Information-theoretic approach to kinetic-energy functionals: the nearly uniform electron gas

We strengthen the connection between information theory and quantum mechanical systems using a recently developed dequantization procedure which results in a decomposition of the kinetic energy as the sum of a classical term and a purely quantum term. For the nearly uniform electron gas, we thereby approximate the noninteracting kinetic energy as the sum of the Thomas-Fermi term, which is exact for the uniform electron gas, and the Weizsäcker term, which is proportional to the Fisher information. Electron correlation is included via a nonlocal analytical expression which is a functional of the (N-1)-conditional probability density. This expression is evaluated via a statistically rigorous Monte-Carlo procedure to obtain the correlation energy as a functional of the electron density. We show that this functional is well aproximated by a term which is proportional to the Shannon entropy. Thus the kinetic energy is expressed as the standard Thomas-Fermi term plus terms which are proportional to two of the cornerstones of information theory: the Fisher information, which is a measure of localization, and the Shannon entropy, which is a measure of delocalization.     

Psychotropic Preparations Sydnophen and Sydnocarb as Donors of Nitrogen Monoxide

The metabolic chain of the antihypertensive drug Molsydomin, which belongs to the group of sydnonimine derivatives, was modelled in vitro with the psychotropic drugs Sydnophen and Sydnocarb, which are also derivatives of sydnonimine. Like Molsydomin, Sydnophen and Sydnocarb are hydrolyzed to N-nitroso compounds which liberate nitrogen monoxide, NO, on subsequent oxidation which may be related to the pharmacological effects of these drugs.     

Adsorption-entanglement layers in flowing high molecular weight polymer solutions IV. The rates of layer formation and decay

Adsorption-entanglement layers are thick (i. e. multimolecular) layers which form at solid surfaces during flow of high molecular weight polymer solutions. This publication, the final part of the present series, is concerned with the rates at which such layers are formed and at which once formed they decay. It is shown that the rate of layer formation depends linearly on the shear rate applied. It is also demonstrated that the rate at which the layers decay is much slower than the rate at which they form. From the results presented in this paper, together with those in previous parts of this series [1–3], a qualitative model which accounts for the observed behaviour is deduced.     

Sorting biomolecules with microdevices

Micro- and nanofabrication techniques have provided an unprecedented opportunity to create a designed world in which separation and fractionation technologies which normally occur on the macroscopic scale can be optimized by designing structures which utilize the basic physics of the process, or new processes can be realized by building structures which normally do not exist without external design. Since microfabrication is exceedingly sophisticated in its development, it is possible to design and construct highly creative microdevices which allow one to probe specific aspects of biological objects. We give examples of uses of micro- and nanofabrication which, as opposed to simply shrinking the size of the vessels or tubes used in macroscopic lab environments, utilize our understanding of the physics of the process to take advantage of fabrication technologies.     

THREE EXPONENTIAL FLUORESCENCE DECAY OF HORSE LIVER ALCOHOL DEHYDROGENASE REVEALED BY IODIDE QUENCHING

Abstract— The time resolved fluorescence decay of horse liver alcohol dehydrogenase was measured using a frequency doubled picosecond dye laser and time-correlated single-photon counting detection. A flow-cell technique is described which eliminates the photodegradation artifacts which commonly occur with laser excitation. A procedure is introduced which uses fluorescence quenching to reveal minor fluorescence lifetime components. The decay of the unquenched tryptophanyl fluorescence could be described by a double exponential decay law, but experiments conducted in the presence of iodide ion showed that the fluorescence decay must be more complex than this. A model is presented in which the fluorescence decay consists of three exponential components, only two of which are susceptible to quenching by iodide ion. Several possibilities are presented for the origin of this minor decay component, the most reasonable of which is that it arises from conformational heterogeneity in the solvent-exposed tryptophanyl residue.     

Excited Fluorophores Enhance the Opening of Vesicles at Electrode Surfaces in Vesicle Electrochemical Cytometry

Electrochemical cytometry is a method developed recently to determine the content of an individual cell vesicle. The mechanism of vesicle rupture at the electrode surface involves the formation of a pore at the interface between a vesicle and the electrode through electroporation, which leads to the release and oxidation of the vesicle's chemical cargo. We have manipulated the membrane properties using excited fluorophores conjugated to lipids, which appears to make the membrane more susceptible to electroporation. We propose that by having excited fluorophores in close contact with the membrane, membrane lipids (and perhaps proteins) are oxidized upon production of reactive oxygen species, which then leads to changes in membrane properties and the formation of water defects. This is supported by experiments in which the fluorophores were placed on the lipid tail instead of the headgroup, which leads to a more rapid onset of vesicle opening. Additionally, application of DMSO to the vesicles, which increases the membrane area per lipid, and decreasing the membrane thickness result in the same enhancement in vesicle opening, which confirms the mechanism of vesicle opening with excited fluorophores in the membrane. Light‐induced manipulation of membrane vesicle pore opening might be an attractive means of controlling cell activity and exocytosis. Additionally, our data confirm that in experiments in which cells or vesicle membranes are labeled for fluorescence monitoring, the properties of the excited membrane change substantially.     

