Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy

We present an extension of our Molecular Transformer model combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state of the art for predicting reactants as well as reagents, solvents and catalysts for each retrosynthetic step. We introduce four metrics (coverage, class diversity, round-trip accuracy and Jensen–Shannon divergence) to evaluate the single-step retrosynthetic models, using the forward prediction and a reaction classification model always based on the transformer architecture. The hypergraph is constructed on the fly, and the nodes are filtered and further expanded based on a Bayesian-like probability. We critically assessed the end-to-end framework with several retrosynthesis examples from literature and academic exams. Overall, the frameworks have an excellent performance with few weaknesses related to the training data. The use of the introduced metrics opens up the possibility to optimize entire retrosynthetic frameworks by focusing on the performance of the single-step model only.

We present an extension of our Molecular Transformer model combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention.     

General method for the synthesis of caged phosphopeptides: tools for the exploration of signal transduction pathways

[reaction: see text] An interassembly approach for the synthesis of peptides containing 1-(2-nitrophenyl)ethyl-caged phosphoserine, -threonine, and -tyrosine has been developed. Photochemical uncaging of these peptides releases the 2-nitrophenylethyl protecting group to afford the corresponding phosphopeptide. The peptides described herein are based on phosphorylation sites of kinases involved in cell movement or cell cycle regulation and demonstrate the versatility of the method and compatibility with the synthesis of polypeptides, including a variety of encoded amino acids.     

A simple protocol for the comparative analysis of the structure and occurrence of biochemical pathways across superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html . The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in Cu(A) assembly in more than a thousand prokaryotes.     

Regio and stereoselective catalytic five-component cascades of diverse heterocyclic bisallenes: tri-directional exploration of biochemical space

We report protecting group free Pd(0) catalyzed cascade syntheses of molecular scaffolds built from heterocyclic bisallenes. These generate novel molecular architecture permitting tri-directional exploration of biochemical space.     

Electrochemistry Enabling Stereoselective Diamination of Alkenes

To achieve the stereoselective and regioselective diamination of alkenes,Xu et al.developed an electrochemical protocol for the diamination of aryl alkenes with sulfamides by using triarylamine as a redox mediator.The chemistry proceeded in an undivided cell under constant current conditions,featuring not only wide scope of substrates and reasonable yields,but also excellent diastereoselectivity(>20:1 dr)and regioselectivity.This work has been published in the Nature Communications and can be reached at https://doi.org/10.1038/s41467-019-13024-5.     

Enabling Heterologous Synthesis of Lupulones in the Yeast Saccharomyces cerevisiae

Lupulones, naturally produced by glandular trichomes of hop (Humulus lupulus), are prenylated phloroglucinol derivatives that contribute the bitter flavor of beer and demonstrate antimicrobial and anticancer activities. It is appealing to develop microbial cell factories such that lupulones may be produced via fermentation technology in lieu of extraction from limited plant resources. In this study, the yeast Saccharomyces cerevisiae transformants harboring a synthetic lupulone pathway that consisted of five genes from hop were constructed. The transformants accumulated several precursors but failed to accumulate lupulones. Overexpression of 3-hydroxy-3-methyl glutaryl co-enzyme A reductase, the key enzyme in precursor formation in the mevalonate pathway, also failed to achieve a detectable level of lupulones. To decrease the consumption of the precursors, the ergosterol biosynthesis pathway was chemically downregulated by a small molecule ketoconazole, leading to successful production of lupulones. Our study demonstrated a combination of molecular biology and chemical biology to regulate the metabolism for heterologous production of lupulones. The strategy may be valuable for future engineering microbial process for other prenylated natural products.

     

Regioselective Magneto-optical Heteronanorods Enabling Chiroptical Activity

Synthesis of colloidal heterostructures with rational design and controllable precision represents a promising strategy for achieving novel properties and applications. Most recently, Zhuang et al. reported a "double-buffer-layer engineering" concept that was capable of regioselectively growing magnetic Fe₃O₄ nanodomains only at single ends of semiconductor Zn_xCd_1-xS(0 ≤ x ≤ 1) nanorods. The resulting composite nanostructures exhibited chiroptical activity due to the local magnetic fields introduced by regiospecific magnetic nanodomains, highlighting the promise of controlled colloidal chemistry in synthesizing chiroptical nanostructures in the absence of chiral molecules and helical geometries. The work has been published online in Nature Nanotechnology on January 20, 2020.     

