正癸烷与二甲苯在超临界压力下的热裂解

采用连续流动装置对正癸烷和二甲苯在超临界压力下的热裂解对比研究. 用气相色谱和色质联用仪对其气相产物和液相产物进行分析, 计算气相产物产率和裂解转化率, 并运用计算化学方法获得正癸烷和二甲苯不同化学键的键能, 从实验和理论上分析其裂解反应的难易程度和裂解规律. 实验结果表明, 在4 MPa和650、700、750 ℃条件下, 正癸烷比二甲苯更容易裂解, 正癸烷裂解产物以C₁-C₃小分子的烃类和氢气为主, 而二甲苯裂解产物主要为乙苯、甲苯和其它芳香类化合物; 键能计算结果表明, 正癸烷碳链骨架的C－C键能和C－H键能均较小, 裂解反应的诱发步骤应该是C－C键断裂, 而二甲苯苯环上C－C和C－H键能均较大, 裂解诱发步骤应该是侧链甲基脱氢反应. 因此正癸烷裂解反应以C－C键断裂和脱氢反应为主, 二甲苯裂解主要发生侧链甲基C－C键断裂和脱氢反应, 而芳环则比较稳定, 理论计算键能分析与裂解实验结果一致.     

激酶ABL与肉豆蔻酰位点小分子作用机理的分子动力学模拟及自由能计算

采用分子动力学方法研究激酶ABL 与ATP 位点小分子imatinib、P16 及变构位点小分子STJ、MS7、MS9、3YY、MYR等的结合, 并用GBSA (generalized Born surface area)方法将结合自由能分解到各残基. 自由能计算结果表明, 小分子STJ、MS7、MS9 有利于imatinib 与ABL 结合; 小分子STJ、MS7、MS9 与激酶ABL的结合自由能接近, 绝对值均大于ABL 与3YY、MYR 的结合自由能. 能量分解表明, ABL 残基ILE502、VAL506、LEU510与STJ和MYR的相互作用是αI 螺旋处于弯曲状态的重要原因. 模拟过程中ABL肉豆蔻酰口袋残基均方根偏差(RMSD)变化值表明, STJ等小分子抑制剂与ABL结合后降低了肉豆蔻酰口袋残基的柔性.     

Improvement of TiO2/Dye/Electrolyte Interface Conditions by Positional Change of Alkyl Chains in Modified Panchromatic Ru Complex Dyes

A series of panchromatic ruthenium sensitizers ( MJ sensitizers) with attached thiophene and phenyl units bearing alkyl chains was synthesized. A new synthetic route was used to examine all possible positions for the alkyl chains. The absorption spectra showed the sum of a ruthenium complex and peripheral organic chromophore units. The hypochromic effect and blueshift of the metal‐to‐ligand charge‐transfer band observed in the modified ruthenium sensitizers were suppressed by changing the positions of the alkyl chains on the attached thiophene ring. Changing only one alkyl chain also influenced the performance of dye‐sensitized solar cells. Ruthenium sensitizer MJ‐10 with bulky substituent harvests visible and near‐infrared light, and solar cells sensitized by MJ‐10 exhibit an efficiency of 9.1 % under 1 sun irradiation.     

Fast,Reversible Lithium Storage with a Sulfur/Long‐Chain‐Polysulfide Redox Couple

The cathodic reactions in Li–S batteries can be divided into two steps. Firstly, elemental sulfur is transformed into long‐chain polysulfides (S₈?Li₂S₄), which are highly soluble in the electrolyte. Next, long‐chain polysulfides undergo nucleation reaction and convert into solid‐state Li₂S₂ and Li₂S (Li₂S₄?Li₂S) by slow processes. As a result, the second‐step of the electrochemical reaction hinders the high‐rate application of Li–S batteries. In this report, the kinetics of the sulfur/long‐chain‐polysulfide redox couple (theoretical capacity=419 mA h g^?1) are experimentally demonstrated to be very fast in the Li–S system. A Li–S cell with a blended carbon interlayer retains excellent cycle stability and possesses a high percentage of active material utilization over 250 cycles at high C rates. The meso‐/micropores in the interlayer are responsible for accommodating the shuttling polysulfides and offering sufficient electrolyte accessibility. Therefore, utilizing the sulfur/long‐chain polysulfide redox couple with an efficient interlayer configuration in Li–S batteries may be a promising choice for high‐power applications.     

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.     

Computational gibberellin‐binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor

Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. In this work, fundamental mechanism of hormone perception by receptor GID1 has been studied by performing computational simulations, revealing a new GA‐binding channel of GID1 and a novel hormone perception mechanism involving only one conformational state of GID1. The novel hormone perception mechanism demonstrated here is remarkably different from the previously proposed/speculated mechanism [Murase et al., Nature 2008 , 456, 459] involving two conformational states (“OPEN” and “CLOSED”) of GID1. According to the new perception mechanism, GA acts as a “conformational stabilizer,” rather than the previously speculated “allosteric inducer,” to induce the recognition of protein DELLA by GID1. The novel mechanistic insights obtained in this study provide a new starting point for further studies on the detailed molecular mechanisms of GID1 interacting with DELLA and various hormones and for mechanism‐based rational design of novel, potent growth regulators that target crops and ornamental plants. © 2013 Wiley Periodicals, Inc.     

PICVib: An accurate,fast, and simple procedure to investigate selected vibrational modes at high theoretical levels

A new approach Procedure for Investigating Categories of Vibrations (PICVib) for estimating vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level is presented and explored. The PICVib has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. The errors are smaller than ca. 0.5% when DFT functionals are combined with high level ab initio methods. The approach is general because it can use any quantum chemical program and electronic structure method. It is very robust because it was validated for a wide range of frequency values (ca. 20–4800 cm^–1) and systems: XH₃ (D_3h) with X = B, Al, Ga, N, P, As, O, S, and Se, YH₄ (D_4h) with Y = C, Si, and Ge, conformers of RDX, S_N2 and E2 reactions, [W(dppe)₂(NNC₅H₁₀)] complex, carbon nanotubes, and hydrogen‐bonded complexes including guanine‐cytosine pair. © 2012 Wiley Periodicals, Inc.     

Multiscale geometric modeling of macromolecules II: Lagrangian representation

Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics, and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X‐ray, NMR, and cryo‐electron microscopy, and theoretical/mathematical models, such as molecular dynamics, the Poisson–Boltzmann equation, and the Nernst–Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger's functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent–solute interaction, and ion channel dynamics, whereas our coarse resolution representations highlight the compatibility of protein‐ligand bindings and possibility of protein–protein interactions. © 2013 Wiley Periodicals, Inc.