Lewis Base Catalyzed Aerobic Oxidative Intermolecular Azide–Zwitterion Cycloaddition

The discovery of a novel aerobic oxidative intermolecular azide–zwitterion reaction catalyzed by an organocatalyst is presented. It is demonstrated that the merger of the Lewis base 1,8‐diazabicyclo[5.4.0]undec‐7‐ene and electron‐deficient olefins generates reactive zwitterion intermediates, which readily participate in cycloaddition reactions with an array of azides, thus providing facile entry to fully or highly substituted 1,2,3‐triazole frameworks. The reaction features an excellent substrate scope, and the products are obtained with high yields and excellent regioselectivities. It is demonstrated that some of these products can be transformed into pharmaceutically important agents. In addition to the experimental results, a detailed mechanistic survey is also provided, including MS studies rationalizing the origin of regioselective control.     

Substoichiometric separation and determination of trace metals

Substoichiometric methods are eminently suitable for the determination of many elements. As a new application of substoichiometry, a substoichiometric speciation of the element in different chemical states is proposed. Substoichiometric speciation of As(III) and As(V) is demonstrated as an example. This is based on a highly selective substoichiometric extraction of As(III) with thionalide and As(V) with tetraphenylarsonium chloride in the presence of an excess amount of pyrogallol. Coexistence of other diverse arsenic species including methylarsenic compounds does not give any interference to the selective determination of As(III) and As(V). For substoichiometric radioactivation, a novel application of the synergistic extraction system in a combination of a substoichiometric amount of thenoyltrifluoroacetone with an excess amount of phenanthroline is demonstrated for Yb as an example. Substoichiometric speciation based on the selective speration and an application of synergistic extraction to substoichiometric separation have additional possibilities in substoichiometry.     

Development and Optimization of Glaser–Hay Bioconjugations

The prevalence of bioconjugates in the biomedical sciences necessitates the development of novel mechanisms to facilitate their preparation. Towards this end, the translation of the Glaser–Hay coupling to an aqueous environment is examined, and its potential as a bioorthogonal conjugation reaction is demonstrated. This optimized, novel, and aqueous Glaser–Hay reaction is applied towards the development of bioconjugates utilizing protein expressed with an alkynyl unnatural amino acid. Unnatural amino acid technology provides a degree of bioorthognality and specificity not feasible with other methods. Moreover, the scope of the reaction is demonstrated through protein–small molecule couplings, small‐molecule–solid‐support couplings, and protein–solid‐support immobilizations.     

Homonuclear correlation experiments of half-integer quadrupolar nuclei using multiple-quantum techniques spinning at a P(4) magic angle

A new approach for obtaining structural information in half-integer quadrupolar nuclei is proposed and demonstrated. In this method, the two-dimensional multiple-quantum experiment is performed, spinning at one of the angles at which the fourth order Legendre polynomial vanishes (P4 magic angle). In such an experiment, the dipolar interaction is retained, whereas the second-order quadrupolar broadening is refocused by the MQ-1Q correlation scheme. By adding an exchange period to this pulse scheme, we performed efficient homonuclear correlation experiments in a regular magic angle spinning probe with minor modifications. The experiment is demonstrated on a model compound, and the results are briefly discussed.     

Parallel density matrix propagation in spin dynamics simulations

Several methods for density matrix propagation in parallel computing environments are proposed and evaluated. It is demonstrated that the large communication overhead associated with each propagation step (two-sided multiplication of the density matrix by an exponential propagator and its conjugate) may be avoided and the simulation recast in a form that requires virtually no inter-thread communication. Good scaling is demonstrated on a 128-core (16 nodes, 8 cores each) cluster.     

Adhesion and wetting in an aqueous environment: theoretical assessment of sensitivity to the solid surface energy

The sensitivity of contact angles in an aqueous environment to the surface energy of the solid is discussed. It is demonstrated that this sensitivity is much higher in an aqueous than in a vapor environment. The Girifalco-Good equation, in combination with the Owens-Wendt equation, is used for the approximate demonstrations. It is shown that the transition from complete wetting to complete dewetting by the aqueous phase in a solid-liquid-liquid system occurs over a much narrower range of the surface energy of the solid than in a solid-liquid-vapor system. It is also demonstrated that the contact angle may be extremely sensitive to small variations in the relationship between surface tensions and the corresponding interfacial tension.     

Synthesis of Camalexin and Related Analogues

Camalexin is synthesized on a gram scale by coupling of thiazole and indole in an amidoalkylation–oxidation sequence. Several high‐yielding implementations of this two‐step approach are demonstrated with variation of either the intermediate acyliminium reagent or the oxidation conditions. Benzo‐analogues and aza‐analogues of the natural product are also obtained by this method. As a side result, a new formylation of indole is demonstrated.     

