Computer-designed repurposing of chemical wastes into drugs.

As the chemical industry continues to produce considerable quantities of waste chemicals1,2, it is essential to devise 'circular chemistry'3-8 schemes to productively back-convert at least a portion of these unwanted materials into useful products. Despite substantial progress in the degradation of some classes of harmful chemicals9, work on 'closing the circle'-transforming waste substrates into valuable products-remains fragmented and focused on well known areas10-15. Comprehensive analyses of which valuable products are synthesizable from diverse chemical wastes are difficult because even small sets of waste substrates can, within few steps, generate millions of putative products, each synthesizable by multiple routes forming densely connected networks. Tracing all such syntheses and selecting those that also meet criteria of process and 'green' chemistries is, arguably, beyond the cognition of human chemists. Here we show how computers equipped with broad synthetic knowledge can help address this challenge. Using the forward-synthesis Allchemy platform16, we generate giant synthetic networks emanating from approximately 200 waste chemicals recycled on commercial scales, retrieve from these networks tens of thousands of routes leading to approximately 300 important drugs and agrochemicals, and algorithmically rank these syntheses according to the accepted metrics of sustainable chemistry17-19. Several of these routes we validate by experiment, including an industrially realistic demonstration on a 'pharmacy on demand' flow-chemistry platform20. Wide adoption of computerized waste-to-valuable algorithms can accelerate productive reuse of chemicals that would otherwise incur storage or disposal costs, or even pose environmental hazards.

Programmed Formation of HCN Oligomers through Organosulfur Catalysis.

An efficient, inexpensive, and reliable synthesis of diaminomaleonitrile (DAMN, 1) is described starting from readily available acetone cyanohydrin as the source of hydrogen cyanide (HCN). Diaminomaleonitrile (DAMN) is known to be an important intermediate in heterocyclic and medicinal chemistry as well as being a possible precursor for the origin of life's hypothesis within prebiotic chemistry. The mechanism of its formation through organosulfur catalysis has been investigated by electrospray ionization mass spectrometry (ESI-MS) using two newly synthesized cationic "marker" molecules as a tool that allows for sensitive detection. As a result, the proposed mechanism of a thiocyanate-mediated synthesis of the HCN tetramer DAMN starting from organic disulfides was confirmed.

Synthesis of multi-substituted pyridines from ylidenemalononitriles and their emission properties.

Numerous methodologies to obtain pyridines from ylidenemalononitriles are described in the literature. Nevertheless, they are limited to the use of microwave or conventional heat and few lead to 2,3,4 or 2,3,4,5-substituted pyridines as multi-proposal molecular scaffolds or even universal pyridines. Herein, we present a mild and facile solvent-free methodology to obtain a scope of multi-substituted pyridines at room temperature. We also report an example where one of the resulting amino-nicotinonitriles exhibits a preliminary evidence of aggregation-induced emission (AIE).

Increasing Scope of Clickable Fluorophores: Electrophilic Substitution of Ylidenemalononitriles.

Recently, we demonstrated that ylidenemalononitriles (YMs) react with amines to form cyclic amidines and that the starting linear YMs are nonemissive in solution and the cyclic amidines are fluorescent. These turn-on systems were of interest to us because of their potential as biosensors and synthons for accessing functionalized pyridines. While our original method was promising, several limitations persisted, including access to more functionalized and polar-solvent-soluble structures as well as increased control over the rate of cyclization. Herein, we report a new approach that allows the electrophilic substitution of YMs. These substituted YMs exhibit faster turn-on rates, color tunability, access to polar-solvent-soluble species, and increased control over cyclization rate. This allowed us to significantly expand the fluorophore's chemical space.

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel-Hauser amides, and magnesium alkoxides.

Magnesium organometallic reagents occupy a central position in organic synthesis. The freshness of these compounds is the key for achieving a high conversion and reproducible results. Common methods for the synthesis of Grignard reagents from metallic magnesium present safety issues and exhibit a batch-to-batch variability. Tubular reactors of solid reagents combined with solution-phase reagents enable the continuous-flow preparation of organomagnesium reagents. The use of stratified packed-bed columns of magnesium metal and lithium chloride for the synthesis of highly concentrated turbo Grignards is reported. A low-cost pod-style synthesizer prototype, which incorporates single-use prepacked perfluorinated cartridges and bags of reagents for the automated on-demand lab-scale synthesis of carbon, nitrogen, and oxygen turbo magnesium bases is presented. This concept will provide access to fresh organomagnesium reagents on a discovery scale and will do so independent from the operator's experience in flow and/or organometallic chemistry.

Continuous Endoperoxidation of Conjugated Dienes and Subsequent Rearrangements Leading to C-H Oxidized Synthons.

We have investigated the continuous flow photooxidation of several conjugated dienes and subsequent rearrangement using a practical and safe continuous-flow homemade engineered setup. End-to-end approaches involving endoperoxidation, Kornblum-DeLaMare rearrangement, and additional rearrangements are comprehensively detailed with optimization, scope, and scale-up to obtain useful hydroxyenones, furans, and 1,4-dicarbonyl building blocks.

