Chapter 1: The Genesis of Organic Chemistry PDF

Chapter 1: The Genesis of Organic Chemistry 1.1: What is Organic Chemistry? – Organic chemistry focuses on molecules that contain – at the bare minimum – carbon and hydrogen Usually, oxygen, sulfur, and nitrogen will make an appearance – Carbon can form stable covalent bond...

Chapter 1: The Genesis of Organic Chemistry 1.1: What is Organic Chemistry? – Organic chemistry focuses on molecules that contain – at the bare minimum – carbon and hydrogen Usually, oxygen, sulfur, and nitrogen will make an appearance – Carbon can form stable covalent bonds with: H, N, O, S, and even other C – Carbon is able to from long chains with itself – either in straight or branched forms Chapter 1: The Genesis of Organic Chemistry 1.1: What is Organic Chemistry? – C6H14 can form five isomers – different molecules with the same formula but different connections Chapter 1: The Genesis of Organic Chemistry 1.1: What is Organic Chemistry? – The arrangement of bonds and mole pairs around a molecule provides the molecular geometry – Geometry and polarity of bonds leads to molecular polarity – Molecular polarity can dictate molecular behavior – affecting the reactivity and behavior with other molecules Polar molecules can exist in the polar environment of your bloodstream Nonpolar molecules will be stored in adipose (fat) tissue Chapter 1: The Genesis of Organic Chemistry 1.1: What is Organic Chemistry? – Bond polarity is dictated by electronegativity differences – you will NEED to memorize the following electronegativity values: H, Li – F, P – Cl, Se – Br, and I Chapter 1: The Genesis of Organic Chemistry 1.2: Review: Bond Types and Polarity – Covalent and ionic bonds exist – covalent bonds may be polar or nonpolar – There is a prediction guide to help you determine bond polarity: ΔEN < 0.5: Nonpolar 0.5 < ΔEN < 1.9: Polar ΔEN > 1.9: Ionic Br-CH3: ΔEN = 0.3 = Br (2.8) – C (2.5) – so, the bond is nonpolar covalent (or just nonpolar) Chapter 1: The Genesis of Organic Chemistry 1.2: Review: Bond Types and Polarity – Calculate the ΔEN and bond polarity for each bond in the following: Chapter 1: The Genesis of Organic Chemistry 1.2: Review: Bond Types and Polarity – Remember: Just because a molecule has polar bonds does not mean that it is a polar molecule – Molecular geometry is used to determine molecular polarity Chapter 1: The Genesis of Organic Chemistry 1.3: Drawing Lewis Structures 1. Find the total number of valence electrons – anions have extra electrons, cations have fewer electrons 2. Lay out the skeleton of the molecule – H and F cannot be central (they make ONE bond only). Avoid oxygen-oxygen bonds, and try to make the molecule symmetrical 3. Determine ho many remaining valence electrons are present 4. Form octets using lone pairs on the outside atoms first 5. Make lone pairs into bonding pairs to satisfy the octet rule on the central atom – C, N, O, and F NEVER violate the octet rule 6. Calculate formal charges – you do not need to show a 0 formal charge, but you DO need to show all others 𝐹𝑜𝑟𝑚𝑎𝑙 𝐶ℎ𝑎𝑟𝑔𝑒 = 𝐺𝑟𝑜𝑢𝑝 # − (# 𝑜𝑓 𝑒𝑙𝑒𝑐𝑡𝑟𝑜𝑛𝑠 𝑖𝑛 𝑙𝑜𝑛𝑒 𝑝𝑎𝑖𝑟𝑠 + # 𝑜𝑓 𝑏𝑜𝑛𝑑𝑠) 7. Evaluate: More bonds are better Structures with a minimized size and formal charge are better Structures with the negative formal charge on the more electronegative atoms are better Chapter 1: The Genesis of Organic Chemistry 1.3: Drawing Lewis Structures – Predict the better structure: SCN- N3- SO32- PO33- Chapter 1: The Genesis of Organic Chemistry 1.3: Drawing Lewis Structures – Octet violations: – Elements in the third period and below can have an “expanded octet” – more than 8 electrons around them when they are the central atom Phosphorus can form 5 bonds (its in Group 5A) – Elements in Group 3A have a “diminished octet” – they can have a maximum of 6 electrons around them Boron and Aluminum will only form 3 bonds Chapter 1: The Genesis of Organic Chemistry 1.3: Drawing Lewis Structures – Oxyacids have the general formula HaXOb and contain polyatomic ions – We will focus on Brønsted-Lowry acids – the H atom must be as positive as possible, and it is bonded to the more