Anion-binding of a chiral tris(2-aminoethyl)amine-based tripodal thiourea: a spectroscopic and computational study

Scholten, Kevin; Merten, Christian

doi:10.1039/d1cp05688c

Cited by 5 publications

(3 citation statements)

References 35 publications

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“…Without dispersion corrections, a different conformer of rotaxane dominated and gave a VCD spectrum in good agreement with experiment. 105 Also Merten and co-workers 106 − 109 and Zehnacker and co-workers 110 , 111 have shown in several works that including dispersion correction results in significant shifts in the conformational preferences, and that the experimental data are in better agreement with spectra calculated without dispersion corrections. On the basis of these previous observations and our results, it appears that VCD is a sensitive probe of molecular conformation and could hence be used to refine the description of dispersion interactions in quantum-chemical calculations.…”

Section: Resultsmentioning

confidence: 92%

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides

2022

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Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( 32073075 Phys. Chem. Chem. Phys. 2020 22 7169 7192 and 30943025 J. Chem. Theory. Comput. 2019 15 2847 2862 ) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.

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Section: Resultsmentioning

confidence: 92%

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides

2022

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“…Relative energy differences and Boltzmann populations χ refer to the zero-point corrected energies of the conformers (Δ E ZPC ), as we regularly find Δ E ZPC -derived populations to better explain the experimental signatures than, for instance, Gibbs Free energies (for a detailed discussion see ref. 8, 9, 12 and 67). Vibrational line broadening was simulated by assigning a Lorentzian band shape with half-width at half-height of 8 cm −1 to the calculated dipole and rotational strength.…”

Section: Methodsmentioning

confidence: 99%

VCD spectroscopy reveals conformational changes of chiral crown ethers upon complexation of potassium and ammonium cations

Weirich

Tusha

Engelage

et al. 2022

Phys. Chem. Chem. Phys.

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“…The mechanism of the high selectivity for Cl − anions is related to the higher binding constant of Cl − with the anion receptor. The corresponding thiourea derivatives are known as effective receptors for chloride [34]. The complexation of the chloride to the anion receptor influences the redox reaction of the cobalt redox center.…”

Section: The Electrochemical Detection Of Chloride Using the Au/mbl A...mentioning

confidence: 99%

Voltammetric Sensing of Chloride Based on a Redox-Active Complex: A Terpyridine-Co(II)-Dipyrromethene Functionalized Anion Receptor Deposited on a Gold Electrode

Malecka-Baturo,

Daniels,

Dehaen

et al. 2024

Molecules

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A redox-active complex containing Co(II) connected to a terpyridine (TPY) and dipyrromethene functionalized anion receptor (DPM-AR) was created on a gold electrode surface. This host-guest supramolecular system based on a redox-active layer was used for voltammetric detection of chloride anions in aqueous solutions. The sensing mechanism was based on the changes in the redox activity of the complex observed upon binding of the anion to the receptor. The electron transfer coefficient (α) and electron transfer rate constant (k0) for the modified gold electrodes were calculated based on Cyclic Voltammetry (CV) experiments results. On the other hand, the sensing abilities were examined using Square Wave Voltammetry (SWV). More importantly, the anion receptor was selective to chloride, resulting in the highest change in Co(II) current intensity and allowing to distinguish chloride, sulfate and bromide. The proposed system displayed the highest sensitivity to Cl− with a limit of detection of 0.50 fM. The order of selectivity was: Cl− > SO42− > Br−, which was confirmed by the binding constants (K) and reaction coupling efficiencies (RCE).

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Anion-binding of a chiral tris(2-aminoethyl)amine-based tripodal thiourea: a spectroscopic and computational study

Abstract: Thioureas are well-known structural motifs in supramolecular anion recognition. Their conformational preferences are typically characterized by detailed NMR spectroscopy and crystallography, which are often complemented with computational results from geometry...

Cited by 5 publications

References 35 publications

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides

VCD spectroscopy reveals conformational changes of chiral crown ethers upon complexation of potassium and ammonium cations

Voltammetric Sensing of Chloride Based on a Redox-Active Complex: A Terpyridine-Co(II)-Dipyrromethene Functionalized Anion Receptor Deposited on a Gold Electrode

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