Solution-State Structure of a Long-Loop G-Quadruplex Formed Within Promoters of Plasmodium falciparum B var Genes.

We report the high-resolution NMR solution-state structure of an intramolecular G-quadruplex with a diagonal loop of ten nucleotides. The G-quadruplex is formed by a 34-nt DNA sequence, d[CAG3T2A2G3TATA2CT3AG4T2AG3T2], named UpsB-Q-1. This sequence is found within promoters of the var genes of Plasmodium falciparum, which play a key role in malaria pathogenesis and evasion of the immune system. The [3+1]-hybrid G-quadruplex formed under physiologically relevant conditions exhibits a unique equilibrium between two structures, both stabilized by base stacking and non-canonical hydrogen bonding. Unique equilibrium of the two closely related 3D structures originates from a North-South repuckering of deoxyribose moiety of residue T27 in the lateral loop. Besides the 12 guanines involved in three G-quartets, most residues in loop regions are involved in interactions at both G-quartet-loop interfaces.

Solid-State Synthesis of B←N Adducts by the Amine-Facilitated Trimerization of the Phenylboronic Acid.

Stable boroxine-amine adducts comprising dative B←N bond(s) were prepared by mechanochemically-induced reactions of phenylboronic acid (PBA) and amines (pyridine, DMAP, 1H-pyrazole, piperidine, DABCO, hexamethylenetetramine, or 4,4'-bipyridine). In-situ Raman monitoring, ex-situ PXRD and DFT calculations were used for product identification. Stoichiometry of the product (3 : 1, 3 : 2 or 6 : 1 adduct) was controlled by the amine structure and the molar ratio of the reactants. The 1 : 2 H-bonded assembly of PBA and 4,4'-bipyridine (bpy) was confirmed as an intermediate in the adduct formation for bpy. Competitive binding experiments indicated that the exchange of the amines in the 3 : 1 adducts follows the computed adduct stabilities that increase with the amine basicity. Following the DFT prediction, the first adduct with two different amines, DMAP and pip, bound to one boroxine moiety was isolated and structurally characterized. Results show that calculations can be used to predict possible and preferred product(s) and their spectral characteristics.

A Detailed Kinetico-Mechanistic Investigation on the Palladium C-H Bond Activation in Azobenzenes and Their Monopalladated Derivatives.

Palladium C-H bond activation in azobenzenes with R1 and R2 at para positions of the phenyl rings (R1 = NMe2, R2 = H (L1); R1 = NMe2, R2 = Cl (L2); R1 = NMe2, R2 = I (L3); R1 = NMe2, R2 = NO2 (L4); R1 = H, R2 = H (L5)) and their monopalladated derivatives, using cis-[PdCl2(DMF)2], has been studied in detail by in situ 1H NMR spectroscopy in N,N-dimethylformamide-d7 (DMF-d7) at room temperature; the same processes have been monitored in parallel via time-resolved UV-vis spectroscopy in DMF at different temperatures and pressures. The final goal was to achieve, from a kinetico-mechanistic perspective, a complete insight into previously reported reactivity results. The results suggest the operation of an electrophilic concerted metalation-deprotonation mechanism for both the mono- and dipalladation reactions, occurring from the coordination compound and the monopalladated intermediates, respectively. The process involves deprotonation of the C-H bond assisted by the presence of a coordinated DMF molecule, which acts as a base. For the first time, NMR monitoring provides a direct evidence of all the intermediate stages: that is, (i) coordination of the azo ligand to the PdII center, (ii) formation of the monopalladated species, and (iii) coordination of the monopalladated species to another PdII unit, which finally result in the (iv) formation of the dipalladated product. All of these species have been identified as intermediates in the dipalladation of azobenzenes, evidenced also by UV-vis spectroscopy time-resolved monitoring. The data also confirm that the cyclopalladation of asymmetrically substituted azobenzenes occurs by two concurrent reaction paths. In order to identify the species observed by NMR and by UV-vis spectroscopy, the final products, intermediates, and the PdII precursor have been prepared and characterized by X-ray diffraction and IR and NMR spectroscopy. DFT calculations have also been used in order to explain the isomerism observed for the isolated complexes, as well to assign their NMR and IR spectra.

Mechanism of Mechanochemical C-H Bond Activation in an Azobenzene Substrate by PdII Catalysts.

Mechanism of C-H bond activation by various PdII catalysts under milling conditions has been studied by in situ Raman spectroscopy. Common PdII precursors, that is PdCl2 , [Pd(OAc)2 ]3 , PdCl2 (MeCN)2 and [Pd(MeCN)4 ][BF4 ]2 , have been employed for the activation of one or two C-H bonds in an unsymmetrical azobenzene substrate. The C-H activation was achieved by all used PdII precursors and their reactivity increases in the order [Pd(OAc)2 ]3

Reversible Gas-Solid Ammonia N-H Bond Activation Mediated by an Organopalladium Complex.

N-H bond activation of gaseous ammonia is achieved at room temperature in a reversible solvent-free reaction using a solid dicyclopalladated azobenzene complex. Monitoring of the gas-solid reaction in real-time by in situ solid-state Raman spectroscopy enabled a detailed insight into the stepwise activation pathway proceeding to the final amido complex via a stable diammine intermediate. Gas-solid synthesis allowed for isolation and subsequent structural characterization of the intermediate and the final amido product, which presents the first dipalladated complex with the PdII-(µ-NH2)-PdII bridge. Gas-solid reaction is readily followed via color changes associated with conformational switching of the palladated azobenzene backbone. The reaction proceeds analogously in solution and was characterized by UV-vis and NMR spectroscopies showing the same stepwise route to the amido complex. Combining the experimental data with density functional theory calculations we propose a stepwise mechanism of this heterolytic N-H bond activation assisted by exogenous ammonia.

Mechanochemical reactions studied by in situ Raman spectroscopy: base catalysis in liquid-assisted grinding.

In situ Raman spectroscopy was employed to study the course of a mechanochemical nucleophilic substitution on a carbonyl group. We describe evidence of base catalysis, akin to catalysis in solution, achieved by liquid-assisted grinding.