# Chemical Sciences: A Manual for CSIR-UGC National Eligibility Test for Lectureship and JRF/Vibrational circular dichroism

Vibrational circular dichroism (VCD) is a spectroscopic technique which detects differences in attenuation of left and right circularly polarized light passing through a sample. It is basically circular dichroism spectroscopy in the infrared and near infrared ranges.
Because VCD is sensitive to the mutual orientation of distinct groups in a molecule, it provides three-dimensional structural information. Thus, it is a powerful technique as VCD spectra of enantiomers can be simulated using ab initio calculations, thereby allowing the identification of absolute configurations of small molecules in solution from VCD spectra. Among such quantum computations of VCD spectra resulting from the chiral properties of small organic molecules are those based on density functional theory (DFT) and gauge-invariant atomic orbitals (GIAO). As a simple example of the experimental results that were obtained by VCD are the spectral data obtained within the carbon-hydrogen (C-H) stretching region of 21 amino acids in heavy water solutions. Measurements of vibrational optical activity (VOA) have thus numerous applications, not only for small molecules, but also for large and complex biopolymers such as muscle proteins (myosin, for example) and DNA.

## Theory of VCD

While the fundamental quantity associated with the infrared absorption is the dipole strength, the differential absorption is proportional also to the rotational strength, a quantity which depends on both the electric and magnetic dipole transition moments. Sensitivity of the handedness of a molecule toward circularly polarized light results from the form of the rotational strength.

## VCD of peptides and proteins

Extensive VCD studies have been reported for both polypeptides and several proteins in solution; several recent reviews were also compiled. An extensive but not comprehensive VCD publications list is also provided in the "References" section. The published reports over the last 22 years have established VCD as a powerful technique with improved results over those previously obtained by visible/UV circular dichroism (CD) or optical rotatory dispersion (ORD) for proteins and nucleic acids.

## VCD of nucleic acids

VCD spectra of nucleotides, synthetic polynucleotides and several nucleic acids, including DNA, have been reported and assigned in terms of the type and number of helices present in A- , B-, and Z- DNA.

## VCD Instrumentation

For biopolymers such as proteins and nucleic acids, the difference in absorbance between the levo- and dextro- configurations is five orders of magnitude smaller than the corresonding (unpolarized) absorbance. Therefore, VCD of biopolymers requires the use of very sensitive, specially built instrumentation as well as time-averaging over relatively long intervals of time even with such sensitive VCD spectrometers. Most CD instruments produce left- and right- circularly polarized light which is then either sine-wave or square-wave modulated, with subsequent phase-sensitive detection and lock-in amplification of the detected signal. In the case of FT-VCD, a photo-elastic modulator (PEM) is employed in conjunction with an FT-IR interferometer set-up. An example is that of a Bomem model MB-100 FT-IR interferometer equipped with additional polarizing optics/ accessories needed for recording VCD spectra. A parallel beam emerges through a side port of the interferometer which passes first through a wire grid linear polarizer and then through an octagonal-shaped ZnSe crystal PEM which modulates the polarized beam at a fixed, lower frequency such as 37.5 kHz. A mechanically stressed crystal such as ZnSe exhibits birefringence when stressed by an adjacent piezoelectric transducer. The linear polarizer is positioned close to, and at 45 degrees, with respect to the ZnSe crystal axis. The polarized radiation focused onto the detector is doubly modulated, both by the PEM and by the interferometer setup. A very low noise detector, such as MCT (HgCdTe), is also selected for the VCD signal phase-sensitive detection. Quasi-complete commercial FT-VCD instruments are also available from a few manufacturers but these are quite expensive and also have to be still considered as being at the prototype stage. To prevent detector saturation an appropriate, long wave pass filter is placed before the very low noise MCT detector, which allows only radiation below 1750 cm$^{−1}$ to reach the MCT detector; the latter however measures radiation only down to 750 cm$^{−1}$. FT-VCD spectra accumulation of the selected sample solution is then carried out, digitized and stored by an in-line computer. Published reviews that compare various VCD methods are also available.

## Magnetic VCD

VCD spectra have also been reported in the presence of an applied external magnetic field. This method can enhance the VCD spectral resolution for small molecules.

## Raman optical activity (ROA)

ROA is a technique complementary to VCD especially useful in the 50—1600 cm$^{−1}$ spectral region; it is considered as the technique of choice for determining optical activity for photon energies less than 600 cm$^{−1}$.

