Microscopic vibrational circular dichroism on the forewings of a European hornet: heterogenous sequences of protein domains with different secondary structures

We developed a microscopic scanning for vibrational circular dichroism (VCD) spectroscopy in which a quantum cascade laser is equipped with a highly focused infrared light source to attain a spatial resolution of 100 μm. This system was applied to the forewing of a European hornet to reveal how the protein domains are organised. Two-dimensional patterns were obtained from the VCD signals with steps of 100 μm. We scanned the 1500-1740 cm-1 wavenumber range, which covers amide I and II absorptions. Zone sequenced α-helical and β-sheet domains within an area of 200 μm2 in membranes close to where two veins cross. The sign of the VCD signal at 1650 cm-1 changed from positive to negative when probed along the zone axis, intermediated by the absence of VCD activity. The significance of this zone is discussed from the viewpoint of the mechanical properties required for flying motion. These features are unattainable using conventional FTIR (Fourier transform infrared) or FT-VCD methods with a spatial resolution of ∼10 mm2.

Circular Polarization-Resolved Raman Optical Activity: A Perspective on Chiral Spectroscopies of Vibrational States

Circular polarization-resolved Raman scattering methods include Raman optical activity (ROA) and its derivative─surface-enhanced Raman optical activity (SEROA). These spectroscopic modalities are rapidly developing due to their high information content, stand-off capabilities, and rapid development of Raman-active chiral nanostructures. These methods enable a direct readout of the vibrational energy levels of chiral molecules, crystals, and nanostructured materials, making it possible to study complex interactions and the dynamic interfaces between them. They were shown to be particularly valuable for nano- and biotechnological fields encompassing complex particles with nanoscale chirality that combine strong scattering and intense polarization rotation. This perspective dives into recent advancements in ROA and SEROA, their distinction from surface-enhanced Raman scattering, and the potential of these information-rich label-free spectroscopies for the detection of chiral biomolecules.

Induced Chirality in Canthaxanthin Aggregates Reveals Multiple Levels of Supramolecular Organization

Carotenoids tend to form supramolecular aggregates via non-covalent interactions where the chirality of individual molecules is amplified to the macroscopic level. We show that this can also be achieved for non-chiral carotenoid monomers interacting with polysaccharides. The chirality induction in canthaxanthin (CAX), caused by heparin (HP) and hyaluronic acid (HA), was monitored by chiroptical spectroscopy. Electronic circular dichroism (ECD) and Raman optical activity (ROA) spectra indicated the presence of multiple carotenoid formations, such as H- and J-type aggregates. This is consistent with molecular dynamics (MD) and density functional theory (DFT) simulations of the supramolecular structures and their spectroscopic response.

Probing solution conformations of l-DOPA: Integration of experiment and simulation via vibrational optical activity

l-DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l-DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l-DOPA itself is necessary. This article presents a thorough examination of the vibrational spectra of l-DOPA, with a particular emphasis on chirally sensitive VOA techniques. We successfully obtained high-quality Raman and ROA spectra of l-DOPA in its cationic form, under low pH conditions, and at a high concentration of 100 mg/ml. These spectra cover a broad spectral range, allowing for precise comparisons with theoretical simulations. We also obtained IR and VCD spectra, but they faced limitations due to the narrow accessible spectral region. Exploration of l-DOPA's conformational landscape revealed its intrinsic flexibility, with multiple coexisting conformations. To characterize these conformations, we employed two methods: one involved potential energy surface scans with implicit solvation, and the other utilized molecular dynamics simulations with explicit solvation. Comparing ROA spectra from different conformer groups and applying spectral decomposition proved crucial in determining the correct conformer ratios. The use of explicit solvation significantly improved the quality of the final simulated spectral profiles. The accurate determination of conformer ratios, rather than solely relying on the number of averaged spectra, played a crucial role in simulation accuracy. In conclusion, our study offers valuable insights into the structure and conformational behavior of l-DOPA and represents a valuable resource for subsequent spectroscopic studies of its deuterated analogs.

