Combining selection valve and mixing chamber for nanoflow gradient generation: Toward developing a liquid chromatography cartridge coupled with mass spectrometer for protein and peptide analysis

Toward developing a micro HPLC cartridge, we have recently built a high-pressure electroosmotic pump (EOP). However, we do not recommend people to use this pump to deliver an organic solvent directly, because it often makes the pump rate unstable. We have experimented several approaches to address this issue, but none of them are satisfactory. Here, we develop an innovative approach to address this issue. We first create an abruption (a dead-volume) within a fluid conduit. We then utilize an EOP to withdraw, via a selection valve, a train of eluent solutions having decreasing eluting power into the fluid conduit. When these solutions are further aspirated through the dead-volume, these solutions are partially mixed, smoothening concentration transitions between two adjacent eluent solutions. As these solutions are pushed back, through the dead-volume again, a smooth gradient profile is formed. In this work, we characterize this scheme for gradient formation, and we incorporate this approach with a high-pressure EOP, a nanoliter injection valve, and a capillary column, yielding a micro HPLC system. We then couple this micro HPLC with an electrospray ionization – mass spectrometer for peptide and protein separations and identifications.     

Electrochromatographic separation on a poly(dimethylsiloxane)/glass chip by integration of a capillary containing an acrylate monolithic stationary phase

In this paper, we present an approach to perform electrochromatographic separations on poly(dimethylsiloxane) chips: a fused-silica capillary containing a stationary phase was introduced directly into the chip. This approach would offer great flexibility since capillary modification methods are well known, and thus, with this kind of chip, different microfluidic devices having various functions could be prepared. Electrophoretic separations were first achieved by integrating an empty capillary into the chip to evaluate the analytical performances of this system. They were compared to those obtained with a classical chip. Finally, an electrochromatographic separation involving a capillary containing a hexyl acrylate-based monolith was performed. These preliminary results show this approach to be promising.     

Setting the Foundations of Aqueous Three-Phase Systems (A3PS) in the Quest for a Rational Design

This work presents the first in-depth study of Aqueous Three-Phase Systems (A3PS) with the main purpose of unveiling their behaviour, hence contributing to the development of this new field. Thus, a complete definition of a quaternary system was carried through by describing all the regions in detail to represent them later on in a regular-tetrahedral diagram. The three aqueous faces of the tetrahedron demonstrated an undeviating influence in the segregation capacity. Furthermore, a method for comparing Aqueous Biphasis Systems (ABS) immiscibilities was set up in order to allow the evaluation and detection of the “limiting ABS” for the three-phase region. Finally, all this information was compiled and utilised to obtain a new strategy for an A3PS rational design, which can be applied with ABS libraries or in an experimental approach. In this sense, this strategy represents an undoubted advance towards future studies and development of A3PS, as this sequential application of the constructed knowledge is assumed to save time and resources.     

Adaptative finite element simulation of currents at microelectrodes to a guaranteed accuracy. Application to a simple model problem

In this series of papers we consider the general problem of numerical simulation of the currents at microelectrodes using an adaptive finite element approach. Microelectrodes typically consist of an electrode embedded (or recessed) in an insulating material. For all such electrodes, numerical simulation is made difficult by the presence of a boundary singularity at the electrode edge (where the electrode meets the insulator), manifested by the large increase in the current density at this point, often referred to as the ‘edge-effect’. Our approach to overcoming this problem involves the derivation of an a posteriori bound on the error in the numerical approximation for the current that can be used to drive an adaptive mesh-generation algorithm. This allows us to calculate the current to within a prescribed tolerance. We begin by demonstrating the power of the method for a simple model problem — an E reaction mechanism at a microdisc electrode — for which the analytical solution is known. In this paper we give the background to the problem, and show how an a posteriori error bound can be used to drive an adaptive mesh-generation algorithm. We then use the algorithm to solve our model problem and obtain very accurate results on comparatively coarse meshes in minimal computing time. We give the technical details of the background theory and the derivation of the error bound in the accompanying paper.     

Asymmetric Allylation Polymerization of Bis(allylsilane) and Dialdehyde

The enantioselective addition of an allylsilane to an aldehyde is an excellent method to give optically active homoallyl alcohols. Applying this reaction to the asymmetric polymerization of bis(allylsilane) and dialdehyde, the synthesis of a new optically active polymer having chirality on the main chain was possible. Chiral acyloxyborane (CAB) was effective as a catalyst in this asymmetric allylation polymerization.     

An approach to the bis-oxazole macrocycle of diazonamides

A convergent approach to a macrocyclic compound embodying the complete "eastern" quadrant of diazonamides is described. The opening sequence in this work relies on an oxazole-forming reaction devised earlier in this group, while a late step involves a Robinson-Gabriel cyclization of an amidoketone to form a second oxazole.     

