Adenine as a Halogen Bond Acceptor: A Combined Experimental and DFT Study
Source abstract
Abstract
In this work, we report the cocrystallization of N9-ethyladenine with 1,2,4,5-tetrafluoro-3,6-diiodobenzene (TFDIB), a classical XB donor. As far as our knowledge extends, this is the first cocrystal reported to date where an adenine derivative acts as a halogen bond acceptor. In the solid state, each adenine ring forms two centrosymmetric H-bonded dimers: one using N1···HA6–N6 and the other N7···HB6–N6. Therefore, only N3 is available as a halogen bond acceptor that, indeed, establishes an N···I halogen bonding interaction with TFDIB. The H-bonded dimers and halogen bonds have been investigated via DFT (Density Functional Theory) calculations and the Bader’s Quantum Theory of Atoms In Molecules (QTAIM) method at the B3LYP/6-311+G* level of theory. The influence of H-bonding interactions on the lone pair donor ability of N3 has also been analyzed using the molecular electrostatic potential (MEP) surface calculations.
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Research context
OpenAlex topics: Crystallography and molecular interactions · X-ray Diffraction in Crystallography · Nonlinear Optical Materials Research
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain
Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), c/ Til·lers, s/n, Campus UAB, 08193 Bellaterra, Spain
Funding
Ministerio de Economía, Industria y Competitividad, Gobierno de España
References (45)
Show source-provided references
1. Lehn, J.M. (1995). Supramolecular Chemistry: Concepts and Perspectives, Wiley VCH. [1th ed.].10.1002/3527607439 ↗
2. Gilli, G., and Gilli, P. (2009). The Nature of the Hydrogen Bond, Oxford University Press.10.1093/acprof:oso/9780199558964.001.0001 ↗
3. σ-Holes10.1002/wcms.1113 ↗
4. Halogen bonding and other σ-hole interactions: A perspective10.1039/c3cp00054k ↗
5. The bright future of unconventional σ/π-hole interactions10.1002/cphc.201500314 ↗
6. Hypervalency, secondary bonding and hydrogen bonding: Siblings under the skin10.1039/C6CS00688D ↗
7. Halogen bonding (X-bonding): A biological perspective10.1002/pro.2201 ↗
8. The halogen bond10.1021/acs.chemrev.5b00484 ↗
9. Definition of the halogen bond (IUPAC Recommendations 2013)10.1351/PAC-REC-12-05-10 ↗
10. The structure of Bromine 1,4-dioxanate10.3891/acta.chem.scand.08-0873 ↗
11. Halogen bonds in biological molecules10.1073/pnas.0407607101 ↗
12. The Protein Data Bank10.1093/nar/28.1.235 ↗
13. Halogen bonds as orthogonal molecular interactions to hydrogen bonds10.1038/nchem.112 ↗
14. Systematic investigation of halogen bonding in protein-ligand interactions10.1002/anie.201006781 ↗
15. Underestimated halogen bonds forming with protein backbone in protein data bank10.1021/acs.jcim.7b00235 ↗
16. Halogen bonding in medicinal chemistry: From observation to prediction10.4155/fmc-2017-0052 ↗
17. Mendez, L., Henriquez, G., Sirimulla, S., and Narayan, M. (2017). Looking back, looking forward at halogen bonding in drug discovery. Molecules, 22.10.3390/molecules22091397 ↗
18. Directing macromolecular conformation through halogen bonds10.1073/pnas.0610531104 ↗
19. Halogen bonding: A powerful tool for modulation of peptide conformation10.1021/acs.biochem.7b00429 ↗
20. The Cambridge Structural Database
21. Reaction of trimethylene–bisadenine with d10 divalent cations10.1016/S0277-5387(98)90351-5 ↗
22. An empirical method for correcting diffractometer data for absorption effects10.1107/S0108767383000252 ↗
23. WinGX suite for small-molecule single-crystal crystallography10.1107/S0021889899006020 ↗
24. Crystal structure determination and refinement via SIR201410.1107/S1600576715001132 ↗
25. Crystal structure refinement with SHELXL
26. Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures10.1107/S0021889807067908 ↗
27. Density-functional thermochemistry. III. The role of exact exchange10.1063/1.464913 ↗
28. Semiempirical GGA-type density functional constructed with a long-range dispersion correction10.1002/jcc.20495 ↗
29. Contracted Gaussian-basis sets for molecular calculations. I. Second row atoms, Z=11-1810.1063/1.438980 ↗
30. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., and Petersson, G.A. (2009). Gaussian 09, Revision C.01, Gaussian, Inc.
31. Ab initio effective core potentials for molecular calculations – potentials for the transition-metal atoms Sc to Hg10.1063/1.448799 ↗
32. A quantum theory of molecular structure and its applications10.1021/cr00005a013 ↗
33. Keith, T.A. (2013). TK Gristmill Software, AIMAll.
34. σ-Hole⋯π and lone pair⋯π interactions in benzylic halides10.1039/C5OB00366K ↗
35. Lone pair–π vs. σ-hole–π interactions in bromine head-containing oxacalix[2]arene[2]triazines10.1039/C8CE00666K ↗
36. Kitaigorodsky, A. (2012). Molecular Crystals and Molecules, Elsevier. Physical Chemistry.
37. Structure validation in chemical crystallography10.1107/S090744490804362X ↗
38. Cyanurate Mimics of Hydrogen-Bonding Patterns of Nucleic Bases: Crystal Structure of a 1:1 Molecular Complex of 9-Ethyladenine and N-Methylcyanuric Acid10.1021/ol006811p ↗
39. The high-temperature phase of 1,2,4,5-tetra-fluoro-3,6-di-iodo-benzene and the phase transition10.1107/S0567740881008406 ↗
40. Switching between halogen- and hydrogen-bonding in stoichiometric variations of a cocrystal of a phosphine oxide10.1039/c2ce25653c ↗
41. Evaluating the Energetic Driving Force for Cocrystal Formation10.1021/acs.cgd.7b01375 ↗
42. A Bond Path: A Universal Indicator of Bonded Interactions10.1021/jp981794v ↗
43. Topological information of the electron-density distribution in hydrogen-bonded systems10.1107/S0108767304096503 ↗
44. First-Principles Crystal Engineering of Nonlinear Optical Materials. II. Effect of Halogen Bonds on the Structure and Properties of Triiodobenzenes10.1021/acs.jpcc.8b04932 ↗
45. Structure and conformation of 2, 3-diethoxycarbonyl-1-methylpyridinium iodide studied by NMR, FTIR, Raman, X-ray diffraction and DFT methods10.1016/j.saa.2013.05.046 ↗