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Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach
Author(s) -
Jalkanen K. J.,
Würtz Jürgensen V.,
Claussen A.,
Rahim A.,
Jensen G. M.,
Wade R. C.,
Nardi F.,
Jung C.,
Degtyarenko I. M.,
Nieminen R. M.,
Herrmann F.,
KnappMohammady M.,
Niehaus T. A.,
Frimand K.,
Suhai S.
Publication year - 2005
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.20863
Subject(s) - chemistry , biomolecule , alanine , amide , raman spectroscopy , molecule , molecular dynamics , stereochemistry , computational chemistry , tryptophan , amino acid , organic chemistry , biochemistry , physics , optics
We report on our work with vibrational absorption, vibrational circular dichroism, Raman scattering, Raman optical activity, and surface‐enhanced Raman spectroscopy to study protein and DNA structure, hydration, and the binding of ligands, drugs, pesticides, or herbicides via a combined theoretical and experimental approach. The systems we have studied systematically are the amino acids ( L ‐alanine, L ‐tryptophan, and L ‐histidine), peptides ( N ‐4271 acetyl L ‐alanine N ′‐methyl amide, N ‐acetyl L ‐tryptophan N ′‐methyl amide, N ‐acetyl L ‐histidine N ′‐methyl amide, L ‐alanyl L ‐alanine, tri‐ L ‐serine, N ‐acetyl L ‐alanine L ‐proline L ‐tyrosine N ′‐methyl amide, Leu‐enkephalin, cyclo‐(gly‐ L ‐pro) 3 , N ‐acetyl ( L ‐alanine) n N ′‐methyl amide), 3‐methyl indole, and a variety of small molecules (dichlobenil and 2,6‐dochlorobenzamide) of relevance to the protein systems under study. We have used molecular mechanics, the SCC‐DFTB, SCC‐DFTB+disp, RHF, MP2, and DFT methodologies for the modeling studies with the goal of interpreting the experimentally measured vibrational spectra for these molecules to the greatest extent possible and to use this combined approach to understand the structure, function, and electronic properties of these molecules in their various environments. The application of these spectroscopies to biophysical and environmental assays is expanding, and therefore a thorough understanding of the phenomenon from a rigorous theoretical basis is required. In addition, we give some exciting and new preliminary results which allow us to extend our methods to even larger and more complex systems. The work presented here is the current state of the art to this ever and fast changing field of theoretical spectroscopic interpretation and use of VA, VCD, Raman, ROA, EA, and ECD spectroscopies. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006