Vibrational Circular Dichroism Intensities Research Articles

Vibrational circular dichroism spectroscopy as a probe for the detection of collagen fibril and fibrillation in solution

The detection of collagen fibrils and fibrillation is crucial for tissue regeneration, biomedical applications of collagen, and for studying the interaction of small molecules with the collagen fibrils in the development of therapeutics for collagen-based diseases. At present, collagen fibrillation is probed by high-value microscopic techniques, which limits real-time monitoring of collagen fibril growth and measurement only in dry form. In this context, a quick sensing method is necessary for detecting these fibrils, especially monitoring fibril growth in solution. Herein, we show that vibrational circular dichroism (VCD), a growing spectroscopic technique, can probe collagen fibrils in aqueous solutions by generating an enhanced amide I VCD signal (intensity) compared to monomer. Unlike regular protein VCD measurements, VCD of collagen fibrils require a very low concentration (5 mg/mL) of collagen and can be probed in a very short time (∼10 min). Moreover, VCD responds to the diameter and height of collagen fibrils as evidenced by an increased VCD intensity (close to 103) with pH and NaCl, making VCD a sensitive tool for monitoring the growth of the fibril diameter and height. VCD was also found to be suitable for detecting the time-dependent increase in fibril diameter under fibrillation conditions. Because no other probe is presently available for rapid detection of collagen fibrils in solution form, the ability of VCD to rapidly probe collagen fibrillation in solution and in real-time opens a new way of studying collagen fibrillation in different fields and applications.

Chiral Lanthanide Complexes with l- and d-Alanine: An X-ray and Vibrational Circular Dichroism Study.

A whole series of [Ln(H2O)4(Ala)2]26+ dimeric cationic lanthanide complexes with both l- and d-alanine enantiomers was synthesized. The single-crystal X-ray diffraction at 100 and 292 K shows the formation of two types of dimers (I and II) in crystals. Between the dimer centers, the alanine molecules behave as bridging (μ2-O,O’-) and chelating bridging (μ2-O,O,O’-) ligands. The first type of bridge is present in dimers I, while both bridge forms can be observed in dimers II. The IR and vibrational circular dichroism (VCD) spectra of all l- and d-alanine complexes were registered in the 1750–1250 cm−1 range as KBr pellets. Despite all the studied complexes are exhibiting similar crystal structures, the spectra reveal correlations or trends with the Ln–O1 distances which exemplify the lanthanide contraction effect in the IR spectra. This is especially true for the positions and intensities of some IR bands. Unexpectedly, the ν(C=O) VCD bands are quite intense and their composed shapes reveal the inequivalence of the C=O vibrators in the unit cell which vary with the lanthanide. Unlike in the IR spectra, the ν(C=O) VCD band positions are only weakly correlated with the change of Ln and the VCD intensities at most show some trends. Nevertheless, this is the first observation of the lanthanide contraction effect in the VCD spectra. Generally, for the heavier lanthanides (Ln: Dy–Lu), the VCD band maxima are very close to each other and the mirror reflection of the band of two enantiomers is usually better than that of the lighter Lns. DFT calculations show that the higher the multiplicity the higher the stability of the system. Actually, the molecular geometry in crystals (at 100 K) is well predicted based on the highest-spin structures. Also, the simulated IR and VCD spectra strongly depend on the Ln electron configuration but the best overall agreement was reached for the Lu complex, which is the only system with a fully filled f-shell.

Density Functional Computations of Vibrational Circular Dichroism Spectra beyond the Born-Oppenheimer Approximation.

Transition-metal complexes provide rich features in vibrational circular dichroism (VCD) spectra, including significant intensity enhancements, and become thus useful in structural and functional studies of molecules. Quite often, however, the vibrational spectral bands are mixed with the electronic ones, and interpretation of such experiments is difficult. In the present study, we elaborate on the theory needed to calculate the VCD intensities beyond the Born-Oppenheimer (BO) approximation. Within a perturbation approach, the coupling between the electronic and vibrational states is estimated using the harmonic approximation and simplified wave functions obtainable from common density functional theory (DFT) computations. Explicit expressions, including Slater determinants and derivatives of molecular orbitals, are given. On a model diamine complex, the implementation is tested and factors affecting spectral intensities and frequencies are investigated. For two larger molecules, the results are in a qualitative agreement with previous experimental data. Typically, the electronic-vibrational interaction Hamiltonian coupling elements are rather small (∼0 to 10 cm-1), which provides negligible contributions to vibrational frequencies and absorption intensities. However, significant changes in VCD spectra are induced due to the large transition magnetic dipole moment associated with the d-d metal transitions. The possibility to model the spectra beyond the BO limit opens the way to further applications of chiral spectroscopy and transition-metal complexes.

