organic chemistry

• Organic chemistry is the study of the structure, properties, composition, reactions, and preparation of carbon-containing compounds
• Most organic compounds contain carbon and hydrogen, but they may also include any number of other elements (e.g., nitrogen, oxygen, halogens, phosphorus, silicon, sulfur)

  
• Originally limited to the study of compounds produced by living organisms, organic chemistry has been broadened to include human-made substances (e.g. pharmaceuticals, plastics....)
• When the Earth was formed 4.5 billion years ago, it was formed without life
• About 3.95 billion years ago, there was life on Earth
• Simultaneous activation of H2, CO2 and N2 on mineral surfaces leading to the formation of a variety of biologically relevant molecules, such as amino acids, nucleic acid bases and cofactors
• Molecules, such as pyruvate, acetate, methanol and ammonia, are known to form on transition metal containing surfaces
• Organic chemistry is the study of compounds containing carbon with the exception of simple compounds e.g. carbonates (CO3^2-), carbon dioxide (CO2) and carbon monoxide (CO)

  
• Organic chemistry describes the structures, properties, preparation, and reactions of a vast array of molecules that we call organic compounds
• There are many different types of organic compounds, but all have carbon as their principal constituent atom

  
• These carbon atoms form a carbon skeleton or carbon backbone that has other bonded atoms such as H, N, O, S, and the halogens (F, Cl, Br, and I)

  
• Why is carbon special?

  Carbon is unlike no other element able to build covalent bonds with himself an other elements

  
• Octet rule


  • C atoms primarily bond to each other to form the molecular skeleton or backbone of organic molecules
  • H atoms bond to the various C atoms, or to other atoms such as N and O

  
• Methane CH4


  The simplest organic molecule

  
• sp3 hybridization


  Mixing of an s orbital and three p orbitals to produce four hybrid orbitals
• ALL tetrahedral carbon and nitrogen atoms in organic chemistry are sp3 hybridized

  
• 1. C single bond


  • Free rotation around single bonds
  • Rotation barrier (12 kJ/mol)
• C=C double bond


  • ALL trigonal carbons such as those found in double bonds are sp2 hybridized
  • The unused p orbital on each carbon overlaps to form the π part of the double bond

  
• Free rotation of the double bond is not possible, a C-C-σ bond can rotate but a C-C-π bond has to be opened, need high energy, spontaneous not possible

  
• C=C triple bond


  • ALL linear carbons such as those found in triple bonds are sp hybridized
  • The unused p orbitals on each carbon overlap to form the π parts of the triple bond

  
• Per C atom in ethyne (acetylene) there is one C-H bond, one C-C-σ bond, and two π bonds by overlapping of the p-orbitals, no free rotation

  
• Types of organic compounds

  • Alkenes (C-C double bond)
  • Alkynes (C-C triple bond)
  • Arenes (special bonds represented as alternating single and double C-C bonds in a six-membered ring)

  
• Looking only at hydrocarbons, there is a huge number of structural varieties possible
• Chemists have learned through years of experience that organic compounds can be classified into families according to their structural features and that the members of a given family often have similar chemical reactivity
• Instead of 40 million compounds with random reactivity, there are a few dozen families of compounds whose chemistry is reasonably predictable
• Classification of organic compounds

  • Cyclic compounds
  • Alicyclic compounds
  • Aliphatic
  • Unsaturated carbohydrates
  • Saturated carbohydrates
  • Carbocyclic
  • Heterocyclic
  • Aromatic
  • Alicyclic
  • Aromatic
  • Saturated
  • Unsaturated
• There are over 40 million known organic compounds, so nomenclature is very important
• The nomenclature is based on the rule of the International Union of Pure Applied Chemistry (IUPAC)
• Alkane names


  • Methane
  • Ethane
  • Propane
  • Butane
  • Pentane
  • Hexane
  • Heptane
  • Octane
  • Nonane
  • Decane

  
• Alkanes


  • Compounds with C-C single bonds and C-H bonds only (no functional groups)
  • Connecting carbons can lead to large or small molecules
  • Alkanes are saturated with hydrogen (no more can be added)
  • Also called aliphatic compounds
  • Universal formula CnH2n+2

  
• The molecular formula of an alkane with more than three carbons can give more than one structural isomer
• Alkane physical properties


  • Boiling points and melting points increase as size of alkane increases
  • Forces between molecules (temporary dipoles, dispersion) are weak Van-der-Waals forces
  • Alkanes are lipophilic and hydrophobic, not soluble in water but soluble in nonpolar solvents
  • C1 - C4 gaseous, C5 – C20 liquid, > C20 solid (paraffin, wax), >> C20 Polymers (polyethylen)
• Alkyl group


  • Remove one H from an alkane (a part of a structure)
  • General abbreviation "R" (for Radical, an incomplete species or the "rest" of the molecule)
  • Name: replace -ane ending of alkane with -yl ending
• Compounds are given systematic names by a process that follows specific rules
• Alkanes


  • Lipophilic and hydrophobic
  • Not soluble in water but soluble in nonpolar solvents
  • Forces between molecules (temporary dipoles, dispersion) are weak Van-der-Waals forces
  • C1 - C4 gaseous
  • C5 – C20 liquid
  • > C20 solid (paraffin, wax)
  • >> C20 Polymers (polyethylen)
• Alkyl group


  • Remove one H from an alkane (a part of a structure)
  • General abbreviation "R" (for Radical, an incomplete species or the "rest" of the molecule)
• Naming alkanes


  • Replace -ane ending of alkane with -yl ending
  • Methyl- (Me-) -CH3 from Methane (1 C)
  • Ethyl- (Et-) -C2H5 from Ethane (2 C)
  • Propyl- (Pr-) -C3H7 from Propane (3C)
  • Butyl- (Bu-) -C4H9 from Butane (4C)
  • Pentyl- (Pen-) -C5H11 from Pentane (5 C)
  • Hexyl- (Hex-) -C6H13 from Hexane (6 C)
  • universal: Alkyl- -R from Alkane
• Naming alkanes


  • Named as longest possible chain
  • Carbons in that chain are numbered in sequence
  • substituents are numbered at their point of attachment, numbered in the way that they get the lowest number
  • Complex substituents are named as compounds would be
  • if the substitute appear several times, prefix di-, tri-, tetra-, ....are used
  • different substituents are named in alphabetical order

  
• Alkyl groups


  • Primary alkyl group (a carbon at the end of a chain)
  • Secondary alkyl group (a carbon in the middle of a chain)
  • Tertiary alkyl group (a carbon with three carbons attached to it)
• Alkanes reactivity


  • primary-, secondary- and tertiary carbon show different reactivity
  • The order of stability for carbocations is as follows – the reactivity of the carbocation is otherwise tertiary > secondary > primary > methyl
  • primary > secondary > tertiary