FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Förster theory

In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C‐phycocyanin (C‐PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C‐PC were examined by model chemistry in gas phase at time‐dependent density functional theory (TDDFT), configuration interaction‐singles (CIS), and Zerner's intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long‐range pigment‐protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short‐range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long‐ and short‐range interactions were properly taken into account, the calculated energy transfer rates (1/K) in the framework of Förster model at TDDFT/B3LYP/6‐31+G* level were in good agreement with the experimental results of C‐PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C‐PC monomer is predominant from β‐155 to β‐84 (1/K = 13.4 ps), however, from α‐84 of one monomer to β‐84 (1/K = 0.3–0.4 ps) in a neighbor monomer in C‐PC trimer. In C‐PC hexamer, an additional energy flow was predicted to be from β‐155 (or α‐84) in top trimer to adjacent β‐155 (or α‐84) (1/K = 0.5–2.7 ps) in bottom trimer. © 2013 Wiley Periodicals, Inc.     

Study on the Interaction Between Bovine Serum Albumin and Potassium Perfluoro Octane Sulfonate

The interactions between potassium perfluorooctanesulfonate (PFOS) and bovine serum albumin (BSA) were studied by fluorescence spectroscopy. The association constants between PFOS and BSA were obtained by fluorescence enhancing and fluorescence quenching respectively. Furthermore, fluorescence quenching was studied at different temperatures, and the binding constant was also determined by the method of fluorescence quenching. According to the thermodynamic parameters, the main binding force could be judged. The experimental results revealed that BSA and PFOS had strong interactions. The mechanism of quenching belonged to dynamic quenching and the main sort of binding force was hydrophobic force. IR-spectra proved the interaction changed the conformation of BSA.     

Solubilization and Transfer Free Energy of Some Organic Compounds from Bulk Aqueous Phase to Micelle of a New Type of Surfactant

A new type of surfactant, 3‐alkoxyl‐2‐hydroxylpropyltrimethyl ammonium bromide (C_nH_2n+1OCH₂CH(OH)CH₂N(CH₃)₃ ⁺Br^?, abbreviated as R_nTAB, n=8, 12, 14, 16) was synthesized. The solubilization of n‐pentanol, n‐hexanol, n‐heptanol, benzyl alcohol, n‐hexane, benzene, toluene, heptane, and carbon tetrachloride in aqueous solutions of R_nTAB, sodium dodecyl sulfonic(R₁₂SO₃N_a), and in the mixed solution of R₁₆TAB/R₁₂SO₃N_a have been studied by the microtitration method. The experimental results show that the solubilized amounts of the organic compounds increase with the growing of the hydrocarbon chain of R_nTAB, and the solubilizing ability of the binary system is lower for polar substances than for a mono‐surfactant aqueous solution. “V” isothermal curves of the solubilized amount of polar substances have been observed, and the minimum solubilized amount is at the molar ratio 1∶1 of R₁₆TAB/R₁₂SO₃N_a. However, the solubilizing ability of mixed surfactants for non polar substances is higher than that for a mono‐surfactant solution, the solubilizing isotherm curves present a “saddle” shape, and the maximum solubilized amount is at the molar ratio 1∶1 of R₁₆TAB/R₁₂SO₃N_a too. The length of hydrophobic chains of surfactant and the polarity of the organic compound affect the transfer free energy from aqueous to micelle phase. The longer the hydrophobic chain of R_nTAB and the lower the polarity of the organic compound, the more easily will the compound transfer from aqueous phase to micelle phase.     

Biofuels–Renewable Energy Sources: A Review

Biodiesel is biodegradable and nontoxic, and it significantly reduces toxic and other emissions when burned as a fuel. The advantages of biodiesel as diesel fuel are its portability, ready availability, renewability, higher combustion efficiency, non-toxicity, higher flash point, and lower sulfur and aromatic content, higher cetane number, and higher biodegradability. The major disadvantages of biodiesel are its higher viscosity, lower energy content, higher cloud point and pour point, higher nitrogen oxide (NO_x) emissions, lower engine speed and power, injector coking, engine compatibility, high price, and greater engine wear. The technical disadvantages of biodiesel/fossil diesel blends include problems with fuel freezing in cold weather, reduced energy density, and degradation of fuel under storage for prolonged periods. The sources of biodiesel are vegetable oils and fats. The direct use of vegetable oils and/or oil blends is generally considered to be unsatisfactory and impractical for both direct injection and indirect type diesel engines because of their high viscosities and low volatilities injector coking and trumpet formation on the injectors, higher level of carbon deposits, oil ring sticking, and thickening and gelling of the engine lubricant oil, acid composition. Biodiesel is obtained by transesterifying triglycerides with methanol. A popular variation of the batch transesterification process which needs high alcohol/acid ratio (several separation problems and high corrosivity and toxicity) is the use of continuous stirred tank reactors in series. This continuous process is heterogeneous and is based on reactive distillation. The key factor is the selection of the right and effective solid catalyst which leads to reduction of energy consumption and investments at all.     