## Notes

* ↑ http://planetphysics.org/?op=getobj;from=objects;id=410 Principles of IR and NIR Spectroscopy
* ↑ "Vibrational Circular Dichroism of Polypeptides XII. Re-evaluation of the Fourier Transform Vibrational Circular Dichroism of Poly-gamma-Benzyl-L-Glutamate," P. Malon, R. Kobrinskaya, T. A. Keiderling, Biopolymers 27, 733-746 (1988).
* ↑ "Vibrational Circular Dichroism of Biopolymers," T. A. Keiderling, S. C. Yasui, U. Narayanan, A. Annamalai, P. Malon, R. Kobrinskaya, L. Yang, in Spectroscopy of Biological Molecules New Advances ed. E. D. Schmid, F. W. Schneider, F. Siebert, p. 73-76 (1988).
* ↑ "Vibrational Circular Dichroism of Polypeptides and Proteins," S. C. Yasui, T. A. Keiderling, Mikrochimica Acta, II, 325-327, (1988).
* ↑ *"Vibrational Circular Dichroism of Proteins Polysaccharides and Nucleic Acids" T. A. Keiderling, Chapter 8 in Physical Chemistry of Food Processes, Vol. 2 Advanced Techniques, Structures and Applications., eds. I.C. Baianu, H. Pessen, T. Kumosinski, Van Norstrand--Reinhold, New York (1993), pp 307-337.
* ↑ "Spectroscopic characterization of Unfolded peptides and proteins studied with infrared absorption and vibrational circular dichroism spectra" T. A. Keiderling and Qi Xu, Advances in Protein Chemistry Volume 62, [Unfolded Proteins, Dedicated to John Edsall, Ed.: George Rose, Academic Press:New York] (2002), pp. 111-161.
* ↑ "Protein and Peptide Secondary Structure and Conformational Determination with Vibrational Circular Dichroism " Timothy A. Keiderling, Current Opinions in Chemical Biology (Ed. Julie Leary and Mark Arnold) 6, 682-688 (2002).
* ↑ Review: Conformational Studies of Peptides with Infrared Techniques. Timothy A. Keiderling and R. A. G. D. Silva, in Synthesis of Peptides and Peptidomimetics, Ed. M. Goodman and G. Herrman, Houben-Weyl, Vol 22Eb, Georg Thiem Verlag, New York (2002) pp. 715-738, (written and accepted in 2000).
* ↑ "Polarization Modulation Fourier Transform Infrared Spectroscopy with Digital SignalProcessing: Comparison of Vibrational Circular Dichroism Methods." Jovencio Hilario, DavidDrapcho, Raul Curbelo, Timothy A. Keiderling, Applied Spectroscopy 55, 1435-1447(2001)--
* ↑ "Vibrational circular dichroism of biopolymers. Summary of methods and applications.", Timothy A. Keiderling, Jan Kubelka, Jovencio Hilario, in Vibrational spectroscopy of polymers and biological systems, Ed. Mark Braiman, Vasilis Gregoriou, Taylor&Francis, Atlanta (CRC Press, Boca Raton, FL) (2006) pp. 253-324 (originally written in 2000, updated in 2003)
* ↑ "Observation of Magnetic Vibrational Circular Dichroism," T. A. Keiderling, Journal of Chemical Physics, 75, 3639-41 (1981).
* ↑ "Vibrational Spectral Assignment and Enhanced Resolution Using Magnetic Vibrational Circular Dichroism," T. R. Devine and T. A. Keiderling, Spectrochimica Acta, 43A, 627-629 (1987).
* ↑ "Magnetic Vibrational Circular Dichroism with an FTIR" P. V. Croatto, R. K. Yoo, T. A. Keiderling, SPIE Proceedings 1145 (7th International Conference on FTS, ed. D. G. Cameron) 152-153 (1989).
* ↑ "Direct Measurement of the Rotational g-Value in the Ground State of Acetylene by Magnetic Vibrational Circular Dichroism." C. N. Tam and T. A. Keiderling, Chemical Physics Letters, 243, 55-58 (1995).
* ↑ . "Ab initio calculation of the vibrational magnetic dipole moment" P. Bour, C. N. Tam, T. A. Keiderling, Journal of Physical Chemistry 99, 17810-17813 (1995)
* ↑ "Rotationally Resolved Magnetic Vibrational Circular Dichroism. Experimental Spectra and Theoretical Simulation for Diamagnetic Molecules." P. Bour, C. N. Tam, B. Wang, T. A. Keiderling, Molecular Physics 87, 299-318, (1996).

