Capturing nitrenes with iron and light for C-N bond formation

Finding new ways to make chemical bonds is not only a fascination for chemists, but also important for developing greener routes in chemical synthesis. Carbon-nitrogen bonds are one such motif of interest; they are ubiquitous in chemical synthesis as part of amine functional groups, which are present in biologically relevant molecules and pharmaceutical compounds. A powerful method for the formation of C-N bonds involves using nitrenes (R-N:) as the nitrogen source. The use of azides (RN3) to generate the nitrene is particularly attractive, as the only by-product is nitrogen gas, and no additional oxidants are required.

Typical drawbacks associated with the use of nitrenes in amination reactions, i.e. forming C-N bonds for amine functionalities, include the necessity for elevated temperatures (to liberate nitrogen gas from the azide to form the nitrene) and competitive side reactivity (since nitrenes are highly reactive intermediates). Research by Che and co-workers in Hong Kong and China now describes a way to circumvent these disadvantages, using visible light in combination with an iron porphyrin complex to catalyse C-N bond formation by either C-H bond amination or alkene aziridination using organic azide substrates.

Iron porphyrin nitrene capture from organic azide

Figure 1: Trapping of the nitrene (NR) generated from an azide (N3R) by the iron porphyrin (bottom), compared to previous work (top) where a free, reactive nitrene is generated.

The iron porphyrin complex, as described by the researchers, has a dual role in the light-driven C-N bond formation reactivity. Firstly, the iron porphyrin acts as a photosensitiser in this reaction, assisting with the nitrene formation from the organic azide by irradiation. More importantly, the porphyrin complex then acts as a trap for the reactive nitrene and forms a resulting metal-nitrene (or imido) intermediate that can then react with carbon-based substrates for C-N bond formation. Capturing the nitrene at a metal centre, as opposed to generating a free nitrene for subsequent reactivity (as shown in Figure 1), allows for greater selectivity, which is reflected in the extensive substrate scope described by Che and co-workers.

The researchers started their investigation by screening a panel of iron porphyrins to serve as a catalyst in the light-driven C-H amination of indane (as a hydrocarbon substrate) with an electron-deficient aryl azide (Scheme 1). They observed the successful conversion to the C-H amination product, 1-aminoindane, in various yields, where the Fe(TF4DMAP)Cl porphyrin complex (as shown in Scheme 1) was the most effective catalyst, resulting in a 99% yield after 24 hours. Control studies confirmed both light irradiation and the iron porphyrin were required for conversion, and further mechanistic experiments supported the formation of an iron-nitrene intermediate, that could subsequently react with a C-H bond (in this case, within indane) via H-atom abstraction for amination. Translating the same reaction conditions to sp2 carbon substrates, by using styrene instead of indane, resulted in olefin aziridination, showing the applicability of this method to other substrates.

Fe-porphyrin catalysed C-H amination of indane scheme

Scheme 1: C-H amination of indane (1a) with the electron-deficient aryl azide (2a) to form 1-aminoindane (3a), using the optimal iron porphyrin catalyst Fe(TF4DMAP)Cl

After determining the optimal conditions in the above example reactions, Che and co-workers demonstrated an impressive substrate scope for this reactivity, varying either the hydrocarbon substrate or the organic azide for C-H amination. Additionally, they also demonstrated this reactivity could be applied to intramolecular C-H amination, for the formation of imidazolidines or α-azidoketones. Ultimately, this reactivity could be translated to natural product synthesis, and preliminary results in this report showed that late-stage C-H amination using azides could be achieved in complex substrates.

This work elegantly demonstrates a new method for C-N bond formation using organic azides and hydrocarbon or olefin substrates, as the first example of a light driven, iron-porphyrin catalysed, C-H amination or alkene aziridination reaction.

To find out more, please read:

Iron porphyrin catalysed light driven C–H bond amination and alkene aziridination with organic azides

Yi-Dan Du, Cong-Ying Zhou, Wai-Pong To, Hai-Xu Wang and Chi-Ming Che

Chem. Sci., 2020,11, 4680-4686

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HOT Articles: May

We are pleased to share a selection of our referee-recommended HOT articles for May. We hope you enjoy reading these articles and congratulations to all the authors whose articles are featured! As always, Chemical Science is free to read & download. You can find our full 2020 HOT article collection here.

