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Experimental and Computational Evidence for “Double Pancake Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines
[Image: see text] Crystal structures are reported for bicyclic 3-CF(3)C(6)H(4)CN(5)S(3) and monocyclic 3-CF(3)C(6)H(4)CN(3)S(2), the latter of which is strongly dimerized in a cis-cofacial geometry [3-CF(3)C(6)H(4)CN(3)S(2)](2). The title compounds have previously been characterized in solution by N...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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American Chemical Society
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644306/ https://www.ncbi.nlm.nih.gov/pubmed/31458400 http://dx.doi.org/10.1021/acsomega.8b03211 |
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author | Boeré, René T. |
author_facet | Boeré, René T. |
author_sort | Boeré, René T. |
collection | PubMed |
description | [Image: see text] Crystal structures are reported for bicyclic 3-CF(3)C(6)H(4)CN(5)S(3) and monocyclic 3-CF(3)C(6)H(4)CN(3)S(2), the latter of which is strongly dimerized in a cis-cofacial geometry [3-CF(3)C(6)H(4)CN(3)S(2)](2). The title compounds have previously been characterized in solution by NMR, displaying spectra that are consistent with the structure of [3-CF(3)C(6)H(4)CN(3)S(2)](2) in the crystal with anti-oriented CF(3) substituents. The interannular binding was investigated using density functional theory (DFT) methods. However, the DFT-optimized geometry spreads the aryl rings too far apart (centroid–centroid distances of ≥4.353 Å versus experimental distance of 3.850 Å). Significant improvements are obtained with dispersion-corrected DFT functionals B3LYP-D3, B3LYP-D3BJ, M062X, and APFD using the 6-311+G(2d,p) basis set. However, all of these overbind the aryl rings with centroid–centroid distances of 3.612, 3.570, 3.526, and 3.511 Å, respectively. After selecting B3LYP-D3BJ/6-311+G(2d,p) as the best method, five alternative dimer geometries were tested, and all were found to be binding; however, anti cofacial-4 (matching the structure in the solid state) is the most stable. Computed energies of the remainder are as follows: +7.0 kJ mol(–1) (syn-cofacial-5), +26.7 kJ mol(–1) (anti-cofacial-64), +27.0 kJ mol(–1) (syn-cofacial-150), +102.0 kJ mol(–1) (S,S-antarafacial), and +103.7 kJ mol(–1) (S,N-antarafacial), where the suffixes are torsional angles around the CN(3)S(2) thiazyl ring centroids. The binding in the four most stable cofacial dimers may be described by “double pancake bonding”. |
format | Online Article Text |
id | pubmed-6644306 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-66443062019-08-27 Experimental and Computational Evidence for “Double Pancake Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines Boeré, René T. ACS Omega [Image: see text] Crystal structures are reported for bicyclic 3-CF(3)C(6)H(4)CN(5)S(3) and monocyclic 3-CF(3)C(6)H(4)CN(3)S(2), the latter of which is strongly dimerized in a cis-cofacial geometry [3-CF(3)C(6)H(4)CN(3)S(2)](2). The title compounds have previously been characterized in solution by NMR, displaying spectra that are consistent with the structure of [3-CF(3)C(6)H(4)CN(3)S(2)](2) in the crystal with anti-oriented CF(3) substituents. The interannular binding was investigated using density functional theory (DFT) methods. However, the DFT-optimized geometry spreads the aryl rings too far apart (centroid–centroid distances of ≥4.353 Å versus experimental distance of 3.850 Å). Significant improvements are obtained with dispersion-corrected DFT functionals B3LYP-D3, B3LYP-D3BJ, M062X, and APFD using the 6-311+G(2d,p) basis set. However, all of these overbind the aryl rings with centroid–centroid distances of 3.612, 3.570, 3.526, and 3.511 Å, respectively. After selecting B3LYP-D3BJ/6-311+G(2d,p) as the best method, five alternative dimer geometries were tested, and all were found to be binding; however, anti cofacial-4 (matching the structure in the solid state) is the most stable. Computed energies of the remainder are as follows: +7.0 kJ mol(–1) (syn-cofacial-5), +26.7 kJ mol(–1) (anti-cofacial-64), +27.0 kJ mol(–1) (syn-cofacial-150), +102.0 kJ mol(–1) (S,S-antarafacial), and +103.7 kJ mol(–1) (S,N-antarafacial), where the suffixes are torsional angles around the CN(3)S(2) thiazyl ring centroids. The binding in the four most stable cofacial dimers may be described by “double pancake bonding”. American Chemical Society 2018-12-24 /pmc/articles/PMC6644306/ /pubmed/31458400 http://dx.doi.org/10.1021/acsomega.8b03211 Text en Copyright © 2018 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
spellingShingle | Boeré, René T. Experimental and Computational Evidence for “Double Pancake Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines |
title | Experimental and Computational Evidence for “Double Pancake
Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly
Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines |
title_full | Experimental and Computational Evidence for “Double Pancake
Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly
Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines |
title_fullStr | Experimental and Computational Evidence for “Double Pancake
Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly
Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines |
title_full_unstemmed | Experimental and Computational Evidence for “Double Pancake
Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly
Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines |
title_short | Experimental and Computational Evidence for “Double Pancake
Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly
Dimerized 5-Aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines |
title_sort | experimental and computational evidence for “double pancake
bonds”: the role of dispersion-corrected dft methods in strongly
dimerized 5-aryl-1λ(2),3λ(2)-dithia-2,4,6-triazines |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644306/ https://www.ncbi.nlm.nih.gov/pubmed/31458400 http://dx.doi.org/10.1021/acsomega.8b03211 |
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