Caspar Harttung vom Hoff (Austria, 1557) Beinecke Library, Yale

39. Carl Wilhelm Scheele (1742-1786) Prerevolutionary Pharmacist Carl Wilhelm Scheele (1742-1786)

40. Scheele's Acids Benzoic Uric Citric Lactic Oxalic Gum Benzoin Rhubarb (?) Lemon Milk Urine (purified as heavy-metal salts) Bismuth, cobalt, antimony, tin, mercury, silver, and gold were attacked by lactic acid either by digestion or by boiling. After standing over tin the acid caused a black precipitate to form in a solution of gold in aqua regia. 7) Lead dissolved after several days of digestion. The solution acquired a sweet, tart taste but did not crystallize. 10) With copper our solution first took on a blue color, then green, finally dark blue, but it did not crystallize. 9) Iron and zinc were dissolved with formation of flammable air. The iron solution was brown and gave no crystallization, but the zinc solution crystallized. 8) On Milk and its Acid (1780) 19 pp. ! Tartaric Tartar (wine cask residue)

41. e.g. "Oxymoron" "Oxy" = Sharp What's sharp about Rhubarb? Acidic taste "acre" to be sour root "ac-" sharp sharp dullness (self-contradiction) Latin "acidus”; Greek (oxus)

42. Scheele's Acids (purified as heavy-metal salts) Benzoic Oxalic Citric Lactic Uric Tartaric Gum Benzoin Rhubarb Lemon Milk Urine Tartar (Wine Casks)

43. vs. Carboxylic Acid Alcohol pK a ~16Carboxylic Acid pK a ~5 Alcohol Carbonyl High HOMO Stabilized Higher HOMO More Stabilized (Note: there will be more to this story involving "inductive effects") pK a depends on energy difference between A-H and A - H +

44. Scheele's Acids (purified as heavy-metal salts) Benzoic Oxalic Citric Lactic Uric Tartaric Gum Benzoin Rhubarb Lemon Milk Urine Tartar (Wine Casks) ?

45. Uric Acid Two C=O LUMOs stabilize the High HOMO of N Two C=O LUMOs stabilize the Higher HOMO of N - pK a 5.8 (vs. 38 for NH 3  NH 2 - + H + )

46. tung sten 7 Elements Discovered or Codiscovered by Scheele nitrogen chlorine manganese molybdenum bariumtungsten oxygen gases heavy stone (Swedish)

47. Scheele (1771) Feuerluft "fire air" Ag + O 2 > 340°C Ag 2 CO 3 Ag 2 O + CO 2  …since I have no large burning glass, I beg you to try with yours…

48. Genealogy Top

49. The Chemical Revolution 1789

50. Werad Radix Latin Licorice (glukos + rhiza) Greek Rutabega Swedish Wort Old English Mathematics (16th Cent) Race? Razza Italian Eradicate Wurzel German Chemistry (18th Cent - France) Politics (18th Cent - England) Radish Radical: Going to the root or origin = Root

51. 1787: Radical Introduced as a Political Term "The necessity of a substantial and radical reform in the representation..." J. Jebb

52. September 17, 1787

53. by Louis Bernard Guyton de M ORVEAU (1737-1816) "Radical" Introduced as a Chemical Term 1787 age 50

54. Méthode de Nomenclature Chimique 1787 Antoine François de F OURCROY (1755-1809) age 32 Claude Louis B ERTHOLLET (1748-1822) age 39

55. Antoine Laurent Lavoisier (1743-1794) age 45 7,000 pounds (~$300,000) Traité Élémentaire de Chemie (1789)

56. Weighing a Gas vacuum Hg P atm - P gas

57. "Lavoisier in his Laboratory Mme. Lavoisier taking his dictation (After a sepia drawing by Mme. Lavoisier) " Lavoisier's Pneumatic Trough

58. Elementary Treatise of Chemistry 1789 PRESENTED IN A NEW ORDER AND ACCORDING TO MODERN DISCOVERIES With Figures

59. Preliminary Discourse (1789) I had no other object, when I began the following Work, than to extend and explain more fully the Memoir which I read at the public meeting of the Academy of Science in the month of April 1787, on the necessity of reforming and completing the Nomenclature of Chemistry. While engaged in this employment, I perceived, better than I had ever done before, the justice of the following maxims of the Abbé de Condillac, in his System of Logic, and some of his other works:

60. Preliminary Discourse (1789) "We think only through the medium of words. --Languages are true analytical methods. --Algebra, which is adapted to its purpose in every species of expression, in the most simple, most exact, and best manner possible, is at the same time a language and an analytical method. --The art of reasoning is nothing more than a language well arranged."

61. Preliminary Discourse (1789) Thus, while I thought myself employed only in forming a Nomenclature, and while I proposed to myself nothing more than to improve the chemical language, my work transformed itself by degrees, without my being able to prevent it, into a treatise upon the Elements of Chemistry.

62. Preliminary Discourse (1789) The impossibility of separating the nomenclature of a science from the science itself, is owing to this, that every branch of physical science must consist of three things; the series of facts which are the objects of the science, the ideas which represent these facts, and the words by which these ideas are expressed. Like three impressions of the same seal, the word ought to produce the idea, and the idea to be a picture of the fact.

63. Preliminary Discourse (1789) And, as ideas are preserved and communicated by means of words, it necessarily follows that we cannot improve the language of any science without at the same time improving the science itself; neither can we, on the other hand, improve a science, without improving the language or nomenclature which belongs to it. However certain the facts of any science may be, and, however just the ideas we may have formed of these facts, we can only communicate false impressions to others, while we want words by which these may be properly expressed.

64. Clarity: FactsIdeas Words “impressions of the same seal”

65. New Order 1) Doctrine 2) Nomenclature 3) Operations

66. Elements …if by the name of elements we mean to desig- nate the simple, indivisible molecules that make up substances, it is probable that we do not know what they are : but if, on the contrary, we associate with the name of elements, or of the principles of substances, the idea of the furthest stage to which analysis can reach, all substances that we have so far found no means to decompose are elements for us…they behave with respect to us like simple substances.

67. Traité É lémentaire de Chimie (1789) Table of Elements imponderable

68. Lavoisier-Laplace Calorimeter (1782) Flame 3 Feet Inner Can Completely Surrounded by Insulating Ice Lamp into Bucket Bucket into Cage Cage into Can Flame Completely Surrounded by Melting Ice Melted by Flame Only!

69. End of Lecture 18 Oct. 11, 2010 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