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A computational approach for modeling electronic circular dichroism of solvated chromophores.

ABSTRACT: The present study consists in a novel computational protocol to model the UV-circular dichroism spectra of solvated species. It makes use of quantum-chemical calculations on a series of conformations of a flexible chromophore or on a series of chromophore/solvent clusters extracted from molecular dynamic simulations. The protocol is described and applied to the aqueous cationic tripeptide GAG⁺ and to the aqueous neutral decapeptide (GVGVP)₂ . The protocol has proven able to: (i) properly consider the conformational motion of solute in the given environment; (ii) give the actual statistical weight of each conformational state; (iii) provide a reliable quantum mechanical method able to reproduce the spectral features. Temperature effects on conformations and spectral properties are properly taken into account. The role of explicit solvent on the conformational analysis and the spectra calculation is discussed. The comparison of the calculated circular dichroism spectra with experimental ones recorded at different temperatures represents a strict validation test of the method.

SUBMITTER: Monti M

PROVIDER: S-EPMC9825941 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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A computational approach for modeling electronic circular dichroism of solvated chromophores.

Monti Marta M Stener Mauro M Aschi Massimiliano M

Journal of computational chemistry 20220922 30

The present study consists in a novel computational protocol to model the UV-circular dichroism spectra of solvated species. It makes use of quantum-chemical calculations on a series of conformations of a flexible chromophore or on a series of chromophore/solvent clusters extracted from molecular dynamic simulations. The protocol is described and applied to the aqueous cationic tripeptide GAG<sup>+</sup> and to the aqueous neutral decapeptide (GVGVP)<sub>2</sub> . The protocol has proven able to ...[more]

PMID: 36134712

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Project description: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 ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and 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.

Dataset Information

A computational approach for modeling electronic circular dichroism of solvated chromophores.

Publications

A computational approach for modeling electronic circular dichroism of solvated chromophores.

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