Biopolymer Spectroscopy

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Biopolymer Spectroscopy

• Introduction to Spectroscopy I
• Vibrational Rotational Spectroscopy

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Figure 19.1
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Table 19.1
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Infrared region of the electromagnetic spectrum
Gunzler and Gremlich, IR Spectroscopy, p. 1
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Infrared Regions
The infrared region may be divided into three
sections near-, mid- and far-infrared
Region Wavelength range Wavenumber range
(mm)
(cm-1)
Near 0.78 - 2.5
12800 - 4000
Middle 2.5 - 50 4000 - 200
Far 50 -1000 200 -
10 The most useful IR region lies between 4000
670 cm-1.
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Figure 19.4

Spontaneous emission is a completely random
process, the emitted photons are incoherent
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In simple diatomic molecules, such as BrCl or CO,
there is a certain distance between the atoms at
which the attractive bonding forces and repulsive
interactions between electrons balance each
other. This distance is referred to as the
equilibrium bond distance, req, and it can be
changed by applying energy
n is the frequency of vibration k is the force
constant of the bond (the resistance of the bond
to vibration and a measure of its strength)
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Vibrational frequencies
Reduced mass (m) (m1 x m2)/(m1 m2)
The frequency of the vibrational transition is
dependent on the nature of the atoms (reduced
mass) and the strength (force constant) of the
bonds between them.
http//www.cem.msu.edu/reusch/VirtualText/Spectrp
y/InfraRed/infrared.htmir3
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Molecular vibrations
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Morse potential, V(x) (red curve), as a function
of the bond length, x, for HCl The zero of energy
is chosen to be the bottom of the potential. The
yellow curve shows a harmonic potential, which is
a good approximation to the Morse potential near
the bottom of the well. The horizontal lines
indicate allowed energy levels in the Morse
potential. De and Do represent the bond energies
defined with respect to the bottom of the
potential and the lowest state, respectively,and
xe is the equilibrium bond length.
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Harmonic/Anharmonic energy levels
The total vibrational energy of a molecule is
quantized, such that the vibrational quantum
number, n, can take on values V 0, 1, 2, 3,
4, ... Vibrational selection rule D V 1 (0
? 1) For a harmonic oscillator, the energy
(Joules) of a particular energy level is given
by Evib h(V ½)nvib For an anharmonic
oscillator, the expression is Evib h(V
½)nvib (V ½)Xcnvib where Xc is an
anharmonicity constant
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Harmonic/Anharmonic energy levels
Selection rule
Hendra, Jones Warnes, Fourier Transform Raman
Spectroscopy, p. 21
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Energy difference between any pairs of adjacent
levels
The frequency of radiation n that can bring about
this change is
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Rotational Selection Rules
Rotational Selection Rules Dipole Moment Change
is parallel to principal rotational axis of
symmetry DJ 1 (no Q fine structure) Dipole
Moment Change is perpendicular to principal
rotational axis of symmetry DJ 1 (Q fine
structure)
Brisdon, p. 23
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Vibrational energy levels rotational energy
levels
DJ 1 (R) DJ -1 (P)
http//www.chemistry.nmsu.edu/studntres/chem435/La
b9/intro.html
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P, Q, and R Branches (NO gas)
http//faculty.augie.edu/kjbetsch/exp5.html
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IR Spectrum
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Baseline
Background absorption
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Absorption maximum
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Shoulder two non-separable bands
Disturbances by absorption of CO2 and H2O in the
air
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Gunzler and Gremlich, IR Spectroscopy, p. 1
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Vibrational excitations

• The main types of bond excitation are stretching
  (nXY) and bending (dYXY) and often the absorption
  of certain wavelengths of infrared radiation may
  be correlated with the stretching or bending of
  certain types of bonds within a molecule.
• Infrared spectra of compounds are complicated by
  bond oscillations in the whole molecule, giving
  rise to overtone and harmonic absorptions.