Analysis of Vibrational Circular Dichroism Spectra of Peptides: A Generalized Coupled Oscillator Approach of a Small Peptide Model Using VCDtools.

Vibrational circular dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work, we study the origin of these VCD signals using the general coupled oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and β-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the through-space coupling of electric dipoles. The crucial role played by intramolecular hydrogen bonds in determining VCD intensities is also illustrated. Moreover, we find that the contributions to the rotational strengths, considered to be insignificant in standard VCD models, may have sizable magnitudes and can thus not always be neglected. In addition, the VCD robustness of the amide I and II modes has been investigated by monitoring the variation of the rotational strength and its contributing terms during linear transit scans and by performing calculations with different computational parameters. From these studies—and in particular, the decomposition of the rotational strength made possible by the GCO analysis—it becomes clear that one should be cautious when employing measures of robustness as proposed previously.

GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra.

As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments.

Vibrational circular dichroism as a probe of solid-state organisation of derivatives of cyclic β-amino acids: Cis- and trans-2-aminocyclobutane-1-carboxylic acid.

Peptide models built from cis- and trans-2-aminocyclobutane-1-carboxylic acids (ACBCs) are studied in the solid phase by combining Fourier-transform infrared spectroscopy (FTIR) absorption spectroscopy, vibrational circular dichroism (VCD), and quantum chemical calculations using density functional theory (DFT). The studied systems are N-tert-butyloxycarbonyl (Boc) derivatives of 2-aminocyclobutanecarboxylic acid (ACBC) benzylamides, namely Boc-(cis-ACBC)-NH-Bn and Boc-(trans-ACBC)-NH-Bn. These two diastereomers show very different VCD signatures and intensities, which of the trans-ACBC derivative being one order of magnitude larger in the region of the ν (CO) stretch. The spectral signature of the cis-ACBC derivative is satisfactorily reproduced by that of the monomer extracted from the solid-state geometry of related ACBC derivatives, which shows that no long-range effects are implicated for this system. In terms of hydrogen bonds, the geometry of this monomer is intermediate between the C6 and C8 structures (exhibiting a 6- or 8-membered cyclic NH⋯O hydrogen bond) previously evidenced in the gas phase. The benzyl group must be in an extended geometry to reproduce satisfactorily the shape of the VCD spectrum in the ν (CO) range, which qualifies VCD as a potential probe of dispersion interaction. In contrast, reproducing the IR and VCD spectrum of the trans-ACBC derivative requires clusters larger than four units, exhibiting strong intermolecular H-bonding patterns. A qualitative agreement is obtained for a tetramer, although the intensity enhancement is not reproduced. These results underline the sensitivity of VCD to the long-range organisation in the crystal.

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.

Intermediate length-scale chirality related to the vibrational circular dichroism intensity enhancement upon fibril formation in a gelation process.

Chiro-optical spectroscopic methods, such as vibrational circular dichroism (VCD) spectroscopy, are regarded as useful measures that provide us information on the structural properties of chiral species, but for correct interpretation of the measured spectra, appropriate modeling that can be compared with the observed spectra is essential. In the present study, the origin of the VCD intensity enhancement observed upon fibril formation in a gelation process is examined theoretically. Comparing with the observed spectroscopic feature and also with the observed scanning electron microscope (SEM) image, it is derived that there are at least three hierarchical tiers of chirality in the gel. The VCD intensity enhancement originates from one of them on the ∼50 nm length scale, which consists of a co-axial antiparallel right-handed double helical structure that persistently continues over ∼100 molecules, indicating that the intermediate length-scale fibril formation plays a crucial role in the VCD intensity enhancement, in a way similar to some fibril-forming peptides examined previously. The time course of the gelation process observed by the time dependence of the VCD intensity is also shown and discussed.

Absolute configuration assignment of (+)-fluralaner using vibrational circular dichroism.

