硼烷缺电子多中心桥键的H-F力研究

Hellmann-Feynman静电力表现了分子中电荷分布及对各原子核的作用。H-F力的方向性可描述电子电荷的数量和位置,具有定量、形象和直观的特点,已在弯键的研究中显示出来。这一方法尚可用于多中心缺电子桥键的研究。 1 理论与方法 按LCAO-MO理论对H-F力进行分解,除有重叠力、极化力和屏蔽力外,还有一     

A method to construct polyelectrolyte multilayers film containing gold nanoparticles

Gold nanoparticles in polyelectrolyte multilayers film can be easily prepared by repeating immersion of a substrate in poly(diallyl dimethylammonium) chloride (PDDA)-AuCl₄⁻ complexes solution followed by reduction Au³⁺ through heating. UV-vis spectroscopy, cyclic voltammetry (CV) and tapping-mode atomic force microscopy (AFM) are used to confirm the successful construction of the polyelectrolyte multilayers film and the formation of gold nanoparticles. The multilayers film shows electrocatalytic activity to dioxygen reduction.     

Scanning force microscopy and amplitude versus distance measurements on single‐crystal oxide surfaces

Dynamic mode imaging and investigations on amplitude versus distance measurements were carried out on surfaces of single‐crystal; SrTiO₃, Al₂O₃ and LaAlO₃. Experiments were performed to optimize the imaging parameters for surfaces having varying elastic properties. The dependence of the amplitude–distance curve on different materials and the amplitude of oscillation was investigated. For SrTiO₃, a low‐drive amplitude provided the linear region necessary for imaging. A large amplitude of oscillation, however, created dips in the amplitude–distance curves, presumably due to complications in the tip dynamics such as bifurcation, period doubling, etc. In the case of Al₂O₃ and LaAlO₃, amplitude–distance curves were characterized by oscillations for lower tip sample separations and step‐like discontinuities in the stiff region. The magnitude of the oscillations and discontinuities was found to decrease with amplitude and eventually could be eliminated. Thus, for these samples a large amplitude of the cantilever provided the linear region required for imaging. It was observed also that two different surfaces of Al₂O₃ (c‐cut and r‐cut) yield totally different amplitude–distance curves consistent with their standard differences. The results indicate the complex behaviour of amplitude–distance curves, which not only vary from one sample to another but from one surface to another for a given sample. Copyright © 2004 John Wiley & Sons, Ltd.     

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Single polymer molecules adsorbed to mica and the oppositely charged polymer/surfactant complexes formed at the air–water interface visualized by atomic force microscopy

In the present study, the structure and morphology of single sodium poly(styrenesulfonate) (PSS) molecules adsorbed to mica surface from the natural aqueous solution is investigated using atomic force microscopy technique. Results show that single PSS molecules are observed which show a morphology of wormlike coils. Meanwhile, single sodium poly(styrenesulfonate) (PSS)/Hexadecyltrimethylammonium bromide (CTAB) complexes deposited on mica from the air–water interface are also observed. However, the PSS/CTA⁺ complexes show different conformations by appearing in the morphology of circular patches. Experimental data are in fair agreement with the theoretical analysis.     

A quantitative method for dual‐pass electrostatic force microscopy phase measurements

Electrostatic force microscopy (EFM) has become a powerful tool for investigating charges on surfaces. The use of phase measurement in EFM is a direct and fast way to detect electrostatic force gradients, but only qualitatively. With the dual‐pass scheme, the phase signal at lifted height is often assumed to exclude any influences from the topography, but it does not. We report the collection of both topography and phase data by EFM on charged, micron‐sized metal wires. In order to quantify the electrostatic force, a cone model and finite element analysis are provided to integrate the force gradient from the phase signal. Copyright © 2007 John Wiley & Sons, Ltd.     

