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Chem 1AA3 - Chapter 26, 27, 11 - Organic Chemistry.docx

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Jeff Landry

Chapter 26, 27, 11: Organic Chemistry Why is organic chemistry important? - To understand how we interact with: o Other organisms (food and nutrients, infections) o Our environment (aromas, pollutants) o Drugs o Ourselves (metabolism, growth, immunity, cancer) o To understand how things are made, what they’re made of, what they react with.. Organic Chemistry Components 1) Structure: the connectivity and 3D nature of compounds 2) Theory: structure and reactivity in term sof atoms and the electrons that bind them together 3) Synthesis: how to design and make new molecules Alkanes (Section 26-1, 26-2) - Hydrocarbons – the simplest organic compounds (CnH2n+2 - Saturated (all bonding electrons used to make single bonds) - Simplest one: Methane – CH4 – tetrahedral, AX4 - Ethane (C2H6) o structural formula shows connectivity o Conformation: eclipsed, completely lined up with one another… o Wedged line: bond is coming forward out of the plane o Dashed line: bond is going backward behind the plane o Straight line: bond (and attached group( is in the plane - Propane (C3H8) o Condensed structural formula: C3 CH2CH3(still gives connectivity and structural info but easier to write) How to Drawn Organic Molecules 1. Draw molecules in a zip-zag shape versus linear structures (each point is a carbon) 2. Assume there are H atoms attached to each carbon in a zig-zag structure, giving valences of 4 have to explicitly show heteroatoms (not carbon) 3. For reactions, draw out the functional groups in detail and include lone pairs (electrons) Hints: count your carbon atoms, count the substituents on carbon atoms including implied H atoms, never more than four bonds to carbon Structural Diversity (Isomers, cycloalkanes; Section 26-1, part of 26-3) - Skeletal or structural isomers have: o The same molecular formula but different connectivity o Different physical properties - Concept check: draw all structural isomers of C5H12 o 2 methyl butane, 2 ethyl propane, pentane, 2, 2 – dimethyl propane/ dimethyl propane Conformations of Alkanes Newman Projections - Looking head on at carbon atoms bonded together so you can’t actually see the bond - Represented by circle with point in the middle - Pink dot is the carbon closest to you ,blue circle is carbon atom further from you - Bonds exactly lined up like an eclipse - If we allow a rotation around the carbon atom with groups behind to rotate, everything is very well separated - Eclipsed one: higher energy because you have repulsion between two H atom s - Staggered: lower energy, less repulsion b/c the H is bisecting the space btwn two H’s behind - Degrees of rotation to get from staggered to eclipsed: 60 degrees - Entropy causes rotation - H atoms in ethane’s eclipsed conformation appear to be far apart, but in reality, they are in contact with each other Conformation vs Configuration - Conformation: arrangement of atoms in a molecule that can be changed by simple rotation of single bonds, without breaking any bonds - Configuration: the permanent geometry of a molecule resulting from the spatial arrangement of its bonds o Must break bonds to change configuration Conformations of “disubstituted ethane” - fixed group in front, rotate one behind - Conformation 2 has the most energy b/c two R groups are repelling each other right beside each other - Unique pictures: 3, unique energies: 2 (2 and 3 have the same energy) - Conformation 1: anti-conformation - Conformation 2 and 3: gauche conformations Eclipsed Conformations - Bonds in front and back are exactly lined up - All eclipsed conformations have higher energy than all staggered conformations - - Middle conformation has the highest energy since R and R’ are repulsing - Energy max, local max, global min, but also local min as we rotate around structures - Any groups with eclipsing cause us to sit at a higher potential energy Conformations and Potential Energies (Ethane) - Relative potential energies, max and min - Max is fully eclipsed, all bonds are completely eclipsing one another - Totally staggered is minimum energy - Second local max, CH3 should be rotating 60 deg clockwise so in th the 5 picture the first H to the left of the bottom should be CH3, the CH3 should be an H - 6 picture the CH3 on the right should be H - Starts with global max then local min local max global min local max local min global max - Rotation occurs during to entropy Iclicker 1: which conformation has the highest (least favourable) energy? Assumr R, R’ is methyl. D) Ring Structures: Cycloalkanes (C H ) n 2n If these molecules were flat: 60 deg 90 