Organic Chemistry Exam Helper Introduction to Organic Chemistry By Matthew Pasek, Ph.D Organic Chemistry Exam Helper: Introduction to Organic Chemistry by Matthew Pasek Published by Free Radical Consulting 2703 Pemberton Creek Drive, Seffner FL 33584 © 2017 Matthew Pasek All rights reserved No portion of this book may be reproduced in any form without permission from the publisher, except as permitted by U.S copyright law For permissions contact: freeradicalconsulting@gmail.com Forward This book is part of a series of organic chemistry study guides It focuses on the introductory material covered by organic chemistry classes: a general overview, details of bonding, molecular formulae, acids and bases, hybridization, nomenclature, and conformations Most important to the student of organic chemistry are the quizzes at the end These quizzes allow you to test your knowledge of key concepts With organic chemistry, practice makes perfect The frequent practice of organic chemistry reactions will help you pass, or even ace, an organic chemistry exam The subjects covered in this book are the introductory materials of organic chemistry Each organic chemistry class is different: some will emphasize specific characteristics not included here, others will be sticklers for certain aspects of organic chemistry (typically if that’s the professor’s area of focus) and may not use the same suite as those shown here, and still others will focus on a bare minimum set of concepts, due either to time constraints or pedagogical concerns This guide is meant to supplement, and not replace, attending the organic chemistry course I am a professor of geochemistry and not an organic chemist However, the organic chemistry fundamentals are an important part of any chemist’s training, and I learned organic chemistry left and right for my own research and for my grants I’ve tutored many students in this subject, but it is possible for there to be errors in these questions as I am not an organic chemist by profession Figures here were drawn using ACD lab’s ChemSketch program This program is great for drawing organic molecules Other sketches are done by hand or with power point TOC Contents What is organic chemistry? Bonds in organic chemistry Molecular formula Saturation Chemistry Resonance Skeletal drawings Molecular hybridization Acids and Bases From 2D to 3D 10 Isomers 11 Stereoisomers 12 Molecular Attractive Forces 13 Hydrogen Bonding 14 Nomenclature 15 Nomenclature 2 16 From diagrams to nomenclature 17 Quiz Me! 18 Conclusion and Cartoon What is organic chemistry? Chemistry is the science of the electron Organic chemistry is a branch of chemistry Organic chemistry is the chemistry of the element carbon, glibly put Nearly all (but NOT all) carbon compounds are organic compounds Organic chemistry arose out of a search for a difference between “alive” and “not alive” Such a search involved a concept called “vitalism”, the belief that there was something fundamentally different between the molecules of life and those that were formed by non-life Well, it turns out there isn’t really any major difference Aside from a bit more radiocarbon in living things (because they actively exchange carbon with the atmosphere, unlike most non-living reactions), the chemistry of organic compounds made by life or by man and nonbiologic reactions is the same Fundamentally, the chemistry of non-living carbon compounds is identical to living carbon compounds The glib definition of “organic chemistry = carbon chemistry” does need some caveats, however For instance, many geologists study a rock called limestone Limestone is mostly composed of a mineral called calcite, which has a formula of CaCO3 The carbon in calcite, and in carbonate (CO32-, HCO3-, CO2) in general, is not considered to be organic, since it forms by non-biologic processes Similarly, several other simple compounds are not considered to be organic These include hydrogen cyanide (HCN), which forms several inorganic salts, and diamond and graphite, which are both carbon minerals, and silicon carbide (SiC) and iron carbide, which are minerals A more exhaustive definition of organic is that the carbon atoms of the molecule should be covalently bound to either hydrogen or carbon (and preferentially hydrogen at some point in the structure) Carbon that forms ionic bonds and metallic bonds is typically not considered organic Similarly, graphite and diamond are essentially pure carbon, and aren’t considered organic Naturally there’s a fair bit of fuzziness with determining whether a carboncontaining compound