Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides

The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.     

Progress on phthalocyanine-conjugated Ag and Au nanoparticles: Synthesis,characterization, and photo-physicochemical properties

Phthalocyanine (Pc) complexes are an important class of dyes with numerous (e.g., biological, photophysical, and analytical) applications. Among the methods used to improve the properties of these complexes, one should mention the introduction of different substituents, variation of the central metal ion, ligand exchange, and conjugation to nanomaterials (e.g., carbon-based nanomaterials and metal nanoparticles (NPs)). This work briefly reviews Pc complex conjugation to Ag and Au NPs, highlights the different NP shapes, and discusses the diversity of conjugation approaches. Moreover, the use of UV–Vis spectroscopy, powder X-ray diffraction, X-ray photoelectron spectroscopy, transmission electron microscopy, atomic force microscopy, dynamic light scattering and Fourier transform infrared spectroscopy to characterize Pc-NP hybrids is summarized. The effect of conjugation on Pc photo-physicochemical properties (fluorescence, singlet oxygen generation, triplet state formation, and optical limiting behavior) is discussed, and future perspectives for the synthesis and applications of new hybrids are provided.     

Surface modification of low density polyethylene (LDPE) film by low pressure O2 plasma treatment

In this work, low pressure glow discharge O₂ plasma has been used to increase wettability in a LDPE film in order to improve adhesion properties and make it useful for technical applications. Surface energy values have been estimated using contact angle measurements for different exposure times and different test liquids. In addition, plasma-treated samples have been subjected to an aging process to determine the durability of the plasma treatment. Characterization of the surface changes due to the plasma treatment has been carried out by means of Fourier transformed infrared spectroscopy (FTIR) to determine the presence of polar species such as carbonyl, carboxyl and hydroxyl groups. In addition to this, atomic force microscopy (AFM) analysis has been used to evaluate changes in surface morphology and roughness. Furthermore, and considering the semicrystalline nature of the LDPE film, a calorimetric study using differential scanning calorimetry (DSC) has been carried out to determine changes in crystallinity and degradation temperatures induced by the plasma treatment. The results show that low pressure O₂ plasma improves wettability in LDPE films and no significant changes can be observed at longer exposure times. Nevertheless, we can observe that short exposure times to low pressure O₂ plasma promote the formation of some polar species on the exposed surface and longer exposure times cause slight abrasion on LDPE films as observed by the little increase in surface roughness.     

聚苯胺纳米点阵列的制备和库仑台阶现象

本文制备了PANI纳米点阵列, 利用导电原子力显微镜(C-AFM)表征了其形貌和导电性能, 在室温下观察到PANI纳米点的库仑台阶(Coulomb staircase)现象, 并利用库仑阻塞效应的理论进行了初步的分析.     

利用DPN技术直接构建磁性纳米图形

在纳米尺度下构建有序的磁性模板和图形是当前的研究热点之一 [1,2 ] .这种模板在生物样品的分离[1] 、磁电子学研究和信息存储 [2 ] 等领域具有重要意义 .目前 ,光刻 [3] 、微触点印刷 [4 ] 和自组装 [5] 等多项技术已被用来构建各种纳米模板 .1 999年 ,美国西北大学 Mirkin小组 [6 ]发明的 Dip- pen纳米刻蚀技术 (简称 DPN技术 )更在可控组装方面显示出巨大优越性 .这项技术是在一定驱动力作用下 ,使吸附在原子力显微镜 ( AFM)针尖上的分子“墨水”逐渐转移到基底表面上 ,实现纳米模板的可控构建 .与传统技术相比 ,DPN技术可在纳米尺…     

Effect of cooperativity on the O-H stretching force constant in associated water species

CNDO/force calculations have been employed to calculate the O-H stretching force constants for various structures of associated water species such as water-dimethylether, water-acetonitrile, water-lithium fluoride, linear and cyclic water polymers. The variation in the O-H stretching force constant in A_m… O-H… D_n species where A_m and D_n represent, respectively,m number of electron-acceptor andn number of electron-donor molecules, is explained on the basis of the cooperativity effect. With increasing electron-acceptor power of A and electron-donor power of D, the hydrogen-bonded O-H stretching force constant is significantly reduced. The results obtained in these studies are in general agreement with experimental observations reported earlier.     

Calculation of harmonic force constants,vibrational frequencies and integrated intensities of some organic molecules using the MINDO—Forces method

The harmonic force constants, vibrational frequencies and integrated intensity ratios of CH₂, H₂O, CH₂O, C₂H₂, CO₂, HCN, CH₃, CH₄, and C₂H₄ have been calculated using the MINDO—FORCES program and the Pulay method for the calculation of the molecular force constants. The results obtained are in general quite satisfactory when compared with available literature values. The results are, however, not as satisfactory in case of molecules containing heteroatoms, due to the neglect of some dipolar repulsion integrals for the heteroatoms by the MINDO/3 method. Calculated integrated intensities for CH₃ and C₂H₄ agree well with experimental results. The calculated integrated intensities for other molecules are obtained for the first time and no comparison with published data is therefore possible.Part of the M.Sc. Thesis of K. H. A. 1978.     

Probing in vitro digestion at oil–water interfaces

Interfacial layers have been widely applied to study the formation and stability of emulsion-based systems. However, the application of isolated interfaces to address digestibility of emulsions is often limited because of the complexity of experimental methods and results. This review summarizes the latest developments in analytical methods and literature data on effects of digestion on interfacial layers. Particular emphasis is given to understand the changes on interfacial magnitudes during oral, gastric, and duodenal digestion, either applied separately or sequentially. Limitations of interfacial aspects and key factors that influence emulsion microstructure in bulk and lipid digestion are identified. Understanding the behavior of interfacial layers upon gastrointestinal digestion promotes an accurate tracking of the physiological fate of emulsions.     

Analysis of First-Order Reactions with Distributed Parameters

Simple methods of analysis of first-order kinetic processes controlled by distributions of parameters (activation energies and/or frequency factors) are presented. Both the isothermal and nonisothermal regimes are considered. The procedures make use of numerically calculated time derivatives of the concentrations of decaying species (reactants in the case of chemical reactions). They do not require any adjustable initial or boundary values of parameters (like concentration at the infinite time) being thus more accurate and reliable than earlier methods in which kinetic parameters were determined from the concentration, and not from its time derivative. The methods were successfully employed in analysis of the thermally driven cis–trans isomerization of a photochromic crown ether containing the azobenzene moiety incorporated in the crown.     

Scaling Function Between the Exponential-6 and the Generalized Lennard-Jones Potential Functions

The van der Waals forces for non-bonded interaction can be expressed either by the Exponential-6 or by the Lennard-Jones(m-n) potential functions, whereby m > n. Hitherto a relationship exists between the Exponential-6 and the Lennard-Jones(12-6) potential functions, with a scaling factor = 13.772 at or near the equilibrium and = 12.0 for long range interaction. This paper attempts to develop relationships between Exponential-6 and a more generalized Lennard-Jones(m-n). Analysis reveals that the relationship exists only when n = 6 and that two sets of scaling factors (as functions of index m) applies for the relationship between Exponential-6 and the Lennard-Jones(m-6), whereby m > 6.