Archive for the ‘Hot Articles’ Category

Chemical Science HOT Articles: May 2021

New month, new HOT articles!

We are pleased to share a selection of our referee-recommended HOT articles for May 2021. We hope you enjoy reading these articles, congratulations to all the authors whose articles are featured! As always, Chemical Science is free to read & download.

You can explore our full 2021 Chemical Science HOT Article Collection here!

Browse a selection of our May HOT articles below:

Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8
Vaibhav Kumar Shukla, Lucas Siemons, Francesco L. Gervasio and D. Flemming Hansen
Chem. Sci., 2021, Advance Article

Blue-conversion of organic dyes produces artifacts in multicolor fluorescence imaging
Do-Hyeon Kim, Yeonho Chang, Soyeon Park, Min Gyu Jeong, Yonghoon Kwon, Kai Zhou, Jungeun Noh, Yun-Kyu Choi, Triet Minh Hong, Young-Tae Chang and Sung Ho Ryu
Chem. Sci., 2021, Advance Article

Controllable DNA strand displacement by independent metal–ligand complexation
Liang-Liang Wang, Qiu-Long Zhang, Yang Wang, Yan Liu, Jiao Lin, Fan Xie and Liang Xu
Chem. Sci., 2021, Advance Article

Spatial-confinement induced electroreduction of CO and CO2 to diols on densely-arrayed Cu nanopyramids
Ling Chen, Cheng Tang, Kenneth Davey, Yao Zheng, Yan Jiao and Shi-Zhang Qiao
Chem. Sci., 2021, Advance Article

Manipulating valence and core electronic excitations of a transition-metal complex using UV/Vis and X-ray cavities
Bing Gu, Stefano M. Cavaletto, Daniel R. Nascimento, Munira Khalil, Niranjan Govind and Shaul Mukamel
Chem. Sci., 2021, Advance Article

Chemical Science, Royal Society of Chemistry

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Chemical domain image recognition using autocatalysis

A reaction in which one of the products speeds up further product formation is called an autocatalytic reaction. Autocatalysis plays an important role in living systems including DNA replication, apoptosis, and even in the origin of life, due to self-sustaining growth and oscillation. Researchers from Brown University employ this nature of autocatalytic click chemistry to generate an artificial neural network that can be used for image classification.

Autocatalytic reaction rate depends on the concentration of product and shows a non-linear dependency of product formation with progress in reaction time. In this view, a network of autocatalytic reactions is analogous to an artificial neural network. An artificial neuron is a basic learning unit, inspired by biological neurons, which multiplies it’s inputs by a set of weights and transforms their sum through a nonlinear operator. Researchers used this resemblance to formulate a winner-take-all neural network.

Fig 1: Kinetics of autocatalysis. (a) Reagent and autocatalytic product evolution over time (b) Rate of product concentration change over time for the reaction simulated in a, showing the accelerated production typical of an autocatalytic process.

Copper-catalyzed azide–alkyne cycloaddition (CuAAC) reaction was chosen for autocatalysis as it is fast, can occur under mild conditions and produce high yield. Also, CuAAC reaction involves colored copper–ligand complexes and can be quantitatively monitored using UV-vis spectroscopy.

In a winner-take-all neural network, winner is determined by it’s achievement to reach to a particular condition. Here, they have used the reaction half-way point (t1/2) as the condition of image classification. Experiment wise, they have used automated liquid handling equipment to remove a certain volume and then added it together into individual pools for potential image class. The pool that reaches the transition time first is determined as the winner.

Fig 2: An overview of the copper (C) catalyzed azide–alkyne cycloaddition reaction, showing the buildup of triazole branches on the amine backbone of (A) after each azide (B) incorporation. The threebranched product (D) catalyzes its own generation by promoting the reduction of Cu(II). Experimental setup for evaluating a chemical WTA network (Right: upper panel). (Right lower panel) Network training and in silico simulation. (a) Example images from each of the considered classes. (b) Trained weights for each class.  

This study shows an interesting adaptation of autocatalysis as a platform for non-linear activation function necessary for artificial neural network classification. The findings are expected to improve future development of chemical-domain computing systems.

