Electronic structure and conductance of large molecules and DNA

Using a new technique based on embedding in a local orbital formalism, the electronic structure and electron transmission properties of long biological molecules are calculated, in particular DNA. The electronic structure is found by adding one structural unit at a time to the molecule, and calculating an embedding potential for adding the next structural unit. At present, an extended Hückel scheme is used for the Hamiltonian. The transmission is also calculated within the embedding scheme, taking the molecule–metal contacts into account. The results for transmission depend greatly on the orbitals to which contact is made, and also on energy. The implications of these calculations for conductance are discussed.     

Separation of niobium and tantalum with benzo- and phenylacetylhydroxamic acids

Benzohydroxamic acid (I) or phenylacetylhydroxamic acid (II) is suggested for the quantitative separation of tantalum from niobium in an oxalate solution. The tantalum precipitate must be ignited for weighing; niobium is determined in the filtrate with another reagent. The pH range for complete separation is 4.0–6.4 for I and 4.5–6.2 for II. Single precipitation is satistactory for Nb: Ta ratios of 18 : 1 to 1 : 20 for I, and 8 : 1 to 1 : 23 for II. Titanium, zirconium, tartrate, citrate and a large excess of oxalate interfere.     

Tutorial and comprehensive computational study of acceptance and transmission of sinusoidal and digital ion guides

A quadrupoles acceptance is a measure of its ability to catch ions with certain trajectories. One way to calculate acceptance is the method of ellipses. The method arose partly from a simplification that trajectories could be calculated for an electrode axis independently of others. It has been used to calculate the acceptance and transmission of sine‐driven quadrupole mass filters for over 50 years. Although the method is straightforward, it is generally described with little detail or presented as a confusing string of equations. As such, it may not be decipherable by all practitioners. For this reason, the first half of this paper presents a practical explanation of the method of ellipses and the concepts that make it work. Only equations necessary to describe the method are introduced. The tutorial also prepares the reader for the second half, which presents an alternative approach for calculating acceptance based on an array of initial trajectories. The alternative approach is used to compare the acceptance of simplified sinusoidal and digital ion guides. The method of ellipses was applied to validate results of the new approach for calculation of acceptance.     

Simultaneous spectrophotometric determination of molybdenum and selenium,and of molybdenum and tellurium

A method is reported for the extraction of molybdenum-phenylfluorone by chloroform. The extraction is complete whether perchlorate ions are present or not but the extractions in the presence of perchlorate ions gave a somewhat more sensitive procedure for the spectrophotometric determination of molybdenum in the solvent phase as the molybdenum-phenylfluorone complex.A procedure is reported for the simultaneous determination of molybdenum and selenium, and molybdenum and tellurium. The method involves first the formation and solvent extraction of the molybdenum-phenylfluorone complex by chloroform in the presence of perchlorate ions, followed by determination of selenium in the remaining aqueous phase as selenium-diethyldithiocarbamate complex after solvent extraction with 2-ethyl-1-hexanol in the presence of perchlorate ions. A similar procedure is reported for the simultaneous determination of molybdenum and tellurium except that in the determination of molybdenum, the phenylfluorone complex is extracted by chloroform in the absence of perchlorate ions. Tellurium is determined in the remaining aqueous phase as tellurium-diethyldithiocarbamate complex after solvent extraction by 2-ethyl-1-hexanol solvent extraction in the presence of perchlorate ions.     

A simple and low-energy strategy for the separation of water and acetonitrile

As acetonitrile is a widely used solvent for the chemical industry, the recovery of acetonitrile from acetonitrile wastewater is significant for both industrial cost reduction and environmental protection. In this article, a simple, low-energy, and low-cost strategy is proposed for the effective separation of acetonitrile from high-concentration acetonitrile wastewater. The approach is based on a sequential combination of two steps: salt-induced phase separation and hydrophobic filtration. The acetonitrile wastewater was first induced to split into two phases by salt, that is, the acetonitrile-rich phase and the water-rich phase, then the above two phases were poured into the hydrophobic filter paper funnel for the separation. It was shown that NaCl is a suitable salting-out reagent, and that hydrophobic filter papers—obtained from modification by butyltrichlorosilane and octyltrichlorosilane were the optimal choice for hydrophobic filtration. The salt-induced phase separation process is able to increase the volume fraction of acetonitrile in the acetonitrile-rich phase up to 92%. The acetonitrile-rich phase can pass through the hydrophobic filter paper, whereas the water-rich phase was intercepted. The hydrophobic filter paper retained strong hydrophobicity and high acetonitrile-separating capacity after 3 months storage, or upon immersion in acetonitrile-water mixtures for 12 h, or applied for 25 consecutive separations.     