is organic or not Some don’t feel that formaldehyde is an organic compound, whereas to others it obviously is The same is true for HCN, which we identified as inorganic Some scientists argue it is better described as organic In the end, most of the cases at the intersection are intuitive As long as there’s more than one carbon, and it’s bound to another carbon or hydrogen, you can generally assume the compound to be organic Note that organic has nothing to do with “coming from nature”, so there’s a vast difference between organic chemistry and the organic food that you might buy at Whole Foods or Trader Joe’s Organic in chemistry provides no real discerning value as to its origin, or its inherent “health” KEY POINTS AND HINTS: Organic chemistry is the chemistry of carbon, but not all carbon-bearing molecules are organic Organic carbon compounds should have covalent bonds, and should have C-C or C-H bonds Bonds in organic chemistry Bonding diagrams in chemistry show how the electrons are distributed in compounds The element carbon has an electronic structure of 1s2 2s2 2p2 (remember that from Gen Chem?) This means that carbon has four valence electrons in the second shell It is capable of forming four bonds with these valence electrons Although five bonds do occur as intermediates or transition states, these are not stable Drawing a structure with five bonds to carbon has been given a colloquial name of “Texas Carbon” (everything’s bigger in Texas!) If you draw a molecule with five bonds to carbon (including double bonds), you’ve probably drawn it wrong Be careful! A common way of representing bonding in molecules is through a Lewis dot structure Lewis dot structures were first used by a chemist Gilbert Lewis, who designed these diagrams to show how electrons were shared or not (not involved in a bond) between different atoms in a bond or molecule You can calculate a “formal charge” of a molecule by: FC = NV – NU – BE/2 Where FC is the formal charge, NV is the number of valence electrons (4 for carbon, 5 for N, 6 for O, etc.), NU is the number of unbonded electrons, and BE is the number of electrons participating in bonds The Lewis dot structure must by definition show all electrons It is often easier to simplify some of this by drawing bonding electrons as a line, instead of dots Two lines show there’s a double bond, and three show there’s a triple bond Electrons that don’t participate in bonds are still shown explicitly in a Lewis dot structure KEY POINTS AND HINTS: Lewis dot structures show bonds and unbonded electrons If a structure has 5 bonds to carbon, it is very likely wrong! Carbon almost never has a free electron pair on it (except for carbenes) Practice Sections 1 & 2? Problem 1 Problem 2 Problem 3 Problem 4 Problem 5 Back to TOC Problem 1 Identify which of these is an organic compound A) CaCO3 B) C60 (AKA a buckyball) C) N2 D) H3C-CH3 Go back to section No Back to question Go back to section Problem 17 The structure for caffeine is shown below What is the hybridization on the highlighted carbon? A) sp2 B) sp C) sigma D) sp3 Go back to section YES! Next question Go back to section No Back to question Go back to section Problem 18 Which of the following is a plausible formula for hexanone? A) C6H14O B) C6H12O2 C) C5H12O D) C6H12O Go back to section YES! Next question Go back to section No Back to question Go back to section Problem 19 This is phenylalanine, an amino acid If an acid is added to phenylalanine, what region will the proton likely add to? A) 2 B) 4 C) 1 D) 3 Go back to section YES! Next question Go back to section No Back to question Go back to section Problem 20 Which of the following structures for C2H4O2 do you predict will be the most acidic? A) C) Go back to section B) D) YES! Back to TOC Previous Exam Go back to section Done! No Back to question Go back to section 18 Conclusion and Cartoon The End! Good luck! .. .Organic Chemistry Exam Helper Introduction to Organic Chemistry By Matthew Pasek, Ph.D Organic Chemistry Exam Helper: Introduction to Organic Chemistry by Matthew Pasek... The frequent practice of organic chemistry reactions will help you pass, or even ace, an organic chemistry exam The subjects covered in this book are the introductory materials of organic chemistry Each organic chemistry class is different: some will emphasize... From diagrams to nomenclature 17 Quiz Me! 18 Conclusion and Cartoon What is organic chemistry? Chemistry is the science of the electron Organic chemistry is a branch of chemistry Organic chemistry is the chemistry of the element carbon, glibly put