Advertisement

Chemical Papers

, Volume 71, Issue 10, pp 1809–1823 | Cite as

Different molecular assemblies in two new phosphoric triamides with the same C(O)NHP(O)(NH)2 skeleton: crystallographic study and Hirshfeld surface analysis

  • Anahid Saneei
  • Mehrdad Pourayoubi
  • Titus A. Jenny
  • Aurelien Crochet
  • Katharina M. Fromm
  • Ekaterina S. Shchegravina
Original Paper
  • 65 Downloads

Abstract

Different molecular assemblies were compared in two new structures [4-CH3-C6H4C(O)NH]P(O)[NH]2(CH2)3, 1, and [4-CH3-C6H4C(O)NH]P(O)[NHC6H3(3,4-CH3)2]2, 2, belonging to the families of “cyclic phosphoric triamide” and “phosphoric triamide”, respectively. The differences in the hydrogen bond motifs were discussed (by single crystal X-ray diffraction) as a result of three factors: (1) action of two N atoms with a non-planar environment in 1 as an H-bond acceptor, (2) different orientations of three N–H bond vectors in two molecules and (3) different conformations of C=O and P=O groups. These differences lead to more complicated hydrogen bond pattern of 1, with respect to that of 2, as structure 1 may be considered as a model of four-acceptor–three-donor versus a two-acceptor–three-donor system in 2. The main discrepancies of 1 and 2, monitored by the Hirshfeld surface analysis, are related to the contribution portions of O···H/H···O contacts, in which compound 1 not only involves the greater existence of classical hydrogen bonds but also contains the further C–H···O weak interactions in its crystal packing with respect to compound 2. Instead, in 2, the shortage of O···H/H···O contacts has been partially compensated by the C···H/H···C interactions, due to the presence of more unsaturated carbon acceptors. The differences in assemblies are also reflected in the solid-state IR spectra, especially for the N–H vibration frequencies. The new compounds were further studied by 1D NMR experiments (1H, 13C, 31P), 2D NMR techniques [HMQC and HMBC (H–C correlation), HSQC (N–H correlation)], high-resolution ESI–MS, EI–MS spectrometry and IR spectroscopy.

Keywords

Phosphoric triamide Molecular assembly Hydrogen bonding pattern Hirshfeld surface analysis NMR spectroscopy 

Notes

Acknowledgements

AS and MP would like to thank the Ferdowsi University of Mashhad for financial supporting this study (Grant No. 28386/3-2013/10/02). Crystallography experiments have been supported by FriMat, University of Fribourg.

Supplementary material

11696_2017_168_MOESM1_ESM.docx (4.3 mb)
Supplementary material 1 (DOCX 4392 kb)

