Microgram-scale testing of reaction conditions in solution using nanoliter plugs in microfluidics with detection by MALDI-MS

This paper describes a microfluidic system to screen and optimize organic reaction conditions on a submicrogram scale. The system uses discrete droplets (plugs) as microreactors separated and transported by a continuous phase of a fluorinated carrier fluid. Previously, we demonstrated the use of a microfabricated PDMS plug-based microfluidic system to perform assays and crystallization experiments in aqueous solutions with optical detection. Here, we developed an approach that does not require microfabrication of microfluidic devices, is applicable to synthetic reactions in organic solvents, and uses detection by MALDI-MS. As a demonstration, conditions for selective deacetylation of ouabain hexaacetate were tested, and the optimum conditions for mono-, bis-, or trisdeacetylation have been identified. These conditions were validated by scale-up reactions and isolating these potentially neurotoxic products. Mono- and bisdeacetylated products are unstable intermediates in the deacetylation and were isolated for the first time. This system enables no-loss handling of submicroliter volumes containing a few micrograms of a compound of interest. It could become valuable for investigating or optimizing reactions of precious substrates (e.g., products of long synthetic sequences and natural products that can be isolated only in small quantities).     

Single-molecule emulsion PCR in microfluidic droplets

The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today's biomedical engineering challenges in single-molecule amplification and analysis.     

Miniaturizing chemistry and biology in microdroplets

By compartmentalizing reactions in aqueous microdroplets of water-in-oil emulsions, reaction volumes can be reduced by factors of up to 10(9) compared to conventional microtitre-plate based systems. This allows massively parallel processing of as many as 10(10) reactions in a total volume of only 1 ml of emulsion. This review describes the use of emulsions for directed evolution of proteins and RNAs, and for performing polymerase chain reactions (PCRs). To illustrate these applications we describe certain specific experiments, each of which exemplifies a different facet of the technique, in some detail. These examples include directed evolution of Diels-Alderase and RNA ligase ribozymes and several classes of protein enzymes, including DNA polymerases, phosphotriesterases, beta-galactosidases and thiolactonases. We also describe the application of emulsion PCR to screen for rare mutations and for new ultra-high throughput sequencing technologies. Finally, we discuss the recent development of microfluidic tools for making and manipulating microdroplets and their likely impact on the future development of the field.     

Solid-phase PCR in a picowell array for immobilizing and arraying 100 000 PCR products to a microscope slide

We present a method for performing highly parallel PCR reactions in a picowell array (PWA) simultaneously immobilizing generated PCR products in a covalent and spatially-resolved manner onto a microscope slide via solid-phase PCR (SP-PCR). This so called PWA-SP-PCR was performed in picowell arrays featuring 100?000 wells cm(-2) of 19 pL reaction volumes with a surface-to-volume ratio of 0.2 μm(-1). Positive signals were obtained in 97.2% of the 110?000 wells in an area of 110 mm(2). Immobilized DNA was either indirectly detected using streptavidin-Cy5 or directly by molecular hybridisation of Cy3- and/or Cy5-labelled probes. Amplification and immobilization was demonstrated for template DNA ranging from 100 bp up to 1513 bp lengths. Even single DNA molecules were successfully amplified and immobilized demonstrating digital solid-phase PCR. Compared to widely established emulsion based PCR (emPCR) approaches, leading to PCR products immobilized onto bead surfaces in a highly parallel manner, the novel technique results in direct spatial registration of immobilized PCR products in a microarray format. This enables the subsequent use for massively parallel analysis similar to standard microarrays.     

Organic Reactions in Microdroplets: Reaction Acceleration Revealed by Mass Spectrometry

The striking finding that reaction acceleration occurs in confined‐volume solutions sets up an apparent conundrum: Microdroplets formed by spray ionization can be used to monitor the course of bulk‐phase reactions and also to accelerate reactions between the reagents in such a reaction. This Minireview introduces droplet and thin‐film acceleration phenomena and summarizes recent methods applied to study accelerated reactions in confined‐volume, high‐surface‐area solutions. Conditions that dictate either simple monitoring or acceleration are reconciled in the occurrence of discontinuous and complete desolvation as the endpoint of droplet evolution. The contrasting features of microdroplet and bulk‐solution reactions are described together with possible mechanisms that drive reaction acceleration in microdroplets. Current applications of droplet microreactors are noted as is reaction acceleration in confined volumes and possible future scale‐up.     

