Growing interest in non-covalent interactions involving chalcogen atoms has been ascribed to their importance in crystal engineering, molecular recognition and macromolecular edifices. The present study is dealing with chalcogen bonds involving divalent Sulphur, Selenium and Tellurium atoms, acting as sigma-hole donors, in small-molecule compounds using the Cambridge Structural Database (CSD) in conjunction with ab initio calculations. Results derived from CSD surveys and computational study revealed that nucleophiles formed complexes with the chalcogen-bond donors R1-X-R2 (X = S, Se or Te). The main forces stabilizing the complexes were chalcogen bonds, enhanced by dispersion interactions. Complexation pattern and energetics show that nucleophile bonding at divalent S, Se and Te atoms is a relatively strong and directed interaction. The bond consists of a charge transfer from a nucleophile atom lone pair to an X-R1 or X-R2 antibonding orbital.
References
[1]
Pal, D. and Chakrabarti, P. (2001) Non-Hydrogen Bond Interactions Involving the Methionine Sulfur Atom. Journal of Biomolecular Structure and Dynamics, 19, 115-128. https://doi.org/10.1080/07391102.2001.10506725
[2]
Politzer, P., Murray, J.S. and Lane, P. (2007) σ-Hole Bonding and Hydrogen Bonding: Competitive Interactions. International Journal of Quantum Chemistry, 107, 3046-3052. https://doi.org/10.1002/qua.21419
[3]
Bleiholdder, C., Werz, D.B., Köppel, H. and Gleiter, R. (2006) Theoretical Investigations on Chalcogen-Chalcogen Interactions: What Makes These Nonbonded Interactions Bonding? Journal of the American Chemical Society, 128, 2666-2674. https://doi.org/10.1021/ja056827g
[4]
Clark, T., Hennemann, M., Murray, J.S. and Politzer, P. (2007) Halogen Bonding: the σ-Hole. Journal of Molecular Modeling, 13, 291-296. https://doi.org/10.1007/s00894-006-0130-2
[5]
Ramos, L.A., Ulic, S.E., Romano, R.M., Erben, M.F., Lehmann, C.W., Bernhardt, E., Beckers, H., Willner, H. and Della Vedova, C.O. (2010) Vibrational Spectra, Crystal Structures, Constitutional and Rotational Isomerism of FC(O)SCN and FC(O)NCS. Inorganic Chemistry, 49, 11142-11157. https://doi.org/10.1021/ic101741e
[6]
Politzer, P., Murray, J.S. and Bulat, F.A. (2010) Average Local Ionization Energy: A Review. Journal of Molecular Modeling, 16, 1731-1742. https://doi.org/10.1007/s00894-010-0709-5
[7]
Politzer, P., Murray, J.S. and Clark, T. (2013) Halogen Bonding and Other σ-Hole Interactions: A Perspective. Physical Chemistry Chemical Physics, 15, 11178-11189. https://doi.org/10.1039/c3cp00054k
[8]
Politzer, P. and Murray, J.S. (2013) Halogen Bonding: An Interim Discussion. ChemPhysChem, 14, 278-294. https://doi.org/10.1002/cphc.201200799
[9]
Politzer, P., Murray, J.S., Janjie, G.V. and Zarie, S.D. (2014) σ-Hole Interactions of Covalently-Bonded Nitrogen, Phosphorus and Arsenic: A Survey of Crystal Structures. Crystals, 4, 12-31. https://doi.org/10.3390/cryst4010012
[10]
Pandiyan, B.V., Deepa, P. and Kolandaivel, P. (2016) Studies on the σ-Hole Bonds (Halogen, Chalcogen, Pnicogen and carbon Bonds) Based on the orientation of Crystal Structure. Molecular Physics, 2016, Article ID: 1255796.
[11]
Zabardasti, A., Afrouzi, H., Kakanejadifard, A. and Jamshidi, Z. (2017) The S···P Noncovalent Interaction: Diverse Chalcogen Bonds. Molecular Physics, 38, 249-263. https://doi.org/10.1080/17415993.2016.1275634
[12]
Bauza, A. and Frontera, A. (2018) Chalcogen Like-Like Interactions Involving Trisulphide and Triselenide Compounds: A Combined CSD and Ab Initio Study. Molecules, 23, 699. https://doi.org/10.3390/molecules23030699
[13]
Bauza, A. and Frontera, A. (2019) Halogen and Chalcogen Bond Energies Evaluated Using Electro Density Properties. ChemPhysChem, 20, 1-7.