Target‐Triggered NIR Emission with a Large Stokes Shift for the Detection and Imaging of Cysteine in Living Cells

Background autofluorescence from biological systems generally reduces the sensitivity of a fluorescent probe for imaging biological targets. Addressing this challenge requires the development of fluorescent probes that produce emission in the near‐infrared region. Herein, we report the design and synthesis of a fluorescent probe that generates an NIR emission with a large Stokes shift upon the selective response to Cys over Hcy and GSH. The probe is designed to consist of two Cys‐sensing sites, an acrylate ester and an aldehyde installed ortho to each other. The reaction of the probe with Cys triggers an excited state intramolecular proton transfer process upon photo‐excitation, thereby producing an NIR emission with a large Stokes shift. Accordingly, this probe hold great promise for the selective detection of Cys in biological systems. We further demonstrate the capacity of this probe for Cys imaging in living cells.     

The de novo design of median molecules within a property range of interest

Summary In this paper an application is presented of the median molecule workflow to the de novo design of novel molecular entities with a property profile of interest. Median molecules are structures that are optimised to be similar to a set of existing molecules of interest as an approach for lead exploration and hopping. An overview of this workflow is provided together with an example of an instance using the similarity to camphor and menthol as objectives. The methodology of the experiments is defined and the workflow is applied to designing novel molecules for two physical property datasets: mean molecular polarisability and aqueous solubility. This paper concludes with a discussion of the characteristics of this method.     

An easy access to an organometallic low molecular weight gelator: a crystal engineering approach

In this Letter, a crystal engineering rationale is exploited to achieve an easy access to an organometallic low molecular weight gelator (LMWG) derived from a salt of ferrocene-1,1′-dicarboxylic acid (FDCA) and dicyclohexyl amine (DCHA). To the best of our knowledge, this is the first report wherein a crystal engineering approach has been exploited to design an organometallic LMWG.     

Efficient assembly consensus algorithms for divergent contig sets

Assembly is a fundamental task in genome sequencing, and many assemblers have been made available in the last decade. Because of the wide range of possible choices, it can be hard to determine which tool or parameter to use for a specific genome sequencing project. In this paper, we propose a consensus approach that takes the best parts of several contigs datasets produced by different methods, and combines them into a better assembly. This amounts to orienting and ordering sets of contigs, which can be viewed as an optimization problem where the aim is to find an alignment of two fragmented strings that maximizes an arbitrary scoring function between matched characters. In this work, we investigate the computational complexity of this problem. We first show that it is NP-hard, even in an alphabet with only two symbols and with all scores being either 0 or 1. On the positive side, we propose an efficient, quadratic time algorithm that achieves approximation factor 3.     

An iridium oxide reference electrode for use in microfabricated biosensors and biochips

In this paper we argue for the use of iridium oxide (IrO(x)) electrodes as quasi-reference electrodes in microfabricated biosensors and biochips that operate in buffered solutions. The simple microfabrication of these electrodes consists of a one-step electrodeposition of IrO(x) onto a microfabricated platinum (Pt) electrode. The IrO(x) electrode potential was found to vary less than 20 mV over 9 days after stabilization for 1 day in a phosphate-buffered saline (PBS) solution; this behavior of the electrode potential was found to be easily reproduced. Moreover, the electrode potential was found to vary by less than 15 mV in the initial hour of its use; this behavior of the electrode potential was also found to be reproducible. The performance of a microfabricated glucose sensor employing an IrO(x) reference electrode is characterized in this paper in order to evaluate the usefulness of this new IrO(x) electrode as a quasi-reference electrode. The glucose sensor consists of a recessed microfabricated Pt electrode array, an electrodeposited IrO(x) film, an inner layer composed of an electropolymerized poly(m-phenylenediamine)/glucose oxidase (PMPD/GOx) film, and an outer or protective layer composed of Teflon and polyurethane (PU) films. The response of this sensor was found to be equivalent to the response of the same sensor employing a commercial Ag/AgCl reference electrode. These results show that a microfabricated IrO(x) electrode can be used as a quasi-reference electrode in microfabricated biosensors and biochips operating in buffered solutions.     

Transition-metal-catalyzed sequential cross-coupling of bis(iodozincio)methane and -ethane with two different organic halides

Bis(iodozincio)methane, prepared from diiodomethane and zinc, reacts with an organic halide in the presence of a transition-metal catalyst to give an iodozinciomethylenated compound; this then reacts with another organic halide to form a C--C bond. The overall process connects two electrophiles with one carbon atom. Bis(iodozincio)ethane can also undergo this transformation, yielding a new stereogenic center. The asymmetric induction of this stereogenic center was investigated by using a chiral palladium catalyst.     

The Use of Chloroformamidine Hydrochloride as a Reagent for the Synthesis of Guanidines from Electron Deficient Aromatic Amines

In efforts to optimize a manufacturing process for an internal development compound, a clean, efficient approach to guanidine synthesis using chloroformamidine hydrochloride was identified. To investigate the general utility of this methodology towards electron‐deficient aromatic amines, a set of favorable conditions were developed from a series of screens, and the scope of the reaction was probed. The successful application of this chemistry to a variety of pyridines, anilines, and heterocyclic compounds highlights its use as an improved, alternative guanylation method for this often challenging set of aromatic amines.     