Activation and Reaction Volumes for [4+2] and [3+2] Additions Involving Maleic Anhydride

The partial molar volumes of reactants and products of the [3+2] addition of C-(p-nitrophenyl)-N-phenylnitrone to maleic anhydride and of the [4+2] addition of 9,10-dimethylanthracene to the same dienophile were determined, and the reaction volumes were calculated. A new method was suggested for determining the reaction volume. The activation volumes of both reactions were calculated from the dependences of the reaction rates on the external pressure. The volume parameters of the reactions involving the reagents of close size are close. The ratios of the activation volumes to the reaction volumes are unity, which suggests a common concerted mechanism of the reactions. Factors that could be responsible for significant changes in the absolute values of the reaction volume parameters are discussed.     

Ultrasonication‐assisted spray ionization‐based micro‐reactors for online monitoring of fast chemical reactions by mass spectrometry

Microfluidics can be used to handle relatively small volumes of samples and to conduct reactions in microliter‐sized volumes. Electrospray ionization can couple microfluidics with mass spectrometry (MS) to monitor chemical reactions online. However, fabricating microfluidic chips is time‐consuming. We herein propose the use of a micro‐reactor that is sustained by two capillaries and an ultrasonicator. The inlets of the capillaries were individually immersed to two different sample vials that were subjected to the ultrasonicator. The tapered outlets of the two capillaries were placed cross with an angle of ~60° close to the inlet of the mass spectrometer to fuse the eluents. On the basis of capillary action and ultrasonication, the samples from the two capillaries can be continuously directed to the capillary outlets and fuse simultaneously to generate gas phase ions for MS analysis through ultrasonication‐assisted spray ionization (UASI). Any electric contact applied on the capillaries is not required. Nevertheless, UASI spray derived from the eluents can readily occur in front of the mass spectrometer. That is, a micro‐reactor was created from the fusing of the eluent containing different reactants from these two UASI capillaries, allowing reactions to be conducted in situ. The solvent in the fused droplets was evaporated quickly, and the product ions could be immediately observed by MS because of the extreme rise in the concentration of the reactants. For proof of concept, pyrazole synthesis reaction and cortisone derivatization by Girard T reagent were selected as the model reactions. The results demonstrated the feasibility of using UASI‐based micro‐reactor for online MS analysis to detect reaction intermediates and products.     

Molecular dynamics calculation of molecular volumes and volumes of activation

Experimentally, the effects of pressure on reaction rates are described by their pressure derivatives, known as volumes of activation. Transition state theory directly links activation volumes to partial molar volumes of reactants and transition states. We discuss a molecular dynamics method for the accurate calculation of molecular volumes, within which the volumes of molecular species are obtained as a difference between the volumes of pure solvent and solvent with a single molecule inserted. The volumes thus obtained depend on the molecular geometry, the strength and type of the solute-solvent interactions, as well as temperature and pressure. The partial molar volumes calculated using this approach agree well with experimental data. Since this method can also be applied to transition state species, it allows for quantitative analysis of experimental volumes of activation in terms of structural parameters of the corresponding transition states. The efficiency of the approach is illustrated by calculation of volumes of activation for three nonpolar reactions in nonpolar solvents. The results agree well with the experimental data.     

