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Chemistry 121(01) Winter 2009

Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@chem.latech.edu Office : 311 Carson Taylor Hall ; Phone: 318-257-4941; Office Hours : MTW 9:00 am - 11:00 am; TR 9::00 - !0:00 am & 1:00-2:00 pm.

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Chemistry 121(01) Winter 2009

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  1. Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@chem.latech.edu Office: 311 Carson Taylor Hall ; Phone: 318-257-4941; Office Hours: MTW 9:00 am - 11:00 am; TR 9::00 - !0:00 am & 1:00-2:00 pm. Chemistry 121(01) Winter 2009 December 19, Test 1 (Chapters 12-14) January 2 Test 1 (Chapters 15-16) February 6 (Chapters 17-19) February 27, (Chapters 20-22) March 2, 2009, Make Up Exam: Bring Scantron Sheet 882-E

  2. Introduction to Organic and biochemistry Chapter 1-12

  3. Introduction to organic & Biochemistry

  4. Introduction to organic & Biochemistry 12.1 Organic and Inorganic Compounds12.2 Bonding Characteristics of the Carbon Atom12.3 Hydrocarbons and Hydrocarbon Derivatives

  5. Organic and Inorganic compounds • Ionic Compounds: Have cations and anions are also called salts made of metlas and non-metals • Covalent Compounds: Consists of neutral molecules connected by covalent bonds to non metallic elements. • Organic Compounds : • have carbon atoms sharing electrons in covalent bonds. Carbon atoms form chains, and many atoms can be joined by covalent bonds. • Inorganic Compounds: • Consist of ions produced by loss or gain of electrons between a metal and non metal.

  6. Covalent or Ionic Identify covalent and ionic compounds: H2O, NaCl, C2H5OH, CH3COOH, Na2CO3, CH3OK, KOH Covalent : Ionic:

  7. Organic or Inorganic Identify organic and inorganic compounds: H2O, NaCl, C2H5OH, CH3COOH, Na2CO3, C3H8, KOH Organic : Inorganic:

  8. Introduction • Organic chemistry is the study of the compounds of carbon with H, N, O and S. • Biochemistry is the study of the chemical processes in living organisms. It deals with the structure and function of cellular components.

  9. More details.. Organic vs. Inorganic • Organic compounds are produced by living things. • Inorganic compounds are produced by non-living naturalprocesses or by human intervention in the laboratory. • This was the most common definition of "organic" until Wohler's1828 synthesis of urea (an organic compound) from ammonium cyanate (a salt, and therefore? Organic/inorganic). But we no longer use this definition, for the simple reason that many compounds that everyone agrees are organic -- including "natural products" which are routinely made by living things -- have been synthesized by humans. • Organic compounds contain carbon. • Inorganic compounds don't. • Organic compounds contain carbon-hydrogen bonds. Inorganic compounds don't.

  10. Bonding Characteristics of the Carbon Atom • C is a small atom • it forms four bonds consisting of single, double, and triplecarbon to carbon bonds or other atoms • Shows tetrahedral (all 4 - ), trigonal planar (2 - & 1 =) and linear ( 1 - & 1) • it forms strong bonds with C, H, O, N, and some metals • form stable covalent bonds to other carbon atoms – catenation: Long carbon chains can be produced.

  11. s and p hybrids Four sp3 hybrids Three sp2 hybrids Two sp hybrids

  12. Hybrid Atomic Orbitals Hybridization is the mixing up of two or more atomic orbitals • There are three types of hybrid atomic orbitals for carbon sp3(one s orbital + three p orbitals give foursp3 orbitals) sp2(one s orbital + two p orbitals give threesp2 orbitals) sp (one s orbital + one p orbital give two sp orbitals)

  13.  and  bonds in single and multiple bonds • single bond - one shared pair of electrons between two atoms; a s bond • double bond - two shared pairs of electrons between two atoms; one s bond and one p bond • triple bond - three shared pairs of electrons between two atoms; one s bond and two p bonds

  14.  and  bonds • Overlap of hybrid orbitals can form two types of bonds, depending on the geometry of the overlap • bondsare formed by “direct” overlap  bondsare formed by “parallel” overlap of unhybrid p prbitlas

  15. Predicting hybridization of atoms in a Lewis structure • Count sigma bonds and unshared electrons around the atom If the total number of pairs: 2 sp hybridization 3 sp2 hybridization 4 sp3 hybridization

