CH1601 Organic and Biological Chemistry I - Lectures 1-9 Notes

Topic 1: Basic Introduction to Organic Chemistry

  • Drawing and naming organic compounds and functional groups.
  • Alkanes, alkenes, alkynes, alcohols, ethers, amines, nitro compounds, alkyl halides, aldehydes, ketones, carboxylic acids, esters, amides, and cyanides.
  • Common abbreviations:
    • Me (methyl)
    • Ph (phenyl)
    • R = alkyl
    • Ar = aryl
    • n-, i-, t- for branched groups
  • Definition of primary, secondary, tertiary, and quaternary positions.
  • Concept of oxidation levels in organic chemistry.

Topic 2: Structure and Bonding I

  • Lewis bonding model.
  • Electronegativity.
  • Ionic and covalent bonding - why does carbon form four covalent bonds?
  • Why do molecules adopt specific shapes?
  • Atomic orbitals, shapes and combining atomic orbitals to form linear combinations - molecular orbitals.
  • H<em>2H<em>2 and He</em>2He</em>2
  • Bonding and antibonding orbitals from overlap of 1s orbitals - formation of σ bonds.
  • Overlap of p orbitals - formation of π bonds.

Topic 3: Structure and Bonding II

  • Hybridisation - model for bonding in methane.
  • Classification of sp3, sp2 and sp terminology and shapes of molecules.
  • Methane and ethane as case studies; introduction to ethane and ethyne.
  • Comparison of borohydride anion, methane and ammonium cation as sp3 hybrids.

Topic 4: Molecular Conformation

  • Dynamics of molecular systems.
  • Concept of conformations using ethane and butane as case studies.
  • Newman projections, staggered and eclipsed conformations.
  • Syn- and anti-periplanar nomenclature; gauche.
  • Shapes and conformations of three to six membered rings; concept of angle strain and torsional strain.
  • Chair, boat, half-chair and twist conformations of cyclohexane, axial and equatorial environments.
  • Conformational analysis of mono-substituted cyclohexane derivatives.

Topic 5: Stereochemistry and Molecular Configuration

  • Definition of isomers, constitutional isomers and stereoisomers.
  • Achiral and chiral molecules - enantiomers; introduction to stereogenic centres.
  • Assignment of absolute configuration to stereocentres - Cahn-Ingold-Prelog rules.
  • Properties of enantiomers and polarimetry - optical activity.
  • Diastereoisomers; compounds with multiple stereocentres; 2n2^n rule and effect of symmetry - meso compounds.

Topic 6: Introduction to mechanism, resonance and delocalisation I

  • Why do molecules react?
  • Nucleophiles, Lewis bases, electrophiles and Lewis acids.
  • Drawing reaction mechanisms and the “curly arrow” notation; what do they mean and rules for their use.
  • Resonance and delocalisation; amides as a case study; hybridisation, bond overlap and forming molecular orbitals.
  • The rules for resonance and delocalisation.

Topic 7: Introduction to mechanism, resonance and delocalisation II

  • The rules for resonance and delocalisation, geometry and effects upon reactivity in amides; other delocalised systems; the allyl cation, allyl anion and common functional groups (nitro, ester, carboxylate, benzene).
  • Introduction to acids and bases I; equilibrium and pKa; definition; factors that affect the strength of an acid with case studies (i). stability of conjugate base.

Topic 8 and 9: Introduction to acids and bases II

  • Topics 8 and 9: Introduction to acids and bases II; (ii). placing negative charge on electronegative element; (iii) bond strength; (iv) inductive effects; (v) hybridisation; Delocalisation; phenols and C-H acidity.

  • Basicity; definition of pKaH; factors that affect the strength of a base with case studies (i). availability of negative charge / lone pair; (ii) delocalisation; (iii) solvent effects.