准经典轨线方法对Ca+CD3Ⅰ→CaⅠ+CD3同位素效应的动力学研究

在扩展Lond-Eyring-Polanyi-Sato(LEPS)势能面上,采用准经典轨线方法对反应Ca+CD3I→CaI+CD3进行了动力学计算,并讨论了该反应的同位素效应.在同位素效应作用下,产物CaI的振动态分布向低振动态转移,反应体系的散射截面在低碰撞能和高碰撞能处有较小的变化.同时,受到反应物的质量因子变化的影响,产物转动取向值减少,产物转动取向增强.仅有产物的角分布受同位素效应的影响不明显.     

锌掺杂对TiO2染料敏化电池光阳极中电荷俘获态分布及电子复合过程的影响

基于瞬态光电压和瞬态光电流技术研究了锌掺杂的TiO2染料敏化太阳能电池中电子复合及传输的动力学行为.通过实验获得了不同阳极掺杂条件下的电子复合时间常数与电子收集时间常数,考察了锌掺杂对电池阳极材料导带能级和电子俘获态的影响.研究结果表明,锌的掺杂在提高TiO2导带能级的同时延长了俘获态电子的复合时间常数,从而大大提高了电池的开路电压.     

高温高压Li3N-hBN体系cBN转变的热力学分析

以经典热力学第二定律ΔG<0为依据,分析了静态高温高压触媒法合成立方氮化硼(cBN)过程中发生的可能反应.考虑温度和压强对反应物相体积的影响,计算了六方氮化硼(Li3N-hBN)体系中hBN+Li3N→Li3BN2,h BN→cBN及Li3BN2→Li3N+cBN反应在高温高压条件下的ΔG.结果证实,Li3BN2由Li3N与hBN在高温高压(T>1300 K,P>3.0 GPa)条件下反应得到,在cBN的合成(T=1600～1800 K,P=4.6～6.0 GPa)条件下,hBN和Li3BN2都有向cBN转化的倾向,但由hBN向cBN直接转变的反应自由能比Li3BN2分解生成cBN的反应自由能更负,反应的可能性更大.探讨了高温高压条件下立方氮化硼的转变机理。     

热解温度对生物质焦理化特性的影响

利用SEM、BET及TGA对在873、1 073和1 273 K下制得的麦秆焦的理化特性进行分析,进行了用制得的麦秆焦还原NO的实验,同时考虑了焦样及NO初始浓度对该反应的影响,得出了热解温度对麦秆焦的各种物理化学特性及其与NO反应活性的影响。结果表明,1 073 K焦样的孔隙特征最为发达,燃烧活性最高,并对应最高的NO还原效率。焦作用下NO的还原率随着焦样浓度的增大线性升高,而随着初始NO浓度的增大呈幂函数的规律下降。不同热解温度下麦秆焦样与NO的反应均在1 173 K附近存在动力学控制和扩散控制的转折温度;在动力学控制的反应温度范围内,热解温度对麦秆焦与NO反应活化能的影响不大(89.78~95.41 kJ/mol),其中,NO浓度项和焦浓度项的反应级数分别为0.89和1.00。     

Transportation of a microdroplet on an oriented liquid crystal surface

Wetting phenomena play important roles in several technological applications and in many physical and biological thin‐film phenomena, such as wetting, adhesion and friction. One of key issues of these studies is to control the surface energy (or wettability) dynamically for liquid transportation. We have developed a liquid crystal (LC) surface for use as a transport substrate since we expected that the surface energy of an LC surface can be controlled rapidly using an electric field. The rapid control of the polarisability (or wettability) of a liquid crystalline surface by an electric field has been demonstrated, together with the transportation of a liquid microdroplet.