Nonconventional Hydrogen Bonds between Silver Anion and Nucleobases: Size-Selected Anion Photoelectron Spectroscopy and Density Functional Calculations

Halogen Bonding to the π-Systems of Polycyclic Aromatics

The propensity of the π-electron system lying above a polycyclic aromatic system to engage in a halogen bond is examined by DFT calculations. Prototype Lewis acid CF3I is placed above the planes of benzene, naphthalene, anthracene, phenanthrene, naphthacene, chrysene, triphenyl, pyrene, and coronene. The I atom positions itself some 3.3-3.4 Å above the polycyclic plane, and the associated interaction energy is about 4 kcal/mol. This quantity is a little smaller for benzene, but is roughly equal for the larger polycyclics. The energy only oscillates a little as the Lewis acid slides across the face of the polycyclic, preferring regions of higher π-electron density over minima of the electrostatic potential. The binding is dominated by dispersion which contributes half of the total interaction energy.

Metal Centers as Nucleophiles: Oxymoron of Halogen Bond-Involving Crystal Engineering

This review highlights recent studies discovering unconventional halogen bonding (HaB) that involves positively charged metal centers. These centers provide their filled d‐orbitals for HaB, and thus behave as nucleophilic components toward the noncovalent interaction. This role of some electron‐rich transition metal centers can be considered an oxymoron in the sense that the metal is, in most cases, formally cationic; consequently, its electron donor function is unexpected. The importance of Ha⋅⋅⋅d‐[M] (Ha=halogen; M is Group 9 (Rh, Ir), 10 (Ni, Pd, Pt), or 11 (Cu, Au)) interactions in crystal engineering is emphasized by showing remarkable examples (reported and uncovered by our processing of the Cambridge Structural Database), where this Ha⋅⋅⋅d‐[M] directional interaction guides the formation of solid supramolecular assemblies of different dimensionalities.

Comparison of Bifurcated Halogen with Hydrogen Bonds

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.

Nucleobase Pair-Metal Dimer/Dinuclear Metal Cation Interaction: A Theoretical Study

Nucleobase pair-metal dimer/dinuclear metal cation interactions play an important role in biological applications because of their highly symmetrical structures and high stabilities. In this work, we have selected five adenine-adenine hydrogen bonding, adenine-thymine (AT), adenine-uracil, adenine-adenine stacking pairs, and Watson-Crick AT stacking pairs and studied their interaction with the coinage metal dimer M2 and M2 2+ metal cations, where M = Ag, Au, and Cu. Quantum chemical calculations have been carried out with density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Electronic structures were analyzed by the partial density of states method. During interactions, we find that M-M distances are shorter than the sum of van der Waals radii of the corresponding two homocoinage metal atoms, which show the existence of significant metallophilic interactions. Results indicated that nucleobase-M2 2+ complexes are stronger as compared to nucleobase-M2 complexes. Also, the replacement of the hydrogen bond by the dinuclear metal cation-coordinated bond forms more stable alternative metallo-DNA sequences in AAST base pairs. TDDFT calculations reveal that nucleobase-Cu2 complexes and nucleobase-Ag2 2+/Au2 2+ complexes can be used for fluorescent markers and logic gate applications. Atom-in-molecules analysis predicted the noncovalent interaction in these complexes.

Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions

This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.

A dinuclear Cu(i)-mediated complex: Theoretical studies of the G2Cu2 4+ cluster ion

Recently, the T-Hg(ii)₂-A base pair containing two equivalents of Hg(ii) has been prepared and characterized experimentally, which implies that there might exist considerable stable metal-mediated base pairs holding two neighbouring metal centers. Here we report a quantum chemical study on geometries, electronic structures, and bonding of various G₂Cu₂ ⁴⁺ (G = guanine) isomers including one di-copper(i) unit. Different density functional methods [Becke 3-parameter-Lee-Yang-Parr, Perdew-Becke-Ernzerhof, Becke-Perdew, Density Functional Theory with Dispersion Corrections (DFT-D)] assign ambiguous relative energies to these isomers with the singlet and triplet states. High-level ab initio [domain-based local pair natural orbital (DLPNO) coupled-cluster with single and double excitations and DLPNO-coupled-cluster with single, double, and perturbative triple excitations] calculations confirm that the lowest-lying isomer of the G₂Cu₂ ⁴⁺ ion has C _2h symmetry with the singlet state and is comparable to the singly and doubly charged homologues (G₂Cu₂ ⁺ and G₂Cu₂ ²⁺). The extended transition state (ETS)-natural orbitals for the chemical valence (ETS-NOCV) calculations point out that it has larger instantaneous interaction energy and bond dissociation energy than the corresponding singly and doubly charged complexes due to its relatively stronger attractive energies and weaker Pauli repulsion. The orbital interactions in the quadruply charged cluster chiefly come from Cu₂ ⁴⁺ ← G⋯G π donations. The results may help the understanding of the bonding properties of other potential metal-base pair complexes with the electron transfer.