Archive for the ‘Uncategorized’ Category

Chemical Science Reviewer Spotlight – November 2021

To further thank and recognise the support from our excellent reviewer community, we are highlighting reviewers who have provided exceptional support to the journal over the past year.

This month, we’ll be highlighting Christine Luscombe, Peng Yang, Shigeyoshi Inoue and Jennifer Brodbelt. We asked our reviewers a few questions about what they enjoy about reviewing, and their thoughts on how to provide a useful review.

Christine Luscombe, Okinawa Institute of Science and Technology, Japan. Christine works on developing organic semiconducting polymers for applications including light-emitting diodes, photovoltaics, mixed ionic-electronic conduction, and stretchable electronics.
Peng Yang, Shaanxi Normal University, China. Peng’s group develop coatings by exploiting the chemical diversity of amyloid-like protein aggregation and use them in applications including bio-interfaces, flexible electronics and adhesives.
Shigeyoshi Inoue, Technische Universität München, Germany. Shigeyoshi’s research focus is on the synthesis, characterization and reactivity investigation of compounds containing low-valent main group elements with unusual structures and unique electronic properties.
Jennifer Brodbelt, University of Texas at Austin, USA. Jennifer’s group develop high performance mass spectrometry strategies, such as ultraviolet photodissociation, to analyze and quantify molecules in complex mixtures, such as proteins and lipids.

 

What encouraged you to review for Chemical Science?

Jennifer Brodbelt: Chemical Science has a broad readership and covers a diverse range of topics. This contributes to its high impact factor and makes it a must-read journal. Serving as a reviewer is a natural part of the whole publishing process, and it is just as important to review manuscripts as it is to submit excellent manuscripts to keep the entire cycle strong.

 

Christine Luscombe: I am big supporter of society journals and I am also a stronger believer in trying to give back to the community. Additionally, Chemical Science is a top tier journal, so I see it as a privilege to be able to be part of the publication process.

 

What do you enjoy most about reviewing?

Shigeyoshi Inoue: By reviewing papers, I will always be able to read and learn from the latest results and may even be able to contribute to the paper in some way.

 

Peng Yang: I can learn from other scientists with a new point of view. The reviewing process is also an evaluation of myself and helps to improve my own work.

 

What makes a paper truly stand out for you when you are reviewing?

Shigeyoshi Inoue: Of course, the quality of the reported results and great research ideas are important. However, I personally like papers that contain a simple and readable introduction and a conclusion that reflects well on the results obtained.

 

Jennifer Brodbelt: I definitely appreciate good quality figures. Good figures can capture the whole story.

 

What would you recommend to new reviewers to ensure their report is helpful?

Peng Yang: Evaluate papers from a scientific perspective and guide authors to do more innovative research rather than simply following others. Guide the authors to do more research on basic mechanism studies and more real or close-to-real applications, instead of only proof-of-concept showcases.

 

What has been your biggest learning point from reviewing?

Christine Luscombe: To treat people with respect and remember that there is someone who spent months/years collecting the data that went into writing the paper. We owe it to them to be careful as possible in our reviewing process.

 

Tune in next month to meet our next group of #ChemSciReviewers!

 

If you want to learn more about how we support our reviewers, check out our Reviewer Hub.

Interested in joining our ever-growing reviewer community? Send us your CV and a completed Reviewer Application Form to becomeareviewer@rsc.org.

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Associate Editor highlight – interview with Professor Tanja Junkers

Professor Tanja Junkers is a polymer chemist. Her research group work to control and manipulate the structure of polymers in any possible way with the aim to create sophisticated materials that can mimic materials made by Nature. Tanja’s group now also explore machine learning and how this can be utilised to advance chemistry and chemical synthesis itself.

What excites you most about your area of research and what has been the most exciting moment of your career so far?

If I think about what brings me joy in my work, it is actually the small things, like when an experiment actually confirms that my predictions were right, or – not so small – when one of my PhD students graduates successfully. That makes me proud! It’s all these little moments that make my research worthwhile.

What do you feel has been the most important development with your area of research since your publication in Chemical Science in 2015?

