Determining the Regiochemistry and Relative Stereochemistry of Small and Druglike Molecules Using an Alignment Algorithm for Infrared Spectra

Böselt, Lennard; Dötzer, Reinhard; Steiner, Sandra; Stritzinger, Michaela; Salzmann, Susanne; Riniker, Sereina

doi:10.1021/acs.analchem.0c01399

Cited by 14 publications

(27 citation statements)

References 17 publications

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“…Vibrational circular dichroism (VCD) spectroscopy is chiroptical spectroscopy that extends circular dichroism into the infrared region. − Even a molecule with no electronic absorption in the ultraviolet–visible (UV–vis) region can be a target. VCD spectra are typically measured 10 4 –10 5 times for several hours on repeated scans to obtain reliable results.…”

mentioning

confidence: 99%

Multidimensional Vibrational Circular Dichroism Apparatus Equipped with Quantum Cascade Laser and Its Use for Investigating Some Peptide Systems Containing d-Amino Acids

Sato

Shimizu²,

Watanabe³

et al. 2021

Anal. Chem.

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We developed a multidimensional vibrational circular dichroism system with a positional coordinate, making it possible to move in both x-and y-directions using an automatic stage. Quantum cascade laser (QCL) was used as a light source to achieve high intensity and narrow focusing. The QCL emitted light in the wavenumber range of 1500−1740 cm −1 , which encompassed absorption bands assigned to the stretching vibrations of amides I and II. The operation of the instrument was analyzed for samples containing amide groups. An aqueous solution of Gly-L-Leu or Gly-D-Leu was measured under the background absorbance as high as 3.5 due to the water medium. The spectra were recorded by scanning at 1.0 cm −1 steps. The time required for performing measurement at each wavenumber was less than 1 s. The mirror-image relation was maintained between the optical antipodes. A peak assigned to amide II appeared clearly at around 1580 cm −1 . In the case of KBr pellets containing the same compounds, peaks assigned to amide I and II were observed. For two-dimensional pattering, a KBr pellet comprising two domains of amino acids (or L-Ala and D-Ser) was investigated. The distribution of each component within the pellet was obtained under the two-dimensional alignment at the spatial interval of 2.5 mm.

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mentioning

confidence: 99%

Multidimensional Vibrational Circular Dichroism Apparatus Equipped with Quantum Cascade Laser and Its Use for Investigating Some Peptide Systems Containing d-Amino Acids

Sato

Shimizu²,

Watanabe³

et al. 2021

Anal. Chem.

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“…Peak alignment was done based on the IRSA algorithm originally developed by Riniker and co-workers. 71 Figure 3 shows the computational and experimental results, for which we adapted the recently presented IRSA algorithm by Riniker and co-workers to continuous spectral densities. 71 Hence, the computational peaks are aligned to their experimental pendants, using a scoring function for peak position and intensity, in order to facilitate the comparison between simulated and experimental spectra (see the SI for details).…”

Section: ∆ Pbcmentioning

confidence: 99%

“…71 Figure 3 shows the computational and experimental results, for which we adapted the recently presented IRSA algorithm by Riniker and co-workers to continuous spectral densities. 71 Hence, the computational peaks are aligned to their experimental pendants, using a scoring function for peak position and intensity, in order to facilitate the comparison between simulated and experimental spectra (see the SI for details). It is important to note that we choose to align the IR spectra, which is more reliable than seeking for an alignment of the congested VCD spectra, but nevertheless improves the significance of predicted VCD peaks.…”

Section: ∆ Pbcmentioning

confidence: 99%

Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge

Jähnigen

Zehnacker‐Rentien

Vuilleumier

2021

J. Phys. Chem. Lett.

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We introduce a new theoretical formalism to compute solid-state vibrational circular dichroism (VCD) spectra from molecular dynamics simulations. Having solved the origin-dependence problem of the periodic magnetic gauge, we present IR and VCD spectra of (1S,2S )-trans-1,2-cyclohexanediol obtained from first-principles molecular dynamics calculations and nuclear velocity perturbation theory, along with the experimental results. As the structure model imposes periodic boundary conditions, the common origin of the rotational strength has hitherto been ill-defined and was approximated by means of averaging multiple origins. The new formalism relies on the velocity representation of VCD and the time-correlation function, whose symmetry properties are exploited to reconnect the periodic model with the finite physical system. It restores the gauge freedom of finite models, but still allows fully accounting for non-local spatial coupling terms from the gauge transport term. We show that even for small simulation cells the rich nature of solid-state VCD spectra found in experiments can be reproduced to a very satisfactory level. While the general workflow to compute solid-state VCD spectra relies on the interplay of experimental data and theoretical simulation, expressions of VCD in liquid state and for isolated systems can be derived as simplification of the general equations.

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“…The above mentioned workflows have been applied multiple times to elucidate the structure of NPS. While chromatography and mass spectrometry are most often used in complementarity with NMR, IR and Raman spectroscopies are rather used as optional tools, and little details are given in the literature [14][15][16].…”

Section: Introductionmentioning

confidence: 99%

High-field and benchtop NMR spectroscopy for the characterization of new psychoactive substances

Castaing‐Cordier

Ladroue

Besacier

et al. 2021

Forensic Science International

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New psychoactive substances (NPS) have become a serious threat for public health in Europe due to their ability to be sold in the street or on the darknet. Regulating NPS is an urgent priority but comes with a number of analytical challenges since they are structurally close to legal products. A number of analytical techniques can be used for identifying NPS, among which NMR spectroscopy is in the limelight. High field NMR is typically used for structural elucidation in combination with others techniques like GC-MS, Infrared spectroscopy, together with databases. In addition to their strong ability to elucidate molecular structures, high field NMR techniques are the gold standard for quantification without any physical isolation procedure and with a single internal standard. However, high field NMR remains expensive and emerging "benchtop" NMR apparatus which are cheaper and transportable can be considered as valuable alternatives to high field NMR. Indeed, benchtop NMR, which has emerged about ten years ago, makes it possible to carry out structural elucidation and quantification of new psychoactive substances despite the gap in resolution and sensitivity as compared to high field NMR. This review describes recent advances in the field of NMR applied to the characterization of NPS. High-field NMR methods are first described in view of their complementarity with other analytical methods, focusing on both structural and quantitative aspects. The second part of the review highlights how emerging benchtop NMR approaches could act as a game changer in the field of forensics.

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Determining the Regiochemistry and Relative Stereochemistry of Small and Druglike Molecules Using an Alignment Algorithm for Infrared Spectra

Cited by 14 publications

References 17 publications

Multidimensional Vibrational Circular Dichroism Apparatus Equipped with Quantum Cascade Laser and Its Use for Investigating Some Peptide Systems Containing d-Amino Acids

Multidimensional Vibrational Circular Dichroism Apparatus Equipped with Quantum Cascade Laser and Its Use for Investigating Some Peptide Systems Containing d-Amino Acids

Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge

High-field and benchtop NMR spectroscopy for the characterization of new psychoactive substances

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