Organic Chemistry PDF

ORGANIC CHEMISTRY I. INTRO & HISTORY OF ORG CHEM II. STRUCTURE AND BONDING Introduction ❖ Structure of the Atom Organic Chemistry atoms are made up of protons (+), - th...

ORGANIC CHEMISTRY I. INTRO & HISTORY OF ORG CHEM II. STRUCTURE AND BONDING Introduction ❖ Structure of the Atom Organic Chemistry atoms are made up of protons (+), - the study of molecules that have neutrons and electrons (-) carbon atoms Almost all of the atom’s mass is in - Carbon, with four valence electrons, the nucleus, but it is the electrons often catenates or bonds with itself that take part in chemical bonding and reactions History Each element is distinguished by Jons Jacob Berzelius (1806) the number of protons in the - First coined the term “organic nucleus (the atomic number) chemistry” for the study of Atoms with the same number of compounds derived from biological protons but different numbers of sources neutrons are called isotopes. - Vital Force Theory: Organic Atomic mass unit (amu) - based chemistry referred to the study of on Carbon 12 chemical compounds that could only be extracted from living things, but ❖ Electron Structure of the Atom not made Electrons that are bound to nuclei are found in orbitals Friedrich Wöhler (1828) Heisenberg Uncertainty - Discover organic matter on Principle - we can never meteorites determine the exact location of - First person to isolate the elements the electron, but we can yttrium, beryllium, and titanium determine the electron density - Most well known for his discovery (the probability of finding the that an inorganic salt, ammonium electron in a particular part of the cyanate, could be used to make orbital) urea without living organisms. Atomic orbitals are grouped into different “shells” at different Key Discoveries/Concepts distances from the nucleus. Each Friedrich August Kekule von Stradonitz shell is identified by a principal (1865) quantum number, n. - Discovered the benzene ring The first electron shell contains structure just the 1s orbital. The second - The benzene ring is characterized electron shell consists of the 2s by three double bonds alternating and 2p orbitals. with single bonds between carbon In addition to the 2s orbital, the atoms and in concept double bonds second shell also contains three are shorter than single bonds, but in 2p atomic orbitals (2px, 2py, 2pz) benzene they are of equal length Node - a region of zero and the explanation behind this is by electron density Kekule as one night he had a dream The three 2p orbitals differ only in of snakes twisting together or eating their spatial orientation, so they its own tal until they formed a circle. have identical energies. Orbitals with identical energies are called Gilbert Newton Lewis degenerate orbitals. - Demonstrated the concept of electron dot structure (Lewis ❖ Lewis Dot Structure structure) Each valence electron (electrons that are in the outermost shell) is Linus Pauling symbolized by a dot ( ). - Responsible for the concepts of A dash ( — ) represents a nature of chemical bond, resonance, bonding pair of electrons hybridization, and molecular orbital — a single bond, 1 σ bond theory = a double bond, 1 σ bond and one π bond  a triple bond, 1 σ bond orbitals from different atoms from and two π bonds which the unpaired electrons interact, form bonds, and share A pair of dots ( ) represents a electron pairs nonbonding (lone) pair of VSEPR (Valence Shell Electron electrons that are not involved in Pair Repulsion Theory) molecular a covalent bond and "belong to" geometry model that helps predict only one atom the shape of a molecule from the Purpose: to arrange atoms to electron pairs that surround the have their appropriate noble-gas central atoms of the molecule. configurations Note: Core is excluded; it does Recall: not participate in hybridization or a. Octet Rule - an atom will be chemical bonding. Also referred most stable when to as “kernel”. surrounded by 8 electrons in the valence shell sp hybridization produces linear molecules at ❖ Bond Polarity and Electronegativity a 180° angle Nonpolar Covalent Bond - bond “diagonal hybridization” with the electrons shared equally a hybrid orbital of one ‘s’ and between the two atoms one ‘p’ orbitals of equal (EN diff 0.0 - 0.3) energy Polar Covalent Bond - unequally 50% s, 50% p shared pair of bonding electrons examples: BeF2, BeH2, BeCl2 (EN diff 0.4 - 1.7) Bond polarity is symbolized by an sp2 hybridization arrow with its head at the 120° angle negative end of the polar bond “trigonal hybridization” and a plus sign at the positive a hybrid orbital of one ‘s’ and end. two ‘p’ orbitals The bond polarity is measured by 33.33% s and 66.67% p its dipole moment (µ) defined to examples: Boron compounds be the amount of charge separation (𝛿+ and 𝛿–) multiplied sp3 hybridization by the bond length (d). 