The Many Measures of Molecular Dimensions

In contrast to the high precision with which masses of atoms and molecules can be specified, their external dimensions remain intrinsically fuzzy. Attention is directed to the difference between measurements of interatomic separations within molecules, that in many instances are cited with error bars of +/– 0.002 Å, and the available approximate magnitudes of over-all sizes, needed for estimating packing densities (in solids or liquids). The following account, is a critical examination of the underlying concepts and of the diversity of data in the literature, regarding internal dimensions (bond lengths), overall extensions, cross-sectional areas, and volumes of molecules that may be derived from a variety of experiments. Historical markers of the evolution of the underlying theories and experiments are included.     

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.     

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.     

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.     

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order M?ller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.     

Thermodynamics of liquid Fe-Si and Fe-Ge alloys

The enthalpies of mixing of liquid binary Fe-Ge (1765±5 K) and Fe-Si (1750±5 K) alloys were determined using a high-temperature isoperibolic calorimeter. The thermodynamic properties of Fe-Ge melts were also studied by electromotive force method in the temperature range of 1250-1580 K. The comparison of our measurement results with literature data has been performed. The extreme negative values of integral enthalpy of mixing and alternating-sign deviations from Raoult's low for germanium can be explained by the influence of binary clusters formation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Radical addition reactions: factors determining the transition-state geometry

Interatomic distances in the reaction centers of the addition reactions of (i) H^· to the C=C, C=O, N≡C, and C≡C bonds, (ii) ^·CH₃ radical to the C=C, C=O, and C≡C bonds, and (iii) alkyl, aminyl, and alkoxyl radicals to olefin C=C bonds were determined using a new semiempirical method for calculating transition-state geometries of radical reactions. For all reactions of the type X^· + Y=Z → X— Y—Z^· the r ^# _X...Y distance in the transition state is a linear function of the enthalpy of reaction. Parameters of this dependence were determined for seventeen classes of radical addition reactions. The bond elongation, Δr ^# _X...Y, in the transition state decreases as the triplet repulsion, electronegativity difference between the atoms X and Y in the reaction center, and the force constant of the attacked multiple bond increase. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 894–902, April, 2005.