 

For further details, please go through:

Leveraging autocatalytic reactions for chemical domain image classification

Christopher E. Arcadia, Amanda Dombroski, Kady Oakley, Shui Ling Chen, Hokchhay Tann, Christopher Rose, Eunsuk Kim, Sherief Reda, Brenda M. Rubensteinb and Jacob K. Rosenstein*

Chem. Sci., 2021, 12, 5464

 

About the blogger

Dr Damayanti Bagchi is a postdoctoral researcher in Irene Chen’s lab at University of California, Los Angeles, United States. She has obtained her PhD in Physical Chemistry from Satyendra Nath Bose National Centre for Basic Sciences, India. Her research is focused on spectroscopic studies of nano-biomaterials. She is interested in exploring light enabled therapeutics. She enjoys travelling and experimenting with various cuisines, which she found resembles with products/ side products of chemical reactions!

You can find her on Twitter at @DamayantiBagchi.

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Chemical Science HOT Articles: April 2021

New month, new HOT articles!

We are pleased to share a selection of our referee-recommended HOT articles for April 2021. We hope you enjoy reading these articles, congratulations to all the authors whose articles are featured! As always, Chemical Science is free to read & download.

You can explore our full 2021 Chemical Science HOT Article Collection here!

 

Browse a selection of our April HOT articles below:

Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts
Simone Gallarati, Raimon Fabregat, Rubén Laplaza, Sinjini Bhattacharjee, Matthew D. Wodrich and Clemence Corminboeuf
Chem. Sci., 2021, Advance Article

Deaminative meta-C–H alkylation by ruthenium(ii) catalysis
Wen Wei, Hao Yu, Agnese Zangarelli and Lutz Ackermann
Chem. Sci., 2021, Advance Article

Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies
Jiahui Chen, Kaifu Gao, Rui Wang and Guo-Wei Wei
Chem. Sci., 2021, Advance Article

Recent advances in single atom catalysts for the electrochemical carbon dioxide reduction reaction
Jincheng Zhang, Weizheng Cai, Fang Xin Hu, Hongbin Yang and Bin Liu
Chem. Sci., 2021, Advance Article

Wavy graphene sheets from electrochemical sewing of corannulene
Carlo Bruno, Eleonora Ussano, Gianni Barucca, Davide Vanossi, Giovanni Valenti, Edward A. Jackson, Andrea Goldoni, Lucio Litti, Simona Fermani, Luca Pasquali, Moreno Meneghetti, Claudio Fontanesi, Lawrence T. Scott, Francesco Paolucci and Massimo Marcaccio
Chem. Sci., 2021, Advance Article

Oxidative additions of alkynyl/vinyl iodides to gold and gold-catalyzed vinylation reactions triggered by the MeDalphos ligand
Jessica Rodriguez, Alexis Tabey, Sonia Mallet-Ladeira and Didier Bourissou
Chem. Sci., 2021, Advance Article

 

Chemical Science, Royal Society of Chemistry

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Chemical Science HOT Articles: March 2021

New month, new HOT articles!

We are pleased to share a selection of our referee-recommended HOT articles for March 2021. We hope you enjoy reading these articles, congratulations to all the authors whose articles are featured! As always, Chemical Science is free to read & download.

You can explore our full 2021 Chemical Science HOT Article Collection here!

 

Browse a selection of our March HOT articles below:

Photoactive electron donor–acceptor complex platform for Ni-mediated C(sp3)–C(sp2) bond formation
Lisa Marie Kammer, Shorouk O. Badir, Ren-Ming Hu and Gary A. Molander
Chem. Sci., 2021, Advance Article

Exploiting host–guest chemistry to manipulate magnetic interactions in metallosupramolecular M4L6 tetrahedral cages
Aaron J. Scott, Julia Vallejo, Arup Sarkar, Lucy Smythe, E. Regincós Martí, Gary S. Nichol, Wim T. Klooster, Simon J. Coles, Mark Murrie, Gopalan Rajaraman, Stergios Piligkos, Paul J. Lusby and Euan K. Brechin
Chem. Sci., 2021, Advance Article

DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations
Zhixin Zhou, Jianbang Wang, R. D. Levine, Francoise Remacle and Itamar Willner
Chem. Sci., 2021, Advance Article

Asymmetric synthesis of dihydro-1,3-dioxepines by Rh(ii)/Sm(iii) relay catalytic three-component tandem [4 + 3]-cycloaddition
Chaoran Xu, Jianglin Qiao, Shunxi Dong, Yuqiao Zhou, Xiaohua Liu and Xiaoming Feng
Chem. Sci., 2021, Advance Article

