On the Bonding of First-Row Transition Metal Cations to Guanine and Adenine Nucleobases

Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal-Nucleic Acid Complexes

Understanding the structure of metal-nucleic acid systems is important for many applications such as the design of new pharmaceuticals, metal detection platforms, and nanomaterials. Herein, we explore the ability of 20 density functional theory (DFT) functionals to reproduce the crystal structure geometry of transition and post-transition metal-nucleic acid complexes identified in the Protein Data Bank and Cambridge Structural Database. The environmental extremes of the gas phase and implicit water were considered, and analysis focused on the global and inner coordination geometry, including the coordination distances. Although gas-phase calculations were unable to describe the structure of 12 out of the 53 complexes in our test set regardless of the DFT functional considered, accounting for the broader environment through implicit solvation or constraining the model truncation points to crystallographic coordinates generally afforded agreement with the experimental structure, suggesting that functional performance for these systems is likely due to the models rather than the methods. For the remaining 41 complexes, our results show that the reliability of functionals depends on the metal identity, with the magnitude of error varying across the periodic table. Furthermore, minimal changes in the geometries of these metal-nucleic acid complexes occur upon use of the Stuttgart-Dresden effective core potential and/or inclusion of an implicit water environment. The overall top three performing functionals are ωB97X-V, ωB97X-D3(BJ), and MN15, which reliably describe the structure of a broad range of metal-nucleic acid systems. Other suitable functionals include MN15-L, which is a cheaper alternative to MN15, and PBEh-3c, which is commonly used in QM/MM calculations of biomolecules. In fact, these five methods were the only functionals tested to reproduce the coordination sphere of Cu²⁺-containing complexes. For metal-nucleic acid systems that do not contain Cu²⁺, ωB97X and ωB97X-D are also suitable choices. These top-performing methods can be utilized in future investigations of diverse metal-nucleic acid complexes of relevance to biology and material science.

Computational design of three Cu-induced triangular pyrimidines based DNA motifs with improved conductivity

Novel DNA triangular pyrimidine derivatives are designed by metal decoration through replacement of H by Cu in the Watson–Crick hydrogen bond region. The DFT method is used to examine the coordination of triangle-arranged Cu with three pyrimidines in nonplanar three-bladed turbine geometries. The Cu···Cu cuprophilic bonds are ascribed to the partially occupied d orbitals without direct molecular orbital (MO) interactions. Four-center bonds depend on Cu–N/O bonds, which are contributed by p orbitals of N/O atoms along or perpendicular to the bond axis. The activity of frontier MOs is modulated, leading to the decrease of gaps, ionization potentials (IPs), and electron affinities (EAs) desired for the improvement of conductivity. The hole trapping ability is assured by virtue of the spin density distributed on Cu. On average, the single electron density is located on π orbitals of three aromatic base rings. There is paramagnetic electron delocalization on the inner d orbitals of triangle region. The analysis of electron localization function ELF-π and electrostatic potential maps reveals that the outer strong π–π stacking interaction together with the inner d orbital channel enable effective transduction of electrical signals along the Cu–DNA nanowires. The 3Cu-induced triangular pyrimidines have important potential applications as structural motifs of molecular electronic devices.

The exocyclic amino group of adenine in PtII and PdII complexes: 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 Pt^II and Pd^II, 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 N6H₂ acting 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.

Intensified effects of multi-Cu modification on the electronic properties of the modified base pairs containing hetero-ring-expanded pyrimidine bases

Novel DNA base pair derivatives (A2CunU, A2CunC, G3CunU, and G3CunC) are designed by aromatic expansion of pyrimidine bases with four kinds of hetero-rings (denoted by nC and nU, n = 1, 2, 3, and 4) and metal-decoration through Cu replacement of hydrogens in the Watson-Crick hydrogen bond region. Their structures and properties are calculated for examining the cooperative effects of the two modification ways. The calculated results reveal that multiple Cu decoration makes up the deficiencies of size-expansion, and exhibits not only increase of structural stability and reduction of ionization potentials, but also ideal shrink of the HOMO-LUMO gaps, notable enhancement of interbase coupling as well as remarkable redshifts of π → π* transitions for all M-x modified base pairs. The decrease extents of the gaps and ionization potentials follow the same order G3CunU > G3CunC > A2CunU > A2CunC, and in each series (denoted by different n), the gaps, ionization potentials and first π → π* transition energies have an order of 4 < 1 < 2 < 3. The Cu d orbitals function as bridges for π electron delocalization on the conjugated aromatic rings of two bases, leading to an enhancement of transverse electronic communication, as verified by spin density delocalization, orbital composition changes, redshift of the π → π* transition and also advocated by the electron-sharing indexes such as delocalization index, Mayer bond orders and multicenter bonding. Electron localization function ELF-π isosurfaces above the molecular plane further suggested that effective longitudinal conduction is closely relevant with the bicyclic domain involving good electron delocalization and strong π-π stacking between layers. This work presents theoretical evidence for the cooperative effects of metal decoration and ring-expansion modifications on the electronic properties of the modified base pairs and also proves that the base pairs designed here could be competent building blocks for the DNA-based nanowires with improved electron activity and excellent conductivity.