  • Neutral nitrogen bases and effect of (i) substitution (ii) electron withdrawing groups (iii) hybridisation (iv) delocalisation; amides revisited, amidines and guanidines

  • Recommended Reading

    • “Organic Chemistry”; (second edition) Klein (Wiley VCH; ISBN 978-1-118-45228-8); Chapters 1-3 and 5.
    • “Organic Chemistry”; (second edition); Clayden, Greaves, Warren (Oxford University Press; Oxford, 2012; ISBN 978-0-19-927029-3); Chapters 2, 4, 7, 8, 14 and 16.
    • “Chemistry3”; Burrows, Holman, Parsons, Pilling, Price, (Oxford University Press, Oxford, 2009; ISBN 978-0-19-927789-6). Chapters 3, 4, 9 and 10.
    • “Organic Chemistry”; Vollhardt and Schore, (Freeman Palgrave Macmillan, 2011; ISBN 978-1-4292-3924-0). Chapters 1-5.

  • Other Recommended Purchases:

    • Molecular Models

  • Other Sources of information:

    • All information for this course including handouts, tutorials (and answers), class tests and recordings of the lectures, as well as supporting recordings for the workshops designed to aid your learning, will all be available through the CH1601 page on moodle.
    • Lecture Recordings will contain the audio for the lectures and will sync with the lecture handouts, and will contain a screen capture of material I draw on the board.
    • QR codes: Some lecture handouts contain embedded QR codes that allow you to see and manipulate molecules in 3-dimensions. Scan the QR code with your phone or tablet and manipulate away! Please try this as it will be bene ficial for your studies.
    • Self-guided learning
    • Workshop Recordings

What is organic chemistry?

  • The study of structure and reactions of compounds composed mainly of hydrocarbon (C,H) atoms but may also contain other atoms, commonly N, O, S, Si, halogens or metals.

What are we interested in?

  • Theory and structure: To identify key chemical components (pharmaceuticals) and understand how they are held together
  • Reaction mechanisms: Can we predict how molecules react with each other?
  • Synthesis and Biology: Can we make designer molecules and understand how their structure relates to biological activity?

Hydrocarbons, Functional groups and drawing them

  • We are interested in the molecular structures of organic compounds
  • All structures can be classified as consisting of hydrocarbon chains (C-H bonds) and Functional groups (that contain N, O, S etc).
  • A hydrocarbon chain is made up of rings and chains of carbon atoms - these are the “supports” for functional group
  • Examples of pentane (chain) and cyclohexane (ring)
  • It is cumbersome and time consuming to draw out all C and H atoms so we simplify the structures. General rules:
    • Draw chains of carbon atoms as zig-zags
    • Miss out Hs attached to carbon atoms and C-H bonds
    • Miss out capital Cs representing carbon atoms

Names for Carbon chains

  • It is often convenient to refer to a chain of carbon atoms by an abbreviated name indicating its length. These common abbreviations are used in drawing structures:
    • methyl (-CH3, Me)
    • ethyl (-CH2CH3, Et)
    • propyl (-CH2CH2CH3, Pr)
    • butyl (-CH2CH2CH2CH3, Bu)
  • These names / abbreviations can only be used for the terminal chains of atoms
  • Alkyl groups can be generalised by “R” - a generic name for any alkyl group

Names for Carbon rings

  • A benzene ring is common; if this group is attached to a molecule by only one of its atoms this is a phenyl group - abbreviation = Ph.
  • Branches in carbon chain - hydrocarbon frameworks are often branched, with some branched chains given names / abbreviations:
  • Consider propanol C3H8O - two possible structures:
    • straight chain n-propanol (n-PrOH)
    • branched chain i-propanol (i-PrOH)
  • These structures are isomers (non-identical molecules with the same molecular formula are isomeric).
  • Isomeric Compounds: For example consider C3H6 and C4H8O (isomers need not necessarily contain the same functional groups!).
  • C3H6 two isomers
  • C4H8O - multiple isomers possible - this leads to molecular complexity. Note that isomers do not need to contain the same functional groups!