References

  1. Allen FH, Bruno IJ (2010) Bond lengths in organic and metal-organic compounds revisited: X–H bond lengths from neutron diffraction data. Acta Crystallogr B 66:380–386. doi: 10.1107/S0108768110012048 CrossRefGoogle Scholar
  2. Altomare A, Cascarano G, Giacovazzo C, Guagliardi A, Burla MC, Polidori G, Camalli M (1994) SIR92—a program for automatic solution of crystal structures by direct methods. J Appl Crystallogr 27:435. doi: 10.1107/S002188989400021X Google Scholar
  3. Bauerschmidt S, Hanebeck W, Schulz KP, Gasteiger J (1992) Elucidation of reactions in the mass spectrometer. Anal Chim Acta 265:169–182. doi: 10.1016/0003-2670(92)85023-Y CrossRefGoogle Scholar
  4. Braga D, Grepioni F (1997) From alkynols to alkynol complexes. A molecular assembly study. Organometallics 16:4910–4919. doi: 10.1021/om970331t CrossRefGoogle Scholar
  5. Brandenburg K, Putz H (1999) DIAMOND. Crystal impact. GbR Bonn, GermanyGoogle Scholar
  6. Carletti E, Colletier J-P, Schopfer LM, Santoni G, Masson P, Lockridge O, Nachon F, Weik M (2013) Inhibition pathways of the potent organophosphate CBDP with cholinesterases revealed by X-ray crystallographic snapshots and mass spectrometry. Chem Res Toxicol 26:280–289. doi: 10.1021/tx3004505 CrossRefGoogle Scholar
  7. Cremer D, Pople JA (1975) General definition of ring puckering coordinates. J Am Chem Soc 97:1354–1358. doi: 10.1021/ja00839a011 CrossRefGoogle Scholar
  8. Desiraju G (2010) Crystal engineering: a brief overview. J Chem Sci 122:667–675. doi: 10.1007/s12039-010-0055-2 CrossRefGoogle Scholar
  9. Gholivand K, Madani Alizadehgan A, Mojahed F, Soleimani P (2008) Crystal structures and mass spectral fragmentation studies of some new carbacylamidophosphate compounds. Polyhedron 27:1639–1649. doi: 10.1016/j.poly.2008.01.023 CrossRefGoogle Scholar
  10. Gholivand K, Shariatinia Z, Mashhadi SM, Daeepour F, Farshidnasab N, Mahzouni HR, Taheri N, Amiri S, Ansar S (2009) Structural diversity in phosphoramidate’s chemistry: syntheses, spectroscopic and X-ray crystallography studies. Polyhedron 28:307–321. doi: 10.1016/j.poly.2008.10.057 CrossRefGoogle Scholar
  11. Groom CR, Bruno IJ, Lightfoot MP, Ward SC (2016) The Cambridge Structural Database. Acta Crystallogr B 72:171–179. doi: 10.1107/S2052520616003954 CrossRefGoogle Scholar
  12. Hirshfeld FL (1977) Bonded-atom fragments for describing molecular charge densities. Theor Chim Acta 44:129–138. doi: 10.1007/BF00549096 CrossRefGoogle Scholar
  13. Macrae CF, Bruno IJ, Chisholm JA, Edgington PR, McCabe P, Pidcock E, Rodriguez-Monge L, Taylor R, van de Streek J, Wood PA (2008) Mercury CSD 2.0—new features for the visualization and investigation of crystal structures. J Appl Crystallogr 41:466–470. doi: 10.1107/S0021889807067908 CrossRefGoogle Scholar
  14. Martin AD, Britton J, Easun TL, Blake AJ, Lewis W, Schröder M (2015) Hirshfeld surface investigation of structure-directing interactions within dipicolinic acid derivatives. Cryst Growth Des 15:1697–1706. doi: 10.1021/cg5016934 CrossRefGoogle Scholar
  15. McKinnon JJ, Spackman MA, Mitchell AS (2004) Novel tools for visualizing and exploring intermolecular interactions in molecular crystals. Acta Crystallogr B 60:627–668. doi: 10.1107/S0108768104020300 CrossRefGoogle Scholar
  16. McKinnon JJ, Jayatilaka D, Spackman MA (2007) Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces. Chem Comm 3814–3816. doi: 10.1039/B704980C
  17. Metrangolo P, Resnati G (2008) Halogen versus hydrogen. Science 321:918–919. doi: 10.1126/science.1162215 CrossRefGoogle Scholar
  18. Michalik S, Maƚecki JG, Mƚynarczyk N (2014) Synthesis of [Re2Cl4(O)2(μ-O)(3,5-lut)4] and investigation of its structure via X-ray and spectroscopic measurements and DFT calculations. Chem Pap 68:689–696. doi: 10.2478/s11696-013-0493-7 CrossRefGoogle Scholar
  19. Mizrahi V, Modro TA (1982) Phosphoric carboxylic imides. 1. Preparation and fragmentation behavior of dialkylphosphoryl (and phosphinyl) acetyl (and benzoyl) imides and related systems. J Org Chem 47:3533–3539. doi: 10.1021/jo00139a030 CrossRefGoogle Scholar
  20. Palatinus L, Chapuis G (2007) SUPERFLIP—a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions. J Appl Crystallogr 40:786–790. doi: 10.1107/S0021889807029238 CrossRefGoogle Scholar
