Estimation of Kováts retention indices using group contributions

We have constructed a group contribution method for estimating Kováts retention indices by using observed data from a set of diverse organic compounds. Our database contains observed retention indices for over 35,000 different molecules. These were measured on capillary or packed columns with polar and nonpolar (or slightly polar) stationary phases under isothermal or nonisothermal conditions. We neglected any dependence of index values on these factors by averaging observations. Using 84 groups, we determined two sets of increment values, one for nonpolar and the other for polar column data. For nonpolar column data, the median absolute prediction error was 46 (3.2%). For data on polar columns, the median absolute error was 65 (3.9%). While accuracy is insufficient for identification based solely on retention, it is suitable for the rejection of certain classes of false identifications made by gas chromatography/mass spectrometry.     

Artificial neural networks based on principal component analysis input selection for clinical pattern recognition analysis

Two clinical data sets were applied for pattern recognition in order to discover the correlation between urinary nucleoside profiles and tumours. One data set contains 168 clinical urinary samples, of which 84 specimens are from female thyroid cancer patients (malignant tumour group), and the other samples were collected from healthy women (normal group). However, 168 clinical urinary samples comprised the second data set, too. In all the specimens, each number of the samples for both uterine cervical cancer patients (malignant tumour group) and healthy females (normal group) is 60, and the other 48 samples were collected from uterine myoma patients (benign tumour group). For the two data sets, the separation and quantitative determination of the clinical urinary nucleosides were performed by capillary electrophoresis (CE). The pattern recognition was achieved applying multiple layer perceptron artificial neural networks (MLP ANN) based on conjugate gradient descent training algorithm. Moreover, applying the proposed principal component analysis (PCA) input selection scheme to MLP ANN, the accuracy rate of the pattern recognition was improved to some extent (or without any deterioration) even by much simpler structure of MLP ANN. The study showed that MLP ANN based on PCA input selection was a promising tool for pattern recognition.     

Bursts in single-file motion mediated conduction

We present a cellular automaton (CA) model of particles in a single-file motion with free particle exchange at the boundaries of a one-dimensional channel connected to two infinite reservoirs in order to study the self-transmission of particles with excluded mutual passage. The parallel, local and homogeneous rule sets of the CA algorithm consider two different interactions of varying strength between particles, without any specific particle-channel interaction. CA model results suggest that one hallmark of single-file motion is the conduction bursts at a particular time scale, which have thus far only been discovered for hydrogen bond networked water translocation. The cumulative transport probabilities of particles through single-file channels of different length follow a single profile, which can be obtained through proper scaling of time. The universal features of our results suggest new experiments in single-file channel with fluids other than water.     

Optical tweezers directed one-bead one-sequence synthesis of oligonucleotides

An optical tweezers directed parallel DNA oligonucleotide synthesis methodology is described in which controlled pore glass (CPG) beads act as solid substrates in a two-stream microfluidic reactor. The reactor contains two parallel sets of physical confinement features that retain beads in the reagent stream for synthetic reaction but allow the beads to be optically trapped and transferred between the reagent and the inert streams for sequence programming. As a demonstration, we synthesized oligonucleotides of target sequence 25-nt, one deletion and one substitution using dimethoxytrityl (DMT) nucleoside phosphoramidite chemistry. In detecting single-nucleotide mismatches, fluorescence in situ hybridization of the bead-conjugated probes showed high specificity and signal-to-noise ratios. These preliminary results suggest further possibilities of creating a novel type of versatile, sensitive and multifunctional reconfigurable one-bead one-compound (OBOC) bead array.     

Reactive and nonreactive scattering of N2 from Ru(0001): a six-dimensional adiabatic study

We have studied the dissociative chemisorption and scattering of N(2) on and from Ru(0001), using a six-dimensional quasiclassical trajectory method. The potential energy surface, which depends on all the molecular degrees of freedom, has been built applying a modified Shepard interpolation method to a data set of results from density functional theory, employing the RPBE generalized gradient approximation. The frozen surface and Born-Oppenheimer [Ann. Phys. (Leipzig) 84, 457 (1927)] approximations were used, neglecting phonons and electron-hole pair excitations. Dissociative chemisorption probabilities are found to be very small even for translational energies much higher than the minimum reaction barrier, in good agreement with experiment. A comparison to previous low dimensional calculations shows the importance of taking into account the multidimensional effects of N(2) rotation and translation parallel to the surface. The new calculations strongly suggest a much smaller role of nonadiabatic effects than previously assumed on the basis of a comparison between low dimensional results and experiments [J. Chem. Phys. 115, 9028 (2001)]. Also in agreement with experiment, our theoretical results show a strong dependence of reaction on the initial vibrational state. Computed angular scattering distributions and parallel translation energy distributions are in good agreement with experiments on scattering, but the theory overestimates vibrational and rotational excitations in scattering.     