electronegative O atom and not to the X atom We can also say they contain –O-H groups Chapter 1: The Genesis of Organic Chemistry 1.3: Drawing Lewis Structures – Smaller organic molecules can have their Lewis structures generated using the steps previously discussed – Larger organic molecules get more complicated – However: Carbon always has 4 bonds – 4 single bonds, 2 double bonds, 2 single bonds and 1 double bond, 1 triple bond and 1 single bond Carbon almost never has lone pairs of electrons Use pi bonds when filling octets in C (forming double or triple bonds) Chapter 1: The Genesis of Organic Chemistry 1.3: Drawing Lewis Structures – Draw a Lewis structure for: (CH3)2CHCHCC(CH3)CH2CO2H (CH3)2 is NOT CH3-CH3 – instead is it TWO CH3 groups attached to the next carbon The second instance of (CH3) means the group is attached to the previous C You MUST learn as soon as possible that CO2H is short for a carboxylic acid and has the structure: Chapter 1: The Genesis of Organic Chemistry 1.3: Drawing Lewis Structures Chapter 1: The Genesis of Organic Chemistry 1.4: Hybridization and Bonding – Recall that electrons populate orbitals and that hybrid orbitals are a blending of different orbital types – for us that will be the s and p orbitals – S orbitals are those that are closest to the nucleus and are always a part of hybrid orbitals – Recall that electrons want to be as far apart from one another as possible – so to make 4 bonds, all three of the p orbitals will need to hybridize with the s orbital This creates the sp3 hybrid orbital, and can make 4 bonds Chapter 1: The Genesis of Organic Chemistry 1.4: Hybridization and Bonding Chapter 1: The Genesis of Organic Chemistry 1.4: Hybridization and Bonding – sp3 hybridized orbitals: Separates four sets of electrons into 4σ and 0π bonds – sp2 hybridized orbitals: Separates three sets of electrons into 3σ and 1π bonds – sp hybridized orbitals: Separates two sets of electrons into 2σ and 2π bonds Hybrid orbitals are used to make σ bonds or to put lone pairs of electrons in Unhybridized p orbitals are used to make π bonds – either double to triple bonds Chapter 1: The Genesis of Organic Chemistry 1.4: Hybridization and Bonding – Hybridization will also tell you the molecular geometry of a molecule – if the central atom has the specified hybridization below, it will have the specified geometry: sp3 hybridization corresponds to tetrahedral geometry sp2 hybridization corresponds to trigonal planar geometry sp hybridization corresponds to linear geometry Chapter 1: The Genesis of Organic Chemistry 1.4: Hybridization and Bonding Chapter 1: The Genesis of Organic Chemistry 1.4: Hybridization and Bonding Chapter 1: The Genesis of Organic Chemistry 1.4: Hybridization and Bonding Chapter 1: The Genesis of Organic Chemistry 1.5: Bond Polarity and Molecular Polarity – Polarity occurs when electrons are shared unequally Bond polarity can be determined using electronegativity values – and using electronegativity can give a rough guide to bond polarity – Molecular polarity is due to the vector aspect of bond polarity and molecular geometry Chapter 1: The Genesis of Organic Chemistry 1.5: Bond Polarity and Molecular Polarity – Dipole vectors represent the magnitude of charge separation – The vector always points toward the more electronegative atom – The size of a vector is proportional to ΔEN Vector dipoles can be added together in any order to determine the overall molecular polarity Chapter 1: The Genesis of Organic Chemistry 1.5: Bond Polarity and Molecular Polarity Chapter 1: The Genesis of Organic Chemistry 1.5: Bond Polarity and Molecular Polarity Chapter 1: The Genesis of Organic Chemistry 1.5: Bond Polarity and Molecular Polarity Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – A molecule’s chemistry is due to a number of factors – polarity, functional groups, geometry – You will be responsible for recognizing (short form and fully drawn) eight functional groups in this course: Aldehydes, ketones, carboxylic acids, carboxylic esters, alcohols, ethers, amines, and amides Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – Representation of