 

Determination of protein–ligand binding modes using fast multi-dimensional NMR with hyperpolarization
Yunyi Wang, Jihyun Kim and Christian Hilty
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC00266F

 

Speciation of Be2+ in acidic liquid ammonia and formation of tetra- and octanuclear beryllium amido clusters
Matthias Müller, Antti J. Karttunen and Magnus R. Buchner
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC01112F

 

Stimulus-responsive surface-enhanced Raman scattering: a “Trojan horse” strategy for precision molecular diagnosis of cancer
Cai Zhang, Xiaoyu Cui, Jie Yang, Xueguang Shao, Yuying Zhang and Dingbin Liu
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC01649G

 

Electro-organic Synthesis – A 21st Century Technique
Dennis Pollok and Siegfried R Waldvogel
Chem. Sci., 2020, Accepted Manuscript
DOI: 10.1039/D0SC01848A

 

Mobility and Versatility of the Liquid Bismuth Promoter in the Working Iron Catalysts for Light Olefin Synthesis from Syngas
Bang Gu, Deizi Vanessa Peron, Alan J Barrios, Mounib Bahri, Ovidiu Ersen, Mykhailo Vorokhta, Břetislav Šmíd, Dipanjan Banerjee, Mirella Virginie, Eric Marceau, Robert Wojcieszak, Vitaly Ordomsky and Andrei Khodakov
Chem. Sci., 2020, Accepted Manuscript
DOI: 10.1039/D0SC01600D

 

Ru-catalyzed isomerization of ω-alkenylboronates towards stereoselective synthesis of vinylboronates with subsequent in situ functionalization
Guo-Ming Ho, Lucas Segura and Ilan Marek
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC02542A


 

 

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Prolonging the Lifetimes of Dye-Sensitized Solar Cells by Positioning Dyes

Dye-sensitized solar cells (DSSCs) are electrochemical devices that can convert solar energy into electricity. The critical component of a DSSC is its dye molecules which are covalently adsorbed on the electrodes of the DSSC. These molecules are responsible for light absorption and energy conversion in the device. DSSCs are more economical than commercial Si-based solar cells, but their lifetimes are limited (~6 years vs. 20-30 years of Si-based counterparts).

A research team from Xiamen University, China, recently demonstrated in Chemical Science (DOI: 10.1039/D0SC00588F) that the anchoring stability of the dyes determined the longevity of DSSCs. They specifically studied N719, a Ru-containing dye, adsorbed on three different crystal facets of rutile TiO2 (electrode). N719 adsorbed on the TiO2(111) facets was the most stable among all the facets studied.

The researchers adopted surface-enhanced Raman spectroscopy (Fig.1) in their research, the setup of which involved two laser beams. One 405-nm laser excited the dye molecules to initiate energy conversion, and another 638-nm laser collected the Raman scattering signals at the dye/TiO2 interface. The obtained Raman spectra showed the peaks associated with the vibrations of N719.

Figure 1. The experimental setup. The 405-nm laser excites N719 dye molecules adsorbed on rutile TiO2. The 638-nm laser probed the Raman scattering signals of N719. The Au nanoparticle (yellow sphere) enhances the Raman signal intensity.

The Raman spectra revealed that the adsorption stability of N719 depended on the crystal facet of TiO2. For TiO2(001), after illumination for 36 min, the Raman peaks of N719 gradually diminished (Fig. 2a), indicating that the dye molecules were either detached from TiO2 or decomposed. A similar trend was observed for N719 on TiO2(110) (Fig. 2b). Mass spectroscopy detected that the electrolytes after 36-min illumination contained N719 molecules missing an S atom. This result indicated that the C=S bond of N719 was broken, leading to the loss of the dye. In contrast, N719 on TiO2(111) exhibited stable Raman signals during the identical illumination duration (Fig. 2c).

The different stability was ascribed to variation in the dissociation energy of the C=S bond. Density functional theory (DFT) simulation proved that the cleavage of the C=S bond on TiO2(111) had an energy barrier of 3.5 eV, about 1.0 eV and 1.5 eV higher than those on TiO2(110) and TiO2(001), respectively. The higher energy barrier suppresses bond dissociation and stabilizes the adsorption of N719.

Figure 2. Raman spectra of N719 adsorbed on (a) TiO2(001), (b) TiO2(110), and (c) TiO2(111). Spectra were collected with an interval of 4 min. Peaks highlighted in yellow and blue are from TiO2 and N719, respectively. The schemes on the right show the simulated structures of dye-adsorbed (top) and desorbed (bottom) TiO2 facets. Ph–N=C=S represents N719 in simulation. The yellow spheres are S.

This work highlights the importance of dye positioning in promoting long-lasting performance of DSSCs.

For expanded understanding, please read:

In Situ Raman Study of the PhotoInduced Behavior of Dye Molecules on TiO2(hkl) Single Crystal Surfaces

Sheng-Pei Zhang, Jia-Sheng Lin, Rong-Kun Lin, Petar M. Radjenovic, Wei-Min Yang, Juan Xu, Jin-Chao Dong, Zhi-Lin Yang, Wei Hang, Zhong-Qun Tian, and Jian-Feng Li

Chem. Sci., 2020, DOI: 10.1039/D0SC00588F

 

Tianyu Liu acknowledges Zacary Croft at Virginia Tech, U.S., for his careful proofreading of this post.

 

About the blogger:

Tianyu Liu obtained his Ph.D. (2017) in Chemistry from the University of California, Santa Cruz, in the United States. He is passionate about the communication of scientific endeavors to both the general public and other scientists with diverse research expertise to introduce cutting-edge research to broad audiences. He is a blog writer for Chem. Comm. and Chem. Sci. More information about him can be found at http://liutianyuresearch.weebly.com/.

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Welcome to our new Associate Editor: Gabriel Merino

We would like to wish a very warm welcome to our new Chemical Science Associate Editor Professor Gabriel Merino!

 

Professor Gabriel Merino

Gabriel is a Professor in the Applied Physics Department at Centro de Investigacion y de Estudios Avanzados Merida (Cinvestav Mérida), México. He studied at the Universidad de las Americas Puebla (BSc in Chemistry, 1997) and Cinvestav Zacatenco (PhD in Chemistry, 2003) under the supervision of Alberto Vela. He then joined the group of Gotthard Seifert and Thomas Heine at TU Dresden as a postdoctoral fellow before returning to Mexico in 2005 to take his first independent research position at the Universidad de Guanajuato. He joined Cinvestav Merida in 2012 and his research group is one of the most active groups in Theoretical and Computational Chemistry in Mexico and Latin America.

Gabriel has also spent time researching at Cornell University (Roald Hoffmann, 2005), and the University of the Basque Country (Jesus Ugalde, 2011). He is a member of the Mexican National Researcher System (Level 3, the highest level), and a member of the Mexican Academy of Sciences. He has been awarded the Research Grant from the Academia Mexicana de Ciencias (2012), the Catedra Marcos Moshinsky (2012), the National Prize “Andres Manuel del Rio” in Chemistry from the Mexican Chemical Society (2017), the Walter Kohn Award (2018) from the International Center of Theoretical Physics, and the Moshinsky Medal (2019) from Institute of Physics (UNAM).

Gabriel has previously served as Associate Editor for RSC Advances (2016-2020) and is currently a member of the editorial board for the International Journal of Quantum Chemistry and ChemistrySelect. His group’s main research interests are the prediction of new chemical entities and the study of central concepts of chemistry, such as chemical bonding and aromaticity. You can find out more on their website.

