Ammoniated Complexes of Uracil and Transition Metal Ions: Structures of [M(Ura-H)(Ura)(NH₃)]⁺by IRMPD Spectroscopy and Computational Methods (M = Fe, Co, Ni, Cu, Zn, Cd)

Abstract

The structures of deprotonated d-block metal dication bound uracil dimers, solvated by a single ammonia molecule, were explored in the gas phase using infrared multiple photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance-mass spectrometer. The IRMPD spectra were then compared with computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31+G(d,p) basis set for all atoms, with the exception of Cd, for which the LANL2DZ basis set with relativistic core potentials was used. The calculations were then repeated using the def2-TZVPP basis set on all atoms and were compared to the first set of calculations. The lowest-energy structures are those in which one uracil is deprotonated at the N3 position and, aside from the Cu complex, the intact uracil is a tautomer in which the N3 hydrogen is at the O4 carbonyl oxygen. The metal displays a tetradentate interaction to the uracil moieties, with the exception of Cu, which is tridentate, and the ammonia molecule is bound directly to the metal center. In the Cu complex, a square planar geometry is observed about the metal center, consistent with Jahn-Teller distortions commonly observed in Cu(II) complexes, and the intact uracil assumes its canonical tautomer. All other metal cation complexes are five-coordinate, square pyramidal complexes, with the intact uracil adopting a tautomer in which the N3 hydrogen is on O4. The IRMPD spectroscopic data are consistent with the computed infrared spectra for the lowest-energy structures in all cases.

Structures of [M(Ura-H)(Ura)]+ and [M(Ura-H)(H2O)n]+ (M = Cu, Zn, Pb; n = 1–3) complexes in the gas phase by IRMPD spectroscopy in the fingerprint region and theoretical studies

“…With a bond length of ∼1.5 Å, this interaction is relatively strong. This isomer is the lowest in energy for the M = Cu and Pb complexes, which is consistent with results previously obtained for Cu [23,29] and Pb [22], and comparable to the ammoniated dimer of Cu [30] as well as similar bare dimers metalated by group 2 dications [24,25]. This structure is only slightly higher in energy for the Zn complex by a nominal amount.…”

“…By contrast, the [Cu(Ura-H)] + complex was shown to be deprotonated at the N1 position of uracil, with Cu bound to N1 and O2 [27,28]. However, the dimeric complex adopts a similar structure to the Pb and Zn dimers, where deprotonation occurs at N3 and metal binding is to N3 and O4 of the deprotonated moiety [23,29,30].…”

Gas‐phase hydration of Mg2+ complexes with deprotonated uracil, thymine, uridine, and thymidine

“…However, the key question is why the efficiency of gas‐phase hydration of the ion [ U + U r ‐H+Mg] + is much higher than that of gas‐phase hydration of the ion [ T + T dr ‐H+Mg] + . It can be taken for granted that for both ions, the metal cation is coordinated by deprotonated N3 atom of nucleobase or nucleoside . On the other hand, the ions [ U + U r ‐H+Mg] + and [ T + T dr ‐H+Mg] + have different fragmentation pathways.…”

“…However, to the best of our knowledge, such studies are limited. There are only a few interesting and detailed papers concerned with hydration of deprotonated uracil with metal cations, including Mg 2+ …”

From 3D to 2D Transition Metal Nitroprussides by Selective Rupture of Axial Bonds

“…Figure 5s hows the optimized geometry for 1m2p, [Zn(1m2p)] and [Cd(1m2p)] species at D3-B3LYPl evel of theory within the SMD(1m2p) continuum solventm odel.T he Becke, 3-parameter,L ee-Yang-Parr (B3LYP) functional hasb een successfully used previouslyi ns ome studies to describe zinc and cadmiumo rganometallic complexes. [23][24][25][26][27] Indeed, D3-B3LYP calculations have been performed recently to explain for spectroscopico bservations on 1m2p solventand to study the spectroscopicp roperties of pyrrolidone-type molecules. [28,29] Additional information for the corresponding calculations is provided in the theoretical detailss ection.…”