Scaling-up VPT2: A feasible route to include anharmonic correction on large molecules

Vibrational analysis plays a crucial role in the investigation of molecular systems. Though methodologies like second-order vibrational perturbation theory (VPT2) have paved the way to more accurate simulations, the computational cost remains a difficult barrier to overcome when the molecular size increases. Building upon recent advances in the identification of resonances, we propose an approach making anharmonic simulations possible for large-size systems, typically unreachable by standard means. This relies on the fact that, often, only portions of the whole spectra are of actual interest. Therefore, the anharmonic corrections can be included selectively on subsets of normal modes directly related to the regions of interest. Starting from the VPT2 equations, we evaluate rigorously and systematically the impact of the truncated anharmonic treatment onto simulations. The limit and feasibility of the reduced-dimensionality approach are detailed, starting on a smaller model system. The methodology is then challenged on the IR absorption and vibrational circular dichroism spectra of an organometallic complex in three different spectral ranges.

Differentiation of solvatomorphs of active pharmaceutical ingredients (API) by solid-state vibrational circular dichroism (VCD)

Here, we present the new application of solid-state Vibrational Circular Dichroism (VCD) spectroscopy to differentiate several dutasteride (DS) solvatomorphs - the model active pharmaceutical ingredient (API). Several crystalline DS hydrochloride hydrates solvated with methanol, ethanol, acetonitrile, acetone, and acetic acid were prepared. In contrast to almost identical IR spectra, the VCD ones were very sensitive to changes in the sample composition. We marked significant differences in the shape of VCD spectra of studied DS solvatomorphs, DS hydrates, and DS polymorphic forms. Our findings, supported by DFT calculations, show that VCD spectroscopy has the pronounced ability to distinguish their crystal arrangements. We believe that this contribution will extend the use of VCD in the pharmaceutical industry for developing and designing new chiral drug products for the identification, description, and in-depth probing of several pharmaceutical solvatomorphs in the future.

Practical phase-space electronic Hamiltonians for ab initio dynamics

Modern electronic structure theory is built around the Born-Oppenheimer approximation and the construction of an electronic Hamiltonian Ĥel(X) that depends on the nuclear position X (and not the nuclear momentum P). In this article, using the well-known theory of electron translation (Γ') and rotational (Γ″) factors to couple electronic transitions to nuclear motion, we construct a practical phase-space electronic Hamiltonian that depends on both nuclear position and momentum, ĤPS(X,P). While classical Born-Oppenheimer dynamics that run along the eigensurfaces of the operator Ĥel(X) can recover many nuclear properties correctly, we present some evidence that motion along the eigensurfaces of ĤPS(X,P) can better capture both nuclear and electronic properties (including the elusive electronic momentum studied by Nafie). Moreover, only the latter (as opposed to the former) conserves the total linear and angular momentum in general.

Diagonalizing the Born-Oppenheimer Hamiltonian via Moyal perturbation theory, nonadiabatic corrections, and translational degrees of freedom

This article describes a method for calculating higher order or nonadiabatic corrections in Born-Oppenheimer theory and its interaction with the translational degrees of freedom. The method uses the Wigner-Weyl correspondence to map nuclear operators into functions on the classical phase space and the Moyal star product to represent operator multiplication on those functions. These are explained in the body of the paper. The result is a power series in κ2, where κ = (m/M)1/4 is the usual Born-Oppenheimer parameter. The lowest order term is the usual Born-Oppenheimer approximation, while higher order terms are nonadiabatic corrections. These are needed in calculations of electronic currents, momenta, and densities. The separation of nuclear and electronic degrees of freedom takes place in the context of the exact symmetries (for an isolated molecule) of translations and rotations, and these, especially translations, are explicitly incorporated into our discussion. This article presents an independent derivation of the Moyal expansion in molecular Born-Oppenheimer theory. We show how electronic currents and momenta can be calculated within the framework of Moyal perturbation theory; we derive the transformation laws of the electronic Hamiltonian, the electronic eigenstates, and the derivative couplings under translations; we discuss in detail the rectilinear motion of the molecular center of mass in the Born-Oppenheimer representation; and we show how the elimination of the translational components of the derivative couplings leads to a unitary transformation that has the effect of exactly separating the translational degrees of freedom.

Close-Up Look at Electronic Spectroscopic Signatures of Common Pharmaceuticals in Solution

Simulating electronic properties and spectral signals requires robust computational approaches that need tuning with the system's peculiarities. In this paper, we test implicit and fully atomistic solvation models for the calculation of UV-vis and electronic circular dichroism (ECD) spectra of two pharmaceutically relevant molecules, namely, (2S)-captopril and (S)-naproxen, dissolved in aqueous solution. Room temperature molecular dynamics simulations reveal that these two drugs establish strong contacts with the surrounding solvent molecules via hydrogen bonds. Such specific interactions, which play a major role in the spectral response and are neglected in implicit approaches, are further characterized and quantified with natural bond orbital methods. Our calculations show that simulated spectra, and especially ECD, are in good agreement with experiments solely when conformational and configurational dynamics, mutual polarization, and solute-solvent repulsion effects are considered.