molecules – as formulas or drawings – is very important – The more complex a molecule – the more time-prohibitive it is to draw a structure – Consider hexane as: Full Lewis Structure Condensed Line Drawing (Stick Figure) Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – Rules: 1. Carbon almost always has 4 bonds 2. The end of the stick represents a C atom, unless otherwise stated 3. Intersections of sticks represent C atoms, unless otherwise stated 4. Hydrogens bonded to carbon are omitted Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – Classifications of carbon and hydrogen: Primary C (1°): The carbon has one bond to another carbon Secondary C (2°): The carbon has two bonds to other carbons Tertiary C (3°): The carbon has three bonds to other carbons Quaternary C (4°): The carbon has four bonds to other carbons – Hydrogens are classified relative to the carbon they are attached to – so a 1° H is attached to a 1° C Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – Practice: Classify each carbon in the following molecule of 2,2-dimethylbutane, (CH3)3CCH2CH3 and draw a stick figure Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – Practice: Classify each carbon in the following molecule of 2,2-dimethylbutane, (CH3)3CCH2CH3 and draw a stick figure Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – Practice: Classify each carbon in the following molecule of isopropyl methyl ether and draw a stick figure Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – Convert the following stick figures into condensed Lewis structures, and give their molecular formulas Chapter 1: The Genesis of Organic Chemistry 1.6: Line Angle Drawings (Stick Figures) in Organic Chemistry – You need to get proficient at writing formulas quickly – as in SOON and as in FAST Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – The carbonyl group (carbon double bonded to oxygen) is present in many organic functional groups: Aldehydes: There is an H attached to the carbonyl – RCHO where R = C or H Ketones: There are two carbons attached to the carbonyl – RCOR’ where R, R’ = C Carboxylic acids: The carbonyl is attached to an OH group on one side and a C on the other – RCOOH or RCO2H where R = C or H Carboxylic esters: The carbonyl is attached to OC on one side and either H or C on the other – RCO2R’ where R = H or C and R’ = C Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – The carbonyl group (carbon double bonded to oxygen) is present in many organic Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – The carbonyl group (carbon double bonded to oxygen) is present in many organic Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Alcohols have a hydroxyl group (OH) – ROH where R = C that is not a carbonyl Methyl: C is attached to no other C 1°: C is attached to one other C atom 2°: C is attached to two other C atom 3°: C is attached to three other C atom – Ethers have C-O-C attachments where neither C is a carbonyl – ROR’ where R, R’ = C Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Amines have a nitrogen attached to 1, 2, or 3 C atoms, where none of the C atoms is a carbonyl – RNR’R’’ where R = C, and R’, R’’ = C or H 1°: N attached to one C atom 2°: N attached to two C atoms 3°: N attached to three C atoms Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Amides have a nitrogen attached to 1, 2, or 3 C atoms, where one C atom is a carbonyl – RCONR’R’’ where R, R’, R’’ = C or H 1°: N attached to one C atom 2°: N attached to two C atoms 3°: N attached to three C atoms Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Aldehydes: Carbonyl attached to hydrogen Simplest: Formaldehyde (methanal) – HCHO Next: Acetaldehyde (ethanal) – H3CCHO – the first metabolite of ethanol by alcohol dehydrogenase Others: Benzaldehyde (almond extract), Vanillin (vanilla), Cinnamaldehyde (cinnamon) Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Ketones: Carbonyl attached to two carbons Simplest: Acetone (propanone) – H3C-CO-CH3 Useful synthetic ketone: methyl vinyl ketone (MVK) for alkylating agent – H2C=CH=CO-CH3 Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Carboxylic acids: