Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

The rapidly growing number of theoretically predicted protein structures requires robust methods that can utilize low-quality receptor structures as targets for ligand docking. Typically, docking accuracy falls off dramatically when apo or modeled receptors are used in docking experiments. Low-resolution ligand docking techniques have been developed to deal with structural inaccuracies in predicted receptor models. In this spirit, we describe the development and optimization of a knowledge-based potential implemented in Q-Dock, a low-resolution flexible ligand docking approach. Self-docking experiments using crystal structures reveals satisfactory accuracy, comparable with all-atom docking. All-atom models reconstructed from Q-Dock's low-resolution models can be further refined by even a simple all-atom energy minimization. In decoy-docking against distorted receptor models with a root-mean-square deviation, RMSD, from native of approximately 3 A, Q-Dock recovers on average 15-20% more specific contacts and 25-35% more binding residues than all-atom methods. To further improve docking accuracy against low-quality protein models, we propose a pocket-specific protein-ligand interaction potential derived from weakly homologous threading holo-templates. The success rate of Q-Dock employing a pocket-specific potential is 6.3 times higher than that previously reported for the Dolores method, another low-resolution docking approach.     

金的化学状态对Au／CoCeOx催化剂CO氧化性能的影响

以CoCeOx复合氧化物为载体,采用沉积沉淀法制备了负载型的金催化剂,并通过不同温度的预处理控制Au的化学状态. 使用粉末X射线衍射、高分辨透射电子显微镜、程序升温还原和X射线光电子能谱对催化剂进行了表征,考察了在室温条件下该系列催化剂的一氧化碳氧化性能. 结果表明, Au/CoCeOx催化剂的CO氧化性能与催化剂表面Au 的含量成正比, Au 可能是反应的主要活性物种. 添加水汽对反应有一定的促进作用,但由于Au 不能稳定存在,特别是当催化剂表面Au 的含量过高时,在水汽的作用下Au 迅速发生歧化反应,使得催化剂的性能下降.     

甲烷氧化偶联纳米SrTiO3催化剂的原位ESR和TPSR表征

采用溶胶-凝胶法制备了纳米钙钛矿型复合氧化物SrTiO3催化剂,并用X射线粉末衍射、透射电子显微镜、原位电子自旋共振和程序升温表面反应等技术对催化剂进行了表征,测定了催化剂对甲烷氧化偶联(OCM)反应的催化性能.结果表明,与相同组成的常规SrTiO3催化剂相比,纳米SrTiO3催化剂具有较好的低温(～650℃)催化性能.通过增大Sr/Ti比可进一步优化纳米SrTiO3的催化性能.纳米SrTiO3催化剂表面的吸附氧物种和F中心均具有活化及催化甲烷分子生成C2烃产物的活性,但吸附氧物种易使OCM反应中间体和产物深度氧化,而F中心具有低温活化甲烷分子及高选择性生成C2烃产物的特性.纳米氧化物粒子因表面原子配位不饱和(配位数低),其表面存在较多的F中心。     

Why the model of non-interacting chains yields adequate description of spin crossover in space structures?

Considering many-body interactions in tetrahedral structures as perturbations of binary potentials by third bodies yields a free energy functional of the binary mixture equivalent to one earlier derived for spin crossover equilibrium in one-dimensional chains. Formal non-ideality parameters of this functional, the excess energy and asymmetries of splittings can be expressed in terms of molecular parameters based on binary potentials.     

How deeply are core electrons perturbed when valence electrons are spin polarized? The case study of transition metal compounds

The ferromagnetic and antiferromagnetic wave functions of the KMnF₃ perovskite have been evaluated quantum-mechanically by using an all electron approach and, for comparison, pseudopotentials on the transition metal and the fluorine ions. It is shown that the different number of α and β electrons in the d shell of Mn perturbs the inner shells, with shifts between the α and β eigenvalues that can be as large as 6 eV for the 3s level, and is far from negligible also for the 2s and 2p states. The valence electrons of F are polarized by the majority spin electrons of Mn, and in turn, spin polarize their 1s electrons. When a pseudopotential is used, such a spin polarization of the core functions of Mn and F can obviously not take place. The importance of such a spin polarization can be appreciated by comparing (i) the spin density at the Mn and F nuclear position, and then the Fermi contact constant, a crucial quantity for the hyperfine coupling, and (ii) the ferromagnetic–antiferromagnetic energy difference, when obtained with an all electron or a pseudopotential scheme, and exploring how the latter varies with pressure. This difference is as large as 50% of the all electron datum, and is mainly due to the rigid treatment of the F ion core. The effect of five different functionals on the core spin polarization is documented.