Exploring machine learning methods for absolute configuration determination with vibrational circular dichroism

Vermeyen, Tom; Brence, Jure; Echelpoel, Robin Van; Aerts, Roy; Acke, Guillaume; Bultinck, Patrick; Herrebout, Wouter A.

doi:10.1039/d1cp02428k

Cited by 8 publications

(12 citation statements)

References 45 publications

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“…A wide range of ML methodologies have been proposed to improve computational accuracy, cost, and speed in IR, Raman, VCD, and ECD spectra (Figure ). − Similar advances must be possible for TCD spectroscopy, too. Although there are no (to the best of our knowledge) ML-based methodologies developed and published for TCD yet, special features of this spectroscopy and its implementation for multidimensional analysis of the biological and abiological structures discussed above make this spectroscopy particularly suitable for the application of ML.…”

Section: Future Directionsmentioning

confidence: 99%

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Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures

et al. 2022

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Chemical, physical, biological and materials engineering disciplines use a variety of chiroptical spectroscopies to probe geometrical and optical asymmetry in molecules and particles. Electronic (ECD) and vibrational (VCD) circular dichroism are the most common of these techniques and collectively enable the studies of electronic and vibronic transitions with energies between 0.1 and 5.0 eV. The vibrational states with characteristic energies in the range of 0.001−0.01 eV carry valuable information about concerted intermolecular motions in molecules and crystals involving multiple atoms. These vibronic transitions located in the terahertz (THz) part of the spectrum become increasingly more important for the chemistry, physics, and biology of complex molecules and materials However, the methodology and hardware of THz circular dichroism (TCD) are much less developed than the chiroptical spectroscopies for ultraviolet, visible, near-and mid infrared photons. Here we provide theoretical foundations, practical implementations, comparative assessments, and exemplary applications of TCD spectroscopy. We show that the sign, intensity, and position of TCD peaks are highly sensitive to the three-dimensional structure and long-range organization of molecular crystals, which offer unique capabilities to study (bio) molecules, their crystals, and nanoscale assemblies and apply the novel data processing methodologies. TCD also offers a convenient toolbox to identify new physical phenomena, such as chiral phonons and their propagation in nanostructured matter. We also discuss the major challenges, emerging opportunities and promising research directions, including broad investigation of chiral phonons observed in chiral (nano) crystals and emerging machine learning methodologies for TCD in biological and nanoscale structures. Ubiquity of low-frequency vibrations with rotational components in biomolecular structures, combined with sharpness of peaks in TCD spectra, enables a variety of technological translations.

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Section: Future Directionsmentioning

confidence: 99%

Section: Future Directionsmentioning

confidence: 99%

Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures

et al. 2022

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“…Visual comparison will be explored in a search of either similar or discriminative vibrational bands for individual molecules. Then, inspired by a recent proof-of-concept study using machine learning (ML) to extract absolute configurations from VCD spectra of decorated α-pinene derivatives, 57 we will extend the application of the ML methodology to identify monoterpenes in complex mixtures, such as essential oils which, to the best of our best knowledge, has not been tested for VCD. In this way, we will assess the feasibility of such an approach and identify possible pitfalls for its future development.…”

Section: Introductionmentioning

confidence: 99%

Pushing the boundaries of VCD spectroscopy in natural product chemistry

Vermeyen

Batista

Valverde

et al. 2023

Phys. Chem. Chem. Phys.

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“…45 For detailed information about the various methods of VCD spectra calculation, the quantum-mechanical theory behind them, MD simulations for the explicit description of solvent effects, and the transfer to machine learning methods, the reader shall be referred to the existing literature. 17,21,25,[46][47][48][49][50][51][52][53][54]…”

Section: Introductionmentioning

confidence: 99%

“…The reader should bear in mind that AC determination is still not a black‐box method and every computational method is prone to error 45 . For detailed information about the various methods of VCD spectra calculation, the quantum‐mechanical theory behind them, MD simulations for the explicit description of solvent effects, and the transfer to machine learning methods, the reader shall be referred to the existing literature 17,21,25,46–54 …”

Section: Introductionmentioning

confidence: 99%

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

Groß,

Kühlborn,

Pusch

et al. 2023

Chirality

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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.

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Exploring machine learning methods for absolute configuration determination with vibrational circular dichroism

Abstract: The added value of supervised Machine Learning (ML) methods to determine the Absolute Configuration (AC) of compounds from their Vibrational Circular Dichroism (VCD) spectra was explored. Among all ML methods...

Cited by 8 publications

References 45 publications

Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures

Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures

Pushing the boundaries of VCD spectroscopy in natural product chemistry

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

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