Catalytic Synthesis of Organolithium and Organomagnesium Compounds and of Lithium and Magnesium Hydrides—Applications in Organic Synthesis and Hydrogen Storage

A recent development in homogeneous catalysis is the discovery of catalysts that are active for the lithiation of 1-alkenes to alkenyllithium compounds and lithium hydride as well as for the hydrogenation of lithium and magnesium under mild conditions. The catalytically prepared magnesium hydride is highly reactive and adds to 1-alkenes to give diorganomagnesium compounds and can also be used in the preparation of, for example, silane and “active” magnesium. The use of metal hydrides in hydrogen storage is discussed: hydrogenation/dehydrogenation experiments show that the catalytically prepared magnesium hydride (which can be doped with a second metal) can be used as a high-temperature hydrogen storage material.     

Liquid chromatographic assay of phenothiazine, thioxanthene and butyrophenone neuroleptics and antihistamines in blood and plasma with conventional and radial compression columns and UV and electrochemical detection

An assay strategy for determining a wide range of phenothiazine, thioxanthene and butyrophenone neuroleptics and antihistamines both alone and in combination in blood and plasma is described. The general method employs liquid chromatography with both conventional and radial compression nitrile bonded columns. Detection is by ultraviolet absorption spectrophotometry or by amperometry depending on the concentrations to be measured. Ultraviolet absorption is suitable down to 10 ng/ml. Below this level amperometry is preferable. The various compounds are used as internal standards for each other. The lower limit of detection is approximately 0.1 ng ml-1 with 10-ml sample. The with-run coefficient of variation is a maximum of 7.3%.     

Rapid and simple determination of aldose reductase and sorbitol dehydrogenase

Rapid and well-reproducible methods were developed for the determination of aldose reductase and sorbitol dehydrogenase. The aldose reductase activity measurement is based on photometric o-toluidine aldose back-measurement, which is widely used in laboratories for the quantitative determination of glucose. The spectrophotometric method based on the quantitative decrease in NADH proved suitable for the measurement of sorbitol dehydrogenase activity.Both methods could well be employed for the measurement of the aldose reductase and sorbitol dehydrogenase activities of normal and diabetic tissue homogenizates, and for the comparison of the measured values.     

Principles and applications of electrochemical and optical biosensors

The principles of biocatalytic and bioaffinity biosensors are reviewed with emphasis on electron transfer-type enzyme sensors, optical enzyme sensors and optical immunosensors for homogeneous immunoassay. An enzyme sensor for ethanol was fabricated by electrochemical polymerization of pyrrole onto the surface of platinized platinum-adsorbed alcohol dehydrogenase—NAD—Meldola Blue. Ethanol was determined amperometrically by measuring the oxidative current through polypyrrole. An optical enzyme sensor is exemplified by an acethylcholine sensor based on an optical pH fibre sensor using a thin polyaniline film. The optical immunosensor for homogeneous immunoassay consists of an optical fibre, the end of the which is coated with an optically transparent platinum electrode. With using luminol as a label, highly sensitive homogeneous immunoassay is carried out by measuring the electrochemical luminescence of the label.     

A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies

In this work we present the experimental and theoretical vibrational absorption (VA) and the theoretical vibrational circular dichroism (VCD) spectra for aframodial. In addition, we present the theoretical VA and VCD spectra for the diasteriomers of aframodial. Aframodial has four chiral centers and hence has 2⁴ = 16 diasteriomers, which occur in eight pairs of enantiomers. In addition to the four chiral centers, there is an additional chirality due to the helicity of the entire molecule, which we show by presenting 12 configurations of the 5S,8S,9R,10S enantiomer of aframodial. The VCD spectra for the diasteriomers and the 12 configurations of one enantiomer are shown to be very sensitive not only to the local stereochemistry at each chiral center, but in addition, to the helicity of the entire molecule. Here one must be careful in analyzing the signs of the VCD bands due to the ‘non-chiral’ chromophores in the molecule, since one has two contributions; one due to the inherent chirality at the four chiral centers, and one due to the chirality of the side chain groups in specific conformers, that is, its helicity. Theoretical simulations for various levels of theory are compared to the experimental VA recorded to date. The VCD spectra simulations are presented, but no experimental VCD and Raman spectra have been reported to date, though some preliminary VCD measurements have been made in Stephens’ lab in Los Angeles. The flexible side chain is proposed to be responsible for the small size of the VCD spectra of this molecule, even though the chiral part of the molecule is very rigid and has four chiral centers. In addition to VCD and Raman measurements, Raman optical activity (ROA) measurements would be very enlightening, as in many cases bands which are weak in both the VA and VCD, may be large in the Raman and/or ROA spectra. The feasibility of using vibrational spectroscopy to monitor biological structure, function and activity is a worthy goal, but this work shows that a careful theoretical analysis is also required, if one is to fully utilize and understand the experimental results. The reliability, reproduceability and uniqueness of the vibrational spectroscopic experiments and the information which can be gained from them is discussed, as well as the details of the computation of VA, VCD and Raman (and ROA) spectroscopy for molecules of the complexity of aframodial, which have multiple chiral centers and flexible side chains. Festschrift in Honor of Philip J. Stephens’ 65th Birthday.     

