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Norcorrole as a Delocalized, Antiaromatic System.

ABSTRACT: Nickel norcorrole provides an unusual example of a molecule that is strongly antiaromatic according to the magnetic criterion, but which exhibits, according to high-quality DFT calculations, a symmetric, delocalized structure with no difference in bond length between adjacent Cmeso-C? bonds. A fragment molecular orbital analysis suggests that these discordant observations are a manifestation of the high stability of the dipyrrin fragments, which retain their electronic and structural integrity even as part of the norcorrole ring system.

SUBMITTER: Conradie J

PROVIDER: S-EPMC6425022 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Norcorrole as a Delocalized, Antiaromatic System.

Conradie Jeanet J Foroutan-Nejad Cina C Ghosh Abhik A

Scientific reports 20190319 1

Nickel norcorrole provides an unusual example of a molecule that is strongly antiaromatic according to the magnetic criterion, but which exhibits, according to high-quality DFT calculations, a symmetric, delocalized structure with no difference in bond length between adjacent C<sub>meso</sub>-C<sub>α</sub> bonds. A fragment molecular orbital analysis suggests that these discordant observations are a manifestation of the high stability of the dipyrrin fragments, which retain their electronic and ...[more]

PMID: 30890733

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Project description:The role of protein-bound water molecules in protein function and catalysis is an emerging topic. Here, we studied the solvation of an excess proton by protein-bound water molecules and the contribution of the surrounding amino acid residues at the proton release site of the membrane protein bacteriorhodopsin. It hosts an excess proton within a protein-bound water cluster, which is hydrogen bonded to several surrounding amino acids. Indicative of delocalization is a broad continuum absorbance experimentally observed by time-resolved Fourier transform infrared spectroscopy. In combination with site-directed mutagenesis, the involvement of several amino acids (especially Glu-194 and Glu-204) in the delocalization was elaborated. Details regarding the contributions of the glutamates and water molecules to the delocalization mode in biomolecular simulations are controversial. We carried out quantum mechanics/molecular mechanics (QM/MM) self-consistent charge density functional tight-binding simulations for all amino acids that have been experimentally shown to be involved in solvation of the excess proton, and systematically investigated the influence of the quantum box size. We compared calculated theoretical infrared spectra with experimental ones as a measure for the correct description of excess proton delocalization. A continuum absorbance can only be observed for small quantum boxes containing few amino acids and/or water molecules. Larger quantum boxes, including all experimentally shown involved amino acids, resulted in narrow absorbance bands, indicating protonation of a single binding site in contradiction to experimental results. We conclude that small quantum boxes seem to reproduce representative extreme cases of proton delocalization modes: proton delocalization only on water molecules or only between Glu-194 and Glu-204. Extending the experimental spectral region to lower wave numbers, a water-delocalized proton reproduces the observed continuum absorbance better than a glutamate-shared delocalized proton. However, a full agreement between QM simulations and experimental results on the delocalized excess proton will require a larger quantum box as well as more sophisticated QM/MM methods.

Dataset Information

Norcorrole as a Delocalized, Antiaromatic System.

Publications

Norcorrole as a Delocalized, Antiaromatic System.

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