The absolute configurations of the separated enantiomers of fluralaner, a racemic animal health product used to prevent fleas and ticks, have been assigned using vibrational circular dichroism (VCD). The crystallographic structure of the active enantiomer (+)-fluralaner has previously been shown to have the (S) configuration using small molecule crystallography. We sought a faster analytical method to determine the absolute configuration of the separated enantiomers. When comparing the measured IR (infrared) and VCD spectra, it is apparent that the amide carbonyl groups appear in the IR but are nearly absent in the VCD. Computational work to calculate the VCD and IR using in vacuo models, implicit solvation, and explicitly solvated complexes has implicated conformational averaging of the carbonyl VCD intensities.

Origin of enhanced VCD in amyloid fibril spectra: Effect of deuteriation and pH.

Supramolecular chirality of amyloid fibrils, protein aggregates related to many neurodegenerative diseases, is a remarkable property associated with fibril structure and polymorphism. Since its discovery almost 10years ago there is still little understanding of this phenomenon, including the cause of the highly enhanced vibrational circular dichroism (VCD) intensity arising from fibril supramolecular chirality. In this study, VCD spectra, enhanced by filament supramolecular chirality, are presented for lysozyme and insulin fibrils above and below pH2 and after deuterium exchange, above and below pD 2. Supramolecular chirality (observed by VCD) and fibril morphology (documented by atomic force microscopy) are not affected by protein deuteriation. In D2 O the fibril VCD sign pattern changes to fewer bands, with implications for the amide I/II origin of enhanced VCD intensity. Separation of amide I and II signals will facilitate calculations of enhanced VCD spectra of amyloid fibrils and enable a better understanding of the origin of the VCD sign pattern.

A Vibrational Circular Dichroism Microsampling Accessory: Mapping Enhanced Vibrational Circular Dichroism in Amyloid Fibril Films.

We report the first vibrational circular dichroism (VCD) measurement of spatial heterogeneity in a sample using infrared (IR) microsampling. Vibrational circular dichroism spectra are typically measured using a standard IR cell with an IR beam diameter of 10 mm or greater making it impossible to investigate the spatial heterogeneity of a solid film sample. We have constructed a VCD sampling assembly with either 3 mm or 1 mm spatial resolution. An XY-translation stage was used to measure spectra at different spatial locations producing IR and VCD maps of the sample. In addition, a rotating sample stage was employed using a dual photoelastic modulator (PEM) setup to suppress artifacts due to linear birefringence in solid-phase or film samples. Infrared and VCD mapping of an insulin fibril film has been carried out at both 3 and 1 mm spatial resolution, and lysozyme films were mapped at 1 mm resolution. The IR spectra of different spots vary in intensity due primarily to sample thickness. The changes in the VCD intensity across the map largely correlate to corresponding changes in the IR map. Closer inspection of the insulin map revealed changes in the relative intensities of the VCD spectra not present in the parent IR spectra, which indicated differences in the degree of supramolecular chirality of the fibrils in the various spatial regions. For lysozyme films, in addition to different degrees of supramolecular chirality, reversal of the net fibril chirality was observed. The large signal-to-noise ratio observed at 1 mm resolution implies the feasibility of further increasing the spatial resolution by one or two orders of magnitude for protein fibril film samples.

Stereochemical Study of Sphingosine by Vibrational Circular Dichroism.

Vibrational circular dichroism (VCD) was first applied to the stereochemical analysis of sphingosine. VCD patterns derived from the C═C stretch as well as other mid-infrared (IR) regions were practical markers to discriminate all the stereoisomers of intact sphingosine. Glutaraldehyde was found as an excellent derivatizing reagent for sphingosine which improves its solubility in VCD-friendly nonpolar solvents such as chloroform and enhances the VCD intensities by forming a rigid cyclized structure.

Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

We present the first implementation of the vibrational circular dichroism (VCD) spectrum of large molecules through the Molecules-in-Molecules (MIM) fragment-based method. An efficient projection of the relevant higher energy derivatives from smaller fragments to the parent molecule enables the extension of the MIM method for the evaluation of VCD spectra (MIM-VCD). The overlapping primary subsystems in this work are constructed from interacting fragments using a number-based scheme and the dangling bonds are saturated with link hydrogen atoms. Independent fragment calculations are performed to evaluate the energies, Hessian matrix, atomic polar tensor (APT), and the atomic axial tensor (AAT). Subsequently, the link atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, as in the ONIOM approach. In the two-layer model, the long-range interactions between fragments are accounted for using a less computationally intensive lower level of theory. The performance of the MIM model is calibrated on the d- and l-enantiomers of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and VCD intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-VCD method is employed to predict the VCD spectra of perhydrotriphenylene and cryptophane-A, yielding spectra in agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-VCD model for exploring vibrational circular dichroism spectra of large molecules.

