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Chemistry 121(01) Winter 2009
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Chem 120: Background for
             Organic and Biochemistry
  • Chapters 1-11
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Chapter 3: Atomic Structure and Periodic Table
  • Chapter 3: Atomic Structure and Periodic Table


      • 3.6 Electron Arrangements Within Atoms
        Chemistry at a Glance: Shell-Sub-shell-Orbital Interrelationships
      • 3.7 Electron Configurations and Orbital Diagrams
        3.8 The Electronic Basis for the Periodic Law and the Periodic Table
      • 3.9 Classification of the Elements
        Chemistry at a Glance: Element Classification Schemes and the Periodic Table
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Shapes of s Atomic Orbitals
  • All s orbitals have the shape of a sphere, with its center at the nucleus
    • of the s orbitals, a 1s orbital is the smallest, a 2s orbital is larger, and a 3s orbital is larger still
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Atomic Orbitals
  • s orbital - a spherical-shaped atomic orbital; can hold a maximum of 2 electrons
  • p orbital - a dumbbell-shaped atomic orbital; the three p orbitals (px, py, pz) can hold a maximum of 2 electrons each
  • Electrons always fill starting with the lowest-energy orbital:
  • lower energy higher energy
  • 1s2 2s2 2p6 3s2 3p6
  • We will be concerned with only the valence electrons which are the outermost electrons involved in forming bonds.
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Shapes of p Atomic Orbitals
    • A p orbital consists of two lobes arranged in a straight line with the center at the nucleus
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Electronic Structure of atoms
  • Ground state electronic configuration of atoms in core format
  • Carbon (C): ): [He] 2s2, 2p2
  •                                       or [He] 2s2, 2px13py13pz0
  • Potassium (K): Ar] 4s1
  • Phosphorous (P): [Ne] 3s2, 3p3


  • Valence shell electronic configuration
  • Carbon (C): ): 3s2, 3p2
  • Potassium (K): 4s1
  • Phosphorous (P): 3s2, 3p3
  • How you get the electronic configuration of an atom from the periodic table?
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Excited State Valence Electron Configuration
  • Carbon (C):
  • Ground state: 2s2, 2p2   or  2s2, 2px13py13pz0








  • Excited State: 2s1, 2p3    or 2s1, 2px13py13pz1
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Chapter 4: Ionic Bond Model
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Lewis structure of atoms (Review)
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Cations and Anions
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Ionic model of bonding model (Review)
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 Chapter 5. Chemical Bonding: The Covalent Bond Model
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Lewis Model of bonding (Review)
  • "octet rule“
  • atoms tend to gain, lose or share electrons so as to have eight electrons in their outer electron shell
  • “Lewis structure of atoms”
  •   Shows only valence electrons, is a convenient way of representing atoms to show their chemical bonding pattern.
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Covalent model of bonding (Review)
  • Covalent bonds - results from the sharing of electrons between two atoms typically involves two nonmetallic elements


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Types of electrons
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Drawing Lewis structure molecules and ions (Review)
  • 3) Draw the skeletal structure by connecting the atoms with single bonds.


  • 4) Give each of the atoms an octet (8 e-).  Adding unshared pairs of electrons


  • 5) Count the total number of e- used through step 4 and compare to the number calculated in step 2.
  •      a) If it results in zero, the structure is correct.
  •     b) For every two electrons too many, another bond is added            (minimize formal charges).
  •       Multiple bonds form only with C, N, O and S.
  •           Total number of bonds  to neutral atoms:
    •           4 bonds to C
    •          3 bonds to N, P
    •          2 bonds to O, S
    •          1 bond to H, F, Cl, Br, I
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Drawing Lewis structure molecules and ions
 (Review)
  • 1) Predict arrangement of atoms.
    • H is always a terminal atom.
    • Halogens and oxygen are often terminal.
    • The central atom of binary compounds is usually written
    • first and has the lowest subscript.
    • Most organic compounds have more than two central atoms.
    • These are mainly C, but N, O and S can also be central atoms.
  • 2) Total number of valence electrons (e-)
    • Add all valence electron of atoms in the molecule from the formula.
    • Add the ion charge for negative ions or subtract for positive ions.



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Calculation of formal charges of atoms in the Lewis structure
  • 1. For a neutral molecule, the sum of the formal charges equals zero.  For a polyatomic ion, the sum of the formal charges equals the charge on the ion.
  • 2. Formal charge of each atom is calculated by:
  •        (group #) - (# unshared e-) -  ½  (# shared e-)
  • 3. Formal charges are shown as  + or - on the atom with that charge.
  • 4. An atom with the same number of bonds as its group number has no formal charge.
  • 5. In a molecule if two different elements can be assigned a negative charge, then the more electronegative element gets the charge; the same sign should not be given to bonded atoms.
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Lewis Structures (Review)
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Draw Lewis structure of molecules
  • CHCl3
  • C2H4
  • C3H8O
  • CH3CH2CH2OH
  • CH3CH2OCH3
  • CH3CO2H
  • CH3CHO
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Draw Lewis structure and assign formal charges
  • CH3NH3+







