Electron localization functions and local measures of the covariance

The electron localization measure proposed by Becke and Edgecombe is shown to be related to the covariance of the electron pair distribution. Just as with the electron localization function, the local covariance does not seem to be, in and of itself, a useful quantity for elucidating shell structure. A function of the local covariance, however, is useful for this purpose. A different function, based on the hyperbolic tangent, is proposed to elucidate the shell structure encapsulated by the local covariance; this function also seems to work better for the electron localization measure of Becke and Edgecombe. In addition, we propose a different measure for the electron localization that incorporates both the electron localization measure of Becke and Edgecombe and the Laplacian of the electron density; preliminary indications are that this measure is especially good at elucidating the shell structure in valence regions. Methods for evaluating electron localization functions directly from the electron density, without recourse to the Kohn-Sham orbitals, are discussed.     

More on basis set quality tests

The quality measure δ of Sordo and Pueyo is computed for 94 orbital basis sets for the atomic helium Hartree-Fock problem and compared with various information theoretic quality measures reported previously by us for this data base. δ is in error often enough that it is unlikely to be a useful general purpose measure.     

A proof of the triangle inequality for the Tanimoto distance

A distance, or dissimilarity measure, can be defined based on the Tanimoto coefficient, a similarity measure widely applied to chemical structures. A new, simple proof that this distance satisfies the triangle inequality is presented. This revised version was published online in July 2006 with corrections to the Cover Date.     

Adequacy and Inadequacy in the Metrology of Chemical Analysis

The adequacy (inadequacy) of samples to each other and reference materials to test samples is an important notion in the metrology of chemical analysis. However, the literature gives no strict definition for this notion. In this paper, it was proposed to determine adequacy based on the measure of inadequacy. For the case of two samples, the measure of inadequacy is the absolute value of the difference between the systematic errors of the results of analyses of the samples; it depends on the difference in the composition and properties of the samples. The measure of inadequacy of a standard reference material to a series of test samples is the maximum distance between the systematic error of the reference material and one of the quantiles of the systematic error distribution of the test samples Q(0.025); Q(0.975); the errors in this case are due to the composition and the properties of the test samples. The samples are considered adequate if the measure of inadequacy can be neglected compared to the normalized error of the analysis. Using the determination of total cholesterol in the blood serum of humans as an example, it was shown that the standard reference material in the analysis of samples of complex composition is often inadequate to test samples.     

Informationsgehalt analytischer Ergebnisse

A general measure for the amount of informationI(p,p ₀) is defined, which allows to determine the relationships specific for different cases of probability distribution before carrying out the analysisp ₀ (x) and after it has been carried outp(x). The relation of this general measure to the Shannon measure of amount of information is discussed and it is demonstrated that the Shannon measure is a special case of the general one for rectangularp ₀ (x).     

A spectral similarity measure using Bayesian statistics

A spectral similarity measure was developed that can differentiate subtle differences between two spectra. The spectra are digitalized into a vector. The difference between the two spectra is defined by a difference vector, which is one spectrum minus the other. The spectral similarity measure is transformed into a hypothesis test of the similarities and differences between the two spectra. The scalar mean of the difference vector is used as the statistical variable for the hypothesis test. A threshold for the hypothesis that the spectra are different was proposed. The Bayesian prior odds ratio was estimated from multiple spectra of the same sample. The posterior odds ratio was used to quantity the spectral similarity measure of the two spectra. Diffuse reflectance near-infrared spectra of tobacco samples of two formulations were used to demonstrate this method. The results show that this new method can detect subtle differences between the spectra.     

Measuring silver nanoparticle dissolution in complex biological and environmental matrices using UV-visible absorbance

