Chemical properties of oxopropenyl adducts of purine and pyrimidine nucleosides and their reactivity toward amino acid cross-link formation

N2-oxopropenyldeoxyguanosine (2) forms in duplex DNA by modification of dG residues with base propenal or malondialdehyde. The pKa of 2 was estimated to be 6.9 from the pH dependence of its ring-closing to the pyrimidopurinone derivative 1. The acidity of 2 may be an important determinant of its miscoding properties and its reactivity to nucleophiles in DNA or protein. To test this hypothesis, analogous N-oxopropenyl derivatives of dA (4), dC (5), and N1-methyl-dG (6) were synthesized and their pKa's were determined by optical titration. The N-oxopropenyl derivatives of dA and dC both exhibited pKa's of 10.5, whereas the N-oxopropenyl derivative of N1-methyldG exhibited a pKa of 8.2. Cross-linking of 2, 4, 5, and 6 to N(alpha)-acetyl-lysine was explored at neutral pH. Adduct 2 did not react with N(alpha)-acetyl-lysine, whereas 4-6 readily formed cross-links. The structures of the cross-links were elucidated, and their stabilities were investigated. The results define the acidity of oxopropenyl deoxynucleosides and highlight its importance to their reactivity toward nucleophiles. This study also identifies the structures of a potential novel class of DNA-protein cross-links.     

Hydration properties of aqueous Pb(II) ion

Using density functional theory and polarized continuum models, we have determined the most probable coordination number and structure of the first hydration shell of aqueous Pb(II). The geometries and hydration free energies of Pb(H2O)(1-9)(2+) were examined and benchmarked against experimental values. The free energies of hydration of Pb(H2O)(6-8)(2+) were found to match the experimental value within 10 kcal/mol. Moreover, based upon our thermochemical results for single water addition, primary hydration numbers of 6, 7, and 8 are all thermally accessible at STP. Use of a small-core 60 electron effective core potential (ECP) with the aug-cc-pvdz-PP basis on Pb resulted in structures that are significantly less hemidirected than predicted when using the large-core 78 electron ECP and the lanl2DZ basis on the metal. Our results imply that the hemi- to holo-directed transition in Pb(II)-water complexes is driven by coordination number and not hybridization of the 6s lone-pair orbital or enhanced covalent bonding in the Pb-OH2 bond. In addition to basis set effects, the influence of different solvation models on hydration reactions has further been examined so as to determine the relative accuracy of the calculated hydration thermochemistry.     

Ab initio study of the one- and two-photon circular dichroism of R-(+)-3-methyl-cyclopentanone

One- and two-photon circular dichroism spectra of R-(+)-3-methyl-cyclopentanone, a system that has been the subject of recent experimental studies of (2+1) resonance-enhanced multiphoton ionization circular dichroism, have been calculated with an origin-invariant density functional theory approximation in the region of the lowest electronic excited states, both for the gas phase and for a selection of solvents. A polarizable continuum model is used in the calculations performed on the solvated system. Two low-lying conformers are analyzed, and a comparison of the intensities and characteristic features is made with the corresponding two-photon absorption for each species, also for the Boltzmann-averaged spectra. The effect of the choice of geometry, basis set, and exchange-correlation functional is carefully analyzed. It is found that a density functional theory approach using the Coulomb attenuating method variant of Becke's three-parameter exchange and the Lee-Yang-Parr correlation functionals with correlation-consistent basis sets of double-zeta quality can reproduce the experimental electronic circular dichroism spectra very well. The features appearing in experiment are characterized in terms of molecular excitations, and the differences in the response of each state in the one- and two-photon processes are highlighted.     

Highly Luminescent Cesium Lead Halide Perovskite Nanocrystals with Tunable Composition and Thickness by Ultrasonication

We describe the simple, scalable, single‐step, and polar‐solvent‐free synthesis of high‐quality colloidal CsPbX₃ (X=Cl, Br, and I) perovskite nanocrystals (NCs) with tunable halide ion composition and thickness by direct ultrasonication of the corresponding precursor solutions in the presence of organic capping molecules. High angle annular dark field scanning transmission electron microscopy (HAADF‐STEM) revealed the cubic crystal structure and surface termination of the NCs with atomic resolution. The NCs exhibit high photoluminescence quantum yields, narrow emission line widths, and considerable air stability. Furthermore, we investigated the quantum size effects in CsPbBr₃ and CsPbI₃ nanoplatelets by tuning their thickness down to only three to six monolayers. The high quality of the prepared NCs (CsPbBr₃) was confirmed by amplified spontaneous emission with low thresholds. The versatility of this synthesis approach was demonstrated by synthesizing different perovskite NCs.     

