Chemical Communications Blog

We’re celebrating researchers who published their first independent article with ChemComm. Professor Sílvia Osuna published her first article in 2017: Computational tools for the evaluation of laboratory-engineered biocatalysts. We wanted to find out more about Sílvia and her research – Read more below.

What are the main areas of research in your lab and how has your research progressed since publishing your first article?
The main research areas in my lab are the application and development of computational tools for evaluating laboratory-engineered enzymes, with the final goal of rationally designing new enzymes. The Feature article published in Chem. Commun. in 2017 focused on providing an overview of the available computational strategies that can be used to evaluate laboratory-engineered enzymes. Since then, we have computationally evaluated a variety of enzymes mostly through extensive Molecular Dynamics simulations (monoamine oxidase, tryptophan synthase, and alcohol dehydrogenases, among others) to unveil the role exerted by distal active site mutations on the enzyme conformational landscape. Most importantly, we have also developed new computational tools for predicting active site and distal mutations for enhanced activity (Shortest Path Map tool), which we are currently applying for altering the conformational dynamics of different enzymes. The key role exerted by remote mutations on the active sites of enzymes suggests that allostery (i.e. regulation of enzyme function by distal positions) might be an intrinsic characteristic of enzymes, which we are exploiting for enzyme evolution. Therefore, our research is now more focused on applying the developed tools to rationally design new enzyme variants rather than evaluating and explaining the enhanced activities of previously reported laboratory-engineered enzymes.

What do you hope your lab can achieve in the coming year?
I hope in the coming year we can further validate our computational tools for predicting distal active site mutations. Due to the broad sequence space of enzymes, the computational prediction of such distal mutations has been proven to be extremely challenging. However, our new tools developed open the door to new protocols based on the introduction of active site and also distal mutations. This is totally unprecedented in the computational enzyme design field, and I hope in the coming year we can further demonstrate that our developed computational tools can be successfully applied for enzyme design.

Describe your journey to becoming an independent researcher.
I received a PhD in 2010 from the University of Girona (UdG) at the Institut de Química Computacional (IQC) under the supervision of Prof. Miquel Solà and Prof. Marcel Swart. I worked on the computational study of the chemical reactivity of carbon-based compounds, such as (metallo)fullerenes and carbon nanotubes. In October 2010 I moved to the group of Prof. Houk at the University of California, Los Angeles (UCLA) thanks to the IOF Marie Curie fellowship. At that time, I started to work in the computational design of enzymes of medical and pharmaceutical interest. In December 2013, I rejoined the Institute of Computational Chemistry and Catalysis (IQCC) at the University of Girona with a postdoctoral Juan de la Cierva position. I was also awarded a Career Integration Grant (CIG) project for developing a computational protocol for designing new enzymes, and also an I+D MINECO Project together with Prof. Swart. In 2015, I obtained a European Research Council – Starting grant project (ERC-StG) to apply network models for the computational design of efficient enzymes (NetMoDEzyme), and also a 5-year Ramón y Cajal position from the Spanish government. In 2018, I was promoted to the current permanent ICREA position I currently hold. My group is now funded by the ERC-StG project, an I+D MINECO project, and a Human Frontier Science Program project.

What is the best piece of advice you have ever been given?
My grandmother used to tell me a Catalan saying “De pressa i bé, mai s’avingué”, which I believe the English equivalent would be “Slow and steady wins the race”. There are of course exceptions to the saying, but I believe it is a generally good advice that also applies in scientific contexts.

Why did you choose to publish your first article in ChemComm?
I received an invitation to submit a Feature article to ChemComm a few months after being awarded the ERC-StG project. I decided this was an excellent idea as I had already done an extensive bibliographic search for writing the ERC project. Most importantly, I like ChemComm, its published Feature articles, and its broad readership. I was also really happy to see that our published Feature article was included in the most downloaded articles of 2017 in physical and environmental chemistry. When I received a second invitation to contribute with a second Feature article in 2018, I didn’t hesitate to accept the invitation.

Sílvia received her PhD in 2010 from the University of Girona (UdG) at the Institut de Química Computacional (IQC) under the supervision of Prof. Miquel Solà and Prof. Marcel Swart. In 2010, she moved to the group of Prof. Houk at the University of California, Los Angeles (UCLA). In 2012, she rejoined the Institute of Computational Chemistry and Catalysis (IQCC) at the University of Girona with a postdoctoral Juan de la Cierva position, which was followed by a Ramon y Cajal contract, and her current permanent ICREA research professor position. Sílvia’s research lies at the interface between computational chemistry and biology. Her research focuses on the study of biochemical processes mainly related to enzyme catalysis.