Facile Conversion of Red Phosphorus into Soluble Polyphosphide Anions by Reaction with Potassium Ethoxide.

Soluble polyphosphide anions were successfully generated in a number of organic solvents by the reaction between shelf-stable red phosphorus and potassium ethoxide. The species were identified by (31)P NMR spectroscopy in solution and by X-ray crystal-structure determination of (Bu4N)2P16 in the solid state. The reaction was scaled up to gram quantities by using a flow-chemistry process.

Synthesis and Reactivity Profile of Ylidenemalononitrile Enamines and Their Ester Analogs Towards Electrophiles and Nucleophiles.

Herein, we describe the synthesis and reactivity of enamines derived from ylidenemalononitriles and ylidenecyanoacetates. The enamine scope was expanded by (1) increasing yields of aldehyde-derived ylidenemalononitriles, (2) incorporating silyl functionalities, and (3) using other amide acetals to expand the substitution patterns of pyridines resulting from enamine cyclization. In addition, methods to produce α-pyrones and polysubstituted pyridines from both ylidenemalononitriles and ylidenecyanoacetates are described.

A concise flow synthesis of efavirenz.

Efavirenz is an essential medicine for the treatment of HIV, which is still inaccessible to millions of people worldwide. A novel, semi-continuous process provides rac-Efavirenz with an overall yield of 45%. This streamlined proof-of-principle synthesis relies on the efficient copper-catalyzed formation of an aryl isocyanate and a subsequent intramolecular cyclization to install the carbamate core of Efavirenz in one step. The three-step method represents the shortest synthesis of this life-saving drug to date.

Ylidenemalononitrile enamines as fluorescent "turn-on" indicators for primary amines.

Ylidenemalononitrile enamines undergo rapid amine exchange followed by a cyclization with primary amines to yield fluorescent products with emission intensities as high as 900 times greater than the starting materials. After identifying the fluorescent species by X-ray crystallography, we demonstrate that the rate of amine exchange is substrate dependent and that by simple structural variation the fluorescence can be tuned over the entire visible spectrum. We further demonstrate their potential application in biomolecule labeling.

Organic reaction systems: using microcapsules and microreactors to perform chemical synthesis.

The appetite for complex organic molecules continues to increase worldwide, especially in rapidly developing countries such as China, India, and Brazil. At the same time, the cost of raw materials and solvent waste disposal is also growing, making sustainability an increasingly important factor in the production of synthetic life-saving/improving compounds. With these forces in mind, our group is driven by the principle that how we synthesize a molecule is as important as which molecule we choose to synthesize. We aim to define alternative strategies that will enable more efficient synthesis of complex molecules. Drawing our inspiration from nature, we attempt to mimic (1) the multicatalytic metabolic systems within cells using collections of nonenzyme catalysts in batch reactors and (2) the serial synthetic machinery of fatty acid/polyketide biosynthesis using microreactor systems. Whether we combine catalysts in batch to prepare an active pharmaceutical ingredient (API) or use microreactors to synthesize small or polymeric molecules, we strive to understand the mechanism of each reaction while also developing new methods and techniques. This Account begins by examining our early efforts in the development of novel catalytic materials and characterization of catalytic systems and how these observations helped forge our current models for developing efficient synthetic routes. The Account progresses through a focused examination of design principles needed to develop multicatalyst systems using systems recently published by our group as examples. Our systems have been successfully applied to produce APIs as well as new synthetic methods. The multicatalyst section is then juxtaposed with our work in continuous flow multistep synthesis. Here, we discuss the design principles needed to create multistep continuous processes using examples from our recent efforts. Overall, this Account illustrates how multistep organic routes can be conceived and achieved using strategies and techniques that mimic biological systems.

Continuous-flow oxidative cyanation of primary and secondary amines using singlet oxygen.

Primary and secondary amines can be rapidly and quantitatively oxidized to the corresponding imines by singlet oxygen. This reactive form of oxygen was produced using a variable-temperature continuous-flow LED-photoreactor with a catalytic amount of tetraphenylporphyrin as the sensitizer. α-Aminonitriles were obtained in good to excellent yields when trimethylsilyl cyanide served as an in situ imine trap. At 25°C, primary amines were found to undergo oxidative coupling prior to cyanide addition and yielded secondary α-aminonitriles. Primary α-aminonitriles were synthesized from the corresponding primary amines for the first time, by an oxidative Strecker reaction at -50 °C. This atom-economic and protecting-group-free pathway provides a route to racemic amino acids, which was exemplified by the synthesis of tert-leucine hydrochloride from neopentylamine.

Fluorescent THF-based fructose analogue exhibits fructose-dependent uptake.