## References
### Peptides and proteins

* Huang R, Wu L, McElheny D, Bour P, Roy A, Keiderling TA. Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip beta-Hairpin Peptide Using (13)C Isotopic Labeling and IR Spectroscopy. The journal of physical chemistry. B. 2009 Apr;113(16):5661-74.
* "Vibrational Circular Dichroism of Poly alpha-Benzyl-L-Glutamate," R. D. Singh, and T. A. Keiderling, Biopolymers, 20, 237-40 (1981).
* "Vibrational Circular Dichroism of Polypeptides II. Solution Amide II and Deuteration Results," A. C. Sen and T. A. Keiderling, Biopolymers, 23, 1519-32 (1984).
* "Vibrational Circular Dichroism of Polypeptides III. Film Studies of Several alpha-Helical and ß-Sheet Polypeptides," A. C. Sen and T. A. Keiderling, Biopolymers, 23, 1533-46 (1984).
* "Vibrational Circular Dichroism of Polypeptides IV. Film Studies of L-Alanine Homo Oligopeptides," U. Narayanan, T. A. Keiderling, G. M. Bonora, and C. Toniolo, Biopolymers 24, 1257-63 (1985).
* "Vibrational Circular Dichroism of Polypeptides, T. A. Keiderling, S. C. Yasui, A. C. Sen, C. Toniolo, G. M. Bonora, in Peptides Structure and Function, Proceedings of the 9th American Peptide Symposium," ed. C. M. Deber, K. Kopple, V. Hruby; Pie rce Chemical: Rockford, IL; 167-172 (1985).
* "Vibrational Circular Dichroism of Polypeptides V. A Study of 310 Helical-Octapeptides" S. C. Yasui, T. A. Keiderling, G. M. Bonora, C. Toniolo, Biopolymers 25, 79-89 (1986).
* "Vibrational Circular Dichroism of Polypeptides VI. Polytyrosine alpha-helical and Random Coil Results," S. C. Yasui and T. A. Keiderling, Biopolymers 25, 5-15 (1986).
* "Vibrational Circular Dichroism of Polypeptides VII. Film and Solution Studies of alpha-forming Homo-Oligopeptides," U. Narayanan, T. A. Keiderling, G. M. Bonora, C. Toniolo, Journal of the American Chemical Society, 108, 2431-2437 (1986).
* "Vibrational Circular Dichroism of Polypeptides VIII. Poly Lysine Conformations as a Function of pH in Aqueous Solution," S. C. Yasui, T. A. Keiderling, Journal of the American Chemical Society, 108, 5576-5581 (1986).
* "Vibrational Circular Dichroism of Polypeptides IX. A Study of Chain Length Dependence for 310-Helix Formation in Solution." S. C. Yasui, T. A. Keiderling, F. Formaggio, G. M. Bonora, C. Toniolo, Journal of the American Chemical Society 108, 4988-499 3 (1986).
* "Vibrational Circular Dichroism of Biopolymers." T. A. Keiderling, Nature, 322, 851-852 (1986).
* "Vibrational Circular Dichroism of Polypeptides X. A Study of alpha-Helical Oligopeptides in Solution." S. C. Yasui, T. A. Keiderling, R. Katachai, Biopolymers 26, 1407-1412 (1987).
* "Vibrational Circular Dichroism of Polypeptides XI. Conformation of Poly(L-Lysine(Z)-L-Lysine(Z)-L-1-Pyrenylalanine) and Poly(L-Lysine(Z)-L-Lysine(Z)-L-1-Napthylala-nine) in Solution" S. C. Yasui, T. A. Keiderling, and M. Sisido, Macromolecules 20, 2 403-2406 (1987).
* "Vibrational Circular Dichroism of Biopolymers" T. A. Keiderling, S. C. Yasui, A. C. Sen, U. Narayanan, A. Annamalai, P. Malon, R. Kobrinskaya, L. Yang, in "F.E.C.S. Second International Conference on Circular Dichroism, Conference Proceedings," ed. M. Kajtar, L. Eötvös Univ., Budapest, 1987, p. 155-161.
* "Vibrational Circular Dichroism of Poly-L-Proline and Other Helical Poly-peptides," R. Kobrinskaya, S. C. Yasui, T. A. Keiderling, in "Peptides: Chemistry and Biology, Proceedings of the 10th American Peptide Symposium," ed. G. R. Marshall, ESCOM, L eiden, 1988, p. 65-67.
* "Vibrational Circular Dichroism of Polypeptides with Aromatic Side Chains," S. C. Yasui, T. A. Keiderling, in "Peptides: Chemistry and Biology, Proceedings of the 10th American Peptide Symposium," ed. G. R. Marshall, ESCOM, Leiden, 1988, p. 90-92.