On the physical adsorption of gases on carbon materials from molecular simulation

In this paper we present a series of work covering a range of aspects relating molecular simulation to experiment. The importance of surface mediation type effects to the adsorption of simple and complex gases is demonstrated. Coupled with the adsorption of simple gases is their projection area when used for surface area determination. The pressure dependence of a projection area is demonstrated for argon at 77 and 87.3 K. A simple model is used to account for the degree of graphitisation of a surface is demonstrated and used to account for the isosteric heat behaviour of non-graphitised carbon blacks. Turning from surfaces to porous solids, an alternative treatment of experiment data (either sub or super critical) is presented that avoids the ambiguity of excess amounts adsorbed. Using this method one is able to obtain pore size distributions and amounts adsorbed without relying on such things as helium expansion volumes. Since this type of method is usually applied to composite solids we also demonstrate the correct method for calculating the heat of adsorption using independent sets of simulations. The final topic covered in this paper is an example of the information that can be gained from the heat capacity of an adsorbed phase.     

Directing the Activation of Donor–Acceptor Cyclopropanes Towards Stereoselective 1,3‐Dipolar Cycloaddition Reactions by Brønsted Base Catalysis

The first stereoselective organocatalyzed [3+2] cycloaddition reaction of donor‐acceptor cyclopropanes is presented. It is demonstrated that by applying an optically active bifunctional Brønsted base catalyst, racemic di‐cyano cyclopropylketones can be activated to undergo a stereoselective 1,3‐dipolar reaction with mono‐ and polysubstituted nitroolefins. The reaction affords functionalized cyclopentanes with three consecutive stereocenters in high yield and stereoselectivity. Based on the stereochemical outcome, a mechanism in which the organocatalyst activates both the donor‐acceptor cyclopropane and nitroolefin is proposed. Finally, chemoselective transformations of the cycloaddition products are demonstrated.     

Virtual Screening in Search for a Chemical Probe for Angiotensin-Converting Enzyme 2 (ACE2)

We elaborate new models for ACE and ACE2 receptors with an excellent prediction power compared to previous models. We propose promising workflows for working with huge compound collections, thereby enabling us to discover optimized protocols for virtual screening management. The efficacy of elaborated roadmaps is demonstrated through the cost-effective molecular docking of 1.4 billion compounds. Savings of up to 10-fold in CPU time are demonstrated. These developments allowed us to evaluate ACE2/ACE selectivity in silico, which is a crucial checkpoint for developing chemical probes for ACE2.     

Ab initio molecular dynamics with dual basis set methods

On-the-fly, ab initio classical molecular dynamics are demonstrated with an underlying dual basis set potential energy surface. Dual-basis self-consistent field (Hartree-Fock and density functional theory) and resolution-of-the-identity second-order M?ller-Plesset perturbation theory (RI-MP2) dynamics are tested for small systems, including the water dimer. The resulting dynamics are shown to be faithful representations of their single-basis analogues for individual trajectories, as well as vibrational spectra. Computational cost savings of 58% are demonstrated for SCF methods, even relative to Fock-extrapolated dynamics, and savings are further increased to 71% with RI-MP2. Notably, these timings outperform an idealized estimate of extended-Lagrangian molecular dynamics. The method is subsequently demonstrated on the vibrational absorption spectrum of two NO(+)(H?O)? isomers and is shown to recover the significant width of the shared-proton bands observed experimentally.     

ULTRAMINE: a high-capacity polyethylene-imine-based polymer and its application as a scavenger resin

The synthesis of a novel high-loading polyethylene-imine resin (ULTRAMINE) is described, and its application as a scavenger resin in various acylation reactions is demonstrated. The inverse suspension polymerization technique was used for the synthesis of well-defined spherical polymer beads. Polymer beads with different cross-linking densities were synthesized according to the degree of acryloylation of the polyethylene-imine polymer. The resin was characterized by various spectroscopic techniques. The size, shape, and morphological features of the resin were demonstrated by microscopy. The resin showed excellent swelling properties in both polar and nonpolar solvents. The chemical stability of the resin in various reagents and solvents was investigated and monitored by IR spectroscopy. The mechanical stability of the beads was determined by a single-bead compressive experiment. The ULTRAMINE beads can be used as an excellent scavenger for excess acylating reagent, as demonstrated for a variety of reactions. ULTRAMINE-red resin was derived from ULTRAMINE through exhaustive reduction of the amide carbonyl groups to yield an all-amine resin.     

