Structural characterization of chiral molecules using vibrational circular dichroism spectroscopy

Peter Rygaard Lassen

Research output: Book/ReportPh.D. thesis

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Abstract

Chiral molecules, i.e., molecules with handedness, are essential to biology, because most amino acids and sugars are chiral. A pair of molecules which are mirror images of each other have identical physical properties, but they differ in their interaction with other chiral molecules. This is the cornerstone of biological specificity. Chiral molecules also interact differently with different polarization states of electromagnetic radiation, because the absorption coefficient depends on the state of polarization. This is called dichroism and gives rise to several spectroscopic techniques targeting chiral molecules. This project is about application of one such technique, circular dichroism (CD) spectroscopy, which measures the difference in absorption of left- and right circularly polarized light - hence the name circular dichroism. This study has focused on the infrared (IR) range because there are many vibrational transitions here compared to the number of electronic transitions in the ultraviolet or visible range - hence the term vibrational circular dichroism (VCD). VCD was used to identify the absolute configuration (chirality) and predominant conformers of chiral molecules by direct comparison of experimental and calculated spectra. Theoretical structures of the sample molecules were constructed and optimized using molecular mechanical force fields followed by the quantum mechanical method density functional theory (DFT). Calculations of IR absorption and VCD spectra were then carried out using the same DFT methods. Here, VCD has the advantage over CD that time-independent DFT calculations are sufficient. During the course of this project, the above methodology has been applied to a range of molecules. Some of them (nyasol, curcuphenol dimers and ginkgolide) are purely organic compounds of pharmaceutical interest. Others are transition metal complexes relevant for the search for parity-violation effects in vibrational spectroscopy (rhenium complexes), for asymmetric catalysis (Schiff-base complexes), or as model systems for metal centres in biology (Schiff-bases and heme). Proteins (primarily myoglobin) have been studied experimentally by VCD, but are far too large for DFT calculations, in which case one must resort to model systems. In the case of organic compounds, the absolute configuration has been determined for molecules as large as ginkgolide B with 11 chiral centres or as flexible as the curcuphenol dimer with 11 variable dihedral angles. This illustrates the capabilities of the method, which are primarily limited by the duration of DFT calculations. In the case of metal complexes, they have only recently become within reach of DFT, which opens new possibilities. Interesting VCD enhancement effects in the vicinity of some transition metal centres have been discovered by a group at Syracuse University, with whom a collaboration was established. A theory for the enhancement has been developed by that group, but is not yet fully implemented in available DFT software. Currently, only part of the enhancement can be reproduced theoretically, as demonstrated for the Schiff-bases. Their conformers and absolute configurations were also identified. As for proteins, the interpretation of their spectra is different, because the immense number of overlapping vibrational modes makes it difficult to obtain information beyond the predominant secondary structure. However, the discovery of enhanced VCD signals around some metal centres allows for probing of the active site. This has been done for myoglobin with a range of different ligands attached. Corresponding DFT calculations have been carried out for just the heme group and ligands.
Original languageEnglish
Place of PublicationKgs. Lyngby
PublisherTechnical University of Denmark
Number of pages217
Publication statusPublished - Nov 2006

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