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Organic and Biological Molecules

Organic and Biological Molecules. Chapter 22. Organic Chemistry and Biochemistry. The study of carbon-containing compounds and their properties. The vast majority of organic compounds contain chains of rings of carbon atoms. The study of the chemistry of living matter.

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Organic and Biological Molecules

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  1. Organic and Biological Molecules Chapter 22

  2. Organic Chemistry and Biochemistry • The study of carbon-containing compounds and their properties. • The vast majority of organic compounds contain chains of rings of carbon atoms. • The study of the chemistry of living matter

  3. Hydrocarbons • compounds composed of carbon and hydrogen. • Saturated compounds (alkanes) have the maximum number of hydrogen atoms attached to each carbon atom • Saturated: carbon-carbon bonds are all single - alkanes [CnH2n+2]

  4. Unsaturated compounds have fewer hydrogen atoms attached to the carbon chain than alkanes • Unsaturated: They contain carbon-carbon multiple bonds (double or triple)

  5. 22.1 Alkanes: Saturated hydrocarbons • Saturated hydrocarbons, CnH2n+2 • “Saturated” because they can’t take any more hydrogen atoms • Straight chains are H3C–(CH2)n–2–CH3 • Waxes, oils, & fuel gases as n decreases.

  6. Alkanes: Saturated Hydrocarbons • Hydrocarbons are molecules composed of carbon & hydrogen • Each carbon atom forms 4 chemical bonds • A saturated hydrocarbon is one where all C - C bonds are “single” bonds & the molecule contains the maximum number of H-atoms • Saturated hydrocarbons are called ALKANES

  7. Methane is a tetrahedral molecule

  8. The Lewis structure of ethane.

  9. A ball-and-stick model of ethane.

  10. Propane

  11. Butane

  12. The First 10 “Normal” Alkanes C1 - C4 are Gases at Room Temperature Name Formula M.P. B.P. # Structural Isomers • Methane CH4 -183 -162 1 • Ethane C2H6 -172 -89 1 • Propane C3H8 -187 -42 1 • Butane C4H10 -138 0 2 • Pentane C5H12 -130 36 3 • Hexane C6H14 -95 68 5 • Heptane C7H16 -91 98 9 • Octane C8H18 -57 126 18 • Nonane C9H20 -54 151 35 • Decane C10H22 -30 174 75 C5 - C16 are Liquids at Room Temperature

  13. The C-H Bonds in Methane

  14. IUPAC Rules for Naming Branched Alkanes • Find and name the parent chain in the hydrocarbon - this forms the root of the hydrocarbon name • Number the carbon atoms in the parent chain starting at the end closest to the branching • Name alkane branches by dropping the “ane” from the names and adding “yl”. A one-carbon branch is called “methyl”, a two-carbon branch is “ethyl”, etc… • When there are more than one type of branch (ethyl and methyl, for example), they are named alphabetically • Finally, use prefixes to indicate multiple branches

  15. Rules for Naming Alkanes 1. For alkanes beyond butane, add -aneto the Greek root for the number of carbons. C-C-C-C-C-C : hexane 2. Alkyl substituents: drop the -aneand add -yl -C2H5 is ethyl

  16. Rules for Naming Alkanes 3. Positions of substituent groups are specified by numbering the longest chain sequentially. C  C-C-C-C-C-C 3-methylhexane • Start numbering at the end closest to the branching 4. Location and name are followed by root alkane name. Substituents in alphabetical order and use di-, tri-, etc.

  17. Normal vs Branched Alkanes • Normal alkanes consist of continuous chains of carbon atoms • Alkanes that are NOT continuous chains of carbon atoms contain branches • The longest continuous chain of carbons is called the parent chain

  18. Structural Isomerism • Structural isomers are molecules with the same chemical formulas but different molecular structures - different “connectivity”. • They arise because of the many ways to create branched hydrocarbons. n-pentane, C5H12 2-methlbutane, C5H12

  19. Isomer Naming • Older conventions would have that as “isooctane,” but a good IUPAC name results from the following: • Name the longest C chain (pentane) • List the side groups in alphabetical order with Greek prefixes (trimethylpentane) • Supply (smallest possible) positional indices (2,2,4 trimethylpentane)

  20. 2 4 1 3 5 Example : Show the structural formula of 2,2-dimethylpentane • The parent chain is indicated by the ROOT of the name - “pentane”. This means there are 5 carbons in the parent chain. • “dimethyl” tells us that there are TWO methyl branches on the parent chain. A methyl branch is made of a single carbon atom. • “2,2-” tell us that BOTH methyl branches are on the second carbon atom in the parent chain.

  21. 2 4 1 3 5 6 7 Example: Structural formula of3-ethyl-2,4-dimethylheptane? • The parent chain is indicated by the ROOT of the name - “heptane”. This means there are 7 carbons in the parent chain. • “2,4-dimethyl” tells us there are TWO methyl branches on the parent chain, at carbons #2 and #4. • “3-ethyl-” tell us there is an ethyl branch (2-carbon branch) on carbon #3 of the parent chain.

  22. 3 5 4 6 2 7 1 8 5 3 2 4 6 7 1 8 Example: 2,3,3-trimethyl-4-propyloctane • The parent chain is indicated by the ROOT of the name - “octane”. This means there are 8 carbons in the parent chain. • “2,3,3-trimethyl” tells us there are THREE methyl branches - one on carbon #2 and two on carbon #3. • “4-propyl-” tell us there is a propyl branch (3-carbon branch) on carbon #4 of the parent chain.

