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Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B(12) Derivatives?
[Image: see text] Aryl corrins represent a novel class of designed B(12) derivatives with biological properties of “antivitamins B(12)”. In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) a...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510309/ https://www.ncbi.nlm.nih.gov/pubmed/37656981 http://dx.doi.org/10.1021/jacs.3c03001 |
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author | Tsybizova, Alexandra Fritsche, Lukas Miloglyadova, Larisa Kräutler, Bernhard Chen, Peter |
author_facet | Tsybizova, Alexandra Fritsche, Lukas Miloglyadova, Larisa Kräutler, Bernhard Chen, Peter |
author_sort | Tsybizova, Alexandra |
collection | PubMed |
description | [Image: see text] Aryl corrins represent a novel class of designed B(12) derivatives with biological properties of “antivitamins B(12)”. In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born–Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both “static” DFT calculations and “dynamic” BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made. |
format | Online Article Text |
id | pubmed-10510309 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-105103092023-09-21 Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B(12) Derivatives? Tsybizova, Alexandra Fritsche, Lukas Miloglyadova, Larisa Kräutler, Bernhard Chen, Peter J Am Chem Soc [Image: see text] Aryl corrins represent a novel class of designed B(12) derivatives with biological properties of “antivitamins B(12)”. In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born–Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both “static” DFT calculations and “dynamic” BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made. American Chemical Society 2023-09-01 /pmc/articles/PMC10510309/ /pubmed/37656981 http://dx.doi.org/10.1021/jacs.3c03001 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Tsybizova, Alexandra Fritsche, Lukas Miloglyadova, Larisa Kräutler, Bernhard Chen, Peter Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B(12) Derivatives? |
title | Cryogenic Ion Vibrational
Predissociation (CIVP) Spectroscopy
of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations
for Vitamin B(12) Derivatives? |
title_full | Cryogenic Ion Vibrational
Predissociation (CIVP) Spectroscopy
of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations
for Vitamin B(12) Derivatives? |
title_fullStr | Cryogenic Ion Vibrational
Predissociation (CIVP) Spectroscopy
of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations
for Vitamin B(12) Derivatives? |
title_full_unstemmed | Cryogenic Ion Vibrational
Predissociation (CIVP) Spectroscopy
of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations
for Vitamin B(12) Derivatives? |
title_short | Cryogenic Ion Vibrational
Predissociation (CIVP) Spectroscopy
of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations
for Vitamin B(12) Derivatives? |
title_sort | cryogenic ion vibrational
predissociation (civp) spectroscopy
of aryl cobinamides in the gas phase: how good are the calculations
for vitamin b(12) derivatives? |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510309/ https://www.ncbi.nlm.nih.gov/pubmed/37656981 http://dx.doi.org/10.1021/jacs.3c03001 |
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