In Situ Quantitative Monitoring of Adsorption from Aqueous Phase by UV-vis Spectroscopy: Implication for Understanding of Heterogeneous Processes

The development of in situ techniques to quantitatively characterize the heterogeneous reactions is essential for understanding physicochemical processes in aqueous phase. In this work, a new approach coupling in situ UV-vis spectroscopy with a two-step algorithm strategy is developed to quantitatively monitor heterogeneous reactions in a compact closed-loop incorporation. The algorithm involves the inverse adding-doubling method for light scattering correction and the multivariate curve resolution-alternating least squares (MCR-ALS) method for spectral deconvolution. Innovatively, theoretical spectral simulations are employed to connect MCR-ALS solutions with chemical molecular structural evolution without prior information for reference spectra. As a model case study, the aqueous adsorption kinetics of bisphenol A onto polyamide microparticles are successfully quantified in a one-step UV-vis spectroscopic measurement. The practical applicability of this approach is confirmed by rapidly screening a superior adsorbent from commercial materials for antibiotic wastewater adsorption treatment. The demonstrated capabilities are expected to extend beyond monitoring adsorption systems to other heterogeneous reactions, significantly advancing UV-vis spectroscopic techniques toward practical integration into automated experimental platforms for probing aqueous chemical processes and beyond.

Absolute configuration assignment of highly fluorinated carboxylic acids via VCD and MRR spectroscopy

Chiral analysis has become a crucial step in studying the stereospecific synthesis of Active Pharmaceutical Ingredients (APIs). Both Vibrational Circular Dichroism (VCD) and Molecular Rotational Resonance (MRR) spectroscopy are capable of determining absolute configurations (ACs) via comparison of experimental and calculated data. In this regard, each technique has its own caveats. In VCD analysis, accurate prediction of the normal modes as well as rigorous conformational searches of both the analyte and potential (self-)aggregation products are required to optimally match experimental spectra. In MRR analysis, chiral species are resolved through complexation with a chiral tag to prepare spectrally distinct diastereomeric complexes. Although individual complex isomers can be distinguished, spectral assignments need to be matched to unique isomer geometries for unambiguous AC assignment. In this work, the ACs of two highly fluorinated carboxylic acids were successfully assigned using VCD and MRR spectroscopy. In the VCD analysis, the M06-2X functional was demonstrated to be superior to B3LYP and B3LYP-GD3 in accurately predicting the C-F normal modes and both monomeric and dimeric spectral contributions were observed. In a similar analysis with broadband MRR, most experimentally identified geometries had more than one possible computational match. Nevertheless, careful consideration of the chiral tag, as well as additional isomer assignments, resulted in successful assignment of the AC. This comparative study demonstrates the power of contemporary VCD analysis and the unique contributions of MRR to the analytical toolbox.

Impact of conformation and intramolecular interactions on vibrational circular dichroism spectra identified with machine learning

Vibrational Circular Dichroism (VCD) spectra often differ strongly from one conformer to another, even within the same absolute configuration of a molecule. Simulated molecular VCD spectra typically require expensive quantum chemical calculations for all conformers to generate a Boltzmann averaged total spectrum. This paper reports whether machine learning (ML) can partly replace these quantum chemical calculations by capturing the intricate connection between a conformer geometry and its VCD spectrum. Three hypotheses concerning the added value of ML are tested. First, it is shown that for a single stereoisomer, ML can predict the VCD spectrum of a conformer from solely the conformer geometry. Second, it is found that the ML approach results in important time savings. Third, the ML model produced is unfortunately hardly transferable from one stereoisomer to another.

Can the absolute configuration of cyclic peptides be determined with vibrational circular dichroism?

