Chem 334 - Summer 1998 - Organic Chemistry I Dr. Carl C. Wamser

Chapter 1 - Structure and Bonding

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?

• 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 ?
• acid/base, oxidation/reduction, addition/elimination, substitution, rearrangement
• substitution - of Cl for OH (identify bonds broken and made)
• Reaction mechanism ?
• how does the reaction occur (step-by-step)

A reaction mechanism

• Break the molecules into atoms
• Reassemble into products
• What's wrong with this mechanism?
• It would take too much energy (unnecessarily)

A better mechanism

• Balance bond breaking with bond making
• First an acid-base reaction:
  CH3OH + HCl --> CH3OH2+ + Cl-
• Then a substitution:
  CH3OH2+ + Cl- --> CH3Cl + H2O

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)

Lewis Structures

• the octet rule
  - atoms strive to get 8 electrons (full shell)
• ionic bonding
  - gaining or losing electrons
  - stabilized by Coulombic attractions
• covalent bonding
  - sharing electrons
  - most common bonding in organic compounds

Typical Valence

• H - 1 valence electron - 1 bond
• C - 4 valence electrons - 4 bonds
• N - 5 valence electrons - 3 bonds + 1 lone pair
• O - 6 valence electrons - 2 bonds + 2 lone pairs
• F - 7 valence electrons - 1 bond + 3 lone pairs

Functional Groups

• characteristic arrangement of atoms that define a family of compounds
• R represents generic carbon group
• alcohols: R-O-H
• ethers: R-O-R
• carbonyl group ( C=O )
  • aldehydes: RCHO
  • ketones: R2CO
• carboxyl group ( COO )
  • carboxylic acids: RCOOH

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

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-Cl is actually d+ H-Cl d-
• where d+ or d- represents a partial charge

Polar Bonds to Carbon

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

Formal Charge

• #valence e- - (# bonds + # lone e-)
• (How many e- is normal for this atom?)
  - (How many e- in this compound?)

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)

Molecular Geometry - VSEPR Approach

• valence-shell electron-pair repulsion
• maximize separation between electron pairs (including lone pairs)
  • 4 pairs - tetrahedral
  • 3 pairs - trigonal planar
  • 2 pairs - linear
• note that multiple bonds are considered a single region of electron density
  • e.g., CH2=O is trigonal planar

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

Hybrid Orbitals

• sp hybrids (one s plus one p)
  - makes two identical orbitals (linear)
• sp2 hybrids (one s plus two p)
  - makes three identical orbitals (trigonal)
• sp3 hybrids (one s plus three p)
  - makes four identical orbitals (tetrahedral)

Why Hybrid Orbitals?

• good shape (directional)
• allows high overlap in bonding
• maximizes electron density between atoms
• good orientation
• minimizes repulsions between orbitals

Identifying the Hybridization of Carbon

• identify sigma and pi bonds around the carbon atom
  (you need one sigma bond for each neighboring atom
  and you need a total of four bonds for carbon)

Neighboring Atoms	Sigma Bonds	Pi Bonds	Hybrid	Structure
4	4	0	sp3	tetrahedral
3	3	1	sp2	trigonal planar
2	2	2	sp	linear

Molecular Orbitals

• overlap of atomic orbitals
• electrons are close to two nuclei
• bonding and antibonding combinations

Sigma Bonds

• cylindrical symmetry
• formed by end-on overlap

Pi Bonds

• nodal plane through bond axis
• formed by side-on overlap

Writing Organic Structures

• Lewis structures
  - all electrons shown
• Kekule structures
  - show bonds as lines
  - lone pairs sometimes omitted
• 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

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)

methane: CH4

penicillin: