Use of spheron for separating flavonoids

Institute of Biology, Ufa Scientific Center, Russian Academy of Sciences, Ufa, fax (3472) 35 6103. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 755-756, September-October, 1995. Original article submitted September 6, 1994.     

Dynamics of Hopfield-Type Neural Networks with Modulo Periodic Unpredictable Synaptic Connections,Rates and Inputs

In this paper, we rigorously prove that unpredictable oscillations take place in the dynamics of Hopfield-type neural networks (HNNs) when synaptic connections, rates and external inputs are modulo periodic unpredictable. The synaptic connections, rates and inputs are synchronized to obtain the convergence of outputs on the compact subsets of the real axis. The existence, uniqueness, and exponential stability of such motions are discussed. The method of included intervals and the contraction mapping principle are applied to attain the theoretical results. In addition to the analysis, we have provided strong simulation arguments, considering that all the assumed conditions are satisfied. It is shown how a new parameter, degree of periodicity, affects the dynamics of the neural network.     

Study of ion specific interactions of alkali cations with dicarboxylate dianions

Alkali metal cations often show pronounced ion-specific interactions and selectivity with macromolecules in biological processes, colloids, and interfacial sciences, but a fundamental understanding about the underlying microscopic mechanism is still very limited. Here we report a direct probe of interactions between alkali metal cations (M(+)) and dicarboxylate dianions, (-)O(2)C(CH(2))(n)CO(2)(-) (D(n)(2-)) in the gas phase by combined photoelectron spectroscopy (PES) and ab initio electronic structure calculations on nine M(+)-D(n)(2-) complexes (M = Li, Na, K; n = 2, 4, 6). PES spectra show that the electron binding energy (EBE) decreases from Li(+) to Na(+) to K(+) for complexes of M(+)-D(2)(2-), whereas the order is Li(+) < Na(+) ≈ K(+) when M(+) interacts with a more flexible D(6)(2-) dianion. Theoretical modeling suggests that M(+) prefers to interact with both ends of the carboxylate -COO(-) groups by bending the flexible aliphatic backbone, and the local binding environments are found to depend upon backbone length n, carboxylate orientation, and the specific cation M(+). The observed variance of EBEs reflects how well each specific dicarboxylate dianion accommodates each M(+). This work demonstrates the delicate interplay among several factors (electrostatic interaction, size matching, and strain energy) that play critical roles in determining the structures and energetics of gaseous clusters as well as ion specificity and selectivity in solutions and biological systems.     

The PyPES library of high quality semi‐global potential energy surfaces

In this article, we present a Python‐based library of high quality semi‐global potential energy surfaces for 50 polyatomic molecules with up to six atoms. We anticipate that these surfaces will find widespread application in the testing of new potential energy surface construction algorithms and nuclear ro‐vibrational structure theories. To this end, we provide the ability to generate the energy derivatives required for Taylor series expansions to sixth order about any point on the potential energy surface in a range of common coordinate systems, including curvilinear internal, Cartesian, and normal mode coordinates. The PyPES package, along with FORTRAN, C, MATLAB and Mathematica wrappers, is available at http://sourceforge.net/projects/pypes-lib . © 2015 Wiley Periodicals, Inc.     

Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations

We present results of a theoretical analysis of the phosphorylation reaction in cAMP-dependent protein kinase using a combined quantum mechanical and molecular mechanics (QM/MM) approach. Detailed analysis of the reaction pathway is provided using a novel QM/MM implementation of the nudged elastic band method, finite temperature fluctuations of the protein environment are taken into account using free energy calculations, and an analysis of hydrogen bond interactions is performed on the basis of calculated frequency shifts. The late transfer of the substrate proton to the conserved aspartate (D166), the activation free energy of 15 kcal/mol, and the slight exothermic (-3 kcal/mol) character of the reaction are all consistent with the experimental data. The near attack conformation of D166 in the reactant state is maintained by interactions with threonine-201, asparagine-177, and most notably by a conserved water molecule serving as a strong structural link between the primary metal ion and the D166. The secondary Mg ion acts as a Lewis acid, attacking the beta-gamma bridging oxygen of ATP. This interaction, along with a strong hydrogen bond between the D166 and the substrate, contributes to the stabilization of the transition state. Lys-168 maintains a hydrogen bond to a transferring phosphoryl group throughout a reaction process. This interaction increases in the product state and contributes to its stabilization.     

Synthesis,Structure and Molecular Docking of New 4,5-Dihydrothiazole Derivatives Based on 3,5-Dimethylpyrazole and Cytisine and Salsoline Alkaloids

The interaction results of 1,2-dibromo-3-isothiocyanatopropane with some pyrazoles as well as cytisine and salsoline alkaloids were presented in this paper. It was shown that the reaction resulted in one one-step and rather mild method for the preparation of the corresponding 1,3-thiazoline bromomethyl derivatives. The yield of this reaction was affected by the presence of a base and an order in which reagents were added. Molecular docking of the synthesized 1,3-thiazoline derivatives for putative antibacterial activity was carried out using the penicillin-binding target protein (PBP4) of the bacteria E. coli “Homo sapiens” and S. aureus “Homo sapiens” as an example. Molecular docking demonstrated that the compounds had insignificant binding energies at the level of selected reference drugs (Cephalotin and Chloramphenicol). The presence of natural alkaloids in the structure of thiazoline derivatives somewhat increased the affinity of these substrates for target proteins selected.     

The Electronic Ground State of [Fe(CO)3(NO)]−: A Spectroscopic and Theoretical Study

During the past 10 years iron‐catalyzed reactions have become established in the field of organic synthesis. For example, the complex anion [Fe(CO)₃(NO)]^?, which was originally described by Hogsed and Hieber, shows catalytic activity in various organic reactions. This anion is commonly regarded as being isoelectronic with [Fe(CO)₄]^2?, which, however, shows poor catalytic activity. The spectroscopic and quantum chemical investigations presented herein reveal that the complex ferrate [Fe(CO)₃(NO)]^? cannot be regarded as a Fe^?II species, but rather is predominantly a Fe⁰ species, in which the metal is covalently bonded to NO^? by two π‐bonds. A metal–N σ‐bond is not observed.     

Synthesis of Diels–Alder adducts of the quinolizidine alkaloids N-methylcytisine, (−)-leontidine,and (−)-thermopsine with N-phenylmaleimide

The Diels–Alder adducts of the quinolizidine alkaloids N-methylcytisine, (?)-leontidine, and (?)-thermopsine with N-phenylmaleimide have been synthesized. The structures and absolute configurations of the new asymmetric centers of the products were determined by NMR spectroscopy experiments, QC-calculations, and X-ray data.     

Chitosan nanostructures deposited from solutions in carbonic acid on a model substrate as resolved by AFM

Chitosan macromolecules can be dissolved in water saturated with CO₂ under high pressure, i.e. in carbonic acid. This unique biocompatible solvent with acidity regulated by the variation of applied CO₂ pressure is rather promising for biomedical applications. In this work the main features of deposition of chitosan structures on the model substrate from solutions in this media were examined. After deposition on the mica surface, the obtained structures have been successfully visualised by atomic force microscopy (AFM). It has been found out that they adsorb as rather peculiar elongated objects with an average length of about 70?nm. Such conformations are believed to appear due to amphiphilic nature of chitosan semiflexible chains in agreement with recent theoretical findings. The well-defined geometry of the elongated monodispersed structures allows them to demonstrate some elements of liquid crystalline-like ordering.