Combinatorial chemistry of materials,polymers and catalysts

The need for new materials and catalysts has never been satisfied by conventional methods. Chemical diversity is much too large to be explored systematically. Combinatorial chemistry applied to the discovery of new materials and catalysts can provide new lead structures, which has already been demonstrated by pioneers in the field. Combinatorial chemistry is much more than just a multiplication of experiments. In order to provide the results expected, combinatorial chemistry requires the combination of library preparation, characterization, identification of the desired properties and retrievable collection of the accumulated data in an intelligent data base. The state of the art of combinatorial chemistry in materials, polymer and catalysis research is reviewed. We have been engaged in the manual and automated preparation of catalyst libraries by liquid phase techniques (sol‐gel‐process and hydrothermal synthesis) for a variety of applications. The chemical nature of the components prepared on the library is not only a product of the liquid phase reaction conditions, but also of the drying and calcination process. High‐throughput characterization of the library components is therefor as important as the identification of desired materials properties. Automated micro‐X‐ray‐fluorescence spectrometry with a commercial instrument has been used successfully to identify chemical compositions of library components. Automated microdiffraction has been used to characterize the microstructure of the materials prepared. For the sensitive detection of reaction energies on catalyst libraries emissivity corrected IR‐thermography has been developed. It is used to identify catalytic activity of library components through the heat of reaction with high efficiency. This method has been applied to total oxidation, selective oxidation and hydrogenation reactions. Although much slower, but more detailed information was obtained with spatially resolved mass spectrometry. In a simple set‐up product composition of selective oxidation reactions have been scanned with the help of a simple gas analyzer (quadrupole mass spectrometer). A remarkable discrimination of product selectivity was recorded on a diverse library containing amorphous microporous mixed oxide catalysts. With high resolution MS more difficult problems, such as the differentiation of products of the same unit mass, such as CO, N₂ and ethylene can be solved in high throughput modes. The selectivities observed correlate well with the behaviour of the materials under conventional reaction conditions.     

Aqueous microwave chemistry: a clean and green synthetic tool for rapid drug discovery

The development of "Greener Organic Chemistry" is due to the recognition that environmentally friendly products and processes will be economical in the long term as they circumvent the need for treating 'end-of-the-pipe' pollutants and by-products generated by conventional synthesis. The fundamentals and significant outcomes of microwave-assisted organic synthesis in aqueous medium are summarized in this tutorial review, which have resulted in the development of relatively sustainable and environmentally benign protocols for the synthesis of drugs and fine chemicals.     

Single-molecule detection in solution: a new tool for analytical chemistry

Single-molecule detection (SMD) is becoming more and more popular in the scientific community and is on the threshold to become a technique for laboratory use. Therefore, conceivable applications as well as optimized conditions for SMD will be discussed. To point out the possibilities of SMD, the signal-to-background ratio and the detection efficiency, in combination with the probability of misclassification, will be contemplated.     

Single-molecular detection in solution: a new tool for analytical chemistry

Single-molecule detection (SMD) is becoming more and more popular in the scientific community and is on the threshold to become a technique for laboratory use. Therefore, conceivable applications as well as optimized conditions for SMD will be discussed. To point out the possibilities of SMD, the signal-to-background ratio and the detection efficiency, in combination with the probability of misclassification, will be contemplated.     

A fully integrated high-throughput screening methodology for the discovery of new polyolefin catalysts: discovery of a new class of high temperature single-site group (IV) copolymerization catalysts

For the first time, new catalysts for olefin polymerization have been discovered through the application of fully integrated high-throughput primary and secondary screening techniques supported by rapid polymer characterization methods. Microscale 1-octene primary screening polymerization experiments combining arrays of ligands with reactive metal complexes M(CH(2)Ph)(4) (M = Zr, Hf) and multiple activation conditions represent a new high-throughput technique for discovering novel group (IV) polymerization catalysts. The primary screening methods described here have been validated using a commercially relevant polyolefin catalyst, and implemented rapidly to discover the new amide-ether based hafnium catalyst [eta(2)-(N,O)[bond](2-MeO[bond]C(6)H(4))(2,4,6-Me(3)C(6)H(2))N]Hf(CH(2)Ph)(3) (1), which is capable of polymerizing 1-octene to high conversion. The molecular structure of 1 has been determined by X-ray diffraction. Larger scale secondary screening experiments performed on a focused 96-member amine-ether library demonstrated the versatile high temperature ethylene-1-octene copolymerization capabilities of this catalyst class, and led to significant performance improvements over the initial primary screening discovery. Conventional one gallon batch reactor copolymerizations performed using selected amide-ether hafnium compounds confirmed the performance features of this new catalyst class, serving to fully validate the experimental results from the high-throughput approaches described herein.     

