Some organic chemicals DNA Essential oils Medicines •Active Pharmaceutical Ingredients •Excipients Materials Fuels Pigments 109 5 109 5 109 5 109 5 Need to be able to represent 3D molecular struct.
Some organic chemicals Medicines DNA •Active Pharmaceutical Ingredients •Excipients Fuels Materials Essential oils Pigments 109.5 109.5 109.5 109.5 Need to be able to represent 3D molecular structure in 2D Bond coming out of plane of screen Bond going into plane of screen e.g H = H H C C H H H Or H H = H C C HH H Angle between any two bonds at a Carbon atom = 109.5o H H H C H H C H 109.5o H H 109.5 o C H H H C H Ethane: a gas b.p ~ -100oC Empirical formula: CH3 Molecular formula C2H6 Structural formula •An organic chemical •Substance composed of organic molecules •Identity and number of atoms comprising each molecule H H H C C H •Atom-to-atom connectivity H H Structural formula showing stereochemistry H H H C H H C H •3D shape Electronic configuration of Carbon Hydrogen H H H C C H H H C 1s2 2s2 2p2 H 1s1 Orbitals available for covalent bonding? Ethane H 1s (1 e ) C 2py C 2pz (vacant) (vacant) •However, know that the geometry of the Carbons in ethane is tetrahedral •Cannot array py and pz orbitals to give tetrahedral geometry •Need a modified set of atomic orbitals - hybridisation 1s 2s 2p 2p 2p Hybridisation 1s (2e-) sp3 sp3 sp3 (1e-) (1e-) (1e-) sp3 (1e-) An sp3 orbital extends mainly in one direction from the nucleus and forms bonds with other atoms in that direction Carbon sp3 orbitals can overlap with Hydrogen 1s orbitals to form Carbon-Hydrogen bonds = H H H C C H H H Each sp3 orbital contributes one electron; each s orbital contributes one electron to form C-H [C H] [Anti-bonding orbitals also formed; not occupied by electrons] bonds: symmetrical about the bond axis Geometry of Carbon in ethane is tetrahedral and is based upon sp3 hybridisation sp3 hybridised Carbon = tetrahedral Carbon Tetrahedral angle 109.5o C 109.5o φ = 60o H H H H Staggered conformation Minimum energy conformation (least crowded possible conformation) H H C-C bonds: symmetrical about the bond axes In principle, no barrier to rotation about C-C bond HH Could have φ H = 0o = H H H H H Eclipsed conformation Maximum energy conformation (most crowded possible conformation) H C C H H H •Eclipsed conformation experiences steric hindrance •Unfavourable interaction between groups which are close together in space HH H H Steric hindrance exists between H H the eclipsing C-H bonds in this conformation •These unfavourable interactions absent in the staggered conformation •Hence, the staggered conformation is lower in energy •Energy difference between eclipsed and staggered conformations of ethane = 12 kJ mol-1 •Each C-H eclipsing interaction contributes kJ mol-1 of torsional strain energy -1 kJ mol HH -1 kJ mol H H Conformations: Total: 12 kJ mol-1 torsional strain H H kJ mol-1 different orientations of molecules arising from rotations about C-C bonds Consider one full rotation about the C-C bond in ethane Start at φ = 0 (eclipsed conformation) HH φ = 0 H H H H Eclipsed conformation strain energy 12 kJ mol-1 Rotate 60 φ = 60 H H H H H H Staggered conformation strain energy kJ mol-1 Rotate 60 HH φ = 120 H H H H Eclipsed conformation strain energy 12 kJ mol-1 Rotate 60 φ = 180 H H H H H H Staggered conformation strain energy kJ mol-1 Rotate 60 HH φ = 240 H H Rotate 60 H H Eclipsed conformation strain energy 12 kJ mol-1 H φ = 300 H H H H H Staggered conformation strain energy kJ mol-1 Rotate 60 HH φ = 360 Full rotation Return to starting position H H Eclipsed conformation strain energy 12 kJ mol-1 H Identical to that at φ = 0 H Hence, in one full rotation about the C-C bond •Pass through three equivalent eclipsed conformations (energy