Targeted 1,3-dipolar cycloaddition with acrolein for cancer prodrug activation
Ambara R. Pradipta, Peni Ahmadi, Kazuki Terashima, Kyohei Muguruma, Motoko Fujii, Tomoya Ichino, Satoshi Maeda and Katsunori Tanaka
Chem. Sci., 2021, Advance Article

Three-membered cyclic digermylenes stabilised by an N-heterocyclic carbene
Zhaowen Dong, Jan Mathis Winkler, Marc Schmidtmann and Thomas Müller
Chem. Sci., 2021, Advance Article

 

Chemical Science, Royal Society of Chemistry

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Gearing up for motion in ruthenium rotors

The mighty gear is essential in machines. Even when scaling down the size of the machine, like from cars to small wristwatches, gears are necessary to transmit motion and mechanical power across the system. Machines can be decreased in size all the way to the nanoscale with molecular machines, where individual molecules can produce mechanical motion in response to external stimuli. Just as in macroscopic machines (e.g. cars), the addition of gears to nanomachines is needed for creating more complex assemblies with controlled motion, extending the applications of these molecules beyond the fundamental.

Figure 1. A schematic representation of the design for trains of molecular gears.

A team of researchers from France and Japan have now reported a series of molecular gears, with the aim of achieving correlated motion within trains of gears across a surface (Figure 1). To achieve this correlated motion, the researchers designed desymmetrised organometallic molecular gears based around star-shaped ruthenium piano-stool complexes. These molecular gears incorporated a facially capping hydrotris(indazolyl)borate ligand at one end, which both anchors the complex to the surface and lifts the central metal centre away to enable a rotational axis around the ruthenium. At the other end, the molecular gears have a cyclopentadienyl core to act as the cogwheel, functionalised with bulky groups that mimic the teeth that allow correlated motion between the gears (Figure 2). The researchers set out to make these molecular gears with lower symmetry to allow for detailed on-surface mechanical studies, by changing one of the five teeth (i.e. the functionalised groups around the cyclopentadienyl core) to include a steric or chemical tag– this is shown in Figures 1 and 2 by the green section.

Figure 2. Chemical structure of the molecular gears, with the anchoring ligand in black beneath the ruthenium centre and the rotating cogwheel cyclopentadienyl ligand in blue. The rectangles represent the teeth of the cogwheel as the bulky groups added to the central cyclopentadienyl core, where one of the five teeth (coloured green rather than blue) is sterically or chemically changed to lower the symmetry.

The researchers developed a modular synthetic approach to achieve desymmetrisation of the star-shaped ruthenium molecular gears, based on post-functionalisation of the central cyclopentadienyl core with Ni(II) porphyrins to act as the teeth of the cogwheels. They used an unsymmetrical 1,2,3,4,5-penta(p-halogenophenyl)cyclopentadienyl as the core; the p-halogenophenyl groups are all pre-activated to allow for further functionalisation, but one of the five is a p-iodophenyl group that chemoselectively reacts over the other four p-bromophenyl groups. Scheme 1 shows a sequential synthetic route towards one of the desymmetrised molecular gears: the p-iodophenyl group is first functionalised with a unique porphyrin (shown in green), before subsequent functionalisation of the four other p-bromophenyl groups with the same porphyrins (shown in blue), all using palladium-catalysed cross-coupling reactions.

Synthetic scheme showing the route towards the desymmetrised molecular gears

Scheme 1. An example synthetic route towards desymmetrised molecular This example shows a sterically tagged cogwheel, where the unique porphyrinic tooth (in green) contains a longer linker than the four other teeth (in blue).

The researchers varied their approach to changing the unique porphyrinic tooth for the molecular gear, using either steric tagging (with one longer linker between the porphyrin and p-halogenophenyl group) or chemical tagging, using either one distinct electron-deficient porphyrin (achieved by using p-cyanophenyl substituents on the tetrapyrrole core) or one distinct metal porphyrin (Zn(II) instead of Ni(II)). The synthesised desymmetrised molecular gears were characterised using spectroscopic and electrochemical techniques, and the researchers are currently undertaking further mechanical studies to understand the correlated motion of these gears on surfaces.