Sensitive, label-free DNA diagnostics based on near-field microwave imaging

Biological assays often rely on "reporter labels" to enhance measurement sensitivity, for example, by incorporation of a fluorescent dye or a nanoparticle into a nucleic acid or a protein. Use of labels, however, complicates sample preparation, increases assay costs, and can cause experimental artifacts by interfering with assay thermodynamics or limiting label stability. We evaluate near-field microwave imaging (NFMI) as an alternative, label-free technique for molecular diagnostics. Using DNA monolayers as an experimental model, NFMI is demonstrated to achieve sensitivities comparable to conventional fluorescence bioassays. Moreover, NFMI is shown to be compatible with imaging at resolutions required by microarray applications, as demonstrated by monitoring DNA hybridization in an array format.     

Single-capillary Teorell oscillator--studies with nonelectrolytes

It has been demonstrated that if in a Teorell oscillator, the membrane is replaced by a single capillary, the system behaves much better and becomes easily reproducible. It has also been demonstrated that oscillatory behavior in a Teorell-type setup is not limited to electrolytes; even nonelectrolytes can show oscillations. The only requirement seems to be that the nonelectrolyte should be capable of generating an electrical double layer in the capillary. This is the first report of a Teorell oscillator with a single capillary. Also, oscillations with nonelectrolytes in a Teorell-type setup have not been reported before.     

Nickeladihydrofuran. Key intermediate for nickel-catalyzed reaction of alkyne and aldehyde

The formation of a nickeladihydrofuran by oxidative cyclization of an alkyne and an aldehyde with nickel(0) has been demonstrated; the transformation of the nickeladihydrofuran into an enone by decomposition, a lactone by carbonylation and an allylic alcohol by treatment with ZnMe(2) suggests that nickeladihydrofuran is an important key intermediate in a variety of catalytic reactions.     

Stereocontrol in a combined allylic azide rearrangement and intramolecular Schmidt reaction

Pre-equilibration of an interconverting set of isomeric allylic azides is coupled with an intramolecular Schmidt reaction to afford substituted lactams stereoselectively. The effect of substitution and a preliminary mechanistic study are reported. The synthetic potential of this method is demonstrated in the context of an enantioselective synthesis of an advanced intermediate leading toward pinnaic acid.     

Interactions between a luminescent conjugated oligoelectrolyte and insulin during early phases of amyloid formation

Aggregates of misfolded proteins play an important role in diseases such as Alzheimer's. Here it is demonstrated how the anionic oligothiophene p-FTAA interacts with and influences pre-fibrillar protein assemblies during the earlier stages of in vitro fibrillation. Conjugated polythiophenes have previously been demonstrated to detect and discriminate between different types of protein aggregates and also introduce luminescent or conductive properties to these nanoscale fiber structures. Fluorescence spectroscopy, DLS, TEM and FCS are employed to follow the interplay between p-FTAA and insulin during in vitro fibrillation.     

Surface-immobilized self-assembled protein-based quantum dot nanoassemblies

Luminescent semiconductor quantum dot (QD)-based optical biosensors have the potential to overcome many of the limitations associated with using conventional organic dyes for biodetection. We have previously demonstrated a hybrid QD-protein-based fluorescence resonance energy transfer (FRET) sensor. Although the QD acted as an energy donor and a protein scaffold in the sensor, recognition and specificity were derived from the proteins. Transitioning this hybrid prototype sensor into flow cells and integrated devices will require a surface-immobilization strategy that allows the QD-based sensor to sample the environment and still maintain a distinct protein-covered QD architecture. We demonstrate a self-assembled strategy designed to accomplish this. Using glass slides coated with a monolayer of neutravidin (NA) as the template, QDs with maltose binding protein (MBP) and avidin coordinated to their surface were attached to the glass slides in discrete patterns using an intermediary bridge of biotinylated MBP or antibody linkers. Control of the surface location and concentration of the QD-protein-based structures is demonstrated. The utility of this self-assembly strategy is further demonstrated by assembling a QD-protein structure that allows the QDs to engage in FRET with a dye located on the surface-covering protein.     

Application of ion-exchange reactions between membranes and resins

The separation of a solution of an electrolyte from an ion-exchange resin by an ion-exchange membrane, where the charge sign of the fixed sites is the same, results in a process that is comparable to Donnan dialysis in its overall effect. That is, the counter-ions from the resin can be exchanged for ions of the same charge sign in the electrolyte. The reaction is demonstrated and the efficiency of the process evaluated by monitoring the metathesis of carbonic acid from sodium carbonate. An application of the metathesis of a non-electrolyte to a preconcentration method for ion chromatography is demonstrated.     

Nickel-catalyzed intermolecular codimerization of acrylates and alkynes

The linear codimerization of acrylates and alkynes to produce 1,3-dienes is successfully demonstrated using a nickel catalyst in association with 2-aminopyridine as an additive.