Raman Optical Activity Spectra Research Articles

Vibrational Raman optical activity of camphor: The importance of electric‐dipole—electric‐quadrupole polarizability contribution

AbstractThe importance of the electric‐dipole—electric‐quadrupole polarizability contribution to the vibrational Raman optical activity (VROA) and dimensionless circular intensity difference spectra of (1S)‐camphor is examined. The spectra are simulated with and without this tensor contribution using density functional theory calculations, and similarity is evaluated for each against the experimental spectra. Careful examination of the comparison between experimental and calculated spectra reveals multiple vibrational bands, in the ~1,130–950 cm−1 region, originating from −C–H bending vibrations that are dominated by the electric‐dipole—electric‐quadrupole polarizability contributions. The similarity overlap analysis also reveals that the similarity overlap between experimental and predicted spectra in the measured spectral range increases, by up to 12%, when electric‐dipole—electric‐quadrupole polarizability contributions are included. The negative VROA band at 1,125 cm−1 in the experimental spectrum of (1S)‐(‐)‐camphor can only be reproduced in the predicted spectra when electric‐dipole—electric‐quadrupole polarizability contribution is included. Investigations on additional molecules indicated that (a) two experimental VROA bands of (1S,4R)‐(+)‐fenchone at ~1,740 and 220 cm−1 originate from dominating electric‐dipole—electric‐quadrupole polarizability contribution and (b) the symmetric and antisymmetric ring deformation modes of dimethyloxirane have dominating electric‐dipole—electric‐quadrupole polarizability contribution. These observations establish the importance of electric‐dipole—electric‐quadrupole polarizability contribution to VROA for the first time.

Simulation of Raman and Raman optical activity of saccharides in solution.

Structural studies of sugars in solution are challenging for most of the traditional analytical techniques. Raman and Raman optical activity (ROA) spectroscopies were found to be extremely convenient for this purpose. However, Raman and ROA spectra of saccharides are challenging to interpret and model due to saccharides' flexibility and polarity. In this study, we present an optimized computational protocol that enables the simulation of the spectra efficiently. Our protocol, which results in good agreement with experiments, combines molecular dynamics and density functional theory calculations. It further uses a smart optimization procedure and a novel adaptable scaling function. The numerical stability and accuracy of individual computational steps are evaluated by comparing simulated and experimental spectra of d-glucose, d-glucuronic acid, N-acetyl-d-glucosamine, methyl β-d-glucopyranoside, methyl β-d-glucuronide, and methyl β-N-acetyl-d-glucosaminide. Overall, our Raman and ROA simulation protocol allows one to routinely and reliably calculate the spectra of small saccharides and opens the door to advanced applications, such as complete 3-dimensional structural determination by direct interpretation of the experimental spectra.

Vibrational (resonance) Raman optical activity with real time time dependent density functional theory.

We present a novel approach for the calculation of vibrational (resonance) Raman optical activity (ROA) spectra based on real time propagation. The ROA linear electronic response tensors are formulated in a propagator formalism in order to treat linear response (LR-) and real time time dependent density functional theory (RT-TDDFT) on equal footing. The length, mixed, and velocity representations of these tensors are discussed with respect to the potential origin dependence of the ROA invariants in the calculations. The propagator formalism allows a straight forward extension of the optical LR tensors in a mixed or velocity representation to a coupling with nonlocal potentials, where an extra term appears in the definition of the momentum operator, in order to maintain the gauge invariance. Using RT-TDDFT paves the way for an innovative, efficient calculation of both on- and off-resonance ROA spectra. Exemplary results are given for the off-resonance and (pre-)resonance spectra of (R)-methyloxirane, considering the resonance effects due to one or more electronically excited states. Moreover, the developed real time propagation approach allows us to obtain entire excitation profiles in a computationally efficient way.

The Raman optical activity of pinane as compared with (-)α- and (-)β-pinene: The perspective of intramolecular enantiomerism

The Raman and Raman optical activity (ROA) spectra of chiral pinane were analyzed by a bond polarizability algorithm. By the differential bond polarizability, the chirality of pinane is compared with our previous results of (-)α- and (-)β-pinene to show the intramolecular enantiomerism. The intramolecular enantiomerism implies the existence of an approximate mirror symmetry. This symmetry is most destroyed by the on-ring CC double in (-)α-pinene. This leads to the decrease of ROA from (-)α-pinene, (-)β-pinene to pinane. Variation of differential bond polarizabilities also follows this trend. This comparison demonstrates the chiral behavior and the roles of the asymmetric centers of (-)α-, (-)β-pinene and pinane from a spectroscopic viewpoint.

