Jagdeesh Bandekar

Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.

FT-IR spectroscopic studies of polyurethanes Part I. Bonding between urethane COC groups and the NH Groups

Abstract Fourier-transform-infrared-attenuated total internal reflectance (FT-IR-ATR) has been used to study polyurethanes containing different hard segments but the same soft segment. The spectra of a series of blended polyurethanes have been systematically studied. The changes in the urethane COC regions of the polyurethanes with respect to the hard segments make a strong case for the existence of hydrogen-bonding interactions between the urethane COC groups and the NH groups. The decreases in the relative intensities of carbonyl bands and shifts of NH stretching bands (as the urethane COC bonding with NH groups increases) are in support of this proposal. The urethane COC region is shown to be a useful region in interpreting ATR spectra of polyurethanes. The implications of these results to the present methods of estimating phase separations in polyurethanes are discussed. Results obtained from ab initio quantum chemical computational methods show this hydrogen bond to be directional and to have an energy of 6.32 kcal mol −1 (compared with carbonyl hydrogen bond energy of 8.37 kcal mol −1 ) which is surprisingly high.

FR-IR spectroscopic studies of polyurethanes—Part II. Ab initio quantum chemical studies of the relative strengths of “carbonyl” and “ether” hydrogen-bonds in polyurethanes

Abstract Ab initio quantum chemical computations were carried out on (a) dimethyl ether, (b) N-methyl formamide, (c) dimethyl ether-N-methyl formamide complex, and (d) N-methyl formamide dimer to compute the strengths of hydrogen bonds (H-bonds) between the NH groups and CO and ether COC groups. The basis set used was the 3-21G set of the GAUSSIAN 80 program obtained from QCPE, Bloomington, IN. Variations in the strengths of these two H-bonds with the N . . O distance (where O is either carbonyl or ether group oxygen) were studied and found to be similar in behavior. The strength of the “ether” hydrogen bond is computed to be 10.32 kcal mol−1, which is quite significant compared to the value of 10.11 kcal mol−1 for the more accepted “carbonyl” hydrogen bond. The “ether” hydrogen bond is found to be directional, specific and non-negligible. Work with two more basis sets has indicated that the results so obtained are not dependent on their choice. Possible importance of such a hydrogen bond in polyurethanes, inhalation anesthetics, and depsi-peptides is indicated.

Vibrational studies of the disulfide group in proteins: Part III. A simplified ab initio force field for diethyl disulfide and SS and CS stretch frequency—conformation correlations for diisobutyl disulfide

Abstract We have obtained a simplified ab initio force field for diethyl disulfide, based on our previous scaled ab initio force field, which can be used in normal coordinate analysis of proteins containing the disulfide bridge. A normal coordinate analysis has been performed for diisobutyl disulfide in all possible conformations. The correlations thus obtained between the SS and CS stretch frequencies and the conformation are useful in understanding similar correlations in proteins containing the disulfide bridge. A simple way is presented to identify local C 2 symmetry in a disulfide bridge through Raman polarization studies.

Vibrational analysis of crystalline triglycine

Abstract We have refined vibrational force fields for polypeptides that permit excellent reproduction of the normal mode frequencies of such molecules. This is demonstrated in the present study, in which 80 IR and Raman bands of crystalline triglycine between 1800 and 200 cm −1 are reproduced with an average error of 6 cm −1 . A deuterated sample is shown by normal mode analysis to have remained protonated at the C-terminal peptide group. Such results show that normal mode analysis can now provide a rigorous base for spectral studies of conformation in peptides and proteins.

Dipole Moment Derivatives and Their Orientations in Uracil, An ab initio Study

Abstract Using the force fields due to Nishimura et al.[1] and to Harsanyi et al.[2], dipole moment derivatives (DMDs) and their orientations have been computed by ab initio techniques. The values so computed using the above two force fields are surprisingly close to each other. The DMDs corresponding to the C = O stretching (s) and CN s are found to be among the most significant. The DMD values of C2 = O s and C4 = O s are found to be comparable in value, both of them thus expected to contribute to C = O s ir band intensities. The DMDs of NH in-plane bending (ipb) modes are found to be surprisingly small, thus explaining the observed absence of splittings due to the corresponding transition dipole- transition dipole coupling (TDC) interactions. The DMD values obtained here are shown to be crucial in deciding which of the observed bands in solid state or condensed phase samples could be due to Fermi resonance and/or overtone and/or combination bands. They could also be used effectively in studying rela...

Copper(II)-Nucleic acid interactions—A conformational study

Abstract The effect of copper complexation upon the conformational angles in mononucleotides and dinucleotides was studied using classical potential energy expressions. The geometrical parameters were taken from crystallographic reports on the base-metal complexes. It was found that the preferred conformations of the complexes were quite different from the preferred conformations of the corresponding pure nucleotides. Notable among the disallowed conformations in case of Cu(II)-dinucleotide complexes were the regions corresponding to RRNAs, RNAs and the A, B and C forms of DNA. It is proposed that the energetics of a single strand is more important than inter-strand interactions in promoting copper-induced denaturation of DNA.