deg 108 deg 120 deg Butterfly envelope actually 109.5 - Carbon atom bonded to 4 other groups wants tetrahedral geometry – 109.5 bond angles - These molecules aren’t flat, they flex a bit to open up bond angles to get close to 109.5 Molecules are not always flat: Cyclohexane Boat Chair - Boat has a lot of eclipsed atoms  higher energy - Chair formation is fully staggered, no eclipses - Equatorial H atoms are pink o Closet to being right on the midline - Axial H atoms (at the poles, like an axis going through the molecule) are blue o Point down / up o C atoms that are down / lower have H atoms that point down o C atoms that are up / higher have H atoms that point up Ring Strain in Cycloalkanes - Propane – bond angles ( at C atoms) 109.5 - Cyclopropane: bond angles (at C atoms) 60, H atoms are eclipsed Naming - Chemistry is a visual science: structures are key to understanding reactivity and physical properties - Systematic nomenclature: IUPAC rules (assumed knowledge) - Choose one with most constituents on it - Give the lower position to the letter that comes first in the alphabet - Name the following compounds: a) 3-methyl hexane b) 3-ethyl - 2,4-dimethylheptane c) 3-ethyl, 5-methylheptane Name of Common Compounds - The acetyl group is not a functional group; it is a commonly seen structural motif More alkyl names (to the right) - Focus on carbon that is the connection point to the R group - How many carbon atoms are bonded to the R looking at the chain itself? - n-butyl usually just called butyl - Sec- butyl (secondary butyl group since 2 side carbon groups) - Carbon tha tis the point of connection with the R and the rest of the molecule - Tert-butyl (tertiary butyl since 3 C’s attached to the connecting carbon) - Isobutyl (like an isopropyl but with an extra C ) o Itself is only bonded to one other C atom in the side chain; like an isomer of a butyl.. iso. - Isobutyl is one word so we alphabetize it according to the i - Sec-butyl and tert-butyl, ignore the first piece and alphabetize according to the butyl Substituents - Allyl group puts carbon between double bond and R, 3 carbon group - Allyl acetate: o ester C double bond O , single bond O with an r group o alkene - diagnostic iclicker: c) ethyl butanoate Reaction of Alkanes C8H18 + O2  1) What are the products of the reaction at 29 8K> 2) Write a balanced eqn 3) Predict the signs of H, S, G: - H 4) What type of reaction is shown? Combustion Halogenation X2 CH4  CH3X + HX + CH3-CH3 light or heat hemolytic – break bonds equally, one e goes one way one e goes the othe rway Applicable also for F2 (often explosive), Br2 (slow), but not I2 (no rxn) Bonding in Alkanes - Hybridization Review: Electronic Structure and Bonding - the atom: a dense nucleus surrounded by a much larger extranuclear space Principal Energy Levels - electrons are confined to shells defined by the principal quantum number (n) - n = 1, 2, 3 2 - each shell can contain electrons 2n electrons - the lower the value of n, the lower the energy of the shell (nearest to the nucleus) Orbitals - shells are divided into sub-shells s, p, d, f - p, d, f orbitals are further divided up based on their sptial orientation - Shell orbitals in that shell n = 1 1s n = 2 2s, 2p x 2p y 2p z n = 3 3s, 3px, 3py, 3pz, + 5 3d Electron Configuration Three principles/rules are used to determine the electron configuration Aufbau principle: Paula exclusion principle: Hund’s rule: - Each type of orbital (s, p, d, f) has a distinct shape - The shape represents the probability of finding an electron (quantum mechanics) - Organic chemists are interested in shells 1, 2, and sometimes 3 S: 2 - spherical, p orbitals : 3 – 90 degrees from one another px py pz Example: Carbon 1s 2s 2p 2 2 - The outer most electrons of atoms (valence electrons) govern the chemical and physical properties p-orbital shapes - The p-orbitals in carbon are at 90 deg to each other - Atoms bonding to a carbon atom should therefore be situated at 90 to each other…? - Problem: the shape of methane is tetrahedral (AX4); bond angles are 109.5, not 90 - Symmetrical, even bond lengths Hybridization - Comes from the word hybrid which means something is of mixed origin or composition - Hybrid orbitals arise by combination of atomic orbitals within an atom sp Hybridization (section 11-3) - Energy is between s and p but not exactly in the middle, offset more towards the p - 3 p orbitals and 1 s; weighted contribution - S orbital overlaps with p orbitals: constructive interference; enhanced blue portion - Overlapping in opposite phase – destructive interference; reduced red portion - The number of hybrid orbitals is equal to the number of combining atomic orbitals - Combine one 2s orbital and three 2p orbitals 3  four