Multidimensional vibrational circular dichroism for insect wings: Comparison of species

This study reports the microscopic measurements of vibrational circular dichroism (VCD) on four different insect wings using a quantum cascade laser VCD system equipped with microscopic scanning capabilities (named multi-dimensional VCD [MultiD-VCD]). Wing samples, including (i) beetle, Anomala albopilosa (female), (ii) European hornet, Verspa crabro flavofasciata Cameron, 1903 (female), (iii) tiny dragonfly, Nannophya pygmae Rambur, 1842 (male), and (iv) dragonfly, Symetrum gracile Oguma, 1915 (male), were used in this study. Two-dimensional patterns of VCD signals (~10 mm × 10 mm) were obtained at a spatial resolution of 100 μm. Measurements covered the absorption peaks assigned to amides I and II in the range of 1500-1740 cm-1 . The measurements were based on the enhancement of VCD signals for the stereoregular linkage of peptide groups. The patterns were remarkably dependent on the species. In samples (i) and (ii), the wings comprised segregated domains of protein aggregates of different secondary structures. The size of each microdomain was approximately 100 μm. In contrast, no clear VCD spectra were detected in samples (iii) and (iv). One possible reason was that the chain of stereoregular polypeptides was too short to achieve VCD enhancement in samples (iii) and (iv). Notably, the unique features were only observed in the VCD spectra because the IR spectra were nearly the same among the species. The VCD results hinted at the connection of protein microscopic structures with the wing flapping mechanisms of each species.

Understanding the surrounding effects on Raman optical activity signatures of a chiral cage system: Cryptophane-PP-111

Cryptophane molecules are cage-like structures consisting in two hemispheres, each made of three benzene rings. These hemispheres are bound together with three O(CH2)nOlinkers of various lengths giving rise to a plethora of cryptophane derivatives. Moreover, they are able to encapsulate neutral guests: CH2Cl2, CHCl3, …; and charged species: Cs+, Tl+, …. Finally, they exhibit chiroptical properties thanks to the anti arrangement of the linkers between the hemispheres. This work focuses on the Raman optical activity (ROA) signatures of Cryptophane-111 (n=1 for each linker). More specifically, we aim at simulating accurately its ROA spectra with and without a xenon atom inside its cavity. Experimental data (Buffeteau et al., 2017) have already demonstrated the effect of the encapsulation in the low-wavenumbers region. To generate the initial structures, we rely on the novel Conformer-Rotamer Ensemble Sampling Tool (CREST) program, developed by S. Grimme and co-workers. This is required due to the flexibility provided by the linkers. The CREST algorithm seems promising and has already been used to sample the potential energy surface (PES) of target systems before the simulation of their vibrational spectroscopies (Eikås et al., 2022). We observe large similarities between the two sets of conformers (one with and one without Xe encapsulated), demonstrating the robustness of the CREST algorithm. For corresponding structures, the presence of xenon pushed the two hemispheres slightly further apart. After optimization at the DFT level, only one unique conformer has a Boltzmann population ratio greater than 1%, pointing out the relative rigidity of the cage. Based on this unique conformer, our simulations are in good agreement with the experimental data. Regarding xenon encapsulation, the (experimental and theoretical) ROA signatures at low wavenumbers are impacted: slight shifts in wavenumbers are observed as well as a decrease in relative ROA intensity for bands around 150 cm-1. The wavenumber shifts were very well reproduced by our simulations, but the experimental decrease in the ROA intensity was unfortunately not reproduced.

Quantitative evaluation of IR and corresponding VCD spectra

Classical electromagnetic theory applied to infrared (IR) and vibrational circular dichroism (VCD) spectra of chiral compounds can provide useful insights, such as the fact that the area of all bands of wavenumber-normalized absorbance above zero must be the same as the area below zero. Additionally, dispersion analysis based on wave optics and dispersion theory, which was extended by Born and Kuhn to include chiral substances, can be used to quantitatively describe the dielectric function and the chiral admittance functions that shape IR and VCD spectra. For dispersion analysis, pairs of coupled oscillators, with five different kinds of parameters, namely oscillator strength, damping, oscillator position, vertical distance between coupled oscillators, and the coupling constant are used to model the dielectric functions and chiral admittance functions. We report the results of such an analysis for α-Pinene and Propylene oxide. For most bands, the oscillator model using two coupled oscillators is sufficient to achieve a good correspondence between experimental and modelled data.