Distinguishing the toxic effects of nanoparticles (NPs) themselves from the well-studied toxic effects of their ions is a critical but challenging measurement for nanotoxicity studies and regulation. This measurement is especially difficult for silver NPs (AgNPs) because in many relevant biological and environmental solutions, dissolved silver forms AgCl NPs or microparticles. Simulations predict that solid AgCl particles form at silver concentrations greater than 0.18 and 0.58 μg/mL in cell culture media and moderately hard reconstituted water (MHRW), respectively. The AgCl NPs are usually not easily separable from AgNPs. Therefore, common existing total silver techniques applied to measure AgNP dissolution, such as inductively coupled plasma mass spectrometry (ICP-MS) or atomic absorption, cannot accurately measure the amount of silver remaining in AgNP form, as they cannot distinguish Ag oxidation states. In this work, we introduce a simple localized surface plasmon resonance (LSPR) UV–visible absorbance measurement as a technique to measure the amount of silver remaining in AgNP form for AgNPs with constant agglomeration states. Unlike other existing methods, this absorbance method can be used to measure the amount of silver remaining in AgNP form even in biological and environmental solutions containing chloride because AgCl NPs do not have an associated LSPR absorbance. In addition, no separation step is required to measure the dissolution of the AgNPs. After using ICP-MS to show that the area under the absorbance curve is an accurate measure of silver in AgNP state for unagglomerating AgNPs in non-chloride-containing media, the absorbance is used to measure dissolution rates of AgNPs with different polymer coatings in biological and environmental solutions. We find that the dissolution rate decreases at high AgNP concentrations, 5 kDa polyethylene glycol thiol coatings increase the dissolution rate, and the rate is much higher in cell culture media than in MHRW.     

A novel k-word relative measure for sequence comparison

In order to extract phylogenetic information from DNA sequences, the new normalized k-word average relative distance is proposed in this paper. The proposed measure was tested by discriminate analysis and phylogenetic analysis. The phylogenetic trees based on the Manhattan distance measure are reconstructed with k ranging from 1 to 12. At the same time, a new method is suggested to reduce the matrix dimension, can greatly lessen the amount of calculation and operation time. The experimental assessment demonstrated that our measure was efficient. What's more, comparing with other methods’ results shows that our method is feasible and powerful for phylogenetic analysis.     

Towards a quantitative definition of perfection in chromatographic analyses

The paper published by Ghaoui and Rothman [J. High Resolut. Chromatogr. 15 (1992) 36] and particularly its Fig. 5, is further considered here because it contains the germ of an idea of how to measure improvements to a chromatographic method, and how to define the goal of perfection in terms of "zero defects" as required by quality assurance schemes. From this, a new role emerges for signal averaging in capillary chromatography: a role to quantify and measure method improvements, and one which can be generally applied to measure improvements in instrument design too.     

Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions

Thermodynamic integration is a widely used method to calculate and analyze the effect of a chemical modification on the free energy of a chemical or biochemical process, for example, the impact of an amino acid substitution on protein association. Numerical fluctuations can introduce large uncertainties, limiting the domain of application of the method. The parametric energy function describing the chemical modification in the thermodynamic integration, the "Alchemical path," determines the amplitudes of the fluctuations. In the present work, I propose a measure of the fluctuations in the thermodynamic integration and an approach to search for a parametric energy path minimizing that measure. The optimal path derived with this approach is very close to the theoretical minimum of the measure, but produces nonergodic sampling. Nevertheless, this path is used to guide the design of a practical and efficient path producing correct sampling. The convergence with this practical path is evaluated on test cases, and compares favorably with that of other methods such as power or polynomial path, soft-core van der Waals, and some other approaches presented in the literature.     

Application of high-performance liquid chromatography based measurements of lipophilicity to model biological distribution

Octanol-water partition coefficients are the most widely used measure of lipophilicity in modelling biological partition/distribution. It has long been recognised that the retention of a compound in reversed-phase liquid chromatography is governed by its lipophilicity/hydrophobicity, and thus shows correlation with an octanol-water partition coefficient. A great number of publications have reported the efforts made to adjust HPLC conditions to measure surrogate octanol-water partition coefficients. However, there is no general consensus in this field. HPLC provides a platform to measure various types of lipophilicity that can provide relevant information about the compounds' property. In this way HPLC can be more valuable than just a surrogate for octanol-water partition. Chromatography using biomimetic stationary phases may provide better insight for biological partition/distribution processes. The research in this field is still ongoing and a large variety of HPLC conditions have been suggested. This review will outline approaches to overcoming the difficulties of standardisation and describe different theoretical approaches for comparison of HPLC lipophilicity data obtained under various conditions, along with the relation of these results to biological partition/distribution.     

Solid angles 5. Chiral molecules and the case of face selectivity

In this paper we present the analytical algorithm to calculate the solid angle of a collection of spheres in a hemisphere and quadrant. The methodology is a reliable and useful measure of partial steric congestion and can readily be applied to chiral and pro-chiral molecules. This algorithm lays the foundation for the application of a steric measure to the prediction of diastereomeric and enantiomeric excess.     

