环多肽晶体的浮动电荷极化力场模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对五种环多肽晶体进行了研究. 与传统力场相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理地体现了分子中的电荷分布. 相对其他极化力场模型, 具有计算量较小的特点. 该模型下计算得到的环多肽分子单元相对实验测得的结构的原子位置、氢键长度和二面角的均方根偏差分别为0.009 nm、0.013 nm和5.16°, 能够很好地重复实验结果. 总体上, 其结果优于或相当于其他力场模型, 适用于对实际蛋白质体系的模拟和研究.     

Study of polymer treatment with tetrafluoromethane plasma: Reactivity of fluorinated species on model surfaces

Polyolefins and their model molecules, some n-alcanes, have been modified by a tetrafluoromethane microwave plasma. The chosen molecules are high-density polyethylene (HDPE) and hexatriacontane (HTC), low-density polyethylene (LDPE) and paraffin, and polycaprolactone (PCL) and octadecyl octadecanoate (ODO). It has been found, except for paraffin, that the model surfaces have the same behavior as the corresponding polymers. Plasma modification is described as the sum of two mechanisms: degradation and fluorination. These reactions seem to be competitive and parallel. Degradation and fluorination rates are dependent on treatment time and are practically independent on substrate position. A domain of fluorination exists near the edge of plasma, whatever the substrate in or outside plasma. © 1993 John Wiley & Sons, Inc.     

用Xα方法对CH4在Ni(Ⅲ)表面吸附解离反应的理论研究

用Ｘ_α方法对ＣＨ_４在Ｎｉ（Ⅲ）表面吸附解离反应的理论研究马晨生,马理,杨忠志（吉林大学理论化学研究所,长春,１３００２３）关键词ＣＨ_４／Ｎｉ（Ⅲ）吸附体系,原子簇模型,ＣＨ_４／Ｍｉ_７,ＭＳ－Ｘ_α－ＳＣＦ方法甲烷在Ｎｉ表面的催化重整反应在工业和国...     

Gas-Chromatographic Studies of the Interaction between Water and Methanol Molecules and the Surface of Carbon Materials

The gas-chromatographic method is used to study the interaction of water and methanol molecules with active hydrophilic centres existing at the surface of thermally exfoliated graphite and graphitized thermal carbon black. The concentration of carboxyl and phenol hydroxyl groups at the surface of these sorbents is determined, and heats of adsorption of the studied molecules are shown to be and 28−25 kJ/mol, respectively. It is also shown that adsorption of water at the hydrophilic centres at lowest relative pressure values takes place with formation of clusters consisting of n = 2 water molecules.     

A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building

Summary A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching -helices (C, D, G, I, J, K and L) and -sheets (3/4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, -helices B, B and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val³⁷⁰, Pro³⁷¹, Leu³⁷², Trp³¹⁶, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp¹⁰⁰ or Asp³⁰¹ was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates. These findings are in accordance with a recently published predictive model for substrates of P450 2D6 [Koymans et al., Chem. Res. Toxicol., 5 (1992) 211].     

The size distribution for theA g RB f−g Model of polymerization

This paper gives the equilibrium distribution of polymer sizes for Flory'sA _g RB _f–g model of polymerization. In this model, the polymers are composed of structural units withg functional groups of the typeA and (f-g) functional groups of the typeB. Reaction is subject to three conditions: (1) Functional groups of the typeA react only with those of typeB, and vice versa. (2) Intramolecular reactions do not occur [and therefore only branched-chain (noncyclic) polymers and formed]. (3) Subject to conditions (1) and (2), all functional groups are equally reactive. The derivation employs Stockmayer's statistical mechanical method (first used on Flory'sRA _f model), coupled with a recursion giving the number of distinct polymers which may be assembled fromk units of theA _g RB _f–g type. We also give distributions for a limiting case of theA _g RB _f–g model, the so-calledA _g RB model. This paper completes the solution of the Smoluchowski coagulation equation (monodisperse case) for the kernelsa _ij =A + B(i +j)+ Cij. The proof will be given in another publication.     

RATE OF INTRA-MOLECULAR CONTACT FORMATION IN SHORT TWO-DIMENSIONAL COMPACT POLYMERS CHAINS

It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p(r) of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p(r) of short two-dimensional compact polymers chains may consist of two parts, i.e. p(r) = p1(r) p2(r), where p1(r) and p2(r) are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k(N) ∝ N-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H (hydrophobic) residues in the sequences of compact chains and the energy parameters of εHH, εHP and εPP . Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.     

Modeling of asymmetric membrane formation by dry-casting method

Many polymeric membranes are produced by phase inversion technique invented by Loeb and Sourirajan in 1962. The dry-casting method is one of the major phase inversion techniques in which a homogeneous polymer solution consisting of solvent(s) and nonsolvent(s) is cast on a support and then evaporation of the casting solution takes place under convective conditions. In this paper, we model membrane formation by the dry-casting method. The model takes into account film shrinkage, evaporative cooling, coupled heat, and mass transfer and incorporates practical and reliable diffusion theory as well as complex boundary conditions especially at the polymer solution/air interface. The predictions from the model provide composition paths, temperature, and thickness of the solution. By plotting the composition paths on the ternary phase diagram, we ascertain the general structural characteristics of the membranes prepared from particular casting conditions. The predictive ability of the model was evaluated by comparing the results with the experimental data obtained from gravimetric measurements for cellulose acetate (CA)–acetone–water system. In an attempt to illustrate the importance of diffusion formalism on the predictions, recently proposed multicomponent diffusion theory and its simplified forms were utilized in the model. The computational results show that the critical factor for capturing the accurate behavior of membrane formation is the diffusion formalism utilized in the model.     

A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.     

A generalization of the Rouse-Zimm model

The idea of consistently averaging the hydrodynamic interaction and its various consequences for Hookean dumbbells are reviewed. For long chains this idea can be used to generalize the Rouse-Zimm model for polymer solutions. Unlike the usual Rouse-Zimm model, the new model for steady shear flow predicts a nonzero second normal stress coefficient and shear rate dependent material functions. In the limit of long chains, the viscosity and the normal stress coefficients are universal functions of the reduced shear rate.This paper was presented at the Frühjahrstagung des Fachausschusses Polymerphysik der Deutschen Physikalischen Gesellschaft at Kaiserslautern (West Germany), March 12–14, 1986.