Cyclic peptides show a wide range of biological activities, among others as antibacterial agents. These peptides are often large and flexible with multiple chiral centers. The determination of the stereochemistry of molecules with multiple chiral centers is a challenging and important task in drug development. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) can distinguish between different stereoisomers. The absolute configuration (AC) of a stereoisomer can be determined by comparing its experimental spectra to computed spectra of stereoisomers with known AC. In this way, the AC of rigid molecules with up to seven chiral centers has been assigned (Bogaerts et al., Phys. Chem. Chem. Phys., 2020, 22, 18014). The question arises whether this is possible with more conformationally flexible molecules such as cyclic peptides. We here investigate to what extent the AC of cyclic peptides can be determined with VCD. More specifically, we investigate the maximum number of chiral centers a cyclic peptide can have in order to be able to unambiguously assign the AC with VCD. We present experimental and computed IR and VCD spectra for a series of eight tetrapeptides and hexapeptides with two, three and four chiral centers. We use our recently developed computational protocol with a conformational search based on sampling with meta-dynamics. We use visual inspection to compare the computed spectra of different stereoisomers with an experimental spectrum of the corresponding cyclic peptide with known AC. We find that the AC of the investigated cyclic peptides with two chiral centers can be unambiguously assigned with VCD. This is however not possible for all of the cyclic peptides with three chiral centers and for none of those with four chiral centers. At best, one can limit the number of possible stereoisomers in those cases. Our work shows that other techniques are needed to assign the AC of cyclic peptides with three or more chiral centers. Our study also constitutes a warning that the spectra of all stereoisomers should be computed before attempting to match to an experimental spectrum, to avoid an accidental erroneous match.

Improving the IR spectra alignment algorithm with spectra deconvolution and combination with Raman or VCD spectroscopy

The relative stereochemistry of organic molecules can be determined by comparing theoretical and experimental infrared (IR) spectra of all isomers and assessing the best match. For this purpose, we have recently developed the IR spectra alignment (IRSA) algorithm for automated optimal alignment. IRSA provides a set of quantitative metrics to identify the candidate structure that agrees best with the experimental spectrum. While the correct diastereomer could be determined for the tested sets of rigid and flexible molecules, two issues were identified with more complex compounds that triggered further development. First, strongly overlapping peaks in the IR spectrum are not treated adequately in the current IRSA implementation. Second, the alignment of multiple spectra from different sources (e.g. IR and VCD or Raman) can be improved. In this study, we present an in-depth discussion of these points, followed by the description of modifications to the IRSA algorithm to address them. In particular, we introduce the concept of deconvolution of the experimental and theoretical spectra with a set of pseudo-Voigt bands. The pseudo-Voigt bands have a set of parameters, which can be employed in the alignment algorithm, leading to improved scoring functions. We test the modified algorithm on two data sets. The first set contains compounds with IR and Raman spectra measured in this study, and the second set contains compounds with IR and VCD spectra available in the literature. We show that the algorithm is able to determine the correct diastereomer in all cases. The results highlight that vibrational spectroscopy can be a valuable alternative or complementary method to inform about the stereochemistry of compounds, and the performance of the updated IRSA algorithm suggests that it is a powerful tool for quantitative-based spectral assignments in academia and industry.

Vibrational Circular Dichroism from DFT Molecular Dynamics: The AWV Method

The paper illustrates the Activity Weighted Velocities (AWV) methodology to compute Vibrational Circular Dichroism (VCD) anharmonic spectra from Density Functional Theory (DFT) molecular dynamics. AWV calculates the spectra by the Fourier Transform of the time correlation functions of velocities, weighted by specific observables: the Atomic Polar Tensors (APTs) and the Atomic Axial Tensors (AATs). Indeed, AWV shows to correctly reproduce the experimental spectra for systems in the gas and liquid phases, both in the case of weakly and strongly interacting systems. The comparison with the experimental spectra is striking especially in the fingerprint region, as demonstrated by the three benchmark systems discussed: (1S)-Fenchone in the gas phase, (S)-(−)-Propylene oxide in the liquid phase, and (R)-(−)-2-butanol in the liquid phase. The time evolution of APTs and AATs can be adequately described by a linear combination of the tensors of a small set of appropriate reference structures, strongly reducing the computational cost without compromising accuracy. Additionally, AWV allows the partition of the spectral signal in its molecular components without any expensive postprocessing and any localization of the charge density or the wave function.

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.

Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution

Sugars are crucial components in biosystems and industrial applications. In aqueous environments, the natural state of short saccharides or charged glycosaminoglycans is floating and wiggling in solution. Therefore, tools to characterize their structure in a native aqueous environment are crucial but not always available. Here, we show that a combination of Raman/ROA and, on occasions, NMR experiments with Molecular Dynamics (MD) and Quantum Mechanics (QM) is a viable method to gain insights into structural features of sugars in solutions. Combining these methods provides information about accessible ring puckering conformers and their proportions. It also provides information about the conformation of the linkage between the sugar monomers, i.e., glycosidic bonds, allowing for identifying significantly accessible conformers and their relative abundance. For mixtures of sugar moieties, this method enables the deconvolution of the Raman/ROA spectra to find the actual amounts of its molecular constituents, serving as an effective analytical technique. For example, it allows calculating anomeric ratios for reducing sugars and analyzing more complex sugar mixtures to elucidate their real content. Altogether, we show that combining Raman/ROA spectroscopies with simulations is a versatile method applicable to saccharides. It allows for accessing many features with precision comparable to other methods routinely used for this task, making it a viable alternative. Furthermore, we prove that the proposed technique can scale up by studying the complicated raffinose trisaccharide, and therefore, we expect its wide adoption to characterize sugar structural features in solution.

Inspecting the structural characteristics of chiral drug penicillamine under different pH conditions using Raman optical activity spectroscopy and DFT calculations

The investigation of the structural characteristics of chiral drugs in physiological environments is a challenging research topic, which may lead to a better understanding of how the drugs work. Raman optical activity (ROA) spectroscopy in combination with density functional theory (DFT) calculations was exploited to inspect the structural changes in penicillamine under different acid-base states in aqueous solutions. The B3LYP/aug-cc-PVDZ method was employed and the implicit solvation model density (SMD) was considered for describing the solvation effect in H₂O. The conformations of penicillamine varied with pH, but penicillamine was liable to stabilize in the form of the P_C conformation (the sulfur atom is in a trans orientation with respect to carboxylate) in most cases for both D- and L-isomers. The relationship between the conformations of penicillamine and the ROA peaks, as well as peak assignments, were comprehensively studied and elucidated. In the fingerprint region, two ROA couplets and one ROA triplet with different patterns were recognized. The intensity, sign and frequency of the corresponding peaks also changed with varying pH. Deuteration was carried out to identify the vibrational modes, and the ROA peaks of the deuterated amino group in particular are sensitive to change in the ambient environment. The results are expected not only to serve as a reference for the interpretation of the ROA spectra of penicillamine and other chiral drugs with analogous structures but also to evaluate the structural changes of chiral molecules in physiological environments, which will form the basis of further exploration of the effects of structural characteristics on the pharmacological and toxicological properties of chiral drugs.

Measurement of Raman Optical Activity with High-Frequency Polarization Modulation

Many chiroptical spectroscopic techniques have been developed to detect chirality in molecular species and probe its role in biological processes. Raman optical activity (ROA) should be one of the most powerful methods, as ROA yields vibrational and chirality information simultaneously and can measure analytes in aqueous and biologically relevant solvents. However, despite its promise, the use of ROA has been limited, largely due to challenges in instrumentation. Here, we report a new approach to ROA that exploits high-frequency polarization modulation. High-frequency polarization modulation, usually implemented with a photoelastic modulator (PEM), has long been the standard technique in other chiroptical spectroscopies. Unfortunately, the need for simultaneous spectral and polarization resolution has precluded the use of PEMs in ROA instruments. We combine a specialized camera system (the Zurich imaging polarimeter, or ZIMPOL) with PEM modulation to perform ROA measurements. We demonstrate performance similar to the current standard in ROA instrumentation while reducing complexity and polarization artifacts. This development should aid researchers in exploiting the full potential of ROA for chemical and biological analysis.

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.

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.

Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity

It is crucial for fundamental physical chemistry techniques to find their application in tackling real-world challenges. Hitherto, Raman optical activity (ROA) spectroscopy is one of the examples where a promising future within the pharmaceutical sector is foreseen, but has not yet been established. Namely, the technique is believed to be able to contribute in investigating the conformational behaviour of drug candidates. We, herein, strive towards the alignment of the ROA analysis outcome and the pharmaceutical expectations by proposing a fresh strategy that ensures a more complete, reliable, and transferable ROA study. The strategy consists of the treatment of the conformational space by means of a principal component analysis (PCA) and a clustering algorithm, succeeded by a thorough ROA spectral analysis and a novel way of estimating the contributions of the different chemical fragments to the total ROA spectral intensities. Here, vancomycin, an antibiotic glycopeptide, has been treated; it is the first antibiotic glycopeptide studied by means of ROA and is a challenging compound in ROA terms. By applying our approach we discover that ROA is capable of independently identifying the correct conformation of vancomycin in aqueous solution. In addition, we have a clear idea of what ROA can and cannot tell us regarding glycopeptides. Finally, the glycopeptide class turns out to be a spectroscopically curious case, as its spectral responses are unlike the typical ROA spectral responses of peptides and carbohydrates. This preludes future ROA studies of this intriguing molecular class.

