Considerable interest in hydrogen bonding involving chalcogen has been growing since the IUPAC committee has redefined hydrogen bonding. Not only the focus is on unconventional acceptors, but also on donors not discussed before. It has been mentioned in previous studies that the proton of the H-C group could be involved in hydrogen bonding, but with conventional acceptors. In this study, we explored the ability of hydrogen bond formation of Se, S and Te acceptors with the H-C donor using Cambridge Structural Database in conjunction with Ab Initio calculations. In the CSD, there are respectively 256, 6249 and 11 R1,R2,-C=Se, R1,R2,-C=S and R1,R2,-C=Te structures that form hydrogen bonds, in which the N,N groups are majority. Except for C=S acceptor which can form a hydrogen bond with its C, C group, both C=Se and C=Te acceptors could form a hydrogen bond only with N,C and N,N groups. CSD analysis shows very similar d (norm) around -0.04 ？, while DFT-calculated interaction for N,C and N,N groups are also similar. Both interaction distances derived from CSD analysis and DFT-calculated interaction energies demonstrate that the acceptors form stable complexes with H-CF3. Besides hydrogen bonds, dispersion interactions are forces stabilizing the complexes since their contribution can reach 50%. Analysis of intra-molecular geometries and Ab Initio partial charges show that this bonding stems from resonance induced Cδ+=Xδ- dipoles. In many respects, both C=Se, C=S and C=Te are similar to C=S, with similar d (norm) and calculated interaction strengths.
References
[1]
Araújo, E.B., Idalgo, E., Moraes, A.P.A. and Souza, F.A.G. (2009) Crystallization Kinetics and Thermal Properties of 20Li2O-80TeO2 Glass. Materials Research Bulletin, 44, 1596-1600. https://doi.org/10.1016/j.materresbull.2009.01.019
[2]
Ferrarini, R.S., Princival, J.L., Comasseto, J.V. and Santos, D. (2008) A Concise Enantioselective Synthesis of (+)-endo-brevicomin Accomplished by a Tellurium/Metal Exchange Reaction. Journal of the Brazilian Chemical Society, 19, 811-812. https://doi.org/10.1590/S0103-50532008000500002
[3]
Liu, Y., Wu, W. and Goddard, A. (2018) Tellurium: Fast Electrical and Atomic Transport along the Weak Interaction Direction. Journal of the American Chemical Society, 140, 550-553. https://doi.org/10.1021/jacs.7b09964
[4]
Luo, Z. (2016) Selenourea: A Convenient Phasing Vehicle for Macromolecular X-Ray Crystal Structures. Scientific Reports, 6, Article No. 37123. https://doi.org/10.1038/srep37123
[5]
Okumura, K. (1974) Photovoltaic Effects at the Interface between Amorphous Selenium and Organic Polymers. Journal of Applied Physics, 45, 5317. https://doi.org/10.1063/1.1663237
[6]
Poborchii, V.V., Kolobov, A.V. and Tanaka, K. (1998) An In Situ Raman Study of Polarization-Dependent Photocrystallization in Amorphous Selenium Films. Applied Physics Letters, 72, 1167-1169. https://doi.org/10.1063/1.121002
[7]
Qi, R. and Cheng, Y. (2019) Synthesis of Se Nanowires at Room Temperature Using Selenourea as Se Source. Journal of Materials Science, 31, 5843-5847. https://doi.org/10.1007/s10854-019-02616-y
[8]
Vargas, F., Toledo, F.T. and Comasseto, J.V. (2010) N-Functionalized Organolithium Compounds via Tellurium/Lithium Exchange Reaction. Journal of the Brazilian Chemical Society, 21, 2072-2078. https://doi.org/10.1590/S0103-50532010001100007
[9]