Recent publications suggest that high dietary fructose might play a significant role in cancer metabolism and can exacerbate a number of aspects of metabolic syndrome. Addressing the role that fructose plays in human health is a controversial question and requires a detailed understanding of many factors including the mechanism of fructose transport into healthy and diseased cells. Fructose transport into cells is thought to be largely mediated by the passive hexose transporters Glut2 and Glut5. To date, no probes that can be selectively transported by one of these enzymes but not by the other have been identified. The data presented here indicate that, in MCF-7 cells, a 1-amino-2,5-anhydro-D-mannitol-based fluorescent NBDM probe is transported twice as efficiently as fructose and that this takes place with the aid of Glut5. Its Glut5 specificity and differential uptake in cancer cells and in normal cells suggest this NBDM probe as a potentially useful tool for cross-cell-line correlation of Glut5 transport activity.

Applying flow chemistry: methods, materials, and multistep synthesis.

The synthesis of complex molecules requires control over both chemical reactivity and reaction conditions. While reactivity drives the majority of chemical discovery, advances in reaction condition control have accelerated method development/discovery. Recent tools include automated synthesizers and flow reactors. In this Synopsis, we describe how flow reactors have enabled chemical advances in our groups in the areas of single-stage reactions, materials synthesis, and multistep reactions. In each section, we detail the lessons learned and propose future directions.

Passive fructose transporters in disease: a molecular overview of their structural specificity.

The SLC2 family of facilitative Glucose transporters (Gluts) contains 14 isoforms divided into three classes based on amino acid sequence. While the majority of these proteins transport glucose, a subset can transport fructose. Recently, fructose and the Gluts responsible for fructose uptake have received increased interest due to the correlation between high fructose consumption and early onset of metabolic syndrome. In addition, the up-regulation of Gluts in certain cancers has made possible the development of a number of fructose probes for imaging cancer. Although structure activity data has defined some aspects of fructose-specific uptake, a far more detailed clarification of the variables governing the onset and progression of fructose-correlated diseases is still needed. Here, we summarize what is known about molecular structure and fructose uptake as it relates to the correlation of fructose and disease.

Flow synthesis of a versatile fructosamine mimic and quenching studies of a fructose transport probe.

We describe the synthesis of 1-amino-2,5-anhydro-D-mannose ("mannitolamine"), a key intermediate to the 7-nitro-1,2,3-benzadiazole conjugate (NBDM), using commercially available fluidic devices to increase the throughput. The approach is the first example of a flow-based Tiffeneau-Demjanov rearrangement. Performing this step in flow enables a ~64-fold throughput enhancement relative to batch. The flow process enables the synthesis to be accomplished three times faster than the comparable batch route. The high throughput enabled the production of larger quantities of the fluorescent fructose transport probe NBDM, enabling us to measure key photophysical properties that will facilitate future uptake studies.

Investigating the continuous synthesis of a nicotinonitrile precursor to nevirapine.

2-Chloro-3-amino-4-picoline (CAPIC) is a strategic building block for the preparation of nevirapine, a widely-prescribed non-nucleosidic reverse transcriptase inhibitor for the treatment of HIV-infected patients. A continuous synthesis to the bromo derivative of a CAPIC intermediate, 2-bromo-4-methylnicotinonitrile, that terminates in a dead-end crystallization is described. The route uses inexpensive, acyclic commodity-based raw materials and has the potential to enable lower cost production of nevirapine as well as other value added structures that contain complex pyridines. The route terminates in a batch crystallization yielding high purity CAPIC. This outcome is expected to facilitate regulatory implementation of the overall process.

Iterative asymmetric allylic substitutions: syn- and anti-1,2-diols through catalyst control.

A copper-catalyzed asymmetric allylic boronation (AAB) gives access to syn- and anti-1,2-diols. The method facilitates an iterative strategy for the preparation of polyols, such as the fully differentiated L-ribo-tetrol and protected D-arabino-tetrol. P=protecting group.

Development of a Practical Synthesis of the 8-FDC Fragment of OPC-167832.

A concise and practical synthesis has been developed to provide the 8-fluoro-5-hydroxy-3,4-diydrocarbostyril (8-FDC) fragment of OPC-167832 in 41% yield and in >99% purity over four steps from 3-amino-4-fluorophenol. The key feature of this process is the development of a telescoped one-pot synthesis of the quinolone via a chemoselective amidation/acid-induced cyclization that allows for simple product isolation without the need for column chromatography.

Stereoconvergent synthesis of chiral allylboronates from an E/Z mixture of allylic aryl ethers using a 6-NHC-Cu(I) catalyst.

We present a 6-NHC-Cu(I) complex that provides α-substituted allylboronates using allylic aryl ether substrates. The method was discovered by comparison of the chemoselectivities exhibited by complexes 1a, 1b, 2, and 3. We observed that 1a preferentially reacts with electron-rich alkenes over electron-deficient alkenes. Development of an asymmetric method revealed that 1b reacts with both the E and Z isomers to provide the same absolute configuration without showing E-Z isomerization. This stereoconvergent reaction occurs with high yields (av 86%), high S(N)2' selectivity (>99:1), and high ee (av 94%) and exhibits wide functional-group tolerance using pure E or Z isomer or E/Z alkene mixtures. The stereoconvergent feature enables the use of many different olefination strategies for substrate production, including cross-metathesis. Chiral allylboronates could be purified by silica gel chromatography and stored in the freezer without decomposition.