1. Biopolymer Spectroscopy
Introduction to Spectroscopy I
Vibrational & Rotational Spectroscopy

2. Figure 19.1

3. Table 19.1

4. Infrared region of the electromagnetic spectrum
Gunzler and Gremlich, IR Spectroscopy, p. 1

5. 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
Middle
Far
The most useful IR region lies between 4000 – 670 cm-1.

6. Figure 19.4
Spontaneous emission is a completely random process, the emitted photons are incoherent

7. 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)

8. 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.

9. Molecular vibrations

10. 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.

11. 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

13. Harmonic/Anharmonic energy levels
Selection rule
Hendra, Jones & Warnes, Fourier Transform Raman Spectroscopy, p. 21

14. Energy difference between any pairs of adjacent levels
The frequency of radiation n that can bring about this change is :

15. 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

16. Vibrational energy levels – rotational energy levels
DJ = +1 (R) DJ = -1 (P)

17. P, Q, and R Branches (NO gas)

19. IR Spectrum 1 Baseline Background absorption 2 Absorption maximum 3
Shoulder; two non-separable bands
Disturbances by absorption of CO2 and H2O in the air 4 5
Gunzler and Gremlich, IR Spectroscopy, p. 1

21. 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.

22. Stretching and Bending Vibrations

23. 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

24. Infrared active stretches and bend
Symmetric stretch
Asymmetric stretch
Bend

25. Active, inactive, and weakly active -C≡C- stretches
CH3-C≡C-H infrared active, significant dipole moment
CH3-C≡C-CH3 infrared inactive, no dipole moment
CH3-C≡C-CH2CH3 weakly infrared active, small dipole moment

26. 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 degrees of vibrational freedom, while a linear molecule has 3n - 5 degrees of freedom

27. Vibrational modes for linear CO2
Linear CO2 – number of modes = 3(3) – 5 = 4
Housecroft and Sharpe, p. 84

28. Infrared Spectrum of CO2 gas
dOCO
nCO

29. Vibrational modes for bent SO2
Bent SO2 - number of modes = 3(3) – 6 = 3
Housecroft and Sharpe, p. 84

30. Infrared Spectrum of H2O

31. Infrared Spectrum of H2O vapour

32. IR absorbance for common functional groups

33. The infrared spectrum of benzyl alcohol displays a broad, hydrogen-bonded -OH stretching band in the region 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.

34. 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 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.

36. 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 C=O 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.

38. Amide A is with more than 95% due to the the N-H stretching vibration
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 1986;38: ).

39. Amide I is the most intense absorption band in proteins
Amide I is the most intense absorption band in proteins. It is primilary goverend by the stretching vibration of the C=O (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.

40. 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.

41. frequency, absorbance at the maximum (Ao), full width at half height (FWHH), surface of Gaussian band st=stretching vibration bd=bending s=symetrical as=asymetrical