Spectral study on the unique enhanced fluorescence of guanosine triphosphate by zinc ions

Binding effect of guanosine triphosphate (GTP) with metal ions is involved in many biologically important processes, and so its investigation has been one interesting research focus for many chemical and biochemical research groups. In this contribution, we presented the unique fluorescence recovery and enhancement of GTP induced by Zn(II) based on the spectrofluorometric method. When excited at 280 nm, GTP is hardly fluorescent at the alkaline condition. However, the presence of Zn(II) caused an obvious fluorescence emission of GTP at 346 nm, and the binding molar ratio between GTP and Zn(II) had been proved to be 1. The investigations of binding property of various nucleotides with metal ions demonstrated that this fluorescence recovery and enhancement of GTP with Zn(II) was highly specific, which could successfully discriminate GTP from other structurally similar nucleotides including GDP and GMP. Furthermore, similar fluorescence response of the bacterial alarmone ppGpp to Zn(II) had also been identified.

Immobilization mechanisms of deoxyribonucleic acid (DNA) to hafnium dioxide (HfO2) surfaces for biosensing applications

Immobilization of biomolecular probes to the sensing substrate is a critical step for biosensor fabrication. In this work we investigated the phosphate-dependent, oriented immobilization of DNA to hafnium dioxide surfaces for biosensing applications. Phosphate-dependent immobilization was confirmed on a wide range of hafnium oxide surfaces; however, a second interaction mode was observed on monoclinic hafnium dioxide. On the basis of previous materials studies on these films, DNA immobilization studies, and density functional theory (DFT) modeling, we propose that this secondary interaction is between the exposed nucleobases of single stranded DNA and the surface. The lattice spacing of monoclinic hafnium dioxide matches the base-to-base pitch of DNA. Monoclinic hafnium dioxide is advantageous for nanoelectronic applications, yet because of this secondary DNA immobilization mechanism, it could impede DNA hybridization or cause nonspecific surface intereactions. Nonetheless, DNA immobilization on polycrystalline and amorphous hafnium dioxide is predominately mediated by the terminal phosphate in an oriented manner which is desirable for biosensing applications.

Site-specific control of N7-metal coordination in DNA by a fluorescent purine derivative

A synthetic strategy that utilizes O6-protected 8-bromoguanosine gives broad access to C8-guanine derivatives with phenyl, pyridine, thiophene, and furan substituents. The resulting 8-substituted 2'-deoxyguanosines are push-pull fluorophores that can exhibit environmentally sensitive quantum yields (Φ=0.001-0.72) due to excited-state proton-transfer reactions with bulk solvent. Changes in nucleoside fluorescence were used to characterize metal-binding affinity and specificity of 8-substituted 2'-deoxyguanosines. One derivative, 8-(2-pyridyl)-2'-deoxyguanosine (2PyG), exhibits selective binding of Cu(II), Ni(II), Cd(II), and Zn(II) through a bidentate effect provided by the N7 position of guanine and the 2-pyridyl nitrogen atom. Upon incorporation into DNA, 2-pyridine-modified guanine residues selectively bind to Cu(II) and Ni(II) with equilibrium dissociation constants (K(d)) that range from 25 to 850 nM; the affinities depend on the folded state of the oligonucleotide (duplex>G-quadruplex) as well as the identity of the metal ion (Cu>Ni≫Cd). These binding affinities are approximately 10 to 1 000 times higher than for unmodified metal binding sites in DNA, thereby providing site-specific control of metal localization in alternatively folded nucleic acids. Temperature-dependent circular-dichroism studies reveal metal-dependent stabilization of duplexes, but destabilization of G-quadruplex structures upon adding Cu(II) to 2PyG-modified oligonucleotides. These results demonstrate how the addition of a single pyridine group to the C8 position of guanine provides a powerful new tool for studying the effects of N7 metalation on the structure, stability, and electronic properties of nucleic acids.

Photoelectron and computational studies of the copper-nucleoside anionic complexes, Cu(-)(cytidine) and Cu(-)(uridine)

The copper-nucleoside anions, Cu(-)(cytidine) and Cu(-)(uridine), have been generated in the gas phase and studied by both experimental (anion photoelectron spectroscopy) and theoretical (density functional calculations) methods. The photoelectron spectra of both systems are dominated by single, intense, and relatively narrow peaks. These peaks are centered at 2.63 and 2.71 eV for Cu(-)(cytidine) and Cu(-)(uridine), respectively. According to our calculations, Cu(-)(cytidine) and Cu(-)(uridine) species with these peak center [vertical detachment energy (VDE)] values correspond to structures in which copper atomic anions are bound to the sugar portions of their corresponding nucleosides largely through electrostatic interactions; the observed species are anion-molecule complexes. The combination of experiment and theory also reveal the presence of a slightly higher energy, anion-molecule complex isomer in the case of the Cu(-)(cytidine). Furthermore, our calculations found that chemically bond isomers of these species are much more stable than their anion-molecule complex counterparts, but since their calculated VDE values are larger than the photon energy used in these experiments, they were not observed.

Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes

Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods. Cationized systems subject to study are those resulting from cation coordination to the main basic sites of the base pair, N7 and N3 of adenine and O2 of thymine. For Cu+ coordinated to N7 or N3 of adenine, only the double proton-transferred product is found to be stable, similarly to the neutral system. However, when Cu+ interacts with thymine, through the O2 carbonyl atom, the single proton transfer from thymine to adenine becomes thermodynamically spontaneous, and thus rare forms of the DNA bases may spontaneously appear. For Cu2+ cation, important effects on proton-transfer processes appear due to oxidation of the base pair, which stabilizes the different single proton-transfer products. Results for hydrated systems show that the presence of the water molecules interacting with the metal cation (and their mode of coordination) can strongly influence the ability of Cu2+ to induce oxidation on the base pair.