Enabling the Li-ion conductivity of Li-metal fluorosulphates by ionic liquid grafting

Recently unveiled ‘alkali metal fluorosulphate (AMSO₄F)’ class of compounds offers promising electrochemical and transport properties. Registering conductivity value as high as 10⁻⁷ S cm⁻¹ in NaMSO₄F phases, we explored the fluorosulphate group to design novel compounds with high Li-ion conductivity suitable for solid electrolyte applications. In the process, we produced sillimanite-structured LiZnSO₄F by low temperature synthesis (T ≤ 300 °C). Examining this phase, we accidentally discovered the possibility of improving the ionic conductivity of poor conductors by forming a monolayer of ionic liquid at their particle surface. This phenomenon was studied by solid-state NMR, XPS and AC impedance spectroscopy techniques. Further, similar trends were noticed in other fluorosulphate materials like tavorite LiCoSO₄F and triplite LiMnSO₄F. With this study, we propose ‘ionic liquid grafting’ as an interfacial route to enable good Li-ion conductivity in otherwise poor conducting ceramics.     

Diastereoselective Alkene Hydroesterification Enabling the Synthesis of Chiral Fused Bicyclic Lactones

Palladium-catalysed diastereoselective hydroesterification of alkenes assisted by the coordinative hydroxyl group in the substrate afforded a variety of chiral γ-butyrolactones bearing two stereocenters. Employing the carbonylation-lactonization products as the key intermediates, the route from the alkenes with single chiral center to chiral THF-fused bicyclic γ-lactones containing three stereocenters was developed.     

Recovery Techniques Enabling Circular Chemistry from Wastewater

In an era where it becomes less and less accepted to just send waste to landfills and release wastewater into the environment without treatment, numerous initiatives are pursued to facilitate chemical production from waste. This includes microbial conversions of waste in digesters, and with this type of approach, a variety of chemicals can be produced. Typical for digestion systems is that the products are present only in (very) dilute amounts. For such productions to be technically and economically interesting to pursue, it is of key importance that effective product recovery strategies are being developed. In this review, we focus on the recovery of biologically produced carboxylic acids, including volatile fatty acids (VFAs), medium-chain carboxylic acids (MCCAs), long-chain dicarboxylic acids (LCDAs) being directly produced by microorganisms, and indirectly produced unsaturated short-chain acids (USCA), as well as polymers. Key recovery techniques for carboxylic acids in solution include liquid-liquid extraction, adsorption, and membrane separations. The route toward USCA is discussed, including their production by thermal treatment of intracellular polyhydroxyalkanoates (PHA) polymers and the downstream separations. Polymers included in this review are extracellular polymeric substances (EPS). Strategies for fractionation of the different fractions of EPS are discussed, aiming at the valorization of both polysaccharides and proteins. It is concluded that several separation strategies have the potential to further develop the wastewater valorization chains.     

Ultrapermeable Gel Membranes Enabling Superior Carbon Capture

Membrane technology is rapidly gaining broad attraction as a viable alternative for carbon capture to mitigate increasingly severe global warming. Emerging CO₂-philic membranes have become crucial players in efficiently separating CO₂ from light gases, leveraging their exceptional solubility-selectivity characteristics. However, economic and widespread deployment is greatly dependent on the boosted performance of advanced membrane materials for carbon capture. Here, we design a unique gel membrane composed of CO₂-philic molecules for accelerating CO₂ transportation over other gases for ultrapermeable carbon capture. The molecular design of such soft membranes amalgamates the advantageous traits of augmented permeation akin to liquid membranes and operational stability akin to solid membranes, effectively altering the membrane's free volume characteristics validated by both experiments and molecular dynamics simulation. Surprisingly, gas diffusion through the free-volume-tuned gel membrane undergoes a 9-fold improvement without compromising the separation factor for the superior solubility selectivity of CO₂-philic materials, and CO₂ permeability achieves a groundbreaking record of 5608 Barrer surpassing the capabilities of nonfacilitated CO₂ separation materials and exceeding the upper bound line established in 2019 even by leading-edge porous polymer materials. Our designed gel membrane can maintain exceptional separation performance during prolonged operation, enabling the unparalleled potential of solubility-selective next-generation materials towards sustainable carbon capture.     

ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways

This article proposes a method to efficiently generate approximate ligand unbinding pathways. It combines an efficient tree‐based exploration method with a morphing technique from Computer Graphics for dimensionality reduction. This method is computationally cheap and, unlike many existing approaches, does not require a reaction coordinate to guide the search. It can be used for finding pathways with known or unknown directions beforehand. The approach is evaluated on several benchmarks and the obtained solutions are compared with the results from other state‐of‐the‐art approaches. We show that the method is time‐efficient and produces pathways in good agreement with other state‐of‐the‐art solutions. These paths can serve as first approximations that can be used, analyzed, or improved with more specialized methods. © 2018 Wiley Periodicals, Inc.     

Enabling a circular economy for chemicals in plastics

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Controlled processing of polymer nanoribbons: Enabling microhelix transformations

Flow‐coated, two‐dimensional polymer ribbon structures undergo a shape‐transformation into a three‐dimensional helix upon their release into a solution. Driven by surface forces and due to geometric asymmetry, the helix radius and spring constant depend upon the ribbon cross‐section dimensions, surface energy, and material elastic modulus. Such spring‐like microhelices offer multiple functionalities combined with mechanical stretching and shape recovery. Fabricating such microhelices requires a sequence of processing steps, beginning with flow‐coating of ribbons on a substrate, followed by etching of a “scum layer” to allow for an independent release into a solution, upon which shape‐transformation occurs. During the deposition‐etch‐release sequence, various control parameters influence the nanoribbon size and geometry, hence the helix properties. The experimental study presented here focuses on the influence of meniscus height, substrate velocity, substrate surface energy, and etch time on nanoribbon size (height and width), scum layer thickness, and helix radius. The results show that meniscus height and contact angle dictate flux toward the meniscus edge and volume available for spatial assembly, allowing control over the aspect ratio of ribbons. We vary the aspect ratio by two orders of magnitude, while maintaining geometric asymmetry needed for helix shape‐transformation. We provide robust scaling for the nanoribbon size and geometry and report the advantages and disadvantages of different parameters, in the control of polymer nanoribbon and helix fabrication. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1270–1278     

Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type—rather than the application domain or energy source—we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.     

An Optochemical Oxygen Scavenger Enabling Spatiotemporal Control of Hypoxia

We present an optochemical O₂ scavenging system that enables precise spatiotemporal control of the level of hypoxia in living cells simply by adjusting the light intensity in the illuminated region. The system employs rhodamine containing a selenium or tellurium atom as an optochemical oxygen scavenger that rapidly consumes O₂ by photochemical reaction with glutathione as a coreductant upon visible light irradiation (560–590 nm) and has a rapid response time, within a few minutes. The glutathione-consuming quantum yields of the system were calculated as about 5 %. The spatiotemporal O₂ consuming in cultured cells was visualized with a hypoxia-responsive fluorescence probe, MAR. Phosphorescence lifetime imaging was applied to confirmed that different light intensities could generate different levels of hypoxia. To illustrate the potential utility of this system for hypoxia research, we show that it can spatiotemporally control calcium ion (Ca²⁺) influx into HEK293T cells expressing the hypoxia-responsive Ca²⁺ channel TRPA1.     

The Rise of Trichlorides Enabling an Improved Chlorine Technology

Chlorine plays a central role for the industrial production of numerous materials with global relevance. More recently, polychlorides have been evolved from an area of academic interest to a research topic with enormous industrial potential. In this minireview, the value of trichlorides for chlorine storage and chlorination reactions are outlined. Particularly, the inexpensive ionic liquid [NEt₃Me][Cl₃] shows a similar and sometimes even advantageous reactivity compared to chlorine gas, while offering a superior safety profile. Used as a chlorine storage, [NEt₃Me][Cl₃] could help to overcome the current limitations of storing and transporting chlorine in larger quantities. Thus, trichlorides could become a key technique for the flexibilization of the chlorine production enabling an exploitation of renewable, yet fluctuating, electrical energy. As the loaded storage, [NEt₃Me][Cl₃], is a proven chlorination reagent, it could directly be employed for downstream processes, paving the path to a more practical and safer chlorine industry.