Vibrational spectra and theoretical calculations of a natural pentacyclic triterpene alcool isolated from Mucuna pruriens

Nematode control is a significant problem in agriculture industry all over the world. The control is often made with the use of toxic chemicals which can bring detrimental effect to humans, animals, and the environment. Therefore, developing an alternative method of control has become an area of interest such as use of antagonistic plant. Among the variety of antagonist plant species, Mucuna genus are most commonly used. We have carried out a study of the secondary metabolites present on the aerial parts of Mucuna pruriens var. utilis, from which it was isolated and purified a pentacyclic triterpene alcohol, named glutinol. This is the first time the isolation of glutinol is described from this plant species. Identification of this natural product was carried out using infrared, Raman, and NMR spectroscopies. The assignment of the vibrational frequencies was assisted by theoretical calculations using two functionals (HF and B3LYP). Raman optical activity (ROA) frequencies were calculated to assist in te detailed identification of the broad band observed at 2926 cm−1 in the experimental Raman spectrum. The calculated ROA spectra for glutinol (S configuration for the carbon bonded to the hydroxyl group) and R-glutinol (R configuration for the carbon bonded to the hydroxyl group) are discussed to show the potential of this technique to determine the absolute configuration of natural products.

Optical properties of S2 and S3 excited states of protonated schiff-base retinal chromophores in TPA, ECD and ROA.

The electronic transitions of the protonated Schiff base of 1l-cis-retinal (PSB11) and protonated Schiff bases of all-trans retinal (PSBT) for the second or higher electronic excited states are hard to be observed experimentally, due to weak intensities of electronic state excitations. In this paper, we propose visualizations method to investigate these weak electronic state transitions of PSB11 and PSBT, using two-photon absorption (TPA), electronic circular dichroism (ECD) and Raman optical activity (ROA) spectra. Because of the resonance excitations of PSB11 and PSB11 in TPA, the transition intensity of the third electronic state is significantly enhanced, which are much larger than that of S1 and S2 electronic transitions. The charge transfer and electron-hole coherence of these electronic transitions in each step in TPA are visualized with charge difference density and transition density matrix. Also, the strong absorptions of S1 and S2 electronic excited states are observed with ECD spectra, and the physical mechanism of electric and magnetic interactions for these electronic transitions are revealed by visualization method. The large intensity of ROA at S3 excited state results from transition electric and magnetic dipole interactions, not from transition electric dipole and transition electric quadrupole interactions. Our results provide a new visualization method to study the optical properties of biological system using TPA and ECD spectra.

Resonance Effects in the Raman Optical Activity Spectrum of [Rh(en)3]3.

Raman optical activity spectra of Λ-tris(ethylenediamine)-rhodium(III) {[Rh(en)3]3+} have been calculated at 16 on-, near-, and off-resonant wavelengths between 290 and 800 nm. The resulting spectra are analyzed in detail with a focus on the observed resonance effects. Because several electronically excited states are involved, the spectra are never monosignate, as is often observed in resonance Raman optical activity spectra. Most normal modes are enhanced through these resonance effects, but in several cases, de-enhancement effects are found. The molecular origins of the Raman optical activity intensity for selected normal modes are established by means of group coupling matrices. In general, this methodology allows one to produce an intuitive explanation for the intensity behavior of a given normal mode. However, due to the complex electronic structure of [Rh(en)3]3+, there are some intriguing resonance effects the origins of which could not be fully clarified in terms of group coupling effects. Therefore, simple and general rules that predict how the intensity of a specific normal mode is affected by resonance effects are difficult to devise.

