Molecular Spectroscopy Identification of Molecular Structure

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Molecular SpectroscopyIdentification of
Molecular Structure

• X-ray diffraction
• -stereostructure of molecules (DNA)
• UV/VIS (???/???)
• -electronic structure of molecules
• Infrared spectroscopy (????)
• -molecular vibration
• NMR or MRI (????/????)
• -nuclear spin
• Mass spectroscopy (???)
• -molecular mass

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Internal Energy of Molecules

• EtotalEtransEelecEvibErotEnucl
• Eelec electronic transitions (UV, X-ray)
• Evib vibrational transitions (Infrared)
• Erot rotational transitions (Microwave)
• Enucl nucleus spin (nuclear magnetic
• resonance) or (MRI magnetic resonance
• imaging)

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The molecular orbital diagram for the ground
state of NO
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The molecular structure of beta-carotene
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The electronic absorption spectrum of
beta-carotene.
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• Ultraviolet 190400nm
• Violet   400 - 420 nm
• Indigo   420 - 440 nm
• Blue   440 - 490 nm
• Green   490 - 570 nm
• Yellow   570 - 585 nm
• Orange   585 - 620 nm
• Red   620 - 780 nm

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Electronic Spectroscopy

• Ultraviolet (UV) and visible (VIS) spectroscopy
• This is the earliest method of molecular
  spectroscopy.
• A phenomenon of interaction of molecules with
  ultraviolet and visible lights.
• Absorption of photon results in electronic
  transition of a molecule, and electrons are
  promoted from ground state to higher electronic
  states.

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UV and Visible Spectroscopy

• In structure determination UV-VIS spectroscopy
  is used to detect the presence of chromophores
  like dienes, aromatics, polyenes, and conjugated
  ketones, etc.

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Electronic transitions

• There are three types of electronic transition
• which can be considered
• Transitions involving p, s, and n electrons
• Transitions involving charge-transfer electrons
• Transitions involving d and f electrons

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Absorbing species containing p, s, and n electrons

• Absorption of ultraviolet and visible radiation
  in organic molecules is restricted to certain
  functional groups (chromophores) that contain
  valence electrons of low excitation energy.

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Vacuum UV or Far UV (?lt190 nm )
UV/VIS
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s s Transitions

• An electron in a bonding s orbital is excited to
  the corresponding antibonding orbital. The energy
  required is large. For example, methane (which
  has only C-H bonds, and can only undergo s s
  transitions) shows an absorbance maximum at 125
  nm. Absorption maxima due to s s transitions
  are not seen in typical UV-VIS spectra (200 - 700
  nm)

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n s Transitions

• Saturated compounds containing atoms with lone
  pairs (non-bonding electrons) are capable of n
  s transitions. These transitions usually need
  less energy than s s transitions. They can be
  initiated by light whose wavelength is in the
  range 150 - 250 nm. The number of organic
  functional groups with n s peaks in the UV
  region is small.

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n p and p p Transitions

• Most absorption spectroscopy of organic compounds
  is based on transitions of n or p electrons to
  the p excited state.
• These transitions fall in an experimentally
  convenient region of the spectrum (200 - 700 nm).
  These transitions need an unsaturated group in
  the molecule to provide the p electrons.

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Chromophore Excitation lmax, nm Solvent
CC p?p 171 hexane
CO n?pp?p 290180 hexanehexane
NO n?pp?p 275200 ethanolethanol
C-X   XBr, I n?sn?s 205255 hexanehexane
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Orbital Spin States

• Singlet state (S)Most molecules have ground
  state with all electron spin paired and most
  excited state also have electron spin all paired,
  even though they may be one electron each lying
  in two different orbital. Such states have zero
  total spin and spin multiplicities of 1, are
  called singlet (S) states.

Total Spin
Multiplicities
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Orbital Spin States

• For some of the excited states, there are states
  with a pair of electrons having their spins
  parallel (in two orbitals), leading to total spin
  of 1 and multiplicities of 3.

Total Spin
Multiplicities
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Orbital Spin States

• For triplet state Under the influence of
  external field, there are three values (i.e. 3
  energy states) of 1, 0, -1 times the angular
  momentum. Such states are called triplet states
  (T).
• According to the selection rule, S?S, T?T, are
  allowed transitions, but S?T, T?S, are forbidden
  transitions.

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Selection Rules of electronic transition

• Electronic transitions may be classed as intense
  or weak according to the magnitude of emax that
  corresponds to allowed or forbidden transition as
  governed by the following selection rules of
  electronic transition
• Spin selection rule there should be no change in
  spin orientation or no spin inversion during
  these transitions. Thus, S?S, T?T, are allowed,
  but S?T, T?S, are forbidden. (?S0 transition
  allowed)

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p?p
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Instrumentation
?? ??? ?? ??? ???
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Components of a SpectrophotometerLight Source

• Deuterium Lamps-a truly continuous spectrum in
  the ultraviolet region is produced by electrical
  excitation of deuterium at low pressure.
  (160nm375nm)
• Tungsten Filament Lamps-the most common source of
  visible and near infrared radiation.

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Components of a SpectrophotometerMonochromator
(???/???)

• Used as a filter the monochromator will select a
  narrow portion of the spectrum (the bandpass) of
  a given source
• Used in analysis the monochromator will
  sequentially select for the detector to record
  the different components (spectrum) of any source
  or sample emitting light.

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MonochromatorCzerny-Turner design
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Grating
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Photomultiplier Detector
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Principle of Photomultiplier Detector

• The type is commonly used.
• The detector consists of a photoemissive cathode
  coupled with a series of electron-multiplying
  dynode stages, and usually called a
  photomultiplier.
• The primary electrons ejected from the
  photo-cathode are accelerated by an electric
  field so as to strike a small area on the first
  dynode.

