Molecular structures of viruses from Raman optical activity.

Raman and vibrational Raman optical activity (ROA) spectra have been calculated for three molecules: H2O2, CHDTF and CHDTOH. The effects of electron correlation on the ROA parameters of these relatively small systems have been investigated by means of the multiconfigurational self-consistent field (SCF) approach. A range of correlation-consistent basis sets has been used in the calculations. The basis set convergence of the calculated ROA parameters is fairly well achieved when sets of at least d-aug-cc-pVTZ quality are used. On the other hand, the aug-cc-pVDZ set seems to be sufficient for a qualitative analysis. Diffuse functions, possibly a double set, are essential to ensure a good quality of the calculated ROA spectrum. In most cases the sign and approximate magnitude of the ROA are correctly predicted at the SCF level, and the corresponding ROA spectra should be considered qualitatively accurate.

Purification and properties of the components of cowpea mosaic virus.

Infrared vibrational circular dichroism (VCD) and vibrational Raman optical activity (ROA) have been measured and compared quantitatively over the frequency range from 835 to 1345 cm−1 for trans-pinane, cis-pinane, α-pinene, and β-pinene. For these molecules in this region of spectral overlap between VCD and ROA, the average ratio of VCD or ROA to its parent vibrational intensity favors ROA by a factor of two to three. Several vibrational modes in each molecule yield both large VCD and large ROA, while several other modes show little propensity toward significant VCD or ROA intensity. Beyond this general property of a few strongly chiral and strongly achiral vibrational modes, little additional correlation between VCD and ROA intensity is found. This quantitative compilation of VCD, infrared, ROA, and Raman intensities provides an experimental basis for computational intensity studies of VCD, ROA, and their theoretical comparison.

Natural resonance electronic Raman optical activity (ROA) is observed for the first time. Coincidently, the first example of vibrational ROA enhanced by low‐lying electronic transition is reported. These new phenomena were measured using the rare‐earth complex Eu(tfc)3 (+)‐tris[3‐trifluoroacetyl‐D‐camphorato]europium(III), where electronic resonance occurs between the 532‐nm laser excitation and the 7F1 → 5D1 transition of the Eu3+ metal center. Electronic Raman spectra involve the Raman transitions terminating on the low‐lying electronic states of Eu(tfc)3. The observed vibrational ROA spectra are enhanced relative to typical ROA spectra by the proximity of vibrational states of Eu(tfc)3 to its low‐lying electronic states with significant magnetic‐dipole character, whereas the parent vibrational Raman spectra do not appear to be resonance‐enhanced since the 532‐nm vibrational Raman spectrum has similar relative intensities to the corresponding Raman spectrum measured with 1064‐nm laser excitation. Copyright © 2010 John Wiley & Sons, Ltd.

Vibrational Spectra:Principles and Applications with emphasis on optical activity

Vibrational Raman optical activity (ROA) is measured in our laboratory as a small intensity difference in Raman scattered light from chiral molecules in right and left circularly polarized incident light.[l, 2] Recently, a series of instrumental advances [3] has opened up the realm of biopolymers, including proteins, polysaccharides and now nucleic acids, to this novel chiroptical technique. For proteins and polysaccharides it has already been demonstrated that ROA can probe key structural elements more incisively than conventional Raman spectroscopy because it can cut through the complexity of the conventional spectra by probing directly the crucial chiral elements of biomolecular structure. In this contribution we focus on some of our recent results on polynucleotides and as an example present the Raman and ROA spectra of poly(rG)•poly(rC) in H2O between 650 and 1750 cm −1 in Figure 1.

