1. Absorption Spectroscopy of Biopolymers Overview

4. Visible & near-UV regionwavelength (nm) Microwave & radiowave regionfrequency (Hz) Infared regionwavenumber (cm -1 ) Far-UV, x-ray,  -rayenergy (  =h )

5. Absorption & Emission Rapid process(10 -15 s)

6. Absorption & Emission

7. Radiation-Induced Transition Absorption Stimulated emission Spontaneous emission

8. UV-Visible Spectroscopy Ultraviolet-visible spectroscopy involves the absorption of ultraviolet/visible light by a molecule causing the promotion of an electron from a ground electronic state to an excited electronic state. Ultraviolet/Visible light: wavelengths ( ) between 190 and 800 nm

9. UV-visible spectrum The two main properties of an absorbance peak are: 1.Absorption wavelength max 2.Absorption intensity A max Housecroft and Sharpe, p. 466

10. Beer-Lambert Law Beer-Lambert Law : log(I 0 /I) =  bc  = A/c b A =  bc A =  c (when b is 1 cm) I 0 = intensity of incident light I = intensity of transmitted light  = molar absoptivity coefficient in cm 2 mol -1 c = concentration in mol L -1 b = pathlength of absorbing solution in cm -1 A = absorbance = log(I o /I) 0.1 cm ℓ http://www.hellma-worldwide.de/en/default.asp

11. Beer-Lambert Law AAbsorbance or optical density (OD)  absorptivity; M -1 cm -1 cconcentration; M Ttransmittance

12. Transmittance, Absorbance, and Cell Pathlength http://www.shu.ac.uk/schools/sci/chem/tutorials/molspec/beers1.htm

13. Deviations from the Beer-Lambert Law The Beer-Lambert law assumes that all molecules contribute to the absorption and that no absorbing molecule is in the shadow of another Low c High c http://www.shu.ac.uk/schools/sci/chem/tutorials/molspec/beers1.htm

14. Sample Concentrations Solution too concentrated Diluted five-fold

15. UV-visible spectrum of 4-nitroanaline Solvent: Ethanol Concentration: 15.4 mg L -1 Pathlength: 1 cm Molecular mass = 138 Harwood and Claridge, p. 18

16. UV-visible spectrum of 4-nitroanaline 1.Determine the absorption maxima ( max ) and absorption intensities (A) from the spectrum: max = 227 nm, A 227 = 1.55 max = 375 nm, A 375 = 1.75 2. Calculate the concentration of the compound: (1.54 x 10 -2 g L -1 )/(138 g/mol) = 1.12 x 10 -4 mol L -1 3.Determine the molar absorptivity coefficients (  ) from the Beer- Lambert Law:  = A/c ℓ  227 = 1.55/(1.0 cm x 1.12 x 10 -4 mol L -1 ) = 13,900 mol -1 L cm -1  375 = 1.75/(1.0 cm x 1.12 x 10 -4 mol L -1 ) = 15,700 mol -1 L cm -1

17. Molar absorptivities (  ) Molar absoptivities are very large for strongly absorbing chromophores (  >10,000) and very small if the absorption is weak (  = 10 to 100). The magnitude of  reflects both the size of the chromophore and the probability that light of a given wavelength will be absorbed when it strikes the chromophore. A general equation stating this relationship may be written as follows:  = 0.87 x 10 20 P x a where P is the transition probability (0 to 1) a is the chromophore area in cm 2 The transition probability depends on a number of factors including where the transition is an “allowed” transition or a “forbidden” transition http://www.cem.msu.edu/~reusch/VirtualText/Spectrpy/UV-Vis/uvspec.htm#uv2

18. UV-visible spectrum of 4-nitroanaline Solvent: Ethanol Concentration: 15.4 mg L -1 Pathlength: 1 cm Molecular mass = 138 Harwood and Claridge, p. 18

19. UV-visible spectrum of 4-nitroanaline 1.Determine the absorption maxima ( max ) and absorption intensities (A) from the spectrum: max = 227 nm, A 227 = 1.55 max = 375 nm, A 375 = 1.75 2. Calculate the concentration of the compound: (1.54 x 10 -2 g L -1 )/(138 g/mol) = 1.12 x 10 -4 mol L -1 3.Determine the molar absorptivity coefficients (  ) from the Beer- Lambert Law:  = A/c ℓ  227 = 1.55/(1.0 cm x 1.12 x 10 -4 mol L -1 ) = 13,900 mol -1 L cm -1  375 = 1.75/(1.0 cm x 1.12 x 10 -4 mol L -1 ) = 15,700 mol -1 L cm -1

20. UV-visible spectroscopy definitions chromophore Any group of atoms that absorbs light whether or not a color is thereby produced. auxochrome A group which extends the conjugation of a chromophore by sharing of nonbonding electrons. bathochromic shift The shift of absorption to a longer wavelength. hypsochromic shift The shift of absorption to a shorter wavelength. hyperchromic effect An increase in absorption intensity. hypochromic effect A decrease in absorption intensity.

