Synthesis,structure, and chemical property of the first fluorine-containing porphycene

[structure: see text] A pyrrolic macrocycle, beta-tetrakis(trifluoromethyl)porphycene, is the first example of a fluorine-containing porphycene. Four electron-withdrawing CF(3) substituents provide a highly distorted structure and an attractive electron-deficient nature for the porphycene framework. From the electrochemical study, it is found that the LUMO energy level for the beta-trifluoromethylporphycene is 1.24 V more stabilized compared to that for etioporphyrin. Moreover, the deprotonation of the inner N[bond]H proton in the porphycene was observed upon the addition of DBU.     

Kernel representations for flux and concentration in ion channel models with time-varying concentrations

This paper explores stochastic models for the study of ion transport in biological cells. It considers one-dimensional models with time-varying concentrations at the boundaries. The average concentration and flux in the channel are obtained as kernel representations, where the kernel functions have a probabilistic interpretation which contributes to a better understanding of the models. In particular, the kernel representation is given for the flux at a boundary point, providing a correct version of a representation found in the literature. This requires special attention because one of the kernel functions exhibits a singularity. This kernel representation is feasible due to the linearity of the system that arises from the assumed independence between ions.     

Support effects on the chemical property and catalytic activity of Co-Mo HDS catalyst in sulfur recovery

Effects of carbon nanotubes (CNT) and alumina (γ-Al2O3) supports on the catalytic activities of hydrodesulfurization (HDS) process over CoMo catalyst have been studied. XRD results indicated that the main active phases in CNT and γ-Al2O3 supported Co-Mo catalysts are MoO2 and MoO3, respectively. The TPR results reveal that the reduction peak temperatures of the active species on CNT supported Co-Mo catalyst is lower than those on alumina supported Co-Mo catalyst, indicating that the CNT supports favor the r...     

Modification of second-sphere communication, leading to an unusually high abundance of the head-to-head conformer of cisplatin cross-link retro models

Rapid atropisomerization of cisplatin-DNA cross-link models, cis-PtA(2)G(2) (A(2) = two amines or a diamine, G = guanine derivative, bold font indicating a guanine not linked to another guanine), makes their NMR spectra uninformative. The conformers [two head-to-tail (DeltaHT and LambdaHT) conformers, one head-to-head (HH) conformer] are detected in (CCC)PtG(2) retro models (CCC = chirality-controlling chelates designed to reduce rotation around the G N7 to Pt bond by destabilizing the transition state). Clear trends are found with four CCC ligands, 2,2'-bipiperidine (Bip) and N,N'-dimethyl-2,3-diaminobutane (each with S,R,R,S and R,S,S,R configurations at the chelate ring N, C, C, and N atoms, respectively). S,R,R,S ligands favor left-handed G base canting and the LambdaHT form; R,S,S,R ligands favor right-handed canting and the DeltaHT form. The HH conformer is normally negligible unless G = 5'-GMP. However, understanding this 5'-phosphate effect is complicated by possible interligand interactions of the 5'-phosphate with the N1H of the cis-5'-GMP and a CCC NH; these interactions are referred to as second-sphere (SSC) and first-to-second-sphere (FSC) communication, respectively. We now investigate the four (CCC)PtG(2) models with 1-Me-5'-GMP, a G lacking the N1H needed for SSC. The phosphate location makes FSC possible in the major but not the minor HT form. The major form should increase from pH 3 to pH 7 because the phosphate is deprotonated at pH 7. However, the major DeltaHT form for the R,S,S,R pair did not change in abundance, and the major LambdaHT form for the S,R,R,S pair actually decreased. Thus, FSC is weak. At pH approximately 7 the HH conformer of the S,R,R,S pair had an abundance (40-44%) higher than that in any reported cis-PtA(2)G(2) adduct. FSC involving one 1-Me-5'-GMP could play a role. The high HH abundance and use of a pH jump experiment with (S,R,R,S)-BipPt(1-Me-5'-GMP)(2) allowed us to obtain the first deconvoluted CD spectrum for a cis-PtA(2)G(2) HH conformer. The CD features for the HH conformer are much weaker than for the HT conformers. Our findings are best interpreted to indicate that FSC is not important in aqueous solution, especially for the HT form. Weak FSC is consistent with recent models of the cross-link in duplexes. In contrast, crystals of fluxional models often reveal FSC, but not the more important SSC. SSC was unrecognized until our retro model studies, and the new results reinforce the value of studying retro models for identifying interactions in solution.     

On property of the invariant of graphical representations of DNA sequences

In this article, we consider the influence of variation of DNA sequence on the leading eigenvalue of graphical representation of the biological sequences. The research interpret the rationality of the graphical representation method that compare different DNA sequences. And we show the result on two different models that presented before.      