  23. 4 3 5 5-ethyl- 3,4-dimethyl octane Example : Name the molecules shown • parent chain has 5 carbons - “pentane” • two methyl branches - start counting from the right - #2 and #3 • 2,3-dimethylpentane • parent chain has 8 carbons - “octane” • two methyl branches - start counting from the left - #3 and #4 • one ethyl branch - #5 • name branches alphabetically

  24. Reactions of alkanes • Combustion reactions 2C4H10 + 13 O2 8CO2 + 10 H2O(g) • Substitution Reactions CH4 + Cl2 CH3Cl + HCl CH3Cl+ Cl2 CH2Cl2 + HCl CH2Cl2 + Cl2 CHCl3 + HCl

  25. Dehydrogenation Reactions CH3CH3 CH2 CH2 Ethylene

  26. Cyclic alkanes • A cycloalkane is made of a hydrocarbon chain that has been joined to make a “ring”. • Note that two hydrogen atoms were lost in forming the ring • What is the general formula for a cycloalkane?

  27. Cyclic alkanes, CnH2n • If the two end C’s lose 1 H each, they have free valence to close a ring • Again, properties similar to straight chains. • Can now have conformational isomers! • E.g., BOAT cyclohexane versus CHAIR

  28. Cyclohexane - Boat & Chair Conformations • Cyclohexane is NOT a planar molecule. To achieve its 109.5° bond angles and reduce angle strain, it adopts several different conformations. • The BOAT and CHAIR (99%) are two conformations

  29. Unsaturated hydrocarbomns22.2 Alkenes and Alkynes Alkenes: hydrocarbons that contain a carbon-carbon double bond. [CnH2n] C=C Ethene CC=C propene Alkynes: hydrocarbons containing a carbon-carbon triple bond. [CnH2n-2] C C Ethyne CCCCC 2-pentyne

  30. Alkenes are hydrocarbons that contain at least one carbon-carbondouble bond Alkynes are hydrocarbons that contain at least one carbon-carbontriple bond The suffix for the parent alkane chains are changed from “ane” to “ene” and “yne” e.g. ethene, ethyne Where it is ambiguous, the BONDS are numbered like branches so that the location of the multiple bond may be indicated Alkenes & Alkynes

  31. Alkenes, CnH2n • Cycle formation isn’t the only possible result of dehydrogenation. • Adjacent C’s can double bond, C=C, making an (unsaturated) alkene. Sp2

  32. The Bonding in Ethylene

  33. Nomenclature for Alkenes 1.Root hydrocarbon name ends in -ene C2H4; CH2=CH2is ethene 2. With more than 3 carbons, double bond is indicated by the lowest numbered carbon atom in the bond. C=CCC is 1-butene

  34. Alkene Isomers • While an sp3 CX2Y2 has only 1 isomer, • (every X and Y is adjacent to all the others) • the sp2alkene C2X2Y2 has cis & trans isomers (where X is or isn’t on the same side of = as X). • For longer hydrocarbons, cis & trans refer to the side the chain extends:

  35. Cis and Trans Isomers • Double bond is fixed • Cis/trans Isomers are possible CH3 CH3 CH3 CH = CH CH = CH cistrans CH3

  36. Addition Reactions • Weaker  bonds are broken and new (stronger)  bonds are formed to atoms being added.

  37. Hydrogenation • Adds a hydrogen atom to each carbon atom of a double bond H H H H Ni H–C=C–H + H2H–C–C–H HH ethene ethane CH3-CH3

  38. Halogenation • Adds a halogen atom to each carbon atom of a double bond H H H H Ni H–C=C–H + Cl2H–C–C–H ClCl ethene dichloro ethane

  39. Halogenation Reactions CH2 CHCH2CH2CH2 + Br2 CH2Br CHBrCH2CH2CH2 1,2-dibromopentane

  40. Alkynes, CnH2n–2 • Carbon-carbon triple bonds • Names end in -yne HCCH ethyne(acetylene) HCC-CH3 propyne

  41. The Bonding in Acetylene

  42. Naming Alkenes and Alkynes When the carbon chain has 4 or more C atoms, number the chain to give the lowest number to the double or triple bond. 1 2 3 4 CH2=CHCH2CH3 1-butene CH3CH=CHCH3 2-butene CH3CHCHCH3 2-butyne

  43. Question Write the IUPAC name for each of the following unsaturated compounds: A. CH3CH2CCCH3 CH3 B. CH3C=CHCH3 2-pentyne 2-methyl-2-butene

  44. Question • Name the following compound 5-ethyl-3-heptyne

  45. Additions reactions:Hydrogenation and Halogenation Hydrogens and halogens also add to the triple bond of an alkyne.

  46. 22.3 Aromatic hydrocarbonsUnsaturated Cyclic hydrocarbons • Alternating single/double bond cycles occur in many organic molecules • This class is called “aromatic” (by virtue of their aroma). • The  structure is often preserved in their chemical reactions; they don’t add, they substitute instead.

  47. Lewis structures for the benzene ring.

  48. Benzene C6H6 sp2 sp2 sp2

  49. Shorthand notation for benzene rings

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