Read more from our ChemComm1st authors in ChemComm Milestones – First Independent Authors

We’re celebrating researchers who published their first independent article with ChemComm. Dr Han Xiao published his first article in 2018: A noncanonical amino acid-based relay system for site-specific protein labeling. We wanted to find out more about Han and his research – Read more below.

What are the main areas of research in your lab and how has your research progressed since publishing your first article?
Understanding complex biological systems and developing novel therapeutic approaches requires explorations at the interface of chemistry and biology. The focus of our research is the development of various chemical tools that allow us to precisely probe and manipulate biological systems. We are interested in (1) adding new building blocks with novel chemical, biological, and physical properties into different biological systems; (2) enhancing the performance of chemical biological tools for a variety of applications; (3) using these tools to better understand and ultimately control various biological processes; and (4) exploring the therapeutic utilities of these tools in the context of cancer, autoimmune, and metabolic diseases. My program has a strong translational focus, seeking to initiate new clinical opportunities, and contribute to advances in chemical biology, glycobiology, and cancer immunology.
Our article demonstrates the first application of autonomous cells with the endogenous ability to biosynthesize different noncanonical amino acids and incorporate them into proteins. Noncanonical amino acid, p-amino-phenylalanine, was biosynthesized in E. coli, followed by site-specific incorporation into a specific protein residue. The resulting protein was ready for functionalization using an oxidative conjugation reaction. We are continuing cells utilizing a 21st amino acid and further examine their utility in protein evolution and therapy development.

What do you hope your lab can achieve in the coming year?
Although I have been building my independent research profile at Rice, I am actively exploring new research directions by collaborating with researchers in different fields. I hope we can tell you more of these exciting works in the coming year.

Describe your journey to becoming independent researcher.
My academic training and research experience have provided me with a broad background in multiple disciplines, which is critical for me to build up my independent research program. As an undergraduate, I supported Dr. Liu-Zhu Gong’s group (USTC) by developing flexible routes to synthesize chiral amines in alkaloid nature products. As a graduate student, I joined Dr. Peter G. Schultz’s lab at the Scripps Research Institute (TSRI). My graduate work was mainly focused on expanding the technique of genetically incorporating noncanonical amino acids in both prokaryotic and eukaryotic organisms and applying this technique for better cancer therapeutics. To further my goal of becoming a professional scientist, I started my post-doctoral research career in Prof. Carolyn R. Bertozzi’s laboratory at Stanford University, whose lab has extensive experience in studying cancer-associated glycosylation. I learned a lot from my previous advisors about how to carry out projects as well as run a lab. The different training experiences from these labs laid the foundation for the interdisciplinary program I would like to build up at Rice University.

What is the best piece of advice you have ever been given?
The best advice was given to me by my parents: Prepare for the Future.

Why did you choose to publish your first article in ChemComm?
ChemComm is a renowned journal with a large readership from all chemistry disciplines as well as interdisciplinary fields. I am very happy to publish our first work in ChemComm.

Biography Han Xiao is an Assistant Professor of Chemistry and Biosciences at Rice University. Han obtained his undergraduate degree from the University of Science and Technology of China (USTC) where he graduated with a B.S. in chemistry and an honors degree in physical science. He conducted undergraduate research in Prof. Liu-Zhu Gong’s group, focusing on organic methodology and synthesis of natural products. After graduating from USTC in 2010, Han joined the Ph.D. program at the Scripps Research Institute (TSRI). His thesis work with Prof. Peter G. Schultz focused on expanding the technique of genetically incorporating unnatural amino acids in both prokaryotic and eukaryotic organisms and applying this technique for better cancer therapeutics. In 2015, Han joined the laboratory of Prof. Carolyn R. Bertozzi as a Good Ventures Postdoctoral Fellow of the Life Science Research Foundation at Stanford University. In his postdoctoral work, he was engaged in the development of novel cancer immune therapy targeting the cell-surface glycans axis of immune modulation. In July 2017, Han started his independent research at Rice University. Find him on Twitter: @Han_Xiao2016

Hiroshi Yamagishi recently published his first independent research article with ChemComm. We wanted to celebrate this exciting milestone by finding out more about Hiroshi and his research. Check out his #ChemComm1st article: Facile light-initiated radical generation from 4-substituted pyridine under ambient conditions

We asked Hiroshi a few questions about his experience in the lab and working with ChemComm. Read more below.

