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The Chemistry of Life: Organic and Biological Chemistry

The Chemistry of Life: Organic and Biological Chemistry. The element carbon forms a vast number of compounds. The study of carbon compounds constitutes a separate branch of chemistry known as organic chemistry . The study of living species is called biological chemistry, or biochemistry.

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The Chemistry of Life: Organic and Biological Chemistry

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  1. The Chemistry of Life: Organic and Biological Chemistry The element carbon forms a vast number of compounds. The study of carbon compounds constitutes a separate branch of chemistry known as organic chemistry. The study of living species is called biological chemistry, or biochemistry Prof. T. L. Meeks

  2. A Look Back The shapes of organic molecules: The three dimensional structures of organic and biochemical molecules play an essential role in determining their physical and chemical behaviors. Carbon forms a tetrahedral geometry normally. Prof. T. L. Meeks

  3. A Look Back VSEPR model of carbon shows four electron pairs. All single bonds are tetrahedrally spaced A double bond with 2 single bonds will be trigonal planar Two double bonds, or a triple bond, will be linear Prof. T. L. Meeks

  4. A Look Back The stabilities of organic substances In chapter 8 we learned about the average strengths of various chemical bonds, including those characteristic to organic chemistry. - double bonds are normally stronger than single, and triple stronger than double Prof. T. L. Meeks

  5. A Look Back The stabilities of organic substances The reaction of a simple organic molecule with oxygen is highly exothermic, however, many organic molecules are stable in air for indeterminate amounts of time due to the extremely high activation energy for combustion to begin. Prof. T. L. Meeks

  6. A Look Back Solubility and Acid-Base properties Most organic compounds have prevalent C-C or C-H bonds which are nonpolar. In general, the molecules are nonpolar and do not dissolve well in water. Prof. T. L. Meeks

  7. A Look Back Solubility and Acid-Base properties Organic molecules that do dissolve in water are those that have polar groups on the surface of the molecule, such as glucose Prof. T. L. Meeks

  8. A Look Back Solubility and Acid-Base properties Many organic substances contain acidic or basic groups. The most important acidic substances are the carboxylic acids which bear the functional group -COOH. Prof. T. L. Meeks

  9. A Look Back Solubility and Acid-Base properties Basic organic substances are amines, which bear the -NH2, -NHR, or -NR2 groups. Amino acids contain both the carboxylic acid group and the amino group, and are therefore amphoteric Prof. T. L. Meeks

  10. Introduction to Hydrocarbons The compounds of carbon are so numerous that it is convenient to organize them into families that exhibit similar structures. The simplest class of organic compounds is the hydrocarbons, compounds composed only of carbon and hydrogen. Identified easily by stable C-C bonds Prof. T. L. Meeks

  11. Introduction to Hydrocarbons Hydrocarbons can be divided into 4 general types • alkanes - single bonds • alkenes - a double bond • alkynes - a triple bond • aromatics - planar ring structure Prof. T. L. Meeks

  12. Introduction to Hydrocarbons Alkanes - single bonds only • saturated hydrocarbons, contain the largest possible number of hydrogen atoms per carbon • general formula is CnH2n+2 Prof. T. L. Meeks

  13. Introduction to Hydrocarbons Alkenes - a double bond exists in molecule • unsaturated hydrocarbons, do not contain the largest possible number of hydrogen atoms per carbon, double bond could be broken to add two more hydrogens • general formula is CnH2n Prof. T. L. Meeks

  14. Introduction to Hydrocarbons Alkynes - a triple bond exists in molecule • unsaturated hydrocarbons, do not contain the largest possible number of hydrogen atoms per carbon, triple bond could be broken to add four more hydrogens • general formula is CnH2n-2 Prof. T. L. Meeks

  15. Introduction to Hydrocarbons Aromatics - planar ring structure • connected by both sigma and pi bonds between carbon atoms • general formula is CnH2n-6 Prof. T. L. Meeks

  16. Introduction to Hydrocarbons Hydrocarbons are relatively nonpolar, thus are nearly insoluble in water, but dissolve easily in nonpolar solvents. - melting points and boiling points are determined by London dispersion forces, in general, the larger the molecule the higher its boiling point Prof. T. L. Meeks

  17. Alkanes Prof. T. L. Meeks

  18. Alkanes Written two ways: Lewis structure Condensed H H - C - H CH4 H Prof. T. L. Meeks

  19. Alkanes Structures • Lewis structures and condensed structural formulas do not tell us anything about the three dimensional shapes • must be predicted using AXE notation based on VSEPR theory Prof. T. L. Meeks

  20. Alkanes Structural Isomers • The alkanes listed in the table are straight-chain hydrocarbons because all the carbons are joined in one continuous chain • alkanes consisting of four or more carbon atoms can also form branched chains Prof. T. L. Meeks

  21. Alkanes Structural Isomers • Compounds with the same molecular formula but with different bonding arrangements are called structural isomers. • Structural isomers differ slightly from one another in physical properties Prof. T. L. Meeks

  22. Alkanes Nomenclature • 1892 IUP met to formulate rules for systematic naming of organic substances • Chemists everywhere subscribe to a common system for naming compounds Prof. T. L. Meeks

  23. Alkanes Nomenclature • Find the longest continuous chain of carbon atoms, and use the name of this chain as the base name of the compound • Number the carbon chains in the longest chain, beginning with the end of the chain that is nearest a substituent Prof. T. L. Meeks