Enantiomeric excesses and electronic chirality measure

We present an approach to measure the amount of chirality in the electronic wave function and apply it to the study of a set of asymmetric aminohydroxylation reactions. The correlation coefficient between the chirality measure and the enantiomeric excesses is larger than 0.9 and suggests that this phenomenological approach can be a valuable tool to investigate and, perhaps in the future, design asymmetric synthesis.     

一种新型密度计及水、丙酮、4-甲基-2-戊酮(MIBK)三元混合物 的密度测定

我们设计了一种小型密度计,它用螺旋测微计作体积置换泵,可测到3×10^-^4mL的体积变化。实验时仅需8mL样品便可精确测定各温度下的密度,其精度≤2×10^-^4g/mL,而且操作简单,用该装置测定了293.15-323.15K水、丙酮、MIBK及相应的二元、三元体系的液体密度,并进行了关联。     

Determination of vapor pressures using gas chromatography

The determination of vapor pressures, p0, of compounds with low vapor pressures (10(-8) Pa < p0 < 10(3) Pa) is becoming increasingly important as a result of the need to measure p0 for environmentally sensitive compounds such as organophosphorus pesticides, biphenyls, dioxins and alkylbenzenes. Under strict conditions, the components of gas-liquid chromatography (GLC) (a volatile solute, an involatile solvent and a mobile carrier gas) are in equilibrium and as a result it is possible to use the technique to measure equilibrium properties such as vapor pressure. The technique is rapid, reliable and reproducible. These advantages have tempted many workers to measure physiochemical properties, including vapor pressures, under conditions for which the basic theories do not hold. In this review, the GLC techniques used to measure vapor pressures from GLC data together with the basic theory, limitations of the techniques and some recent measurements are discussed.     

Topological characterization of crystallization of gold nanoclusters

In this study we use a new topological structure measure to analyze the local environment of 923 atom gold clusters quenched from the melt, at various quench rates, by molecular dynamics. The crystallization and geometrical rearrangements of the core atoms upon freezing can be clearly observed using our structure measure which is based on planar graphs. Our results support the hypothesis that crystallization is initiated from the surface and proceeds into the cluster core.     

Rapid measurement of three-dimensional diffusion tensor

In this article, the authors demonstrate a rapid NMR method to measure a full three-dimensional diffusion tensor. This method is based on a multiple modulation multiple echo sequence and utilizes static and pulsed magnetic field gradients to measure diffusion along multiple directions simultaneously. The pulse sequence was optimized using a well-known linear inversion metric (condition number) and successfully tested on both isotropic (water) and anisotropic (asparagus) diffusion systems.     

Communication: Exciton-phonon information flow in the energy transfer process of photosynthetic complexes

Non-Markovian and nonequilibrium phonon effects are believed to be key ingredients in the energy transfer in photosynthetic complexes, especially in complexes which exhibit a regime of intermediate exciton-phonon coupling. In this work, we utilize a recently developed measure for non-Markovianity to elucidate the exciton-phonon dynamics in terms of the information flow between electronic and vibrational degrees of freedom. We study the measure in the hierarchical equation of motion approach which captures strong coupling effects and nonequilibrium molecular reorganization. We propose an additional trace distance measure for the information flow that could be extended to other master equations. We find that for a model dimer system and for the Fenna-Matthews-Olson complex the non-Markovianity is significant under physiological conditions.     

Quantitative analysis of (styrene/acrylonitrile/methyl methacrylate) co-polymer systems by infrared resonance spectroscopy

A detailed careful analysis of the infrared resonance (IR) spectra of polystyrene (PSt), polymethyl methacrylate (PMMA), polyacrylonitrile (PAN) and their co-mixtures were performed. Through this study the absorption peak area to weight ratios as well as working curves were obtained to test for their reliability as well as their suitability. Satisfactory results were achieved and these working curves were then used to measure the polymerized components of binary and ternary co-polymers. By investigating the acquired data we conclude that the monomer preferential polymeric sequence is St > MMA > AN. A quantitative method to measure P (St/AN/MMA) concentrations by IR spectroscopy is proposed in this work.