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CHAPTER 4: ALKANES AND CYCLOALKANES

  1. Cis-trans stereoisomerism
    Problems: 1. Draw the structures for the following two compounds, using wedges and dashes: a. cis-1,3-dimethylcyclobutane; b. trans-1-ethyl-2-methylcyclopentane. 2. For cis-1,3-diethylcyclobutane draw a. a stereoisomer and b. a constitutional isomer.
  2. Combustion of alkanes and cycloalkanes: we covered these reactions in class: the two products are always CO2 and H2O; you just need to balance the equations.
    Problem: Write the products of combustion for each of the following alkanes: a. CH3-CH2-CH2-CH2-CH(CH3)2; b. methylcyclohexane; c. ethylcyclopentane

CHAPTER 5: CONFORMATIONS

  1. Constitutional isomers and conformational isomers
  2. Alkane chain conformations: at room temperature,  bonds allow for free rotation of the atoms connected by the bond.
  3. Eclipsed and staggered conformations
  4. Drawing Newman projections – the dihedral angle
  5. Determining relative stability of conformational isomers
  6. Cycloalkane conformations – angle strain: cycloalkanes distort from planarity to alleviate angle strain (except for cyclopropane)
  7. Drawing cyclohexane chair forms: the axial (a) and equatorial (e) positions. Make sure that in your drawing the (a) and (e) can be distinguished.
  8. Stability of chair forms
  9. Mono-and disubstituted cylcohexanes.

CHAPTER 6: CONFIGURATIONAL ISOMERS – STEREOCHEMISTRY

  1. Two Major Classes of Isomers. Definition of isomers, constitutional isomers, and stereoisomers. You should be able to identify constitutional and stereoisomers.
  2. Introduction to stereoisomerism. Chiral and Achiral Molecules. Draw the enantiomer of a given chiral molecule.
  3. Chirality (or Stereogenic) Centers. You should be able to identify/locate all stereogenic centers present in each molecule.
  4. Enantiomers – what they are, and how do you recognize them?
  5. Designating Configuration using the Cahn-Ingold-Prelog system. Should be able to label stereogenic centers with R and S. For this, you should be able to apply the rules to assign priority to various substituents.
    Problems: Draw all possible stereoisomers for the compound below, label pairs of enantiomers and diastereomers, and label the meso compound! a. CH3-CH(OH)-CH(OH)-CH2-CH3; b. CH3-CH(Cl)-CH2-CH(Br)-CH3. Label compounds as R or S.
  6. Diastereomers. Calculate the maximum number of stereoisomers for a given molecule (2n, where n is the number of stereogenic centers).
  7. Symmetry and chirality. Meso Compounds.
  8. Optical Activity. Definition. How do enantiomers rotate plane-polarized light? Dextrorotatory and levorotatory isomers. Specific rotation and its equation. Racemic mixture: definition, properties, and how does it differ from the meso compound? The Table below was discussed in class. Racemic Mixture Meso Compound
    Stereogenic Centers Present Present
    Optical Activity None None
    Cancellation of Optical Activity Intermolecular (1:1, mol/mol mixture
    of the enantiomers) Intramolecular
    Can you render it optically active? Yes! E.g., by chiral chromatography, microbial activity Impossible!

CHAPTER 7: INTRODUCTION TO REACTIONS
7.1. Enthalpy or heat of reaction
Steps and species involved in reactions:
Radicals, carbanions, and carbocations