Chirality plays a crucial role in drug discovery and development. As a result, a significant number of commercially available drugs are structurally dissymmetric and enantiomerically pure. The determination of the exact 3D structure of drug candidates is, consequently, of paramount importance for the pharmaceutical industry in different stages of the discovery pipeline. Traditionally the assignment of the absolute configuration of druggable molecules has been carried out by means of X-ray crystallography. Nevertheless, not all molecules are suitable for single-crystal growing. Additionally, valuable information about the conformational dynamics of drug candidates is lost in the solid state. As an alternative, vibrational optical activity (VOA) methods have emerged as powerful tools to assess the stereochemistry of drug molecules directly in solution. These methods include vibrational circular dichroism (VCD) and Raman optical activity (ROA). Despite their potential, VCD and ROA are still unheard of to many organic and medicinal chemists. Therefore, the present review aims at highlighting the recent use of VOA methods for the assignment of the absolute configuration of chiral small-molecule drugs, as well as for the structural analysis of biologics of pharmaceutical interest. A brief introduction on VCD and ROA theory and the best experimental practices for using these methods will be provided along with selected representative examples over the last five years. As VCD and ROA are commonly used in combination with quantum calculations, some guidelines will also be presented for the reliable simulation of chiroptical spectra. Special attention will be paid to the complementarity of VCD and ROA to unambiguously assess the stereochemical properties of pharmaceuticals.

Experimental and ab initio theoretical vibrational Raman optical activity of alanine

Simultaneous haemo-filtration and haemo dialysis

Determination of the absolute handedness, known as absolute configuration (AC), of chiral molecules is an important step in any field related to chirality, especially in the pharmaceutical industry. Vibrational optical activity (VOA) has become a powerful tool for the determination of the AC of chiral molecules in the solution state after nearly forty years of evolution. VOA offers a novel alternative, or supplement, to X-ray crystallography, permitting AC determinations on neat liquid, oil, and solution samples without the need to grow single crystals of the pure chiral sample molecules as required for X-ray analysis. By comparing the sign and intensity of the measured VOA spectrum with the corresponding ab initio density functional theory (DFT) calculated VOA spectrum of a chosen configuration, one can unambiguously assign the AC of a chiral molecule. Comparing measured VOA spectra with calculated VOA spectra of all the conformers can also provide solution-state conformational populations. VOA consists of infrared vibrational circular dichroism (VCD) and vibrational Raman optical activity (ROA). Currently, VCD is used routinely by researchers in a variety of backgrounds, including molecular chirality, asymmetric synthesis, chiral catalysis, drug screening, pharmacology, and natural products. Although the application of ROA in AC determination lags behind that of VCD, with the recent implementation of ROA subroutines in commercial quantum chemistry software, ROA will in the future complement VCD for AC determination. In this review, the basic principles of the application of VCD to the determination of absolute configuration in chiral molecules are described. The steps required for VCD spectral measurement and calculation are outlined, followed by brief descriptions of recently published papers reporting the determination of AC in small organic, pharmaceutical, and natural product molecules.

We present a systematic study of the basis set dependence of the backscattering vibrational Raman intensities and Raman Optical Activity (ROA) intensity differences. The accuracies of computed Raman intensities and ROA intensity differences for a series of commonly used basis sets are reported, relative to large reference basis sets, using the B3LYP density functional. This study attempts to separately quantify the relative accuracies obtained from particular basis set combinations: one for the geometry optimization and force field computation and the other for the computation of Raman and ROA tensors. We demonstrate here that the basis set requirements for the geometry and force fields are not similar to those of the Raman and ROA tensors. The Raman and ROA tensors require basis sets with diffuse functions, while geometry optimizations and force field computations typically do not. Eleven molecules were examined: (S)-methyloxirane, (S)-methylthirane, (R)-epichlorhydrin, (S)-CHFClBr, (1S,5S)-α-pinene, (1S,5S)-β-pinene, (1S,4S)-norborneneone, (M)-σ-[4]-helicene, an enone precursor to a cytotoxic sesquiterpene, the gauche-gauche conformer of the monosaccharide methyl-β-d-glucopyranose, and the dipeptide Ac-(alanine)2-NH2. For the molecules examined here, intensities and intensity differences obtained from Raman and ROA tensors computed using the aug-cc-pVDZ basis set are nearly equivalent to those computed with the larger aug-cc-pVTZ basis set. We find that modifying the aug-cc-pVDZ basis set by removing the set of diffuse d functions on all atoms (while keeping the diffuse s and p sets), denoted as aug(sp)-cc-pVDZ, results in a basis set which is significantly faster without much reduction in the overall accuracy. In addition, the popular rDPS basis set introduced by Zuber and Hug offers a good compromise between accuracy and efficiency. The combination of either the aug(sp)-pVDZ or rDPS basis for the computation of the Raman and ROA tensors with the 6-31G* basis set for the geometry optimization and force field calculation is a reliable and cost-effective method for obtaining Raman intensities and ROA intensity differences.

