Cargando…

Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative

The mol­ecular structure of the title compound {systematic name: 3′,6′-bis(di­ethyl­amino)-2-[(2-hy­droxy­benzyl­idene)amino]­spiro­[isoindoline-1,9′-xan­then]-3-one}, C(35)H(36)N(4)O(3) or RbSa, can be seen as being composed of two parts sharing a central quaternary carbon atom. Both the xanthene a...

Descripción completa

Detalles Bibliográficos
Autores principales: Suramitr, Songwut, Teanwarawat, Jitpinan, Ithiapa, Nuttapong, Wattanathana, Worawat, Suramitr, Anwaraporn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336787/
https://www.ncbi.nlm.nih.gov/pubmed/32695446
http://dx.doi.org/10.1107/S2056989020007197
_version_ 1783554390597042176
author Suramitr, Songwut
Teanwarawat, Jitpinan
Ithiapa, Nuttapong
Wattanathana, Worawat
Suramitr, Anwaraporn
author_facet Suramitr, Songwut
Teanwarawat, Jitpinan
Ithiapa, Nuttapong
Wattanathana, Worawat
Suramitr, Anwaraporn
author_sort Suramitr, Songwut
collection PubMed
description The mol­ecular structure of the title compound {systematic name: 3′,6′-bis(di­ethyl­amino)-2-[(2-hy­droxy­benzyl­idene)amino]­spiro­[isoindoline-1,9′-xan­then]-3-one}, C(35)H(36)N(4)O(3) or RbSa, can be seen as being composed of two parts sharing a central quaternary carbon atom. Both the xanthene and iso­indole moieties are nearly planar: 14 atoms in the former moiety show an r.m.s. deviation of 0.0411 Å and eleven atoms in the latter moiety show an r.m.s. deviation of 0.0545 Å. These two planes are almost perpendicular to each other, the angle between the mean planes being 87.71 (2)°. The title compound appears to be in its enol form. The corresponding H atom was located and freely refined at a distance of 1.02 (3) Å from the O atom and 1.72 (2) Å from the N atom. The strong intra­molecular hydrogen bond O—H⋯N bridging the hydroxyl group and its neighboring nitro­gen atom forms an S(6) graph-set motif. Apart from the intra­molecular O—H⋯N hydrogen bond, C—H⋯O inter­actions are observed between two neighbouring RbSa mol­ecules related by an inversion center. The C—O donor–acceptor distance is 3.474 (2) Å. Moreover, C—H⋯π inter­actions are observed between the C—H bond of one of the ethyl groups and the centroid of the benzene ring of the iso­indole moiety. The C⋯centroid distance is 3.8191 (15) Å. No π–π inter­actions are observed in the crystal structure as the shortest distance between ring centroids is more than 4 Å. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H, C⋯H/H⋯C, O⋯H/H⋯O and N⋯H/H⋯N inter­actions. DFT calculations at the CAM-B3LYP/6–31 G(d) level were carried out to gain a better understanding of the relative energies and the tautomerization process between two possible conformers (keto and enol), as well as the transition state of the title compound.
format Online
Article
Text
id pubmed-7336787
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher International Union of Crystallography
record_format MEDLINE/PubMed
spelling pubmed-73367872020-07-20 Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative Suramitr, Songwut Teanwarawat, Jitpinan Ithiapa, Nuttapong Wattanathana, Worawat Suramitr, Anwaraporn Acta Crystallogr E Crystallogr Commun Research Communications The mol­ecular structure of the title compound {systematic name: 3′,6′-bis(di­ethyl­amino)-2-[(2-hy­droxy­benzyl­idene)amino]­spiro­[isoindoline-1,9′-xan­then]-3-one}, C(35)H(36)N(4)O(3) or RbSa, can be seen as being composed of two parts sharing a central quaternary carbon atom. Both the xanthene and iso­indole moieties are nearly planar: 14 atoms in the former moiety show an r.m.s. deviation of 0.0411 Å and eleven atoms in the latter moiety show an r.m.s. deviation of 0.0545 Å. These two planes are almost perpendicular to each other, the angle between the mean planes being 87.71 (2)°. The title compound appears to be in its enol form. The corresponding H atom was located and freely refined at a distance of 1.02 (3) Å from the O atom and 1.72 (2) Å from the N atom. The strong intra­molecular hydrogen bond O—H⋯N bridging the hydroxyl group and its neighboring nitro­gen atom forms an S(6) graph-set motif. Apart from the intra­molecular O—H⋯N hydrogen bond, C—H⋯O inter­actions are observed between two neighbouring RbSa mol­ecules related by an inversion center. The C—O donor–acceptor distance is 3.474 (2) Å. Moreover, C—H⋯π inter­actions are observed between the C—H bond of one of the ethyl groups and the centroid of the benzene ring of the iso­indole moiety. The C⋯centroid distance is 3.8191 (15) Å. No π–π inter­actions are observed in the crystal structure as the shortest distance between ring centroids is more than 4 Å. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H, C⋯H/H⋯C, O⋯H/H⋯O and N⋯H/H⋯N inter­actions. DFT calculations at the CAM-B3LYP/6–31 G(d) level were carried out to gain a better understanding of the relative energies and the tautomerization process between two possible conformers (keto and enol), as well as the transition state of the title compound. International Union of Crystallography 2020-06-05 /pmc/articles/PMC7336787/ /pubmed/32695446 http://dx.doi.org/10.1107/S2056989020007197 Text en © Suramitr et al. 2020 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Research Communications
Suramitr, Songwut
Teanwarawat, Jitpinan
Ithiapa, Nuttapong
Wattanathana, Worawat
Suramitr, Anwaraporn
Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative
title Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative
title_full Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative
title_fullStr Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative
title_full_unstemmed Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative
title_short Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B–salicyl­aldehyde Schiff base derivative
title_sort crystal structure, hirshfeld surface analysis and computational study of a rhodamine b–salicyl­aldehyde schiff base derivative
topic Research Communications
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336787/
https://www.ncbi.nlm.nih.gov/pubmed/32695446
http://dx.doi.org/10.1107/S2056989020007197
work_keys_str_mv AT suramitrsongwut crystalstructurehirshfeldsurfaceanalysisandcomputationalstudyofarhodaminebsalicylaldehydeschiffbasederivative
AT teanwarawatjitpinan crystalstructurehirshfeldsurfaceanalysisandcomputationalstudyofarhodaminebsalicylaldehydeschiffbasederivative
AT ithiapanuttapong crystalstructurehirshfeldsurfaceanalysisandcomputationalstudyofarhodaminebsalicylaldehydeschiffbasederivative
AT wattanathanaworawat crystalstructurehirshfeldsurfaceanalysisandcomputationalstudyofarhodaminebsalicylaldehydeschiffbasederivative
AT suramitranwaraporn crystalstructurehirshfeldsurfaceanalysisandcomputationalstudyofarhodaminebsalicylaldehydeschiffbasederivative