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Principle of Photomultiplier Detector

• The impinging electrons strike with enough energy
  to eject two to five secondary electrons, which
  are accelerated to the second dynode to eject
  still more electrons.
• A photomultiplier may have 9 to 16 stages, and
  overall gain of 106109 electrons per incident
  photon.

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Single and Double Beam Spectrometer

• Single-Beam There is only one light beam or
  optical path from the source through to the
  detector.
• Double-Beam The light from the source, after
  passing through the monochromator, is split into
  two separate beams-one for the sample and the
  other for the reference.

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Quantitative AnalysisBeers Law

• Aebc
• e the molar absorptivity (L mol-1 cm-1)
• b the path length of the sample
• c the concentration of the compound in solution,
  expressed in mol L-1

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Transmittance
I0
I
b
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External Standard and the Calibration Curve
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Vibrational Spectroscopy
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The potential curve for a diatomic molecule
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Morse energy curve for a diatomic molecule.
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IR spectrum
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Selection Rule of Infrared Spectrum

• There must be a change in the dipole moment
  during a vibrational cycle.
• Homonuclear diatomic molecules will have no IR
  spectrum.

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Molecules with permanent dipole moments (µ) are
IR active
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Types of Molecular VibrationsStretch-change in
bond length

• symmetric stretching

• asymmetric stretching

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Types of Molecular Vibrations Bend-change in
bond angle
scissoring
wagging
rocking
twisting/torsion
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Normal Modes of Vibration

• Linear molecule of N atoms normal modes 3N -
  5  
• Nonlinear molecule of N atoms normal modes 3N
  - 6

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Only some modes may be IR active
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The three fundamental vibrations for sulfur
dioxide
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How many vibrational modes?

• 2 atoms (H2) - 1 vibration
• 3 atoms (H2O) - 3 vibrations
• 3 atoms (CO2) - 4 vibrations
• 4 atoms (H2CO) - 6 vibrations

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Rotational Spectroscopy
Selection Rule A molecule must have a permanent
dipole moment
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Vibrational-Rotational Spectrum
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Calculate Bond Length of Heteronuclear Diatomic
Molecule
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Nuclear Magnetic Resonance Spectroscopy

• The rules for determining the net spin of a
  nucleus
• 1. If the number of neutrons and the number of
  protons are both even, then the nucleus has NO
  spin.
• 2. If the number of neutrons plus the number of
  protons is odd, then the nucleus has a
  half-integer spin (i.e. 1/2, 3/2, 5/2)
• 3. If the number of neutrons and the number of
  protons are both odd, then the nucleus has an
  integer spin (i.e. 1, 2, 3)

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Nuclei Unpaired Protons Unpaired Neutrons Net Spin
1H 1 0 1/2
2H 1 1 1
31P 1 0 1/2
23Na 1 2 3/2
14N 1 1 1
13C 0 1 1/2
19F 1 0 1/2

• A nucleus of spin I will have 2I 1 possible
  orientations.

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Larmor Precession
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• In the absence of an external magnetic field,
  these orientations are of equal energy.
• If a magnetic field is applied, then the energy
  levels split. Each level is given a magnetic
  quantum number, m.

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Nucleus in a Magnetic Field

• The lower energy level will contain slightly more
  nuclei than the higher level.
• It is possible to excite these nuclei into the
  higher level with electromagnetic radiation.
• The frequency of radiation needed is determined
  by the difference in energy between the energy
  levels.

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Calculating transition energy
g magnetogyric ratio and is a fundamental
nuclear constant which has a different value for
every nucleus. B the strength of the magnetic
field at the nucleus ?E?B?
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The Absorption of Radiation by a Nucleus in a
Magnetic Field

• If energy is absorbed by the nucleus, then the
  angle of precession, q, will change.
• For a nucleus of spin 1/2
• , absorption of radiation "flips" the
  magnetic moment so that it opposes the applied
  field.

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Chemical Shift

• The magnetic field at the nucleus is not equal to
  the applied magnetic field electrons around the
  nucleus shield it from the applied field.
• The difference between the applied magnetic field
  and the field at the nucleus is termed the
  nuclear shielding.

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Electrons in s-orbitals

• Spherical symmetry and circulate in the applied
  field
• A magnetic field which opposes the applied field.
  
• Applied field strength must be increased for the
  nucleus to absorb at its transition frequency.
• This upfield shift is also termed diamagnetic
  shift.

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Electrons in p-orbitals

• No spherical symmetry.
• They produce comparatively large magnetic fields
  at the nucleus, which give a low field shift.
• This "deshielding" is termed paramagnetic shift.

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Proton Chemical Shift Ranges
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Spin - Spin coupling

• The protons on neighboring carbons will generate
  magnetic fields whose magnetic moments will
  interact with the magnetic moment of the external
  magnetic field.
• This results in the splitting of the NMR signal.

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NMR of Ethanol
-CH3
-CH2-
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Methyl peak splitting into a triplet
the ratio of areas 121
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Methylene peak splitting into a quartet
the ratio of areas 1331
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The molecular structure of bromoethane
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The NMR spectrum of CH3CH2Br (bromoethane) with
TMS reference
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The molecule (2-butanone)
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(C)
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(B)
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(D)
(A)
(B)
(C)
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(C)
(B)
(A)
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A technician speaks to a patient before heis
moved intot eh cavity of a magnetic resonance
imaging (MRI).
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A colored Magnetic Resonance Imaging (MRI) scan
through a human head, showing a healthy brain in
side view.