Chemistry%20121(01)%20Winter%202009

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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_at_chem.latech.edu
Office 311 Carson Taylor Hall Phone
318-257-4941 Office Hours MTW 900 am - 1100
am TR 900 - !000 am 100-200 pm.
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
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Introduction to Organic and biochemistry

• Chapter 1-12

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Introduction to organic Biochemistry
Test 1 12. Saturated Hydrocarbons 13. Unsaturated Hydrocarbons 14. Alcohols, Phenols, and Ethers Test 3 18. Carbohydrates 19. Lipids 20. Proteins
Test 2 15. Aldehydes and Ketones 16. Carboxylic Acids, Esters, and Other Acid Derivatives 17. Amines and Amides Test 4 21. Enzymes and Vitamins 22. Nucleic Acids 23. Biochemical Energy Production
Self Study 24. Carbohydrate Metabolism 25. Lipid Metabolism 26. Protein Metabolism
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Introduction to organic Biochemistry

• 12.1 Organic and Inorganic Compounds12.2
  Bonding Characteristics of the Carbon Atom12.3
  Hydrocarbons and Hydrocarbon Derivatives

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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.

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Covalent or Ionic

• Identify covalent and ionic compounds
• H2O, NaCl, C2H5OH, CH3COOH, Na2CO3, CH3OK, KOH
• Covalent
• Ionic

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Organic or Inorganic

• Identify organic and inorganic compounds
• H2O, NaCl, C2H5OH, CH3COOH, Na2CO3, C3H8, KOH
• Organic
• Inorganic

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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.

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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's 1828 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.

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Bonding Characteristics of the Carbon Atom

• C is a small atom
• it forms four bonds consisting of single,
  double, and triple carbon 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.

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s and p hybrids
Four sp3 hybrids
Three sp2 hybrids
Two sp hybrids
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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 four
  sp3 orbitals)
• sp2 (one s orbital two p orbitals give three
  sp2 orbitals)
• sp (one s orbital one p orbital give two sp
  orbitals)

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? 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

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? and ? bonds

• Overlap of hybrid orbitals can form two types of
  bonds, depending on the geometry of the overlap
• bonds are formed by direct overlap
• ? bonds are formed by parallel overlap of
  unhybrid p prbitlas

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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

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Counting ? and ? bonds in Lewis structure
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Draw Lewis structure of molecules

• CHCl3
• C2H4
• C3H8O
• CH3CH2CH2OH
• CH3CH2OCH3
• CH3CO2H
• CH3CHO

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

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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
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Bond Properties

• Bond strength
• strongest weakest
• Bond length
• longest
  shortest

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Formula

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

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Condensed formula

• Condensed formula
• Shorthand way of writing a formula.
• Lists all atoms in order and tells how they are
  bound together.
• Example. Propane C3H8 CH3CH2CH3
• This is a convenient format for describing a
  molecule using text.

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Structural Formula of hydrocarbons

• One simple class of compound is the alkane which
  has only C, H and single bonds.
• methane ethane propane
  butane
• CH4 CH3CH3 CH3CH2CH3
  CH3CH2CH2CH3

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Line Formula of hydrocarbons

• One simple class of compound is the alkane which
  has only C, H and single bonds.
• methane ethane propane
  butane
• CH4 CH3CH3 CH3CH2CH3
  CH3CH2CH2CH3

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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.

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Models

• Three dimensional representations

Ball and Stick
Space Filling
Both are models of propane.
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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

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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

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Common Functional Groups
Alcohol(carbon, hydrogen and oxygen) CH3-CH2-OH
Thiol (thioalcohol)   thio means sulfur CH3-CH2-SH
Amine CH3-CH2-NH2
Ether CH3-CH2-O-CH2-CH3
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Common Functional Groups (continued)
Carbonyl group or unit            
Aldehyde          
ketones         
Carboxylic acids    
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Classification of organic compounds
Class Functional group Example

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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
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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

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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 double bond or triple bonds

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Classification of Hydrocarbons
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Examples of Alkanes, Alkenes, Alkynes and
Arenes
ethane ethene ethyne benzene C2H6 C2H4 C
2H2 C6H6 CnH2n2 CnH2n CnH2n-2 CnHn
saturated unsaturated unsaturated
Aromatic alkane alkene alkyne Arene
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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