Effective fully polarizable QM/MM approaches to compute Raman and Raman Optical Activity spectra in aqueous solution

Raman and Raman Optical Activity (ROA) signals are amply affected by solvent effects, especially in the presence of strongly solute-solvent interactions such as Hydrogen Bonding (HB). In this work, we extend the fully atomistic polarizable Quantum Mechanics/Molecular Mechanics approach, based on the Fluctuating Charges and Fluctuating Dipoles force field to the calculation of Raman and ROA spectra. Such an approach is able to accurately describe specific HB interactions, by also accounting for anisotropic contributions due to the inclusion of fluctuating dipoles. To highlight the potentiality of the novel approach, Raman and ROA spectra of L-Serine and L-Cysteine dissolved in aqueous solution are computed and compared both with alternative theoretical approaches and experimental measurements.

Solid-state vibrational circular dichroism: Methodology and application for amphetamine derivatives

Amphetamine derivatives are considered most seized substances worldwide. In this study, solid-state vibrational circular dichroism (VCD) measurements of enantiomerically pure substances were performed for spectroscopic discrimination between (S)- and (R)-enantiomers. First, we have developed a universal experimental approach to obtain reliable and reproducible solid-state VCD spectra. First, the samples were prepared as pellets composed of mixtures of camphor as a model compound and a crystalline matrix powder. In order to obtain the best results without artifacts and with a maximum signal-to-noise ratio, the following experimental conditions were optimized: pellet thickness and diameter and sample rotation speed. The optimized parameters were then used for the analysis of amphetamine and its derivatives (methamphetamine and 3,4-methylendioxymethamphetamine). Our high-quality spectra and results suggest that solid-state VCD spectroscopy represents a cost-effective and easy-to-use method for the analysis of conformation changes and molecular packing in solid-state with potential applications in pharmaceutical and forensic practice.

Molecular Vibrations in Chiral Europium Complexes Revealed by Near-Infrared Raman Optical Activity

Raman optical activity (ROA) is commonly measured with green light (532 nm) excitation. At this wavelength, however, Raman scattering of europium complexes is masked by circularly polarized luminescence (CPL). This can be avoided using near-infrared (near-IR, 785 nm) laser excitation, as demonstrated here by Raman and ROA spectra of three chiral europium complexes derived from camphor. Since luminescence is strongly suppressed, many vibrational bands can be detected. They carry a wealth of structural information about the ligand and the metal core, and can be interpreted based on density functional theory (DFT) simulations of the spectra. For example, jointly with ROA experimental data, the simulations make it possible to determine absolute configuration of chiral lanthanide compounds in solution.

Unveiling chiral optical constants of α-pinene and propylene oxide through ATR and VCD spectroscopy in the mid-infrared range

Optical constants functions of analytes are indispensable for the effective design of plasmonic sensors. Such sensors are potentially able to enhance the sensitivity by several order of magnitudes which can greatly facilitate the determination of the generally weak spectral signals caused by vibrational circular dichroism. Accordingly, to demonstrate how to obtain these functions, we have determined the dielectric and chirality admittance functions of α-Pinene and Propylene oxide in the mid-infrared spectral range using attenuated total reflection and vibrational circular dichroism spectroscopy. Our iterative formalism starts with an estimation of the absorption index function, followed by the calculation of the refractive index function using the Kramers-Kronig relation and a modelled spectrum based on Fresnel's equations. By comparing the experimental and modelled spectra, we improve the absorption index function. To determine the chirality admittance function, we use the same iterative formalism, but with a modified 4x4 matrix formalism formulated by Berreman. Our results show that the experimental absorbance difference is independent of the dielectric function of the chiral substance and depends linearly on the cuvette thickness. Additionally, we provide a sum rule that can be used to assess the quality of VCD spectra and determine the position of the baseline. Our findings provide crucial insights into the optical properties of chiral substances in the mid-infrared spectral range, which have important implications for a range of applications in fields such as analytical chemistry and materials science.