 

Browse a selection of Gabriel’s latest work published by the Royal Society of Chemistry:

Origin of the isotropic motion in crystalline molecular rotors with carbazole stators
Abraham Colin-Molina, Marcus J. Jellen, Eduardo García-Quezada, Miguel Eduardo Cifuentes-Quintal, Fernando Murillo, Jorge Barroso, Salvador Pérez-Estrada, Rubén A. Toscano, Gabriel Merino and Braulio Rodríguez-Molina
Chem. Sci., 2019, 10, 4422-4429
DOI: 10.1039/C8SC04398A

Filling the void: controlled donor–acceptor interaction facilitates the formation of an M–M single bond in the zero oxidation state of M (M = Zn, Cd, Hg)
Ranajit Saha, Sudip Pan, Pratim K. Chattaraj and Gabriel Merino
Dalton Trans., 2020, 49, 1056-1064
DOI: 10.1039/C9DT04213J

Triggering the dynamics of a carbazole-p-[phenylene-diethynyl]-xylene rotor through a mechanically induced phase transition
Andrés Aguilar-Granda, Abraham Colin-Molina, Marcus J. Jellen, Alejandra Núñez-Pineda, M. Eduardo Cifuentes-Quintal, Rubén Alfredo Toscano, Gabriel Merino and Braulio Rodríguez-Molina
Chem. Commun., 2019, 55, 14054-14057
DOI: 10.1039/C9CC05672F

Exhaustive exploration of MgBn (n = 10–20) clusters and their anions
Yonghong Tian, Donghe Wei, Yuanyuan Jin, Jorge Barroso, Cheng Lu and Gabriel Merino
Phys. Chem. Chem. Phys., 2019, 21, 6935-6941
DOI: 10.1039/C9CP00201D

 

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Real World data for protein modeling

It should go without saying that NMR is an incredibly important characterization technique with profoundly broad applicability across the entirety of chemistry. Rarely do you find something that people who work on proteins and wacky main-group synthesis both consider crucial to their work. Given powerful enough magnets and high-quality samples, rich structural information can be obtained for all manner of molecules large and small. Large molecules do pose a problem with the sheer volume of information contained within a single spectrum. Because of this, there exists a need to develop computational programs that can translate spectra into detailed structural models. Currently, existing methods predict NMR spectra based on a combination of experimentally based databases with chemical shift heuristics. These simulations, while useful, lack high predictive rigor and often have difficulty simulating the messiness of real world data. This is particularly challenging because experimental spectra can often have significant chemical shift deviations from predicted values, with those peaks discarded as outliers.

Figure 1. The overall design of the novel UCBShift chemical shift prediction algorithm, combining both a transfer prediction module a machine learning module.

To face these challenges and generate more accurate results, researchers in the US developed a new algorithm that uses both machine learning and transfer prediction (Figure 1). Transfer prediction has been widely used and relies on the similarities of NRM peak sequences between known data, typically clean datasets, and the experimental sample in question. The advantage of the new approach is that it allows for data that would previously have been dismissed as anomalous to be utilized and to give more accurate predictions. The researchers used high-quality datasets that they modified for accuracy. In particular, they retained the water and ligand molecules that co-crystallized with the proteins that would likely be associated with the solvated forms of the proteins. As the interactions of these small molecules can alter the spectral shifts of NMR peaks, their inclusion increases the likelihood that peaks previously considered outliers will be incorporated and analyzed.

Figure 2. Difference between UCBShift-Y and SHIFTY+ (previous method) showing that overall the new algorithm is making better predictions.

Initial analysis with the new dataset produced some anomalous results, which were then mitigated by removing paramagnetic and other outlier proteins that would bias the results against the earlier algorithms. Once those were removed, the new algorithm still outperformed prior methods (Figure 2). While these advances are extremely useful for current researchers, they are approaching the limit of accuracy for systems that rely heavily on transfer predictions. In order to generate fully accurate models and structures intense work on combining deep learning with human expertise is necessary.

To find out more, please read:

Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data

Jie Li, Kochise C. Bennett, Yuchen Liu, Michael V. Martin and Teresa Head-Gordon

Chem. Sci., 2020,11, 3180-3191

About the blogger:

Dr. Beth Mundy is a recent PhD in chemistry from the Cossairt lab at the University of Washington in Seattle, Washington. Her research focused on developing new and better ways to synthesize nanomaterials for energy applications. She is often spotted knitting in seminars or with her nose in a good book. You can find her on Twitter at @BethMundySci.

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Welcome to Associate Editor Maja Köhn

We would like to wish a very warm welcome to our new Chemical Science Associate Editor Professor Maja Köhn!

