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

Rotational Spectroscopy of the Acetone-Water Complex: Large Amplitude Motions

Acetone (CH3COCH3), the simplest ketone, has recently attracted considerable attention for its important role in atmospheric chemistry and in the formation of ices in extraterrestrial sources that contain complex organic molecules. In this study, we employed a combination of experimental rotational spectroscopy and quantum chemistry calculations to investigate the structure and dynamics of the acetone-water complex. Our aim was to understand how non-covalent interactions with water affect the methyl internal rotation dynamics of acetone, and how water-centered large amplitude motions alter the observed physical properties compared to those predicted at the equilibrium position. Detailed rotation-tunneling analyses of acetone-H2O and -D2O reveal that the interactions with water disrupt the equivalence of the two methyl rotors, resulting in a noticeably lower methyl rotor barrier for the top with the close-by water compared to that of free acetone. The barrier for the methyl group further from water is also lower, although to a lesser degree. To gain further insights, extensive theoretical modelling was conducted, focusing on the associated large amplitude motions. Furthermore, quantum theory of atoms in molecules and non-covalent interactions analyses were utilized to visualize the underlying causes of the observed trends.

Conformational distributions of tetrahydro-2-turoic acid in water at different pH values by their IR and vibrational circular dichroism spectra

Infrared (IR) and vibrational circular dichroism (VCD) spectra of tetrahydro-2-furoic acid (THFA) in aqueous solutions under several different pH conditions were recorded. To interpret the IR and VCD spectra of THFA obtained in highly acidic and basic aqueous solutions, extensive and systematic conformational searches were conducted to acquire the low-energy minima for both the neutral and deprotonated forms of THFA species, as well as their hydrated clusters. This was accomplished by using the conformer-rotamer ensemble sampling tool (CREST) with an implicit solvation model for water. The CREST candidates were further optimized at the B3LYP-D3BJ/def2-TZVP level of theory. The simulated VCD spectra of the neutral THFA conformers in the polarizable continuum model (PCM) of water alone exhibit little agreement with the experimental data under highly acidic conditions. Applying the clusters-in-a-liquid solvation model by considering the monohydrate THFA conformers in the PCM of water, significantly improved agreement with the experimental data. Similarly, the deprotonated THFA species solvated with one to four explicit water molecules in the PCM of water were considered. While the IR and VCD spectra of the deprotonated THFA monohydrate conformers offer the best agreement with the experimental data, other larger hydrated clusters, particularly the dihydrates, also contribute to the spectra. Through the synergistic combined experimental and theoretical approach used in the study, comprehensive conformational distributions of the predominant THFA species across various pH conditions were extracted.

Influence of microsolvation on vibrational circular dichroism spectra in dimethyl sulfoxide solvent: A Bottom-Up approach using Quantum cluster growth

Chiroptical spectroscopic measurements serve as routine methods to assign the absolute configuration of chiral compounds and interpret their conformational behavior in solution. One common challenge is the use of strongly hydrogen-bonding solvents, which can significantly bias the conformational ensemble and affect the vibrational circular dichroism (VCD) active bands in solution. One such solvent is dimethyl sulfoxide (DMSO)-an excellent solvent for stubborn compounds-that must be explicitly considered in VCD analysis. Explicit consideration of solvent remains a critical challenge in chiroptical spectroscopy due to the need to explore solute-solvent conformational space and the computational expense in modeling these clusters. Interested in the recent development of the Quantum Cluster Growth (QCG) program by the Grimme lab, we set out to model and interpret previously reported VCD spectra for several molecules using their efficient program. Our purposes are two-fold: (1) to investigate the applicability of the QCG program to the problem of reproducing VCD spectra in DMSO solvent and (2) to identify limitations in using this approach. We find that we can conveniently model and analyze the VCD spectra of investigated molecules in DMSO. However, the final set of conformers used for VCD calculations are functional dependent and different sets of conformers can provide satisfactory quantitative agreement between experimental and predicted VCD spectra. We hope that this study provides guidance for future chiroptical studies in the challenging DMSO solvent.

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 in the C-D, XY, and XYZ stretching region

Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.

Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics

Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.