Other common branched carbon chain types (for butyl chain)

  • The prefixes “sec” and “tert” are short for secondary and tertiary
  • This refers to the substitution of the carbon atom that attaches a group to the structure
  • A primary carbon is attached to only one other C atom; a secondary to 2 other C atoms and so on
  • The names primary, secondary, tertiary and quaternary tell us something about the structure of a molecule and so are often used when we describe chemical reactions:
    • straight chain n-butyl (n-Bu)
    • branched chain iso-butyl (i-Bu)
    • branched chain sec-butyl (s-Bu)
    • branched chain tert-butyl (t-Bu)

Functional groups

  • Functional groups: are the reactive sites of molecules; we will talk about their reactions and properties in detail, but for now we will just name the functional groups you will see in this course:
    • Alkenes (olefins) contain C-C double bonds (C=C)
      • shape: alkenes are planar
    • Alkynes contain C-C triple bonds (C≡C)
      • shape: alkynes are linear
    • Alcohols - contain a hydroxyl group (R-OH)
    • Ethers (R1-O-R2) contain an alkoxy group; ethers have 2 alkyl groups linked through a single oxygen atom
    • Amines (R-NH2) contain the NH2 (amino group)
    • Nitro compounds - (R-NO2) contain the nitro group - too many nitro groups in a molecule can make it explosive (TNT)
    • Alkyl halides - contain a bond to a halogen
      • Alkyl fluorides (R-F) contain the fluoro group
      • Alkyl chlorides (R-Cl) contain the chloro group
      • Alkyl bromides (R-Br) contain the bromo group
      • Alkyl iodides (R-I) contain the iodo group.
      • Alkyl halides have broadly similar properties but different reactivities and are sometimes given the “wild-card” abbreviation -X; R-X refers to any alkyl halide
    • Many functional groups contain the carbonyl group; (C=O)
      • Aldehydes = RCHO =
      • Ketone = R1COR2 =
    • Carboxylic acids (R-CO2H) contain the carboxyl group CO2H
    • Esters - (R1-CO2R2) contain a carboxyl group with an additional alkyl group CO2R
    • Amides - (RCONH2; R1-CONHR2; R1-CONR2R3)
      • Proteins are amides formed when a carboxylic acid of one amino acid reacts with the amino group of another.
      • Paracetamol is an amide
    • Nitriles or cyanides (R-CN); contain the cyano group (C≡N)
      • An organic nitrile group is very different to lethal inorganic cyanide!

The concept of oxidation level

  • Carbon atoms carrying functional groups can be grouped into similar classifications according to their oxidation level. For example, a carboxylic acid, ester and amide all have the carbon bearing the functional group bonded to two heteroatoms (any atom not C or H - commonly O,N, halogen,S)
  • To classify the oxidation level of an organic molecule, count the number of bonds formed at C to a heteroatom (multiple bonds count as appropriate number of single bonds)
  • Therefore acid and ester are at the same oxidation level
  • To get from a compound with a high oxidation level to a lower oxidation level - do a REDUCTION
  • To get from a compound with a low oxidation level to a higher oxidation level - do an OXIDATION

Naming Organic Compounds

  • Systematic nomenclature to name organic compounds has been introduced by IUPAC.
  • Names are divided into three parts that:
    • Describe the hydrocarbon framework
    • Describe the functional groups
    • Indicates where the functional groups are attached to the skeleton
  • The IUPAC naming system is made up of these three parts and is sometimes known as the suffix, the parent chain and the prefix
  • The name of a functional group is simply combined with that of the relevant hydrocarbon framework
  • Numbers are then used to locate the functional groups. If they are necessary the carbon atoms are counted from one end of the framework; if you have a choice the lowest possible number is used (look for the longest carbon chain….)
  • Application to branched hydrocarbon frameworks; treat as a derivative of the longest carbon chain