Vibrational Spectra:Principles and Applications with emphasis on optical activity

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.

A comparison of the aqueous solution vibrational Raman optical activity (ROA) spectra of poly-L-lysine in random coil and α-helix conformations with those of bovine serum albumin and insulin, which are both rich in α-helix, is reported. Possible ROA signatures of α-helix include a broad positive band in the range ∼900-1000 cm -1 and a couplet, negative at low wavenumber and positive at high, centred at ∼1103 cm -1 , both features originating in backbone C α -C and C α -N stretch modes; a negative-positive couplet centred at ∼1275 cm -1 originating in backbone amide III C α H and NH deformations; and a positive band in the amide I region peaking at ∼1665 cm -1

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.

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.

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.

We present an analytical time-dependent Hartree-Fock algorithm for the calculation of the derivatives of the electric dipole-magnetic dipole polarizability with respect to atomic Cartesian coordinates. Combined with analogous procedures to determine the derivatives of the electric dipole-electric dipole and electric dipole-electric quadrupole polarizabilities, it enables a fully analytical evaluation of the three frequency-dependent vibrational Raman optical activity (VROA) invariants within the harmonic approximation. The procedure employs traditional non-London atomic orbitals, and the gauge-origin dependence of the VROA intensities has, therefore, been assessed for the commonly used aug-cc-pVDZ and rDPS:3-21G basis sets.

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

Determining the absolute configuration of a molecule is possible by means of various chiroptical spectroscopic methods, one of them being vibrational Raman optical activity (VROA). By adopting a laser excitation wavelength in resonance with an electronic transition, the weak spectral signals can be selectively enhanced. We implement a Kohn-Sham methodology for the calculation of resonance and off-resonance VROA spectra to (S)-naproxen and (S)-ibuprofen and discuss their band patterns. The resonance enhancement of the VROA spectrum of (S)-naproxen at an incident wavelength of 514.5 nm caused by an absorption tail as well as the typical off-resonance behavior of the VROA spectrum of (S)-ibuprofen at the same incident wavelength can be well reproduced. VROA spectra are also predicted under full resonance conditions.

Chiroptical spectroscopyis sensitive to the formation of intermolecularinteractions for chiral molecules. Experimental Vibrational CircularDichroism (VCD), Vibrational Raman Optical Activity (ROA), and OpticalRotatory Dispersion (ORD) data of (−)-[5]-ladderanoic acidin chloroform have been analyzed using theoretical predictions forboth monomeric and dimeric structures of (R)-[5]-ladderanoicacid to better understand their utility for the interpretation ofexperimental data. B3LYP, B3PW91, and M06-2X functionals, with andwithout dispersion corrections, and the 6-31+G­(2d,p) basis set wereused for theoretical predictions. It is found that dimer contributionsare important to better reproduce the experimental vibrational absorptionand associated VCD spectra, and a monomer:dimer ratio of 30:70 isindicated at the B3LYP level. However, no significant improvementis evident from dimer contributions to reproduce the experimentalRaman and associated ROA spectra, and a monomer:dimer ratio of 100:0is indicated at the B3LYP level. Boltzmann population-weighted specificrotations are predicted to be negative for both monomeric and dimericconformations of (R)-[5]-ladderanoic acid, and quantitativeagreement with the experimental ORD of (−)-[5]-ladderanoicacid is obtained with a 70:30 mixture of monomers and dimers.

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.

A vibrational Raman optical activity (ROA) study of a range of different structural types of virus exemplified by filamentous bacteriophage fd, tobacco mosaic virus, satellite tobacco mosaic virus, bacteriophage MS2 and cowpea mosaic virus has revealed that, on account of its sensitivity to chirality, ROA is an incisive probe of their aqueous solution structures at the molecular level. Protein ROA bands are especially prominent from which, as we have shown by comparison with the ROA spectra of proteins with known structures and by using a pattern recognition program, the folds of the major coat protein subunits may be deduced. Information about amino acid side-chain conformations, exemplified here by the determination of the sign and magnitude of the torsion angle chi(2,1) for tryptophan in fd, may also sometimes be obtained. By subtracting the ROA spectrum of the empty protein capsid (top component) of cowpea mosaic virus from those of the intact middle and bottom-upper components separated by means of a caesium chloride density gradient, the ROA spectrum of the viral RNA was obtained, which revealed that the RNA takes up an A-type single-stranded helical conformation and that the RNA conformations in the middle and bottom-upper components are very similar. This information is not available from the X-ray crystal structure of cowpea mosaic virus since no nucleic acid is visible.

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.

Comment on a sum rule for vibrational raman optical activity

Simultaneous haemo-filtration and haemo dialysis