Desiraju, G.R. (1996) The C-H···O Hydrogen Bond: Structural Implications and Supramolecular Design. Accounts of Chemical Research, 29, 441-449. https://doi.org/10.1021/ar950135n
[10]
Marques, M.P.M., Amorim da Costa, A.M. and Paulo, J.A. (2001) Evidence of C-H···O Hydrogen Bonds in Liquid 4-Ethoxybenzaldehyde by NMR and Vibrational Spectroscopies. The Journal of Physical Chemistry A, 105, 5292-5217. https://doi.org/10.1021/jp0046041
[11]
Madzhidov, T.I. and Chmutova, G.A. (2010) The Nature of Hydrogen Bonds with Divalent Selenium Compounds. Journal of Molecular Structure: THEOCHEM, 959, 1-7. https://doi.org/10.1016/j.theochem.2010.07.041
[12]
Mishra, K.K., Singh, K., Gosh, P., Gosh, D. and Das, A. (2017) Nature of Selenium Hydrogen Bonding: Gas Phase Spectroscopy and Quantum Chemistry Calculations. Physical Chemistry Chemical Physics, 19, 24179-24187. https://doi.org/10.1039/C7CP05265K
[13]
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
[14]
Bibelayi, D.D., Lundemba, A.S., Allen, F.H., Galek, P.T., Pradon, J., Reilly, A.M., Groom, C.R. and Yav, Z.G. (2016) Hydrogen Bonding at C = Se Acceptors in Seleno-Ureas, Seleno-Amides and Selones. Acta Crystallographica Section B, 72, 317-325. https://doi.org/10.1107/S2052520616003644
[15]
Groom, C.R. and Allen, F.H. (2014) The Cambridge Structural Database in Retrospect and Prospect. Angewandte Chemie International Edition in English, 53, 662-671. https://doi.org/10.1002/anie.201306438
[16]
Allen, F.H. (2002) The Cambridge Structural Database: A Quarter of a Million Crystal Structures and Rising. Acta Crystallographica Section B, 58, 380-388. https://doi.org/10.1107/S0108768102003890
[17]
Frisch, M.J., et al. (2014) GAUSSIAN09. Gaussian Inc., Wallingford.
[18]
Becke, A.D. (1993) Density-Functional Thermochemistry. III. The Role of Exact Exchange. The Journal of Chemical Physics, 98, 5648-5652. https://doi.org/10.1063/1.464913
[19]
Lee, C., Yang, W. and Parr, R.G. (1988) Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Physical Review B, 37, 785-789. https://doi.org/10.1103/PhysRevB.37.785
[20]
Stephens, P.J., Devlin, F.J., Habalowski, C.F. and Frisch, M.J. (1994) Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. The Journal of Physical Chemistry, 98, 11623-11627. https://doi.org/10.1021/j100096a001
[21]
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
[22]
Grimme, S., Anthony, J., Ehrlich, S. and Krieg, H. (2010) A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. The Journal of Chemical Physics, 132, Article ID: 154104. https://doi.org/10.1063/1.3382344
[23]
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
[24]
Politzer, P., Murray, J.S. and Clark, T. (2013) Halogen Bonding and Other σ-Hole Interactions: A Perspective. Physical Chemistry Chemical Physics, 15, 11178. https://doi.org/10.1039/c3cp00054k
[25]
Allen, F.H., Bird, C.M., Rowland, R.S. and Raithby, P.R. (1997) Resonance-Induced Hydrogen Bonding at Sulphur Acceptors in R1R2C=S and R1CS2- Systems. Acta Crystallographica Section B, 53, 680-695. https://doi.org/10.1107/S0108768197002656
[26]
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
[27]
Blessing, R.H. (1983) Interdependence of Carbon-Nitrogen and Carbon-Oxygen Bond Lengths in Urea Structures and in Ureido Ring Structures. Journal of the American Chemical Society, 105, 2776-2783. https://doi.org/10.1021/ja00347a043
[28]
Wood, P.A., Allen, F.H. and Pidcock, E. (2009) Hydrogen-Bond Directionality at the Donor H Atom—Analysis of Interaction Energies and Database Statistics. CrystEngComm, 11, 1563-1571. https://doi.org/10.1039/b902330e
