Building A Toolset

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Building A Toolset For The Identification of
Organic Compounds
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• Study of the Interaction of Electromagnetic
  Radiation (Energy) and Matter
• When Energy is applied to matter it can be
• Absorbed
• Emitted
• Cause a chemical change (reaction)
• Transmitted.
• Electromagnetic Spectrum

Cosmic ? (Gamma) X-Ray Ultraviolet Visible Infr
ared Microwave Radio
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• Spectroscopy Types
• Mass Spectrometry (MS) Hi-Energy Electron
  Bombardment
• Use Molecular Weight, Presence of Nitrogen,
  Halogens
• Ultraviolet Spectroscopy (UV) Electronic Energy
  States
• Use Presence of Conjugated Molecules Carbonyl
  Group
• Infrared Spectroscopy (IR) Vibrational Energy
  States
• Use Functional Groups Compound Structure
• Nuclear Magnetic Resonance Spectroscopy (NMR)
  Nuclear Spin States
• Use The number, type, and relative position of
  protons (Hydrogen nuclei) and Carbon-13
  nuclei

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• High energy electrons bombard organic molecules
  breaking some or all of the original molecules
  into fragments.
• The process usually removes a single electron to
  produce a positive ion (cation radical) that can
  be separated in a magnetic field on the basis of
  the mass / charge ratio.
• Removal of the single electron produces a charge
  of 1 for the cation.
• Thus, the cation represents the Molecular Weight
  of the original compound or any of the fragments
  that are produced.
• The mass spectrum produced is a plot of relative
  abundance of the various fragments versus the
  Mass / Charge (M/Z) ratio.
• The most intense peak is called the Base Peak,
  which is arbitrarily set to 100 abundance all
  other peaks are reported as percentages of
  abundance of Base Peak.

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Typical Mass Spectrum
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• Molecular Ion Peak (M) Molecular Wgt of
  Original Molecule
• Largest mass/charge ratio and it is always the
  last peak on the right side of spectrum
• Molecular Ion Peak may or may not be the base
  peak!
• The Molecular Ion Peak(s) abundance can be quite
  small.
• The presence of Nitrogen in the compound If the
  Mass / Charge (m/z) ratio for the Molecular Ion
  peak is Odd, then the molecule contains an Odd
  number of Nitrogen atoms, i.e., 1, 3, 5, etc.
• Note An Even value for the Mass / Charge
  ratio could represent a compound with an even
  number of Nitrogen atoms, i.e., 0, 2, 4 etc., but
  the actual presence of Nitrogen in the compound
  is not explicitly indicated as it is with an
  Odd value for the ratio.

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• Most elements exist in several isotopic forms
• Ex. 1H1, 2H1, 12C6, 13C6, 35Cl17, 37Cl17, 79Br35,
  81Br35
• Each peak in a Mass Spectrum represents the
  Integral Molecular Weight of the fragment not
  the Average Molecular Weight usually reported
• Integral Molecular Weight represents an
  integral number of protons and neutrons, i.e.,
  a specific isotope.
• Average Molecular Weight represents the average
  molecular weight of All isotopes present.
• Thus, all peaks in a Mass Spectrum for a given
  fragment reflect the naturally occurring isotopic
  mixture of the elements in the fragment.

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• The Presence of Chlorine in a Compound
• The two (2) principal Chlorine Isotopes in nature
  are Cl-35 and Cl-37 (2 additional Neutrons in
  Cl-37)
• The relative abundance ratio of Cl-35 to Cl-37 is
  100 32.6 or 75.8 24.2 or ?
  3 1
• Therefore, a Molecule containing a single
  Chlorine atom will show two Mass Spectrum
  Molecular Ion peaks, one for Cl-35 (M) and one
  for Cl-37 (M2)
• Note M2 denotes 2 more neutrons than M
• Based on the natural abundance ratio of 100 /
  32.6 (about 31), the relative intensity (peak
  height) of the Cl-35 peak will be 3 times the
  intensity of the Cl-37 peak.