CHEMILUMINESCENCE INVOLVING PEROXIDE DECOMPOSITIONS

Abstract— It is a reasonable assumption that many of the known cherniluminescent organic compounds react to give a carbonyl group in an excited state. By extension of this hypothesis we were led to test several substituted acridinium salts. Oxidation of these with hydrogen peroxide in the presence of base resulted in the formation of N-methylacridone in high yield, and the emission of light from an excited state of this ketone. Mechanisms for this process are discussed. Interest in indole derivatives aroused by the finding of a tryptamine residue in the luminescent cypridina luciferin, in conjunction with the hypothesis mentioned above, has led to an investigation of some indoles, and in particular, the important isolable peroxide of tetrahydrocarbazole. A preliminary account of this work is given.     

Concise Construction of the ACDE Ring System of Calyciphylline A Type Alkaloids by a [5+2] Cycloaddition

A concise route for construction of the ACDE ring skeleton in calyciphylline A type alkaloids was developed using an intramolecular [5+2] cycloaddition reaction of an oxidopyrylium species bearing a tetrasubstituted olefin. Key to the success of this reaction was the combination of acid and base, which accelerated the construction of this skeleton containing a spiro ring and vicinal quaternary carbon centers. The resultant tricyclic ADE ring compound was converted to an ACDE ring model through C−H oxidation and an aza-Wittig reaction.     

Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4

Actinobacteria generate a large number of structurally diverse small molecules with potential therapeutic value. Genomic analyses of this productive group of bacteria show that their genetic potential to manufacture small molecules exceeds their observed ability by roughly an order of magnitude, and this revelation has prompted a number of studies to identify members of the unknown majority. As a potential window into this cryptic secondary metabolome, pairwise assays for developmental interactions within a set of 20 sequenced actinomycetes were carried out. These assays revealed that Amycolatopsis sp. AA4, a so-called "rare" actinomycete, produces a novel siderophore, amychelin, which alters the developmental processes of several neighboring streptomycetes. Using this phenotype as an assay, we isolated amychelin and solved its structure by NMR and MS methods coupled with an X-ray crystallographic analysis of its Fe-complex. The iron binding affinity of amychelin was determined using EDTA competition assays, and a biosynthetic cluster was identified and annotated to provide a tentative biosynthetic scheme for amychelin.     

Signal Generation at an Electrochemical Immunosensor via the Direct Oxidation of an Electroactive Label

In this paper, we report the development of an electrochemical immunosensor with a direct signal generation scheme. To achieve this, ferrocenecarboxylic acid was conjugated as an electroactive label to an immunocomplex immobilized on an electrochemically pretreated glassy carbon electrode. The pregnancy hormone and tumor marker, human chorionic gonadotrophin (hCG), was employed as a model analyte. Direct oxidation of ferrocenecarboxylic acid facilitated a signal generation scheme for the quantification of hCG at the immunosensor. Evaluation of the immunosensor performance has yielded statistically acceptable agreement in hCG levels present in several human serum samples compared to those reported by a Sydney hospital.     

A Complete Switch of the Directional Selectivity in the Annulation of 2‐Hydroxybenzaldehydes with Alkynes

Controlling reaction selectivity is an eternal pursuit for chemists working in chemical synthesis. As part of this endeavor, our group has been exploring the possibility of constructing different natural product skeletons from the same simple starting materials by using different catalytic systems. In our previous work, an isoflavanone skeleton was obtained from the annulation of a salicylaldehyde and an alkyne when a gold catalyst was employed. In this paper, it is shown that a coumarin skeleton can be efficiently obtained through an annulation reaction with the same starting materials, that is, terminal alkynes and salicylaldehydes, by simply switching to a rhodium catalyst. A plausible reaction mechanism is proposed for this new annulation based on isotopic substitution experiments.     

Synthesis of labeled 1-amino-2-methylenecyclopropane-1-carboxylic acid, an inactivator of 1-aminocyclopropane-1-carboxylate deaminase

1-Amino-2-methylenecyclopropane-1-carboxylic acid (2-methylene-ACC) is an irreversible inhibitor for a bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which catalyzes the conversion of ACC to alpha-ketobutyrate and ammonia. The inactivation has been proposed to proceed with the ring scission induced by an addition of an enzyme nucleophile, resulting in the formation of a reactive turnover product that then traps an active-site residue. To gain further insight into this unique enzymatic reaction, the tritiated 2-methylene-ACC was prepared and incubated with ACC deaminase to locate and identify the entrapped amino acid residue. The synthesis of this radiolabeled compound and the results of its incubation with ACC deaminase are reported in this paper.     

A nucleophilic 1,3-rearrangement leading to 3,4-disubstituted 3,4-dihydroquinolines

A new nucleophilic 1,3-rearrangement is observed when treating 2-methoxyquinolino-3-lithium with an α-C substituted deoxybenzoin,and this rearrangement yielded an unusual 3,4-disubstituted 3,4-dihydroquinoline.Several similar reactions were designed and executed to investigate this novel 1,3-rearrangement,and a mechanism involving a nucleophilic addition and a following 1,3-rearrangement with an unusual dearomatization on the quinoline ring is proposed.