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Self-adjusting MOFs

Recent decades have established that metal-organic frameworks (MOFs) are a pretty cool class of materials, with potential applications across a range of fields. In particular, their high porosities make them extremely attractive for storing a variety of gases, including possible fuels like methane and hydrogen. Two primary strategies have emerged to store H2 and CH4 in MOFs – synthesizing materials with unsaturated metals that can strongly bind to the target and synthesizing materials with small pores where multiple weak interactions combine to produce strong binding. Of course, these MOFs are designed with a single specific target in mind, making them synthetically complex and useful for storing only one type of molecule. Ideally, new MOFs with relatively straightforward syntheses that can bind multiple targets could be developed.

Figure 1. (a) Single crystal X-ray diffraction structure of 1–H2O. (b,c) View of the pores of 1–H2O showing binding pocket.

Scientists in the United States took a hybrid approach, creating MOFs with small, but flexible binding pockets. While the concept feels relatively straightforward and intuitive, it’s of course more complicated in practice. The MOF needs to hit a Goldilocks zone in terms of flexibility, where only a small number of select targets will bind rather than a wide range of gases. The researchers accomplished this by using an actinide (depleted uranium) as the metal nodes for their MOF as its tendency to adopt high coordination numbers should result in smaller pockets and limit possible rearrangements of the flexible linker. Also, the descriptor “as it is only mildly radioactive” is something I hadn’t read about a material before and rather caught my attention. The crystalline material, referred to as 1-H2O (Figure 1), was straightforwardly synthesized in an autoclave and isolated in relatively high yields. It features pores with two pockets that are capped by the bowl-shaped linkers. As synthesized, the pockets are occupied by water molecules that can be removed by heating the MOF under a dynamic vacuum.

Figure 2. (a) Neutron powder diffraction structure of D2 adsorbed at site I in 1–D2. (b) Neutron powder diffraction structure of CD4 adsorbed at site I in 1–CD4. (c) Powder X-ray diffraction structure of DMF adsorbed inside the pore of U(bdc)2.

The MOF maintains its structural integrity after water removal, actually expanding slightly. This indicates that the MOF will contract upon binding, locking the target into place in the pocket. The researchers found that the MOF rapidly uptakes both H2 and CH4 at low temperatures, but the precise nature of the binding pocket adjustments can’t be determined by gas adsorption studies. To probe the structural details, the researchers turned to neutron powder diffraction to probe the binding of deuterated molecules to the MOF (Figure 2). The obtained structures show clear, cooperative effects that cause the adjustments to the binding pocket. The multiple different interactions allow the flexible structure to fit the two different adsorbates of interest, binding them both strongly. This work demonstrates the utility and versatility of flexible MOFs for adsorbing different gases with design principles that should be transferrable to non-radioactive materials.

To find out more, please read:

Self-adjusting binding pockets enhance H2 and CH4 adsorption in a uranium-based metal–organic framework

Dominik P. Halter, Ryan A. Klein, Michael A. Boreen, Benjamin A. Trump, Craig M. Brown and Jeffrey R. Long

Chem. Sci., 2020, Advance Article

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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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

 

 

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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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HOT Chemical Science articles for November

We are happy to present a selection of our HOT articles for October. To see all of our HOT referee-recommended articles from 2019, please find the collection here.

As always, Chemical Science articles are free to access.

CsAlB3O6F: a beryllium-free deep-ultraviolet nonlinear optical material with enhanced thermal stability

Chem Sci., 2019, Advance Article


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Programmable dynamic covalent nanoparticle building blocks with complementary reactivity

Chem Sci., 2020, Advance Article


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Aqueous microdroplets containing only ketones or aldehydes undergo Dakin and Baeyer–Villiger reactions

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Significantly improved electrocatalytic oxygen reduction by an asymmetrical Pacman dinuclear cobalt(ii) porphyrin–porphyrin dyad

Chem. Sci., 2020, Advance Article

 

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Ptychographic X-ray tomography reveals additive zoning in nanocomposite single crystals

Johannes Ihli, Mark A. Levenstein, Yi-Yeoun Kim, Klaus Wakonig, Yin Ning, Aikaterini Tatani, Alexander N. Kulak, David C. Green, Mirko Holler, Steven P. Armes and Fiona C. Meldrum

Chem. Sci., 2020, Advance Article

 

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Biosynthesis of plant tetrahydroisoquinoline alkaloids through an imine reductase route

Chem. Sci., 2020, Advance Article

 

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Molecular Switches from DNA

The idea of using DNA-based devices to create highly specific sensors, diagnostic tools, and therapeutics has inspired widespread research. DNA molecular switches, a basic class of DNA nanostructures, turn some process on and off depending on whether a substrate binds to the switch. They are typically coupled with some form of signal amplification process to increase sensitivity and should theoretically provide enhanced signal-to-noise. Unfortunately, current amplification procedures have a significant amount of background reactions, called leakage, that limit their current utility. One approach to design better switches is to find ways to observe single molecule dynamics. Combining transient binding of complimentary oligonucleotides with high resolution fluorescence microscopy allows for the development of highly sensitive molecular switches without leakage problems.

