Organic chemistry - key points

• organic chemistry - carbon based (unique character) with unique chemical and physical properties - useful in synthesis and structure 
• Inorganic carbon compounds include: 
• Carbonates, Bicarbonates, Metal carbides, Metal cyanides, Oxides of carbon 
• Organic compounds: 
• generally, low solubility in water and high solubility in non-polar solvents
• mostly flammable 
• covalent bonding 
• slower chemical reactions between molecules 
• classifications: functional groups, skeletal structures, homologous series 
• isomerism common
• Inorganic compounds:
• high solubility in water and low solubility in non-polar solvents
• mostly non flammable
• often ionic bonding 
• faster and quantitative chemical reactions between ions 
• classifications: acids, bases, salts 
• few isomers present: only in transition metal complexes

Functional groups associated with the following organic compounds: 

• aspirin - aryl, carboxylic acid, ester 
• cis-11-retinal - alkene, aldehyde 
• adrenaline - phenol, amine, alcohol 
• soap - ester 

Hydrocarbons - classified as saturated (alkanes - linear (CnH2n+2)or cyclic (CnH2n)) or unsaturated (alkenes, aromatics and alkynes)

Mono-alkenes - 1 double C=C bond, CnH2n 

Mono-alkynes - 1 triple C bond, CnH2n-2 

aromatics: usually contain 1 or more rings of 6 C atoms called benzene rings 

Naming isomers: prefix: 

• n - alkane = unbranched 
• iso - alkane = contains (CH3)2CH- and no other branches
• neo - alkane = contains (CH3)3C- and no other branches 

• aliphatic - open chain of carbon atoms, saturated vs unsaturated 
• alicyclic - ring of saturated carbon atoms 
• aromatic - ring where all the carbon atoms are unsaturated and conjugated 
• heterocyclic - ring of carbon and at least one other element such as N, S or O
• functional group; 
  • gives its characteristic chemical properties 
  • acts as a site of chemical reactivity
  • serves as the basis for nomenclature 
  • classifies its family 
• polyfunctional compounds = more than one functional group, principal functional group determines the class, secondary FGs treated as substituents 
• Order of preference mneumonic made
• homologous series - similar chemical properties where members (homologues) have the same functional group, general formula, similar chemical properties and are prepared by similar methods, except they differ by length of the carbon chain (adjacent members differ by CH2) - gradual variation in physical properties with increasing molecular weight

• Bonding - 
  • orbitals combine to form hybrid atomic orbitals (combination of atomic orbitals from the same atom) and molecular orbitals (combination of atomic, or hybrid atomic, orbitals from different atoms) - second row elements hybridise using their 2s and 2p orbitals 
• s orbital = lower in energy compared to other orbitals in the same shell
• 3 p orbitals in the same shell, px, py, pz 
• hybridisation - enables carbon to form 4 bonds due to 4 unpaired electrons in the hybrid atomic orbitals compared to the 2 unpaired electrons shown in it's electronic configuration 
  • one of the 2s electrons is promoted to the vacant p orbital which requires energy but is favourable as it decreases electron pair repulsion 
  • - the 2s and 2p orbitals now mix to form various hybrid atomic orbitals 
  • same number of orbitals out as put in 
• sp3 hybridisation: 2s orbital mixed with all 3 of the p orbitals; used for saturated compounds
  • the 4 orbitals hybridise/combine to give 4 new hybrid atomic orbitals which are all equivalent with the same energy - degenerate (sp3)
  • orbitals point towards the corners of a tetrahedron
  • overlap produces sigma bonds 

• sp2 hybridisation: s and two p orbitals combine to give three new hybrid atomic orbitals 
  • sp2 orbitals point towards the corners of the triangle - used for sigma bonding 
  • the third p orbital [unchanged] is perpendicular to them - used for pi bonding 
  • sp2 = used for bonding in alkenes, carbonyls and aromatic rings [double bonds]
• sp hybridisation: s and p orbital combine to give 2 new hybrid atomic orbitals 
  • the sp orbitals are 180 degrees to each other = linear molecule - used for sigma bonding
  • the p orbitals are perpendicular to them - used for pi bonding 
  • sp = used for bonding in alkynes and nitriles 

• note: 
• single bond = 1 sigma bond = sp3 
• double bond = 1 sigma and 1 pi bond = sp2
• triple bond = 1 sigma and 2 pi bonds = sp 

Properties of hybrid orbitals 

• hold electrons closer to the nucleus 
• bonds become shorter, stronger and more directional so they have more effective bonding interactions 
• the more s-character in an orbital, the lower the energy so the stability of the electron increases in that orbital 

