Molecular structure and organic chemistry
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Molecular structure and organic chemistry
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 molecularstructures.

  • Ethyl Alcohol C2H6O Dimethyl Ether C2H6O

Importance of molecular structure








Importance of Molecular Structure

  • Ethyl Alcohol C2H6O Dimethyl Ether C2H6O


  • 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






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.

Some vibrational modes


Some Vibrational Modes

Show clip of various vibrational modes here.

Molecular vibrations
Molecular Vibrations

Covalent bonds vibrate at only certain allowable frequencies.


Vibrations as a key to structure
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.

Stretching frequencies
Stretching Frequencies

  • Frequency decreases with increasing atomic weight.

  • Frequency increases with increasing bond energy. =>

Infrared absorbtions
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.

The ir region
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. =>

Infrared absorbtions1
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

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 chemistry’s and have similar absorbance values of the IR Specs.

  • Show clip of absorbtion frequencies for various functional groups.

O h and n h stretching
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) =>

An amine ir spectrum
An Amine IR Spectrum


Carbonyl stretching
Carbonyl Stretching

  • The C=O bond of simple ketones, aldehydes, and carboxylic acids absorb around 1710 cm-1.

  • Usually, it’s the strongest IR signal.

  • Carboxylic acids will have O-H also.

  • Aldehydes have two C-H signals around 2700 and 2800 cm-1. =>

A ketone ir spectrum
A Ketone IR Spectrum


An aldehyde ir spectrum
An Aldehyde IR Spectrum


O h stretch of a carboxylic acid
O-H Stretch of a Carboxylic Acid

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


Variations in c o absorption
Variations in C=O Absorption

  • Conjugation of C=O with C=C lowers the stretching frequency to ~1680 cm-1.

  • The C=O group of an amide absorbs at an even lower frequency, 1640-1680 cm-1.

  • The C=O of an ester absorbs at a higher frequency, ~1730-1740 cm-1.

  • Carbonyl groups in small rings (5 C’s or less) absorb at an even higher frequency. =>

An amide ir spectrum
An Amide IR Spectrum


Carbon nitrogen stretching
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 .=>

A nitrile ir spectrum
A Nitrile IR Spectrum


Ir spectrophotometers
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.

The hydrocarbon skeleton
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

Carbon carbon bond stretching
Carbon-Carbon Bond Stretching

  • Stronger bonds absorb at higher frequencies:

    • C-C 1200 cm-1

    • C=C 1660 cm-1

    • CC 2200 cm-1 (weak or absent if internal)

  • Conjugation lowers the frequency:

    • isolated C=C 1640-1680 cm-1

    • conjugated C=C 1620-1640 cm-1

    • aromatic C=C approx. 1600 cm-1 =>

Carbon hydrogen stretching
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 =>