Valency and molecular structure

Valency is defined for each molecular orbital. The molecular orbital valency values are shown to be a good measure of the bonding nature of the molecular orbital. Comparisons are made with photoelectron spectral studies and Mulliken overlap population analysis.The variation of molecular valency and molecular orbital valency with bond angle is studied. It is found that for all the molecules presently considered, energy is linearly related to valency and that the molecular valency reaches a maximum at the equilibrium bond angle. It is also shown that the molecular orbital valency can serve as a quantitatively reliable ordinate for Mulliken-Walsh diagrams.     

Electronic and Magnetic Properties of Linear and Dimerized Titanium Nanochains Under Compressive and Tensile Strain

The magnetic and electronic properties of both linear and dimerized nanochains of titanium at different atomic distances are calculated within density functional theory with the generalized gradient approximation. Titanium which is a nonmagnetic in its bulk form is shown to become magnetic in its nanochain structure. Also, a close relationship is found between magnetic state and geometry of chain structure and the dependence of electronic properties on the atomic structures of chains is revealed. It is found that, for dimerized nanochains from equilibrium constant, compressive strain leads to a reduction in magnetism. Moreover, characteristics of the systems near the Fermi level are investigated and the charge densities of both nanostructures are studied in the ferromagnetic order. The results show that metallic bonding is mainly responsible for the linear structure; however, for the dimerized structure, the bonding is more directional, i.e. has a more covalent character. With increasing tension along the axis of the nanostructures, a change in the types of bonding is found.     

Critical point and vapor pressure of ionic fluids including NaCl and KCl

The critical properties and the vapor and liquid densities of NaCl, KCl, and the primite-model ionic fluid are compared on a corresponding-states basis. In preparation for these comparisons the vapor density of NaCl at very high temperature is calculated from the accurate molecular parameters. The very recent treatment of Gillan is adopted for the primitive model. The liquid properties of KCl and NaCl follow corresponding states exactly but there is some discrepancy for the ion pair in the vapor. The differences are greater for the primitive model but again the agreement is quite good for the liquid. Critical properties are reported for all three fluids.     

AB initio and Dft investigations of Al, Ga, and In tricyanides and triisocyanides

Structural parameters, standard entropies, and vibrational spectra of cyanides and isocyanides of trivalent AI, Ga, and In were obtained for the first time by ab initio and B3LYP density functional methods. The isocyanide form is found to be preferable for Al; for Ga and In, the cyanide form is more stable. The considerable discrepancy between the results obtained by the SCF and B3LYP methods shows that it is important to take electron correlation energy into account; however, a comparison between the DZP and LANL2DZP basis sets demonstrates that basis sets with the effective core potential are not adequate for describing molecular tricyanides of group IIIa elements. This situation is probably characteristic for molecular systems with a cyano group in the molecule. Translated from Zhumal Struktumoi Khimii, Vol. 41, No. 1, pp. 42-48, January-February, 2000.     

Prediction and molecular insights into fungal adhesins and adhesin like proteins

Adhesion is the foremost step in pathogenesis and biofilm formation and is facilitated by a special class of cell wall proteins known as adhesins. Formation of biofilms in catheters and other medical devices subsequently leads to infections. As compared to bacterial adhesins, there is relatively less work for the characterization and identification of fungal adhesins. Understanding the sequence characterization of fungal adhesins may facilitate a better understanding of its role in pathogenesis. Experimental methods for investigation and characterization of fungal adhesins are labor intensive and expensive. Therefore, there is a need for fast and efficient computational methods for the identification and characterization of fungal adhesins. The aim of the current study is twofold: (i) to develop an accurate predictor for fungal adhesins, (ii) to sieve out the prominent molecular signatures present in fungal adhesins. Of the many supervised learning algorithms implemented in the current study, voting ensembles resulted in enhanced prediction accuracy. The best voting-ensemble consisting of three support vector machines with three different kernels (PolyK, RBF, PuK) achieved an accuracy of 94.9% on leave one out cross validation and 98.0% accuracy on blind testing set. A preference/avoidance list of molecular features as well as human interpretable rules are also extracted giving insights into the general sequence features of fungal adhesins. Fungal adhesins are characterized by high Threonine and Cysteine and avoidance for Phenylalanine and Methionine. They also have avoidance for average hydrophilicity. The current analysis possibly will facilitate the understanding of the mechanism of fungal adhesin function which may further help in designing methods for restricting adhesin mediated pathogenesis.     

