Competition among weak C-H⋯O/S/H interactions in the crystal structure of {(C2H5O)2P(S)}2N2C4H8 bis(thiophosphoramide): experimental/computational studies
Status PubMed-not-MEDLINE Language English Country Great Britain, England Media electronic-ecollection
Document type Journal Article
PubMed
40606187
PubMed Central
PMC12218915
DOI
10.1039/d5ra01306b
PII: d5ra01306b
Knihovny.cz E-resources
- Publication type
- Journal Article MeSH
Supramolecular assembly driven by weak C-H⋯S[double bond, length as m-dash]P/O and CH⋯HC contacts was studied in a new bis(thiophosphoramide) structure, {(C2H5O)2P(S)}2N2C4H8, using X-ray crystallography and DFT computational methods. Combined QTAIM/noncovalent interaction (NCI) and natural bond orbital (NBO) analyses were used to gain deeper insights into the nature, energy and strengths of these contacts. The C-H⋯O hydrogen bond was found to be the strongest interaction, followed by two H⋯H and then H⋯S contacts. Crystal lattice energy calculations were performed, and the components contributing to the intermolecular interactions were investigated and discussed (electrostatic, polarization, dispersion and repulsion). The dispersion forces were found to be the most prominent in the network energy. The relative contributions of the intermolecular contacts were visualized by Hirshfeld surfaces and two-dimensional fingerprint diagrams. Some topics related to geometry and conformation were also studied.
Department of Chemistry Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
Department of Chemistry Masaryk University Kotlarska 2 61137 Brno Czech Republic
UNESCO UNISA ITL NRF Africa Chair in Nanoscience and Nanotechnology Pretoria South Africa
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Ugwu D. I. Conradie J. J. Mol. Struct. 2023;1293:136275.
Khorramaki M. Pourayoubi M. Yazdan-Abad V. R. Darugar V. Vakili M. Eigner V. Dušek M. J. Mol. Struct. 2025;1321:140068.
Darugar V. Vakili M. Tayyari S. F. Hansen P. E. Kamounah F. S. J. Mol. Liq. 2021;334:116035.
Wang J. Li H. Xu B. RSC Chem. Biol. 2021;2:289–305. PubMed PMC
Baker E. N., International Tables for Crystallography, ed. M. G. Rossmann and E. Arnold, Springer, Dordrecht, 2006, ch. 22.2, vol. F, pp. 546–552
Colmenero F. Plášil J. Cobos J. Sejkora J. Timón V. Čejka J. Bonales L. J. RSC Adv. 2019;9:15323–15334. PubMed PMC
Lin Z.-J. Mahammed S. A. R. Liu T.-F. Cao R. ACS Cent. Sci. 2022;8:1589–1608. PubMed PMC
Cai Y. Peng W. Vana P. Nanoscale Adv. 2022;4:2787–2793. PubMed PMC
van der Lubbe S. C. C. Fonseca Guerra C. Chem.–Asian J. 2019;14:2760–2769. PubMed PMC
Hosseinpoor S. Pourayoubi M. Dušek M. Skořepová E. Phosphorus, Sulfur Silicon Relat. Elem. 2022;197:747–757.
Galvez C. E. Piro O. E. Echeverría G. A. Robles N. L. Lezama J. O. G. Sankaran S. V. Thamotharan S. Villecco M. B. Loandos M. del H. Gil D. M. New J. Chem. 2022;46:5690–5704.
de Almeida L. R. Carvalho P. S. Napolitano H. B. Oliveira S. S. Camargo A. J. Figueredo A. S. de Aquino G. L. B. Carvalho-Silva V. H. Cryst. Growth Des. 2017;17:5145–5153.
Britvin S. N. Rumyantsev A. M. Silyutina A. A. Padkina M. V. ChemistrySelect. 2017;2:8721–8725.
Wagner J. P. Schreiner P. R. J. Chem. Theory Comput. 2016;12:231–237. PubMed
Echeverría J. Aullón G. Danovich D. Shaik S. Alvarez S. Nat. Chem. 2011;3:323–330. PubMed
Reilly A. M. Tkatchenko A. Chem. Sci. 2015;6:3289–3301. PubMed PMC
Danovich D. Shaik S. Neese F. Echeverría J. Aullón G. Alvarez S. J. Chem. Theory Comput. 2013;9:1977–1991. PubMed
Riu M. L. Y. Bistoni G. Cummins C. C. J. Phys. Chem. A. 2021;125:6151–6157. PubMed
Wagner J. P. Schreiner P. R. Angew. Chem., Int. Ed. 2015;54:12274–12296. PubMed
Ghosh S. Chopra P. Wategaonkar S. Phys. Chem. Chem. Phys. 2020;22:17482–17493. PubMed
Fargher H. A. Sherbow T. J. Haley M. M. Johnson D. W. Pluth M. D. Chem. Soc. Rev. 2022;51:1454–1469. PubMed PMC
Liu W. Zhang L. Zhou H. Yang C. Miao Z. Zhao Y. Nucleosides, Nucleotides Nucleic Acids. 2013;32:161–173. PubMed
Penchovsky R. Georgieva A. V. Dyakova V. Traykovska M. Pavlova N. Antibiotics. 2024;13:221. PubMed PMC
Langner H. K. Jastrzebska K. Caruthers M. H. J. Am. Chem. Soc. 2020;142:16240–16253. PubMed
Gholivand K. Ebrahimi Valmoozi A. A. Bonsaii M. Pestic. Biochem. Physiol. 2014;112:40–50. PubMed
Cantarella H. Otto R. Soares J. R. Silva A. G. de. B. J. Adv. Res. 2018;13:19–27. PubMed PMC
Safin D. A. Babashkina M. G. Bolte M. Garcia Y. CrystEngComm. 2012;14:774–778.