[14]
Bauza, A. and Frontera, A. (2020) σ/π-Hole Noble Gas Bonding Interactions: Insights from Theory and Experiment. Coordination Chemistry Reviews, 404, Article ID: 213112. https://doi.org/10.1016/j.ccr.2019.213112
[15]
Murray, J.S., Lane, P., Clark, T. and Politzer, P. (2007) σ-Hole Bonding: Molecules Containing Group VI Atoms. Journal of Molecular Modeling, 13, 1033-1038. https://doi.org/10.1007/s00894-007-0225-4
[16]
Murray, J.S. and Politzer, P. (2011) The Electrostatic Potential: An Overview. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1, 153-163. https://doi.org/10.1002/wcms.19
[17]
Politzer, P. and Murray, J.S. (2017) σ-Hole Interactions: Perspectives and Misconceptions. Crystals, 7, 212-227. https://doi.org/10.3390/cryst7070212
[18]
Goettel, J.T. and Gerken, M. (2016) Synthesis and Characterization of Adducts between SF4 and Oxygen Bases: Examples of O···S(IV) Chalcogen Bonding. Inorganic Chemistry, 55, 12441-12450. https://doi.org/10.1021/acs.inorgchem.6b02373
[19]
Karjalainen, M.M., Perez, C.S., Rautiainen, J.M., Oilunkaniemi, R. and Laitinen, R.S. (2016) Chalcogen-Chalcogen Secondary Bonding Interactions in Trichalcogenide Ferrocenophanes. CrystEngComm, 18, 4538-4545. https://doi.org/10.1039/C6CE00451B
[20]
Bruno, I.J., Cole, J.C., Edgington, P.R., Kessler, M., Macrae, C.F., McCabe, P., Pearson, J. and Taylor, R. (2002) New Software for Searching the Cambridge Structural Database and Visualizing Crystal Structures. Acta Crystallographica Section B, 58, 389-397. https://doi.org/10.1107/S0108768102003324
[21]
Macrae, C.F., Bruno, I.J., Chisholm, J.A., Edgington, P.R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. and Wood, P.A. (2008) Mercury CSD 2.0—New Features for the Visualization and Investigation of Crystal Structures. Journal of Applied Crystallography, 41, 466-470. https://doi.org/10.1107/S0021889807067908
[22]
Macrae, C.F., Edgington, P.R., McCabe, P., Pidcock, E., Shields, G.P., Taylor, R., Towler, M. and van de Streek, J. (2006) Mercury: Visualization and Analysis of Crystal Structures. Journal of Applied Crystallography, 39, 453-457. https://doi.org/10.1107/S002188980600731X
[23]
Sykes, R.A., McCabe, P., Allen, F.H., Battle, G.M., Bruno, I.J. and Wood, P.A. (2011) New Software for Statistical Analysis of Cambridge Structural Database Data. Journal of Applied Crystallography, 44, 882-886. https://doi.org/10.1107/S0021889811014622
[24]
Wood, P.A., Pidcock, E. and Allen, F.H. (2008) Interaction Geometries and Energies of Hydrogen Bonds to C=O and C=S Acceptors: A Comparative Study. Acta Crystallographica Section B, 64, 491-496. https://doi.org/10.1107/S0108768108015437
[25]
Bondi, A. (1964) Van der Waals Volumes and Radii. The Journal of Physical Chemistry, 68, 441-451. https://doi.org/10.1021/j100785a001
[26]
Murray, J.S. and Politzer, P. (2011) The Electrostatic Potential: An Overview. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1, 153-163. https://doi.org/10.1002/wcms.19
[27]
Lundemba, A.S., Bibelayi, D.D., Wood, P.A., Pradon, J. and Yav, Z.G. (2020) σ-Hole Interactions in Small-Molecule Compounds Containing Divalent Sulfur Groups R1-S-R2. Acta Crystallographica Section B, 76, 707-718. https://doi.org/10.1107/S2052520620008598
[28]
Grimme, S.J. (2006) Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction. Journal of Computational Chemistry, 27, 1787-1799. https://doi.org/10.1002/jcc.20495
[29]
Politzer, P. and Murray, J.S. (2009) An Overview of σ-Hole Bonding, an Important and Widely-Occurring Noncovalent Interaction. In: Leszczynski, J. and Shukla, M.K., Eds., Practical Aspects of Computational Chemistry, Springer, Heidelberg, 149-163. https://doi.org/10.1007/978-90-481-2687-3_6
[30]
Murray, J.S., Lane, P. and Politzer, P. (2009) Expansion of the σ-Hole Concept. Journal of Molecular Modeling, 15, 723-729. https://doi.org/10.1007/s00894-008-0386-9
[31]
Murray, J.S., Macaveiu, L. and Politzer, P. (2014) Factors Affecting the Strengths of σ-Hole Electrostatic Potentials. Journal of Computational Science, 5, 590-596. https://doi.org/10.1016/j.jocs.2014.01.002
[32]
Guo, X., Liu, Y.W., Li, Q.Z., Li, W.Z. and Cheng, J.B. (2015) Competition and Cooperativity between Tetrel Bond and Chalcogen Bond in Complexes Involving F2CX (X = Se and Te). Chemical Physics Letters, 620, 7-12. https://doi.org/10.1016/j.cplett.2014.12.015