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• The presence of Bromine in a compound
• The two (2) principal Bromine Isotopes in nature
  are Br-79 and Br-81 (2 additional Neutrons in
  Br-81)
• The relative abundance ratio of Br-79 to Br-81 is
  100 97.1 or 50.5 49.5 or ? 1
  1
• Molecules containing a single Bromine atom will
  also show two molecular ion peaks one for Br-79
  (M) and one for Br-81 M2).
• Based on the natural abundance ratio of 100 /
  97.1 (about 11), the relative intensity of the
  Br-79 peak will be about the same as the Br-81
  peak.
• Note Fluorine exists in nature principally as a
  single isotope - 19F9
• Therefore, single Molecular Ion peak
  (assuming no other Halogens present.

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• Compounds containing two (2) Chlorine atoms will
  produce three (3) Molecular Ion peaks
  representing the 3 possible isotope combinations
  available
• 35Cl17 35Cl17 (Rel Peak Intensity - 100.0)
• 35Cl17 37Cl17 (Rel Peak Intensity -
  65.3)
• 37Cl17 37Cl17 (Rel Peak Intensity -
  10.6)
• Compounds containing three (3) Chlorine atoms
  will produce four (4) Molecular Ion peaks
  representing the 4 possible isotope combinations
  available
• 35Cl17 35Cl17 35Cl17 (Rel Peak Intensity
  - 100.0)
• 35Cl17 35Cl17 37Cl17 (Rel Peak Intensity
  - 97.8)
• 35Cl17 37Cl17 37Cl17 (Rel Peak Intensity
  - 31.9)
• 37Cl17 37Cl17 37Cl17 (Rel Peak Intensity
  - 3.5)

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• UV-Visible Spectrum 200 nm 700 nm
• Most organic molecules and functional groups are
  transparent in the Ultraviolet and Visible
  portions of the electromagnetic spectrum.
• Thus
• Absorption Spectroscopy in theUltraviolet /
  Visible Range is of Limited Utility
• In the case of ultraviolet and visible
  spectroscopy, the energy absorption transitions
  that occur are between electronic energy levels
  of valence electrons, that is, orbitals of lower
  energy are excited to orbitals of higher energy.
• Thus, UV / Visible spectra are often called
  Electronic Spectra

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• Molecules have many excited modes of vibration
  and rotation at room temperature. The rotational
  and vibrational levels are superimposed on the
  electronic levels
• Electron transitions may occur from any of
  several vibrational and rotational states of one
  electronic level to any of several vibrational
  and rotational states of a higher electronic
  level.
• Thus, the UV spectrum of a molecule consists of a
  broad band of absorption centered near the
  wavelength of the major transition

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• UV Spectroscopy is generally limited to the
  determination of the presence of a Conjugated
  Unsaturated System and Carbonyl Groups.
• Conjugated Unsaturated Systems
• Conjugated unsaturated systems are molecules with
  two or more double or triple bonds each
  alternating with a single bond.
  Ex. CH2CH ? CHCH2
• Conjugated unsaturated systems are species that
  have delocalized ? bonds, i.e. a p-orbital on an
  atom adjacent to a double bond producing ? ? ?
  transitions.
• Single electron as in the allyl radical
  (CH2CH?CH2)
• Vacant p orbital as in allyl cation (CH2CH?CH2)
• P orbital of another double bond (CH2CH ?CHCH2

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• Compounds whose molecules contain conjugated
  multiple bonds have absorption maxima at
  wavelengths longer than 200 nm, i.e. in the UV
  range.
• Conjugated systems absorb strongly in the UV /
  Visible portion of the electromagnetic spectrum,
  therefore they can be investigated with
  Ultraviolet Spectroscopy.
• More complicated alkenes (carbon-carbon double
  bond) and nonconjugated dienes usually have
  absorption maxima below 200 nm, i.e. do not
  absorb in the UV range).