A valveless microfluidic device for integrated solid phase extraction and polymerase chain reaction for short tandem repeat (STR) analysis

A valveless microdevice has been developed for the integration of solid phase extraction (SPE) and polymerase chain reaction (PCR) on a single chip for the short tandem repeat (STR) analysis of DNA from a biological sample. The device consists of two domains--a SPE domain filled with silica beads as a solid phase and a PCR domain with an ~500 nL reaction chamber. DNA from buccal swabs was purified and amplified using the integrated device and a full STR profile (16 loci) resulted. The 16 loci Identifiler? multiplex amplification was performed using a non-contact infrared (IR)-mediated PCR system built in-house, after syringe-driven SPE, providing an ~80-fold and 2.2-fold reduction in sample and reagent volumes consumed, respectively, as well as an ~5-fold reduction in the overall analysis time in comparison to conventional analysis. Results indicate that the SPE-PCR system can be used for many applications requiring genetic analysis, and the future addition of microchip electrophoresis (ME) to the system would allow for the complete processing of biological samples for forensic STR analysis on a single microdevice.     

Simultaneous estimation of detection sensitivity and absolute copy number from digital PCR serial dilution

Digital polymerase chain reaction (dPCR) is a refinement of the conventional PCR approach to nucleic acid detection and absolute quantification. Digital PCR works by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions. Current quantification methods rely on the assumption that the PCR reactions are always able to detect single target molecules. When the assumption does not hold, the copy numbers will be severely underestimated. We developed a novel dPCR quantification method which determines whether the single copy assumption is violated or not by simultaneously estimating the assay sensitivity and the copy numbers using serial dilution data sets. The implemented method is available as an R package “digitalPCR”.     

A modified next reaction method for simulating chemical systems with time dependent propensities and delays

Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the Gillespie algorithm or the next reaction method. In this paper we make explicit use of the fact that the initiation times of the reactions can be represented as the firing times of independent, unit rate Poisson processes with internal times given by integrated propensity functions. Using this representation we derive a modified next reaction method and, in a way that achieves efficiency over existing approaches for exact simulation, extend it to systems with time dependent propensities as well as to systems with delays.     

Supramolecular reactor in an aqueous environment: aromatic cross Suzuki coupling reaction at room temperature

[reaction: see text] We have investigated supramolecular reactors for the Suzuki coupling reactions of aryl halides with phenyl boronic acids by using self-assembly of amphiphilic rod-coil molecules in aqueous solution at room temperature. All the rod-coil molecules synthesized in this work showed to self-assemble into discrete micelles consisting of aromatic rod bundles encapsulated by hydrophilic poly(ethylene oxide) coils. We present a comparative study of rod-coil molecules' efficiency as supramolecular reactors for Suzuki coupling reaction. The closed-packed aromatic bundles play an efficient role in supramolecular reactors for the coupling reactions at room temperature. The supramolecular reactor based on hexa-p-phenylene confers unprecedented activity, allowing reactions to be performed at very low catalyst levels, without conventional heating or microwave.     

Introduction of a calibration-free reaction calorimeter that combines the benefits of DSCS and reaction calorimeters

The reaction calorimeter CAP202 (chemical process analyzer) determines thermal effects by measuring the true heat flow (THF) based on unique design principles. In particular, measurements can be performed without requiring any calibration procedures and the obtained results are most reliable and exhibit extremely stable baselines. The benefits in respect of experimental speed, data quality and long term performance are obvious. Due its broad dynamic range the instrument can be employed for measurements ranging from small physical heat to energetic chemical reactions. The CPA allows running experiments seamlessly with reaction volumes between 10 and 180 mL. This volume flexibility simplifies the investigation of multi-step operations and is the basis for various applications employing precious or highly energetic compounds. Due to the fact that calibrations are not required, altering conditions during a single experiment like changes in viscosities, liquid levels or stirring speeds do not affect the results of the measurements.     

Simultaneous in-situ monitoring of parallel polymerization reactions using light scattering; a new tool for high-throughput screening

A recently introduced technique, simultaneous multiple sample light scattering (SMSLS), was used to monitor parallel polymerization reactions in situ. SMSLS is designed for real-time, high-throughput screening and provides a time-dependent light scattering signature for each reaction, which contains both qualitative and semiquantitative information. Qualitatively, the signature immediately indicates whether the reaction occurs or not, whether there is an initial lag period, and how long the reaction takes until it stops. The signature also provides estimates of the reaction rate and weight average molecular mass M(w), and its shape can help identify mechanistic aspects, for example, controlled versus free radical polymerization, presence of impurities, etc. The method is inherently adapted to small sample volumes and requires no special sample preparation or postpolymerization characterization. The demonstration here involved the free radical polymerization of acrylamide under varying conditions and should be readily applicable to a wide variety of other reactions. Results were cross-checked with multi-detector gel permeation chromatography.     