Efficient Prediction of Mole Fraction Related Vibrational Frequency Shifts

While so far it has been possible to calculate vibrational spectra of mixtures at a particular composition, we present here a novel cluster approach for a fast and robust calculation of mole fraction dependent infrared and vibrational circular dichroism spectra at the example of acetonitrile/(R)-butan-2-ol mixtures. By assigning weights to a limited number of quantum chemically calculated clusters, vibrational spectra can be obtained at any desired composition by a weighted average of the single cluster spectra. In this way, peak positions carrying information about intermolecular interactions can be predicted. We show that mole fraction dependent peak shifts can be accurately modeled and, that experimentally recorded infrared spectra can be reproduced with high accuracy over the entire mixing range. Because only a very limited number of clusters is required, the presented approach is a valuable and computationally efficient tool to access mole fraction dependent spectra of mixtures on a routine basis.

Vibrational Circular Dichroism Spectroscopy of Chiral Molecular Crystals: Insights from Theory

Chirality is a curious phenomenon that appears in various forms. While the concept of molecular (RS-)chirality is ubiquitous in chemistry, there are also more intricate forms of structural chirality. One of them is the enantiomorphism of crystals, especially molecular crystals, that describes the lack of mirror symmetry in the unit cell. Its relation to molecular chirality is not obvious, but still an open question, which can be addressed with chiroptical tools. Vibrational circular dichroism (VCD) denotes chiral infrared (IR) spectroscopy that is susceptible to both, the molecular as well as the intermolecular space by means of vibrational transitions. When carried out in the solid state, VCD delivers a very rich set of non-local contributions that are determined by crystal packing and collective motion. Since its discovery in the 1970s, VCD has become the method of choice for the determination of absolute configurations, but its applicability reaches beyond towards the study of different crystal forms and polymorphism. This brief review summarises the theoretical concepts of crystal chirality and how computations of solid-state VCD can shed light into the intimate connection of chiral structure and vibrational optical activity.

Unveiling the Configurational Landscape of Carbamate: Paving the Way for Designing Functional Sequence-Defined Polymers

Carbamate is an emerging class of a polymer backbone for constructing sequence-defined, abiotic polymers. It is expected that new functional materials can be de novo designed by controlling the primary polycarbamate sequence. While amino acids have been actively studied as building blocks for protein folding and peptide self-assembly, carbamates have not been widely investigated from this perspective. Here, we combined infrared (IR), vibrational circular dichroism (VCD), and nuclear magnetic resonance (NMR) spectroscopy with density functional theory (DFT) calculations to understand the conformation of carbamate monomer units in a nonpolar, aprotic environment (chloroform). Compared with amino acid building blocks, carbamates are more rigid, presumably due to the extended delocalization of π-electrons on the backbones. Cis configurations of the amide bond can be energetically stable in carbamates, whereas peptides often assume trans configurations at low energies. This study lays an essential foundation for future developments of carbamate-based sequence-defined polymer material design.

Molecular Properties of 3d and 4f Coordination Compounds Deciphered by Raman Optical Activity Spectroscopy

Molecular properties of coordination compounds can be efficiently studied by vibrational spectroscopy. The scope of Raman spectroscopy has been greatly enhanced by the introduction of Raman optical activity (ROA) sensitive to chirality. The present review describes some of its recent applications to study the coordination compounds. 3d and 4f metal complexes often absorb the excitation light, or exhibit luminescence. Therefore, effects caused in ROA spectra by electronic circular dichroism (ECD) and circularly polarized luminescence (CPL) must be taken into consideration.In 3d metal complexes ECD and circularly-polarized Raman scattering compete with the resonance ROA (RROA) signal. Pure RROA spectrum can thus be obtained by subtracting the so-called ECD-Raman component. CPL is frequently encountered in 4f systems. While it can mask the ROA spectra, it is useful to study molecular structure. These electronic effects can be reduced by using near-infrared excitation although vibrational ROA signal is much weaker compared to the usual green laser excitation scenario. The ROA methodology is thus complex, but capable of providing unique information about the molecules of interests and their interaction with light.

Pushing the boundaries of VCD spectroscopy in natural product chemistry

Vibrational circular dichroism (VCD) is one of the most powerful techniques to assess the stereochemistry of chiral molecules in solution state. The need for quantum chemical calculations to interpret experimental data, however, has precluded its widespread use by non-experts. Herein, we propose the search and validation of IR and VCD spectral markers to circumvent the requirement of DFT calculations allowing for absolute configuration assignments even in complex mixtures. To that end, a combination of visual inspection and machine learning based methods is used. Monoterpene mixtures are selected for this proof-of-concept study.