There are so many! It’s hard to pick a favourite, but I would probably say that within my very specific area of research, an important development is that we now have the ability to control the shape of the molecular weight distribution of a polymer. This is something that has just emerged in the last few years, and it provides so many new possibilities. It is a whole new dimension that’s opening up at the moment, and it is an important thing for us to be able to do as chemists if we want to bridge the synthetic gap between the materials that we can develop in the lab and those that nature creates. It has a tremendous influence, so I’m really excited about this development.

Why do you feel that researchers should choose to publish their work in Chemical Science

Chemical Science is the flagship chemistry journal of the Royal Society of Chemistry, which I see as being in the same league as Angew or JACS.  Whenever I talk to colleagues and they ask me, would you choose Journal of the American Chemical Science or would you choose Chemical Science, I always point them to the fact that Chemical Science is Diamond Open Access!

The Diamond Open Access service that Chemical Science offers is what makes the real difference. I feel very strongly about open access. As scientists, our research should not be exclusive. The majority is funded by taxpayer’s money. I therefore feel that it is our duty to make our research openly available to all, including non-scientists who may not completely understand what we are doing but should have the opportunity to read it. It is also our duty to make our content as accessible to a general reader as possible.

Of course, I know that you can’t change the system overnight. You must work with what is currently available, and I do feel that the community is headed in the right direction. Long-term, I believe that we must find a way to publish Open Access as standard.

What are you most looking forward to when acting as Associate Editor for the journal?

I see this as a great opportunity to gain experience myself. I’ve learnt a lot during my time with Polymer Chemistry and I’m pretty sure I’m going to learn even more at Chemical Science. As it is a general chemistry journal, rather than a focused polymer journal, I will need to carry out my own research on new ideas and topics in the literature that I wouldn’t have needed to research before.

Mostly I’m looking forward to seeing some really cool science!

What impact do you feel your area of research can make over the next 10 years? 

This is where I think that machine learning and the whole concept of digitisation will really have an impact. Currently, the utilisation of machine learning in my area of research is not widespread, but it is becoming more commonplace. I’m an advocate for the incorporation of machine learning. Chemists, on the whole, are very traditional, and chemistry is basically still carried out the same as it was 150 years ago. I think that’s about to change. We are finally going to see digitisation of the chemical sciences, and that will change the way we do chemistry fundamentally.

For Chemical Science, it is important that we have an open and inclusive board. How do you feel we are advancing in this area?

Progress is being made! Though I sometimes wonder if people define inclusivity in the right way. People usually think mostly about race and gender equity, which, of course, is very, very important, but I think we also need to think about other aspects of inclusivity.

One thing that I often think about is the dominance of the Western world in science, which is of course connected to money. If you go to a smaller university in a poorer country, researchers based there can’t always carry out the most impactful chemistry because they don’t have the financial means to, or they don’t have access to the right information. This makes it difficult to promote inclusivity, because it is harder for these institutes and researchers to compete with others from larger institutes with greater funding. These researchers have incredible ideas and are incredible scientists, but don’t always have the means to carry out what we in the ‘developed’ world deem cutting edge research. This is something that we must work on and acknowledge more.

I also think that this a question that should really be answered by the more stereotypical chemist in higher positions. We will only reach our diversity and inclusion targets if those who are in these higher positions are on board and advocate for increased diversity and inclusivity. It’s easy for those from a minority background to say that things should be more integrated. For example, I can say that of course trans people should be much more visible because I have a personal interest in that, but it’s a totally different thing if a person who is not personally affected actually makes the call for more inclusion and diversity. Therefore, I think this question should really be directed to people who belong to the traditional majority.

On a good note, this is why I like the Royal Society of Chemistry. I know that, as an organisation, the Royal Society of Chemistry is really trying to promote inclusion and diversity. Of course everyone knows that women, for example, have less opportunities in the chemical sciences, but actually publishing a study [through the gender bias report] which the community can refer to and which highlights the statistics is really, really important.

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.