• Types of bonding - sigma and pi 

  • sigma bonds - the bonding in MP is lower in energy than the original AO
    • formed by direct overlap between s-s, s-p, p-p or hybridised orbitals, electron density is along the line of the bond (covalent bond type), symmetric rotation about the bond 
  • pi bonds - formed, after sigma bonds, by parallel overlap of p orbitals where the electron density is above and below the plane of the bond, higher in energy therefore weaker and more easily broken

• increased bond length = decreased bond strength; strongest bond is a triple bond 

no of bonds t c        hybridisation           bond angle 

4                              sp3                         109.5               = one sigma bond, sp3-sp3

3                              sp2                          120                  = one sigma and one pi, sp2-sp2, p-p

2                              sp                            180 - linear      = one sigma and 2 pi, sp-sp, p-p, p-p

examples of bonding on lecture slides - e.g. benzene 

• isomerism = molecules which have the same molecular formula but differ in their arrangement of their atoms - structural isomerism and stereoisomerism 
• structural isomers - positional, functional group, chain, tautomerism [movement of bond and a proton] and ring-chain 
  • usually different compounds with different physical and chemical properties 
• stereoisomers - same structural formula but different 3D arrangement of atoms in space 
  • cis/trans and optical
    • geometrical: cis/trans 
  • refer to carbon chain, requires different groups at each end of the bond = different physical and chemical properties 
  • cis = 2 alkyl groups are on the same side of the double bond [highest priority groups - Z)
  • trans = 2 alkyl groups are on opposite sides of the double bond [highest priority groups - E]
    • optical isomerism
  • optical isomers have the ability to rotate plane polarised light in opposite directions 
  • right/clockwise = dextrorotary - d isomer [+]
  • left/anti-clockwise = laevorotary - l isomer [-]
  • d and l = only refer to the optical rotation/direction 

• a chiral molecule - has no plane of symmetry, carbon has 4 diff groups attached
• compounds with chiral centres = chemically identical isomers = no symmetry = non-superimposable mirror image = show optical activity 
• compounds with achiral centres = chemically identical isomers = plane of symmetry = superimposable mirror image = do not show optical activity 

How are optical isomers drawn? 

• perspective view shows a tetrahedral carbon 
• normal lines are in plane of page, wedges come out of page, dashed lines go into page 

R ans S = systematic nomeclature for chiral carbon - assigned relating to the arrangement of groups around a chiral carbon e.g. is the H above or below once double bond broken 

• assigned by configuration to glyceraldehyde / studying structure 
• neither system is related to +/- [optical rotation] 

• fischer projections - flat drawing representing 3D molecules

  • a carbon is at the intersection of horizontal and vertical lines
  • horizontal lines are forward, out of plane 
  • vertical lines are behind the plane
  • rules; rotation of 180 degrees doesn't change the molecule, do not rotate 90 degrees, do not turn over out of plane, carbon chain is on the vertical line

  mirror images FP - easy to draw, easy to find enantiomers, easy to find internal mirror planes 

• Enantiomers = non superimposable mirror images which forms a chiral molecule - represent 2 optical isomers: + and - where their rotatory powers are due to opposite arrangements of groups around each asymmetric/chiral carbon
  • have identical physical and chemical properties except in their interaction with plane of polarised light
  • enantiomers interact differently with other chiral molecules 
• a racemic mixture = 1:1, equal quantities of 2 enantiomers of a compound, no optical activity as effects of rotating plane polarised light cancel out 
  • mixture may have different BP and MP from the enantiomers 
• diastereomers = a structure with n chiral centres has 2 ^n possible isomers 
  • stereoisomers that are not mirror images to each other/the enantiomers 
  • e.g. molecules with 2 or more chiral carbons where at least 1, but not all, differ 
  • diastereomers which differ at only 1 carbon = epimer 
  • 2 distereomers will have different physical properties e.g. MP/BP
  • they also have different chemical reactivities with both chiral and achiral reagants 

comparison of enantiomers vs diastereomers in lecture notes 

Properties of hybrid orbitals 

• hold electrons closer to the nucleus 
• bonds become shorter, stronger and more directional so they have more effective bonding interactions 
• the more s-character in an orbital, the lower the energy so the stability of the electron increases in that orbital 

• he 4 orbitals hybridise/combine to give 4 new hybrid atomic orbitals which are all equivalent with the same energy - degenerate (sp3)
• orbitals point towards the corners of a tetrahedron
• overlap produces sigma bonds