  16. Counting  and  bonds in Lewis structure

  17. Draw Lewis structure of molecules • CHCl3 • C2H4 • C3H8O • CH3CH2CH2OH • CH3CH2OCH3 • CH3CO2H • CH3CHO

  18. Resonance For many molecules and ions with double bonds, two or more Lewis structure could be written

  19. Curved arrow Electron pushing • Curved arrow:a symbol used to show the redistribution of valence electrons • In using curved arrows, there are only two allowed types of electron redistribution: • from a bond to an adjacent atom • from an atom to an adjacent bond • Electron pushing by the use of curved arrows is also used in explaining reaction mechanisms

  20. Drawing Curved Arrows To show the movement of electrons in breaking and forming bonds. The tail of the arrow is started at the site of electron density (negative character such as a pi bond or lone pair of electrons) and proceeds to the arrowhead which is drawn to the site of electron deficiency (positive character). NEGATIVE TO POSITIVE! Arrows can be drawn from: 1) lone pair bond lone pair 2) bond bond 3) bond

  21. Bond Properties • Bond strength: • strongest weakest • Bond length: • longest shortest

  22. Formula • Molecular formula • kind and number of each type of atoms • Structural formula • each atom and bond in a molecule

  23. Condensed formula • Condensed formula • Shorthand way of writing a formula. • Lists all atoms in order and tells how they are bound together. • Example. Propane C3H8CH3CH2CH3 • This is a convenient format for describing a molecule using text.

  24. Structural Formula of hydrocarbons • One simple class of compound is the alkane which has only C, H and single bonds. methane ethane propane butane CH4CH3CH3CH3CH2CH3 CH3CH2CH2CH3

  25. Line Formula of hydrocarbons One simple class of compound is the alkane which has only C, H and single bonds. methane ethane propane butane CH4CH3CH3CH3CH2CH3 CH3CH2CH2CH3

  26. OH N H H H H H H H H H 2 2 2 2 2 2 2 2 C C C C C C C C H 2 OH N H H C CH C H C H C H C H C H C 2 2 2 2 2 2 2 C C C C C C C C CH 3 H H H H H H H H 2 2 2 2 2 2 2 2 Line formula • Similar to structural formula. • Each line represents a bond. • Carbons are assumed to be present at the end of each line segment. • Hydrogen is not shown when bound to carbon.

  27. Models • Three dimensional representations Ball and Stick Space Filling Both are models of propane.

  28. I see much memorization in your future! Base names of organic compounds Prefix Carbons • Meth- 1 • Eth- 2 • Prop- 3 • But- 4 • Pent- 5 • Hex- 6 • Hept- 7 • Oct- 8 • Non- 9 • Dec- 10

  29. Functional Groups in Organic Compounds • Functional group: an atom or group of atoms within a molecule that shows a characteristic set of physical and chemical properties • Functional group • divide organic compounds into classes • the sites of characteristic chemical reactions • the basis for naming organic compounds

  30. Common Functional Groups

  31. Common Functional Groups (continued)

  32. Classification of organic compounds Class Functional group Example

  33. IUPAC - a general system: Examples prop-en-e = propene eth-an-ol = ethanol but-an-one = butanone but-an-al = butanal pent-an-oic acid = pentanoic acid cyclohex-an-ol = cyclohexanol eth-yn-e = ethyne eth-an-amine = ethanamine cyclo-pent-en-e

  34. The IUPAC system: Naming Organic Compounds • As a general system of nomenclature • prefix-infix-suffix • prefix tells the number of carbon atoms in the parent • infix tells the nature of the carbon-carbon bonds • suffix tells the class of compound

  35. Hydrocarbons • Composed of only carbon and hydrogen; in petroleum and coal • Saturated - hydrocarbons with all • C-C single bonds • Unsaturated - hydrocarbons with at • least one C-C doublebond or triple bonds

  36. Classification of Hydrocarbons

  37. Examples of Alkanes, Alkenes, Alkynes and Arenes: ethane ethene ethyne benzene C2H6 C2H4 C2H2 C6H6 CnH2n+2 CnH2n CnH2n-2 CnHn saturated unsaturated unsaturated Aromatic alkanealkenealkyneArene

  38. Biochemical Principles • Structures of Monomers and Polymers found in living systems • Carbohydrates (glucose, starch, cellulose) • Proteins (amino acids, proteins) • Nucleic acids (Nucleotides-A,T,G,C and RNA & DNA) • Functions of Biological molecules • Enzymes and Vitamins • Nucleic Acids and hereditary • Biochemical Energy Production • Carbohydrate Metabolism • Lipid Metabolism • Protein Metabolism

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