Design of multitarget activity landscapes that capture hierarchical activity cliff distributions

An activity landscape model of a compound data set can be rationalized as a graphical representation that integrates molecular similarity and potency relationships. Activity landscape representations of different design are utilized to aid in the analysis of structure-activity relationships and the selection of informative compounds. Activity landscape models reported thus far focus on a single target (i.e., a single biological activity) or at most two targets, giving rise to selectivity landscapes. For compounds active against more than two targets, landscapes representing multitarget activities are difficult to conceptualize and have not yet been reported. Herein, we present a first activity landscape design that integrates compound potency relationships across multiple targets in a formally consistent manner. These multitarget activity landscapes are based on a general activity cliff classification scheme and are visualized in graph representations, where activity cliffs are represented as edges. Furthermore, the contributions of individual compounds to structure-activity relationship discontinuity across multiple targets are monitored. The methodology has been applied to derive multitarget activity landscapes for compound data sets active against different target families. The resulting landscapes identify single-, dual-, and triple-target activity cliffs and reveal the presence of hierarchical cliff distributions. From these multitarget activity landscapes, compounds forming complex activity cliffs can be readily selected.     

Discrete variable representations and sudden models in quantum scattering theory

An exact formalism in which the scattering problem may be described by sets of coupled equations labeled either by basis functions or quadrature points is presented. Use of each frame and the simply evaluated unitary transformation which connects them results in an efficient procedure for performing quantum scattering calculations. Two approximations are compared with the IOS.     

Dependency of ligand free energy landscapes on charge parameters and solvent models

We performed replica-exchange molecular dynamics (REMD) simulations of six ligands to examine the dependency of their free energy landscapes on charge parameters and solvent models. Six different charge parameter sets for each ligand were first generated by RESP and AM1-BCC methods using three different conformations independently. RESP charges showed some conformational dependency. On the other hand, AM1-BCC charges did not show conformational dependency and well reproduced the overall trend of RESP charges. The free energy landscapes obtained from the REMD simulations of ligands in vacuum, Generalized-Born (GB), and TIP3P solutions were then analyzed. We found that even small charge differences can produce qualitatively different landscapes in vacuum condition, but the differences tend to be much smaller under GB and TIP3P conditions. The simulations in the GB model well reproduced the landscapes in the TIP3P model using only a fraction of the computational cost. The protein-bound ligand conformations were rarely the global minimum states, but similar conformations were found to exist in aqueous solution without proteins in regions close to the global minimum, local minimum or intermediate states.     

Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)

Background  

Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the β-tubulin protein binding site.     

UV-shielding property, photocatalytic activity and photocytotoxicity of ceria colloid solutions

UV-shielding property, photocatalytic activity and cytotoxicity (including photocytotoxicity) of citrate-stabilized ceria colloid solutions were studied. It was established that UV-shielding property (namely, the sun protection factor, the critical absorption wavelength and the UVA/UVB-ratio) of ceria nanoparticles are as good as those of titanium dioxide and zinc oxide nanoparticles. It was further demonstrated that ceria nanoparticles possesses substantially lower photocatalytic activity, which additionally decreases upon decrease in ceria particle size. It was found that colloid ceria solutions are non-toxic to mouse fibroblasts (L929) and fibroblast-like cells of African Green monkey (VERO). Moreover, ceria nanoparticles are capable to protect these cells from UV-irradiation-induced damage. It was proposed that nanocrystalline ceria could be used not only as UV-blocking material, but also as prophylactic and even therapeutic compound for sunburns treatment.     

Joule-Thomson coefficient in systems with multiple chemical equilibria

Multiple chemical equilibria under adiabatic conditionsH, P = const. are considered. It is shown that in this case the Joule-Thomson coefficient may also be expressed in terms of response equilibria, which were previously introduced in the study of equilibria achieved underT, P = const. Nevertheless, our approach reveals some noteworthy differences between the isothermic and adiabatic equilibria.     

Point chirality functions,symmetry rules for chiral representations in one-centre molecular and field models

There are many problems (e.g. intermolecular forces, molecule-radiation field interactions) in which the separate entities (molecules, photons, or sources of static fields) many be represented by point moments (electric and magnetic. permanent or transition). Such point models lead to expressions containing moment products, which reduce on averaging to orientation-independent product functions that are characteristic of the species and its moment representation. Those functions that change sign when the chirality of the system is changed may be referred to as point chirality functions. In this paper, the point chirality functions generated from a given set of moments are defined, and in turn yield the conditions under which a given moment set is chiral; i.e. gives a chiral representation of the species it represents. They are shown to constitute a set of transferable parameters that lead to a unified approach to orientationally averaged chiral interactions of various kinds. By determining the point chirality functions of isolated chiral systems, the results are applied to interactions between various combinations of molecular, static field and radiation field systems without the need of considering the forms of each interaction in detail.     

Extension of the J-based configuration analysis to multiple conformer equilibria: an application to sapinofuranone A

[structure: see text] A new strategy that extends the application of the J-based configuration analysis to systems characterized by multiple conformer equilibria is described and applied to sapinofuranone A (1), a phytotoxic molecule produced by three strains of Sphaeropsis sapinea. This method, based on a combination of computational techniques and NMR spectroscopy, uses ab initio calculations to predict a set of theoretical homo- and heteronuclear J values which can be compared against experimental NMR data.     

