Hydrogen Bonds of C=S, C=Se and C=Te with C-H in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD)
Open Access
- 1 January 2022
- journal article
- research article
- Published by Scientific Research Publishing, Inc. in Crystal Structure Theory and Applications
- Vol. 11 (01), 1-22
- https://doi.org/10.4236/csta.2022.111001
Abstract
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 Å, 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.Keywords
This publication has 42 references indexed in Scilit:
- Synthesis of Se nanowires at room temperature using selenourea as Se sourceJournal of Materials Science: Materials in Electronics, 2019
- The Cambridge Structural Database in Retrospect and ProspectAngewandte Chemie, 2014
- The nature of hydrogen bonds with divalent selenium compoundsJournal of Molecular Structure: THEOCHEM, 2010
- Synthesis, spectral, and antimicrobial evaluation of some new 8-membered phosphorus heterocyclic compoundsMedicinal Chemistry Research, 2010
- Crystallization kinetics and thermal properties of 20Li2O–80TeO2 glassMaterials Research Bulletin, 2009
- Expansion of the σ-hole conceptJournal of Molecular Modeling, 2008
- σ‐Hole bonding and hydrogen bonding: Competitive interactionsInternational Journal of Quantum Chemistry, 2007
- Semiempirical GGA‐type density functional constructed with a long‐range dispersion correctionJournal of Computational Chemistry, 2006
- Application of hydrogen bonding calculations in property based drug designDrug Discovery Today, 2002
- Theoretical studies on electron delocalisation in selenoureaJournal of Chemical Sciences, 2002