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Associate Editor highlight – interview with Professor Graeme Day

Chemcial Science Associate Editor Graeme Day

Professor Graeme Day joined the Chemical Science Editorial Board in 2021. To celebrate this occasion, we met virtually with Graeme to discuss his area of research and how he hopes to see his field progress in the next 10 years.

Graeme’s research focuses on the development of computational approaches for predicting the structures and properties of materials, focussing mainly on organic molecular crystals and their applications in a range of areas from pharmaceuticals to organic electronics. Graeme’s research group have also started to explore the use of machine learning methods for exploring chemical space to find new molecules with exceptional properties.

What excites you most about your area of research and what has been the most exciting moment of your career so far?

Being able to predict the structure of a new material computationally, with the structure then going on to be found experimentally, is very exciting. Going back about 20 years, this is not something that was thought to be possible! The idea that I have seen the crystal structure of a molecule, possibly before that molecule has ever been synthesised, is pretty cool. I feel lucky that we can collaborate and combine our computational work with the experimental work from other groups to uncover new materials. It’s exciting to think about all of the possibilities of these kinds of structure and property prediction methods.

With regards to the most exciting moment of my career, it is difficult to pinpoint one moment. However, in 2004, I was able to take part in my first blind crystal structure prediction test as an independent researcher. This was exciting! Being the only entrant to correctly predict one of the targets gave me a lot of confidence that I had valuable ideas and methods to bring to the field. The field has moved forward dramatically since 2004, but we still use some of the methods that I was working on back then.

What has been the most challenging moment of your career so far?

It’s probably the supervision of a research group that I have found the most challenging, but also very rewarding. Within a few years, I went from carrying out a lot of the research on my own, to receiving an ERC grant and being able to recruit a group of ten or so researchers. I had a very short period of time to learn how to make that transition and accept that I would spend more time discussing results, with less time doing hands-on research. Thankfully, I’ve had the opportunity to work with lots of great people and I hope that they have enjoyed their time in my research group.

Which of your Chemical Science publications are you most proud of and why?

That’s a tough one. Looking back, I’m quite proud of the range of work that we have published in Chemical Science, from fundamental questions about crystal packing, prediction of co-crystallisation, and machine learning applications for structure prediction. I really liked our 2014 contribution, which investigated the conformational preferences of molecules in their crystal structures. This work has important implications for crystal structure prediction.

However, it’s probably our 2020 paper that I’m most proud of because it demonstrates an approach to materials discovery that has been a vision of mine for quite a few years: combining chemical space exploration to identify new molecules with crystal structure prediction to evaluate their likely solid state properties.

What do you feel has been the most important development with your area of research since your first publication in Chemical Science in 2011?

The most important thing has been the increasing trust that people put in computational methods for studying materials. Even just a decade ago, there was a lot of scepticism surrounding methods like crystal structure prediction. This has changed, partly because of the improved methods that are now available, but also due to better communication of the limitations and uncertainties in computational predictions.

What do you hope to be able to contribute to the community through your new role as Associate Editor?

I have tried to keep up a broad level of knowledge of computational chemistry methods and their applications and I hope that I can use this to make informed and fair decisions on what to publish in Chemical Science. I’m really excited to see what people submit because there’s so much interesting work going on.

Why do you feel that researchers should choose to publish their work in Chemical Science?

I feel that I’m joining an editorial board that has done a great job in attracting the highest quality work and building a strong reputation for this flagship journal of the RSC. This means that people read Chemical Science when looking for exciting work. That’s important for researchers: knowing that you’re publishing your best work in a journal where it will be picked up quickly by the community. I think that this is particularly true in the area of computational chemistry, machine learning and AI applications in chemistry. The journal has been a great place for work in these areas that are of broad interest. The journal being Diamond Open Access is, of course, also a great thing. Researchers can make their work freely available without needing to find the budget to pay open access fees.

How do you see your field progressing in the next 10 years?

One big area will be the increasing integration of computational methods with experiments, where automation and robotics will play a big role. I’m looking forward to seeing more experiments where ideas are seeded by computational modelling and machine learning. I also hope that we see some artificial boundaries fall away, particularly between theoretical and experimental chemists. Of course, we need specialisation, but I want to see more people working across that boundary.