 

To find out more, please read:

Desymmetrised pentaporphyrinic gears mounted on metallo-organic anchors

Seifallah Abid, Yohan Gisbert, Mitsuru Kojima, Nathalie Saffon-Merceron, Jérôme Cuny, Claire Kammerer* and  Gwénaël Rapenne*

Chem. Sci., 2021, Advance Article

 

About the blogger:

Photograph of the author, Samantha AppsDr. Samantha Apps recently finished her post as 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.

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Chemical Science HOT Articles: February 2021

New month, new HOT articles!

We are pleased to share a selection of our referee-recommended HOT articles for February 2021. We hope you enjoy reading these articles, congratulations to all the authors whose articles are featured! As always, Chemical Science is free to read & download.

You can explore our full 2021 Chemical Science HOT Article Collection here!

 

Browse a selection of our February HOT articles below:

Towards the rational design of ylide-substituted phosphines for gold(i)-catalysis: from inactive to ppm-level catalysis
Jens Handelmann, Chatla Naga Babu, Henning Steinert, Christopher Schwarz, Thorsten Scherpf, Alexander Kroll and Viktoria H. Gessner;
Chem. Sci., 2021, Advance Article

Ruthenium-catalyzed formal sp3 C–H activation of allylsilanes/esters with olefins: efficient access to functionalized 1,3-dienes
Dattatraya H. Dethe, Nagabhushana C. Beeralingappa, Saikat Das and Appasaheb K. Nirpal
Chem. Sci., 2021, Advance Article

Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes
Jaeseung Yu, Jinsol Yang, Chaok Seok and Woon Ju Song
Chem. Sci., 2021, Advance Article

Desymmetrised pentaporphyrinic gears mounted on metallo-organic anchors
Seifallah Abid, Yohan Gisbert, Mitsuru Kojima, Nathalie Saffon-Merceron, Jérôme Cuny, Claire Kammerer and Gwénaël Rapenne
Chem. Sci., 2021, Advance Article

The atomic-level regulation of single-atom site catalysts for the electrochemical CO2 reduction reaction
Qingyun Qu, Shufang Ji, Yuanjun Chen, Dingsheng Wang and Yadong Li
Chem. Sci., 2021, Advance Article

Chemical tuning of spin clock transitions in molecular monomers based on nuclear spin-free Ni(ii)
Marcos Rubín-Osanz, François Lambert, Feng Shao, Eric Rivière, Régis Guillot, Nicolas Suaud, Nathalie Guihéry, David Zueco, Anne-Laure Barra, Talal Mallah and Fernando Luis
Chem. Sci., 2021, Advance Article
Chemical Science, Royal Society of Chemistry

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Methylene in the middle: from Zn to Ti

Methylene (-CH2) is one of the simplest and most important building blocks for chemical synthesis. Methylenation reactions add methylene groups to molecules and often proceed using transition metal methylene complexes. Titanium methylene complexes are excellent for methylenations and have been used in a variety of reactions such as olefin metathesis, polymerisations or olefination of carbonyls. Early examples of such titanium methylenation reagents include Tebbe’s reagent that can generate a terminally bound mononuclear titanium methylidene, Cp2Ti=CH2 (Figure 1a), or a methylenation reagent prepared from CH2Br2, Zn and TiCl4 (with catalytic lead), referred to as ‘CH2X2-Zn(Pb)-TiCl4’.

Figure 1. (a) The titanium methylidene methylenating reagent from the Tebbe or Petasis reagents. (b) The first key step for the ‘CH2X2-Zn(Pb)-TiCl4’ methylenating reagent: generation of the zinc methylene. (c) The second key step for ‘CH2X2-Zn(Pb)-TiCl4’ methylenating reagent: reduction of Ti(IV) to Ti(III).

Researchers from Japan have been interested in the ‘CH2X2-Zn(Pb)-TiCl4’ methylenation reagent and in particular, deducing the molecular structure of the reactive species. Earlier studies have revealed two key steps in the preparation of this methylenating reagent: the first is that a zinc methylene species, ‘CH2(ZnX2)’, is formed by the reaction of CH2X2 with Zn and catalytic lead (Figure 1b), and the second is that the Ti(IV) chloride reagent is reduced to Ti(III) chloride by Zn(0) simultaneously (Figure 1c). The researchers hypothesised that a reactive titanium methylidene species (similar to that generated from Tebbe’s reagent in Figure 1a) should form via a transmetallation event between the zinc methylene species and the Ti(III) chloride, and thus be the reactive methylenating species of the ‘CH2X2-Zn(Pb)-TiCl4’ methylenation reagent.