Extraction and spectrophotometric determination of nickel with 2-hydroxyacetophenone oxime and simultaneous determination of copper and nickel

It is observed that 2-hydroxyacetophenone oxime can be used for the quantitative extraction of nickel in the pH range 6.6-7.8 into methyl isobutyl ketone. The organic layer shows maximum absorbance at 375 nm. Beer's law is obeyed over the range 1-6 ppm. The colour of the organic layer is stable for more than 48 hr. Interferences have been studied and methods are suggested for their elimination. Copper and nickel are both quantitatively extracted at pH 7 and can be determined simultaneously and accurately in the range 1-6 microg/ml for copper and 1-4 microg/ml for nickel.     

Analytical and environmental aspects of the flame retardant tetrabromobisphenol-A and its derivatives

The present article reviews the available literature on the analytical and environmental aspects of tetrabromobisphenol-A (TBBP-A), a currently intensively used brominated flame retardant (BFR). Analytical methods, including sample preparation, chromatographic separation, detection techniques, and quality control are discussed. An important recent development in the analysis of TBBP-A is the growing tendency for liquid chromatographic techniques. At the detection stage, mass-spectrometry is a well-established and reliable technology in the identification and quantification of TBBP-A. Although interlaboratory exercises for BFRs have grown in popularity in the last 10 years, only a few participating laboratories report concentrations for TBBP-A. Environmental levels of TBBP-A in abiotic and biotic matrices are low, probably due to the major use of TBBP-A as reactive FR. As a consequence, the expected human exposure is low. This is in agreement with the EU risk assessment that concluded that there is no risk for humans concerning TBBP-A exposure. Much less analytical and environmental information exists for the various groups of TBBP-A derivatives which are largely used as additive flame retardants.     

Determination of acetylsalicylic acid and salicylic acid in blood and plasma by HPLC

A method is described for the determination of acetylsalicylic acid and salicylic acid in human whole blood and plasma which uses liquid chromatography with UV detection. The enzymatic degradation of acetylsalicyclic acid in blood and plasma is examined. Addition of potassium fluoride as enzyme inhibitor and deep freezing after plasma preparation allows storage of plasma for one week. A mixture of acetonitrile and diluted acetic acid as mobile phase give the best peak shape. Traces of iron lead to slight peak broadening; addition of EDTA results in excessive tailing. The detection limit for acetylsalicylic acid and salicylic acid is about 250 ng/ml for a 1.0 ml primary sample. The method is sensitive enough for the monitoring of both drugs in bioavailability studies.     

中微肥的生产及其应用

综述了中量和微量元素肥料生产的必要性、生产工艺的改进和在不同土壤条件、作物品种、肥料形式和栽培条件下的应用方法.解决好这一重要问题的关键在于:中微肥的生产,只有综合利用矿产资源和工业废弃资源,才能有效地降低生产成本;只有采取有机螯合的方法,才能保持中微肥的活性;以大量元素肥料为载体,可方便农民使用.     

Formation and stability of prolinol and prolinol ether enamines by NMR: delicate selectivity and reactivity balances and parasitic equilibria

Enamine key intermediates in organocatalysis, derived from aldehydes and prolinol or J?rgensen-Hayashi-type prolinol ether catalysts, were generated in different solvents and investigated by NMR spectroscopy. Depending on the catalyst structure, trends for their formation and amounts are elucidated. For prolinol catalysts, the first enamine detection in situ is presented and the rapid cyclization of the enamine to the oxazolidine ("parasitic equilibrium") is monitored. In the case of diphenylprolinol, this equilibrium is fully shifted to the endo-oxazolidine ("dead end") by the two geminal phenyl rings, most probably because of the Thorpe-Ingold effect. With bulkier and electron-withdrawing aryl rings, however, the enamine is stabilized relative to the oxazolidine, allowing for the parallel detection of the enamine and the oxazolidine. In the case of prolinol ethers, the enamine amounts decrease with increasing sizes of the aryl meta-substituents and the O-protecting group. In addition, for small aldehyde alkyl chains, Z-configured enamines are observed for the first time in solution. Prolinol silyl ether enamines are evidenced to undergo slow desilylation and subsequent rapid oxazolidine formation in DMSO. For unfortunate combinations of aldehydes, catalysts, solvents, and additives, the enamine formation is drastically decelerated but can be screened for by a rapid and facile NMR approach. Altogether, especially by clarifying the delicate balances of catalyst selectivity and reactivity, our NMR spectroscopic findings can be expected to substantially aid synthetically working organic chemists in the optimization of organocatalytic reaction conditions and of prolinol (ether) substitution patterns for enamine catalysis.