What are the main areas of research in your lab and what motivated you to take this direction?

After receiving the PhD for the synthesis and fundamental structural investigation of supramolecular porous fibers and crystals, I was motivated to expand this research topic in regard to their functionality. Our group in University of Tsukuba is now focusing on the synthesis of molecular porous aggregates and investigating their host–guest chemistry and optical functions.

Can you set this article in a wider context?
The host porous crystal, Pyopen, is an attracting and counterintuitive compound. Although the constituent organic molecules are bound together via labile van der Waals-like forces (C–H···N bonds), the porous framework exhibits high thermal stability. Distinct from the conventional MOFs, COFs, or HOFs, the stability of Pyopen is based on the packing mode or the interdigitation of the molecules. We expect that the difference in the bonding regime should result in novel outcomes, and we are now investigating a series of chemical and physical characters of such molecular porous crystals sustained by van der Waals crystals. This article highlights one of the intriguing optical and chemical features of the van der Waals crystals.

What do you hope your lab can achieve in the coming year?

One of the fundamental yet challenging topics in the field of van der Waals porous crystal is to establish a molecular design strategy. Distinct from the MOFs, COFs, or HOFs, the prediction or designing of van der Waals porous crystal is yet to be established due to the extremely low bonding energy and the low directionality of van der Waals force. This topic is what I am now trying to overcome in the coming year.

Describe your journey to becoming independent researcher.

In the course of the PhD, I fortunately received an offer as a researcher from a chemical company and was really willing to join after I got the PhD. However, when I visited the UK as a guest researcher for half a year before joining the company, I occasionally met with a colleague in the University of Tsukuba there, who also visited UK for Sabbatical and proposed to me a position in University of Tsukuba. Through this experience, I understood from the heart the meaning of the sentence: “Nobody knows the future”.

What is the best piece of advice you have ever been given?

An advice from a colleague of mine was indeed impressive and encouraging to me. In the course of a discussion about a research result, he said “I hate the word ‘failure’. You did not fail, but revealed a novel fact that the reaction proceeded in a different way from what you expected”.

Why did you choose to publish in ChemComm?

ChemComm is a renowned journal that covers the diverse chemical sciences. Chemical Science is also attractive to me, but I prefer the communication format for publishing our results with urgency. Therefore, I chose ChemComm.

I am an Assistant Professor in Department of Materials Science, University of Tsukuba since 2018. I was educated at the University of Tokyo, gaining a PhD in 2018 for the development of intricate nanoporous organic and metal¬–organic architectures with distinct structural flexibility. I am currently focusing on optical resonators based on supramolecular aggregates with a view to realizing flexible lasers, displays, optical circuits and sensors. Compounds of interest covers organic linear and dendritic polymers, organic and metal–organic crystals, and organic liquid.

Malte Fischer recently published his first article as a corresponding author with ChemComm. We wanted to celebrate this exciting milestone by finding out more about Malte and his research. Check out his #ChemComm1st article: B(C6F5)3- and HB(C6F5)2-mediated transformations of isothiocyanates.

We asked Malte a few questions about his experience in the lab and working with ChemComm. Read more below.

What are your main areas of research and what motivated you to take this direction?

I would like to summarize the research I am doing and I am interested in, simply under the term “synthetic chemistry”. Specifically, I mean research within the interfaces of organic chemistry, main group chemistry and organometallic chemistry. I am enthusiastic about the progress – especially in recent years – in synthesis, method development and in the search for applications for new molecules. I am convinced that there will always be a need for effective synthesis routes to access unusual and new molecules and I very much hope that I can contribute to this.

Can you set this article in a wider context?

The article is settled in main group chemistry. During my PhD I became more and more interested in this exciting field of research. Based on the reported results I will continue the research in this field.

What do you hope you and your research can achieve in the coming year?

Despite this difficult time, I am simply looking forward to going back to the laboratory at some point to continue having fun in doing research.

Describe your journey to becoming an independent researcher.