How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State

Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P2₁ crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.

Anharmonic Vibrational Raman Optical Activity of Methyloxirane: Theory and Experiment Pushed to the Limits

Combining Raman scattering and Raman optical activity (ROA) with computer simulations reveals fine structural and physicochemical properties of chiral molecules. Traditionally, the region of interest comprised fundamental transitions within 200-1800 cm^-1. Only recently, nonfundamental bands could be observed as well. However, theoretical tools able to match the observed spectral features and thus assist their assignment are rather scarce. In this work, we present an accurate and simple protocol based on a three-quanta anharmonic perturbative approach that is fully fit to interpret the observed signals of methyloxirane within 150-4500 cm^-1. An unprecedented agreement even for the low-intensity combination and overtone transitions has been achieved, showing that anharmonic Raman and ROA spectroscopies can be valuable tools to understand vibrations of chiral molecules or to calibrate computational models.

Amide Spectral Fingerprints are Hydrogen Bonding-Mediated

The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N-acetylglycine-N-methylamide (NAGMA) and N-acetylalanine-N-methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.

A Raman optical activity spectrometer can sensitively detect lanthanide circularly polarized luminescence

Recently, many studies have appeared in which the Raman optical activity (ROA) instrument was found to be convenient for measuring circularly polarized luminescence (CPL). Typically, weak lanthanide luminescence including circular polarization could be detected. The new detection scheme is referred to as ROA-CPL spectroscopy. It is particularly useful when also the vibrational (ROA) itself is detectable as the molecule structure can be examined more reliably. In this review, development of this chiroptical approach and its applications in structural studies of biomolecules are summarized.

Insights in the vibrational optical activity spectra of the antibiotic vancomycin in DMSO

Vibrational circular dichroism (VCD) and Raman optical activity (ROA) are two spectroscopic techniques that are sensitive towards the conformational behaviour of molecules, and are often complementary herein. In this work we pursue the determination of the conformational ensemble of the antibiotic glycopeptide vancomycin in DMSO through comparison of experimental and computational spectra, both for VCD and ROA. ROA is found to be highly suitable for the task, identifying an ensemble that strongly resembles the NMR conformation. In the case of VCD, however, a too high sensitivity of the intensities with respect to minor conformational changes hampers a reliable conformational analysis. Whence attempting to improve the match between the VCD experiment and calculations by any means - e.g., by inducing minor conformational changes or including solvent effects in the calculations - we show that there is the risk of going down the rabbit hole. In conclusion, this work contributes to the broader understanding of where, when and how VCD and ROA can be deployed as techniques for conformational analysis.

New chiral ECD-Raman spectroscopy of atropisomeric naphthalenediimides

In this study, we found that a recently discovered ECD-Raman effect dominated over the natural Raman optical activity in a series of atropisomeric naphthalenediimides, and we investigated the kind of information about the molecular structure that could be obtained from the spectra. The ECD-Raman effect is polarised Raman scattering modulated by electronic circular dichroism. We showed that the spectra significantly depended on the substitution of the solute and/or the change of the solvent. Moreover, the spectra could be well-predicted by the theory, thus providing an interesting tool to monitor the chirality of the binaphthyl compounds.

A Holistic Approach to Determining Stereochemistry of Potential Pharmaceuticals by Circular Dichroism with β-Lactams as Test Cases

This paper's main objective is to show that many different factors must be considered when solving stereochemical problems to avoid misleading conclusions and obtain conclusive results from the analysis of spectroscopic properties. Particularly in determining the absolute configuration, the use of chiroptical methods is crucial, especially when other techniques, including X-ray crystallography, fail, are not applicable, or give inconclusive results. Based on various β-lactam derivatives as models, we show how to reliably determine their absolute configuration (AC) and preferred conformation from circular dichroism (CD) spectra. Comprehensive CD analysis, employing both approaches, i.e., traditional with their sector and helicity rules, and state-of-the-art supported by quantum chemistry (QC) calculations along with solvation models for both electronic (ECD) and vibrational (VCD) circular dichroism ranges, allows confident defining stereochemistry of the β-lactams studied. Based on an in-depth analysis of the results, we have shown that choosing a proper chiroptical method/s strictly depends on the specific case and certain structural features.