  • CH3O-
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Valence-Shell Electron-Pair Repulsion (VSEPR) model (Review)
  • For predicting shapes of molecules and polyatomic Ions based on the repulsion of valence pairs of electrons making them as far apart as possible  around an atom of a Lewis structure.
  • 1) Draw the Lewis structure for the molecule or ion.
  • 2) Determine the number of bonding and unshared pairs attached to the central atom.
  • One single, double or triple bond counted as a bonding pair
  • 3) Choose the appropriate case from the given chart.
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Orbital Overlap Model
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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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s and p hybrids
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Electronegativity (Review)

  • H
  • 2.1
  • Li       Be B C N O F
  • 1.0 1.5 2.0 2.5 3.0 3.5 4.0
  • Na Mg Al Si P S Cl
  • 0.9 1.2 1.5 1.8 2.1 2.5 3.0
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Nonpolar/polar-covalent and ionic bonds. (Review)
  • We classify chemical bonds as polar covalent, nonpolar covalent and ionic based on the difference in electronegativity between the atoms


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



  • Ionic:



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Classify following bonds nonpolar-covalent, polar-covalent or ionic bonds
  • N-H nonpolar-covalent, polar-covalent or ionic bonds
  • O-H nonpolar-covalent, polar-covalent or ionic bonds
  • C-H nonpolar-covalent, polar-covalent or ionic bonds
  • C-F nonpolar-covalent, polar-covalent or ionic bonds
  • Na-Cl nonpolar-covalent, polar-covalent or ionic bonds
  • Al-Cl  nonpolar-covalent, polar-covalent or ionic bonds


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Polar and nonpolar molecules
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Predict the bond angles of molecules from their Lewis structures. (Review)
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Molecular Shape and Polarity (Review)
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s and p 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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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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Chapter 10. Acids, Bases, and Salts
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Acids and Bases
  • There are many compounds when dissolved in water changes the Hydrogen ion (H+) (related to pH) concentration of to water to acid or basic sides


    • Binary acids: E.g. HF, HCl, HBr, HI, H2S
    • Oxyacid: E.g. HNO3, H2SO4 , HClO4
    • Organic acids: E.g.





    • d)   Hydroxy bases: NaOH, Ca(OH)2
    • e)   Amine bases:    CH3NH2 (methylamine)
    •       (CH3)2NH (dimethylamine)


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Arrhenius acids and bases
  • This is the first acid/base concept to be developed to describe typical acid/base reactions.
  • Arrhenius Acid:
  •      A substance that produces H+, or (protons) H+3O, (hydronium ion) in an aqueous solution.
  •  Arrhenius Base:
  •     A substance that produces OH-, or hydroxide ion  in an aqueous solution.
  • E.g.  HCl (acid),  NaOH (base).
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Bronsted Lowery acid and bases
  • This is the second acid/base concept to be developed to include proton, H+ transfer reactions to base other than those containing OH-.  This definition also uses
  •     conjugate acid/base concept .
  • Bronsted Acid:
  •       A substance that donates protons (H+): E.g. HCl (acid),
  • Bronsted Base:
  •       A substance that accepts protons.  E.g. NH3 (base) non-hydroxy bases such as amines.
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Lewis acid and bases
  • Lewis was successful in including acid and bases that catalyze organic reactions without proton or hydroxyl ions.
  • Lewis Acid: A substance that accepts an electron pair.
  • Lewis base: A substance that donates an electron pair.
  • E.g. BF3(g)     +    :NH3(g) ®     F3B:NH3(s)
  •      Lewis Acid    Lewis base     Lewis acid/base adduct
  • the Lewis base donates a pair of electrons to the acid forming a coordinate covalent bond common to coordination compounds. Lewis acids/bases will be discussed later in describing reaction mechanism
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Bronsted Lowery Equilibria Acids/bases
and Conjugate Acid/bases

  • H2O(l)  + HCl(aq)               H3+O(aq)          + Cl¯(aq)
  • base                   acid                             conjugate acid      conjugate base






  • NH3(aq) + H2O(l)                   NH4+  +   OH¯(aq)
  • base                acid                                     conjugate acid      conjugate base
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Strength of conjugate acid/bases
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pH of Aqueous Solutions
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Ka    and    pKa from acid/base equilibria
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Relative acidity/basity
  • Higher  the Ka : higher the acidity.
  • Higher  the Kb : higher the basity.


  • Higher  the pKa : lower the acidity.
  • Higher  the pKb : lower the basity.
  • Which one is weaker acid?
  • HNO2    ;   Ka= 4.0 x 10-4.    pKa= 3.39
  • HOCl2   ;   Ka= 1.2 x 10-2.    pKa= 1.92
  • HOCl     ;  Ka= 3.5 x 10-8.    pKa= 7.46
  • HCN      ;  Ka= 4.9 x 10-10.  pKa= 9.31



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pKa in Acid-Base Equilibrium
  • Equilibrium favors reaction of the stronger acid and stronger base to give the weaker acid and the weaker base
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Molecular Structure and acidity
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Molecular Structure and acidity
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Electronegativity of the atom bonded to H in HA