Sequential photostimulated reactions of trimethylstannyl anions with aromatic compounds followed by palladium-catalyzed cross-coupling processes

The photostimulated reactions of several mono-, di-, and trichloroarenes and aryltrimethylammonium salts with Me(3)Sn(-) ions in liquid ammonia gave good yields of stannanes by the S(RN)1 mechanism. If the chloroarenes are not soluble in liquid ammonia, diglyme is another solvent to perform these reactions. The stannanes thus obtained can be arylated by further reaction with haloarenes through palladium-catalyzed reactions. If the palladium-catalyzed reaction is performed with a chloroiodoarene as substrate, the stannane reacts faster by the C-I bond via chemoselective cross-coupling reaction to give a chloroarene as product, which can be further arylated by a consecutive S(RN)1-Stille reaction or react with other substrates by another palladium-catalyzed reaction. These sequential reactions can also be performed with substrates with two leaving groups to give products in high yields.     

Continuous‐Flow Technology—A Tool for the Safe Manufacturing of Active Pharmaceutical Ingredients

In the past few years, continuous‐flow reactors with channel dimensions in the micro‐ or millimeter region have found widespread application in organic synthesis. The characteristic properties of these reactors are their exceptionally fast heat and mass transfer. In microstructured devices of this type, virtually instantaneous mixing can be achieved for all but the fastest reactions. Similarly, the accumulation of heat, formation of hot spots, and dangers of thermal runaways can be prevented. As a result of the small reactor volumes, the overall safety of the process is significantly improved, even when harsh reaction conditions are used. Thus, microreactor technology offers a unique way to perform ultrafast, exothermic reactions, and allows the execution of reactions which proceed via highly unstable or even explosive intermediates. This Review discusses recent literature examples of continuous‐flow organic synthesis where hazardous reactions or extreme process windows have been employed, with a focus on applications of relevance to the preparation of pharmaceuticals.     

Miniaturized isothermal nucleic acid amplification, a review

Micro-Total Analysis Systems (μTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.     

Adjustment of Heating Rate for Maximum Resolution in TG and TMA (MaxRes)

Conventional thermogravimetric analysis (TG) uses constant heating rates to determine decomposition rates of a material and compositional analysis. Often, the decomposition steps can not be separated clearly enough due to parallel or consecutive reactions. If the reaction rates and the respective activation energies are enough different the TG resolution can be much enhanced by lowering the heating rate during the decomposition steps. The automated discrete adjustment of the heating rate is controlled by a set of parameters, such as threshold values, waiting times and rate factors. This technique, called MaxRes, allows for faster compositional analysis without loss of resolution. The same technique is also applicable to thermomechanical analysis (TMA) if time/temperature dependent events such as softening are to be separated. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effect of pressure on free-radical copolymerization kinetics. I. A concept of additivity of partial molar volumes of activation

A short review of the effect of pressure on copolymerization kinetics shows the necessity of simple models for a better understanding of activation volumes. Therefore, a simple concept, possibly generally valid for free-radical polymerization, is proposed, based on the assumption that molar volumes of activation can be expressed as an addition of a characteristic radical and a monomer contribution, regardless of the combination involved. The scheme may facilitate the visualization of the transition state and contribute to the understanding of reaction mechanisms of radical polymerizations. Ethylene–vinyl acetate copolymerization at 62°C with tert-butyl alcohol as solvent agrees with the proposed scheme, appearing from the pressure independence of the product of reactivity ratios at the different levels (35,600, and 1200 kg/cm²). Implicitly it can be shown that an ethylene monomer contributes about 2 cm³/mole more to the activation volumes of the propagation reactions than does the vinyl acetate monomer, whereas for the radicals the difference of the respective contributions to the activation volumes is opposite in sign.