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• Carbonyl Compounds
• Compounds with carbon-oxygen double bonds
  (carbonyl) also absorb light in the UV region.
• The carbonyl excitation process involves movement
  of an electron from one of the unshared
  (nonbonding) pair to the ? orbital of the
  carbon-oxygen double bond.
  Transitions - n ? ?
• Non-bonding electrons, such as those in a
  carbonyl group (and some alkyl halides), will
  absorb in the UV region, but at lower intensity
  than conjugated systems.
• Carbonyl absorption in the UV does not require
  additional conjugation in the molecule.
• If a molecule does not absorb in the UV, then it
  does not contain a conjugated system of
  alternating double bonds or a carbonyl group

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Ultraviolet / Visual Spectrophotometers

• Produce an absorption spectrum, which is a plot
  of the wavelength in nanometers (nm) over the
  entire Ultraviolet / Visible region versus the
  absorbance (A) of the radiation at each
  wavelength.
• Note Absorption by the solvent is measured
  first and then electronically
  subtracted from the solvent / sample
  mixture.
• A log (Ir / Is)
• Is Intensity of Sample
  Beam
• Ir Intensity of Reference
  Beam
• The Wavelength of Maximum Absorption ( ?max ) is
  obtained from the Absorption Spectrum

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• Molar Absorptivity (?) - also called the Molar
  Extinction Coefficient - is a measure of the
  strength or intensity of the absorption.
• It is the proportionality constant relating the
  observed absorbance (A) at a particular
  wavelength to the molar concentration (C) of the
  sample and the length (l) of the path of the
  light beam through the sample cell (cm).
• A ? C
  l
• ? A / (C
  l )

2,5-Dimethyl-2,4-Hexadiene (in
Methanol) Wavelength of Maximum Absorbance
(?max) 242.5 nm Molar Absorptivity ( ? )
13,100 M-1 cm-1 (Log ? 4.1)
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Conjugated systems show large values of ? ?
1000 100,000 (Log ? 3 - 5) Carbonyl
compounds show smaller values of ? ? 10 100
(Log ? 1 - 2)
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Wavelength of Maximum Absorbance ?max 230
nm Molar
Absorptivity ? 15,000 cm-1
Log ? 4.2 ?
Conjugated Molecule (Benzene Ring)
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Infrared Radiation That part of the
electromagnetic spectrum between the visible and
microwave regions 0.8 ?m (12,500 cm-1) to 50
?m (200 cm-1). Area of Interest in Infrared
Spectroscopy The Vibrational portion of infrared
spectrum 2.5 ?m (4,000 cm-1) to 25 ?m (400
cm-1) Radiation in the vibrational infrared
region is expressed in units called wavenumbers (
) Wavenumbers are expressed in units of
reciprocal centimeters (cm-1) i.e. the reciprocal
of the wavelength (?) expressed in centimeters.
(cm-1) 1 / ?
(cm)
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• Molecular Vibrations
• Absorption of infrared radiation corresponds to
  energy changes on the order of 8-40 KJ/mole (2-10
  Kcal/mole
• The frequencies in this energy range correspond
  to the stretching and bending frequencies of the
  covalent bonds with dipole moments.
• Stretching (requires more energy than bending)
• Symmetrical
• Asymmetrical
• Bending
• Scissoring (in-plane bending)
• Rocking (in-plane bending)
• Wagging (out-of-plane bending)
• Twisting (out of plane bending)

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• No two molecules of different structure will have
  exactly the same natural frequency of vibration,
  each will have a unique infrared absorption
  pattern or spectrum.
• Two Uses
• IR can be used to distinguish one compound from
  another.
• Absorption of IR energy by organic compounds will
  occur in a manner characteristic of the types of
  bonds and atoms in the functional groups present
  in the compound thus, infrared spectrum gives
  structural information about a molecule.
• The absorptions of each type of bond (NH, CH,
  OH, CX, CO, CO, CC, CC, CC, CN, etc.) are
  regularly found only in certain small portions of
  the vibrational infrared region, greatly
  enhancing analysis possibilities.

