New light on an old debate: does the RCN–PtCl2 bond include any back-donation? RCN←PtCl2 backbonding vs. the IR νCN blue-shift dichotomy in organonitriles–platinum(ii) complexes. A thorough density functional theory – energy decomposition analysis study
For a series of organonitrile [RCN (R = Me, CF3, Ph, CH3Ph, CF3Ph)] ligands, the nature of the N–Pt bond in the related cis-/trans-(RCN)2PtCl2 complexes has been computationally investigated by Density Functional Theory. A fragment based bond analysis has been performed in the canonical Kohn–Sham molecular orbitals framework, and it has been ultimately assessed that this bond is characterized both by N→Pt σ and by N←Pt π contributions. Voronoi Deformation Density charges further confirms the occurrence of N←Pt π interactions. Moreover, the Energy Decomposition Analysis-Natural Orbital for Chemical Valence (EDA-NOCV) method shows that the strength of the N←Pt π interaction is not negligible …
B-DNA Structure and Stability as Function of Nucleic Acid Composition. Dispersion-Corrected DFT Study of Dinucleoside-Monophosphate Single and Double Strands
actions of the sugar-phosphate skeleton with water; (6) hydrophobic interactions of the DNA cylindrical core, made up by the hydrogen-bonded and stacked nitrogen bases, with the water solvent. Recently, there has been increasing effort in developing and applying quantum chemical methods able to reproduce the structure of native B-DNA and to correctly describe the energy involved in the intrastrand and interstrand noncovalent interactions between the nucleotide monomers. This topic has been approached by both wave function methods and density functional theory. [2] Water solvent and sodium counterions also play an important role in the formation and relative stabilization of the double-helic…
B‐DNA structure and stability: the role of nucleotide composition and order
Abstract We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double‐stranded B‐DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson–Crick base pairing, using dispersion‐corrected DFT at the BLYP‐D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better‐known eff…
Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug
We have computationally studied the intercalation of the antitumor drug daunomycin into six stacks of Watson-Crick DNA base pairs i.e., AT-AT, AT-TA, GC-AT, CG-TA, GC-GC, GC-CG) using density functional theory (DFT). The proton affinity of the DNA intercalater daunomycin in water was computed to be 159.2 kcal/mol at BP86/TZ2P, which is in line with the experimental observation that daunomycin is protonated under physiological conditions. The intercalation interaction of protonated daunomycin with two stacked DNA base pairs was studied through a hybrid approach in which intercalation is treated at LDA/TZP while the molecular structure of daunomycin and hydrogen-bonded Watson-Crick pairs is c…
A Push-Pull Mechanism Helps Design Highly Competent G-Quadruplex-DNA Catalysts
International audience; Massive efforts are currently being invested to improve the performance, versatility, and scope of applications of nucleic acid catalysts. G-quadruplex (G4)/hemin DNAzymes are of particular interest owing to their structural programmability and chemical robustness. However, optimized catalytic efficiency is still bottleneck and the activation mechanism is unclear. Herein, we have designed a series of parallel G4s with different proximal cytosine (dC) derivatives to fine-tune the hemin-binding pocket for G4-DNAzymes. Combining theoretical and experimental methods, we have assessed the dependence of catalytic enhancement on the electronic properties of proximal dCs and…