 

 

Maja Köhn is a Professor for Integrative Signaling Research at the Faculty of Biology, University of Freiburg, Germany. She studied chemistry at the University of Kiel and moved afterwards to the Max-Planck-Institute and the University in Dortmund, where she obtained her PhD under the direction of H. Waldmann in 2005. After Maja’s postdoctoral work with G. L. Verdine at Harvard University, she started her independent career in 2007 as a group leader at the European Molecular Biology Laboratory in Heidelberg, Germany. In 2016 Maja moved to Freiburg for her current position. Research in her group focuses on the development and application of tools using synthetic chemistry and molecular cell biology to study and target phosphatases in health and disease. Maja’s ORCiD: https://orcid.org/0000-0001-8142-3504

 

Development of a solid phase synthesis strategy for soluble phosphoinositide analogues
Miriam Bru, Shriram P. Kotkar, Nilanjana Kar and Maja Köhn
Chem. Sci., 2012, 3, 1893-1902
DOI: 10.1039/C2SC01061E

Chemical Science, Royal Society of Chemistry

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HOT articles: April

We are pleased to share a selection of our referee-recommended HOT articles for April. We hope you enjoy reading these articles and congratulations to all the authors whose articles are featured! As always, Chemical Science is free to read & download. You can find our full 2020 HOT article collection here.

 

What is the role of acid–acid interactions in asymmetric phosphoric acid organocatalysis? A detailed mechanistic study using interlocked and non-interlocked catalysts
Dennis Jansen, Johannes Gramüller, Felix Niemeyer, Torsten Schaller, Matthias C. Letzel, Stefan Grimme, Hui Zhu, Ruth M. Gschwind and Jochen Niemeyer
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC01026J

10.1039/D0SC01026J

 

Structural properties of ultra-small thorium and uranium dioxide nanoparticles embedded in a covalent organic framework
Liane M. Moreau, Alexandre Herve, Mark D. Straub, Dominic R. Russo, Rebecca J. Abergel, Selim Alayoglu, John Arnold, Augustin Braun, Gauthier J. P. Deblonde, Yangdongling Liu, Trevor D. Lohrey, Daniel T. Olive, Yusen Qiao, Julian A. Rees, David K. Shuh, Simon J. Teat, Corwin H. Booth and Stefan G. Minasian
Chem. Sci., 2020, Advance Article
DOI: 10.1039/C9SC06117G

 

Iron porphyrin catalysed light driven C–H bond amination and alkene aziridination with organic azides
Yi-Dan Du, Cong-Ying Zhou, Wai-Pong To, Hai-Xu Wang and Chi-Ming Che
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC00784F

 

The assemble, grow and lift-off (AGLO) strategy to construct complex gold nanostructures with pre-designed morphologies
Xin Luo, Christophe Lachance-Brais, Amy Bantle and Hanadi F. Sleiman
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC00553C

 

Geometric Landscapes for Material Discovery within Energy-Structure-Function Maps
Seyed Mohamad Moosavi, Henglu Xu, Linjiang Chen, Andrew Cooper and Berend Smit
Chem. Sci., 2020, Accepted Manuscript
DOI: 10.1039/D0SC00049C

 

Expedient synthesis of conjugated triynes via alkyne metathesis
Idriss Curbet, Sophie Colombel-Rouen, Romane Manguin, Anthony Clermont, Alexandre Quelhas, Daniel S. Müller, Thierry Roisnel, Olivier Baslé, Yann Trolez and Marc Mauduit
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC01124J

 

Transferring Axial Molecular Chirality Through a Sequence of On-Surface Reactions
Néstor Merino-Díez, Mohammed S. G. Mohammed, Jesus Castro, Luciano Colazzo, Alejandro Berdonces-Layunta, James Lawrence, Jose Ignacio Pascual, Dimas G. de Oteyza and Diego Peña
Chem. Sci., 2020, Accepted Manuscript
DOI: 10.1039/D0SC01653E

 

Chemical Science, Royal Society of Chemistry

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HOT articles: March

We are pleased to share a selection of our referee-recommended HOT articles for March. We hope you enjoy reading these articles and congratulations to all the authors whose articles are featured! As always, Chemical Science is free to read & download. You can find our full 2020 HOT article collection here.

