It can be proven, you have an area call amide A and amide B, this region bet the 3300-3000 cm-1, can give you info about the tertiary structure of the molecule, the OH stretching vibrations are include in this area, so if you have shift upon binding, this will give an idea.

The other region of interest will be in the far infrared below 300 cm-1, in this area arise the hydrogen bonding collective modes, meaning the intra and inter-molecular hydrogen bonds,

I recommend you to do a titration, the same concentration of the protein, different ratios of the effector molecule.

There are three papers you can check about it:

1.Andreas Barth: What vibrations tells us about proteins

Infrared spectroscopy of proteins

2. Functional waters in intraprotein proton transfer

monitored by FTIR difference spectroscopy

3. Probing the Hydrogen Bonding Structure in the Rieske

Protein

4. Signatures of the hydrogen bonding in the infrared bands of water

This publications will give you an idea how to start.

Good luck!

Certainly, hydrogen bonds influence the strength of the primary bonds to which they form, and cause vibrational frequency change. The problem is to find the right references for the "undisturbed" state, without hydrogen bonds. The vibrations of the H-bonds are found in the far infrared region. I recommend two papers by us on the subject: Adv. Funct. Mater. 19, 1-8 (2009) and J. Phys. Chem. B. 116, 4626-4633 (2012). In the latter, we used matrix isolation spectroscopy to determine the spectra of the molecules without H-bonds. Hope this helps.

Theoretically might be. In practice, I don't think so. Because of many OH groups in the ribose unit

Thank you very much, this really helped. I think I will give this a shot.

I agree with the last two comments: the difficulty is to obtain specifity among the many OH groups.

Thank you Prof.Siebert. That is why I was hoping to find a marker signal originating from the ring, to which the OH groups are attached. For example the carbon ring of tyrosine has a specific marker signal but I have no experience with nucleotides. Does the ring in adenosine has a distinguished signal so that I can detect the H-bondings?

Yes, there are ring vibrations which are sensitive to H-bonding. I myself am also not an expert on vibrational spectroscopy. But I remember earlier work back in the 70-80-ies. Eliane Taillandier has publshed many interesting paper on IR spectroscopy of nucleotides.

Once again, thank you so much Prof.Siebert. I have checked some of the works of Taillandier in 80s as you suggested. I could not find a direct answer to my question yet; however, there I found very good reviews and list of band assignments in nucleotides. At least, I have a starting point and have a lot of papers to read in the weekend.

Hola Filiz, I think its possible but you should have good controls. In the other hand it depends if you will put the organic molecule in inorganic surfaces or will be in liquids and so on but, yes. I think its possible.

If the core problem is that the extremely broad alcohol peak may be composed of other components besides those from the alcohols participating in hydrogen bonding, I wonder if it's possible to do a deconvolution to separate out the components. Perhaps one could either use Mathlab, or adapt NMR signal processing software fir the job.

Mark Rozenberg,

Pay attention on couple of papers about FTIR spectra of polycristalline adenosine and several oligos, possibly they can be useful for you.

1. M Rozenberg et al, Spectrochimica acta A61 (2005) 733

2. M.Rozenberg, G.Shoham, Spectrochimica acta A71 (2009) 1804

I agree with Mark above very much. His papers are a must for everyone working in this field.

There are also interesting Raman studies performed by Pierre-Yves Turpin's group on nucleotides H-bonding. It wothrs having a look.

If you are truly interested in seeing the H-bond, then you should be looking into Terahertz Spectroscopy. In the THz region the signatures of H-bonding are unique. Look into the link below for some ideas

http://kb.osu.edu/dspace/handle/1811/30569?show=full

Thank you Dr.Rozenberg for suggested papers and Dr.Ishai for the suggestion. I will check out them.