To do this, researchers in China developed a series of three-way junction DNA-based molecular switches. These TWJs possess a recognition domain, which interacts with the target of interest and induces a structural change in the TWJ, and a transduction domain, which then becomes accessible and binds to a fluorescent molecule (Figure 1).

Figure 1. General scheme of three-way junction molecular switch with two domains noted.

Experimentally, the TWJs were captured on the imaging surface and only fluorophores bound to a TWJ would remain in place long enough for signal to be acquired by the camera with a 500 ms integration time. The researchers found that shorter transduction domains with 5 or fewer base pairs were not stable enough to allow the fluorescent probes access in the absence of a bound target. The next generation of TWJs feature a hybridization probe to allow the switch to recognize specific DNA inputs. In the presence of inputs, the researchers observed transient binding behavior of the fluorophore, whereas they observed only nonspecific binding in the absence of inputs. The ability to differentiate between non-specific and transient binding in the single-molecule system gives a detection limit of 10 fM without concerns about leakage.

Building on this work, the researchers utilized the same general framework and substituted aptamer sequences for the hybridization probe in the recognition domain. They utilized split aptamer fragments that only draw together when bound to a target molecule. This motif was tested on ATP, a small molecule, and thrombin, a protein. These aptamer-coupled TWJs exhibited sensitivity to concentrations as low as 20 – 50 pm with high sensitivity (Figure 2). In the presence of molecular analogs to ATP or thrombin, the signal level showed no significant difference from that of a blank.

Figure 2. A) Split aptamer-based molecular switch schematic. B) Single-molecule fluorescence-time trajectory data in the presence (top) or absence (bottom) of targets. C) and D) Linear relationship between thrombin concentration and signal and specificity when compared to analogs. E) and F) Linear relationship between ATP concentration and signal and specificity when compared to analogs.

Another advantage of this system is its ability to provide information on the binding affinity of substrates, as it should impact the kinetics of the fluorescent probes. The dwell times of the fluorescence on and off states demonstrated exponential trends with changing input concentrations and could be fit to extract time constants. These time constants can then be used to derive the kinetics parameters and binding affinities of the target species. The general stability of the molecular switch framework allows for studying these types of interactions in a range of pH and salinity conditions, useful for mimicking different environments relevant to future applications. This provides a platform for studying the fundamental interactions that will allow DNA-based nanotechnology to move forward.

To find out more, please read:

Single-molecule dynamic DNA junctions for engineering robust molecular switches

Shuang Cai, Yingnan Deng, Shengnan Fu, Junjie Li, Changyuan Yu and Xin Su

Chem. Sci., 2019, 10, 9922-9927.

About the blogger:

Beth Mundy is a PhD candidate in chemistry in the Cossairt lab at the University of Washington in Seattle, Washington. Her research focuses 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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HOT Chemical Science articles for October

We are happy to present a selection of our HOT articles for October. To see all of our HOT referee-recommended articles from 2019, please find the collection here.

As always, Chemical Science articles are free to access.

Development of a DUB-selective fluorogenic substrate

ChemSci., 2019, 10, 10290-10296

 

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Facile triflic acid-catalyzed α-1,2-cis-thio glycosylations: scope and application to the synthesis of S-linked oligosaccharides, glycolipids, sublancin glycopeptides, and TN/TF antigens

Sanyong Zhu, Ganesh Samala, Eric T. Sletten, Jennifer L. Stockdill and Hien M. Nguyen

ChemSci., 2019, 10, 10475 – 10480

 

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Preferential binding of unsaturated hydrocarbons in aryl-bisimidazolium·cucurbit[8]uril complexes furbishes evidence for small-molecule π–π interactions

Steven J. Barrow, Khaleel I. Assaf, Aniello Palma, Werner M. Nau and Oren A. Scherman

ChemSci., 2019, 10, 10240 – 10246

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Synthesis of bicyclo[3.1.0]hexanes by (3 + 2) annulation of cyclopropenes with aminocyclopropanes

Bastian Muriel, Alec Gagnebina and Jerome Waser

ChemSci., 2019, Advance Article

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Development of a hydrolysis-based small-molecule hydrogen selenide (H2Se) donor

Turner D. Newton and Michael D. Pluth

ChemSci.,  2019, Advance Article

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Ruthenium based antimicrobial theranostics – using nanoscopy to identify therapeutic targets and resistance mechanisms in Staphylococcus aureus

Kirsty L. Smitten, Simon D. Fairbanks, Craig C. Robertson, Jorge Bernardino de la Serna, Simon J. Foster and Jim A. Thomas

ChemSci.,  2019, Advance Article

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1st International Conference on Noncovalent Interactions

Last month, Chemical Science sponsored the 1st International Conference on Noncovalent Interactions, in Lisbon, Portugal. The talks highlighted the important role of noncovalent interactions in a range of disciplines, such as theoretical chemistry, synthesis, catalysis, crystal engineering, molecular recognition, medicinal chemistry, biology, materials science, and electrochemical immobilization.