sp orbitals - Must end up with 4 orbitals since you started with 4, maintain the same number Bonding Methane - Overlap of sp orbitals from carbon and 1s- orbitals from hydrogen - End on (or end-to-end) overlap produces sigma bonds - End-on overlap of sp -orbitals also produces sigma-bonds - Sigma bonds stich all atoms of molecules together, hold together the framework Iclicker 2: how many sigma bonds are there in this molecule? C) 7 - Overlap between C-C and overlap between 6 C-H’s Moving Beyond Alkanes: Functional Groups Sample problem: What functional groups do you see? - Amine NH2 - Amide – carbonyl group C = O right next to a N - Attached to nitrogen atom there is one C atom – primary - Ester O-C=O - Carboxylic acid CO2H - Arene functional group – phenyl ring - Arene – any hydrocarbon containing an aromatic group (eg. A benzene-like ring) Organic Compounds: Medicines/Drugs - Tamoxifen - Viagara (erectile dysfunction) - Lipitor (cholesterol) - Stanozolol (anabolic steroid) – 4 rings joined together as a base structure - Industrial cheimcals: o indigo dye o aspartame (sweetener) – formed of 2 amino acids formed by amide bond  risk of brain cancer.. in rats only on aspartame, amide bond is heat sensitive o sucralose doesn’t get metabolized passes right through, heat stable - natural products: o cocaine o quinine – anti-malarial Alkenes (C H ) n 2n - CH2 = CH2: ethene (ethylene) - CH3CH2CH = CH2: 1-butene (but-1-ene) - CH3CH2CH2C=CH2 CH2CH3 - 2-ethyl-1-pentene (chose the shorter chain due to the double bond) Multiple Covalent Bonds - Ethylene has a double bond in its lewis structure - VSEPR says trigonal planar shape at C - Sp2 hybrid orbitals 2 - Combine one 2s orbital + 2 2p orbitals  3 sp orbitals ( + one 2p orbital left over) - Hybrid orbital lobes pointing in the direction of an equilateral triangle: 120 deg - The extra p orbital can be used to form a pi bond - Pi bond are covalent bonds that form by the sideways overlap of parallel p-orbitals - Eclipsed p-orbitals: = bond - Staggered p-orbitals: no pi bond - 2 electrons making up the second bond are located anywhere within that system - Sigma bond in the middle between the C’s, pi bonds surrounding it Ethene - Must have overlap of p orbitals in double bonds - Prevents rotation around C-C bond - Overlap above and below plane of atoms given one pi bond (in total) Alkenes have restricted rotation - Restricted rotation leads to different configurations - Rotation requires breaking a pi bond to change configuration - Geometric isomers – relative positions of things to each other; everything attached in the exact same spot, but relative positions have changed ; cis / trans - Structural isomers – things attached in diff locations Cis vs trans fatty acid: impact of geometry - Cis-9-octadecenoic acid (bent) vs trans – 9-octadecenoic acid (straight chain ) Chains with double bonds: Less efficient packing b/c of kin in chain geometry, therefore weaker intermolecular forces and lower melting point The E,Z System of Nomenclature - Neither are cis or trans. - Cis trans isomerism talks about whether cabrons ar eon the same side or opposite side - No rule around other functional groups being attached; only in ref to carbon chains - E: entgegen - Z: zussamen - Prioritized based on larger atomic number (larger number = higher priority) - Z: If the two higher priority groups are on the same side - E: high priority groups are on opposite sides On right side of the double bond.. Cl has higher atomic number than C so it takes priority. On left side, carbon is attached to another carbon over the carbon attached to 3 H’s so bottom C gets priority Therefore both high priority chains are on the same side COH (C double bonded O, single bond H) vs COH3 (C single bonded OH, single bonded two H’s) priority goes to COH because you count the O twice when there’s a double bond Tamoxifen (Z-isomer, left) is used to treat hormone dependent breast cancer Iclicker 3: which of the molecules has/have a Z configuration? I) and ii). E configuration? Iii Organic Compounds: Biological - Cis (or Z) d ouble bon dis at D - We can use the term cis here because there is only one non-H substituent on each carbon atom o that double bond Reactions with Alkenes Chemical Reactions - Charge attractions draw molecules together - In organic chem, there is often not a full cation reacting with an anion - more common to have a charged reagent be attracted to an organic compound that has a dipole - The reagent does not necessarily need to be charged: lone electron pairs would also be attracted to a dipole - The majority of rxns in organic chem involve the flow of electrons from one molecule to another - Nucleophil
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