Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.     

煤的孔结构特征对水煤浆性质的影响

本文选用１７种不同变质程度的中国煤，详细研究了煤孔结构特征对煤浆性质的影响。发现煤孔体积通过影响煤在分散体系中的吸水性，从而影响煤之成浆性。但由于不同变质程度煤表面亲水性的显著差异，煤孔体积在影响煤成浆性的能力方面差别很大，这使得煤吸水性和浆体最高煤浓度与煤孔体积并不存在直接的相关性，而是取决于煤孔体积Ｖ和以煤－水接触角（θ）的余弦值表示的煤表面亲水性因子的乘积，即煤之有效孔体积：Ｖ×ｃｏｓ（θ／     

Flexibility and Rigidity of Proteins and Protein–Pigment Complexes

Proteins may be rigid or flexible to various degrees as required for optimal function. Flexibility of large parts of a protein, which rearrange or move, is particularly interesting and will be discussed in this article. We differentiate between several categories, although the boundaries between them are diffuse: flexibility of peptide segments, order–disorder transitions of spatially contiguous regions, and domain motions. The domains may be flexibly linked to allow rather unrestricted motions or the motions may be constrained to certain modes. The various categories of large-scale flexibility will be illustrated with the following examples: (1) Small protein proteinase inhibitors are rather rigid molecules which provide binding surfaces complementary to their cognate proteases but show also limited segmental flexibility and adaptation. (2) Large plasma proteinase inhibitors exhibit large conformational changes after interaction with proteases probably for regulatory purposes. (3) Pancreatic serine proteases employ a disorder–order transition of their activation domain as a means to regulate enzymic activity. (4) Immunoglobulins show rather unrestricted and also hinged domain motions in different parts of the molecule probably to allow binding to antigens in different arrangements. (5) Citrate synthase adopts open and closed forms by a hinged domain motion to bind substrates and release products and to perform the catalytic condensation reaction, respectively. (6) Riboflavin synthase, a bifunctional multienzyme complex, catalyzes two consecutive reactions by means of two subunits, α and β. The β-subunits form a shell, in which the α-subunits are enclosed. Diffusional motion of the catalytic intermediates is therefore restricted. In addition, rearrangement of the N-terminal segment occurs during the assembly of the β-subunit. In contrast, rigidity is dominant in the structures of the light-harvesting complexes and the photosynthetic reaction centers involved in photosynthetic light reactions. These are large protein–pigment complexes in which the proteins serve as matrices to hold the pigments in the appropriate conformation and relative arrangement. Since motion would contribute to deactivation of the photoexcited states of the pigments and diminish the efficiency of light-energy and electron transfer, the functional role of rigidity is easy to rationalize for these proteins.     

Fourth-order diagrammatic MB-RSPT calculations of the interaction energy between two helium atoms

The efficiency of the MB-RSPT in the calculations of the correlation contributions to the interaction energies was investigated, using He₂ as a model Van der Waals system. The attention has been focused on the convergency of the perturbation expansion in the calculations of the interaction energy and on the analysis of the fourth-order terms of MB-RSPT. The rôle of the renormalization term in the correct long-range behaviour of the interaction potential has been emphasized.     

Micro construction of poly(epsilon-caprolactone)/poly(L-lactic acid) blend film by solution casting under microwave irradiation

The micro construction of poly(epsilon-caprolactone) (PCL) and poly(L-lactic acid) (PLLA) blend films fabricated by solution casting under microwave irradiation was investigated by selective enzymatic degradation and scanning electron microscopy (SEM). The results were totally different from the blends obtained by conventional methods. The blend was more homogeneous and the PCL continuous phase more compact as no spherulites and tiny zone separation were observed from the film surface and no PCL network was observed inside the film, and the degradation of a PCL plank by Pseudomonas lipase was significantly retarded. The distributed PLLA micro spheres were enlarged and amorphous. The thermal behavior of the blend by microwave heating revealed that PCL and PLLA underwent a melting process, which induced the variations of the PCL phase and PLLA spheres. The weight loss caused by degradation of the PCL/PLLA blend obtained by conventional methods (B50c) is greater than that of the blend obtained by microwave methods (B50m), which reflects the change in morphology from a loose PCL network (B50c) to a dense PCL plank (B50m).     