* "Vibrational Circular Dichroism of Polypeptides XII. Re-evaluation of the Fourier Transform Vibrational Circular Dichroism of Poly-gamma-Benzyl-L-Glutamate," P. Malon, R. Kobrinskaya, T. A. Keiderling, Biopolymers 27, 733-746 (1988).
* "Vibrational Circular Dichroism of Biopolymers," T. A. Keiderling, S. C. Yasui, U. Narayanan, A. Annamalai, P. Malon, R. Kobrinskaya, L. Yang, in Spectroscopy of Biological Molecules New Advances ed. E. D. Schmid, F. W. Schneider, F. Siebert, p. 73-76 (1988).
* "Vibrational Circular Dichroism of Polypeptides and Proteins," S. C. Yasui, T. A. Keiderling, Mikrochimica Acta, II, 325-327, (1988).
* "(1R,7R)-7-Methyl-6,9,-Diazatricyclo[6,3,0,01,6]Tridecanne-5,10-Dione, A Tricyclic Spirodilactam Containing Non-planar Amide Groups: Synthesis, NMR, Crystal Structure, Absolute Configuration, Electronic and Vibrational Circular Dichroism" P. Malon, C . L. Barness, M. Budesinsky, R. K. Dukor, D. van der Helm, T. A. Keiderling, Z. Koblicova, F. Pavlikova, M. Tichy, K. Blaha, Collections of Czechoslovak Chemical Communications 53, 2447-2472 (1988).
* "Vibrational Circular Dichroism of Poly Glutamic Acid" R. K. Dukor, T. A. Keiderling, in Peptides 1988 (ed. G. Jung, E. Bayer) Walter de Gruyter, Berlin (1989) pp 519–521.
* "Biopolymer Conformational Studies with Vibrational Circular Dichroism" T. A. Keiderling, S. C. Yasui, P. Pancoska, R. K. Dukor, L. Yang, SPIE Proceeding 1057, ("Biomolecular Spectroscopy," ed. H. H. Mantsch, R. R. Birge) 7-14 (1989).
* "Vibrational Circular Dichroism. Comparison of Techniques and Practical Considerations" T. A. Keiderling, in "Practical Fourier Transform Infrared Spectroscopy. Industrial and Laboratory Chemical Analysis," ed. J. R. Ferraro, K. Krishnan (Academic Press, San Diego, 1990) p. 203-284.
* "Vibrational Circular Dichroism Study of Unblocked Proline Oligomers," R. K. Dukor, T. A. Keiderling, V. Gut, International Journal of Peptide and Protein Research, 38, 198-203 (1991).
* "Reassessment of the Random Coil Conformation. Vibrational CD Study of Proline Oligopeptides and Related Polypeptides" R. K. Dukor and T. A. Keiderling, Biopolymers 31 1747-1761 (1991).
* "Vibrational CD of the Amide II band in Some Model Polypeptides and Proteins" V. P. Gupta, T. A. Keiderling, Biopolymers 32 239-248 (1992).
* "Vibrational Circular Dichroism of Proteins Polysaccharides and Nucleic Acids" T. A. Keiderling, Chapter 8 in Physical Chemistry of Food Processes, Vol. 2 Advanced Techniques, Structures and Applications., eds. I.C. Baianu, H. Pessen, T. Kumosinski, Van Norstrand—Reinhold, New York (1993), pp 307–337.
* "Structural Studies of Biological Macromolecules using Vibrational Circular Dichroism" T. A. Keiderling, P. Pancoska, Chapter 6 in Advances in Spectroscopy Vol. 21, Biomolecular Spectroscopy Part B eds. R. E. Hester, R. J. H. Clarke, John W iley Chichester (1993) pp 267–315.
* "Ab Initio Simulations of the Vibrational Circular Dichroism of Coupled Peptides" P. Bour and T. A. Keiderling, Journal of the American Chemical Society 115 9602-9607 (1993).
* "Ab initio Simulations of Coupled Peptide Vibrational Circular Dichroism" P. Bour, T. A. Keiderling in "Fifth International Conference on The Spectroscopy of Biological Molecules" Th. Theophanides, J. Anastassopoulou, N. Fotopoulos (Eds), Kluwen Aca demic Publ., Dortrecht, 1993, p. 29-30.
* "Vibrational Circular Dichroism Spectroscopy of Peptides and Proteins" T. A. Keiderling, in "Circular Dichroism Interpretations and Applications," K. Nakanishi, N. Berova, R. Woody, Eds., VCH Publishers, New York, (1994) pp 497–521.