Stereostructural Elucidation of Glucose Phosphorylation by Raman Optical Activity

Phosphorylation of glucose is the prime step in sugar metabolism and energy storage. Two key glucose phosphates are involved, that is, glucose 6-phosphate (G6P) and α-glucose 1-phosphate (αG1P). The chiral conformation of glucose, G6P, and αG1P plays an essential role in enzyme-mediated conversions. However, few techniques were able to give a direct view of the conformational changes from glucose to G6P and αG1P. Here, Raman optical activity (ROA) was used to elucidate the stereochemical evolution of glucose upon phosphorylation. ROA was found to be extremely sensitive to different phosphorylation sites. A characteristic ROA marker of (+)980 cm-1, originated from the phosphate group symmetric stretching vibration, is observed for αG1P with phosphorylation at chiral C1, while no corresponding ROA signal for G6P with phosphorylation at achiral C6 is observed. Phosphorylation-induced gauch-gauch (gg)/gauch-trans (gt) rotamer distribution changes can be sensitively probed by the sign of the ROA band around 1460 cm-1. A positive ROA band at 1465 cm-1 of glucose corresponds to a higher gt ratio, while a negative band at 1455 cm-1 of G6P suggests a dominant gg population, and the disappearance of this ROA band for αG1P indicates a nearly balanced gg/gt distribution. Meanwhile, the phosphorylation at C6 and C1 could cause dramatic reduction of the conformational flexibility of the adjacent C4-OH and C2-OH, respectively. These stereochemical changes revealed by ROA spectra offer a structural basis on the understanding of sugar phosphorylation from the perspective of chirality.

On/off resonance Raman optical activity of human serum transferrin

AbstractThe transferrin proteins exhibit two high affinity Fe(III) binding pockets and are responsible for the iron transport into cells of higher order organisms. Previously, transferrins have been studied as possible transporter molecules for drugs delivery. In this study, Raman optical activity (ROA) was employed to investigate human serum transferrin. Due to the presence of Fe(III) in the holo form of the protein, it is in resonance with the the laser excitation wavelength (of 532 nm) used in the experiments. Consequently, resonance enhanced ROA bands were observed in the spectrum of the holo form. Nevertheless, far from resonance bands, arising from the protein backbone, could simultaneously be observed in the ROA spectrum of the holo form. This implies that ROA can be used to provide simultaneously information on the metal binding pocket as well as on the secondary structure of the protein. Furthermore, it was found that the amount of observed resonance enhanced ROA signals can be tuned by partially removing the iron present in the protein. Electronic circular dichroism (ECD) was employed to verify the Raman/ROA results.

Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity.

Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.

The nature of chirality induced by molecular aggregation and self-assembly.

In this paper, we theoretically analyze the nature of chirality induced by molecular self-assembly with molecular dynamics and visualization methods. Firstly, the dynamics of molecular self-assembly of biphenylenes system are demonstrated in detail. Secondly, the molecular interactions for the assembled molecules are analyzed with the weak intermolecular forces. Thirdly, electron-hole coherence and charge transfer in optical absorption are demonstrated with a transition density matrix and charge difference density, respectively. The detailed visualized analysis of electric and magnetic transition dipole moment integrals reveals the nature of chirality of assembled molecules in electronic circular dichroism (ECD) spectroscopy. The Raman optical activity (ROA) spectra demonstrate that the chirality of assembled molecules is strongly dependent on the pre-resonance Raman spectra, based on the optical absorption and ECD spectroscopy. Our visualized analysis method can well reveal the nature and origin of chirality of molecular self-assembly.

The effect of protein backbone hydration on the amide vibrations in Raman and Raman optical activity spectra.

Raman and specifically Raman optical activity (ROA) spectroscopy are very sensitive to the solution structure and conformation of biomolecules. Because of this strong conformational sensitivity, density functional theory (DFT) calculations are often used to get a better understanding of the experimentally observed spectral patterns. While e.g. for carbohydrate structure the water molecules that surround the solute have been demonstrated to be of vital importance to get accurate modelled ROA spectra, the effect of explicit water molecules on the calculated ROA patterns of peptides and proteins is less well studied. Here, the effect of protein backbone hydration was studied using DFT calculations of HCO-(l-Ala)5-NH2 in specific secondary structure conformations with different treatments of the solvation. The effect of the explicit water molecules on the calculated spectra mainly arises from the formation of hydrogen bonds with the amide C[double bond, length as m-dash]O and N-H groups. Hydrogen bonding of water with the C[double bond, length as m-dash]O group determines the shape and position of the amide I band. The C[double bond, length as m-dash]O bond length increases upon formation of C[double bond, length as m-dash]OH2O hydrogen bonds. The effect of the explicit water molecules on the amide III vibrations arises from hydrogen bonding of the solvent with both the C[double bond, length as m-dash]O and N-H group, but their contributions to this spectral region differ: geometrically, the formation of a C[double bond, length as m-dash]OH2O bond decreases the C-N bond length, while upon forming a N-HH2O hydrogen bond, the N-H bond length increases.