Comparison of the electronic and vibrational optical activity of a europium(III) complex.

The geometry and the electronic structure of chiral lanthanide(III) complexes are traditionally probed by electronic methods, such as circularly polarised luminescence (CPL) and electronic circular dichroism (ECD) spectroscopy. The vibrational phenomena are much weaker. In the present study, however, significant enhancements of vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectral intensities were observed during the formation of a chiral bipyridine-Eu(III) complex. The ten-fold enhancement of the vibrational absorption and VCD intensities was explained by a charge-transfer process and the dominant effect of the nitrate ion on the spectra. A much larger enhancement of the ROA and Raman intensities and a hundred-fold increase of the circular intensity difference (CID) ratio were explained by the resonance of the λ = 532 nm laser light with the (7)F0 → (5)D0 transitions. This phenomenon is combined with a chirality transfer, and mixing of the Raman and luminescence effects involving low-energy (7)F states of europium. The results thus indicate that the vibrational optical activity (VOA) may be a very sensitive tool for chirality detection and probing of the electronic structure of Eu(III) and other coordination compounds.

Aggregates from perylene bisimide oligopeptides as a test case for giant vibrational circular dichroism.

Vibrational circular dichroism (VCD) spectroscopy has become an excellent tool to study biological nanostructures and biomimetic materials in their functional environment and is thus complementary to otherwise employed diffraction, imaging, and spectroscopy methods. However, it is still difficult to relate the observed exceptionally large VCD signals to specific structural elements. Here, we systematically studied the VCD signatures of structurally well-defined and thoroughly characterized nanofibrils from oligopeptide-substituted perylene bisimides that comprise single parallel β-sheets. These nanofibrils show a giant VCD signal in the absence of β-sheet stacking and a negative VCD couplet despite their right-handed helicity. The giant VCD signal was very sensitive to subtle changes in the molecular structure as well as (13)C-labeling, which caused a strong disruption of the exciton system as confirmed by two-dimensional infrared spectroscopy. Simulations based on the commonly applied transition dipole coupling model qualitatively reproduced the IR spectra but failed to account for the observed giant VCD or the strong isotope effect. Because our model system and isotope labeling imposes stringent structural constraints of the observed spectroscopic features, our results challenge current assumptions regarding the structural parameters determining VCD sign and intensity. The investigated system may, hence, serve as a benchmark for more sophisticated models with better predictive power for the investigation of protein aggregates in biomedical context or novel oligopeptide-based nanomaterials.

Arrangement of fibril side chains studied by molecular dynamics and simulated infrared and vibrational circular dichroism spectra.

Highly ordered assemblies of β-sheet-forming peptide and protein fibrils have been the focus of much attention because of their multiple and partially unknown biological functions, in particular as related to degenerative neuronal disorders. Recently, vibrational circular dichroism (VCD) spectra have been shown to provide a unique means of detection for such extended structures utilizing modes of the peptide main chain backbone. In the case of poly-glutamic acid, surprising VCD responses were also found for side chain modes. In this study, in an attempt to explain this latter observation and obtain a link between fibrillar structure and its optical spectral properties, molecular dynamics (MD) methods are used to model the geometry and dynamics of assemblies containing repeating β-strands of Glu(n). A crystal-like model was adopted for the MD structure simulations. Infrared and VCD spectra for segments of MD modeled fibrillar geometries were first calculated using density functional theory (DFT), and then, those parameters were applied to larger structures by means of Cartesian coordinate transfer (CCT) of atomic tensors from the segments. The computations suggest the side chains exhibit residual conformational constraints, resulting in local coupling giving rise to non-negligible VCD intensity, albeit with an overall broad distribution. Calculated spectral distributions are qualitatively consistent with the experimental results but do differ in magnitude. The possibility of realistic modeling of vibrational spectra significantly broadens the potential for application of optical spectroscopies in structural studies of these aggregated biopolymers.