109.5° angle Electronegativity is a chemical “tetrahedral hybridization” property that describes the a hybrid orbital of one ‘s’ and tendency of an atom or a three ‘p’ orbitals functional group to attract 25% s, 75% p electrons toward itself. examples: ethane and Pauling Electronegativity Scale methane is useful for predicting the polarity of covalent bonds. Bonds associated: Higher EN = more attraction for Sigma (σ) bonds - head-on bonding electrons overlap of orbitals. Formal Charge - the charge a Pi (π) bonds - overlap of bonded atom in a molecule would unhybridized p-orbitals. have if the bonding electrons are shared equally. Bond Strength and Length “the shorter the bond, the stronger it is” ( ) − − # 𝑜𝑓 𝑏𝑜𝑛𝑑𝑖𝑛𝑔 𝑒 𝐹𝐶 = (# 𝑜𝑓 𝑣𝑎𝑙𝑒𝑛𝑐𝑒 𝑒 ) − 2 + # 𝑜𝑓 𝑙𝑜𝑛𝑒 𝑝𝑎𝑖𝑟𝑠 III. RESONANCE & ACID-BASE CHEMISTRY ❖ Hybridization Resonance process of combining two atomic - Way of describing delocalized orbitals (AOs) to create a new electron with certain molecules type of hybridized orbitals (HOs). where the bonding cannot be expressed by one Lewis structure Recall: Valence Bond Theory - - It occurs because of the explains covalent bonds as the delocalization of pi electrons results of overlapping atomic  For example, the reaction between hydrochloric acid and hydroxide ion. A proton is transferred from HCl (the acid) to hydroxide ion (the base). After a Take Note: Bronsted-Lowry acid donates a proton, what 1. Electron in pi bonds and electron as remains is called the conjugate base which in this lone pairs (adjacent to pi bonds) are reaction is the chloride ion. Conversely, when a the ones that participate in Brønsted-Lowry base accepts a proton it is resonance converted into its conjugate acid form: water is thus Can we shift delocalize electrons in the conjugate acid of hydroxide ion. In this sigma bonds? NO reactions, H+ ions serve as the proton. 2. Atoms must be connected in exactly the same way IV. ALKANES, CYCLOALKANES, AND Example: FUNCTIONAL GROUP Which of the following are pairs of contributing resonance structures? Functional Groups - A group of atoms responsible for the characteristic reactions of a particular compound. It serves as the site of organic reactions. 3. Knowledge of curved arrow formalism or the movement of electrons from electron rich atom to electron poor Alkanes atom. The arrow head depicts the - The carbons present in alkanes are sp3 destination of the electron hybridized. 4. Resonance is STABILIZING. - For every “n” C present in a straight chain Because the energy is being distributed alkane, there are “2n” H attached + 2H in evenly. The goal of resonance is to the terminal side which come up to the lower the overall energy of a molecule general equation of alkanes: via electron delocalization CnH2n+2 Mortal Sins in Resonance: The Illegal Physical Properties Moves 1. Never resonate onto sp^3 carbon The physical properties of alkanes depend 2. Never disrupt an octet of a halogen on the no. of carbon present in the 3. If a molecule starts out positive or compound. negative, you may not create any additional charges C1 - C4: gases C5 - C17: liquids Acid-Base Chemistry >C18: solids Acid - proton donor - Most acids contain hydrogen (HF, HCl, H3O+, NH4+, CH3COOH) Base - proton acceptor - Such as OH-, F-, NH3, CH3COO-)  Naming Organic Compounds The naming of organic compounds is based on IUPAC which contains the following: Prefix: What and where are the substituents (attached to main chain) Parent: Longest carbon chain [first: #C, last: type] The boiling point, melting point, and density Suffix: Highest priority functional group of alkane increases as the number of carbon increases. Steps in naming compounds: 1. Determine the longest chain containing the functional group of highest priority. 2. Number the chain from the end closest to the highest functional Degree of Substitution of C group. This will dictate primarily the 3. Determine the substituents. reactivity of organic molecule particularly hydrocarbon or any The table below shows the order of groups carbon-containing molecule based on decreasing order of priority. The use of pencil trick is a way to easily determine the degree of substitution of C if the structure given is in line bond notation. Classification of H Similar to the degree of substitution of C, the number of R-groups connected to the carbon determines whether the hydrogen is primary, secondary or tertiary. Intermolecular Forces London Dispersion Force or Van Der Waals - This force is present in all molecules. It has the weakest force. However, if the molecules have more electrons, the force is stronger.  