The exocyclic amino group of adenine in PtIIand PdIIcomplexes: a critical comparison of the X-ray crystallographic structural data and gas phase calculations.
A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H2, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH+) and deprotonated forms (9MeA-H), free and metal-complexed, has been conducted. The metals are PtIIand PdII, bonded to nitrogen-containing co-ligands (NH3, dien, bpy), with N1, N6, and N7 being the metal-binding sites, individually or in different combinations. The results obtained from gas phase calculations are critically compared with X-ray crystallography data, whenever possible. In the majority of cases, there is good qualitative agreement between calculated and experimentally determined C6-N6 bond lengths, but calculated values always show a trend to larger values, by 0.02-0.08 Å. Both methods indicate, with few exceptions, a high degree of double-bond character of C6-N6, consistent with an essentially sp2-hybridized N6 atom. The shortest values for C6-N6 distances in X-ray crystal structures are around 1.30 Å. Exceptions refer to cases in which DFT calculations suggest the existence of a hydrogen bond with N6H2acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp3. Nevertheless, even in these cases the C6-N6 bond (1.392 Å) is still halfway between a typical C-N single bond (1.48 Å) and a typical C=N double bond (1.28 Å). This scenario is, however, not borne out by X-ray crystallographic results, and is attributed to the absence of counter anions and solvent molecules in the calculated structures.
Department of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, 400028, Romania. rsilaghi@chem.ubbcluj.ro.
Radu
R
Silaghi-Dumitrescu
Department of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, 400028, Romania.|Fakultät Chemie und Chemische Biologie (CCB), Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221, Dortmund, Germany.
Béla
B
Mihály
Department of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, 400028, Romania.|Fakultät Chemie und Chemische Biologie (CCB), Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221, Dortmund, Germany.
Timea
T
Mihály
Department of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, 400028, Romania.
Amr A A
AAA
Attia
Departamento de Química Inorgánica, Instituto de Sintesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza-CSIC, 50009, Saragossa, Spain. pablo.sanz@unizar.es.
Pablo J
http://orcid.org/0000-0002-8220-6031
PJ
Sanz Miguel
Fakultät Chemie und Chemische Biologie (CCB), Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221, Dortmund, Germany. bernhard.lippert@tu-dortmund.de.
Bernhard
B
Lippert
D000225:Adenine / Q000737:chemistry*; D018360:Crystallography, X-Ray; D005740:Gases / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D009942:Organometallic Compounds / Q000138:chemical synthesis / Q000737:chemistry*; D010165:Palladium / Q000737:chemistry*; D010984:Platinum / Q000737:chemistry*; D011789:Quantum Theory
D005740:Gases; D009942:Organometallic Compounds; D010984:Platinum; D010165:Palladium; D000225:Adenine
Adenine; DFT calculations; Hybridization state; Metal complexes; Nucleobase amino group