Methods for Spectroscopy

Vibrational Circular Dichroism – VSA Algorithm

Vibrational circular dichroism (VCD) spectroscopy allows the determination of the absolute configuration of chiral molecules. As the measurements can be performed in solution, it is an attractive alternative to X-ray crystallography. The interpretation of experimental VCD spectrum and thus the assignment of the absolute configuration rely on ab initio quantum-mechanical (QM) calculations. For rigid molecules with a single conformation, the gas-phase QM calculations are straightforward and the theoretical VCD spectra agree well with the experimental ones. However, for flexible molecules it becomes challenging to estimate the correct conformational ensemble in solution, which has hampered a broader usage of the VCD technique. To address this issue, we have developed and evaluated a VCD sequence alignment (VSA) algorithm to match theoretical and experimental VCD spectra [1]. A simple in silico conformational search followed by optimization of the spectra alignment was found sufficient to obtain the relevant conformers with appropriate weights. Parametrized on a small set of rigid molecules, the VSA algorithm was successfully tested on a diverse set of flexible molecules, including drug molecules.

[1] external pageBöselt et al., J. Chem. Inf. Model. (2019), 59, 1826.

The fundamental theory behind absorption of circularly polarised light by chiral molecules can be described by the Rosenfeld equation for randomly oriented samples. It describes the difference in absorption belonging to a vibrational or electronic transition between two states. The evaluation of the Rosenfeld equation in the infrared regime requires “beyond Born-Oppenheimer” theories such as Stephen’s magnetic field perturbation (MFP) approach, which offers a computationally easily accessible form. However, these approaches are only valid for isotropic solutions. To address this and enable future experiments with partial alignment of the chiral molecules during measurement, we have developed an anisotropic VCD method [2]. Our calculations found that VCD spectra of anisotropic solutions deviate substantially from isotropic solutions. Moreover, since spherical symmetry is broken, additional structural information can be obtained, which potentially provides a basis for future developments.

[2] external pageSidler et al., J. Chem. Theory Comput. (2019), 15, 2492.

Infrared Spectroscopy – IRSA Algorithm

Infrared spectroscopy (IR) can provide additional information about relative stereochemistry in cases when NMR spectra are non-conclusive, since IR represents a molecule comprehensively by depiction of the complete set of its normal vibrations. The challenge is thereby that diastereomers and substitution isomers often give rise to highly similar IR spectra, and visual distinction is insufficient and may be biased. We have adapted our spectra alignment algorithm, originally developed for vibrational circular dichroism (VCD) spectroscopy [1], to automatically match IR spectra and provide a quantitative measure of the goodness of fit, which can be used to distinguish all possible isomers [3]. The approach can be applied in different use cases: diastereomers of flexible drug-like molecules, E/Z-isomers, as well as substitution isomers. The IRSA algorithm was applied successfully for the stereo assignment of a cyclic peptide [4].

[3] external pageBöselt et al., Anal. Chem. (2020), 92, 9124.
[4] external pagePultar er al., J. Am. Chem. Soc. (2021), 143, 10389.

Peaks in IR spectra can strongly overlap, which poses a challenge for spectra matching algorithms. In addition, we found that the combination of spectra from different sources (e.g., IR and Raman, or IR and VCD) can improve the robustness of the assignment. To address these points, we further developed the IRSA algorithm by introducing the concept of deconvolution of the experimental and theoretical spectra with a set of pseudo-Voigt bands and modifications to the scoring function [5]. The improved IRSA algorithm was tested on 14 compounds with IR and Raman spectra, as well as 3 compounds with IR and VCD spectra.

[5] external pageBöselt et al., Phys. Chem. Chem. Phys. (2023), 25, 2063.