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The Infrared Spectrum A plot of absorption
intensity ( Transmittance) on the y-axis vs.
frequency (wavenumbers) on the x-axis.
Methyl IsopropylKetone
Aliphatic C-H Stretch
CH3
CO Carbonyl
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Principal Frequency Bands (from left to right in
spectrum) OH 3600 cm-1 (Acids - Very Broad,
Alcohols - Broad) NH 3300-3500 cm-1 (2, 1, 0
peaks 1o, 2o, 3o) CN 2250 cm-1 (Nitrile) CC 21
50 cm-1 (Acetylene) CO 1685-1725
cm-1 (Carbonyl) CC 1650 cm-1 (Alkene) CC 1450-16
00 (Aromatic - 4 absorptions) CH2 1450
cm-1 (Methylene) CH3 1375 cm-1 (Methyl) CO 900-11
00 cm-1 (Alcohol, Acid, Ester, Ether,
Anhydride) CH Sat Alkanes Right side of 3000
cm-1 CH Unsat Alkenes Left side of 3000 cm-1,
1650 cm-1 CH Aromatic Verify at 16672000
cm-1, 1450-1600-1
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Analyzing the Spectrum A Suggested Approach

• Step 1. Check for the presence of the Carbonyl
  group (CO) at 1715 cm-1. If molecule is
  conjugated, the strong (CO) absorption will be
  shifted to the right by 30 cm-1, i.e.
  1685 cm-1
• If the Carbonyl absorption is present, check for
• Carboxylic Acids - Check for OH group (broad
  absorption near 3300-2500 cm-1)
• Amides - Check for NH group (1 or 2
  absorptions near 3500 cm-1)
• Esters - Check for 2 C-O group (medium
  absorptions near 1300-1000 cm-1)
• Anhydrides - Check for 2 CO absorptions near
  1810 and 1760 cm-1
• Aldehydes - Check for Aldehyde CH group (2 weak
  absorptions near 2850 and 2750 cm-1)
• Ketones - Ketones (The above groups have been
  eliminated)

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• Step 2. - If the Carbonyl Group is Absent Check
  for Alcohols, Amines, or
  Ethers.
• Alcohols Phenols - Check for OH group (Broad
  absorption near 3600 - 3300 cm-1 Confirm
  present of CO near 1300 - 1000 cm-1
• Amines - Check for NH stretch (Medium
  absorptions) near 3500 cm-1
• Primary Amine - 2 Peaks
• Secondary Amine - 1 Peak
• Tertiary Amine - No peaks
• N-H Scissoring at 1560 - 1640 cm-1
• N-H Bend at 800 cm-1
• Ethers - Check for CO absorption near 1300 -
  1000 cm-1 and absence of OH
• Esters Unbalanced Ethers will show 2 CO
  groups

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• Step 3. Refine the Structure Possibilities by
  Looking for Double Bonds,
  Triple Bonds and Nitro Groups
• Double Bonds - Unsaturated CC (and CC) stretch
  show absorptions on the left side of 3000 cm-1
• Alkene CC weak absorption near 1650 cm-1
• Aromatic CC (4 absorptions 1450-1600 cm-1)
• (Verify Aromatic at 1667 2000 cm-1)
• Triple Bonds C N Nitrile - medium, sharp
  absorption (stretch near 2250 cm-1) R
  C C R Alkyne - weak, sharp absorption
  (stretch) near 2150 cm-1 R C C H
  Terminal Acetylene
  (stretch at 3300 cm-1)
• Nitro Groups - Two strong absorptions 1600 1500
  cm-1 and 1390 - 1300 cm-1

