Excited-state intramolecular proton transfer distinguishes microenvironments in single- and double-stranded DNA

Herein, the efficient interaction of an environment-sensitive fluorophore that undergoes excited-state intramolecular proton transfer (ESIPT) with DNA has been realized by conjugation of a 3-hydroxychromone (3HC) with polycationic spermine. On binding to a double-stranded DNA (dsDNA), the ratio of the two emission bands of the 3HC conjugates changes up to 16-fold, so that emission of the ESIPT product increases dramatically. This suggests an efficient screening of the 3HC fluorophore from the water molecules in the DNA complex, which is probably realized by its intercalation into dsDNA. In sharp contrast, the 3HC conjugates show only moderate changes in the dual emission on binding to a single-stranded DNA (ssDNA), indicating a much higher fluorophore exposure to water at the binding site. Thus, the 3-hydroxychromone fluorophore being conjugated to spermine discriminates the binding of this polycation to dsDNA from that to ssDNA. Consequently, ESIPT-based dyes are promising for monitoring the interaction of polycationic molecules with DNA and probing the microenvironment of their DNA binding sites.     

Ab initio comprehensive conformational analysis of 2'-deoxyuridine, the biologically significant DNA minor nucleoside, and reconstruction of its low-temperature matrix infrared spectrum

A comprehensive conformational analysis of isolated 2'-deoxyuridine (dU), a minor DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G (d,p)//DFT B3LYP/6-31G (d,p) level of theory. At 298.15 and 420 K, all 94 allowed conformers of dU are within 8.96 and 7.91 kcal/mol Gibbs energy ranges, respectively. Syn orientation for the base and South (S) conformers for the sugar dominate at 298.15 K: syn/anti=62.3%:37.7% and S/N=77.2%:22.8%. At 420 K in the majority of conformers, the base is anti oriented and the population of North (N) sugars increases: syn/anti=39.3%:60.7% and S/N=63.0%:37.0%. Values of all conformational parameters and correlations between them, as well as their correlations with valence bonds, and also correlations between valence bonds and angles were estimated. In general, 14 types of intramolecular H-bonds were detected (1-3 H-bonds per conformer, the total number 175), namely, C1'H...O2 (16 H-bonds), C2'H1...O5' (9), C2'H2...O2 (21), C3'H...O2 (21), C5'H1...O2 (14), C5'H2...O2 (11), C6H...O4' (37), C6H...O5' (22), C3'H...HC6 (4), O5'H...HC6 (2), O3'H...O5' (5), O5'H...O4' (1), O5'H...O3' (4), and O5'H...O2 (8). Geometric, vibrational, structural-topological, and energetic features of the OH...O intramolecular H-bonds in dU conformers were determined. The close similarity between energetic and geometric characteristics of dU and thymidine DNA-like conformers in anti and relevant syn conformations and their transition states of the anti-->syn interconversion implies that mismatch DNA glycosylase discriminates between the two nucleosides, mainly because of the difference in the shapes of their bases. Convolution of calculated IR spectra of all the dU conformers within the limits 3400-3700 cm(-1) appears to be consistent with its low-temperature matrix IR spectrum (Ivanov et al. Spectrochim. Acta, Part A 2003, 59, 1959), wavenumber discrepancy not exceeding 1%. It was concluded that, for a reliable reproduction of the experimental spectrum, the whole set of conformers should be taken into consideration. The suggested method makes reconstruction of the isolated nucleoside IR spectrum at a physiological interval of temperature reasonably possible.     

Direct synthesis of mesostructured lamellar molybdenum disulfides using a molten neutral n-alkylamine as the solvent and template

A series of novel mesostructured lamellar molybdenum disulfides with the d spacings from 17 to 30 A can be prepared by the reaction of Mo(CO)6 with elemental sulfur using a molten n-alkylamine as the solvent as well as the template at 140 degrees C. Such intercalated phases can be transformed into mesoporous molybdenum disulfides by slow thermal treatments at 200 degrees C.     