Systems biology and systems chemistry: new directions for drug discovery

Improvements in drug design have historically been centered around structure-based optimization of molecule specificity for a targeted protein, in an effort to reduce unintentional binding to other proteins and off-target effects. Although the "one-to-one" drug design strategy has been successful in impairing function of targets associated with a number of diseases, recent reports of drug promiscuity, which are a potential source of adverse reactions in patients, make a case to refine the drug design strategy such that it includes an awareness of multiple interactions from both ligand and protein perspectives. Polypharmacology and chemical biology studies are amassing interaction data at rapid rates, and the integration of such data into an interpretable model requires zooming our perspective out from the single ligand-target level to the larger network-wide level. We review some of the recent developments in systems-level research for drug design and discovery, and discuss the directions that some drug design efforts are heading toward.     

Lambda-display: a powerful tool for antigen discovery

Since its introduction in 1985, phage display technology has been successfully used in projects aimed at deciphering biological processes and isolating molecules of practical value in several applications. Bacteriophage lambda, representing a classical molecular cloning and expression system has also been exploited for generating large combinatorial libraries of small peptides and protein domains exposed on its capsid. More recently, lambda display has been consistently and successfully employed for domain mapping, antigen discovery and protein interaction studies or, more generally, in functional genomics. We show here the results obtained by the use of large libraries of cDNA and genomic DNA for the molecular dissection of the human B-cell response against complex pathogens, including protozoan parasites, bacteria and viruses. Moreover, by reviewing the experimental work performed in recent investigations we illustrate the potential of lambda display in the diagnostics field and for identifying antigens useful as targets for vaccine development.     

In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery

Here, we propose an in silico fragment-mapping method as a potential tool for fragment-based/structure-based drug discovery (FBDD/SBDD). For this method, we created a database named Canonical Subsite–Fragment DataBase (CSFDB) and developed a knowledge-based fragment-mapping program, Fsubsite. CSFDB consists of various pairs of subsite–fragments derived from X-ray crystal structures of known protein–ligand complexes. Using three-dimensional similarity-matching between subsites on one protein and another, Fsubsite compares the surface of a target protein with all subsites in CSFDB. When a local topography similar to the subsite is found on the surface, Fsubsite places a fragment combined with the subsite in CSFDB on the target protein. For validation purposes, we applied the method to the apo-structure of cyclin-dependent kinase 2 (CDK2) and identified four compounds containing three mapped fragments that existed in the list of known inhibitors of CDK2. Next, the utility of our fragment-mapping method for fragment-growing was examined on the complex structure of tRNA-guanine transglycosylase with a small ligand. Fsubsite mapped appropriate fragments on the same position as the binding ligand or in the vicinity of the ligand. Finally, a 3D-pharmacophore model was constructed from the fragments mapped on the apo-structure of heat shock protein 90-α (HSP90α). Then, 3D pharmacophore-based virtual screening was carried out using a commercially available compound database. The resultant hit compounds were very similar to a known ligand of HSP90α. As a result of these findings, this in silico fragment-mapping method seems to be a useful tool for computational FBDD and SBDD.     

Metal-mediated thiol-disulfide interconversion--a new tool for metallosupramolecular chemistry

Metal-mediated redox-interconversion of the new ligand 2,2':6',2'-terpyridine-6(1H)-thione and the corresponding disulfide allows the programmed assembly of dinucleating ligands.     

High-throughput approaches for the discovery and optimization of new olefin polymerization catalysts

The discovery of new olefin polymerization catalysts is currently a time-intensive trial-and-error process with no guarantee of success. A fully integrated high-throughput screening workflow for the discovery of new catalysts for polyolefin production has been implemented at Symyx Technologies. The workflow includes the design of the metal-ligand libraries using custom-made computer software, automated delivery of metal precursors and ligands into the reactors using a liquid-handling robot, and a rapid primary screen that serves to assess the potential of each metalligand-activator combination as an olefin polymerization catalyst. "Hits" from the primary screen are subjected to secondary screens using a 48-cell parallel polymerization reactor. Individual polymerization reactions are monitored in real time under conditions that provide meaningful information about the performance capabilities of each catalyst. Rapid polymer characterization techniques support the primary and secondary screens. We have discovered many new and interesting catalyst classes using this technology.     

Infrared intensities: A new tool in chemistry.

The interpretation of the infrared intensities in terms of atomic polar tensors and of electrooptical parameters allows to derive rich information on the charge distribution in the molecules. Using the results of several studies of this kind, it is now possible to derive information on intramolecular and intermolecular interactions even from “poor” data such as absolute intensities of whole regions in the spectrum or even from relative intensities.     