Exploring machine learning methods for absolute configuration determination with vibrational circular dichroism

The added value of supervised Machine Learning (ML) methods to determine the Absolute Configuration (AC) of compounds from their Vibrational Circular Dichroism (VCD) spectra was explored. Among all ML methods considered, Random Forest (RF) and Feedforward Neural Network (FNN) yield the best performance for identification of the AC. At its best, FNN allows near-perfect AC determination, with accuracy of prediction up to 0.995, while RF combines good predictive accuracy (up to 0.940) with the ability to identify the spectral areas important for the identification of the AC. No loss in performance of either model is observed as long as the spectral sampling interval used does not exceed the spectral bandwidth. Increasing the sampling interval proves to be the best method to lower the dimensionality of the input data, thereby decreasing the computational cost associated with the training of the models.

Tackling Stereochemistry in Drug Molecules with Vibrational Optical Activity

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.

The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss the effect of the hydrogen bond network on the aggregation behaviour of the acid: while aggregates of the solute represent conditions encountered in a weakly interacting solvent, the presence of water drastically interferes with the clusters - more strongly than originally anticipated. For both scenarios we computed the VCD spectra by means of nuclear velocity perturbation theory (NVPT). The comparison with experimental data allows us to establish a VCD-structure relationship that includes the solvent network around the chiral solute. We suggest that fundamental modes with strong polarisation such as the carbonyl stretching vibration can borrow VCD from the chirally restructured solvent cage, which extends the common explanatory models of VCD generation in aqueous solution.

Mapping of Supramolecular Chirality in Insect Wings by Microscopic Vibrational Circular Dichroism Spectroscopy: Heterogeneity in Protein Distribution

The supramolecular chirality of the hindwing of Anomala albopilosa (male) was investigated using a microscopic vibrational circular dichroism (VCD) system, denoted as MultiD-VCD. The source of intense infrared (IR) light for the system was a quantum cascade laser. Two-dimensional maps of IR and VCD spectra were taken by scanning the surface area (ca. 2 mm × 2 mm) of the insect hindwing tissue. The spectra ranged from 1500 to 1700 cm^-1, and the maps have a spatial resolution of 100 μm. The distribution of proteins, including their supramolecular structures, was analyzed from the location-dependent spectral shape of the VCD bands assigned to amides I and II. The results revealed that the hindwing consists of segregated domains of proteins with different secondary structures: an α-helix (in one part of the membrane), a hybrid of α-helix and β-sheet (in another part of the membrane), and a coil (in a vein).

Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review

Circular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24 000 papers published in the past decade have included CD characterisations of proteins; many of those studies have also included other complementary chemical, biophysical, and computational chemistry methods. This tutorial review describes the background to the technique of CD spectroscopy and good practice methods for high quality data collection. It specifically focuses on both established and new methods and tools available for experimental design and interpretation, data processing, visualisation, analysis, validation, archiving, and accession, including tools developed to enhance the complementarity of this method with other structural and chemical biology studies.

Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge

We introduce a new theoretical formalism to compute solid-state vibrational circular dichroism (VCD) spectra from molecular dynamics simulations. Having solved the origin-dependence problem of the periodic magnetic gauge, we present IR and VCD spectra of (1S,2S)-trans-1,2-cyclohexanediol obtained from first-principles molecular dynamics calculations and nuclear velocity perturbation theory, along with the experimental results. Because the structure model imposes periodic boundary conditions, the common origin of the rotational strength has hitherto been ill-defined and was approximated by means of averaging multiple origins. The new formalism reconnects the periodic model with the finite physical system and restores gauge freedom. It nevertheless fully accounts for nonlocal spatial couplings from the gauge transport term. We show that even for small simulation cells the rich nature of solid-state VCD spectra found in experiments can be reproduced to a very satisfactory level.

Vibrational circular dichroism of D-amino acid-containing peptide NdWFamide in the crystal form

Microcrystals of l-Asn-d-Trp-l-Phe-NH₂ (NdWFamide), a tripeptide derived from Aplysia kurodai that exhibits invertebrate cardiac activity, were evaluated by vibrational circular dichroism (VCD). The chirality of the tryptophan residue at the second position in NdWFamide was associated with the conformation and biological characteristics. The VCD spectrum of NdWFamide was a mirror image of its enantiomer; however, it was significantly different from that of its diastereomer, NWFamide, which is its precursor. The obtained VCD signals of NdWFamide were in good agreement with the VCD signals that were calculated based on the optimized aggregates of NdWFamide, which formed a helical-like backbone conformation. The evaluation of the VCD results revealed the conformation of NdWFamide in the crystalline state and succeeded in distinguishing its stereoisomers. Therefore, this study demonstrates VCD as a useful method for the structural analysis of naturally occurring d-amino acid-containing peptides.