A group contribution method to estimate the densities of ionic liquids

Densities of ionic liquids at different temperature and pressure were collected from 84 references. The collection contains 7381 data points derived from 123 pure ionic liquids and 13 kinds of binary ionic liquids mixtures. In terms of the collected database, a group contribution method based on 51 groups was used to predict the densities of ionic liquids. In group partition, the effect of interaction among several substitutes on the same center was considered. The same structure in different substitutes may have different group values. According to the estimation of pure ionic liquids’ densities, the results show that the average relative error is 0.88% and the standard deviation (S) is 0.0181. Using the set of group values three pure ionic liquids densities were predicted, the average relative error is 0.27% and the S is 0.0048. For ionic liquid mixtures, they are thought considered as idea mixtures, so the group contribution method was used to estimate their densities and the average relative error is 1.22% with S is 0.0607. And the method can also be used to estimate the densities of MCl_x type ionic liquids which are produced by mixing an ionic liquid with a Cl^? anion and a kind of metal chloride.     

A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphs

We developed a spin adapted full configuration interaction (FCI) method which was expected to be effective for parallel processing. The graphical symmetric group approach (GSGA) was employed, where a configuration graph was partitioned into several sets of closed-shell and open-shell graphs. The configuration state functions (CSFs) bearing the same number of closed-shells and open-shells were assembled in a configuration group. The graphical approach provided a number to identify each CSF in a sequential order within the group. Combination of this partitioning and an intermediate configuration-driven algorithm in calculating the so-called σ vectors allowed us to use symbolic coupling constants. Furthermore, this combination made it easy to implement an efficient algorithm suitable to task-distributed parallel procedure for evaluating σ vectors. A program was written and some test calculations were carried out with high parallel efficiency. The largest size of FCI used 10 million CSFs (20 million determinants).     

Comparison of procedures for measurements of dissolved gaseous mercury in seawater performed on a Mediterranean cruise

A comparison of manual procedures for measurements of dissolved gaseous mercury (DGM) in seawater was accomplished. The experiments were performed on board the Italian research vessel Urania during July 2000 as a subtask in the CNR "Med-Oceanor Project 2000". Water samples for DGM were collected by Go-Flo bottles and subsequently analysed for DGM on board the ship. Determinations of DGM were made in parallel by two groups using different analytical routines. The two sets of data obtained compare favourably. Based on the fieldwork and an additional laboratory study, analytical procedures are discussed and an optimised method to determine DGM is presented. In addition, a method for automated in situ measurements of DGM positioned in the water body was tested. This method has the potential to simplify studies of DGM dynamics, that is variation in concentration as a function of water temperature and solar radiation etc.     

Parallel synthesis of a lipopeptide library by hydrazone-based chemical ligation

alpha-Melanocyte-stimulating hormone (alpha-MSH) is an endogeneous linear tridecapeptide with potential application for the modulation of skin tanning. To evaluate the interest of introducing a lipid moiety onto this peptide, we developed an efficient chemoselective parallel method to prepare a large series of analogues of alpha-melanocortin with high purity, varying the nature or the relative position of the lipid moiety. Two sets of building blocks containing lipidic alpha-oxo-aldehydes or alpha-hydrazinoacetyl peptides were combined to obtain a 102-membered library of amphiphilic alpha-MSH analogues. This library was pharmacologically tested at 1 x 10(-7) M for the ability to induce AMPc production in M4Be melanoma cell line after stimulation of the human melanocortin MC1 receptor. Among theses lipopeptides, 84 compounds exhibited an AMPc induction higher than Melitane, a patented alpha-MSH agonist. These results provide strong evidence of the interest of introduction of a lipid tail for the pharmacomodulation of bioactive peptides.     

锌矿原料有机物含量监测方法探究

采用测定化学需氧量(COD)法和有机溶剂抽提法分别对企业常用的两种锌矿原料(A,B)有机物进行监测。通过采用测定化学需氧量(COD)法对锌矿原料中含有的有机物进行定性及半定量分析,实验结果表明,矿粉A中COD为84.9mg/L,矿粉B中COD为96.9mg/L,各自进行了3次平行实验,都能得到稳定的结果,同时确定矿粉A和B中分别含有不同量的有机物。采用有机溶剂抽提法来确定锌矿原料中有机物的含量。考察了溶剂种类、溶剂量、抽提时间对矿粉中的有机物提取效果的影响,得到最佳实验条件,对矿粉的测定结果为:矿粉A中有机物含量为7.6‰,矿粉B中有机物含量为10.1‰。在各自的最佳实验条件下,进行了3次平行实验,都能得到稳定的结果,方法准确、可靠。     

Structure determination of a sildenafil analogue contained in commercial herb drinks

It was found from HPLC analysis that a commercial herb drink contains a putative sildenafil analog. In order to identify the sildenafil-like compound, separation and purification were carried out. The structure determination was performed based on routine 1D and 2D NMR experiments. Unlike sildenafil, the compound contains an ethylpiperazine instead of a methylpiperazine group. In addition, the piperazine and phenyl groups are connected through an acetyl group instead of the sulfonyl group of sildenafil.     