Flow electrochemistry: a safe tool for fluorine chemistry

The heightened activity of compounds containing fluorine, especially in the field of pharmaceuticals, provides major impetus for the development of new fluorination procedures. A scalable, versatile, and safe electrochemical fluorination protocol is conferred. The strategy proceeds through a transient (difluoroiodo)arene, generated by anodic oxidation of an iodoarene mediator. Even the isolation of iodine(iii) difluorides was facile since electrolysis was performed in the absence of other reagents. A broad range of hypervalent iodine mediated reactions were achieved in high yields by coupling the electrolysis step with downstream reactions in flow, surpassing limitations of batch chemistry. (Difluoroiodo)arenes are toxic and suffer from chemical instability, so the uninterrupted generation and immediate use in flow is highly advantageous. High flow rates facilitated productivities of up to 834 mg h⁻¹ with vastly reduced reaction times. Integration into a fully automated machine and in-line quenching was key in reducing the hazards surrounding the use of hydrofluoric acid.

A scalable, efficient and safe electrochemical fluorination protocol is conferred. A broad range of iodine(iii) mediated transformations were performed in high yields without exposure to toxic HF.     

Reversible Michael addition of thiols as a new tool for dynamic combinatorial chemistry

The Michael addition of thiols to enones is reported as a new method for dynamic combinatorial library synthesis.     

Combinatorial discovery of new methanol-tolerant non-noble metal cathode electrocatalysts for direct methanol fuel cells

Combinatorial synthesis and screening were used to identify methanol-tolerant non-platinum cathode electrocatalysts for use in direct methanol fuel cells (DMFCs). Oxygen reduction consumes protons at the surface of DMFC cathode catalysts. In combinatorial screening, this pH change allows one to differentiate active catalysts using fluorescent acid-base indicators. Combinatorial libraries of carbon-supported catalyst compositions containing Ru, Mo, W, Sn, and Se were screened. Ternary and quaternary compositions containing Ru, Sn, Mo, Se were more active than the "standard" Alonso-Vante catalyst, Ru(3)Mo(0.08)Se(2), when tested in liquid-feed DMFCs. Physical characterization of the most active catalysts by powder X-ray diffraction, gas adsorption, and X-ray photoelectron spectroscopy revealed that the predominant crystalline phase was hexagonal close-packed (hcp) ruthenium, and showed a surface mostly covered with oxide. The best new catalyst, Ru(7.0)Sn(1.0)Se(1.0), was significantly more active than Ru(3)Se(2)Mo(0.08), even though the latter contained smaller particles.     

Lectin microarrays: a powerful tool for glycan-based biomarker discovery

Cell surfaces, especially mammalian cell surfaces, are heavily coated with complex poly- and oligosaccharides, and these glycans have been implicated in many functions, such as cell-to-cell communication, host-pathogen interactions and cell matrix interactions. Not surprisingly then, the aberrations of glycosylation are usually indicative of the onset of specific diseases, such as cancer. Therefore, glycans are expected to serve as important biomarkers for disease diagnosis and/or prognosis. Recent development of the lectin microarray technology has allowed researchers to profile the glycans in complex biological samples in a high throughput fashion. This relatively new tool is highly suitable for both live cell and cell lysate analyses and has the potential for rapid discovery of glycan-based biomarkers. In this review, we will focus on the basic concepts and the latest advances of lectin microarray technology. We will also emphasize the application of lectin microarrays for biomarker discovery, and then discuss the challenges faced by this technology and potential future directions. Based on the tremendous progress already achieved, it seems apparent that lectin microarrays will soon become an indispensible tool for glycosylation biomarker discovery.     

Deoxyribozymes: DNA catalysts for bioorganic chemistry

Deoxyribozymes are DNA molecules with catalytic activity. For historical and practical reasons, essentially all reported deoxyribozymes catalyze reactions of nucleic acid substrates, although this is probably not a fundamental limitation. In vitro selection strategies have been used to identify many deoxyribozymes that catalyze RNA cleavage, RNA and DNA ligation, and a variety of covalent modification reactions of nucleic acid substrates. Many deoxyribozymes are capable of catalysis with substantial rate enhancements reaching up to 10(10)-fold over background, and their very high selectivities would often be difficult or impossible to achieve using traditional organic synthesis approaches. This report summarizes the current utility and potential future applications of deoxyribozymes from the bioorganic chemistry perspective.     

Chromatography: An important tool for drug discovery

Despite substantial developments of extraction and separation techniques, isolation of natural products from natural sources is still a challenging task. Undoubtedly hybrid methods like liquid chromatography with NMR spectroscopy or liquid chromatography coupled with mass spectrometry made on‐line structure elucidation possible and provided impressive examples of natural product identification without prior isolation, however, in many cases the necessity to get the purified compounds in hand is still a fact. The process begins with the collection of desired plant material which is subjected to the suitable extraction process. The complex crude extracts are then monitored by various chromatographic procedures to separate and quantify the desired compounds. The active plant extracts are then fractionated to isolate the bioactive compounds in their pure form. The fully identified compound is used as a lead for the production of related analogues to modulate the biological activity and to carry out structure‐activity relationship. The major isolated bioactive compound is used for semi‐synthetic modification or total synthesis should be carried out such that it is relatively easy to modify the structure of the lead compound. This is a simple and cost‐effective way to increase the chance to discover lead compounds. The biological activity in vitro and in vivo has to be done after purification.