Chemical Science, along with Dalton Transactions and RSC Advances, sponsored poster prizes at the conference. Congratulations to Anh Tuan Pham (University of Geneva, Switzerland) who received the Chemical Science poster prize, Sara R. G. Fernandes (University of Lisbon, Portugal) who received the Dalton Transactions poster prize, and Errui Li (Zhejiang University, China) who received the RSC Advances poster prize. There was a fantastic array of posters on display at the meeting, and we would like to extend a huge congratulations to all those who presented.

       

 

 

 

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10th National Conference on Inorganic Chemistry of the Chinese Chemical Society

Chemical Science was pleased to support the 10th National Conference on Inorganic Chemistry of the Chinese Chemical Society which took place at Shandong University last month. Poster prizes were given on behalf of Chemical Science as well as Inorganic Chemistry Frontiers, Materials Chemistry Frontiers, Catalysis Science & Technology, Physical Chemistry Chemical Physics, Green Chemistry, Dalton Transactions, RSC Advances, Nanoscale, Nanoscale Advances, Materials Horizons and Journal of Materials Chemistry A, B and C. Energy & Environmental Science and Sustainable Energy & Fuels also provided a joint prize. The winners are:

Poster prize winners of the 10th National Conference on Inorganic Chemistry of the Chinese Chemical Society

Yuan Xiong 熊昱安 东南大学
Southeast University
Lingling Xu 徐令令 西安交通大学
Xi’an Jiaotong University
Fan Guo 郭帆 南京大学
Nanjing University
Wenbin Wang 王文彬 华中科技大学
Huazhong University of Science and Technology
Mengfei Li 李梦菲 中国石油大学(华东)
China University Of Petroleum
Jing Dong 董婧 北京理工大学
Beijing Institute Of Technology
Bingqi Han 韩冰琪 吉林大学
Jilin University
Wenzhu Yu 于文竹 山东大学
Shandong University
Liang Zhou 周亮 北京大学
Peking University
Genfeng Feng 冯根锋 南京大学
Nanjing University
Peipei Cui 崔培培 德州学院
Dezhou University
Xiaoting Liu 刘晓婷 南开大学
Nankai University
Dong Li 李冬 厦门大学
Xiamen University
Zhi Wang 王芝 山东大学
Shandong University
Shuang Liu 刘爽 东北师范大学
Northeast Normal University

Congratulations to all the winners!

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Chemical biology symposium 2019

The Chemical biology symposium 2019 was recently held at Burlington House in London, UK on 20th May. Chemical Science and Organic & Biomolecular Chemistry were proud to support the meeting, and Chemical Science Senior Editor James Moore attended to meet with delegates and represent the Royal Society of Chemistry.

The symposium showcased the state of the art in chemical biology, bringing together the wider community with leading national and international experts in the field. The programme explored all aspects of chemical biology and highlighted the wider scope and impact of the field.

Chemical Science were proud to present Tiffany Chan from Imperial College London with the poster prize for her poster on ‘Targeted delivery of metal complexes across the blood-brain barrier for the treatment of Alzheimer’s disease’.

Organic & Biomolecular Chemistry were proud to present Sophie Newgas from King’s College London with the runner up poster prize for her poster on ‘Understanding the role of nitric oxide synthase in biosynthetic nitration’.

Congratulations to them both!

Tiffany Chan

Sophie Newgas

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17th Symposium on Host-Guest and Supramolecular Chemistry

The 17th Symposium on Host-Guest and Supramolecular Chemistry was held in Kanazawa, Japan, on 18th and 19th of May, chaired by Professor Shigehisa Akine of Kanazawa University. Professor Tatsuya Nabeshima of the University of Tsukuba and president of the Association of Research for Host-Guest and Supramolecular Chemistry was also in attendance, as was Hiromitsu Urakami on behalf of the Royal Society of Chemistry.

The Chemical Science poster prize was awarded to Mr. Akihiro Kanamori of Kanazawa University for his poster on the ‘Synthesis of Salicylideneimine-Based Cryptophane Derivatives through Chiral Self-sorting and Their Guest Recognition Behavior’.

The Chemical Communications poster prize was awarded to Mr. Lingyun Hu of the University of Tokyo for his poster on the ‘Construction of Metal-responsive DNAzymes by Incorporating CuII-mediated Imidazole-4-carboxylate Base Pairing’.

The Organic & Biomolecular Chemistry poster prize was awarded to Mr. Sota Yonemura of the University of Tsukuba for his poster on the ‘Formation of Chiral Single Isomer by Metal Complexation of a β-Cyclodextrin Derivatives introduced Seven Bipyridyl Groups and Origomer Complex of the Isomer’.

Congratulations to Akihiro, Lingyun & Sota!

(From left) Hiromitsu Urakami, Tatsuya Nabeshima, Akihiro Kanamori (ChemSci poster winner), Shigehisa Akine

Organic & Biomolecular Chemistry poster winner Sota Yonemura

(From left) Hiro Urakami, Tatsuya Nabeshima, Lingyun Hu (ChemComm poster winner), Shigehisa Akine

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