ECD spectroelectrochemistry: A review

The electronic circular dichroism (ECD) spectroscopy is probably the most important chiraloptical method, and the role of chirality in contemporary chemistry, pharmacy, and material science constantly increases. On the other hand, the electrochemical methods are also very sensitive tools for studying multivarious redox processes. Nevertheless, the first ECD spectroelectrochemical (SEC) study was only published by Daub, Salbeck and Aurbach in 1988, and since then, the ECD SEC method has been mentioned in only thirty papers. By the summer of 2020, the ECD SEC studies were mainly focused around molecular systems for organic, and marginally, inorganic chiroptical switching studies of biochemical redox reactions. The review provides more details about the ECD SEC studies carried out so far. At the end, we suggest some future applications for the ECD spectroelectrochemistry.

Polarimetric Measurements of Surface Chirality Based on Linear and Nonlinear Light Scattering

A molecule, molecular aggregate, or protein that cannot be superimposed on its mirror image presents chirality. Most living systems are organized by chiral building blocks, such as amino acids, peptides, and carbohydrates, and any change in their molecular structure (i.e., handedness or helicity) alters the biochemical and pharmacological functions of the molecules, many of which take place at surfaces. Therefore, studying surface chirogenesis at the nanoscale is fundamentally important and derives various applications. For example, since proteins contain highly ordered secondary structures, the intrinsic chirality can be served as a signature to measure the dynamics of protein adsorption and protein conformational changes at biological surfaces. Furthermore, a better understanding of chiral recognition and separation at bio-nanointerfaces is helpful to standardize chiral drugs and monitor the synthesis of adsorbents with high precision. Thus, exploring the changes in surface chirality with polarized excitations would provide structural and biochemical information of the adsorbed molecules, which has led to the development of label-free and noninvasive measurement tools based on linear and nonlinear optical effects. In this review, the principles and selected applications of linear and nonlinear optical methods for quantifying surface chirality are introduced and compared, aiming to conceptualize new ideas to address critical issues in surface biochemistry.

A Unified Mathematical Formalism for First to Third Order Dielectric Response of Matter: Application to Surface-Specific Two-Colour Vibrational Optical Spectroscopy

To take advantage of the singular properties of matter, as well as to characterize it, we need to interact with it. The role of optical spectroscopies is to enable us to demonstrate the existence of physical objects by observing their response to light excitation. The ability of spectroscopy to reveal the structure and properties of matter then relies on mathematical functions called optical (or dielectric) response functions. Technically, these are tensor Green’s functions, and not scalar functions. The complexity of this tensor formalism sometimes leads to confusion within some articles and books. Here, we do clarify this formalism by introducing the physical foundations of linear and non-linear spectroscopies as simple and rigorous as possible. We dwell on both the mathematical and experimental aspects, examining extinction, infrared, Raman and sum-frequency generation spectroscopies. In this review, we thus give a personal presentation with the aim of offering the reader a coherent vision of linear and non-linear optics, and to remove the ambiguities that we have encountered in reference books and articles.

On Raman optical activity sign-switching between the ground and excited states leading to an unusual resonance ROA induced chirality

Raman optical activity (ROA) spectra recorded for a chiral naphthalene diimide derivative (nBu-NDI–BINAM) dissolved in a series of solvents exhibit strong solute to solvent induced chirality with: (1) dominating bands of solvents, (2) nBu-NDI–BINAM resonance ROA (RROA) bands which are barely visible, (3) monosignate RROA Solvent spectra with an unexpected sign concordant with that of the ECD band of the resonant electronic state, (4) bisignate RROA bands for a few solvents, and (5) superposition of non-resonant and resonant ROA bands of the chiral solvents. The unusual ROA enhancement was explained in terms of resonance energy transfer with resonant Raman emission. The surprising RROA sign-switching was found to be due to specific conformational equilibria where one solute conformer dominates in the ground and the other in the first excited singlet state, and, the signs of the related ECD bands of these two conformers are opposite.

Unusual solute to solvent induced chirality in ROA comes from specific conformer equilibria in the ground and the excited states.

Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems

Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.