* "Conformational Study of Sequential Lys-Leu Based Polymers and Oligomers using Vibrational and Electronic Circular Dichroism Spectra" V. Baumruk, D. Huo, R. K. Dukor, T. A. Keiderling, D. LeLeivre and A. Brack Biopolymers 34, 1115-1121 (1994).
* "Vibrational Optical Activity of Oligopeptides" T. B. Freedman, L. A. Nafie, T. A. Keiderling Biopolymers (Peptide Science) 37 (ed. C. Toniolo) 265-279 (1995).
* "Characterization of ß-bend ribbon spiral forming peptides using electronic and vibrational circular dichroism" G. Yoder, T. A. Keiderling, F. Formaggio, M. Crisma, C. Toniolo Biopolymers 35, 103-111 (1995).
* "Vibrational Circular Dichroism as a Tool for Determination of Peptide Secondary Structure" P. Bour, T. A. Keiderling, P. Malon, in "Peptides 1994 (Proceedings of the 23rd European Peptide Symposium,1994," (H.L.S. Maia, ed.), Escom, Le iden 1995, p. 517-518.
* "Helical Screw Sense of homo-oligopeptides of C-alpha-methylated alpha-amino acids as Determined with Vibrational Circular Dichroism." G. Yoder, T. A. Keiderling, M. Crisma, F. Formaggio, C. Toniolo, J. Kamphuis, Tetrahedron Asymmetry 6, 687 -690 (1995).
* "Conformational Study of Linear Alternating and Mixed D- and L-Proline Oligomers Using Electronic and Vibrational CD and Fourier Transform IR." W. M&#228stle, R. K. Dukor, G. Yoder, T. A. Keiderling Biopolymers 36, 623-631 (1995).
* Review: "Vibrational Circular Dichroism Applications to Conformational Analysis of Biomolecules" T. A. Keiderling in Circular Dichroism and the Conformational Analysis of Biomolecules ed. G. D. Fasman, Plenum, New York (1996) p. 555-585.
* "Mutarotation studies of Poly L-Proline using FT-IR, Electronic and Vibrational Circular Dichroism" R. K. Dukor, T. A. Keiderling, Biospectroscopy 2, 83-100 (1996).
* "Vibrational Circular Dichroism Applications in Proteins and Peptides" T. A. Keiderling, Proceedings of the NATO ASI in Biomolecular Structure and Dynamics, Loutrakii Greece, May 1996, Ed. G. Vergoten (delayed second volume to 1998).
* "Transfer of Molecular Property Tensors in Cartesian Coordinates: A new algorithm for simulation of vibrational spectra" Petr Bour, Jana Sopkova, Lucie Bednarova, Petr Malon, T. A. Keiderling, Journal of Computational Chemistry 18, 6 46-659 (1997).
* "Vibrational Circular Dichroism Characterization of Alanine-Rich Peptides." Gorm Yoder and Timothy A. Keiderling, "Spectroscopy of Biological Molecules: Modern Trends," Ed. P. Carmona, R. Navarro, A. Hernanz, Kluwer Acad. Pub., Netherlands (1997) p p. 27-28.
* "Ionic strength effect on the thermal unfolding of alpha-spectrin peptides." D. Lusitani, N. Menhart, T.A. Keiderling and L. W. M. Fung. Biochemistry 37(1998)16546-16554.
* "In search of the earliest events of hCGb folding: structural studies of the 60-87 peptide fragment" S. Sherman, L. Kirnarsky, O. Prakash, H. M. Rogers, R.A.G.D. Silva, T.A. Keiderling, D. Smith, A.M. Hanly, F. Perini, and R.W. Ruddon, American Pep tide Symposium Proceedings, 1997.
* "Cold Denaturation Studies of (LKELPKEL)n Peptide Using Vibrational Circular Dichroism and FT-IR". R. A. G. D. Silva, Vladimir Baumruk, Petr Pancoska, T. A. Keiderling, Eric Lacassie, and Yves Trudelle, American Peptide Symposium Proceedings, 1997.
* "Simulations of oligopeptide vibrational CD. Effects of isotopic labeling." Petr Bour, Jan Kubelka,T. A. Keiderling Biopolymers 53, 380-395 (2000).
* "Site specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution" R. A. G. D. Silva, Jan Kubelka, Petr Bour, Sean M. Decatur, Timothy A. Keiderling, Proceedings of the National Academy of Sciences (PNAS:USA) 97, 8318-8323 (2000).
