Unusual Noncovalent Interaction Between the Chelated Cu(II) Ion and the π Bond in the Vitamin B13 Complex, cis-Diammine(orotato)copper(II): Theoretical and Vibrational Spectroscopy Studies

• Published in: The journal of physical chemistry. B 2009-06, Vol.113 (23), p.8158-8169
• Main Authors: Helios, K, Wysokiński, R, Zierkiewicz, W, Proniewicz, L. M, Michalska, D
• Format: Article
• Language: English
• Subjects: B: Biophysical Chemistry
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp901912v

The crystal structure of the Cu(II) complex with Vitamin B13 (orotic acid), cis-[Cu(oro)(NH3)2] has revealed the presence of unusual, noncovalent π-type interaction between the chelated Cu(II) ion and the CC bond of the uracilate ring [Michalska et al. Polyhedron 2007, 26, 4303]. In this work, the origin and strength of this interaction is thoroughly investigated. Comprehensive studies of the molecular structures and vibrational spectra of the title complex have been performed by using the unrestricted density functional theory methods, B3LYP, and the newly developed M05-2X functional. Calculations at the UMP2 level were also carried out for comparison. A variety of basis sets have been employed in the DFT calculations, including aug-cc-pVTZ, D95V(d,p), SDD, and LanL2DZ. The 63Cu/65Cu isotope substitution technique was applied to identify the copper−ligand vibrations in the infrared spectra. The clear-cut assignment of all the bands in the FT-IR and Raman spectra of the title complex has been made on the basis of the calculated potential energy distribution, PED. It is shown that an extremely intense band at 1210 cm−1 in the Raman spectrum of cis-[Cu(oro)(NH3)2] is diagnostic for the N-1 deprotonation of the uracilate ring and coordination to the copper(II) ion. The B3LYP functional performs better than M05-2X in predicting vibrational frequencies of this complex in the solid state. Intermolecular interactions in crystal were modeled by the supramolecular system consisting of cis-[Cu(oro)(NH3)2], ethylene (above), and formaldehyde (below the copper coordination plane). The stable structure of this system has been predicted only by the M05-2X and MP2 methods, which include dispersion energy, whereas the B3LYP calculations failed in geometry optimization. The distance between the Cu atom and the CC bond, predicted by the M05-2X method (3.00 Å) is similar to the van der Waals contacts between the stacking bases in DNA. The calculated interaction energy between the chelated Cu(II) complex and ethylene amounts to −7.33 kcal mol−1, which is similar to that determined for stacked uracil dimer. It is concluded that the London dispersion energy plays a significant role in the noncovalent interaction between the chelated Cu(II) ion and the uracilate ring in the crystal of cis-[Cu(oro)(NH3)2]. Many copper enzymes in their active sites contain the chelated Cu(II) ion and the aromatic groups (Phe, Tyr and Trp) as the potential binding sites; therefore, the noncovalen