From Hexaoxy‐[6]Pericyclynes to Carbo‐Cyclohexadienes,Carbo‐Benzenes,and Dihydro‐Carbo‐Benzenes: Synthesis,Structure, and Chromophoric and Redox Properties

When targeting the quadrupolar p‐dianisyltetraphenyl‐carbo‐benzene by reductive treatment of a hexaoxy‐[6]pericyclyne precursor 3 with SnCl₂/HCl, a strict control of the conditions allowed for the isolation of three C₁₈‐macrocyclic products: the targeted aromatic carbo‐benzene 1 , a sub‐reduced non‐aromatic carbo‐cyclohexadiene 4 A , and an over‐reduced aromatic dihydro‐carbo‐benzene 5 A . Each of them was fully characterized by its absorption and NMR spectra, which were interpreted by comparison with calculated spectra from static structures optimized at the DFT level. According to the nucleus‐independent chemical shift (NICS) value (NICS≈?13 ppm), the macrocyclic aromaticity of 5 A is indicated to be equivalent to that of 1 . This is confirmed by the strong NMR spectroscopic deshielding of the ortho‐CH protons of the aryl substituents, but also by the strong shielding of the internal proton of the endocyclic trans‐CH?CH double bond that results from the hydrogenation of one of the C?C bonds of 3 . Both the aromatics 1 and 5 A exhibit a high crystallinity, revealed by SEM and TEM images, which allowed for a structural determination by using an X‐ray microsource. A good agreement with calculated molecular structures was found, and columnar assemblies of the C₁₈ macrocycles were evidenced in the crystal packing. The non‐aromatic carbo‐cyclohexadiene 4 A is shown to be an intermediate in the formation of 1 from 3 . It exhibits a remarkable dichromism in solution, which is related to the occurrence of two intense bands in the visible region of its UV/Vis spectrum. These properties could be attributed to the dibutatrienylacetylene (DBA) unit that occurs in the three chromophores, but which is not involved in a macrocyclic π‐delocalization in 4 A only. A versatile redox behavior of the carbo‐chromophores is evidenced by cyclic voltammetry and was analyzed by calculation of the ionization potential, electron affinity, and frontier molecular orbitals.     

The role of attractive interactions in rod-sphere mixtures

We present a computer simulation study of binary mixtures of prolate Gay-Berne particles and Lennard-Jones spheres. Results are presented for three such rod-sphere systems which differ from each other only in the interaction between unlike particles. Both the mixing-demixing behavior and the transitions between the isotropic and any liquid crystalline phases are studied for each system, as a function of temperature and concentration ratio. For systems which show macroscopic demixing, the rod-sphere interaction is shown to give direct control over interfacial anchoring properties, giving rise to the possibility of micellar phase formation in the case of homeotropic anchoring. Additionally, it is shown that on incorporating high concentrations of spheres into a system of rods with weak demixing properties, microphase-separated structures can be induced, including bicontinuous and lamellar arrangements.     

Virtual Screening in Search for a Chemical Probe for Angiotensin-Converting Enzyme 2 (ACE2)

We elaborate new models for ACE and ACE2 receptors with an excellent prediction power compared to previous models. We propose promising workflows for working with huge compound collections, thereby enabling us to discover optimized protocols for virtual screening management. The efficacy of elaborated roadmaps is demonstrated through the cost-effective molecular docking of 1.4 billion compounds. Savings of up to 10-fold in CPU time are demonstrated. These developments allowed us to evaluate ACE2/ACE selectivity in silico, which is a crucial checkpoint for developing chemical probes for ACE2.     

Pattern selection processes and noise induced pattern-forming transitions in periodic systems with transient dynamics

We apply the phase field crystal method for nonequilibrium patterning to stochastic systems with an external source in which transient dynamics is essential. Considering a prototype model for a one-component periodic system subjected to external influence kind of irradiation we study properties of pattern selection processes and external noise induced pattern-forming transitions. These processes are examined by means of the structure function dynamics analysis. Nonequilibrium pattern-forming transitions are analyzed numerically.