Hydrophilic-interaction chromatography of peptides on hydrophilic and strong cation-exchange columns

Hydrophilic-interaction chromatography (HILIC) was recently introduced as a potentially useful separation mode for the purification of peptides and other polar compounds. The elution order of peptides in HILIC, which separates solutes based on hydrophilic interactions, should be opposite to that obtained in reversed-phase chromatography, which separates solutes based on hydrophobic interactions. Three series of peptides, two of which consisted of positively charged peptides (independent of pH at pH less than 7) and one of which consisted of uncharged or negatively charged peptides (dependent on pH), and which varied in overall hydrophilicity/hydrophobicity, were utilized to examine the separation mechanism and efficiency of HILIC on hydrophilic and strong cation-exchange columns.     

The signal vs. concentration relationships in fluorimetry

Formulae for the fluorescence signal are derived which take into account some factors hitherto neglected. From these formulae conditions are deduced, for which a linear relationship exists between the concentration of the fluorescent components and the intensity of the fluorescence. In some cases of practical interest the fulfilment of these conditions cause too low a sensitivity. For such cases a method of optimization is outlined, by means of which the conditions are found which lead to the least deviation from linearity at the required sensitivity.     

A Process Theory of Enzyme Catalytic Power – the Interplay of Science and Metaphysics

Enzymes are protein catalysts of extraordinary efficiency, capable of bringing about rate enhancements of their biochemical reactions that can approach factors of 10²⁰. Theories of enzyme catalysis, which seek to explain the means by which enzymes effect catalytic transformation of the substrate molecules on which they work, have evolved over the past century from the “lock-and-key” model proposed by Emil Fischer in 1894 to models that explicitly rely on transition state theory to the most recent theories that strive to provide accounts that stress the essential role of protein dynamics. In this paper, I attempt to construct a metaphysical framework within which these new models of enzyme catalysis can be developed. This framework is constructed from key doctrines of process thought, which gives ontologic priority to becoming over being, as well as tenets of a process philosophy of chemistry, which stresses environmentally responsive molecular transformation. Enzyme catalysis can now be seen not as enzyme acting on its substrate, but rather as enzyme and substrate entering into a relation which allows them to traverse the reaction coordinate as an ontologic unity.     

The mass spectra of griseofulvin analogues. Characteristic fragmentation processes in the mass spectra of spiro-cyclohexenones and spiro-cyclohexanones containing the griseofulvin skeleton

The mass spectra of a number of griseofulvin analogues have been examined and the fragmentations, which are characteristic of the basic skeleton of the molecule, have been determined. In all of the different structural types examined, the ring cleavages which predominate are found tol occur by fission of one or more of the bonds attached to the spiro carbon atom. The degree of unsaturation in the spiro-cyclohexane ring system is found to controll the type of fragmentation which occurs and the type of ring system which is present can therefore be identified by its mass spectrum.     

大豆分离蛋白改性的研究进展

首先介绍了大豆分离蛋白的基本组成与结构,然后分别从化学改性、酶改性和物理改性三个方面对大豆分离蛋白改性进行了综述.其中,在化学改性方面,针对大豆分离蛋白中含有的氨基、羧基、巯基等不同活性基团的改性原理及研究现状进行了介绍.在酶改性方面,主要介绍了谷胺酰胺转胺酶、木瓜蛋白酶等对大豆分离蛋白的改性作用.在物理改性方面,介绍了共混、加热改性等目前研究较多的方法.通过化学、物理和酶等方法等来引起分子结构的微变化,可使人们获得各种符合预期的性能优良的产品,开发其在医药、化工等领域的应用潜力.     

Epsilon -N,N,N-trimethyllysine-specific ions in matrix-assisted laser desorption/ionization-tandem mass spectrometry

Epsilon -N,N,N-trimethyllysine (K(me3)) is a component of a number of proteins and plays an important role in the expression of their biological functions. Trimethylation, which causes an incremental increase in mass of 42.0470 Da from that of the corresponding MH(+) ion, cannot be distinguished from the acetylation (+42.0106 Da), which also occurs on epsilon-amino groups of Lys or alpha-amino groups in many proteins, without high-accuracy mass measurement which is accurate to within the second decimal place. MALDI-MS and MS/MS have been applied for the analyses of post-translational modifications of histone H3, which is known to contain both multiple acetylation and methylation sites in its sequence. During the measurements of the modified peptides, a novel fragmentation which involves the loss of trimethylamine from K(me3) was found. This characteristic fragmentation, which was observed to produce ions separated by 59 Da from the conventional precursor ion or sequence ions, would be useful for probing K(me3) units in the sequence.     