Substituent effect in theoretical VCD spectra

A correlational study shows for the first time a quantitative substituent effect on Vibrational Circular Dichroism intensity.

Anharmonicity Effects in the Vibrational CD Spectra of Propylene Oxide

This study reports the first vibrational circular dichroism (VCD) spectra of propylene oxide isolated in an argon matrix. The narrow bandwidth achieved, in addition to the rich VCD features, allows a thorough analysis of the spectra and detailed comparison with the calculated harmonic and anharmonic IR and VCD spectra. Several bands in the fingerprint region are identified as nonfundamental modes based on the harmonic calculation, and three of them feature significant VCD intensity. Anharmonic VCD intensity calculations were carried out using a newly developed methodology based on the second-order level of vibrational perturbation theory. All new bands observed can be undoubtedly assigned to combination or overtone modes except the band at 1486.4 cm–1, which is tentatively identified to contain contributions from an overtone and a combination mode. The study also reveals that the current theoretical approach for anharmonic contributions to VCD spectra needs to be further improved when there is an accident...

Infrared, Vibrational Circular Dichroism, and Raman Spectral Simulations for β-Sheet Structures with Various Isotopic Labels, Interstrand, and Stacking Arrangements Using Density Functional Theory

Infrared (IR), Raman, and vibrational circular dichroism (VCD) spectral variations for different β-sheet structures were studied using simulations based on density functional theory (DFT) force field and intensity computations. The DFT vibrational parameters were obtained for β-sheet fragments containing nine-amides and constrained to a variety of conformations and strand arrangements. These were subsequently transferred onto corresponding larger β-sheet models, normally consisting of five strands with ten amides each, for spectral simulations. Further extension to fibril models composed of multiple stacked β-sheets was achieved by combining the transfer of DFT parameters for each sheet with dipole coupling methods for interactions between sheets. IR spectra of the amide I show different splitting patterns for parallel and antiparallel β-sheets, and their VCD, in the absence of intersheet stacking, have distinct sign variations. Isotopic labeling by (13)C of selected residues yields spectral shifts and intensity changes uniquely sensitive to relative alignment of strands (registry) for antiparallel sheets. Stacking of multiple planar sheets maintains the qualitative spectral character of the single sheet but evidences some reduction in the exciton splitting of the amide I mode. Rotating sheets with respect to each other leads to a significant VCD enhancement, whose sign pattern and intensity is dependent on the handedness and degree of rotation. For twisted β-sheets, a significant VCD enhancement is computed even for sheets stacked with either the same or opposite alignments and the inter-sheet rotation, depending on the sense, can either further increase or weaken the enhanced VCD intensity. In twisted, stacked structures (without rotation), similar VCD amide I patterns (positive couplets) are predicted for both parallel and antiparallel sheets, but different IR intensity distributions still enable their differentiation. Our simulation results prove useful for interpreting experimental vibrational spectra in terms of β-sheet and fibril structure, as illustrated in the accompanying paper.

Vibrational Circular Dichroism Spectra of Lysozyme Solutions: Solvent Effects on Thermal Denaturation Processes

Vibrational spectroscopy has been applied to the study of conformational variation of lysozyme during thermal denaturation. An infrared and vibrational circular dichroism (VCD) analysis of lysozyme in D2O, D2O/EtOD, and D2O/DMSO at different solvent compositions and pH's was accomplished. Complete deuteration effects on amidic groups were revealed through the analysis of the amide I band of lysozyme dissolved in deuterated water. The comparison of IR absorption and VCD spectra of lysozyme in D2O revealed the higher sensitivity of the VCD technique to the presence of partially or fully deuterated secondary structure of lysozyme. Aggregation was induced by thermalization of lysozyme at different solvent compositions and pH values. Interestingly, IR and VCD showed different sensitivities to reveal intermolecular β-sheet aggregation under thermal denaturation. The VCD intensity enhancement was observed as the aggregate dimension increased, whereas IR was sensitive to the nucleation step of the process. Moreover, chirality of supramolecular species was revealed through the analysis of the VCD sign pattern. For the first time, we demonstrate how aggregates produced under different solvent compositions but similar pH's showed the same VCD sign pattern and consequently the same sense of growth.