maxima) •Pass through three equivalent staggered conformations (energy minima) •Pass through an infinite number of other conformations Can plot torsional angle φ as a function of strain energy Steric Strain Energy / kJ mol-1 12 kJ mol-1 60 120 180 240 300 360 Torsional angle / degrees 12 kJ mol-1 = energy barrier to rotation about the C-C bond in ethane Too low to prevent free rotation at room temperature Ethane C2 H6 •Contains Carbon and Hydrogen only (is a hydrocarbon) •Contains bonds only (C-C and C-H single bonds only) •Contains only sp3 hybridised Carbon Do other molecules exist which have these properties? Yes, e.g propane C3H8 H H H H C C C H H H H How many such compounds could exist? In principle, an infinite number In reality, a vast unknown number There exists a vast (and potentially infinite) number of compounds consisting of molecules which: •Contain only C and H •Contain only bonds •Contain only sp3 hybridised C These are known as alkanes C2H6 ethane C3H8 propane CnH2n+2 General formula for alkanes n Molecular Formula CH4 C2H6 C3H8 Structural formula H H C H H Name methane H H H C C H H H CH4 ethane H H H H C C C H CH3CH3 propane H H H C4H10 H H H H H C C C C H H H H H C5H12 H H H H H H C C C C C H H H H H H C6H14 H H H H H H H C C C C C C H H H H H H H Condensed structural formula butane pentane hexane CH3CH2CH3 CH3CH2CH2CH3 CH3CH2CH2CH2CH3 CH3CH2CH2CH2CH2CH3 Further members of the series Heptane CH3CH2CH2CH2CH2CH2CH3 Octane CH3CH2CH2CH2CH2CH2CH2CH3 Nonane CH3CH2CH2CH2CH2CH2CH2CH2CH3 Decane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3 Undecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3 Dodecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3 Etc., etc Some points concerning this series of alkanes Series is generated by repeatedly adding ‘CH2’ to the previous member of the series A series generated in this manner is known as an homologous series Nomenclature (naming) Names all share a common suffix, i.e.’ …ane’ The suffix ‘…ane’ indicates that the compound is an alkane The prefix indicates the number of carbons in the compound ‘Meth…’ = Carbon ‘Hept…’ = Carbons ‘Eth…’ = Carbons ‘Oct…’ = Carbons ‘Prop…’ = Carbons ‘Non…’ = Carbons ‘But…’ = Carbons ‘Dec…’ = 10 Carbons ‘Pent…’ = Carbons ‘Undec…’ = 11 Carbons ‘Hex…’ = Carbons ‘Dodec…’ = 12 Carbons Heptane CH3CH2CH2CH2CH2CH2CH3 ‘Hept…’ implies Carbons ‘…ane’ implies compound is an alkane Representation and conformation H H H H H C C C C H H H H H Butane (full structural formula) H H C H H H H C C C H H H H Same structural formula •Structural formulae: give information on atom-to-atom connectivity •Do not give information on stereochemistry H H C H H H C C H H H C H H H H H H H C C C C H H H H H Have the same information content Propane CH3-CH2-CH3 Both C-C bonds identical Consider the different conformations that can arise during one full rotation about C-C Energy maxima and minima: H H CH3 H kJ mol-1 H CH3 H H H kJ mol-1 H Staggered conformation (energy minimum) H H kJ mol-1 Eclipsed conformation (energy maxmium) Eclipsed conformation of propane possesses 14 kJ mol-1 of torsional strain energy relative to the staggered conformation ... bonds only (C-C and C-H single bonds only) •Contains only sp3 hybridised Carbon Do other molecules exist which have these properties? Yes, e.g propane C3H8 H H H H C C C H H H H How many such compounds... reality, a vast unknown number There exists a vast (and potentially infinite) number of compounds consisting of molecules which: •Contain only C and H •Contain only bonds •Contain only sp3 hybridised... ethane is tetrahedral •Cannot array py and pz orbitals to give tetrahedral geometry •Need a modified set of atomic orbitals - hybridisation 1s 2s 2p 2p 2p Hybridisation 1s (2e-) sp3 sp3 sp3 (1e-)