TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble

Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence‐based template‐free predictor (TargetATPsite) to identify the Adenosine‐5′‐triphosphate (ATP) binding sites with machine‐learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under‐samplings is used as the prediction model, which is effective for dealing with imbalance phenomenon between the positive and negative training samples. Compared with the existing ATP‐specific sequence‐based predictors, TargetATPsite is featured by the second step of possessing the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Experimental results on three benchmark datasets demonstrate the efficacy of TargetATPsite. © 2013 Wiley Periodicals, Inc.     

Micellar Effects on Alkaline Hydrolysis of 3,5-Dinitro-2-chloro Benzotriflouride and 2,4-Dinitrochloro Benzene in Aqueous-Acetonitrile Mixtures

Reaction rate for alkaline hydrolysis of the substrates 3,5-dinitro-2-chloro benzotriflouride (DNCBTF) (1) at 30°C and 2,4-dinitrochloro benzene (DNCB) (2) at 50°C separetely with NaOH as nucleophile is carried out spectrophotometrically in mixed aqueous-acetonitrile solvents. In each system, cationic surfactant as dodecyltrimethyl ammonium bromide (DoTAB), or anionic one as sodium dodecyle sulfate (SDS) is used in wide range of concentrations to study the effect of micelle on the reaction rate. The micellar effect is explained in term of modified pseudo phase ion exchange model. Pseudo first order rate constant, k_obs is obtained for each of the nucleophile and for both substrates 1 and 2 at all range of X_AN · k_obs at given [OH^?] and in presence of any substrate is found to increase with the increase of DoTAB,while decrease with the increase of SDS as micellar phases. Critical micelle concentrations (CMCs) in similar trend are observed to increase in DoTAB while decrease in SDS systems by increasing acetonitrile (AN) content. Micellar binding constant (K_S) between any type of given substrate and the formed micelle, is found to decrease in presence of DoTAB and increase in SDS micellar phases by increasing AN content. Finally, the ratios between pseudo first order rate constants for hydrolysis in micellar phase k_M to that in the bulk phase k_w for DoTAB and SDS systems are found to be greater than and smaller than unity respectively at any given X_AN where the data indicated for (1) is always higher than those for (2). The results concluded that micelle DoTAB is working as a catalyst for the reaction rate, while that for SDS is considered as an inhibitor.     

Co-Mo/γ-Al2O3催化剂的原位红外光谱表征研究

采用CO和NO作为探针分子,应用原位红外光谱法(in-situ FT-IR)和程序升温还原(H₂-TPR)对Mo/γ-Al₂O₃和Co-Mo/γ-Al₂O₃加氢催化剂进行表征,并对催化剂进行了加氢脱硫(HDS)活性评价。实验结果表明,在Co-Mo/γ-Al₂O₃催化剂表面存在三个吸附位;在Mo/γ-Al₂O₃催化剂中加入助剂钴对钼吸附位起到显著的改性作用,并且引入新的活性中心,提高了催化剂的催化活性;随着钼含量的增加,活性中心数目逐渐增多;用CO-NO共吸附原位红外光谱研究了Co-Mo/γ-Al₂O₃催化剂表面活性中心的信息,证明不同的Mo中心分别吸附CO和NO,并将它们区分开来,解决了不同活性中心的光谱互相重叠的问题。     

制备方法对Al2O3掺杂Pt/WO3-ZrO2催化剂上正庚烷异构化反应的影响

采用恒pH法和非恒pH法制备了Al₂O₃掺杂的Pt/WO₃/ZrO₂催化剂,并用N₂吸附-脱附、X射线衍射、紫外-可见漫反射、CO化学吸附、X射线光电子能谱、²⁷Al魔角旋转核磁共振和吡啶吸附红外等技术对催化剂进行了表征.结果表明,相比于非恒pH法制备的催化剂,恒pH法制备的催化剂具有较高的比表面积和Pt分散度,在H₂气氛中产生更多的B酸位,从而表现出更高的催化正庚烷临氢异构化反应活性; 在200℃和质量空速0.9h^-1的反应条件下,正庚烷转化率达70.0%,明显高于非恒pH法制备的催化剂(43.5%).     

碱液后处理对纳米ZSM-5沸石孔道和酸度的影响

采用XRD、N2物理吸附、NH3-TPD以及TEM、IR和NMR手段,系统研究了NaOH碱液后处理对低硅铝比纳米ZSM-5沸石(Si/Al摩尔比为14.5、晶粒度为20～50 nm)孔道和酸度的影响.结果表明,在碱液中,低硅铝比纳米ZSM-5沸石主要发生限域脱硅,而且低硅铝比纳米ZSM-5沸石的碱液脱硅难度大于高硅铝比沸石.但在适当的碱液处理条件下(碱硅比为0.19～0.35,温度为60～80℃,处理时间为2～5 h)可以在其晶体内产生大量介孔,增加比表面积和孔容;同时增加弱酸和中强酸的浓度,并提高L酸比例.L酸的大量增加主要是由于产生了裸露的骨架铝(≡Alδ+),这与文献的观点有所不同.     

