Bonding and Structure

Organic chemistry

• carbon has unique chemistry
  • bonds to every other element
  • bonds to itself in long chains
• organic chemistry involves enormous variety
  • many possible structures
  • many possible reactions

Organic chemists

• what do organic chemists do?
  • understanding structures, reactions
  • correlation of structures with properties
  • synthesis of compounds with specific properties
• who else needs organic?
  • basis of all life processes
    - the great variety of structures and reactions make life possible

How to handle variety

• nomenclature - clear methods for naming structures and reactions
• structures - organized by functional groups
• reactions - organized by reaction types (what happens?)
• reactions - organized by reaction mechanisms (how does it happen?)

What should you get out of organic chemistry?

• from complex names, be able to derive a structure
• from complex structures, be able to identify functional groups, predict characteristic properties
• work through reaction mechanisms - what is a molecule likely to do under certain conditions
• "think like a molecule"

A reaction example

• CH3OH + HCl --> CH3Cl + H2O
• Reaction type
  • what happens ?
• Reaction mechanism
  • how does the reaction occur ? (step-by-step)

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The Periodic Table

• atomic number (defines element)
• atomic weight (isotopes)
• electron shells (rows)
• groups (similar properties)
• filled shells (the noble gases)
• valence electrons (for bonding)

Bonding - Lewis structures

• the octet rule
• ionic bonding
• covalent bonding
  - most common bonding in organic compounds

Typical valence - neutral atoms in normal bonding patterns

• H has 1 valence electron - makes 1 bond
• C has 4 valence electrons - makes 4 bonds
• N has 5 valence electrons - makes 3 bonds + 1 lone pair
• O has 6 valence electrons - makes 2 bonds + 2 lone pairs
• F has 7 valence electrons - makes 1 bond + 3 lone pairs
• Recognize the appearance of these common atoms in correct structures
• Also recognize the common charged forms:

Atom	Bonds	Lone Pairs	Charge
H	1	0	0
H+	0	0	+1
H-	0	1	-1
C	4	0	0
C+	3	0	+1
C.	3	1 e-	0
C-	3	1	-1
N	3	1	0
N+	4	0	+1
N-	2	2	-1
O	2	2	0
O-	1	3	-1
O+	3	1	+1
F	1	3	0
F-	0	4	-1

Writing organic structures

• Lewis structures
  - all electrons shown
• Kekule structures
  - show bonds as lines
  - lone pairs sometimes omitted
• condensed structures
  - common groups are abbreviated (e.g., CH3CH2 = ethyl or Et)
• line structures
  - omit lone pairs
  - omit hydrogens on carbons
  - omit carbons
  (assumed to be at the end of every bond)

3-Dimensional structures

• dotted-line / wedge
• ball-and-stick
• space-filling

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Visualizing chemical structures

• Name (common or systematic)
• Condensed Formula (as usually typed out)
• Lewis Structure (all atoms and bonds shown)
• Line Structure (omit hydrogens, assume carbons at vertices)
• 3-D Structure (show bond orientations)
• Ball-and-Stick Structure (like a molecular model you could make)
• Space-Filling Model (approximates full size of electron distribution)

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methane: CH4

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benzene: C6H6

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penicillin:

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Atomic orbitals

• wavefunctions
  - describe location of electrons
• s orbital (spherical)
• p orbitals (three: x,y,z)
  - (dumbbell shape - 2 lobes)
• d orbitals (4 lobes)
  - not usually needed for organic chemistry
• hybrid orbitals
  - combination orbitals

Bonding

• attraction between negative electrons and positive nuclei
  - repulsions between electrons
  - repulsions between nuclei
• bonding is a balance between the attractions and repulsions
• characteristic bond lengths and strengths

Molecular geometry by VSEPR

• electron pairs repel one another, maximize their separation
• BeH2 is linear (2 pairs of electrons, both in covalent bonds)
• BH3 is trigonal planar (3 pairs of electrons, all in covalent bonds)
• CH4 is tetrahedral (4 pairs of electrons, all in covalent bonds)
• atoms that satisfy the octet rule have 4 pairs of electrons - overall tetrahedral
• H2O molecular structure is bent (2 covalent bonds, 2 lone pairs)
• NH3 molecular structure is pyramidal (3 covalent bonds, one lone pair)

Electronegativity

• tendency of an atom to attract electrons in a covalent bond
• in the Periodic Table, electronegativity increases to the right and up
• F > O > Cl ~ N > Br > C > H > metals

Polar covalent bonds

• electrons in a covalent bond may not be equally shared
  H-F is polarized with excess electron density closer to F
  

Polar bonds to carbon

• C-C bonds are nonpolar
• C-H bonds are generally considered nonpolar
• C-X bonds are polarized with carbon partially +
  for X = F, Cl, Br, I, O, S, N
• C-M bonds are polarized with carbon partially -
  for M = metals

Functional Groups

• a specific arrangement of atoms
• define chemical families
• determine chemical properties
• basis of nomenclature
• organization of textbooks
• examples - the simple oxygen families:
  • alcohols, ethers, aldehydes, ketones, carboxylic acids

Resonance

• more than one possible Lewis structure for a compound
• What's the best Lewis structure?
  • follow the octet rule
  • electronegativity determines the best place to locate charges
    carbon monoxide (CO)
    nitromethane (CH3NO2)

Electron-pushing

• keeping track of electrons is crucial in organic chemistry
• curved electron arrows indicate electron pair movement
  - in converting resonance forms, or later, in reactions

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Review of Acid-Base Reactions

Bronsted-Lowry Acid/Base

• acid - donates H+
• base - accepts H+
  NH3 + H2O <==> NH4+ + OH-
  base + acid <==> acid + base
• note conjugate acid-base pairs
  (differ by H+)

Acidity Constant (Ka)

• HA + H2O <==> H3O+ + A-

usually simplified to
HA <==> H+ + A-

• Ka = [H+] [A-] / [HA]

Acid Strength (pKa)

• stronger acids have higher Ka
  for HCl, Ka = 10E7
  for CH3COOH, Ka = 10E-5
  (acetic acid, found in vinegar)
  
• pKa = - log Ka
• stronger acids have a lower pKa
  for HCl, pKa = -7
  for CH3COOH, pKa = 5

pH and pKa

• Ka = [H+][A-]/[HA]
• pKa = pH - log([A-]/[HA])
• for pH = pKa, [A- ] = [HA]
• for pH < pKa, HA predominates
• for pH > pKa, A- predominates
  e.g., for acetic acid at pH = 7
  [CH3COO-] > [CH3COOH]

Structural Effects on Acid Strength

• electronegativity
  HF > H2O > NH3 > CH4
• weaker bond to H
  HI > HBr > HCl > HF
• inductive effects - electron withdrawal
  H2SO4 > H2SO3
  Cl-CH2-COOH > CH3-COOH
• hybridization with greater s-character
  sp C-H > sp2 C-H > sp3 C-H
• delocalization
  RCOOH > ROH

Acid-Base Reactions

CH3COOH + OH- <==> CH3COO- + H2O
acid (pKa = 5) + base <==> base + acid (pKa = 15.7)
reaction favored for stronger acid

reaction favored to the right

Lewis Acids

• acid - accepts an electron pair
• base - donates an electron pair
  (making a new covalent bond)