HDDR过程中三元和多元Nd-Fe-B合金磁畴结构的MFM研究

用磁力显微镜研究了三元Nd-Fe-B合金在HDDR过程的不同阶段(铸态、不充分吸氢歧化、充分吸氢歧化和脱氢再复合)的破畴结构。在铸态样品表面清楚地观察到了易磁化轴互相垂直的柱状晶表面的两类磁畴图型。当样品不充分吸氢歧化和充分吸氢歧化时，破畴结构明显发生变化，反映了Nd-Fe-B的分解产物NdH2，α-Fe和Fe2B及其微晶结构的变化。脱氢再复合后形成的微晶的磁畴结构则表明样品保留了铸态样品柱状晶的构型。此外，还对比研究了多元Nd-Fe-B合金在HDDR过程中的磁畴结构，并根据微磁结构分析，指出过量的Ga元素添加可抑制Nd2(Fe，M)14B相的吸氢歧化，从而导致相应HDDR粘结磁体性能降低。     

A case study in conformation design: learning by doing

Efforts are described to design simple, fully flexible but conformationally preorganised omega-hydroxy-nonanoic acids that could serve as the conformation controlling unit in analogues of the potent protein-kinase C activator aplysiatoxin. Such analogues are macrodilactones incorporating the designed omega-hydroxy-nonanoic acid and 3,4-dihydroxy-pentanoic acid, which contains the pharmacophoric groups. The design process (replacement of CH(2) groups by an oxygen atom, annelation of a six-membered ring and placement of alkyl substituents) of the omega-hydroxy-nonanoic acids was monitored by force-field calculations. In the end of this process simple analogues of aplysiatoxin are proposed in which the proper disposition of the pharmacophoric groups is secured by a conformationally flexible but preorganised template structure as part of the macrodilactone ring.     

ELASTIC BEHAVIOR OF PROTEIN-LIKE SINGLE CHAIN

The conformational properties and elastic behaviors of protein-like single chains in the process of tensile elongation were investigated by means of Monte Carlo method. The sequences of protein-like single chains contain two types of residues: hydrophobic (H) and hydrophilic (P). The average conformations and thermodynamics statistical properties of protein-like single chains with various elongation ratio λ were calculated. It was found that the mean-square end-to-end distance r increases with elongation ratio,λ. The tensor eigenvalues ratio of : decreases with elongation ratio λ for short (HP)x protein-like polymers, however, the ratio of : increases with elongation ratioλ,especially for long (H)x sequence. Average energy per bond increases with elongation ratioλ, especially for(H)x protein-like single chains. Helmholtz free energy per bond also increases with elongation ratioλ. Elastic force (f), energy contribution to force (fU) and entropy contribution to force (fs) for different protein-like single chains were also calculated.These investigations may provide some insights into elastic behaviors of proteins.     

Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes

Summary A computer procedure TFIT, which uses a molecular superposition force field to flexibly match test compounds to a 3D pharmacophore, was evaluated to find out whether it could reliably predict the bioactive conformations of flexible ligands. The program superposition force field optimizes the overlap of those atoms of the test ligand and template that are of similar chemical type, by applying an attractive force between atoms of the test ligand and template which are close together and of similar type (hydrogen bonding, charge, hydrophobicity). A procedure involving Monte Carlo torsion perturbations, followed by torsional energy minimization, is used to find conformations of the test ligand which cominimize the internal energy of the ligand and the superposition energy of ligand and template. The procedure was tested by applying it to a series of flexible ligands for which the bioactive conformation was known experimentally. The 15 molecules tested were inhibitors of thermolysin, HIV-1 protease or endothiapepsin for which X-ray structures of the bioactive conformation were available. For each enzyme, one of the molecules served as a template and the others, after being conformationally randomized, were fitted. The fitted conformation was then compared to the known binding geometry. The matching procedure was successful in predicting the bioactive conformations of many of the structures tested. Significant deviation from experimental results was found only for parts of molecules where it was readily apparent that the template did not contain sufficient information to accurately determine the bioactive conformation.