  21. Pourayoubi M, Sabbaghi F (2009) Synthesis, spectroscopic characterization and crystal structure of a new acetyl phosphorylamidate P(O)[NHC(O)C6H4(4-NO2)][N(CH(CH3)2)(CH2C6H5)]2. J Chem Crystallogr 39:874–880. doi: 10.1007/s10870-009-9582-4 CrossRefGoogle Scholar
  22. Pourayoubi M, Izadyar M, Elahi B, Parvez M (2013) Combination of X-ray crystallography and theoretical study to evaluate the effect of N–H···O=P versus N–H···O=C hydrogen bonds on the N–H stretching frequencies. J Mol Struct 1034:354–362. doi: 10.1016/j.molstruc.2012.10.055 CrossRefGoogle Scholar
  23. Pourayoubi M, Toghraee M, Zhu J, Dušek M, Bereciartua PJ, Eigner V (2014) Database analysis of hydrogen bond patterns in phosphoric triamides completed with seven new compounds: a crystallographic and 15N NMR study. CrystEngComm 16:10870–10887. doi: 10.1039/C4CE01793E CrossRefGoogle Scholar
  24. Prins LJ, Reinhoudt DN, Timmerman P (2001) Noncovalent synthesis using hydrogen bonding. Angew Chem Int Ed 40:2382–2426. doi: 10.1002/1521-3773(20010702)40:13<2382:AID-ANIE2382>3.0.CO;2-G CrossRefGoogle Scholar
  25. Resnati G, Boldyreva E, Bombicz P, Kawano M (2015) Supramolecular interactions in the solid state. IUCrJ 2:675–690. doi: 10.1107/S2052252515014608 CrossRefGoogle Scholar
  26. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122. doi: 10.1107/S0108767307043930 CrossRefGoogle Scholar
  27. Sheldrick GM (2015) Crystal structure refinement with SHELXL. Acta Crystallogr C 71:3–8. doi: 10.1107/S2053229614024218 CrossRefGoogle Scholar
  28. Spackman MA, Byrom PG (1997) A novel definition of a molecule in a crystal. Chem Phys Lett 267:215–220. doi: 10.1016/S0009-2614(97)00100-0 CrossRefGoogle Scholar
  29. Spackman MA, Jayatilaka D (2009) Hirshfeld surface analysis. CrystEngComm 11:19–32. doi: 10.1039/b818330a CrossRefGoogle Scholar
  30. Spackman MA, McKinnon JJ (2002) Fingerprinting intermolecular interactions in molecular crystals. CrystEngComm 4:378–392. doi: 10.1039/b203191b CrossRefGoogle Scholar
  31. Steiner T (2002) The hydrogen bond in the solid state. Angew Chem Int Ed 41:48–76. doi: 10.1002/1521-3773(20020104)41:1<48:AID-ANIE48>3.0.CO;2-U CrossRefGoogle Scholar
  32. Tarahhomi A, Pourayoubi M, Rheingold AL, Golen JA (2011) Different orientations of C=O versus P=O in P(O)NHC(O) skeleton: the first study on an aliphatic diazaphosphorinane with a gauche orientation. Struct Chem 22:201–210. doi: 10.1007/s11224-010-9682-y CrossRefGoogle Scholar
  33. Toghraee M, Pourayoubi M, Divjakovic V (2011) Study on H-bond patterns in phosphoric triamides having a P(O)NHC(O) skeleton, a gauche orientation of P(O) vs C(O) in new compounds. Polyhedron 30:1680–1690. doi: 10.1016/j.poly.2011.03.045 CrossRefGoogle Scholar
  34. Upadhyay LSB (2012) Urease inhibitors: a review. IJBT 11:381–388Google Scholar
  35. Wolff SK, Grimwood DJ, McKinnon JJ, Turner MJ, Jayatilaka D, Spackman MA (2012) CrystalExplorer (Version 3.1), University of Western AustraliaGoogle Scholar
  36. Wu X, Hu L (2016) Design and synthesis of peptide conjugates of phosphoramide mustard as prodrugs activated by prostate-specific antigen. Bioorg Med Chem 24:2697–2706. doi: 10.1016/j.bmc.2016.04.035 CrossRefGoogle Scholar
  37. Yang L, Powell DR, Houser RP (2007) Structural variation in copper(I) complexes with pyridylmethylamide ligands: structural analysis with a new four-coordinate geometry index, τ4. Dalton Trans 955–964. doi: 10.1039/B617136B
  38. Yizhak RV, Znovjyak KO, Ovchynnikov VA, Sliva TY, Konovalova IS, Medviediev VV, Shishkin OV, Amirkhanov VM (2013) Synthesis and crystal structures of new dioxouranium(VI) complexes based on carbacylamidophosphates (CAPh). Investigation of extraction properties of some CAPh ligands in respect of dioxouranium(VI) nitrate. Polyhedron 62:293–299. doi: 10.1016/j.poly.2013.06.043 CrossRefGoogle Scholar

Copyright information

© Institute of Chemistry, Slovak Academy of Sciences 2017

Authors and Affiliations

  1. 1.Department of Chemistry, Faculty of SciencesFerdowsi University of MashhadMashhadIran
  2. 2.Department of ChemistryUniversity of FribourgFribourgSwitzerland
  3. 3.Fribourg Centre for Nanomaterial’s, FriMatUniversity of FribourgFribourgSwitzerland
  4. 4.Department of Organic ChemistryUNN Lobachevsky State UniversityNizhny NovgorodRussia

Personalised recommendations