New alkyl derivatives phosphine sulfonate (P-O) ligands. Catalytic activity in Pd-catalysed Suzuki-Miyaura reactions in water

Two novel bis(o-methoxyphenyl) phosphinoalkylsulfonate (P-O) ligands have been prepared through a new and sustainable synthetic route; they are air stable as well as water soluble and have been applied in Pd-catalysed Suzuki-Miyaura cross-coupling reactions in neat water in conjunction with microwave heating.     

Chemical and electrochemical oxidation of C8-arylamine adducts of 2'-deoxyguanosine

The electrochemical and chemical oxidation of a series of C8-arylamine adducts of 2'-deoxyguanosine has been examined. The oxidations were found to be reversible by cyclic and square-wave voltammetry in both aqueous buffer and aprotic organic solvent. The mechanism of the oxidation in protic media was either one- or two-electron, depending on the aryl group. The chemical oxidation resulted in guanidinohydantoin and spiroiminodihydantoin rearrangement products similar to those observed for 8-oxo-7,8-dihydro-2'-deoxyguanosine.     

Beyond exciton theory: a time-dependent DFT and Franck-Condon study of perylene diimide and its chromophoric dimer

The diimide perylene motif exhibits a dramatic intensity reversal between the 0 --> 0 and 0 --> 1 vibronic bands upon pi-pi stacking; this distinct spectral property has previously been used to measure folding dynamics in covalently bound oligomers and synthetic biological hybrid foldamers. It is also used as a tool to assess organization of the pi-stacking, indicating the presence of H- or J-aggregation. The zeroth-order exciton model, often used to describe the optical properties of chromophoric aggregates, is solely a transition dipole coupling scheme, which ignores the explicit electronic structure of the system as well as vibrational coupling to the electronic transition. We have therefore examined the optical properties of gas-phase perylene tetracarboxylic diimide (PTCDI) and its chromophoric dimer as a function of conformation to relate the excited-state distributions predicted by exciton theory with that of time-dependent density functional theory (TDDFT). Using ground- and excited-state geometries, the Franck-Condon (FC) factors for the lowest energy molecular nature electronic transition have been calculated and the origin of the intensity reversal of 0 --> 0 and 0 --> 1 vibronic bands has been proposed.     

Conformation-specific infrared and ultraviolet spectroscopy of tyrosine-based protonated dipeptides

We present the spectroscopy and photofragmentation dynamics of two isomeric protonated dipeptides, H+AlaTyr and H+TyrAla, in a cold ion trap. By a combination of infrared-ultraviolet double resonance experiments and density functional theory calculations, we establish the conformations present at low temperature. Interaction of the charge at the N-terminus with the carbonyl group and the tyrosine pi-cloud seems to be critical in stabilizing the low-energy conformations. H+AlaTyr has the flexibility to allow a stronger interaction between the charge and the aromatic ring than in H+TyrAla, and this interaction may be responsible for many of the differences we observe in the former: a significant redshift in the ultraviolet spectrum, a much larger photofragmentation yield, fewer stable conformations, and the absence of fragmentation in excited electronic states.     

Effect of surfactant structure on the residual fluorescence of micelle-based fluorescent probes

In the present paper we have investigated some photo-physical characteristics of different micellar-based fluorescent probes containing a fluorophore (pyrene) and a quencher unit (dodecyl-dioxo 2,3,2). The fluorescent response of the probe in the presence of Cu(II) ions was studied using different micellar substrates, and it was found that the pH at which the On-Off jump occurs is not influenced by the chemical structure of surfactant. In addition, the experimental residual fluorescence is not proportionally affected by microviscosity or by the size of the micellar aggregates. The signal of the native fluorescence of pyrene was observed even when the quencher's occupancy number was greater than one. Moreover, we observed discrepancies between experimental values and calculated residual fluorescence using Laplace data. These results were interpreted suggesting that the residual fluorescence has two main components, one that seems to be independent on micellar properties, while the other is directly related to location of molecules inside the surfactant aggregates that serve as substrate.     

Microwave‐assisted synthesis of 2‐(2‐pyridyl)azoles. Study of their corrosion inhibiting properties

An efficient and fast procedure for the synthesis of 2‐(2‐pyridyl)azoles is described using ionic liquids as catalysts under microwave irradiation. The X‐ray crystallographic analyses for three of the four synthesized compounds are presented. Potentiodynamic polarization studies were carried out to analyze the electrochemical behavior of the compounds in corrosive acidic media. Of the four derivatives, one compound was detected to be an effective corrosion inhibitor prototype for oil refinery environments.