Absolute Configurations of Naturally Occurring [5]- and [3]-Ladderanoic Acids: Isolation, Chiroptical Spectroscopy, and Crystallography.

We have isolated mixtures of [5]- and [3]-ladderanoic acids 1a and 2a from the biomass of an anammox bioreactor and have separated the acids and their phenacyl esters for the first time by HPLC. The absolute configurations of the naturally occurring acids and their phenacyl esters are assigned as R at the site of side-chain attachment by comparison of experimental specific rotations with corresponding values predicted using quantum chemical (QC) methods. The absolute configurations for 1a and 2a were independently verified by comparison of experimental Raman optical activity spectra with corresponding spectra predicted using QC methods. The configurational assignments of 1a and 2a and of the phenacyl ester of 1a were also confirmed by X-ray crystallography.

The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins.

The Raman optical activity (ROA) spectra of proteins show distinct patterns arising from the secondary structure. It is generally believed that the spectral contributions of the side-chains largely cancel out because of their flexibility and the occurrence of many side-chains with different conformations. Yet, the influence of the side-chains on the ROA patterns assigned to different secondary structures is unknown. Here, the first systematic study of the influence of all amino acid side-chains on the ROA patterns is presented based on density functional theory (DFT) calculations of an extensive collection of peptide models that include many different side-chain and secondary structure conformations. It was shown that the contributions of the side-chains to a large extent average out with conformational flexibility. However, specific side-chain conformations can have significant contributions to the ROA patterns. It was also shown that α-helical structure is very sensitive to both the exact backbone conformation and the side-chain conformation. Side-chains with χ1 ≈-60° generate ROA patterns alike those in experiment. Aromatic side-chains strongly influence the amide III ROA patterns. Because of the huge structural sensitivity of ROA, the spectral patterns of proteins arise from extensive conformational averaging of both the backbone and the side-chains. The averaging results in the fine spectral details and relative intensity differences observed in experimental spectra.

Conformational Disorder and Dynamics of Proteins Sensed by Raman Optical Activity.

Raman optical activity (ROA) spectra of proteins hold a lot of information about their structure in solution. To create a better understanding of the ROA spectra of, among others, the intrinsically disordered proteins (IDPs), involved in neurodegenerative diseases, the effect of conformational disorder and dynamics on the ROA spectra was studied. Density functional theory (DFT) calculations of small ensembles of model peptides with increasing disorder show that the ROA patterns of α-helical and polyproline II (PPII) structure reflect the average backbone angles in the ensemble. The amide III region in the ROA spectra of the α-helical peptides is shown to retain its typical −/+/+ pattern, while the amide III region of PPII secondary structure diminishes in intensity with increasing structural disorder. The results show that the ROA spectra of IDPs hence more likely stem from short stretches of well-defined PPII helices rather than a very flexible chain. Further DFT calculations support that mixing of PPII with helical secondary structure is consistent with experimental spectra of IDPs, while mixing with β-strand results in spectral patterns that are not observed experimentally. The detailed information obtained from these results contributes to a better understanding of the spectrum–structure relation.

Is Raman Optical Activity Spectroscopy Sensitive to β-Turns in Proteins? Secondary Structure and Side-Chain Dependence.

β-turns are essential for the structure and function of proteins. The spectroscopic technique Raman optical activity (ROA) has been suggested to be sensitive to such structural elements of proteins in solution. Three spectral features have been reported to mark β-turns in protein ROA spectra: being a negative band at 1220 cm-1 , positive intensity around 1290 cm-1 and negative intensity around 1340-1380 cm-1 . In this work, density functional theory calculations demonstrated that these assignments are inaccurate as these spectral regions are not robust and sense the exact secondary structure surrounding the β-turn as well. Furthermore, it was demonstrated that the amino acid side-chains affect the exact ROA patterns which can direct future research to perform a systematic analysis of the contributions of the side-chains.

Redox-Active Chiroptical Switching in Mono- and Bis-Iron Ethynylcarbo[6]helicenes Studied by Electronic and Vibrational Circular Dichroism and Resonance Raman Optical Activity.