* "Folding studies on the human chorionic gonadotropin b -subunit using optical spectroscopy of peptide fragments" R. A. G. D. Silva, S. A. Sherman, F. Perini, E. Bedows, T. A. Keiderling, Journal of the American Chemical Society, 122, 8623-8630 (2000).
* "Peptide and Protein Conformational Studies with Vibrational Circular Dichroism and Related Spectroscopies", Timothy A. Keiderling, (Revised and Expanded Chapter) In Circular Dichroism: Principles and Applications, 2nd Edition. (Eds. K. Nakanishi, N. Berova and R. A. Woody, John Wiley & Sons, New York (2000) p. 621-666.
* "Conformation studies with Optical Spectroscopy of peptides taken from hairpin sequences in the Human Chorionic Gonadotropin " R. A. G. D. Silva, S. A. Sherman, E. Bedows, T. A. Keiderling, Peptides for the New Millenium, Proceedings of the 16th American Peptide Symposium, (June, 1999 Minneapolis, MN) Ed.G. B. Fields, J. P. Tam, G. Barany, Kluwer Acad. Pub., Dordrecht,(2000) p. 325-326.
* "Analysis of Local Conformation within Helical Peptides via Isotope-Edited Vibrational Spectroscopy." S. M. Decatur, T. A. Keiderling, R. A. G. D.Silva, and P. Bour, Peptides for the New Millenium, Proceedings of the 16th American Peptide Symposium, (June, 1999 Minneapolis, MN) Ed. Ed.G. B. Fields, J. P. Tam, G. Barany, Kluwer Acad. Pub., Dordrecht, (2000) p. 414-416.
* "The anomalous infrared amide I intensity distribution in C-13 isotopically labeled peptide beta-sheets comes from extended, multiple stranded structures. An Ab Initio study." Jan Kubelka and T. A. Keiderling , Journal of the American Chemical Society. 123, 6142-6150 (2001).
* "Vibrational Circular Dichroism of Peptides and Proteins: Survey of Techniques, Qualitative and Quantitative Analyses, and Applications" Timothy A. Keiderling, Chapter in Infrared and Raman Spectroscopy of Biological Materials, Ed. Bing Yan and H.-U. Gremlich, Marcel Dekker, New York (2001) p. 55-100.
* "Chirality in peptide vibrations. Ab initio computational studies of length, solvation, hydrogen bond, dipole coupling and isotope effects on vibrational CD. " Jan Kubelka, Petr Bour, R. A. Gangani D. Silva, Sean M. Decatur, Timothy A. Keiderling, ACS Symposium Series 810, ["Chirality: Physical Chemistry," (Ed. Janice Hicks) American Chemical Society, Washington, DC] (2002), pp. 50–64.
* "Spectroscopic Characterization of Selected b-Sheet Hairpin Models", J. Hilario, J. Kubelka, F. A. Syud, S. H. Gellman, and T. A. Keiderling. Biopolymers (Biospectroscopy) 67: 233-236 (2002)
* " Discrimination between peptide 3$_{10}$- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra " Jan Kubelka, R. A. Gangani D. Silva, and T. A. Keiderling, Journal of the American Chemical Society, 124, 5325-5332 (2002).
* "Ab Initio Quantum Mechanical Models of Peptide Helices and their Vibrational Spectra" Petr Bour, Jan Kubelka and T. A. Keiderling, Biopolymers 65, 45-59 (2002).
* "Discriminating 3$_{10}$- from alpha-helices. Vibrational and electronic CD and IR Absorption study of related Aib-contining oligopeptides" R. A. Gangani D. Silva, Sritana Yasui, Jan Kubelka, Fernando Formaggio, Marco Crisma, Claudio Toniolo, and Timothy A. Keiderling, Biopolymers 65, 229-243 (2002).
* "Spectroscopic characterization of Unfolded peptides and proteins studied with infrared absorption and vibrational circular dichroism spectra" T. A. Keiderling and Qi Xu, Advances in Protein Chemistry Volume 62, [Unfolded Proteins, Dedicated to John Edsall, Ed.: George Rose, Academic Press:New York] (2002), pp. 111–161.
* "Protein and Peptide Secondary Structure and Conformational Determination with Vibrational Circular Dichroism " Timothy A. Keiderling, Current Opinions in Chemical Biology (Ed. Julie Leary and Mark Arnold) 6, 682-688 (2002).