 

DP4-AI automated NMR data analysis: straight from spectrometer to structure
Alexander Howarth, Kristaps Ermanis and Jonathan M. Goodman
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC00442A

 

Completing the triad: synthesis and full characterization of homoleptic and heteroleptic carbonyl and nitrosyl complexes of the group VI metals
Jan Bohnenberger, Manuel Schmitt, Wolfram Feuerstein, Ivo Krummenacher, Burkhard Butschke, Jakub Czajka, Przemysław J. Malinowski, Frank Breher and Ingo Krossing
Chem. Sci., 2020, 11, 3592-3603
DOI: 10.1039/C9SC06445A

 

Recent developments in nickel-catalyzed intermolecular dicarbofunctionalization of alkenes
Joseph Derosa, Omar Apolinar, Taeho Kang, Van T. Tran and Keary M. Engle
Chem. Sci., 2020, Advance Article
DOI: 10.1039/C9SC06006E

 

Enhancing the selectivity of prolinamide organocatalysts using the mechanical bond in [2]rotaxanes
María Calles, Julio Puigcerver, Diego A. Alonso, Mateo Alajarin, Alberto Martinez-Cuezva and Jose Bern
Chem. Sci., 2020, 11, 3629-3635
DOI: 10.1039/D0SC00444H

 

Simultaneous and ultrasensitive detection of multiple microRNAs by single-molecule fluorescence imaging
Hongding Zhang, Xuedong Huang, Jianwei Liu and Baohong Liu
Chem. Sci., 2020, 11, 3812-3819
DOI: 10.1039/D0SC00580K

 

 

Chemical Science, Royal Society of Chemistry

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Most Popular 2018 – 2019 Chemical Science Articles By Subject

The ongoing COVID-19 pandemic has had wide reaching implications on the global research community. In addition to limitations on the ability to conduct research, many in our community are experiencing restricted or no access to institutional resources and published research articles. In-line with our continuing efforts to support the chemical sciences community, we have put together some subject-specific collections of our most popular Chemical Science content from 2018 and 2019. These specially curated collections are designed to highlight some of the exceptional research published in Chemical Science – and like all Chemical Science articles, they are free to access and read from anywhere on the globe with no restrictions. We hope you will find them useful during this time.

Many of the articles selected in the collections below are also included in our 20182019 and 2020 ChemSci Pick of the Week Collections, as well as our 20182019 and 2020 Chemical Science HOT Article Collections.

 

Organic chemistry

This collection presents some outstanding contributions to the field, ranging from dual vicinal functionalisation of heterocycles via an interrupted Pummerer coupling/[3,3]-sigmatropic rearrangement cascade to a review of C4-H indole functionalisation. Browse the full collection

 

Catalysis Chemistry

This specially curated collection pulls together some of the most popular articles from 2018 and 2019 in the field of catalysis. Articles range from Pd doped with Te for the highly selective electrocatalytic reduction of aqueous CO2 to a review of catalyst characterization in the presence of solvent through liquid phase structure-activity relationships.
Browse the full collection

 

Analytical chemistry

This collection ranges from high throughput reaction screening using desorption electrospray ionization mass spectrometry to a review of fluorescent probes for organelle-targeted bioactive species imaging.
Browse the full collection

 

Materials chemistry

This collection presents some outstanding contributions to the field, ranging from the rational design of a water-soluble NIR AIEgen to a review of the mechanical properties of metal-organic frameworks.
Browse the full collection

 

Main group, inorganic & organometallic chemistry

This collection presents articles ranging from the reactivity of diborane(4) towards pyridine and isocyanide to a review of spin states, vibrations and spin relaxation in molecular nanomagnets and spin qubits.
Browse the full collection

 

Chemical biology

This collection includes articles ranging from dual-biomarker-triggered fluorescence probes for differentiating cancer cells to a review of the biomedical applications of copper-free click chemistry.
Browse the full collection

 

Physical & theoretical chemistry

This collection presents some outstanding contributions to the field, ranging from a study that asks why are photosynthetic reaction centres dimeric to a review of polariton chemistry.
Browse the full collection

 

Supramolecular chemistry

This collection presents some outstanding contributions to the field, ranging from a halogen-bond assembled supramolecular catalyst, XBphos-Rh, to a review of electrochemically switchable rotaxanes.
Browse the full collection

 

Chemical Science, Royal Society of Chemistry

Submit to Chemical Science today! Check out our author guidelines for information on our article types or find out more about the advantages of publishing in a Royal Society of Chemistry journal.