Heat of reaction: exothermic and endothermic reactions. Energy diagrams (do not forget to label the axes: Energy vs. Reaction coordinate)
7.2. Entropy: the state of randomness of a system. The entropy increases, when a gas is released in a reaction, e.g., CH3–CH3  CH2=CH2 + H2. The entropy decreases, when a cycle forms out of an open chain molecule (e.g., X-CH2-CH2 CH2-CH2-Y forms a cyclobutene); the reverse of this reaction, where the cycle cleaves, so that it gains more freedom of motion involves an increase in entropy.
7.3. Gibbs free energy change (Go = Ho – T So) predicts whether a reaction is allowed or not.
Thermodynamics: Equilibrium constant and change in free energy (Go). What does it mean, when Go < 0 and when Go > 0? How can you get this information from an energy diagram?
7.4. Equilibria. Equilibrium constant and free energy changes. You should be able to correlate the magnitude of Keq with Go; Go = -2.303RT*log Keq. Remember that a reaction is spontaneous, when Keq > 1, which translates into Go < 0. 7.5. Reaction Kinetics. Energy diagrams. Be acquainted we the physical measures represented on the two axes. Activation energy (Ea) and the thermal effect (Ho) 7.6. Reading Energy Diagrams. Energy diagram of a one-step reaction and of a two-step reaction. Identification of the rate determining step (rds): the highest energy of its transition state is the highest. Transition state. Kinetics. Rate equations: 1st order and 2nd order.) One-step and two-step mechanisms. Golden rule: one-step reaction is 2nd order, while 2-steps reaction is 1st order. Catalysts. Be able to provide a complete definition and to draw comparative energy diagrams for catalyzed and uncatalyzed reactions. Types of reactions: (i) Redox reactions (generic); (ii) for organic reactions: substitution, elimination, addition, and rearrangement 7.7. Nucleophiles and electrophiles. Ionic reactions. Nucleophiles contain an excess of electrons, which can be donated to another reactant:  Charged nucleophiles (OH-, R-O-, SH-, CN-, CH3-COO-, etc.)  Neutral nucleophiles (H2O, CH3-OH, NH3, R-NH2, CH3-COOH, etc.) Electrophiles have an empty orbital, where they can accept a pair of electrons 7.8. Reaction mechanisms Note that curved arrows always start from lone pair electrons or from an electron-rich multiple bond! Nucleophilic attack: is performed onto the substrate molecule by a charged or neutral nucleophile. Leaving groups: good leaving groups are: –I > –Br > –Cl; H2O
Poor leaving groups: –F, –OH, –R, –H

CHAPTER 8: SUBSTITUTION REACTIONS
8.1. Alkyl halides. Aryl halides, vinyl halides, and benzylic halides.
Nomenclature.
Structure of alkyl halides
8.2. Possible mechanisms for substitution reactions: concerted (one-step) vs. sequential (2-steps) mechanisms.
8.3. SN2 Mechanism
One-step process, 2nd order, rate law: r = k•[nucleophile][substrate]
How does the identity of the alkyl group (methyl, 1o, 2o, and 3o) affect the reaction?
Problem: Explain why (CH3)3C-CH2-Br, a 1o alkyl halide, undergoes SN2 reactions very slowly!
8.4. Stereospecificity of SN2 reactions: backside attack with inversion of configuration at a stereogenic center, like flipping the umbrella (Walden inversion): R center  S center, and conversely. This applies only when there is a stereogenic (chiral) center in the molecule.
8.5. SN1 Mechanism
Two-step process, 1st order, rate law: r = k•[substrate]
The stereochemistry of SN1: attack from both sides of the sp2 hybridized planar carbocation – racemization. How does the identity of the alkyl group (methyl, 1o, 2o, and 3o) affect the reaction?
How does the structure of the substrate impact this reaction? Explanation resides in the stability of carbocation which forms as the intermediate
8.6. Drawing the Complete Mechanism of an SN1 reaction.
8.7. Drawing the Complete Mechanism of an SN2 reaction.
8.8. Determining which mechanism predominates: When is the Mechanism SN1 or SN2?
Be proficient with the effect of (i) the alkyl halide, (ii) the nucleophile, (iii) the leaving group, and (iv): the solvent effect (polar protic or polar aprotic).
ELIMINATION REACTIONS
8.9. Introduction to elimination reactions
8.10. Nomenclature of Alkenes: parent chain should contain the double bond, even if not the longest possible carbon chain in the molecule.
8.11. Stereoisomerism of Alkenes: cis/trans and E/Z, respectively
8.12. Alkene Stability:
Increases in the order monosubstituted < disubstituted < trisubstituted < tetrasubstituted.
8.13. Possible Mechanisms for Elimination
8.14. The E2 Mechanism: energy diagram, rate law, effect of substrate – rate increases in the order 1o C < 2o C < 3o C
Regioselectivity of E2 Reactions: Zaitsev and Hofmann elimination products: when smaller base molecules are used, Zaitsev product dominates; upon using bulky, sterically hindered bases, Hofmann product becomes major. (We discussed this in class without mentioning Hofmann’s name. Bulky, sterically hindered bases can only access the outermost hydrogen atoms, cannot get to the carbons inside the chain.)
Stereoselectivity of E2 Reactions: trans elimination product will be major relative to the cis isomer
8.15. The E1 Mechanism: energy diagram, rate law, effect of substrate – reaction rate increases in the order 1o C < 2o C < 3o C
Regioselectivity of E1 Reactions: the Zaitsev elimination product will be major.
Stereoselectivity of E1 Reactions: trans elimination product will be major relative to cis isomer.
8.16. Substitution vs. Elimination: Identifying the reagent
8.17. Substitution vs. Elimination: Identifying the mechanism