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Stretching and Bending Vibrations
http//www.shu.ac.uk/schools/sci/chem/tutorials/mo
lspec/irspec1.htm
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Infrared Active and Inactive Modes
For a vibration mode to be infrared (IR) active,
it must be accompanied by a change in the
molecular electric dipole moment
eg. linear CO2
No change in dipole moment Change in
dipole moment
Housecroft and Sharpe, p. 84
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Infrared active stretches and bend
Symmetric stretch
Asymmetric stretch
Bend
http//sis.bris.ac.uk/sd9319/spec/IR.htm
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Active, inactive, and weakly active -CC-
stretches
CH3-CC-H infrared active, significant
dipole moment CH3-CC-CH3 infrared
inactive, no dipole moment CH3-CC-CH2CH3 we
akly infrared active, small dipole moment
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Vibrational Degrees of Freedom
A molecule containing n atoms has 3n degrees of
freedom, which describe the translational,
rotational, and vibrational motions of the
molecule translational 3 degrees of freedom
(x, y, and z Cartesian axes) rotational a
non-linear molecule has 3 degrees of
rotational freedom, while a linear
molecule has 2 degrees of freedom vibrational a
non-linear molecule has 3n - 6
degrees of vibrational freedom, while
a linear molecule has 3n - 5 degrees
of freedom
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Vibrational modes for linear CO2
Linear CO2 number of modes 3(3) 5 4
Housecroft and Sharpe, p. 84
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Infrared Spectrum of CO2 gas
dOCO
nCO
http//chemistry.beloit.edu/Warming/moviepages/gre
enIR.htm
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Vibrational modes for bent SO2
Bent SO2 - number of modes 3(3) 6 3
Housecroft and Sharpe, p. 84
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Infrared Spectrum of H2O
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Infrared Spectrum of H2O vapour
http//chemistry.beloit.edu/Warming/moviepages/gre
enIR.htm
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IR absorbance for common functional groups
http//www.askthenerd.com/ocol/SPEC/IR/F1.HTM
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The infrared spectrum of benzyl alcohol displays
a broad, hydrogen-bonded -OH stretching band in
the region 3400 cm-1, a sharp unsaturated (sp2)
CH stretch at about 3010 cm-1 and a saturated
(sp3) CH stretch at about 2900 cm-1 these bands
are typical for alcohols and for aromatic
compounds containing some saturated carbon.
Acetylene (ethyne) displays a typical terminal
alkyne C-H stretch, as shown in the second panel.
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Saturated and unsaturated CH bands also are shown
clearly in the spectrum of vinyl acetate (ethenyl
ethanoate). This compound also shows a typical
ester carbonyl at 1700 cm-1 and a nice example
of a carbon-carbon double bond stretch at about
1500 cm-1. Both of these bands are shifted to
slightly lower wave numbers than are typically
observed (by about 50 cm-1) by conjugation
involving the vinyl ester group.
http//www.askthenerd.com/ocol/SPEC/IR/F1.HTM
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Amide vibrations

• The peptide group, the structural repeat unit of
  proteins, gives up to 9 characteristic bands
  named amide A, B, I, II ... VII.
• The amide A band (about 3500 cm-1) and amide B
  (about 3100 cm-1) originate from a Fermi
  resonance between the first overtone of amide II
  and and the N-H stretching vibration.
• Amide I and amide II bands are two major bands of
  the protein infrared spectrum.
• The amide I band (between 1600 and 1700 cm-1) is
  mainly associated with the CO stretching
  vibration(70-85)and is directly related to the
  backbone conformation.
• Amide II results from the N-H bending vibration
  (40-60) and from the C-N stretching vibration
  (18-40). This band is conformational sensitive.
• Amide III and IV are very complex bands resulting
  from a mixture of several coordinated is
  placements. The out-of-plane motions are found in
  amide V, VI and VIII.

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Amide A is with more than 95 due to the the N-H
stretching vibration. This mode of vibration is
not depend on the backbone conformation but is
very sensitive to the strength of a hydrogen bond
(between 3225 and 3280 cm-1 for hydrogen bond
length from 2.69 to 2.85 angstrom, (Krimm
Bandekar Adv Protein Chem 198638181-364).
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Amide I is the most intense absorption band in
proteins. It is primilary goverend by the
stretching vibration of the CO (70-85) and C-N
groups (10-20). Its frequency is found in the
range between 1600 and 1700 cm-1. The exact band
position is determined by the backbone
conformation and the hydrogen bonding pattern.
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Amide II is found in the 1510 and 1580 cm-1
region and it is more complex than amide I. Amide
II derives mainly from in-plane N-H bending
(40-60 of the potential energy). The rest of the
potential energy arises from the C-N (18-40) and
the C-C (about 10) stretching vibrations.
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frequency, absorbance at the maximum (Ao), full
width at half height (FWHH), surface of Gaussian
band ststretching vibration bdbending
ssymetrical asasymetrical