The correlation between the proportions of virus-related products and the infectious component during the synthesis of tobacco ringspot virus

The molecular basis of the interactions between plant virus satellites and their helper viruses is not understood. The features of the satellite tobacco mosaic virus (STMV) genome that determine tobamovirus helper specificity were investigated using two independent strategies. The first tested the possible significance of regions of nearly identical sequence within the 3'-terminal 150 bases of the genomes of STMV and its natural helper virus, tobacco mild green mosaic virus (TMGMV). A chimeric STMV clone containing the 3' terminus of tobacco mosaic virus (TMV-U1) RNA was infectious in coinfections with TMGMV, but it did not replicate with TMV-U1. In the second strategy, populations of STMV adapted to replication with four alternative helper tobamoviruses were generated by serial passage in tobacco. RNase protection analyses of these RNA populations showed that in all cases there had been a genetic change 50 to 60 bases from the 5' terminus of the STMV genome. Similar changes were detected in several progenies of STMV clones replicated with TMV-U1, indicating that change at this site was essential for replication with a helper virus other than TMGMV. Sequence analyses of the changes at this 'helper adaptation domain' showed consistently the deletion of a single G from five consecutive Gs at bases 61 to 65. Infectivity experiments with STMV clones containing this G deletion showed that this change alone was not sufficient to modify helper specificity, so additional factors which remain to be identified must also be involved. Nevertheless, these experiments show the ability of STMV populations to undergo rapid, reproducible evolution by both selection of pre-existing variants and de novo mutation, and constitute the first molecular demonstration that the helper virus acts as a selection pressure on the evolution of satellite populations.

Polyglutamic acid (PGA) is an excellent model system to study peptide and protein folding. Its conformation in solution can be conveniently studied by vibrational optical activity. To better understand the behavior of the molecule in different protonation states and advance the spectroscopic methodology, we obtained infrared (IR), vibrational circular dichroism (VCD), Raman, and Raman optical activity (ROA) spectra of various PGA forms and interpreted them on the basis of molecular dynamics (MD) and density functional theory (DFT) computations. The spectra include the ROA of PGA fibrils, which have been rather unexplored so far. The fibrils provided a distinct ROA pattern, which could be verified by the measurement of both enantiomers. Advancements in the use of vibrational spectroscopy for amyloid fibrils may contribute to the understanding of the biological role of these protein forms, often accompanying neurodegenerative diseases. The computations provided a reliable link between the spectral shapes and molecular geometry, and the simulated spectra reproduced the most important experimental features, although band-to-band simulations of the fibril vibrational optical activity remain challenging. The results nevertheless clearly show that vibrational optical activity combined with spectral simulations appears as a handy tool to study the geometry of proteins, including their aggregates.

Five isolates of the beetle-transmitted cowpea mosaic virus were studied. The symptoms produced by each on a number of hosts were described. The occurrence of amorphous inclusion bodies in the epidermal cells of infected cowpea and pea plants was reported. A purification procedure was described. Three peaks were invariably associated with the purified virus in the analytical ultracentrifuge, the sedimentation coefficients of these components being 58, 100 and 119 S after separation. The components could be purified by density-gradient centrifugation. The top component was not infective; the middle component was far more infective than the bottom component. Purified preparations showed, by electron-microscopy, polyhedral particles of about 25 mμdiameter. Negative staining of the preparations with phosphotungstate revealed empty particles, and of particles apparently containing nucleic acid. An icosahedral model with 60 subunits and 5: 3: 2 axial symmetry was most compatible with the structure of the particles seen on the electron-micrographs. On the basis of homologous and heterologous serological reactions the five isolates could be divided into two groups. They proved also to be serologically related to bean pod mottle virus and to an isolate of red clover mottle virus.