[29]
Bondi, A. (1964) van der Waals Volumes and Radii. The Journal of Physical Chemistry, 68, 441-451. https://doi.org/10.1021/j100785a001
[30]
Rowland, R.S. and Taylor, R. (1996) Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii. The Journal of Physical Chemistry, 100, 7384-7391. https://doi.org/10.1021/jp953141+
[31]
Desiraju, G.R. (2002) Hydrogen Bridges in Crystal Engineering: Interactions without Borders. Accounts of Chemical Research, 35, 565-573. https://doi.org/10.1021/ar010054t
[32]
Jin, L., Li, B., Cui, Z., Shang, J., Wang, Y., Shao, C., Pan, T., Ge, Y. and Qi, Z. (2019) Selenium Substitution-Induced Hydration Changes of Crown Ethers as Tools for Probing Water Interactions with Supramolecular Macrocycles in Aqueous Solutions. The Journal of Physical Chemistry B, 123, 9692-9698. https://doi.org/10.1021/acs.jpcb.9b09618
[33]
Custelcean, R. (2008) Crystal Engineering with Urea and Thiourea Hydrogen-Bonding Groups. Chemical Communications, No. 3, 295-307. https://doi.org/10.1039/B708921J
[34]
Michael, H.A., Ibrahim, A., Zissimos, A.M., Zhao, Y.H., Comer, J. and Reynolds, D.P. (2002) Application of Hydrogen Bonding Calculations in Property Based Drug Design. Drug Discovery Today, 7, 1056-1063. https://doi.org/10.1016/S1359-6446(02)02478-9
[35]
Uma, R.S.A., Subba, R.S., Chandra, S.R.G., Veera, N.R.M. and Naga, R.C. (2011) Synthesis, Spectral, and Antimicrobial Evaluation of Some New 8-membered Phosphorus Heterocyclic Compounds. Medicinal Chemistry Research, 20, 962-967. https://doi.org/10.1007/s00044-010-9425-z
[36]
Kilembe, J.T., Lundemba, A.S., Bibelayi, D.D., Ndefi, G.M., Pradon, J. and Yav, Z.G. (2019) Docking of Human Heat Shock Protein 90 with Selenoderivatives of Geldanamycin. Crystal Structure Theory and Applications, 8, 13-27. https://doi.org/10.4236/csta.2019.82002
[37]
Moudgil, R., Bharatam, P.V., Kaur, R. and Kaur, D. (2002) Theoretical Studies on Electron Delocalisation in Selenourea. Journal of Chemical Sciences, 114, 223-230. https://doi.org/10.1007/BF02704266
[38]
Metrangolo, P., Neukirch, H., Pilati, T. and Resnati, G. (2005) Halogen Bonding Based Recognition Processes: A World Parallel to Hydrogen Bonding. Accounts of Chemical Research, 38, 386-395. https://doi.org/10.1021/ar0400995
[39]
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 Sulphur Groups R1-S-R2. Acta Crystallographica Section B, 76, 707-718. https://doi.org/10.1107/S2052520620008598
[40]
Bauza, A., Quinonero, D., Deya, P.M. and Frontera, A. (2013) Halogen Bonding versus Chalcogen and Pnicogen Bonding: A Combined Cambridge Structural Database and Theoretical Study. CrystEngComm, 15, 3137-3144. https://doi.org/10.1039/C2CE26741A
[41]
Bleiholder, C., Werz, D.B., Koppel, H. and Gleiter, W. (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
[42]
Bleiholder, C., Gleiter, W., Werz, D.B. and Koppel, H. (2007) Theoretical Investigations on Heteronuclear Chalcogen-Chalcogen Interactions: On the Nature of Weak Bonds between Chalcogen Centers. Inorganic Chemistry, 46, 2249-2260. https://doi.org/10.1021/ic062110y
[43]
Garrett, G.E., Gibson, G.L., Straus, R.N., Seferos, D.S. and Taylor, M.S. (2015) Chalcogen Bonding in Solution: Interactions of Benzotelluradiazoles with Anionic and Uncharged Lewis Bases. Journal of the American Chemical Society, 137, 4126-4133. https://doi.org/10.1021/ja512183e
