Statistical Validation of Absolute Configuration Assignment in Vibrational Optical Activity

Stereochemistry of natural products from vibrational circular dichroism

Secondary metabolites from land and marine (micro)organisms have been at the focus of the drug discovery process for many years. One of the reasons for this success is nature's incredible ability to create intricate molecular scaffolds. Such structural richness, however, makes the structural elucidation, and the absolute configuration assignment in particular, a challenging process. Vibrational circular dichroism (VCD) has emerged as one of the most reliable and versatile methods to unambiguously assign both the absolute configuration and conformations of chiral molecules in solution. Although VCD is no longer a curiosity in the field of molecular spectroscopy after 50 years since its first report, it is still underutilized by natural product chemists worldwide for varying reasons. Herein, we highlight the evolution of the application of VCD to natural product chemistry, focusing on its strengths as well as points that still need improvement. General guidelines for the correct application of VCD to stereochemical studies are also provided.

Comparison of different density functional theory methods for the calculation of vibrational circular dichroism spectra

The determination of the absolute configuration (AC) of an organic molecule is still a challenging task for which the combination of spectroscopic with quantum-mechanical methods has become a promising approach. In this study, we investigated the accuracy of DFT methods (480 overall combinations of 15 functionals, 16 basis sets, and 2 solvation models) to calculate the VCD spectra of six chiral organic molecules in order to benchmark their capability to facilitate the determination of the AC.

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.

Vibrational Circular Dichroism study of chiral food additives: γ-valero- and γ-caprolactone

γ-valerolactone and γ-caprolactone are commonly used as flavor additives in the food industry. In the present work we fully explore the molecular structure and conformational distribution of enantiopure γ-valerolactone and γ-caprolactone in solution state by using Vibrational Circular Dichroism (VCD) spectroscopy assisted by quantum chemical calculations. In order to establish the most accurate DFT method for this type of samples a set of methods and basis sets have been implemented and their performances have been compared. Subsequently, we have performed a complete vibrational assignment, which allowed to detect certain key vibrational features related to specific solution-state conformational speciation. In spite of the rigidity of the samples being studied, our results point to the incidence of conformational mixture in CCl₄ solution in both samples.

A Mechanism-Based Sphingosine-1-phosphate Lyase Inhibitor

The synthesis of a series of vinylated analogues of sphingosine-1-phosphate together with their unambiguous configurational assignment by VCD methods is reported. Among them, compound RBM10-8 can irreversibly inhibit human sphingosine-1-phosphate lyase (hS1PL) while behaving also as an enzyme substrate. These findings, together with the postulated mechanism for S1PL activity, reinforce the role of RBM10-8 as a new mechanism-based hS1PL inhibitor.

Comparative Study of the Vibrational Optical Activity Techniques in Structure Elucidation: The Case of Galantamine

The absolute configuration of the alkaloid galantamine was studied using a range of solution-state techniques; nuclear magnetic resonance (NMR), vibrational circular dichroism (VCD), and Raman optical activity (ROA). While the combined use of NMR and VCD does provide a fast, high-resolution methodology for determining the absolute configuration of galantamine, both techniques were needed in concert to achieve this goal. ROA, on the other hand, proved to be sensitive enough to assign the full absolute configuration without relying on other techniques. In both cases, statistical validation was applied to aid the determination of absolute configuration. In the case of galantamine, ROA combined with statistical validation is shown to be a powerful stand-alone tool for absolute configuration determination.

CDSpecTech: A single software suite for multiple chiroptical spectroscopic analyses

The program CDSpecTech was developed to facilitate the analysis of chiroptical spectra, which include the following: vibrational circular dichroism (VCD) and corresponding vibrational absorption (VA) spectra; vibrational Raman optical activity (VROA) and corresponding vibrational Raman spectra; electronic circular dichroism (ECD) and corresponding electronic absorption (EA) spectra. In addition, the program allows for generating optical rotatory dispersion (ORD) as the Kramers-Kronig transform of ECD spectra. The simulation of theoretical spectra from transition strengths can be achieved using different bandshape profiles. The experimental and simulated theoretical spectra can be visually compared by displaying them together. A unique feature of CDSpecTech is performing spectral analysis using the ratio spectra; i.e., the dimensionless dissymmetry factor (DF) spectrum, which is the ratio of CD to absorption spectra, and the dimensionless circular intensity difference (CID) spectrum, which is the ratio of VROA to vibrational Raman spectra. The quantitative agreement between experimental and simulated theoretical spectra can also be assessed from the numerical similarity overlap between them. Two different similarity overlap methods are available. The program uses a graphical user interface which allows for ease of use and facilitates the analysis. All these features make CDSpecTech a valuable tool for the analysis of chiroptical spectra. The program is freely available on the World Wide Web.

Model-averaging of ab initio spectra for the absolute configuration assignment via vibrational circular dichroism

Unescapable errors of calculations are taken into account through a model-averaging technique, opening the way to a quantitative comparison with experiment.

Absolute configuration of the antimalarial erythro-mefloquine – vibrational circular dichroism and X-ray diffraction studies of mefloquine and its thiourea derivative

The long-standing discussion of the absolute configuration of erythro-mefloquine is revisited, showcasing the strength of a combination of experimental and calculated vibrational circular dichroism spectroscopy.

Calculation of Raman optical activity spectra for vibrational analysis

This review provides the necessary knowledge to accurately model ROA spectra of solvated systems and interpret their vibrational characteristics.

Absolute Configuration of a Rare Sesquiterpene: (+)-3-Ishwarone

To determine the absolute configuration of 3-ishwarone, the experimental electronic circular dichroism (ECD), electronic dissymmetry factor (EDF), optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and vibrational dissymmetry factor (VDF) spectra of (+)-3-ishwarone are analyzed with the corresponding density functional theoretical predictions for different diastereomers. ECD and ORD spectra by themselves could not facilitate the determination of the absolute configuration of this molecule. However, the magnitude of the experimental EDF of (+)-3-ishwarone is found to match better with that predicted for the (1R,2S,4S,5R,9R,11R) diastereomer. The analyses of similarity measures between experimental and predicted spectra for VCD and VDF clearly suggested that the absolute configuration of (+)-3-ishwarone is (1R,2S,4S,5R,9R,11R).

Comparison of experimental and calculated chiroptical spectra for chiral molecular structure determination

For three different chiroptical spectroscopic methods, namely, vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and Raman optical activity (ROA), the measures of similarity of the experimental spectra to the corresponding spectra predicted using quantum chemical theories are summarized. In determining the absolute configuration and/or predominant conformations of chiral molecules, these similarity measures provide numerical estimates of agreement between experimental observations and theoretical predictions. Selected applications illustrating the similarity measures for absorption, circular dichroism, and corresponding dissymmetry factor (DF) spectra, in the case of VCD and ECD, and for Raman, ROA, and circular intensity differential (CID) spectra in the case of ROA, are presented. The analysis of similarity in DF or CID spectra is considered to be much more discerning and accurate than that in absorption (or Raman) and circular dichroism (or ROA) spectra, undertaken individually.