Infrared and vibrational circular dichroism spectra of methyl β-D-glucopyranose in water: The application of the quantum cluster growth and clusters-in-a-liquid solvation models

The infrared (IR) and vibrational circular dichroism (VCD) spectra of methyl β-D-glucopyranose in water were measured. Both implicit and explicit solvation models were utilized to explain the observed spectra. The vast body of existing experimental and theoretical data suggested that about eight explicit water molecules are needed to account for the solvent effects, supported by the current Quantum Cluster Growth (QCG) analysis. Extensive manual and systematic conformational searches of the molecular target and its water clusters were carried out by using a recently developed conformational searching tool, conformer-rotamer ensemble sampling tool (CREST), and the microsolvation model in the associated QCG code. The Boltzmann averaged IR and VCD spectra of the methyl β-D-glucopyranose-(water)n (n = 8) conformers in the PCM of water provide better agreement with the experimental ones than those with n = 0, 1, and 2. The explicit solvation with eight water molecules was shown to greatly modify the conformational preference of methyl β-D-glucopyranose from its monomeric form. Further analyses show that the result is consistent with the existence of long-lived methyl β-D-glucopyranose monohydrates with the additional explicit water effects being accounted for with the quantum mechanical treatment of the other seven close-by water molecules in the PCM of water.

Conformations of Steroid Hormones: Infrared and Vibrational Circular Dichroism Spectroscopy

Steroid hormone molecules may exhibit very different functionalities based on the associated functional groups and their 3D arrangements in space, i.e., absolute configurations and conformations. Infrared (IR) and vibrational circular dichroism (VCD) spectra of four different steroid hormones, namely dehydroepiandrosterone (DHEA), 17α-methyltestosterone (MTTT), (16α,17)-epoxyprogesterone (Epoxy-P4), and dehydroepiandrosterone acetate (AcO-DHEA), were measured in deuterated dimethyl sulfoxide and some also in carbon tetrachloride. Extensive conformational searches were carried out using the recent developed conformer-rotamer ensemble sampling tool (CREST) which also accounts for solvent effects using an implicit solvation model. All the CREST conformational candidates were then reoptimized at the B3LYP-D3BJ/def2-TZVPD with the PCM of solvent. The good agreements between the experimental IR and VCD spectra and the theoretical simulations provide a conclusive information about their conformational distribution and absolute configurations. The experimental and theoretical IR and VCD spectra of AcO-DHEA in the carbonyl and alkene stretching region showed some discrepancies, and the possible causes related to solvent effects, large amplitude motions and levels of theory used in the modelling were explored in detail. As part of the investigation, additional calculations at the B3LYP-D3BJ/6-31++G (2d,p) and B3LYP-D3BJ/cc-pVTZ levels, as well as some 'mixed' calculations with the double-hybrid functional B2PLYP-D3 were also carried out. The results indicate that the double-hybrid functional is important for predicting the correct IR band pattern in the carbonyl and alkene stretching region.

Chirality transfer observed in Raman optical activity spectra

Chirality transfer (also called induced chirality) is a phenomenon present in chiroptical spectra that manifests itself as a new band or bands of an achiral molecule interacting with a chiral one. In the Raman optical activity (ROA) spectroscopy, the bands of achiral solvents have been recently observed, but the latest papers have shown that they corresponded to the new ECD-Raman (eCP-Raman) effect. Here, we show an unambiguous example of chirality transfer observed in the ROA spectra. The spectra registered for the (1:1) mixtures of achiral benzonitrile with the enantiomers of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol, and 1-phenylethylamine exhibited the v(CN) vibration band at about 2230 cm^-1. The ROA measurements were repeated several times to ensure the reliability of the phenomenon. Calculations revealed the CN···HO or CN···HNH hydrogen bond formation accompanied by the π···π or CH···π interactions. The interaction strength was shown to be an important factor for the pronouncement of the ROA chirality transfer effect.

Alternating 1-Phenyl-2,2,2-Trifluoroethanol Conformational Landscape With the Addition of One Water: Conformations and Large Amplitude Motions

The 1:1 adduct of 1-phenyl-2,2,2-trifluoroethanol (PhTFE), a chiral fluoroalcohol, with water was investigated using chirped pulse Fourier transform microwave spectroscopy and computational methods. While PhTFE itself was predicted to have three minima, I (gauche+), II (trans), and III (gauche-), only I and II were stable and only I was observed experimentally. A systematic search of the PhTFE···H₂O conformational landscape identified 110 stable minima, 14 of which are within a 15 kJ mol^-1 energy window. Rotational spectra of the two PhTFE···H₂O conformers along with several deuterium and ¹⁸O isotopologues were assigned, and the isotopic data were used to verify the corresponding structures. In the two observed monohydrate conformers, one contains PhTFE I where the water subunit is inserted into the existing intramolecular OH···F contact of I, and the binary adduct is stabilized by two intermolecular contacts: OH···O_W and H_W···F, whereas the other contains PhTFE II where the water subunit interacts with both the alcohol hydrogen and phenyl ring of II, demonstrating that interaction with water sufficiently stabilizes II for its observation in a jet expansion. Interestingly, the predicted electric dipole moment components at the identified minima deviate considerably from the experimental ones. Such deviations were analyzed in terms of dynamic effects associated with the large amplitude motions of the unbound H_W. In addition, tunnelling effects associated with the exchange of the bonded and nonbonded H_W were also discussed.

