Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments

Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed

SITE-SPECIFIC CONFORMATIONAL RAMAN AND IR SPECTRA STUDIES OF SELECTIVELY ISOTOPIC LABELED PEPTIDES

Author Institution: Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607In an effort to determine any underlying interactions that might discriminate between the two most common helical protein structures, $\alpha$ helix and $3_{10}$ helix, we have carried out detailed spectral analysis and quantum mechanical simulations based on density functional theory (DFT) computations of the amide vibrational force fields (FF) and intensities for Raman and IR spectra, at various levels of theory, mostly BPW91/6-31G*. Short structures cannot develop stable helical conformations,consequently, parameters from these ab initio calculations on short peptides were then transferred onto corresponding larger oligopeptides (normally 20 residues) of the same conformation which are representative of molecules studied experimentally. To visualize intricate structural differences between the two types of helices, selected amide positions were isotopically labeled with $^{13}$C=O and $^{15}$N on the amide link or $^{13}$C and $^{18}$O on the amide C=O. The spacing between these labels along the sequence was varied, one residue at a time, to test position sensitivity. A similar approach was followed for 3$_{1}$ helices and $\beta$ sheets. There is a distinct difference in adjacent and alternate labels in a helical sequence, since the sign of the coupling constant changes, which makes the more intense component of the exciton coupled pair opposite in the two cases and leads to a shift in frequency for the apparent $^{13}$C=O Raman or IR band. In terms of discriminating between structures, this sign change is the same in $\alpha$ and 3$_{10}$ helices, however the intensity distribution is somewhat different, indicating the mixing of modes shifts in the two structures. The coupling constants are of the same order of magnitude as well. There is little apparent shift of the amide III, even with $^{15}$N labeling, presumably due to the extensive mixing of these modes. This work is supported by the National Science Foundation, (grant CHE07-18043 to TAK)

Pretransitional structural changes in the thermal denaturation of ribonuclease S and S protein.

Two mechanisms have been proposed for the thermal unfolding of ribonuclease S (RNase S). The first is a sequential partial unfolding of the S peptide/S protein complex followed by dissociation, whereas the second is a concerted denaturation/dissociation. The thermal denaturation of ribonuclease S and its fragment, the S protein, were followed with circular dichroism and infrared spectra. These spectra were analyzed by the principal component method of factor analysis. The use of multiple spectral techniques and of factor analysis monitored different aspects of the denaturation simultaneously. The unfolding pathway was compared with that of the parent enzyme ribonuclease A (RNase A), and a model was devised to assess the importance of the dissociation in the unfolding. The unfolding patterns obtained from the melting curves of each protein imply the existence of multiple intermediate states and/or processes. Our data provide evidence that the pretransition in the unfolding of ribonuclease S is due to partial unfolding of the S protein/S peptide complex and that the dissociation occurs at higher temperature. Our observations are consistent with a sequential denaturation mechanism in which at least one partial unfolding step comes before the main conformational transition, which is instead a concerted, final unfolding/dissociation step

INTRACONFIGURATIONAL ABSORPTION SPECTROSCOPY OF IrX62−IrX_{6}{^{2-}} IN A2MX6A_{2}MX_{6} - TYPE HOST CRYSTALS

Address of Yoo and Keiderling: Department of Chemistry, University of Illinois at Chicago, Box 4348, Chicago, Illinois, 60680, USA.Author Institution:Results of near-ir absorption spectra for $Ir^{+4}$in $A_{2}MX_{6} (A=K, Rb, NH_{4}, M=Sn, Pt, X=Cl, Br)$ type host at $2^{\circ}K$ are discussed and compared to earlier work. Our data indicate that the effect of reduced host symmetry is quite small in this $d^{5}$ system and that the spectra of $IrCl_{6}{^{2-}}$ can be interpreted in a manner paralleling previous studies on $Ir^{+4}$ in cubic hosts. The $IrBr_{6}{^{2-}}$ appears to have a somewhat different vibronic pattern. Shifts of zero-phonon origin and the nature of a vibronic progression were analyzed to correlate with host lattice counter-ions. By comparison to luminescence results of Flint and Paulusz, the latter data are proposed to be indicative of a strongly Jahn-Teller active $e{_g}$ mode