Carbonyl attached to a hydroxyl group Simplest: Formic acid (methanoic acid) – H-CO-OH – an antigen from ant bites Next: Acetic acid (ethanoic acid) – H3C-CO-OH – vinegar is about 5% acetic acid Others: Butyric acid (butanoic acid, found in rancid butter), Benzoic acid (a breakdown of benzaldehyde), Cinnamic acid (a breakdown of cinnamaldehyde), Stearic and Oleic acids (found in animal fat and olive oil, respectively) Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Carboxylic esters: Carbonyl that is attached to an oxygen also attached to another carbon Simplest: Methyl acetate – H3C-CO-OCH3 Next: Ethyl acetate – H3C-CO-OCH2CH3 – found in nail polish remover Others: Ethyl butyrate – H3CCH2CH2-CO-OCH2CH3 – found in fruits and used for many artificial flavors, like cherry, bubblegum, and apricot – Many fruit odors/flavors are due to the presence of carboxylic esters in a mix with aldehydes, ketones, and other select hydrocarbons – unlike flavors that are derived from a single source (like vanilla from vanillin or wintergreen from methyl salicylate) Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Esters are not just carboxylic – phosphate, nitrate, sulfite, and sulfate esters exist, too – A carbon group is used in place of the acidic hydrogen from the oxyacid in these forms Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Alcohols: A hydroxyl group bonded to a carbon that is not a carbonyl Simplest: Methanol (methyl alcohol) – H3C-OH – which breaks down via ADH to formaldehyde Next: Ethanol (ethyl alcohol) – H3CCH2-OH – which breaks down via ADH to acetaldehyde Others: Isopropanol (isopropyl alcohol, rubbing alcohol) – (CH3)2CH-OH – which breaks down via ADH to acetone, carbolic acid (phenol) – C6H5-OH Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Ethers: An oxygen makes σ bonds to two carbons Example: Diethyl ether – H3CCH2-O-CH2CH3 – Ethers were and are used as anesthetics Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Amines: Nitrogen is attached to a carbon that is not a carbonyl Simplest: Methyl amine – H3C-NH2 – Methyl amine – and many amines – have an unpleasant, fishy smell Chapter 1: The Genesis of Organic Chemistry 1.7: Functional Groups in Organic Chemistry – Amides: Nitrogen is attached to a carbonyl Example: Dimethyl formamide (DMF) – CHO-N(CH3)2 – a universal solvent, and tertiary amide Polyamides are useful organic molecules formed between amines and carboxylic acids – nylon is a polyamide – The same condensation reaction combines amino acids to form proteins – ALL amino acids have H2N-CHR-CO2H where the R group determines the identity of the amino acid Chapter 1: The Genesis of Organic Chemistry 1.8: Connecting with Chemistry - The Evolution of Antibiotics – Antibiotics either kill or slow the growth of bacteria – Ancient cultures (and modern ones) had or have varied ways and compounds used to treat or fight infection Chapter 1: The Genesis of Organic Chemistry 1.8: Connecting with Chemistry - The Evolution of Antibiotics – Arsenic antibiotics were the first modern antibiotics – beginning in 1908 with Dr. Paul Ehrlic, who coined the term chemotherapy – The arsenic compounds had several issues, whoever – oxidizing quickly, as well as the toxicity associated with arsenic Chapter 1: The Genesis of Organic Chemistry 1.8: Connecting with Chemistry - The Evolution of Antibiotics – “Sulfa” drugs made their appearance around the same time (1909) and had varied uses from treating polio to pneumonia – The sulfa drugs lead to the creation of laws within the FDA (1938) to ensure drug safety before distribution to the public Chapter 1: The Genesis of Organic Chemistry 1.8: Connecting with Chemistry - The Evolution of Antibiotics – Penicillin is a class of antibiotics first noticed by Alexander Flemming in 1928 and isolated in the 1940s – These chemicals which contain β–lactam are necessary for covalently attaching to enzymes – Cephalosporins are similar in mechanism to penicillin, but are more resistant and are effective over longer periods of time Chapter 1: The Genesis of Organic Chemistry 1.8: Connecting with Chemistry - The Evolution of Antibiotics