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides

Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.

Raman Optical Activity of N-Acetyl-L-Cysteine in water and in methanol: the "clusters-in-a-liquid" model and ab initio molecular dynamics simulations

Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, i.e. the DFT based clusters-in-a-liquid solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations , which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.

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.

Competition between inter and intramolecular hydrogen bond evidenced by vibrational circular dichroism spectroscopy: The case of (1S,2R)-(-)-cis-1-amino-2-indanol

The infrared (IR) absorption and vibrational circular dichroism (VCD) spectra of an intramolecularly hydrogen-bonded chiral amino-alcohol, (1S,2R)-(-)-cis-1-amino-2-indanol, are studied in DMSO-d₆ . The spectra are simulated at the density functional theory (DFT) level within the frame of the cluster-in-the-liquid model. Both IR and VCD spectra show a clear signature of the formation of intermolecular hydrogen bonds at the detriment of the intramolecular OH … N interaction present in the isolated molecule. Two solvent molecules are necessary to reproduce the experimental spectra. Whereas the first DMSO molecule captures the main spectral modifications due to hydrogen bond formation between the solute and the solvent, the second DMSO molecule is necessary for a good description of the Boltzmann contribution of the different complexes, based on their Gibbs free energy.

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.

Looking for the Elusive Imine Tautomer of Creatinine: Different States of Aggregation Studied by Quantum Chemistry and Molecular Spectroscopy

New spectroscopic experiments and state-of-the-art quantum-chemical computations of creatinine in different aggregation states unequivocally unveiled a significant tuning of tautomeric equilibrium by the environment: from the exclusive presence of the amine tautomer in the solid state and aqueous solution to a mixture of amine and imine tautomers in the gas phase. Quantum-chemical calculations predict the amine species as the most stable tautomer by about 30 kJ mol^-1 in condensed phases. On the contrary, moving to the isolated forms, both Z and E imine isomers become more stable by about 7 kJ mol^-1 . Since the imine isomers and one amine tautomer are separated by significant energy barriers, all of them should be present in the gas phase. This prediction has indeed been confirmed by high-resolution rotational spectroscopy, which provides the first experimental characterization of the elusive imine tautomer. The interpretation of the complicated hyperfine structure of the rotational spectrum, originated by three ¹⁴ N nuclei, makes it possible to use the spectral signatures as a sort of fingerprint for each individual tautomer in the complex sample.

Modifying conformational distribution of chiral tetrahydro-2-furoic acid through its interaction with water: a rotational spectroscopic and theoretical investigation

Rotational spectrum of a binary complex formed between tetrahydro-2-furoic acid (THFA) and water was measured using a chirped pulse Fourier transform microwave spectrometer. A comprehensive theoretical conformational search procedure was carried out using CREST, a conformational searching tool, and DFT calculations to aid the spectral assignment and interpretation. The final conformer ensemble is classified into two structural groups: Type 1 conformers showing a classic carboxylic acid monohydrate structure with two strong hydrogen-bonds formed between the COOH group of cis-THFA and water, and the much less stable Type 2 conformers with trans-THFA and weaker intermolecular interactions with water. The 'cis-' and 'trans-' labels refer to the configurations where the carboxylic C[double bond, length as m-dash]O and OH functional groups are on the same or opposite side, respectively. Only the two most stable Type 2 conformers containing trans-THFA I and II were observed experimentally in a neon jet expansion with an abundance ratio of 1 : 1. This relative abundance observation differs greatly from that of the THFA monomer, i.e. with trans-THFA I : trans-THFA II : cis-THFA III of 10 : 1 : 1 in a neon jet expansion, reported previously. The observation indicates a kinetically controlled formation process of different types of the monohydrates in a jet expansion, whereas a thermodynamically controlled process dominates within each type of structures. The relative stability of the THFA ring conformations is altered by interaction with water, showing a noticeable water induced conformational preference.

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.

Aggregation of lactic acid in cold rare-gas matrices and the link to solution: a matrix isolation-vibrational circular dichroism study

Crucial insight into lactic acid self-aggregation in solution is obtained by following its unique VCD spectral features in cold matrices.

Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking

The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.