Raman optical activity tackles the complex conformational space of glycopeptide antibiotics.

Chiral Molecular Propellers of Triarylborane Ammonia Adducts

Chiral molecular propeller conformations have been induced to various triaryl structures including trityl derivatives and triaryl boranes. For borane-amine adducts, such induced propeller chirality has not been reported yet due to the low energy barrier for racemization in common triarylboranes such as B(C6 H5 )3 or B(C6 F5 )3 . Herein, we demonstrate that point chirality in side chains of chiral triarylborane-ammonia adducts, which feature intramolecular hydrogen bonds in addition to the dative N→B bond, can efficiently be transferred to triarylborane propeller chirality. Employing X-ray crystallography and ECD/VCD spectroscopy for structural characterizations, we investigate three examples with different steric demands of the incorporated chiral alkoxy side groups. We elucidate the conformational preferences of the molecular propellers. Furthermore, we show that computationally predicted conformational preferences obtained for the isolated, only implicitly solvated molecules are actually opposite to the experimentally observed ones.

Employing complementary spectroscopies to study the conformations of an epimeric pair of side-chain stapled peptides in aqueous solution

Understanding the conformational preferences of free ligands in solution is often necessary to rationalize structure-activity relationships in drug discovery. Herein, we examine the conformational behavior of an epimeric pair of side-chain stapled peptides that inhibit the FAD dependent amine oxidase lysine specific demethylase 1 (LSD1). The peptides differ only at a single stereocenter, but display a major difference in binding affinity. Their Raman optical activity (ROA) spectra are most likely dominated by the C-terminus, obscuring the analysis of the epimeric macrocycle. By employing NMR spectroscopy, we show a difference in conformational behavior between the two compounds and that the LSD1 bound conformation of the most potent compound is present to a measurable extent in aqueous solution. In addition, we illustrate that Molecular Dynamics (MD) simulations produce ensembles that include the most important solution conformations, but that it remains problematic to identify relevant conformations with no a priori knowledge from the large conformational pool. Furthermore, this work highlights the importance of understanding the scope and limitations of the available techniques for conducting conformational analyses. It also emphasizes the importance of conformational selection of a flexible ligand in molecular recognition.

CFA-18: a homochiral metal-organic framework (MOF) constructed from rigid enantiopure bistriazolate linker molecules

In this work, we introduce the first enantiopure bistriazolate-based metal-organic framework, CFA-18 (Coordination Framework Augsburg-18), built from the R-enantiomer of 7,7,7',7'-tetramethyl-6,6',7,7'-tetrahydro-3H,3'H-5,5'-spirobi[indeno[5,6-d]-[1,2,3]triazole] (H2-spirta). The enantiopurity and absolute configuration of the new linker were confirmed by several chiroselective methods. Reacting H2-spirta in hot N,N-dimethylformamide (DMF) with manganese(ii) chloride gave CFA-18 as colorless crystals. The crystal structure with the composition [Mn2Cl2(spirta)(DMF)2] was solved using synchrotron single-crystal X-ray diffraction. CFA-18 shows a framework topology that is closely related to previously reported metal-azolate framework (MAF) structures in which the octahedrally coordinated manganese(ii) ions are triazolate moieties, and the chloride anions form crosslinked one-dimensional helical chains, giving rise to hexagonal channels. In contrast to MAFs crystallizing in the centrosymmetric space group R3[combining macron], the handedness of the helices found in CFA-18 is strictly uniform, leading to a homochiral framework that crystallizes in the trigonal crystal system within the chiral space group P3121 (no. 152).

Assessing cluster models of solvation for the description of vibrational circular dichroism spectra: synergy between static and dynamic approaches

Solvation effects are essential for defining the shape of vibrational circular dichroism (VCD) spectra.