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• Step 3 (Cont)
• Aromatic Ring Absorptions
• If the absorptions on the left side of 3000 cm-1
  are due to the presence of aromatic (benzene
  ring) CC bonds, the aromaticity and subsequent
  ring substitution patterns can be verified and
  further elucidated in three other regions
• The presence of 1-4 weak absorptions in the
  Overtone region (1667 2000 cm-1)
• The presence of 1-3 strong absorptions in the
  out-of-plane (OOP) region (900 - 690 cm-1)
• Four medium to strong absorptions in region 1650
  - 1450 cm-1
• The relative shapes and numbers of the Overtone
  and OOP absorptions can be used to tell whether
  the aromatic ring is monosubstituted or di-,
  tri-, tetra-, penta-, or hexa-substituted.
• In addition, the ortho-, meta-, para-
  substitutions can also be distinguished for the
  di-substituted isomers.

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• Step 3 (Cont)
• Aromatic Ring Absorptions (Cont)
• The unsaturated C-H Out-of-Plane (OOP) bending
  absorptions in the region 900 690 cm-1 can also
  be used to determine the type of ring
  substitution.
• The number of absorptions and their relative
  positions are unique to each type of
  substitution.
• Although these absorptions are in the
  Fingerprint region they are particularly
  reliable for rings with Alkyl group
  substitutions.
• They are less reliable for Polar substituents.

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Step 4. If none of the above apply then the
compound is most likely a Hydrocarbon.Generally,
a very simple spectrum Hydrocarbons - Check for
saturated Alkane absorptions near right side of
3000 cm-1
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IR Analysis Scheme
Carbonyl (CO) _at_ 1715-1685 (Conjugation moves
absorption to right 30 cm-1
Yes
No
Acid Ester Amide Anhydride Aldehyde Ketone
Alcohol Amine Ether
Saturation lt 3000 cm-1
Unsaturation gt 3000 cm-1
Alkanes -C-H Methylene -CH2 Methyl -CH3
Alkenes (Vinyl) -CC Aromatic -CC
Nitriles
Nitro
Hydrocarbons
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Carbonyl (CO) is Present Acid - Broad OH
Absorption _at_ 3300-2500 cm-1 Ester - C-O
Absorption _at_ 1300-1000 cm-1 Amide - NH Absorption
_at_ 3500 cm-1 (1 or 2 peaks) Anhydride - 2 CO
Absorptions 1810 1760 cm-1 Aldehyde - Aldehyde
C-H Absorptions _at_ 2850 2750 cm-1 Ketone - None
of the above except CO
Carbonyl is Absent Alcohol - Broad OH absorption
_at_ 3300 - 3000 cm-1 Also C-O
absorption _at_ 1300 - 1000 cm-1 Amine - 1 to 2
equal NH absorptions _at_ 3500 cm-1 Ether - C-O
absorption _at_ 1300 - 1000 cm-1
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Saturation
Alkanes -C-H Stretch several absorptions to
right of 3000 cm-1 Methylene -CH2 1450
cm-1 Methyl -CH3 1375 cm-1
Unsaturation
Double Bonds C-H Stretch several absorptions
to left of 3000 cm-1 OOP bending at 1000
650 cm-1 Alkenes (Vinyl) -CC- Stretch (weak) _at_
1675 1600 cm-1
Conjugation moves absorption to
the right Alkynes CC-H Terminal Acetylene
Stretch at 3300 cm-1 Alkynes (Acetylenes) -CC Str
etch _at_ 2150 cm-1
Conjugation moves absorption to the
right Aromatic C-H Stretch absorptions also to
left of 3000 cm-1 OOP bending at 900 690
cm-1 OOP absorption patterns allow
determination of ring substitution (p.
902 Pavia text) -CC 4 Sharp absorptions (2
pairs) _at_ 1600 1450 cm-1 Overtone absorptions
_at_ 2000 1667 cm-1 Relative shapes and numbers
of peaks permit determination of ring
substitution pattern (p. 902 Pavia text).