Analytic solutions to sets of first-order rate equations with up to six rate constants using a symbolic computer language SMP and application to biochemical kinetics

A symbolic computer language SMP* is employed to analytically solve sets of first-order linear differential equations which occur in kinetic rate-reaction studies. The solutions studied are fully analytic functions of time and the rate constants. Two typical systems are studied: the first contains four species and four rate constants, corresponding to four parallel and consecutive first-order reactions; and the second contains four species and six rate constants, including two additional reverse reactions. These analytic functions allow insight into the mechanism, analytic expressions for the rate constants, and more rapid and precise solutions for the species concentrations than a completely numerical solution of the differential rate equations themselves. The results of the first system are applied to a recent experimental study of enzyme kinetics in which constituent amino acid residues of an enzyme are photooxidized and the corresponding catalytic activity measured with time. A second application of the SMP gives rise to a rapid semianalytic method for obtaining the values of the four and six exponentially nonlinear rate constants from the experimental data.     

Distributed data parallel coupled-cluster algorithm: Application to the 2-hydroxypyridine/2-pyridone tautomerism

The recently developed parallel coupled-cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett., 194 , 84 (1992)] is extended to allow four-indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed-memory parallel processors. Quantities such as the double-excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2-hydroxypyridine/2-pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed-memory supercomputers. The largest coupled-cluster calculations contained over 2 million double-excitation amplitudes. © John Wiley & Sons, Inc.     

Liquid‐phase synthesis of mixture‐based bicyclic β‐lactam libraries

Five sets of 27‐membered combinatorial libraries of alicyclic β‐lactams were prepared via liquid‐phase Ugi 4‐center 3‐component reactions (U‐4C‐3CR) utilizing 3 different cis β‐amino acids, 3 different isonitriles and 5×3 sets of aldehydes. Through combinations of the building blocks of one of these libraries, all of the possible sublibraries were also generated. A few azetidinone derivatives were synthesized individually by parallel synthesis.     

Conformational and electronic effects on the regioselectivity of the glycosylation of different anomers of N-dimethylmaleoyl-protected glucosamine acceptors

In a previous paper (Bohn et al., Carbohydr. Res., 2007, 342, 2522) the relative O3/O4 reactivities of both alpha- and beta-methyl glycosides of N-dimethylmaleoyl (DMM) glucosamine acceptors protected at O6 with three different groups were assessed by us, using two glycosyl donors. The alpha-anomers showed preferential or exclusive substitution at O3, whereas the beta-anomers gave preferential or exclusive substitution at O4. A DFT study of analogs of the reported acceptors indicates that whereas the beta-anomers carry the DMM ring parallel to the C2-H2 bond for steric reasons, the alpha-anomers tilt this ring producing a strong hydrogen bond between the H(O)3 and one of the DMM carbonyl groups. In this way, the O3 group becomes more nucleophilic and thus more reactive: both charge and Fukui functions on O3 and O4 in the model compounds support the experimental results. Surprisingly, the previously mentioned hydrogen bond is not the only driving force for the slant of the DMM group: the axial methoxyl group of the alpha-anomers also plays a role. The ease of rotation around the C2-N2 bond for DMM-protected analogs was assessed with different models. MP2 calculations using higher basis sets yield similar relative energy and charge values to those calculated using DFT.     

Wetting study of imidazolium ionic liquids

In this work, we present a systematic contact angles study of a series of 1-alkyl, 3-methyl-imidazolium ionic liquids (ILs) on well-defined polar and nonpolar monolayer surfaces supported on Si wafers. The advancing and receding contact angles of ILs were used to determine the surface energy of the monolayer surfaces using Neumann's equation-of-state and Zisman's critical surface tension approaches. In parallel, the contact angles of conventional probe fluids (molecular liquids) including water, formamide, methylene iodide, ethylene glycol, and hexadecane were determined on the same surfaces. The results obtained showed a great deal of similarity in wetting behavior of ionic vs molecular probe fluids: the contact angles of both sets of liquids followed the same patterns in accord with the surface tension of the fluid. A good agreement was found between the surface energy determined by different sets of liquids.     

Reaction kinetics of multiphoton excited BCI3 with H2S

In order to investigate unique behaviors in kinetics of the reaction of multiphoton excited BCl₃ with H₂S, two kinds of experiments were performed. The first, parallel beam experiment, gives the activation energy of the primary reaction pathway considerably smaller than the bond strength. The second, focussed beam experiment, shows that the isotope selectivity increase with incident pulse energy. Both results were found different from typical multiphoton dissociation experiments, showing its own characteristics.     

Latex aging: The effects of coalescing agents and thermal annealing on the morphology of composite latex particles

Many composite polymer latices are produced with nonequilibrium particle morphologies and these can be prone to structural changes with the time of storage. Here we report on the use of coalescing agents, and separately thermal annealing to follow the morphology changes with aging time. Two coalescing agents with very different water solubilities were used to plasticize the latex polymers. During months of storage time the polymer particles were analyzed via differential scanning calorimetry and transmission electron microscopy. A parallel set of aging experiments were carried out for the same latices where the change agent was simple thermal annealing. Both latex and dry polymer samples were annealed at temperatures above 100 °C and for various periods of time. Both sets of experiments lead to the conclusion that when the aging temperature is at or above the effective glass transition temperature (taking into account solvent plasticization) of the glassiest of the polymers in a two‐component latex, morphological change can be rather fast and easily characterized. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1583–1589, 2011