在四氯合锌离子诱导下反式六元瓜环与碱金属离子构筑的配位超分子自组装体

在盐酸介质中,通过四氯合锌离子诱导,碱金属离子能与反式六元瓜环端口羰基氧原子直接配位构筑形成超分子自组装体。单晶结构表明在HCl介质中,四氯合锌离子形成"蜂巢结构",而且在[ZnCl₄]^2-诱导作用下,碱金属离子和反式六元瓜环端口羰基氧直接配位形成一维超分子自组装体而填充在"蜂巢结构"中。     

酸洗脱矿对胜利褐煤热解过程中N迁移转化的影响

在石英管流化床反应器中对胜利褐煤进行快速热解实验,考察了773~1 173 K下酸洗脱矿对胜利褐煤热解过程中N迁移转化规律的影响。通过比较原煤和酸洗后煤中N的不同逸出规律可以得出,影响酸洗前后胜利褐煤热解过程中N迁移转化规律的主要是碱金属Na及碱土金属Ca;热解过程中,煤中的Na和Ca促使煤中的N向NH3转化并有效抑制了HCN的生成,金属离子的存在对催化焦油N转化为NH3的作用较为明显;原煤中的碱金属和碱土金属的赋存使半焦裂解反应加剧,降低了固体半焦的产率,半焦N的产率也随之减少;与原煤相比,酸洗煤热解半焦中的吡啶型N(N-6)含量较多,而吡咯型N(N-5)和季N(N-Q)相对较少。     

The Effect of Alkaline Addition in Hydrothermal Pretreatment of Empty Fruit Bunches on Enzymatic Hydrolysis Efficiencies

In general, lignocellulosic biomass contains three major components, namely lignin, hemicellulose and cellulose which are the polymers of C5 and C6 sugars. Thus, there is potential to utilize of this biomass for bioethanol production. The hydrolysis of cellulose into glucose was difficult due to the more fibrous nature and thus inhibit enzyme penetration into the cellulose. In order to solve this problem, hydrothermal pretreatment can be used for breaking the bonds within the lignin structure and increase the accessibility of enzyme into the cellulose. In this study, the effect of chemical addition, sodium hydroxide (NaOH) and calcium oxide (CaO) in hydrothermal pretreatment at 180 °C and 30 minutes reaction time of palm oil empty fruit bunches (EFB) on the enzymatic hydrolysis efficiencies was investigated. The enzymatic hydrolysis of hydrothermally pretreated EFB give the highest concentration of glucose at 0.67 g/L while the hydrothermally pretreated of EFB in the presence of NaOH gives the lowest glucose concentration 0.45 g/L.     

铁基分子筛活性位点的制备控制及对NH3-SCR活性的影响

采用离子交换法,通过不同制备条件制备Fe-beta分子筛,并探讨不同制备条件对催化剂活性位点和NH3-SCR活性的影响。通过UV-Vis分析,将不同位置的吸收峰归属于不同的铁活性位点,300nm以下的高能谱区可以归属于孤立的Fe3+位点,300nm-400nm间归属于低聚的FexOy簇,而400nm以上为Fe2O3大颗粒聚合物。对比不同催化剂的SCR活性发现,孤立的Fe3+和低聚态的Fe3+是主要的活性位点,这两种物种的所占比例高低直接影响了催化剂的活性。而大尺度的Fe2O3为非活性位点,因尽量控制并降低其所占比例。另外低聚态的Fe3+所占比例越高,N2O的生成量越高,N2的选择性越差。因此,在制备过程中,除了控制大尺度的Fe2O3的含量,同时要尽量降低低聚态的Fe3+的含量,以增加N2的选择性。采用离子交换法制备Fe-beta催化剂,pH、交换温度、前驱体种类、硅铝比、煅烧条件等制备条件会对Fe-beta的活性位点造成影响,从而导致活性差异。根据实际应用需求,调控制备条件,可有效控制活性物种的分布,制备具有高效NH3-SCR活性的铁基分子筛催化剂。     

Galvanostatically Deposited PtNi Thin-Films as Electrocatalysts for the Hydrogen Evolution Reaction

The synthesis of hybrid platinum materials is fundamental to enable alkaline water electrolysis for cost-effective H₂ generation. In this work, we have used a galvanostatic method to co-deposit PtNi films onto polycrystalline gold. The surface concentrations of Ni (Γ_Ni) and Pt (Γ_Pt) were calculated from electrochemical measurements; the Γ_Pt/Γ_Ni ratio and electrocatalytic activity of these materials towards hydrogen evolution reaction (HER) in 1 M KOH show a strong dependence on the current density pulse applied during the electrodeposition. Analysis of the Tafel parameters hints that, on these deposits, HER proceeds through a Volmer-Heyrovsky mechanism. The galvanostatically deposited PtNi layers present a high current output per Pt gram, 3199 A g_Pt⁻¹, which is significantly larger compared to other PtNi-based materials obtained by more extended and more complex synthesis methods.