Improved absolute configuration determination of complex molecules with VCD

All biological systems are three-dimensional and determining the exact configuration of the system is important for pharmaceutical applications and drug design. However, determining 3D-structures is complicated and difficult. Vibrational circular dichroism is a method using circular polarized light to see differences between different stereoisomers.

In comparison to other methods that determine stereochemistry, calculating VCD spectra is relatively easy since only electronic ground state calculations are performed. In practice, however, absolute configuration determination can be quite challenging due to floppy modes, solvent interactions, and other complications.

Dr. Mark Koenis recently obtained his doctoral degree in this field where he expanded application of VCD calculations to larger, biologic systems such as peptides containing multiple stereocenters and dynamic systems such as rotaxanes. He also provide computational, workflow and visual tools to help researchers with more confident assignment of the absolute stereochemistry.

After using AMS-DFTB to perform conformer searches of the system and DFT to optimize the obtained geometries, VCD- spectra were calculated and evaluated to obtain important information regarding the stereochemistry of the system.

Want to get started yourself with VCD-spectra calculations? Check out our video tutorial and manual!

Do you want try for yourself? Request a free 30-day evaluation for the whole Amsterdam Modeling Suite.

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Mark A. J. Koenis, Olivier Visser, Lucas Visscher, Wybren Jan Buma and Valentin P. Nicu, GUI Implementation of VCDtools, a Program to Analyse Computed Vibrational Circular Dichroism Spectra, J. Chem. Inf. Model. (2019).

Mark A. J. Koenis, Lucas Visscher, Wybren Jan Buma and Valentin P. Nicu, Analysis of Vibrational Circular Dichroism Spectra of Peptides: a Generalised Coupled Oscillator Approach Using VCDtools, J. Phys. Chem. B (2020).

Yiyin Xia, Mark A. J. Koenis, Juan F. Collados, Pablo Ortiz, Syuzanna R. Harutyunyan, Lucas Visscher, Wybren Jan Buma and Valentin P. Nicu, Regional Susceptibility in VCD Spectra to Dynamic Molecular Motions: The Case of a Benzyl α−Hydroxysilane, ChemPhysChem 19, 561 (2019).

Mark A. J. Koenis, Yiyin Xia, Sergio R. Domingos, Lucas Visscher, Wybren Jan Buma and Valentin P. Nicu, Taming Conformational Heterogeneity in and with Vibrational Circular Dichroism Spectroscopy, Chem. Sci. 10, 7680 (2019).

Mark A. J. Koenis, Eveline H. Tiekink, Davita M. E. van Raamsdonk, Nadav U. Joosten, Susanne A. Gooijer, Valentin P. Nicu, Lucas Visscher and Wybren Jan Buma, Analytical Chemistry on Many-Center Chiral Compounds Based on Vibrational Circular Dichroism: Absolute Configuration Assignments and Determination of Contaminant Levels, Anal. Chim. Acta. 1090, 100 (2019).

Mark A. J. Koenis, Artem Osypenko, Gad Fuks, Nicolas Giuseppone, Valentin P. Nicu, Lucas Visscher and Wybren Jan Buma, Self-Assembly of Supramolecular Polymers of N-Centered Triarylamine Trisamides in the Light of Circular Dichroism: Reaching Consensus between Electrons and Nuclei, J. Am. Chem. Soc. 142, 1020 (2020).

Habiburrahman Zulfikri, Mark A. J. Koenis, Michael M. Lerch, Mariangela Di Donato, Wiktor Szymanski, Claudia Filippi, Ben L. Feringa, Wybren Jan Buma, Taming the Complexity of Donor-Acceptor Stenhouse Adducts: Infrared Motion Pictures of the Complete Switching Pathway, J. Am. Chem. Soc. 141, 7376 (2019).

Check out Mark’s thesis, which he recently defended successfully (cum laude – congratulations!)

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