  24. Alkanes Nomenclature • Name and give the location of each substituent group - a substituent group that is formed by removing an H from an alkane is called an alkyl group Prof. T. L. Meeks

  25. Alkanes Nomenclature • When two or more substituents are present, list them in alphabetical order Prof. T. L. Meeks

  26. Alkanes Sample exercise: Name the following alkane: CH3 - CH - CH3 CH3 - CH - CH2 CH3 Prof. T. L. Meeks

  27. Alkanes Sample exercise: Name the following alkane: CH3 - CH - CH3 CH3 - CH - CH2 CH3 pentane Prof. T. L. Meeks

  28. Alkanes Sample exercise: Name the following alkane: CH3 - CH - CH3 CH3 - CH - CH2 CH3 2,4 dimethyl pentane Prof. T. L. Meeks

  29. Alkanes Sample exercise: Write the condensed structural formula for 2,3 dimethyl hexane. Prof. T. L. Meeks

  30. Alkanes Sample exercise: Write the condensed structural formula for 2,3 dimethyl hexane. CH3CH2CH2CH2CH2CH3 Prof. T. L. Meeks

  31. Alkanes Sample exercise: Write the condensed structural formula for 2,3 dimethyl hexane. CH3 CH3CHCHCH2CH2CH3 CH3 Prof. T. L. Meeks

  32. Alkanes Cycloalkanes: alkanes can form not only branched chains, but also rings or cycles. - sometimes drawn as a simple polygon in which each corner represents a CH2 group - the amount of strain on the bonds increases in the smaller rings Prof. T. L. Meeks

  33. Alkanes Reactions of Alkanes: most alkanes are unreactive - at room temp, they do not react with acids, bases, or strong oxidizers - they are not completely inert, a very important reaction is combustion in air - when they do react, they will substitute another atom for a bonded hydrogen (ASS) Prof. T. L. Meeks

  34. Unsaturated Hydrocarbons The presence of one or more multiple bonds makes unsaturated hydrocarbons significantly different from alkanes both in terms of their structures and their activity Prof. T. L. Meeks

  35. Unsaturated Hydrocarbons Alkenes: contain C=C bond • Names of alkenes are based on the longest continuous chain of carbon atoms that contain the double bond • the location of the double bond along the chain is indicated by the number of the carbon atom nearest the end of the chain • Simplest alkene is ethene (ethylene) • it is a plant hormone, important in seed germination and fruit ripening Prof. T. L. Meeks

  36. Unsaturated Hydrocarbons Alkenes: when the placement of alkyl groups differ in the geometric attachment to double bond, geometric isomers occur Prof. T. L. Meeks

  37. Unsaturated Hydrocarbons Alkenes: Cis isomer: the similar groups are on the same side of the double bond Trans isomer: the similar groups are on opposite sides of the double bond Prof. T. L. Meeks

  38. Unsaturated Hydrocarbons Alkenes: geometric isomerism arises because double bonds are resistant to twisting Prof. T. L. Meeks

  39. Unsaturated Hydrocarbons Alkynes: unsaturated hydrocarbons containing one or more C C bonds • Simplest alkyne is acetylene, C2H2 Prof. T. L. Meeks

  40. Unsaturated Hydrocarbons Addition reactions: double and triple bonds markedly increases their chemical reactivity. The most characteristic reactions are addition reactions. - the bond is broken and the reactant is added to the carbons that formed the multiple bond Prof. T. L. Meeks

  41. Unsaturated Hydrocarbons Addition reactions: halogenation Prof. T. L. Meeks

  42. Unsaturated Hydrocarbons Addition reactions: hydrogenation Prof. T. L. Meeks

  43. Unsaturated Hydrocarbons Sample exercise: Addition of HCl to an alkene leads to the formation of 2- chloropropane. What is the alkene? Prof. T. L. Meeks

  44. Unsaturated Hydrocarbons Sample exercise: Addition of HCl to an alkene leads to the formation of 2- chloropropane. What is the alkene? propene Prof. T. L. Meeks

  45. Unsaturated Hydrocarbons Mechanism of Addition Reaction: • An explanation of how the reaction occurs is a reaction mechanism • addition reactions occur in two basic steps • first step is the rate determining step • the binary molecule being added transfers an electron to one of the two carbons • second step involves the addition of the remaining half of the molecule to the second carbon Prof. T. L. Meeks

  46. Unsaturated Hydrocarbons Mechanism of Addition Reaction: • An explanation of how the reaction occurs is a reaction mechanism • addition reactions occur in two basic steps • a pair of electrons can also be donated to form a new covalent bond Prof. T. L. Meeks

  47. Unsaturated Hydrocarbons Aromatics • members of a large and important class of hydrocarbons • simplest member of the series is benzene • planar, highly symmetrical • greater stability is due to delocalization of electrons across the pi bonds Prof. T. L. Meeks

  48. Unsaturated Hydrocarbons Aromatics • each aromatic ring system is given a common name • aromatic rings are written as hexagons with circles in the center Prof. T. L. Meeks

  49. Unsaturated Hydrocarbons Aromatics • although aromatics are unsaturated, they do not readily undergo addition reactions • the delocalized electrons cause aromatics to behave differently • aromatics undergo substitution reactions Prof. T. L. Meeks

  50. Functional Groups: Alcohols and Ethers The reactivity of organic compounds can be attributed to particular atoms or groups of atoms A site of reactivity in an organic molecule is called a functional group because it controls how the molecule behaves or functions Each distinct functional group often undergoes the same kind of reaction Prof. T. L. Meeks

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