Eupatorium capillifolium essential oil: chemical composition, antifungal activity, and insecticidal activity

Natural plant extracts often contain compounds that are useful in pest management applications. The essential oil of Eupatorium capillifolium (dog-fennel) was investigated for antifungal and insecticidal activities. Essential oil obtained by hydrodistillation of aerial parts was analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC/MS). The major components were determined to be thymol methyl ether (=methyl thymol) (36.3%), 2,5-dimethoxy-p-cymene (20.8%) and myrcene (15.7%). Antifungal activity of the essential oil was weak against the plant pathogens Colletotrichum acutatum, C. fragariae, and C. gloeosporioides in direct bioautography assay. The E. capillifolium oil showed promising repellent activity against the yellow fever mosquito Aedes aegypti, whereas the oil exhibited moderate activity against the mosquito's first instar larvae in a high throughput bioassay. Topical applications of the oil showed no activity against the blood-feeding female adults of A. aegypti. Eupatorium capillifolium essential oil showed a linear dose response between adult lace bug (Stephanitis pyrioides) mortality and increasing oil concentration in an adulticidal activity bioassay. The dog-fennel oil was more potent than the conventional insecticide malathion. In conclusion, these combined results showed Eupatorium capillifolium oil is a promising novel source of a biological insecticide with multiple modes of action.     

具有表面活性的杂环缓蚀剂的合成及性能评价

以2-氨基苯并咪唑、氰尿酰氯、正己胺以及N,N-二甲基-1,3-丙二胺为原料,合成一种具有表面活性的杂环类缓蚀剂。通过测定含不同浓度缓蚀剂的盐酸溶液的表面张力来研究其表面性能。采用失重法和动电位极化及电化学阻抗谱方法考察了其与2-氨基苯并咪唑在盐酸介质中对碳钢的缓蚀行为,并通过扫描电镜观察了腐蚀碳钢试片的外貌形态。结果表明,表面活性以及多活性吸附中心的引入提高了缓蚀剂在碳钢表面的吸附能力,合成的缓蚀剂的缓蚀性能比2-氨基苯并咪唑有显著提高。在实验范围内,缓蚀剂的缓蚀效率随浓度增大而提高,电化学测试表明其为一种混合型缓蚀剂。     

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

Recently, we have introduced a new method, metadynamics, which is able to sample rarely occurring transitions and to reconstruct the free energy as a function of several variables with a controlled accuracy. This method has been successfully applied in many different fields, ranging from chemistry to biophysics and ligand docking and from material science to crystal structure prediction. We present an important development that speeds up metadynamics calculations by orders of magnitude and renders the algorithm much more robust. We use multiple interacting simulations, walkers, for exploring and reconstructing the same free energy surface. Each walker contributes to the history-dependent potential that, in metadynamics, is an estimate of the free energy. We show that the error on the reconstructed free energy does not depend on the number of walkers, leading to a fully linear scaling algorithm even on inexpensive loosely coupled clusters of PCs. In addition, we show that the accuracy and stability of the method are much improved by combining it with a weighted histogram analysis. We check the validity of our new method on a realistic application.     

Subduction of coset representations. An application to enumeration of chemical structures with achiral and chiral ligands

Molecules derived from a parent skeleton are enumerated where both achiral ligands as well as chiral ligands are allowed. Chirality fittingness of an orbit is proposed in order to permit chiral ligands. The enumeration is conducted with and without consideration of obligatory minimum valency (OMV). The effect of the OMV is formulated by assigning different weights to the respective orbits of the parent skeleton. The importance of coset representations and their subduction by subgroups is discussed. The subduced representations are classified into three classes through their chirality fittingness, which determines the mode of substitution with chiral and achiral ligands. Several novel concepts such as a unit subduced cycle index and a subduced cycle index are given in general forms.     

Comparison of quantitative conformer analyses by nuclear magnetic resonance and Raman optical activity spectra for model dipeptides

Interpretation of the Raman optical activity (ROA) of peptides is difficult because of molecular flexibility and interaction with the solvent. Typically, simulations and experiments are compared in terms of a qualitative agreement between the spectra. However, on a series of the Pro-Gly, Gly-Pro, Pro-Ala, and Ala-Pro dipeptides more precise conformer ratios could be obtained with the aid of the density functional computations and numerical decomposition of the spectral shapes. All observed transitions were assigned, and the computed transition frequencies were scaled accordingly. Then the populations predicted by the optical spectroscopy agreed within a few percent with an analysis of the spin-spin coupling constants based on the Karplus equations, which was confirmed also by a comparison of calculated and experimental NMR couplings. The results are supported by molecular dynamics simulations and related to the previous conformational studies of similar molecules.     

Cellular automata models of chemical systems

This paper describes the use of kinematic, asynchronous, stochastic cellular automata to model liquid properties, solution phenomena and kinetic phenomena encountered in complex biological systems. Cellular automata models of dynamic phenomena represent in silico experiments designed to assess the effects of competing factors on the physical and chemical properties of solutions and other complex systems. Specific applications include solution behavior, separation of immiscible liquids, micelle formation, diffusion, membrane passage, first- and second-order chemical kinetics, enzyme activity and acid dissociation. Cellular automata is thus considered as providing an exploratory method for the analysis of dynamic phenomena and the discovery and understanding of new, unexpected phenomena.