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.

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Associate Editor highlight – interview with Professor Hemamala Karunadasa

Hemamala Karunadasa Chemical Science Associate Editor

Professor Hemamala Karunadasa joined the Chemical Science Editorial Board in 2021. In 2020, the year of Chemical Science‘s 10th anniversary, we met virtually with Hemamala to discuss her research. In celebration of Hemamala joining the Editorial Board, we have taken the opportunity to revisit this interview.

Hemamala’s research focuses on the preparation of solid-state materials using the tools of solution-state chemistry. Through careful design, Hemamala and her group prepare new materials that can be utilised for clean energy applications.

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Browse a selection of Hemamala’s work below:

Dimensional reduction of the small-bandgap double perovskite Cs2AgTlBr6
Bridget A. Connor, Raisa-Ioana Biega, Linn Leppert and Hemamala I. Karunadasa
Chem. Sci., 2020, 11, 7708-7715
DOI: 10.1039/D0SC01580F, Edge Article

A pencil-and-paper method for elucidating halide double perovskite band structures
Adam H. Slavney, Bridget A. Connor, Linn Leppert and Hemamala I. Karunadasa
Chem. Sci., 2019, 10, 11041-11053
DOI: 10.1039/C9SC03219C, Edge Article

Tuning the bandgap of Cs2AgBiBr6 through dilute tin alloying
Kurt P. Lindquist, Stephanie A. Mack, Adam H. Slavney, Linn Leppert, Aryeh Gold-Parker, Jonathan F. Stebbins, Alberto Salleo, Michael F. Toney, Jeffrey B. Neaton and Hemamala I. Karunadasa
Chem. Sci., 2019, 10, 10620-10628
DOI: 10.1039/C9SC02581B, Edge Article

Structural origins of broadband emission from layered Pb–Br hybrid perovskites
Matthew D. Smith, Adam Jaffe, Emma R. Dohner, Aaron M. Lindenberg and Hemamala I. Karunadasa
Chem. Sci., 2017, 8, 4497-4504
DOI: 10.1039/C7SC01590A, Edge Article

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Associate Editor highlight – interview with Professor Jinlong Gong

In 2021, Chemical Science was delighted to welcome Professor Jinlong Gong as an Associate Editor, handling manuscripts within the area of heterogenous catalysis. To celebrate this occasion, we met virtually with Jinlong to discuss his research and to discuss the kind of manuscripts that he is looking forward to handling for the journal.

Jinlong’s research focuses on understanding the catalytic processes occurring during alkane dehydrogenation and CO2 hydrogenation by developing advanced catalytic materials, as well as optimised industrial processes.

What excites you most about your area of research and what has been the most exciting moment of your career so far?

The major motivation of my research is to provide constructive solutions for a sustainable society, particularly associated with the chemical industry. For example, propane dehydrogenation is a traditional chemical process which has been under development over the past 60-80 years. Our research therefore focuses on trying to develop new catalytic processes to reduce the energy consumption with enhanced catalytic performance. Another example is about the utilisation of CO2 with sustainable energy to produce renewable fuels and help reduce emissions. President Xi Jinping has announced that China’s aim is to achieve a carbon neutral society by 2060. Actually, my work on photocatalytic reduction of CO2 follows such a direction. The big challenge in this area is to improve the efficiency, which is currently still low.

Some of the most exciting moments of my career have been when former students of mine have been recruited into faculty positions at top universities. It is always a pleasure to see young researchers grow up independently and then go on to do amazing things! Another exciting moment for me was when we were able to find new oxide materials that displayed very high efficiency for propane dehydrogenation. We believe that this is going to be the next generation of catalysts for this process.

What has been the most challenging moment of your career so far?

It is always challenging to navigate research into a scientifically critical direction at the right time, rather than staying in a comfortable zone. Transitioning the direction of your research into a new but important area tends be exhausting, especially at the start. On the other hand, the potential reward can be more exciting. Sometimes, it is also challenging to convince funders to support an unrevealed but potentially important research direction, which can be a common issue for most scientists.