21. Absorption and Emission of Photons http://micro.magnet.fsu.edu/optics/lightandcolor/frequency.html

22. Absorption and Emission Emission AbsorptionAbsorption: A transition from a lower level to a higher level with transfer of energy from the radiation field to an absorber, atom, molecule, or solid. EmissionEmission: A transition from a higher level to a lower level with transfer of energy from the emitter to the radiation field. If no radiation is emitted, the transition from higher to lower energy levels is called nonradiative decay. Absorption http://www.chemistry.vt.edu/chem-ed/spec/spectros.html

23. Singlet and Triplet Excited States http://www.shu.ac.uk/schools/sci/chem/tutorials/molspec/lumin1.htm

24. Absorption and emission pathways McGarvey and Gaillard, Basic Photochemistry at http://classes.kumc.edu/grants/dpc/instruct/index2.htm http://classes.kumc.edu/grants/dpc/instruct/index2.htm

25. Selection Rules In electronic spectroscopy there are three selection rules which determine whether or not transitions are formally allowed: 1.Spin selection rule:  S = 0 allowed transitions: singlet  singlet or triplet  triplet forbidden transitions: singlet  triplet or triplet  singlet Changes in spin multiplicity are forbidden http://www.shu.ac.uk/schools/sci/chem/tutorials/molspec/lumin1.htm

26. Selection rules 2. Laporte selection rule: there must be a change in the parity (symmetry) of the complex Laporte-allowed transitions: g  u Laporte-forbidden transitions: g  g or u  u g stands for gerade – compound with a center of symmetry u stands for ungerade – compound without a center of symmetry 3. Selection rule of  ℓ = ± 1 (ℓ is the azimuthal or orbital quantum number, where ℓ = 0 (s orbital), 1 (p orbital), 2 (d orbital), etc.) allowed transitions: s  p, p  d, d  f, etc. forbidden transitions: s  s, d  d, p  f, etc.

28.  and  * orbitals http://www.cem.msu.edu/~reusch/VirtualText/intro3.htm#strc8a

29.  and  * orbitals http://www.cem.msu.edu/~reusch/VirtualText/intro3.htm#strc8a

30. Electronic Transitions:    * McGarvey and Gaillard, Basic Photochemistry at http://classes.kumc.edu/grants/dpc/instruct/index2.htm http://classes.kumc.edu/grants/dpc/instruct/index2.htm The    * transition involves orbitals that have significant overlap, and the probability is near 1.0 as they are “symmetry allowed”. http://www.cem.msu.edu/~reusch/VirtualText /Spectrpy/UV-Vis/uvspec.htm#uv2

31.  * transitions - Triple bonds Organic compounds with -C≡C- or -C≡N groups, or transition metals complexed by C≡N - or C≡O ligands, usually have “low- lying”  * orbitals http://www.cem.msu.edu/~reusch/VirtualText/intro3.htm#strc8a

32. Electronic Transitions: n   * McGarvey and Gaillard, Basic Photochemistry at http://classes.kumc.edu/grants/dpc/instruct/index2.htm http://classes.kumc.edu/grants/dpc/instruct/index2.htm The n-orbitals do not overlap at all well with the  * orbital, so the probability of this excitation is small. The  of the n  * transition is about 10 3 times smaller than  for the  * transition as it is “symmetry forbidden”. http://www.cem.msu.edu/~reusch/VirtualText /Spectrpy/UV-Vis/uvspec.htm#uv2

34. Lycopene from Tomatoes http:// www.purdue.edu/UNS/html4ever/020617.Handa.lycopene.html

35. Chlorophyll B-carotene hemoglobin

36. Quantitative Analysis A plot of absorption versus wavelength is the absorption spectrum

37. Solutions containing the amino acids tryptophan and tyrosine can be analyzed under alkaline conditions (0.1 M KOH) from their different uv spectra. The extinction coefficients under these conditions at 240 nm and 280 nm are A 10-mg smaple of the protein glucagon is hydrolyzed to its constituent amino acids and diluter to 100 mL in 0.1 M KOH. The absorbance of this solution (1 cm path) was 0.717 at 240 nm and 0.239 at 280 nm. Estimate the content of tryptophan and tyrosine in mol (g protein) -1

38. Isosbestic points Isosbestic wavelength the wavelength at which two or more components have the same extinction coefficient The occurrence of two or more isosbestics in the spectra of a series of solutions of the same total concentration demonstrates the presence of two and only two components absorbing in that spectra region.

39. Isosbestic points

40. UV spectrum of BSA UV spectrum of DNA from E. coli

41. UV Absorption of amino acid

42. Effect of Secondary structure

43. Origin of Spectroscopic Changes 1.Change in local charge distribution 2.Change in dielectric constant 3.Change in bonding interaction 4.Change in dynamic coupling between different parts of the molecule

49. Human EyeRetina Retina Outer segment Light sensitive protein http://www2.mrc-lmb.cam.ac.uk/groups/GS/eye.html

50. Rhodopsin is a protein in the membrane of the photoreceptor cell in the retina of the eye. It catalyses the only light sensitive step in vision. The 11-cis-retinal chromophore lies in a pocket of the protein and is isomerised to all- trans retinal when light is absorbed. The isomerisation of retinal leads to a change of the shape of rhodopsin which triggers a cascade of reactions which lead to a nerve impulse which is transmitted to the brain by the optical nerve http://www2.mrc-lmb.cam.ac.uk/groups/GS/rmovie.html 1BRD

51. 1BM1