* Review: Conformational Studies of Peptides with Infrared Techniques. Timothy A. Keiderling and R. A. G. D. Silva, in Synthesis of Peptides and Peptidomimetics, Ed. M. Goodman and G. Herrman, Houben-Weyl, Vol 22Eb, Georg Thiem Verlag, New York (2002) pp. 715–738, (written and accepted in 2000).
* "Spectroscopic Studies of Structural Changes in Two beta-Sheet Forming Peptides Show an Ensemble of Structures That Unfold Non-Cooperatively" Serguei V. Kuznetsov, Jovencio Hilario, T. A. Keiderling, Anjum Ansari, Biochemistry, 42 :4321-4332, (2003).
* "Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution" Jovencio Hilario, Jan Kubelka, T. A. Keiderling, Journal of the American Chemical Society 125, 7562-7574 (2003).
* "Synthesis and conformational study of homopeptides based on (S)-Bin, a C2-symmetric binapthyl-derived Caa-disubstituted glycine with only axial chirality" J.-P. Mazaleyrat, K. Wright, A. Gaucher, M. Wakselman, S. Oancea, F. Formaggio, C. Toniolo, V. Setnicka, J. Kapitan, T. A. Keiderling, Tetrahedron Asymmetry, 14, 1879-1893 (2003).
* "Empirical modeling of the peptide amide I band IR intensity in water solution," Petr Bour, Timothy A. Keiderling, Journal of Chemical Physics, 119, 11253-11262 (2003)
* "The Nature of Vibrational Coupling in Helical Peptides: An Isotope Labeling Study” by R. Huang, J. Kubelka, W. Barber-Armstrong, R. A. G. D Silva, S. M. Decatur, and T. A. Keiderling, Journal of the American Chemical Society, 126, 2346-2354 (2004).
* "The Complete Chirospectroscopic Signature of the Peptide 3$_{10}$ Helix in Aqueous Solution" Claudio Toniolo, Fernando Formaggio, Sabrina Tognon, Quirinus B. Broxterman, Bernard Kaptein, Rong Huang, Vladimir Setnicka, Timothy A. Keiderling, Iain H. McColl, Lutz Hecht, Laurence D. Barron, Biopolymers 75, 32-45 (2004).
* "Induced axial chirality in the biphenyl core for the Ca-tetrasubstituted a-amino acid residue Bip and subsequent propagation of chirality in (Bip)n/Val oligopeptides" J.-P. Mazaleyrat, K. Wright, A. Gaucher, N. Toulemonde, M. Wakselman, S. Oancea, C. Peggion, F. Formaggio, V. Setnicka, T. A. Keiderling, C. Toniolo, Journal of the American Chemical Society 126; 12874-12879 (2004).
* Ab initio modeling of amide I coupling in anti-parallel b-sheets and the effect of the 13C isotopic labeling on vibrational spectra” Petr Bour, Timothy A. Keiderling, Journal of Physical Chemistry B, 109, 5348-5357 (2005)
* Solvent Effects on IR And VCD Spectra of Helical Peptides: Insights from Ab Initio Spectral Simulations with Explicit Water” Jan Kubelka and Timothy A. Keiderling, Journal of Physical Chemistry B 109, 8231-8243 (2005)
* IR Study of Cross-Strand Coupling in a beta-Hairpin Peptide Using Isotopic Labels., Vladimir Setnicka, Rong Huang, Catherine L. Thomas, Marcus A. Etienne, Jan Kubelka, Robert P. Hammer, Timothy A. Keiderling Journal of the American Chemical Society 127, 4992-4993 (2005).
* Vibrational spectral simulation for peptides of mixed secondary structure: Method comparisons with the trpzip model hairpin. Petr Bour and Timothy A. Keiderling, Journal of Physical Chemistry B 109, 232687-23697 (2005).
* Isotopically labeled peptides provide site-resolved structural data with infrared spectra. Probing the structural limit of optical spectroscopy, Timothy A. Keiderling, Rong Huang, Jan Kubelka, Petr Bour, Vladimir Setnicka, Robert P. Hammer, Marcus *A. Etienne, R. A. Gangani D. Silva, Sean M. Decatur Collections Symposium Series, 8, 42-49 (2005)—["Biologically Active Peptides" IXth Conference, Prague Czech Republic, April 20-22, 2005.