Scheme 1. The synthesis of the titanium methylene complex 3 generated via transmetallation.

To confirm their hypothesis, the researchers studied the reactivity of multiple combinations of a zinc methylene species (1) and titanium(III or IV) chloride reagents, with and without additional ligands (such as phosphines, amines or ethers). The researchers found that most combinations of reagents resulted in methylene loss via the generation of methane or ethylene, but the combination of TMEDA adducts of the zinc methylene (1a) and Ti(III) chloride (2) gave clean conversion to a new titanium methylene species 3 (Scheme 1). Although the researchers originally hypothesised the formation of a mononuclear titanium methylidene via methylene transmetallation from zinc to titanium, the new species 3 was revealed to be a dinuclear, bridging methylene complex. The dinuclear species was characterised using NMR spectroscopy and single-crystal X-ray diffraction techniques, and the connectivity of the bridging methylene was conclusively established by the X-ray crystal structure.

After elucidating the structure of the dinuclear titanium methylene complex, the researchers tested 3 as a methylenating reagent and observed successful methylene transfer reactions from 3 to esters, terminal olefins and 1,3-dienes. A further computational mechanistic study for the reactivity of 3 and a 1,3-diene was performed, where the DFT calculations indicated a mononuclear titanium methylidene as the reactive species, generated from the dinuclear titanium methylene complex. These calculations corroborate the researchers’ initial hypothesis and correlate with Tebbe’s reagent, where the reactive methylenating agent is also a mononuclear titanium methylidene that is generated from a dinuclear bridging methylene complex.

 

To find out more, please read:

Structural elucidation of a methylenation reagent of esters: synthesis and reactivity of a dinuclear titanium(III) methylene complex

Takashi Kurogi,* Kaito Kuroki, Shunsuke Moritani and Kazuhiko Takai*

Chem. Sci., 2021, Advance Article

 

About the blogger:

Photograph of the author, Samantha AppsDr. Samantha Apps recently finished her post as 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.

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Chemical Science HOT Articles: January 2021

New year, new HOT article collection!

We are pleased to share a selection of our referee-recommended HOT articles for January 2021. 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 explore our full 2021 Chemical Science HOT Article Collection here!

 

Browse a selection of our January HOT articles below:

Directed evolution of cyclic peptides for inhibition of autophagy
Joshua P. Gray, Md. Nasir Uddin, Rajan Chaudhari, Margie N. Sutton, Hailing Yang, Philip Rask, Hannah Locke, Brian J. Engel, Nefeli Batistatou, Jing Wang, Brian J. Grindel, Pratip Bhattacharya, Seth T. Gammon, Shuxing Zhang, David Piwnica-Worms, Joshua A. Kritzer, Zhen Lu, Robert C. Bast, Jr. and Steven W. Millward
Chem. Sci., 2021, Advance Article

Conformational analysis by UV spectroscopy: the decisive contribution of environment-induced electronic Stark effects
Jeremy Donon, Sana Habka, Michel Mons, Valérie Brenner and Eric Gloaguen
Chem. Sci., 2021, Advance Article

Identifying key mononuclear Fe species for low-temperature methane oxidation
Tao Yu, Zhi Li, Wilm Jones, Yuanshuai Liu, Qian He, Weiyu Song, Pengfei Du, Bing Yang, Hongyu An, Daniela M. Farmer, Chengwu Qiu, Aiqin Wang, Bert M. Weckhuysen, Andrew M. Beale and Wenhao Luo
Chem. Sci., 2021, Advance Article

A feasible approach for automatically differentiable unitary coupled-cluster on quantum computers
Jakob S. Kottmann, Abhinav Anand and Alán Aspuru-Guzik
Chem. Sci., 2021, Advance Article

A photoswitchable strapped calix[4]pyrrole receptor: highly effective chloride binding and release
David Villarón, Maxime A. Siegler and Sander J. Wezenberg
Chem. Sci., 2021, Advance Article

Controlling multiple orderings in metal thiocyanate molecular perovskites Ax{Ni[Bi(SCN)6]}
Jie Yie Lee, Sanliang Ling, Stephen P. Argent, Mark S. Senn, Laura Cañadillas-Delgado and Matthew J. Cliffe
Chem. Sci., 2021, Advance Article

