New 3-hydroxyflavone derivatives for probing hydrophobic sites in microheterogeneous systems

Nine new 3-hydroxyflavone derivatives as fluorescent molecular sensors having two well-separated emission bands were synthesized. These sensors can occupy well-determined locations and orientations in macromolecular ensembles, such as micelles due to their finely-tuned designs. These polarity-sensitive dyes can incorporate into the anhydrous hydrophobic core of aqueous micelles.     

Study of chemical bonds in a-B/C:H films by electron probe microanalysis

This paper describes the study of chemical bonds in amorphous hydrogen rich boron/carbon (a-B/C:H) films by electron probe microanalysis. The films were deposited on Si single crystals by plasma chemical vapour deposition with a precursor-carborane (C₂B₁₀H₁₂) in a laboratory setup. A film thickness and B/C ratio up to a value of 8000 Å and 4, respectively, have been obtained. The analysis of boron and carbon X-ray emission spectra has shown that the nearest order in the films is characterized by the coexistence of C-C, B-C and B-B bonds for B/C 1 and of B-B and B-C bonds for B/C 4. After two years exposure in air the oxygen content in the films increases from 2–5 to 15–20 at.%.     

Quantum coherence,evolution of the Wigner function,and transition from quantum to classical dynamics for a chaotic system

The paper deals with dynamics of a quantum chaotic system under influence of an environment. The effect of an environment is known to destroy the quantum coherence and can convert the quantum dynamics of a system to classical. We use a semiclassical technique for studying the process of decoherence. The condition for transition from quantum to classical dynamics is obtained in general form and checked numerically for a particular chaotic system, known as quantum the standard map on a torus. The relevance of the obtained results to the problem of correspondence between quantum and classical mechanics is briefly discussed. (c) 1996 American Institute of Physics.     

TDS and XPS study of oxygen diffusion into subsurface layers of Pd(110)

Summary The interaction of O₂with Pd(110) has been studied by TDS and XPS at T = 400 K and at pressures P_{O2 from 2.6x10}^-6to 10 Pa. At low exposures in O₂(e￡1-5 L), an adsorption layer withqof ca.0.5 and with the O1s peak at BE = 529.3 eV has been found to form on the surface. Whenegrows from 5 to 10⁸L, the position and intensity of the oxygen O1s peak remain practically constant. At the same time, as much as 5 mL of oxygen is absorbed according to the TDS data. The results obtained by TDS and XPS indicate that oxygen penetrates deep into the subsurface layers of palladium (315-20 ?) and is distributed in its bulk in a low concentration.     

Raman spectroscopy of tris-(hydroxymethyl)aminomethane as a model system for the studies of α-chymotrypsin activation by crown ether in organic solvents

Raman spectroscopy is employed to study tris-(hydroxymethyl)aminomethane and its complexes with 18-crown-6. The results obtained are used to interpret the known effect of α-chymotrypsin activation by crown ether in organic solvents. Raman spectra of the samples lyophilized from aqueous solutions at various pH values are measured in solid state, acetonitrile and cyclohexane.     

Oxidative coupling of malononitrile with formation of 1,1,2,3,3-pentacyanopropene salts

A simple and convenient route for the synthesis of 1,1,2,3,3-pentacyanopropene salts is reported. These salts are formed by interaction of malononitrile with SeO₂ in presence of organic N-containing bases or pyridinium salts.     

Pore formation coupled to ion transport through lipid membranes as induced by transmembrane ionic charge imbalance: atomistic molecular dynamics study

We have employed atomic-scale molecular dynamics simulations to address ion transport through transient water pores in phospholipid membranes. The formation of a water pore is induced by a transmembrane ionic charge imbalance, which gives rise to a significant potential difference across the membrane. The subsequent transport of ions through the pore discharges the transmembrane potential and makes the water pore metastable, leading eventually to its sealing. The findings highlight the importance of ionic charge fluctuations in spontaneous pore formation and their role in ion leakage through protein-free lipid membranes.     

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Synthesis, structure, and X-band (9.5 GHz) EPR characterization of the new series of pH-sensitive spin probes: N,N-disubstituted 4-amino-2,2,5,5-tetramethyl-3-imidazoline 1-oxyls

[reaction: see text] An approach to the synthesis of new imidazoline nitroxides bearing an N',N'-disubstituted amidine group is reported. The approach is based on the alkylation of diamagnetic 4-R-amino-1,2,2,5,5-pentamethyl-3-imidazolines with bromoacetic acid ethyl ester; the products of alkylation are further oxidized to the corresponding nitroxides. The approach allows a variety of functional groups to be introduced into the nitroxide molecule structure. Alkylation with bromoacetic acid ethyl ester was found to proceed with high regioselectivity and afford the products of exo-alkylation. The regiochemical assignment is made on the basis of 13C NMR spectra and confirmed by X-ray diffraction study. All of the nitroxides synthesized here were shown to have pH-dependent EPR spectra with pKa ranging from 3.5 to 6.2. For nitroxides 13 bearing the carboxylic group remote to the nitroxide moiety, the changes in isotropic magnetic parameters of EPR spectra due to reversible deprotonation of the carboxylic group were found to be small. For these nitroxides, we demonstrate an alternative approach for pKa determination that is based on measuring the peak-to-peak line width of the EPR spectrum in the presence of the paramagnetic broadening agent potassium ferricyanide. The partition coefficients of nitroxides in octanol/H2O and octanol/phosphate buffer solution mixtures were measured to reveal a range of their lipophilicities.     

The index of ideality of correlation: improvement of models for toxicity to algae

Toxicity to algae is important characteristic of substances from ecologic point of view. The CORAL software (http://www.insilico.eu/coral) gives possibility to build up model of toxicity to algae using data on the molecular architecture and experimental toxicity, without additional data on physicochemical and/or biochemical parameters. Considerable improvement of the model is observed in the case of using the index of ideality of correlation (IIC) in the role of additional criterion of predictive potential. The IIC is calculated with using of the correlation coefficient between experimental and calculated values of endpoint for the calibration set, with taking into account the positive and negative dispersions between experimental and calculated values. The best model calculated with use the IIC is characterized (the validation set) by n?=?50, r²?=?0.947, RMSE?=?0.401 whereas, model calculated without use the IIC is characterized by n?=?50, r²?=?0.805, and RMSE?=?0.539. The suggested models are built up in accordance to five OECD principles.