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How to Identify Diverse Acids with High-Throughput Research

Have you ever heard of nonulosonic acids? As a materials chemist I hadn’t, as most of the acids I’ve dealt with are either acting as ligands or inorganic and I tend to forget that sugars are actually acids. These nine-carbon sugars are critical for a wide range of cellular functions throughout living organisms. Over 100 different members of this broad group of acids have been identified, all of which can undergo diversification at multiple positions, generating an even larger library of derivatives. What types of modifications can occur has yet to be fully realized, as novel compounds are continually discovered, particularly in prokaryotes. Even when examining a limited number of modifications, say 15, the number of possible derivatives is staggering, reaching several thousand without stereochemical considerations. Identifying these acids is key, as they have been linked to virulence in pathogenic bacteria and their previously mentioned diversity makes them challenging to genomically analyze.

Given these challenges, current detection practices rely on staining and fluorescent labeling which can be labor intensive and specific to a small number of acids. Early approaches based on mass spectroscopy were limited due to the complex backgrounds produced and the difficulties separating signal and noise. However, developments in high-resolution spectrometers and increased data processing abilities have led to successful analysis of increasing numbers of known metabolites. Researchers in the Netherlands and Russia extended this work to develop a screening approach to identify a diverse range of nonulosonic acids via small mass channel mass spectroscopy from previously unexplored environmental microbes (Figure 1).

Figure 1. Outline of the general procedure for the survey pipeline, beginning from the cells to the final structural analysis of the identified acids.

To successfully identify these unknown derivatives, the researchers identified specific ulosonic acid fragments invariant to functionalization. They used 1,2-diamino-4,5-methylene dioxybenzene, an alpha-keto-acid specific labeling reagent, to shift the double bond equivalents from the general cellular background and help conserve the core ulosonic acid structure. By screening a known range of acids with different functional group moieties, they were able to identify universal features for this category of molecules (Figure 2). From there, they created a full process for rapid-throughput studies that automated everything from initial identification of a potential acid molecule through filtering and structural analysis.

Figure 2. A) Universal fragmentation route used to identify nonulasonic acids in the screening, B) data output of various ulosonic acid derivatives identified in the study, and C) differences seen from the chemical labeling introduced in the procedure.

After the pipeline was established, the researchers used various standard cell lines, plant, animal, and algal, for a molecular level survey to confirm the validity of their approach for full-cell analysis. In general, the plants and yeast cells contained no nonulosonic acids, as expected, while the microalgae and animal cells had a range of different nonulosonic acids present. As these acids are thought to play a role in bacterial virulence, a bacteria known to display the acids was screened and several subtypes of animal and bacterial acids were identified as incorporated into the cells. With that validation, the researchers moved on to a wide range of non-pathogenic bacteria. They discovered that over half of these bacteria possess nonulosonic acids; in fact, some have only slightly lower acid abundance than mammalian cells. While much of this data was obtained from single cultures, it represents exciting validation of a broad new approach that could be used to identify potential targets for medical applications and continue to extend our understanding of the diversity of nonulosonic acids.

To find out more, please read:

Tackling the chemical diversity of microbial nonulosonic acids – a universal large-scale survey approach

Hugo B. C. Kleikamp, Yue Mei Lin, Duncan G. G. McMillan, Jeanine S. Geelhoed, Suzanne N. H. Naus-Wiezer, Peter van Baarlen, Chinmoy Saha, Rogier Louwen, Dimitry Y. Sorokin, Mark C. M. van Loosdrecht and Martin Pabst

Chem. Sci., 2020, 11, 3074-3080.

About the blogger:

Dr. Beth Mundy is a recent PhD in chemistry from the Cossairt lab at the University of Washington in Seattle, Washington. Her research focused on developing new and better ways to synthesize nanomaterials for energy applications. She is often spotted knitting in seminars or with her nose in a good book. You can find her on Twitter at @BethMundySci.

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