Structural elucidation of a methylenation reagent of esters: synthesis and reactivity of a dinuclear titanium(iii) methylene complex
Takashi Kurogi, Kaito Kuroki, Shunsuke Moritani and Kazuhiko Takai
Chem. Sci., 2021, Advance Article
Chemical Science, Royal Society of Chemistry

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Magnesium activates all the halogenated benzenes

Activating a bond is the first step towards bond breaking processes for synthesis and catalysis. Despite the major role of transition metals in a variety of bond activation processes, C–X bond activation of halogenated benzenes (PhX, X = F, Cl, Br, I) is still challenging; there are very few examples of metal···XPh complexes, even though they are crucial for C–X bond activation and catalysis. There are even fewer examples of main group metal···XPh complexes, with no examples of main group complexes of bromobenzene or iodobenzene.

Researchers in Germany have been studying cationic magnesium complexes with the β-diketiminate ligand (RBDI, R = methyl or t-butyl), where their extreme Lewis acidity makes them ideal candidates for halobenzene complex formation for C–X activation. Building upon their previous findings of the formation of a Mg-chlorobenzene complex, the researchers have now demonstrated the preparation of the full series of halobenzene complexes, including the first examples of coordination of bromobenzene and iodobenzene to a main group metal, as shown in Scheme 1.

Scheme showing syntheses of Mg-XPh complexes (X = F, Cl, Br, I)

Scheme 1. Syntheses of Mg-XPh complexes (X = F, Cl, Br, I)

The researchers found that both the smaller methyl-substituted complex, (MeBDI)Mg+, and the bulkier t-butyl substituted complex, (tBuBDI)Mg+, were able to bind fluorobenzene to form Mg···FPh complexes (13 in, Scheme 1), owing to the high polarity of PhF that can compete with the Mg···B(C6F5)4 (the magnesium–anion) interaction. The other halobenzene complexes (Mg···XPh for X = Cl, Br, I; VI, 4, 5) could only be accessed with the use of the bulkier tBuBDI ligand. This was attributed to the fact that the bulky t-butyl substituents essentially turn off the Mg···B(C6F5)4 interaction, which in turn allows the less polar PhX halobenzenes to bind to the magnesium centre.

The researchers isolated and fully characterised the Mg-halobenzene complexes, and used X-ray crystallography and DFT calculations to further understand their properties. The interaction of the strongly Lewis acidic (BDI)Mg+ cation with the halobenzene resulted in C–X activation as shown by elongation of the C–X bonds in the crystal structures. Additionally, the solid-state structures showed that the Mg···X–Ph angle is the most linear for PhF and decreases in size (i.e. bends more) for the larger halogens. This increased bending for the larger halogens is explained by the halogen σ-hole, which is a region of positive electrostatic potential on the surface of the halogen opposite to the C–X bond, that increases with halogen size. As shown by the schematic in Figure 1, the presence of a larger halogen hole forces a more acute Mg···X interaction relative to the C–X bond.

Figure 1. Top: Schematic showing the halogen σ-hole (red = positive electrostatic potential, blue = negative electrostatic potential), with possible coordination sites for Mg. Bottom: Electrostatic maps for the halobenzenes.

Figure 1. Top: Schematic showing the halogen σ-hole (red = positive electrostatic potential, blue = negative electrostatic potential), with possible coordination sites for Mg. Bottom: Electrostatic maps for the halobenzenes.

DFT calculations were also performed and were in good agreement with the solid-state experimental parameters. The researchers calculated complexation enthalpies between 11 and 13 kcal mol-1, which are weak but still indicate a Mg···X–Ph interaction. This interaction ultimately indicates C–X bond activation, signifying that these main group complexes show potential for C–X bond breaking processes in future catalytic applications.

 

To find out more, please read:

Magnesium–halobenzene bonding: mapping the halogen sigma-hole with a Lewis-acidic complex

Alexander Friedrich, Jürgen Pahl, Jonathan Eyselein, Jens Langer, Nico van Eikema Hommes, Andreas Görling and Sjoerd Harder*

Chem. Sci., 2021, Advance Article

 

About the blogger:

Photograph of the author, Samantha AppsDr. Samantha Apps recently finished her post as 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.

