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.     

Sample capacity in open tubular and micro-packed columns for GC

Equations have been derived from which the maximum sample size which may be loaded on a column without significantly affecting the performance may be calculated. It is shown that micro-packed columns can handle a sample which is as much as forty times larger than that which can be loaded onto wall-coated open tubular columns with comparable conditions.     

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.     

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.     

Generation and rearrangement of a 1-norbornene in pyrolysis of 1-sila-2-oxynorbornanes

Gas phase pyrolysis of 1-sila-2-oxynorbornenes yields a nortricyclene which is proposed to arise from a β-elimination to form a 1-norbornene, which isomerizes to a 2-norbornacylidene which undergoes γ-CH insertion.     

Modeling of stimulated hydrogel volume changes in photonic crystal Pb2+ sensing materials

We modeled the stimulated hydrogel volume transitions of a material which binds Pb2+ and is used as a photonic crystal chemical sensing material. This material consists of a polymerized crystalline colloidal array (PCCA) hydrogel which contains a crown ether molecular recognition group. The PCCA is a polyacrylamide hydrogel which embeds a crystalline colloidal array (CCA) of monodisperse polystyrene spheres of approximately 100 nm. The array spacing is set to diffract light in the visible spectral region. Changes in the hydrogel volume induced by Pb2+ binding alter the array spacing and shift the diffracted wavelength. This system allows us to sensitively follow the hydrogel swelling behavior which results from the immobilization of the Pb2+ by the crown ether chelating groups. Binding of the Pb2+ immobilizes its counterions. This results in a Donnan potential, which results in an osmotic pressure which swells the hydrogel. We continue here our development of a predictive model for hydrogel swelling based on Flory's theory of gel swelling. We are qualitatively able to model the PCCA swelling but cannot correctly model the large responsivity observed at the lowest Pb2+ concentrations which give rise to the experimentally observed low detection limits for Pb2+. These PCCA materials enable stimulated hydrogel volume transitions to be studied.     

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.     

Thermal degradation of fire retardant chloroparaffin-metal compound mixtures: Part II—Bismuth compounds

The mechanisms of reactions which occur on heating mixtures of Bi compounds and a chloroparaffin, which are suitable fire retardant additives for polymers, have been studied.BiCl₃, which is evolved at a high initial rate by reaction of Bi compounds with HCl eliminated by the chloroparaffin, has a strong catalytic effect on the dehydrochlorination process of the chloroparaffin itself. BiCl₃ evolution occurs in a two-stage process: a fast step characterised by a maximum rate at 300°C followed by a slower step which occurs between 300 and 500°C.     

A graph theory data base for storage of chemical structures organized by the block-cutpoint tree technique

The method presented for organizing a data base according to graph theory, is based on representation of chemical structures in terms of BCT (block-cutpoint tree). It is useful for quick substructure searches and is convenient for structure generation. The data base consists of four files: a master file, a bit sequence file of fixed length records which gives block components of compounds, a BCT file which gives the BCT structures of compounds, and a block file which specifies the blocks. These files are organized recursively and hierarchally, which simplifies the processing of structural information on compounds.     

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.     

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.     

Liquid-induced reversible long-spacing changes in polyethylene single crystals and their implications for the fold-surface problem

The long spacing of single-crystal mats of polyethylene was found to increase reversibly on addition of liquids which normally act as swelling agents. The magnitude of the increase follows the sequence of the solvent power which these liquid exhibit at higher temperatures. The increase in long spacing depends to a minor extent on crystallization conditions, such as concentration and crystallization temperature, but increases very markedly with the molecular weight of the polymer. Heat treatment reduces the amount of swelling, even in the range of low treatment temperatures which do not produce a foldlength increase, implying a reorganization of the fold surface. It is inferred that there is a layer along the fold surface which expands by swelling which in turn implies a disordered amorphous component. Nevertheless, such disordered material need not be an intrinsic consequence of chain folding, as its amount can be reduced to insignificant proportions, e.g., by taking molecules which are short but still fold. Thus both, the presence of amorphous disorder and the nonunique nature of such a disorder along the surface is demonstrated. Further implications for the fold-surface problem are discussed.     