The formation of low-dimensional inorganic nanotube crystallites in carbon nanotubes

The filling of carbon nanotubes, which vary in diameter and morphology, is directly observed by molecular dynamics computer simulation with a potential model which thermodynamically favors a four-coordinate bulk crystal structure. Inorganic nanotube (INT) structures form which are based on percolating hexagonal nets. For small carbon nanotube diameters the filling is shown to proceed via an "internal wetting" mechanism, which depends on the internal carbon nanotube area rather than the free volume. Both single- and double-walled INTs are predicted to form. The atomistic formation mechanisms are discussed and an intermediate structure identified. The INT structures, including the observed intermediate, are discussed by reference to a simple energy landscape. The formation energetics are discussed in terms of a simple analytical model which combines the INT strain energy and the tube-tube interactions. An effective phase diagram, which predicts the INT morphologies as a function of carbon nanotube diameter, is derived and discussed with respect to the analytical model.     

An automated method for predicting the positions of hydrogen-bonding atoms in binding sites

Hydrogen bonds are the most specific, and therefore predictable of the intermolecular interactions involved in ligand–protein binding. Given the structure of a molecule, it is possible to estimate the positions at which complementary hydrogen-bonding atoms could be found. Crystal-survey data are used in the design of a program, HBMAP, that generates a hydrogen-bond map for any given ligand, which contains all the feasible positions at which a complementary atom could be found. On superposition of ligands, the overlapping regions of their maps represent positions of receptor atoms to which each molecule can bind. The certainty of these positions is increased by the incorporation of a larger number and diversity of molecules. In this work, superposition is achieved using the program HBMATCH, which uses simulated annealing to generate the correspondence between points from the hydrogen-bonding maps of the two molecules. Equivalent matches are distinguished on the basis of their steric similarity. The strategy is tested on a number of ligands for which ligand–protein complexes have been solved crystallographically, which allows validation of the techniques. The receptor atom positions of thermolysin are successfully predicted when the correct superposition is obtained.     

SSC: a tool for constructing libraries for systematic screening of conformers

Even a relatively small molecule with 10-20 atoms might have a few local minima, which correspond to different conformers. The number of local minima quickly increases with molecular size and the most common algorithms, driven by calculated forces, frequently identify a minimum, which is closest to the initial structure, rather than the most stable conformer. Here we discuss how to perform a systematic search of the conformational space for a chain-like molecule. Our approach is fully automated and a user has control which chemical bonds will be probed and with which increments. Moreover, whole fragments of the molecule, which are adjacent to each selected rotational bond, are rotated in a properly selected cylindrical coordinate system and unchemical hybridizations and some "clashes" between neighboring groups, which are common when standard Z-matrices are used, are avoided. A library of potentially relevant conformers is created with a tool, which we call SSC, denoting Systematic Screening of Conformers. Each member of the library is prescreened at a predefined level of theory and the most promising conformers are identified. Finally, they are further evaluated at a higher level of theory to identify the most stable structures and their physicochemical properties. As an example, we demonstrate the results of this approach for 2'-deoxycytidine.     

Elastomer reinforcement from a glassy polymer polymerized in situ

Cross-linked networks of poly(dimethylsiloxane) were swelled with styrene containing benzoyl peroxide. Polymerization of the styrene in situ, by increasing the temperature, gave novel elastomeric composites. Scanning electron micrographs suggest that low concentrations of styrene (～ 14 wt.%) gave primarily low-molecular-weight polystyrene (PS), which acted merely as a diluent in the networks. Larger amounts gave PS which phase separated into glassy particles having diameters in the approximate range 0.05–1.5 μm. In these cases, an increase in wt.% PS gave networks showing large increases in ultimate strength, which was to be expected. Surprisingly, there were also increases in maximum extensibility, which usually decreases in response to modifications which increase the ultimate strength.     

In Process Citation

The variation in heat capacity and the thermal shifts which accompany a thermometric determination make the thermogram, even in the case of a very rapid and irreversible reaction, hyperbolic instead of formed of straight segments. These departures from linearity, which are inconvenient in the interpretation and exploitation of the thermograms, can be calculated as a function of the degree of titration. The relation obtained introduces a parameter which the authors call the apparent change of capacity at the equivalence point, and which takes into account the two causes of deviation from linearity. This relationship is confirmed experimentally.     

Unprecedented Coordination-Induced Bright Red Emission from Group 12 Metal-Bound Triarylazoimidazoles

Arylazoimidazoles are important dyes which were intensively studied in the past. In contrast, triarylazoimidazoles (derivatives which carry aryl substituents at the imidazole core) received almost no attention in the scientific literature. Here, we report a new family of simple and easily accessible triarylazoimidazole-group 12 metal complexes, which feature highly efficient photo-luminescence emission (Φ up to  0.44). Novel compounds exhibit bright red emission in solution, which could be excited with a visible light.     

The origin of life

The theory of the evolution of the species, which is today widely accepted, requires a starting point. It is postulated that the biological starting point could have emerged only if chemical evolution had preceded it. Experiments are described which show the formation of organic substances from inorganic gases under conditions which prevailed on earth in the prebiotic era; also demonstrated is the polymerization of such organic substances into biological macromolecules. Hypotheses are discussed whereby these macromolecules could be transformed into dynamic structures which might finally lead to self-reproduction.