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The more the merrier for hydrogen bonds in selective fluorescent probes

Hydrogen bonding is all around us. The intermolecular force of attraction between a hydrogen atom bound to an electronegative centre (the hydrogen bond donor, HBD) and another nearby electronegative atom with a lone pair of electrons (the hydrogen bond acceptor, HBA) is present in many chemical structures and can be seen in many biological motifs such as in enzymes or proteins. Beyond a simple HBD-HBA pair (Figure 1a), hydrogen bonding can cascade between multiple HBD-HBA pairs (Figure 1b). In these paired units, the presence of a central proton mediator (e.g. imidazole) can induce polarisation to make the resulting hydrogen bonds stronger, promoting further reactivity and selectivity (Figure 1c).

Chemical structures depicting hydrogen bonds between donor (D, coloured blue) and acceptor (A, coloured pink), with the hydrogen bonds as dashed lines between the H connected to the D, and the A acceptor atom

Figure 1. Hydrogen bonding between donor (D) and acceptor (A) atoms, with the net dipole shown by the arrows beneath. (a) Simple HBD-HBA pair. (b) Cascade hydrogen bonding around a central imidazole proton mediator, that can promote further reactivity with a larger net additive dipole (c).

Some enzymes cleverly make use of cascade hydrogen bonding to control the strength of the hydrogen bonds that form between the limited number of available amino acids. One example is a class of enzymes with a ‘catalytic triad’, whereby a hydrogen bonding array exists between the hydroxyl group of serine, the imidazole group of histidine and the carboxylate group of aspartate residues (Figure 2a). Researchers from South Korea took inspiration from such catalytic triads to create a ‘synthetic triad’ with a biomimetic hydrogen bonding network (Figure 2b, compound 1). The researchers employed a central benzimidazole to their synthetic triad to act as a platform to align the HBD-HBA pairs, instead of the precise three-dimensional structure that would anchor these pairs in enzymes.

A) Structure shows central imidazole of a histidine, with hydrogen bond on the left from the imidazole nitrogen to a serine hydroxyl H atom, and a hydrogen bond on the right from the imidazole N-H hydrogen atom to a carboxylate O atom on the aspartate residue. B) Structure of the triad, with a central benzimidazole, and 4 sets of hydrogen bonding pairs around this.

Figure 2. (a) Chemical (left) and X-ray (right) structures of the ‘catalytic triad’ in the active site of the enzyme serine protease. (b) Chemical structure (left) and computational model (right) of the ‘synthetic triad’ designed by the researchers.

The researchers envisioned that their biomimetic small molecule could be used as a fluorescent probe owing to the photophysical properties of the chosen benzimidazole motif. They designed the probe for cyanide detection, where capture of a toxic cyanide ion turns on fluorescence in the probe (Figure 3c). The design of the probe was therefore influenced with the target application in mind, so the researchers systematically added each HBD-HBA pair around the benzimidazole, as shown in Figure 3b.

A) Another schematic of the HBD-HBA pair concept around benzimidazole. B) Chemical structures of the evolution of the probe, from compound 2 with one HBD-HBA pair, to compound 3 with two pairs, compound 4 with three pairs and compound 1 with four pairs. C) Structural mechanism showing greyed out ‘off’ fluorescence before cyanide attack, with arrow showing new structure with cyanide bound at the aldehyde, and blue coloured benzimidazole to signify fluorescence is turned on.

Figure 3. (a) Cascade hydrogen bonding around a benzimidazole core. (b) The systematic design of the probe, starting from one HBD-HBA pair up to four pairs. (c) Mechanism of capture of the cyanide ion to turn on fluorescence.

An aldehyde functional group was selected for the first HBD-HBA pair, due to its ability to form hydrogen bonds that can quench the fluorescence in the absence of cyanide (compound 2). The researchers tested compound 2 for cyanide detection and indeed observed fluorescence, but found that the fluorescence also occurred in the presence of a simple Brønsted base. The design of the probe was then iteratively modified until fluorescence was selective for cyanide addition, with a total of four HBD-HBA pairs around the benzimidazole centre that mutually reinforced one another. This strategy shows promise for the design of other fluorescent probes and could also be utilised for other biological targeting applications.

 

To find out more, please read:

Biomimetic hydrogen-bonding cascade for chemical activation: telling a nucleophile from a base

Hyunchang Park and Dongwhan Lee*

Chem. Sci., 2021, Advance Article

 

About the blogger:

Photograph of the author, Samantha AppsDr. Samantha Apps recently finished her post as 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.

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