### Nucleic acids and polynucleotides

* "Application of Vibrational Circular Dichroism to Synthetic Polypeptides and Polynucleic Acids" T. A. Keiderling, S. C. Yasui, R. K. Dukor, L. Yang, Polymer Preprints 30, 423-424 (1989).
* "Vibrational Circular Dichroism of Polyribonucleic Acids. A Comparative Study in Aqueous Solution." A. Annamalai and T. A. Keiderling, Journal of the American Chemical Society, 109, 3125-3132 (1987).
* "Conformational phase transitions (A-B and B-Z) of DNA and models using vibrational circular dichroism" L. Wang, L. Yang, T. A. Keiderling in Spectroscopy of Biological Molecules., eds. R. E. Hester, R. B. Girling, Special Publication 94 Roya l Society of Chemistry, Cambridge (1991) p. 137-38.
* "Vibrational Circular Dichroism of Proteins Polysaccharides and Nucleic Acids" T. A. Keiderling, Chapter 8 in Physical Chemistry of Food Processes, Vol. 2 Advanced Techniques, Structures and Applications eds. I. C. Baianu, H. Pessen, T. Kumosinski, Van Norstrand—Reinhold, New York (1993) pp. 307–337.
* "Structural Studies of Biological Macromolecules using Vibrational Circular Dichroism" T. A. Keiderling, P. Pancoska, Chapter 6 in Advances in Spectroscopy Vol. 21, "Biomolecular Spectroscopy Part B" ed. R. E. Hester, R. J. H. Clarke, John W iley Chichester (1993) pp 267–315.
* "Detection of Triple Helical Nucleic Acids with Vibrational Circular Dichroism," L. Wang, P. Pancoska, T. A. Keiderling in "Fifth International Conference on The Spectroscopy of Biological Molecules" Th. Theophanides, J. Anastassopoulou, N. Fotopoul os (Eds), Kluwen Academic Publ., Dortrecht, 1993, p. 81-82.
* "Helical Nature of Poly (dI-dC) � Poly (dI-dC). Vibrational Circular Dichroism Results" L. Wang and T. A. Keiderling Nucleic Acids Research 21 4127-4132 (1993).
* "Detection and Characterization of Triple Helical Pyrimidine-Purine-Pyrimidine Nucleic Acids with Vibrational Circular Dichroism" L. Wang, P. Pancoska, T. A. Keiderling, Biochemistry 33 8428-8435 (1994).
* "Vibrational Circular Dichroism of A-, B- and Z- form Nucleic Acids in the PO2- Stretching Region" L. Wang, L. Yang, T. A. Keiderling, Biophysical Journal 67, 2460-2467 (1994).
* "Studies of multiple stranded RNA and DNA with FTIR, vibrational and electronic circular dichroism," Zhihua Huang, Lijiang Wang and Timothy A. Keiderling, in Spectrosopy of Biological Molecules, Ed. J. C. Merlin, Kluwer Acad. Pub., Dordrecht, 1995, pp . 321-322.
* "Vibrational Circular Dichroism Applications to Conformational Analysis of Biomolecules" T. A. Keiderling in "Circular Dichroism and the Conformational Analysis of Biomolecules" ed G. D. Fasman, Plenum, New York (1996) pp. 555–598.
* "Vibrational Circular Dichroism Techniques and Application to Nucleic Acids" T. A. Keiderling, In "Biomolecular Structure and Dynamics", NATO ASI series, Series E: Applied Sciences- Vol.342, Eds: G. Vergoten and T. Theophanides, Kluwer Academ ic Publishers, Dordrecht, The Netherlands,pp. 299–317 (1997).