Chemical Science Blog

We are pleased to share a selection of our referee-recommended HOT articles for June. 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.

Mapping protein–polymer conformations in bioconjugates with atomic precision
Kevin M. Burridge, Ben A. Shurina, Caleb T. Kozuszek, Ryan F. Parnell, Jonathan S. Montgomery, Jamie L. VanPelt, Nicholas M. Daman, Robert M. McCarrick, Theresa A. Ramelot, Dominik Konkolewicz and Richard C. Page
Chem. Sci., 2020, 11, 6160-6166
DOI: 10.1039/D0SC02200D

Methylbismuth: an organometallic bismuthinidene biradical
Deb Pratim Mukhopadhyay, Domenik Schleier, Sara Wirsing, Jacqueline Ramler, Dustin Kaiser, Engelbert Reusch, Patrick Hemberger, Tobias Preitschopf, Ivo Krummenacher, Bernd Engels, Ingo Fischer and Crispin Lichtenberg
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC02410D

Formicamycin biosynthesis involves a unique reductive ring contraction
Zhiwei Qin, Rebecca Devine, Thomas J. Booth, Elliot H. E. Farrar, Matthew N. Grayson, Matthew I. Hutchings and Barrie Wilkinson
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC01712D

Unravelling the intricate photophysical behavior of 3-(pyridin-2-yl)triimidazotriazine AIE and RTP polymorphs
Elena Lucenti, Alessandra Forni, Andrea Previtali, Daniele Marinotto, Daniele Malpicci, Stefania Righetto, Clelia Giannini, Tersilla Virgili, Piotr Kabacinski, Lucia Ganzer, Umberto Giovanella, Chiara Botta and Elena Cariati
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC02459G

Molecular-level insight in supported olefin metathesis catalysts by combining surface organometallic chemistry, high throughput experimentation, and data analysis
Jordan De Jesus Silva, Marco A. B. Ferreira, Alexey Fedorov, Matthew S. Sigman and Christophe Copéret
Chem. Sci., 2020, Advance Article
DOI: 10.1039/D0SC02594A

Conformationally Adaptable Macrocyclic Receptors for Ditopic Anions: Analysis of Chelate Cooperativity in Aqueous Containing Media
Stuart N. Berry, Lei Qin, William Lewis and Katrina A. Jolliffe
Chem. Sci., 2020, Accepted Manuscript
DOI: 10.1039/D0SC02533J

Templating S100A9 amyloids on Aβ fibrillar surfaces revealed by charge detection mass spectrometry, microscopy, kinetic and microfluidic analyses
Jonathan Pansieri, Igor Iashchishyn, Hussein Fakhouri, Lucija Ostojić, Mantas MM Malisauskas, Greta Musteikyte, Vytautas Smirnovas, Matthias M. Schneider, Tom Scheidt, Catherine K. Xu, Georg Meisl, Ehut Gazit, Rodolphe Antoine and Ludmilla A. Morozova-Roche
Chem. Sci., 2020, Accepted Manuscript
DOI: 10.1039/C9SC05905A

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Nature is the ultimate molecular designer. The complex structures of proteins are crucial for allowing the many processes that support life, including the many chemical transformations that occur. A diverse array of biological reactions are catalysed by iron porphyrin active sites (also known as hemes), and rely on the local protein environments to envelop and stabilise the reactive intermediates that can form in the process. Whilst chemists can easily synthesise iron porphyrins to imitate the reactive centre, mimicking the surrounding protein superstructure is less trivial.

Metal-organic frameworks (MOFs) represent one strategy (as an alternative to proteins) to support iron porphyrins for chemical catalysis. These frameworks can precisely separate each heme unit, thereby sequestering each active site in a similar fashion to a protein, and the porous nature allows for diffusion of reagents into the catalyst. Importantly, the pore environment can be precisely controlled and modified, allowing for enhancements to the catalytic activity of the supported heme.

Researchers in the US have now reported a new method to modify a heme-containing metal-organic framework to enhance the catalytic activity towards C-H bond activation. They studied the porphyrinic Zr-based framework, PCN-224, where the porphyrin is suspended between Zr₆ nodes (Figure 1).  Exchange of the formate and benzoate ligands around the Zr₆ node in PCN-224 was achieved by initial treatment with acetic anhydride to give acetate ligands in the new material (PCN-224’, 1), and further reactivity with methanol resulted in Zr-hydroxy ligands (2) – see insert to Figure 1. Additionally, iron was installed into the modified framework 1 by reaction with FeCl₃ and base, to give 1FeCl. Here, an FeCl was installed in each porphyrin unit in the MOF, and further hydroxylation reactivity (similar to the 1 to 2 transformation) resulted in the formation of 2FeCl.

Figure 1. The structure of the PCN-224 framework. Insert (below) shows modifications to PCN-224 to give 1 and 2, with varying ligands around the Zr6 node (in green).

The modified PCN-224 frameworks were characterised by various techniques. Powder X-ray diffraction showed the retention of bulk crystallinity of the material upon ligand substitution. UV-Vis and ⁵⁷Fe Mössbauer spectroscopy confirmed iron coordination within the porphyrin units of the framework. Importantly, the modification of the Zr₆ ligands was structrually confirmed by single-crystal X-ray analysis, and DRIFTS spectra showed the expected O-H stretches for the hydroxy ligands in 2 and 2FeCl. The porosity of the framework was maintained upon the modifications, as shown by surface area measurements, making the new materials ideal candidates for catalytic testing.

Figure 2. A chart showing the catalytic activity of the heme-frameworks (1FeCl and 2FeCl) compared to the molecular iron porphyrin complex ((TPP)FeCl) for cyclohexane oxidation.

The researchers studied the effects of the framework modifications using the catalytic oxidation of cyclohexane as a model reaction. The researchers compared the oxidation of cyclohexane with iodosylbenzene in CH₂Cl₂ using either the molecular iron porphyrin complex, or the metallated porphyrin frameworks 1FeCl or 2FeCl. Whilst low yields of oxidation products (cyclohexanol, cyclohexanone and chlorocyclohexane) were observed for the molecular iron porphyrin complex, higher yields of 68% and 26% were noted for the frameworks 1FeCl and 2FeCl, with corresponding turnovers of 14 and 5, respectively (Figure 2). The higher catalytic activity for the acetylated framework (1FeCl) was attributed to the lack of acidic protons within the framework that would impair any oxidation reactivity at the heme centre. Ultimately, the results show an enhancement to the catalysis when the heme is supported and protected, demonstrating that MOFs are ideal supports for modelling enzymatic reactions.

To find out more, please read:

Enhancing catalytic alkane hydroxylation by tuning the outer coordination sphere in a heme-containing metal–organic framework

David Z. Zee and T. David Harris

Chem. Sci., 2020, 11, 5447-5452

About the blogger:

Dr. Samantha Apps is a Postdoctoral Research Associate in the Lu Lab at the University of Minnesota, USA, and obtained her PhD in 2019 from Imperial College London, UK. She has spent the last few years, both in her PhD and postdoc, researching synthetic nitrogen fixation and transition metal complexes that can activate and functionalise dinitrogen. Outside of the lab, you’ll likely find her baking at home, where her years of synthetic lab training has sparked a passion in kitchen chemistry too.

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.

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.

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

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

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.

Keep up to date with our latest articles, reviews, collections & more by following us on Twitter. You can also keep informed by signing up to our E-Alerts.

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/.

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.