You have published over 10 papers with Chemical Science since your first publication with us in 2015. Of these papers, which one do you feel has made the most significant contribution to your area of research and why?

One of the pieces that I like the most is a paper that we published in 2019 – hydroxyl-mediated ethanol selectivity of CO2 hydrogenation. In this paper, we developed a catalyst based on Rh, where we simply added some Fe and Li metals as promoters. One interesting thing we found was that, with various oxide supports, we can tune the surface coverage of hydroxyl groups bound on Rh-based catalysts, which has a very important correlation with ethanol selectivity for CO2 hydrogenation. I believe that this story will provide researchers with a deeper understanding of the formation mechanism of ethanol on this kind of catalyst, particularly in understanding the C-C coupling mechanism for this reaction, which is very important if we want to have a high C2 selectivity.

It’s been over a year after China’s first lockdown started. What changes have you witnessed in the Chinese researcher community? Do you think there are any new challenges or opportunities for chemistry researchers from this ongoing global pandemic?

This is a very good question! Last spring, early in the pandemic, many online seminars were arranged by researchers from all over the world and involved various publishers, which was great for scientific communication. In terms of academic activities, I noticed that there weren’t any big delays in the publication process, which again was great. Since last fall, the situation in China has become much better, with most academic meetings now being able to take place on-site.

One noticeable opportunity from the overall research strategy in China is the focus on health. Funding agencies will now put even more emphasis on bio-relevant research. I think there will be a big boom in this area in China in the next few decades. Globally, I believe we will see lots of joint projects taking place between research groups that work in chemical engineering, chemistry, materials and medicine, which will promote multidisciplinary collaboration.

Why do you feel that researchers should choose to publish their work in Chemical Science

Chemical Science, as flagship journal of the Royal Society of Chemistry, has a prestigious reputation in the chemistry and physical science community. Chemical Science publishes cutting-edge papers that provide deep and novel understanding of the chemistry of important reactions. Multidisciplinary research, including radical physical chemistry, is also welcome. For example, AI methods used to screen candidate materials or analyse chemical reactions can be attractive. This kind of research, in turn, will reward the scientific community. Chemical Science, as an open-access journal, provides a highly fair publishing platform, and the Editorial Office is also very efficient – manuscripts are turned around in a very timely manner. It is one of best journals publishing chemical research.

What attracted you to join the Editorial Board of Chemical Science?

I have served on the Advisory Board for Chemical Science since 2013, and I am also a regular referee for the journal. Now, I feel that I am very fortunate to have the opportunity to handle submissions to Chemical Science, particularly in the area of heterogeneous catalysis. Chemical Science has a high-profile impact on the scientific community, which provides me with the opportunity to handle exciting scientific research, communicate with diverse groups of scientists, and most importantly, serve the research community. Together with the warm editorial team, we can provide authors with a professional publication experience.

It is important for Chemical Science to have an open and inclusive Editorial Board. Do you feel that we are achieving this goal?

I received a lot of warm greetings when May introduced me to the other members of the Editorial Board. Looking at the profiles of our members in the editorial team, we have great diversity among the board, including Associate Editors from all over the world, with expertise spanning across the chemical sciences. So far, I think we are achieving the goal. They are all renowned scientists.

What impact do you feel that your area of research can make over the next 10 years?

First of all, I would like to highlight the impact that I feel light alkane dehydrogenation can make in the next 10 years. This is a major industrial process to produce ethylene/propylene, which are building blocks for preparing polymers. The development of new technology as well as catalytic materials will further decrease the energy consumption during this process, and also increase the catalytic efficiency overall. This can help to ensure a better and greener industrial process in the future.

My second area of research focuses on the photocatalytic reduction of CO2. It’s very important for us to transform from a fossil fuel society into a renewable energy society. Energy conversion and storage technologies will play critical roles in this area. In the next 10-20 years, I think this type of research will definitely have more impact. There has already been a lot of investment into the research as well as infrastructure to support this initiative, so I hope that this goal will be able to be realised.

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.

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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

 

 

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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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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