制备方法对WO_3/ZrO_2结构的影响

用XRD、比表面测定、LRS定性和定量的方法对用Zr（OH）4和已晶化的ZrO2作载体制得的两类WO3／ZrO2催化剂进行了表征．揭示了样品比表面、载体物相、活性组分的存在状态与制备方法、WO3含量、焙烧温度之间的关系．结果表明，WO3能单层分散在ZrO2上；单层覆盖在Zr（OH）4上的WO3使载体在焙烧时晶粒生长受阻，形成介稳的四方ZrO2，并阻止载体微粒间的烧结，使从Zr（OH）4出发制得的WO3／ZrO2比表面明显增大，在WO3含量达到单层分散容量时以上作用表现得最充分；WO3与Zr（OH）4（或四方ZrO2）在高温（～800℃）可能发生了某种化学结合，开创出超强酸位．用以上观点可对文献中已报导的主要实验事实作出较满意的解释.     

Electron and light microscopical investigation of defect structures in mesophases of pharmaceutical substances

 Transmission electron microscopy of freeze fractured and replicated samples (TEM) and polarizing light microscopy (PLM) are used to investigate the defect structures of the thermotropic and lyotropic mesophases of the non-steroidal antiinflammatory drug fenoprofen sodium and of the thermotropic mesophase of the nonionic surfactant sucrose oleate (O1570). All mesophases have a layered, smectic structure. The thermotropic liquid crystal of feno-profen sodium is an interdigitated smectic A phase (smectic Ad) having the highest viscosity of the investigated samples. The thermotropic mesophase of the sugar ester is also of the type smectic A, likely to be of subtype smectic A2 (bilayered smectic structure). The lyotropic mesophase is of lamellar liquid crystalline nature and has a much lower viscosity than the thermotropic mesophases. In the PLM the lyotropic fenoprofen mesophase has a strong tendency to form a pseudoisotropic texture, indicating a strong tendency to form undisturbed layered structures. Other textures exhibited in the PLM are fan-shaped texture and maltese-cross texture. Confocal domains, cylinders, pits and peaks as well as screw dislocations are found in great number in the TEM. However, no greater regions of undisturbed lamellar arrangement in the lyotropic mesophase could be detected. The only texture of the thermotropic fenoprofen mesophase visible in the PLM is the fan-shaped texture, indicating confocal domains as predominant structural elements. However, no confocal domains (tori or Dupin cyclides) are found in the TEM. In the PLM the sugar–ester mesophase exhibited a fan-shaped texture, maltese crosses and oily streaks as dominant textures. In the TEM only a few +π and −π disclinations and imperfect confocal domains could be detected. The discrepancies in the appearance of defect structures and textures between the mesophases as well as the discrepancies in the findings in the PLM and in the TEM investigations are caused by the different sample preparation and the different viscosities of the mesophases. Received: 28 May 1997 Accepted: 2 September 1997     

Spin density distributions in radical anions of heterocyclic amine N-oxides

The unrestricted Hartree-Fock (UHF) method of Snyder and Amos is used to calculate, in the -electron approximation, the spin density distributions in radical anions of heterocyclic amine N-oxides. The computed spin densities are observed to be in good agreement with the experimental values. The computed spin density distribution of the radical anion of pyridine N-oxide is consistent with the greater susceptibility of pyridine N-oxide relative to pyridine to electrophilic nitration. Also, the calculations are consistent with the lower basicity of the N-oxides relative to the parent bases.     

Kinetics of no decomposition over Cu/ZSM-5 catalyst

The kinetics of catalytic decomposition of NO over Cu/ZSM-5 catalyst has been studied in an integral flow reactor at atmospheric pressure. Kinetic analysis is based on the assumption that the surface reaction represents the rate-determining step. On the basis of theoretical considerations of different interactions between reactants and catalyst, and experimental evidences, three different mechanistic kinetic models were chosen. Also a power-law model was tested. The best agreement has been achieved with the model