Sample Solution

The Last Great Explorer GuidesorSubmit my paper for examination By Brook Wilensky-Lanford The journey to discover the Garden of Eden seems like an occupation that ought to have fallen by the wayside a long time before the nineteenth century. Never again did the whimsical medieval topographies of Prester John or Columbus take into consideration the presence of a fascinating, pristine natural heaven. This was a more up to date, smarter age. We had vanquished the wild areas of the world. What's more, Darwin's Origin of Species, distributed in 1859, was gradually demonstrating that individuals and, state, the fowls of the air, were not made at the same time in a solitary spot on the globe. Darwin himself rejected the quest for a land purpose of sources in his 1871 Descent of Man. He permitted that: "It is to some degree progressively likely that our initial ancestors lived on the African mainland than somewhere else." But, he announced, there was additionally a huge gorilla that wandered Europe in the relatively recent past, and at any rate the earth is mature enough for primate species to have moved right around it at this point. In this way, "It is pointless to estimate regarding this matter." Victoria Woodhull, women's activist radical and free-love advocate, was less discretionary in her epic discourse "The Garden of Eden," which she conveyed oftentimes during the 1870s. Eden on Earth was rubbish: "Any school kid of twelve years old who should peruse the portrayal of this nursery and not find that it has no topographical centrality whatever, should be criticized for his ineptitude." Perhaps she was alluding to the minister voyager David Livingstone, who had proclaimed, while frantic with jungle fever in 1871, that heaven existed at the wellspring of the Nile, which he made a decision to be in the Lake Bangweulu area of Zambia. Livingstone was by all account not the only one despite everything searching for Eden. This valiant modern lifestyle was flipping around time-respected convictions. Advancement was proposing that people had rose after some time from our less-canny, carnal primate sources. In any case, Christianity had been demanding for quite a long time that people had slipped, through unique sin, from close heavenly statures in the Garden of Eden to the hopeless, debased society of the late nineteenth century. What was a cutting edge, loyal individual to accept? Enter William Fairfield Warren, recognized Methodist pastor and instructor. As the leader of Boston University, he realized science would characterize what's to come. However, he was reluctant to surrender his religious philosophy to the new order. How to weave the two points of view together? Irrationally, Warren looked to Eden. He set about making an interpretation of the Bible into science: Eden was "the one spot on Earth where the natural conditions are the most great." Genesis says Eden contains "each tree that is lovely to the eye or useful for nourishment"; Warren set "widely varied vegetation of practically unheard of force and extravagance." He observed a newfound actuality: a large number of years back, Earth had been a lot hotter. He followed the revealing of phenomenal animals without a moment's delay well-known and legendary, similar to the wooly mammoth, the dinosaur, and the goliath sequoia. He knew there was as yet one clear spot on the world guide, a spot where no one had been. Furthermore, he come to the unavoidable end result: the Garden of Eden is at the North Pole. It seemed well and good, as it were. Both Eden and the Pole had frustratingly opposed endeavors to find and guarantee them, regardless of hundreds of years of risky, costly undertakings. Warren distributed this hypothesis in 1881 as Paradise Found, The Cradle of the Human Race at the North Pole. The tome emphatically smelled with scholastic power. There were long sections in French, German, and antiquated Greek in the references. He drew on his claim to fame, near folklore, which he portrayed as "the study of the most seasoned conventional convictions and recollections of humanity." He knew the incredible epic old stories of the Hindus, the Celts, the Chinese, the Persians. In the nineteenth century, this was an uncommon, recondite assortment of information, brimming with allegorical echoes of Bible stories, and goal "proof" of Christian realities. The list of "creators alluded to or cited" in Paradise Found records 580 sources—for 495 pages of content. Directly by Darwin, there is Ignatius Donnelly, who guaranteed the lost mainland of Atlantis was genuine; it was demolished by the close impact of Earth with a comet. His 1882 book Atlantis was uncontrollably well known (Donnelly had another hypothesis—that Shakespeare's plays may really be composed by Francis Bacon—yet at that point, that was considered too crazy to be in any way paid attention to). A few commentators felt that Warren's wanton reference did his contention no favors, however obviously numerous perusers were not disturbed. The second printing of Paradise Found, discharged just months after the first, was peppered with tributes. Warren composed gladly of a "plain unschooled Bible understudy," Mr. Alexander Skelton, a mechanical