Molecular Structure and Organic Chemistry

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Molecular Structure and Organic Chemistry

• The structure of a molecule refers to the
  arrangement of atoms within the molecule. The
  structure of a molecule is critical to the
  chemical and physical properties of a substance.
  In fact so vital is structure to molecular
  identity that the same molecular formula may
  represent more than one substance based upon
  their differing structures.
• Example Two totally different substances share
  the same molecular formula, C2H6O, but are
  different because of their differing molecular
  structures.
• Ethyl Alcohol C2H6O Dimethyl Ether C2H6O

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Importance of Molecular Structure

• Ethyl Alcohol C2H6O Dimethyl Ether C2H6O

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Isomers

• Molecules that have the same molecular formulas
  but different structures are called isomers
• There are 2 isomers corresponding to the
  molecular formula C4H10 , 3 corresponding to
  C5H12 and 39 corresponding to the molecular
  formula C9H20

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CH3CH2CH2CH3
CH(CH3)3
CH3CH2CH2CH2CH3
CH3CH2CH(CH3)2
C(CH3)4
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Infrared Spectrophotometry

• using molecular vibrations as a key to structure
• Although ball and stick models of molecules are
  very effective at approximating the actual shapes
  of molecules, they do have one major flaw they
  leave you with the false impression that
  molecules are rigid objects
• The atoms that make up molecules are in constant
  motion. They are continually flexing about their
  bonds. This flexing is referred to as
  vibrational motion. There are several types of
  vibrations, the two most basic vibrational modes
  are stretching and bending.

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Some Vibrational Modes

• Show clip of various vibrational modes here.

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Molecular Vibrations

• Covalent bonds vibrate at only certain allowable
  frequencies.

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Vibrations as a Key to Structure

• Each type of vibration has a frequency that
  depends upon the
• For a constant bond type (single, double or
  triple) the frequency of the vibration is low for
  a bond between heavy atoms. Conversely, for a
  given bond type the frequency of vibrations is
  high for light atoms.
• Multiple bonds vibrate at a higher frequency than
  do single bonds

the mass of the vibrating atoms and the nature of
the bond between them.
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Stretching Frequencies

• Frequency decreases with increasing atomic
  weight.
• Frequency increases with increasing bond energy.
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Infrared Absorbtions

• Vibrations as a key to structure- the entire
  range of vibrations for all organic molecules
  falls within the Infrared Region of the
  Electromagnetic Spectrum(2500nm 25000nm). If a
  beam of IR radiation is directed at a molecular
  sample and if the beam has the same frequency as
  one of the vibrational modes of the molecule then
  the molecule will absorb the energy of the IR
  radiation and the molecular vibration will
  increase in intensity.

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The IR Region

• Just below red in the visible region.
• Wavelengths usually 2.5-25 mm.
• More common units are wavenumbers, or cm-1, the
  reciprocal of the wavelength in centimeters.
• Wavenumbers are proportional to frequency and
  energy. gt

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Infrared Absorbtions

• If in order for absorption to occur, the IR
  frequency must match the frequency of the
  vibrating atoms, and if the frequency of the
  vibrating atoms is dependent upon the mass of the
  atoms and the bond type then the frequency at
  which absorbance occurs is dependant upon the
  mass of the atoms and the bond type. Therefore,
  the same two bonded atoms, regardless of the
  molecule that they are in, will have the same
  absorbance frequency in the IR region. This is
  the major strength of IR Spectrophotometry. IR
  Spec identifies the
• present in an organic molecule.

functional groups
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functional groups

• Functional Group- this is an atom or group of
  atoms that imparts a unique set of chemistry to
  whatever organic molecule it is bonded to. If
  the same functional group is attached to two
  different organic molecules then the two organic
  molecules will have similar chemistrys and have
  similar absorbance values of the IR Specs.
• Show clip of absorbtion frequencies for various
  functional groups.

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O-H and N-H Stretching

• Both of these occur around 3300 cm-1, but they
  look different.
• Alcohol O-H, broad with rounded tip.
• Secondary amine (R2NH), broad with one sharp
  spike.
• Primary amine (RNH2), broad with two sharp
  spikes.
• No signal for a tertiary amine (R3N) gt

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An Alcohol IR Spectrum
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An Amine IR Spectrum
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Carbonyl Stretching

• The CO bond of simple ketones, aldehydes, and
  carboxylic acids absorb around 1710 cm-1.
• Usually, its the strongest IR signal.
• Carboxylic acids will have O-H also.
• Aldehydes have two C-H signals around 2700 and
  2800 cm-1.
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A Ketone IR Spectrum
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An Aldehyde IR Spectrum
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O-H Stretch of a Carboxylic Acid

• This O-H absorbs broadly, 2500-3500 cm-1, due to
  strong hydrogen bonding.

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Variations in CO Absorption

• Conjugation of CO with CC lowers the stretching
  frequency to 1680 cm-1.
• The CO group of an amide absorbs at an even
  lower frequency, 1640-1680 cm-1.
• The CO of an ester absorbs at a higher
  frequency, 1730-1740 cm-1.
• Carbonyl groups in small rings (5 Cs or less)
  absorb at an even higher frequency. gt

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An Amide IR Spectrum
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Carbon - Nitrogen Stretching

• C - N absorbs around 1200 cm-1.
• C N absorbs around 1660 cm-1 and is much
  stronger than the C C absorption in the same
  region.
• C ? N absorbs strongly just above 2200 cm-1. The
  alkyne C ? C signal is much weaker and is just
  below 2200 cm-1 .
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A Nitrile IR Spectrum
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IR Spectrophotometers

• Because every molecule has a unique set of atoms
  and bonds that compose it, each molecule will
  absorb IR radiation only at certain frequencies.
  These frequencies are related to the types of
  bonds and arrangements of atoms in a molecule.
• An IR Spectrophotometer is an instrument that
  measures the absorbance of IR radiation by a
  sample as a function of frequency.

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The Hydrocarbon Skeleton

• All organic molecules consist of nothing more
  than a hydrocarbon skeleton with functional
  groups hung off that skeleton at various
  positions.
• We have just seen that functional groups can be
  identified by their characteristic IR
  absorbtions.
• Let us now investigate the characteristic IR
  absorbtions of the hydrocarbon skeleton

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Carbon-Carbon Bond Stretching

• Stronger bonds absorb at higher frequencies
• C-C 1200 cm-1
• CC 1660 cm-1
• C?C 2200 cm-1 (weak or absent if internal)
• Conjugation lowers the frequency
• isolated CC 1640-1680 cm-1
• conjugated CC 1620-1640 cm-1
• aromatic CC approx. 1600 cm-1
  gt

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Carbon-Hydrogen Stretching

• Bonds with more s character absorb at a higher
  frequency.
• sp3 C-H, just below 3000 cm-1 (to the right)
• sp2 C-H, just above 3000 cm-1 (to the left)
• sp C-H, at 3300 cm-1
  
  gt

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An Alkane IR Spectrum
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An Alkene IR Spectrum
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An Alkyne IR Spectrum
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Vibrational Motions