Density matrix methods in orbital optimization for MCSCF calculations

The problem considered is that of selecting the finite orbital basis which will minimize the energy in a given size CI calculation. (1) A one-body operator is defined which has as eigenfunctions the desired optimal basis. The operator is defined in terms of the basis which leads to a self-consistency problem of Hartree-Fock type. (2) A method of successive orbital rotations is defined which is shown to have desirable convergence properties.     

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.     

Self-consistent field study of the alignment by an electric field of a cylindrical phase of block copolymer

Self-consistent field theory is applied to a film of cylindrical-forming block copolymer subject to a surface field which tends to align the cylinders parallel to electrical plates, and to an external electric field tending to align them perpendicular to the plates. The Maxwell equations and self-consistent field equations are solved exactly, numerically, in real space. By comparing the free energies of different configurations, we show that for weak surface fields, the phase of cylinders parallel to the plates makes a direct transition to a phase in which the cylinders are aligned with the field throughout the sample. For stronger surface fields, there is an intermediate phase in which cylinders in the interior of the film, aligned with the field, terminate near the plates. For surface fields which favor the minority block, there is a boundary layer of hexagonal symmetry at the plates in which the monomers favored by the surface field occupy a larger area than they would if the cylinders extended to the surface.     

Pulsed laser powered homogeneous pyrolysis: A computational analysis

The use of the pulsed laser powered homogeneous pyrolysis technique for measuring unimolecular decomposition rate constants under unambiguously homogeneous conditions is investigated by numerical simulation of the experiment. The coupled partial differential equations which govern the gas dynamics and chemical kinetics are solved numerically and the results analyzed. Conditions under which rate constants can be extracted from the experimental data using a simplified analysis are determined. The effects of five sources of error in the simplified analysis are computed. A correlation is presented which may be used to correct for overestimation of the rate constant which is inherent in the simple analysis. Conditions under which the other four sources of error become negligible are presented. Overall, it is expected that this technique will be capable of routinely measuring rate constants within a factor of 2, and will do much better when a high power laser with a uniform beam profile is used and/or a well characterized thermal monitor molecule is available which decomposes with kinetic parameters close to that of the reactant being investigated. © 1994 John Wiley & Sons, Inc.     

Spintronics birefringence with an extended molecular loop-wire or spiral coupling

A ring with spin-orbit effects coupled to a conducting wire is shown to exhibit a phase delay which is spin dependent. The key is that the coupling of the ring to the wire is over an extended spatial range and not just along a single point; this breaks the symmetry and makes the ring states couple differently to forward and backward moving wire states. This results, for properly injected spin states, in a spin-flipping probability which is dependent on the energy of the injected electron and can therefore be easily controlled. Several systems are presented and shown to exhibit this effect including the basic ring which couples to a wire as well as a ring which mediates between two wires, and a spiral between two wires.     

A general approach for atom-type assignment and the interconversion of molecular structure files

In molecular modeling projects which require use of several different computer programs, one encounters problems in sharing data between programs. One difficult problem is the conversion of atom types from one program's definition to another. A second problem is the conversion of a polymer, such as a protein or polynucleotide molecule, from a “general” program, which understands molecules as a collection of atoms, to a “polymer” program, which understands molecules as a collection of molecular fragments stored in some library. We describe here a new method by which atom types are deduced from the environment of each atom. We use the Daylight Chemical Information Systems library of programs to deduce the atom types based only on the atomic symbol, connectivity and formal charge of each atom in the molecule. We also describe a method by which the polypeptide nature and sequence of a molecule can be deduced from minimal information about the atoms in the molecule. We have written a computer program which demonstrates this method. This program deduces atom types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will also produce input files for the AMBER/PREP fragment library preparation program.     

Analysis of a Chemostat Model with Variable Yield Coefficient

We investigate a chemostat model in which the growth rate is given by a Monod expression with a variable yield coefficient. This model has been investigated by previous researchers using numerical integration. We combine analytical results with path-following methods. The conditions for washout to occur are found. When washout does not occur we establish the conditions under which the reactor performance is maximised at either a finite or infinite residence time. We also determine the parameter region in which oscillations may be generated in the reactor, which was the primary feature of interest to earlier workers on this problem.