engineer and metal forger of Paterson, New Jersey, who had freely landed at his own "strikingly complete and apt" contention for a North Pole Eden. Warren gloated that one Professor Heer, a haughty Swiss scientist, guaranteed that Warren was copying him. He likewise distributed a tribute from the British classicist, and reliable Anglican, Archibald Henry Sayce: "Temporarily, I may state that your view appears to me famously sensible… " (regardless of that Sayce was really alluding to a prior work of Warren's, about the cosmology of Homer's Iliad). Warren's hypothesis was "quickly overriding each previous speculation" on the two sides of the Atlantic—regardless of whether Warren said so himself. In this way, it involved jumbling dissatisfaction for him that other Eden hypotheses kept on showing up. A German paleologist, Moritz Engel of Leipzig, had the nerve to distribute The Solution to the Paradise Question all the while with Paradise Found. Engel's Eden was a desert spring in the desert outside of Damascus. His four waterways were flood downpours that vanish in the dry season, come May or June. Warren retaliated: Engel's Eden was terrible. Maybe Mr. Engel had never at any point understood Genesis, with its image of plenitude and bounty! It was additionally biased, as though he never at any point saw that there were "legends of the Happy Garden" found in many other antiquated customs! To top it all off, Engel's Eden was informal, putting forth no attempt to join "the realities and speculations of ethnologists and zoologists with regards to the beginnings of human life… . The ideal opportunity for investigations of such limitation as this is past." Warren's request that the North Pole Eden was the abrogating, definitive record was genuine. Yet, it might have been a little gullible, given the mystery that Warren himself uncovered on the absolute last page of his book: he didn't really figure his heaven could be found. He composes, sorrowfully: "Tragically deceased Eden is found, yet its doors are banned against us. Presently, as toward the start of our outcast, a sword turns each approach to keep the Way of the Tree of Life… " Arriving at Polar Eden, we could sit idle "however swiftly bow in the midst of a solidified destruction and, moronic with an anonymous wonderment, let fall a couple of hot tears over the covered and destroyed hearthstone of Humanity's soonest and loveliest home." The best way to return to Eden was in death, on the off chance that we acknowledge the penance of Christ. Follow Jesus throughout everyday life, and in death you can walk directly past the cherubim with their blazing swords. Furthermore, much the same as that, regardless of his earnest attempts to be the final word on Eden, Warren had accidentally opened the entryway for a totally different age of Eden-searchers. They started to spring up very quickly, and many even refered to Warren as legitimate proof for their own cases, similarly as Warren had finished with his 580 sources. It began with Warren's own partners in the Methodist church. Reverend E. D. Ledyard declared to a group of people of 5,000 at a retreat in upstate New York that Eden was fairly nearer to home. "In Chautauqua, we see one spot where Edenic benefits have been reestablished. Christ is the focal figure here. During that time Adam heaven is being recovered." In 1890, a three-section article in the San Jose, California evening paper entitled "Nursery of Eden: Its Position on the Globe Has Been Definitely Located" clarified that California's Santa Clara Valley had all the qualities of an Eden—flawless state, immaculate atmosphere, and the goliath sequoia. On the off chance that Warren was so enthused about the sequoia, the author notes, for what reason didn't he pick California? "In coming so close to reality, it appears to be abnormal that the capable logical essayist didn't get the genuine light with regards to the area of the first home of man." Warren couldn't have been glad to discover his work lauded by Wyoming author Willis George Emerson in the introduction to his 1908 sci-fi novel The Smoky God. The book professed to be the genuine record of a Norwegian angler who in 1829 had fallen through an opening at the North Pole into the inside of the Hollow Earth—where the Garden of Eden is reachable by monorail. "In his painstakingly arranged volume, Mr. Warren nearly stubbed his toe against the genuine truth, yet missed it apparently by just a tiny bit." Dr. George C. Allen, a Boston University philologist, trusted him associate Warren that Eden was at the North Pole—yet he made one significant change. In 1921, he guaranteed that the North Pole moves altogether around the globe at regular intervals, so "cautious scientific calculations bring the first heaven where Ohio presently is." Warren himself, who passed on in 1929 at 96 years old, remained totally, outreachingly persuaded of his unique hypothesis' veracity. The North Pole Eden "has shown itself the preeminent and unavoidable speculation from the real factors of current information regarding man and the world. It has fit the most seasoned customs of religion and the most recent accomplishments of science…
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