Introducing one or two alkynyl-iron moieties onto a carbo[6]helicene results in organometallic helicenes (2 a,b) that display strong chiroptical activity combined with efficient redox-triggered switching. The neutral and oxidized forms have been studied in detail by electronic and vibrational circular dichroism, as well as by Raman optical activity (ROA) spectroscopy. The experimental results were analyzed and spectra were assigned with the help of first-principles calculations. In particular, a recently developed method for ROA calculations under resonance conditions has been used to study the intricate resonance effects on the ROA spectrum of mono-iron ethynylhelicene 2 a.

IR, Raman, and Vibrational Optical Activity Spectra of Methyl Glycidate in Chloroform and Water: The Clusters-in-a-liquid Solvation Model.

Solvent effects, in particular those involving water as the solvent, are of significant interest to the chemistry and physics communities. IR, vibrational circular dichroism (VCD), Raman, and Raman optical activity (ROA) spectra of methyl glycidate in two very different solvents, namely CCl4 and water, have been measured experimentally and simulated theoretically. The observed spectra in CCl4 could be well modelled using the polarizable continuum model for the solvent, whereas the situation is much different in water. The experimental VCD spectrum of methyl glycidate in water reveals strong induced VCD signatures in the water bending region, indicating the presence of the relatively long-lived methyl glycidate-watern complexes. We applied the clusters-in-a-liquid approach to identify the dominant methyl glycidate-water1,2 complexes which are the long-lived species responsible for all the spectra observed in water. We examined the influences of solvent dielectric environment and the hydrogen-bonding interactions on the conformational distribution of methyl glycidate. The geometry optimizations, frequency calculations, IR, VCD, Raman and ROA intensity calculations were performed at the B3LYP/6-311++G(2d,p) and aug-cc-pVTZ levels of theory with D3BJ dispersion correction. It is particularly satisfying to note that the clusters-in-a-liquid approach has captured all main experimental features in IR, VCD, Raman and ROA spectra of methyl glycidate in water.

Optically Active Vibrational Spectroscopy of α-Aminoisobutyric Acid Foldamers in Organic Solvents and Phospholipid Bilayers.

Helical α-aminoisobutyric acid (Aib) foldamers show great potential as devices for the communication of conformational information across phospholipid bilayers, but determining their conformation in bilayers remains a challenge. In the present study, Raman, Raman optical activity (ROA), infrared (IR) and vibrational circular dichroism (VCD) spectroscopies have been used to analyze the conformational preferences of Aib foldamers in solution and when interacting with bilayers. A 310 -helix marker band at 1665-1668 cm-1 in Raman spectra was used to show that net helical content increased strongly with oligomer length. ROA and VCD spectra of chiral Aib foldamers provided the chiroptical signature for both left- and right-handed 310 -helices in organic solvents, with VCD establishing that foldamer screw-sense was preserved when the foldamers became embedded within bilayers. However, the population distribution between different secondary structures was perturbed by the chiral phospholipid. These studies indicate that ROA and VCD spectroscopies are valuable tools for the study of biomimetic structures, such as artificial signal transduction molecules, in phospholipid bilayers.

Resveratrol's Hidden Hand: A Route to the Optical Detection of Biomolecular Binding.

Resveratrol is a stilbenoid phytoalexin with promising myriad health benefits predominantly contributed by the trans ( E) diastereomeric form. A recent study has implicated the cis ( Z) diastereomer in human health. This stereoisomer binds with high affinity to human tyrosyl-tRNA synthetase, initiating a downstream cascade that promotes the expression of genes associated with the cellular stress response. We discovered that the nonplanar structure of the cis-resveratrol conformer possesses certain chiral signals in its simulated vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra. These features may be used for the optical detection of the binding event and in understanding the more diversified biological roles of trans-resveratrol over cis-resveratrol. We use a density functional theory model, which is validated against the known results for the E diastereomer. The Z diastereomer is significantly nonplanar and can exist in two helical atropisomeric forms. These forms exchange rapidly in solution, but only one is observed to bind with the synthetase. This suggests that the binding may generate an enantiomeric excess, leading to detectable changes in the vibrational optical activity spectra. We identify candidate features at 998, 1649, and 1677 cm-1 in the ROA and at 1642 and 3834 cm-1 in the VCD spectra of Z-resveratrol that may be useful for this purpose.