Khorramaki M. Abad M. Darugar V. Pourayoubi M. Vakili M. Nečas M. Choquesillo-Lazarte D. Andreev P. V. Shchegravina E. S. Polyhedron. 2022;228:116157.
Safin D. A. Babashkina M. G. Klein A. Nöth H. Bolte M. Krivolapov D. B. Polyhedron. 2010;29:1837–1841.
Mitoraj M. P. Sagan F. Babashkina M. G. Isaev A. Y. Chichigina Y. M. Safin D. A. Eur. J. Org. Chem. 2019;2019:493–503.
Nazir R. Gaan S. J. Appl. Polym. Sci. 2020;137:1–27.
Chang S. Nguyen M. Condon B. Smith J. Fibers Polym. 2017;18:666–674.
Gholivand K. Ebrahimi Valmoozi A. A. Bonsaii M. J. Agric. Food Chem. 2014;62:5761–5771. PubMed
Nguyen T.-M. Chang S. Condon B. Smith J. Mater. Sci. Appl. 2014;5:789–802.
Vahdani Alviri B. Pourayoubi M. Farhadipour A. Nečas M. Bertolasi V. Acta Crystallogr., Sect. C: Struct. Chem. 2018;74:1610–1621. PubMed
Torabi Farkhani E. Pourayoubi M. Izadyar M. Andreev P. V. Shchegravina E. S. Dalton Trans. 2019;48:17908–17918. PubMed
Sheldrick G. M. Acta Crystallogr., Sect. A: Found. Adv. 2015;71:3–8. PubMed PMC
Sheldrick G. M. Acta Crystallogr., Sect. C: Struct. Chem. 2015;71:3–8. PubMed PMC
Pourayoubi M. Abrishami M. Eigner V. Nečas M. Dušek M. Delavar M. Acta Crystallogr., Sect. C: Struct. Chem. 2014;70:1147–1152. PubMed
Allen F. H. Bruno I. J. Acta Crystallogr., Sect. B: Struct. Sci. 2010;66:380–386. PubMed
Cremer D. Pople J. A. J. Am. Chem. Soc. 1975;97:1354–1358.
Sabbaghi F. Pourayoubi M. Dušek M. Eigner V. Bayat S. Damodaran K. Nečas M. Kučeráková M. Struct. Chem. 2016;27:1831–1844.
Sabbaghi F. As’habi A. Saneei A. Pourayoubi M. Abdul Salam A. A. Nečas M. Dušek M. Kučeráková M. Acharya S. Acta Crystallogr., Sect. C: Struct. Chem. 2021;77:68–80. PubMed
Wood P. A. Allen F. H. Pidcock E. CrystEngComm. 2009;11:1563–1571.
Spackman M. A. Jayatilaka D. CrystEngComm. 2009;11:19–32.
Spackman M. A. McKinnon J. J. CrystEngComm. 2002;4:378–392.
Spackman P. R. Turner M. J. McKinnon J. J. Wolff S. K. Grimwood D. J. Jayatilaka D. Spackman M. A. J. Appl. Crystallogr. 2021;54:1006–1011. PubMed PMC
Mackenzie C. F. Spackman P. R. Jayatilaka D. Spackman M. A. IUCrJ. 2017;4:575–587. PubMed PMC
Spackman M. A. CrystEngComm. 2018;20:5340–5347.
Turner M. J. Grabowsky S. Jayatilaka D. Spackman M. A. J. Phys. Chem. Lett. 2014;5:4249–4255. PubMed
Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Mennucci B., Petersson G. A., Nakatsuji H., Caricato M., Li X., Hratchian H. P., Izmaylov A. F., Bloino J., Zheng G., Sonnenberg J. L., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Montgomery J. A., Peralta J. E., Ogliaro F., Bearpark M., Heyd J. J., Brothers E., Kudin K. N., Staroverov V. N., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J. C., Iyengar S. S., Tomasi J., Cossi M., Rega N., Millam J. M., Klene M., Knox J. E., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Martin R. L., Morokuma K., Zakrzewski V. G., Voth G. A., Salvador P., Dannenberg J. J., Dapprich S., Daniels A. D., Farkas Ö., Foresman J. B., Ortiz J. V., Cioslowski J. and Fox D. J., Gaussian 09, Gaussian Inc, Wallingford, CT, USA, 2009, https://www.gaussian.com
Lu T. Chen F. J. Comput. Chem. 2012;33:580–592. PubMed
Weinhold F.. Glendening E. D., Badenhoop J. K., Reed A. E., Carpenter J. E., Bohmann J. A. and Morales C. M., NBO 5.0, Theor. Chem. Institute, Univ. Wisconsin, Madison, WI
Zhurko G. A. and Zhurko D. A., ChemCraft, Version 1.8, https://www.chemcraftprog.com
Espinosa E. Molins E. Lecomte C. Chem. Phys. Lett. 1998;285:170–173.
Contreras-García J. Johnson E. R. Keinan S. Chaudret R. Piquemal J.-P. Beratan D. N. Yang W. J. Chem. Theory Comput. 2011;7:625–632. PubMed PMC
Reed A. E. Curtiss L. A. Weinhold F. Chem. Rev. 1988;88:899–926.
Kaya Kınaytürk N. Kalaycı T. Tunalı B. Spectrosc. Lett. 2021;54:693–706.
Johnson E. R. Keinan S. Mori-Sánchez P. Contreras-García J. Cohen A. J. Yang W. J. Am. Chem. Soc. 2010;132:6498–6506. PubMed PMC