Theoretical Study on the Gas-Phase Acidity of Multiple Sites of Cu+−Adenine and Cu2+−Adenine Complexes

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.

Adenine-stabilized carbon dots for highly sensitive and selective sensing of copper(II) ions and cell imaging

Adenine-stabilized carbon dots (A-CDs) are shown to be a viable fluorescent probe for highly sensitive detection and imaging of Cu²⁺. The probe has a linear fluorometric response in the 1-700 nM concentration range and a 0.3 nM detection limit. The probe, with excitation/emission maxima at 380/435 nm, is highly selective for Cu²⁺ over other metal ions, anions, amino acids, and biomolecules. The fluorescence quenching mechanism of the A-CDs by Cu²⁺ is investigated using transmission electron microscopy images coupled with elemental mapping, X-ray photoelectron spectroscopy, X-ray-excited Auger electron spectroscopy, fluorescence lifetime, UV-visible spectroscopy, and cyclic voltammetry. The experimental results show that the fluorescence quenching is caused by the combination of Cu²⁺-coordination-induced aggregation of the A-CDs, the reduction of Cu²⁺ by the A-CDs, and the nonradiative photoinduced electron transfer process from the A-CDs to Cu²⁺ or metallic Cu. The high sensitivity and high selectivity of the sensor are ascribed to the chemical interactions between the A-CDs and Cu²⁺, the photophysical process between the A-CDs and Cu²⁺, and the high fluorescence quantum yield of the A-CDs (44.6%). The A-CDs have excellent water solubility, good stability to variation of pH values, high photostability, fast response time, and low cytotoxicity. They are successfully employed for intracellular imaging of Cu²⁺ in HepG2 cells and Cu²⁺ detection in the tap water samples.

The influence of Cu+ binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study

In the present work, the influence of Cu⁺ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine-guanine, hypoxanthine-adenine, hypoxanthine-cytosine, hypoxanthine-thymine and hypoxanthine-hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu⁺ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu⁺ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu⁺ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Communicated by Ramaswamy H. Sarma.

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.

INFLUENCE OF CATION-HETEROATOM (Li+, Na+, AND K+) INTERACTION ON THE STRUCTURAL AND THERMOCHEMICAL PROPERTIES OF 2′-DEOXYTHYMIDINE NUCLEOSIDE: QTAIM AND NBO ANALYZES

Density functional theory (DFT) method and B3LYP/6-311++G(d,p) basis set were used to determine coordination geometries, binding strength, and metal ion affinity (MIA) for interaction of 2′-deoxythymidine (dT) with alkali metal cations including Li+, Na+ , and K+ . Calculations demonstrated that the interaction of dT with these cations is tri-coordinated η (O2, O4′, O5′). Among these cations, Li+ cation exhibited the most tendency for interaction with dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of base unit with respect to sugar ring and the acidity of O5′H, O3′H, and N3H groups in 2′-dT nucleoside. Natural bond orbital (NBO) analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of interactions. It was shown that in these complexes, (dT- Li+ , dT- Na+ , and dT- K+ ), the bonds are an electrostatic (closed-shell) interaction in the nature.

Interactions of coinage metal clusters with histidine and their effects on histidine acidity; theoretical investigation

Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M(3) clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M(3) clusters is governed by two major bonding factors: (a) the anchoring N-M and O-M bonds and (b) the nonconventional N-H···M and O-H···M hydrogen bonds. The nature of these chemical bonds has been investigated based on quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. In the next step, the effects of Au, Ag and Cu metal clusters on the gas-phase acidity of weak organic acid (histidine) have been explored. The acidity of isolated histidine was compared with the acidity of its Au(3)-, Ag(3)- and Cu(3)-complexed species. Results indicate that upon complexation with M(3) clusters (at 298 K), the gas-phase acidity (GPA) of histidine varies from 339.5 to 312.3, 315.0, and 313.7 kcal mol(-1) for Au(3)-, Ag(3)- and Cu(3)-His complexes, respectively (i.e., its dissociation becomes much less endothermic). These values indicate that a weak organic acid can be converted to a super acid when it is complexed with metal clusters. Also, in order to investigate the acidity value of the imidazole moiety in histidine, histidine methyl ester (His-OMe) was selected. Similarly, the acidity of this compound was compared with the acidity of their Au(3), Ag(3) and Cu(3)-complexed species. After complexation with M(3) clusters at 298 K, the gas-phase acidity (GPA) of His-OMe varies from 333.0 to 280.0, 304.2 and 291.5 kcal mol(-1), respectively. Moreover, pK(a) values were determined in water for isolated and complexed species of His and His-OMe. The resulting pK(a) values were found to decrease upon complexation with M(3) clusters.

6-Amino-9H-purine-1,7-diium bis-(4-methyl-benzene-sulfonate) monohydrate

The asymmetric unit of the title compound, C(5)H(7)N(5) (2+)·2C(7)H(7)O(3)S(-)·H(2)O, consists of one diprotonated adeninium cation, two p-toluene-sulfonic acid anions and one water mol-ecule. In the crystal, the cations and anions are connected through N-H⋯O hydrogen bonds forming R(2) (2)(8) and R(2) (2)(9) graph-set motifs. The solvent water mol-ecule links cations and anions through O-H⋯O and N-H⋯O hydrogen bonds, generating a two-dimensional layer parallel to (10).