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Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism.

ABSTRACT: The chiral molecular structures of four different substituted indans, namely, (S)-1-methylindan, (R)-1-methylindan-1-d, (R)-1-aminoindan, and (S)-1-indanol, were investigated using experimental vibrational absorption and vibrational circular dichroism spectra and corresponding spectra predicted using quantum chemical (QC) calculations. All of these molecules possess two ring puckering conformations, with ring puckering leading to the pseudoequatorial substituent being approximately four times more abundant over that leading to the pseudoaxial substituent. The amino group in 1-aminoindan has three conformations arising from the rotation of NH₂ group, for each ring puckering conformation, resulting in a total of six conformations. Whereas 1-indanol in the nonhydrogen-bonding solvent CCl₄ also has six conformations similar to those of 1-aminoindan, 1-indanol in the hydrogen-bonding solvent DMSO-d ₆ adopts numerous conformations, of which 30 conformers are considered to have at least ?1% or more population. In DMSO solution, ring puckering leading to pseudoequatorial substituent accounts for 77% population and 23% for pseudoaxial substituent. The QC spectra predicted for the geometry optimized conformers are found to be in excellent quantitative agreement with corresponding experimental spectra in all of the molecules considered. The procedures suggested in this work are hoped to provide successful pathways for future chiral molecular structural analyses.

SUBMITTER: Johnson JL

PROVIDER: S-EPMC6648482 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism.

Johnson Jordan L JL Polavarapu Prasad L PL

ACS omega 20190306 3

The chiral molecular structures of four different substituted indans, namely, (S)-1-methylindan, (R)-1-methylindan-1-d, (R)-1-aminoindan, and (S)-1-indanol, were investigated using experimental vibrational absorption and vibrational circular dichroism spectra and corresponding spectra predicted using quantum chemical (QC) calculations. All of these molecules possess two ring puckering conformations, with ring puckering leading to the pseudoequatorial substituent being ...[more]

PMID: 31459680

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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

Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism.

Publications

Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism.

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