Dipole-Dipole - The force between polar nonmetal bonds. Hydrogen Bond - It occurs when hydrogen is bonded with fluorine, oxygen, or nitrogen (FON). 3. Termination - all the remaining Ion-Dipole radicals in the propagation step must - The force when metals bond to be combined in all possible manner nonmetals. to form a more stable product. Ion-ion - The strongest force which occurs when a metal bonds to another metal. Degree of Unsaturation (Index of Hydrogen Deficiency) Reaction of Alkanes COMBUSTION - Process of combining alkanes with oxygen V. AROMATIC COMPOUNDS alkane + oxygen → carbon dioxide + water + heat ❖ The benzene molecule is composed of six carbon atoms joined in a planar General balance equation for combustion of hexagonal ring with one hydrogen atom alkanes: attached to each. ❖ The stability of Benzene is due to the delocalization of electrons across its ring structure. HALOGENATION - It is a gateway to the rest of organic ❖ Aromatic Compounds - are a special synthesis. class of organic molecules that exhibit unique properties due to their specific Detailed Reaction Mechanism of Alkane structural characteristics. Halogenationz CRITERIA FOR AROMATICS 1. Initiation - decomposing or 1. The molecule is cyclic (a ring of separating the halogen molecule into atoms) its corresponding radical. 2. The molecule is fully planar (all atoms in the molecule lie in the same plane) 3. The molecule is fully conjugated (p 2. Propagation - step in producing orbitals at every atom in the ring) more radicals, specifically alkyl 4. Huckel’s Rule: The molecule has radicals and halogen radicals. 4n+2=π electrons (n=0 or any positive integer). NOMENCLATURE OF AROMATIC COMPOUNDS  VI. STEREOCHEMISTRY A. Monosubstituted Benzene Mono-substituted benzene rings, with a Stereochemistry substituent not on the list above, are - Three-dimensional arrangement of atoms named with benzene being the parent - It deals with the spatial arrangement of name. These compounds are named atoms and groups in molecules as such: Name of the substituent + - Recall the concepts on: Benzene. - Functional groups - Sense of direction - Atomic weight of The 10 organic elements Unlike aliphatic organics, (R)-Thalidomide - has sedative effect benzene-derived compounds can have (S)-Thalidomide - has teratogenic effect multiple names, including common and systematic ones, with IUPAC allowing some widely used common names, which often replace the benzene base name. Stereoisomers - Stereoisomers have the same molecular formula and chemical bonds but they have different spatial arrangements. B. Disubstituted Benzene - Stereoisomers can be subdivided into two Three distinct positional isomers: parts that are configurational and ortho- (o-): 1,2- (next to each other in conformational isomers. a benzene ring) meta- (m): 1,3- (separated by one Configurational carbon in a benzene ring) - This type of isomerism is para- (p): 1,4- (across from each other non-superimposable and in a benzene ring) non-interconvertible by rotation around single bonds. - They can be interconverted by breaking and making bonds. - Types are enantiomers and diastereomers Conformational Examples: - These are non-superimposable but easily interconvertible by rotation about single bonds. - Cycloalkane and alkanes show this type of isomerism. Chirality - Also termed as handedness - Means that molecules cannot be superimposed with its mirror image by any rotations or translations  Cis-trans Isomers - Applicable for alkenes - Only applicable if the atoms on the left are not the same and the atoms on the right are not the same. Chiral Carbon - Has four (4) unique substituents Visual representation: - Asymmetric center R and S Configuration - Could be identified only on chiral carbons - Involves consideration of ranking the atoms around the chiral carbon through its ATOMIC NUMBER (Cahn-Ingold-Prelog system) - Once the atoms were ranked, #4 has to be at the back and will be crossed out. Stereoisomers Possible Numbers - An arc would be traced from 1 to 3. - To identify the maximum number of - R configuration if arrow is towards right stereoisomers possible for a given structure, - S configuration if arrow is towards left the following formula must be used: Important Elements in Organic Chemistry - Hydrogen - Carbon - Nitrogen - Oxygen - Flourine - Phosphorus - Sulfur - Chlorine - Bromine - Iodine Example: