Download PDF
Synlett 2023; 34(10): 1113-1121
DOI: 10.1055/a-2071-4235
cluster
Dispersion Effects

Dispersion in Crystal Structures of 1-Chloro-3-aryl-5-trihalomethyl-1λ4,2,4,6-thiatriazines: Towards an Understanding of the Supramolecular Organization of Covalent Thiazyl Chlorides

Savini Suduweli Kondage
a   Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4, Canada
,
Tracey L. Roemmele
a   Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4, Canada
,
René T. Boeré  ∗
a   Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4, Canada
b   The Canadian Centre for Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4, Canada
› Author AffiliationsResearch funding for this work was provided by ongoing Discovery Grants from the Natural Sciences and Engineering Research Council of Canada. The funding of the Bruker D8-Apex II diffractometer from the NSERC-C Research Tools and Instruments program, with a generous contribution from the University of Lethbridge, is gratefully acknowledged.
› Further Information
    Permissions and Reprints All articles of this category


Abstract

The syntheses of five new 1-chloro-3-aryl-5-trichloromethyl-1λ4,2,4,6-thiatriazines, aryl = 4-R-C6H4- (R = CH3O, CH3, H, Cl and CF3), are reported with full characterization. Single-crystal X-ray diffraction structure determinations on all, as well as the 5-CF3 analogue which also has R = CF3, with models produced by Hirshfeld atom refinement, produced high-accuracy structures. All six exemplars form lateral dimers with short contacts that define a centrosymmetric {δ+S···Nδ−}2 motif, with interaction distances from 3.0473(9) to 3.422(3) Å, which do not vary in an expected manner with R. Normal population analysis charges computed by B3LYP-D3/6-311++G(d,p) DFT methods show small variations, and entirely as expected from the inductive effects of R. Gas-phase minimization of the dimers with M06-2X/aug-cc-pVDZ or B3LYP-D3/6-311++G(d,p) methods, with full counterpoise correction, replicate the experimental geometries for the 5-CF3, the 5-CCl3/CH3OC6H4 and the 5-CCl3/CH3C6H4 experimental structures, but diverge for other CCl3 exemplars. Interaction energies are more than double those computed for [(HC)2N2S]2. Using a geometry-optimized model with H in place of CX3, the interaction energy reduces to a very realistic –22 to –24 kJ/mol for just the {δ+S···Nδ−}2 motif, suggesting that CX3 interactions contribute 21% (CF3) to 37% (CCl3) of the total.

Key words

chlorothiatriazine - thiazyl - supramolecular interaction - dispersion correction - counterpoise correction - density functional theory - X-ray crystallography - molecular squares

Supporting Information

    Supporting information for this article is available online at https://doi.org/10.1055/a-2071-4235.
  • Supporting Information


Publication History

Received: 26 February 2023

Accepted after revision: 12 April 2023

Accepted Manuscript online:
12 April 2023

Article published online:
23 May 2023

© 2023. Thieme. All rights reserved

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

 

  • References and Notes

  • 1 Tiekink ER. T. CrystEngComm 2023; 25: 9
    CrossrefSearch in Google Scholar
  • 2 Scheiner S. J. Phys. Chem. A 2022; 126: 1194
    CrossrefPubMedSearch in Google Scholar
  • 3 Stephaniuk NT, Nascimento MA, Nikoo S, Heyer E, Watanabe LK, Rawson JM. Chem. Eur. J. 2022; 28: e202103846
    CrossrefPubMedSearch in Google Scholar
  • 4 Wen C, Shi Y, Lu X, Xu Z, Liu H. J. Phys. Chem. A 2021; 125: 8572
    CrossrefPubMedSearch in Google Scholar
  • 5 Nikoo S, Rawson JM. Cryst. Growth Des. 2021; 21: 4878
    CrossrefSearch in Google Scholar
  • 6 Nascimento MA, Heyer E, Less RJ, Pask CM, Arauzo A, Campo J, Rawson JM. Cryst. Growth Des. 2020; 20: 4313
    CrossrefSearch in Google Scholar
  • 7 Galmés B, Adrover J, Terraneo G, Frontera A, Resnati G. Phys. Chem. Chem. Phys. 2020; 22: 12757
    CrossrefPubMedSearch in Google Scholar
  • 8 Mills MB, Young HK. S, Wehrle G, Verduyn WR, Feng X, Boyle PD, Dechambenoit P, Johnson ER, Preuss KE. Cryst. Growth Des. 2021; 21: 5669
    CrossrefSearch in Google Scholar
  • 9 Mills MB, Wohlhauser T, Stein B, Verduyn WR, Song E, Dechambenoit P, Rouzières M, Clérac R, Preuss KE. J. Am. Chem. Soc. 2018; 140: 16904
    CrossrefPubMedSearch in Google Scholar
  • 10 Haynes DA, Rawson JM. Eur. J. Inorg. Chem. 2018; 3554
    Crossref
  • 11 Beldjoudi Y, Sun R, Arauzo A, Campo J, Less RJ, Rawson JM. Cryst. Growth Des. 2018; 18: 179
    CrossrefSearch in Google Scholar
  • 12 Bates D, Robertson CM, Leitch AA, Dube PA, Oakley RT. J. Am. Chem. Soc. 2018; 140: 3846
    CrossrefPubMedSearch in Google Scholar
  • 13 Commonly referred to in the recent literature as ‘molecular squares’; see for example refs. 2 and 4.
  • 14 Boeré RT. ACS Omega 2018; 3: 18170
    CrossrefPubMedSearch in Google Scholar
  • 15 Ho PC, Wang JZ, Meloni F, Vargas-Baca I. Coord. Chem. Rev. 2020; 422: 213464
    CrossrefSearch in Google Scholar
  • 16 Boeré RT, Hill ND. D. CrystEngComm 2017; 19: 3698
    CrossrefSearch in Google Scholar
  • 17 Chivers T, Laitinen RS. Chalcogen-Nitrogen Chemistry (updated edition). World Scientific; Singapore: 2022. 88f
    Search in Google Scholar
  • 18 A CSD search of covalent thiazyl chlorides returned 22 hits, of which 11 report having the {δ+S···Nδ−}2 motif; refcodes: CILSAR, COSPIT, DESLIW, ECEBY, EXOVOV, JABRAF, LEDZEZ, LOCZOQ, YAVCON, YAVCUT, ZIJZEX.
  • 19 Groom CR, Bruno IJ, Lightfoot MP, Ward SC. Acta Crystallogr., Sect. B: Struct. Sci., Cryst. Eng. Mater. 2016; 72: 171
    CrossrefPubMedSearch in Google Scholar
  • 20 Chen S.-J, Behrens U, Fischer E, Mews R, Pauer F, Sheldrick GM, Stalke D, Stohrer W.-D. Chem. Ber. 1993; 126: 2601
    CrossrefSearch in Google Scholar
  • 21 Cordes AW, Haynes PJ, Josephy PD, Koenig H, Oakley RT, Pennington WT. J. Chem. Soc., Chem. Commun. 1984; 1021
    Crossref
  • 22 Ramakrishna TV. V, Elias AJ, Vij A. Inorg. Chem. 1999; 38: 3022
    CrossrefSearch in Google Scholar
  • 23 Boeré RT, Roemmele TL, Yu X. Inorg. Chem. 2011; 50: 5123
    CrossrefPubMedSearch in Google Scholar
  • 24 Kleemiss F, Dolomanov OV, Bodensteiner M, Peyerimhoff N, Midgley L, Bourhis LJ, Genoni A, Malaspina LA, Jayatilaka D, Spencer JL, White F, Grundkotter-Stock B, Steinhauer S, Lentz D, Puschmann H, Grabowsky S. Chem. Sci. 2020; 12: 1675
    CrossrefPubMedSearch in Google Scholar
  • 25 Boeré RT. Crystals 2023; 13: 293
    CrossrefSearch in Google Scholar
  • 26 Hill ND. D, Lilienthal E, Bender CO, Boeré RT. J. Org. Chem. 2022; 87: 16213
    CrossrefPubMedSearch in Google Scholar
  • 27 Marszaukowski F, Boeré RT, Wohnrath K. Cryst. Growth Des. 2022; 22: 2512
    CrossrefSearch in Google Scholar
  • 28 Ibrahim MA, Boeré RT. New J. Chem. 2022; 46: 5479
    CrossrefSearch in Google Scholar
  • 29 Boeré RT, Roemmele TL, Kondage SS, Zhou J, Parvez M. Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 2011; 67: o273
    CrossrefPubMedSearch in Google Scholar
  • 30 Roemmele TL, Boeré RT. Acta Crystallogr., Sect. E: Struct. Rep. Online 2011; 67: o3137
    CrossrefPubMedSearch in Google Scholar
    • 31a HAR was employed using NoSpherA2 (ref. 24) within Olex2 1.5-alpha on all six structures (Section 3 of the Supporting Information). The first five refined extremely well, but 4e proved challenging due to borderline data quality (twinning and disorder). Nevertheless, all the HAR models represent improvements on the precision of refinements (mean 32.3% improvement on average C–C distances; see Table S5) compared to exactly parallel models in the independent atom model (IAM). For details, see the Experimental and Table S5 in the Supporting Information. The most obvious feature of the HAR, clearly visible in Figure 3, are the full positional and anisotropic positional refinements of the hydrogen atoms (except for the C10H3 methyl group in 4b, which is rotationally disordered). Still, even such a disorder would have been difficult to pick out in an IAM model, further validating the impressive performance of NoSpherA2 (refs. 25–28). Full details on the SC-XRD structures and refinement are provided in the Supporting Information.
    • 31b CCDC 2244424–2244429 contain the supplementary crystallographic data for this paper. The data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/structures
  • 32 Graham JB. III, Cordes AW, Oakely RT, Boeré RT. Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 1985; 41: 1835
    CrossrefSearch in Google Scholar
  • 33 Boeré RT, Oakely RT, Cordes AW. Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 1985; 41: 1686
    CrossrefSearch in Google Scholar
  • 34 Chivers T, Richardson JF, Smith NR. M. Inorg. Chem. 1986; 25: 47
    CrossrefSearch in Google Scholar
  • 35 Wiegers GA, Vos A. Acta Crystallogr. 1966; 20: 192
    CrossrefSearch in Google Scholar
  • 36 Macrae DF, Edgington PR, McCabe P, Pidcock E, Shields GP, Taylor R, Towler M, van de Streek J. J. Appl. Crystallogr. 2006; 39: 453
    CrossrefSearch in Google Scholar
  • 37 Zhao Y, Truhlar DG. Theor. Chem. Acc. 2008; 120: 215
    CrossrefPubMedSearch in Google Scholar
  • 38 Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Chem. Rev. 2016; 116: 5105
    CrossrefPubMedSearch in Google Scholar
  • 39 Gray M, Bowling PE, Herbert JM. J. Chem. Theory Comput. 2022; 18: 6742
    CrossrefPubMedSearch in Google Scholar
  • 40 A reviewer suggested investigating these interactions by the Quantum Theory of Atoms in Molecules approach. We therefore took the CC-optimized geometry at the B3LYP-D3/6-311++G(d,p) level of theory of 4c into AIMAll for an AIM analysis (ref. 41). This calculation confirmed the presence of (3,−1) critical points, usually taken as indicative of the presence of ‘bonds’, for both the (S···N) and (CCl3···S) type contacts (corresponding to the dashed lines in Figure 4) with average ∇2ρ of 0.035 a.u. for the first and 0.016 a.u. for the second type, corresponding to ‘bond’ strengths of 8.7 and 2.8 kJ/mol, respectively. So yes, BCPs exist in these optimized lateral dimers. It would, however, take a systematic comparison of these BCP energetics with those at the crystallographic geometries to be able to provide an adequate interpretation of their meanings. If anything, these preliminary results substantiate the importance of dispersion in the contributions of the chloro groups to the intermolecular interactions, since the (CCl3···N) component is shown to contribute almost 40% of the total energy (see the remaining text), exceeding this AIM estimate of 24% in the absence of dispersion.
  • 41 AIMAll (Version 19.10.12). Keith TA. TK Gristmill Software; Overland Park KS: 2019. aim.tkgristmill.com (accessed May 10, 2023
    Search in Google Scholar
  • 42 In ref. 2, Scheiner computes interaction energies for hypothetical selenazole dimers, where the CH moieties in the rings are replaced sequentially by one or two nitrogen atoms. It is claimed that for each additional N atom, the interaction energy almost doubles in magnitude. Of course, there is no way to test this experimentally, but our result of a higher interaction energy in the C2N3S thiatriazine fits to this prediction.