I think the moment when I was able to synthesize and characterize my first molecule unknown in literature (happened during my bachelor thesis) inspired me so much that since then I have had the goal of doing independent research and realizing my own ideas. I am definitely still in the beginning of becoming an independent researcher and I am currently working on laying the foundation for it – and this work has given me a lot of pleasure so far.

What is the best piece of advice you have ever been given?

The best advice was given to me by my parents and I try to live by it as much as possible: Pursue what interests you most and captivates you – the rest will come naturally.

Why did you choose to publish in ChemComm?

ChemComm simply stands for publications of the highest quality and with a large readership from all chemistry sub-disciplines. I am immensely pleased to have become a small part of this journal with my first publication as the corresponding author.

Malte’s Bio:

The publication ‘B(C6F5)3- and HB(C6F5)2-Mediated Transformations of Isothiocyanates’ originates from the phase as a research scientist within the group of Prof. Beckhaus in Oldenburg.

05/2019 – 02/2020      Research Scientist/ PostDoc – Carl von Ossietzky University Oldenburg, Germany. Supervisor: Prof. Dr. Rüdiger Beckhaus

10/2015 – 05/2019      PhD in Chemistry. Carl von Ossietzky University Oldenburg, Germany. Supervisor: Prof. Dr. Rüdiger Beckhaus

10/2013 – 10/2015      Master of Science in Chemistry

10/2010 – 10/2013      Bachelor of Science in Chemistry

Find Malte on Twitter: @FiMalte

Rob Woodward recently published his first independent research article with ChemComm. We wanted to celebrate this exciting milestone by finding out more about Rob and his research. Check out his #ChemComm1st article: ‘The design of hypercrosslinked polymers from benzyl ether self-condensing compounds and external crosslinkers’

We asked Rob a few questions about his experience in the lab and publishing with ChemComm. Read more below.

What are the main areas of research in your lab and what motivated you to take this direction?

Our primary research focus is the design and production of new porous organic polymers and carbons for a variety of separation and storage applications. These include solid-state extraction to remove pollutants from water, fractionation of complex mixtures, gas separation and storage, energy storage, and even catalysis. In order to approach such a wide variety of applications, we utilise a class of densely crosslinked porous polymers, known as hypercrosslinked polymers. The key feature of these networks is their simple and robust synthesis, allowing a vast array of aromatic compounds to be used as monomeric building blocks.

Our motivation is to try to use hypercrosslinked polymers to establish a platform for targeted adsorbent design. This would enable the engineering of networks customised to tackle specific problems. For example, if certain chemical functionalities or textural properties are known to be beneficial for a given application, we can envision a sort of ‘plug-and-play’ approach, in which various building blocks are used to produce adsorbents with the desired properties. Hypercrosslinked polymers are generally low-cost and have excellent chemical and thermal stabilities, issues that plague many classes of porous materials. Coupled with tailored design, these features may make hypercrosslinked polymers suitable for a broad range of applications, while remaining technically competitive with leading adsorbents.

Can you set this article in a wider context?

The article represents a new approach to the formation of hypercrosslinked polymers, in which conventional aliphatic crosslinkers are replaced with these benzyl ether aromatic compounds. The synthetic process remains the same, but the textural properties of the resulting polymer can be vastly improved, simply by changing a reagent. These compounds also showed unexpected benefits for hypercrosslinking reactions, allowing better control over the porous properties of networks and for reductions in the amount of catalyst required during synthesis, something currently considered a significant setback for hypercrosslinked polymers.

In a wider context, this work opens new routes to hypercrosslinked polymers where conventional approaches may fail or give poor results, presenting synthetic chemists more options with respect to designing new and improved adsorbents.

What do you hope your lab can achieve in the coming year?

Although I have been building my independent research profile while at Imperial College, I was just very recently appointed to an Assistant Professor position in The University of Vienna’s Faculty of Chemistry. This is really the beginning of my independent academic career with regards to establishing my own lab and research group. So, in all honesty, this year will look like a success to me if we can get the laboratory up and running, begin to build a strong research foundation, and establish a network in Vienna to try to begin some local collaborative work. We do have some exciting work due to come out soon which we hope to build from in the short term, but I won’t say too much about that just yet…

Describe your journey to becoming an independent researcher.

I was awarded both my MChem (2008) and PhD (2013) from The University of Liverpool, which is also my hometown. My PhD focused on the synthesis of responsive polymeric surfactants and colloidal systems. I then took up a short post-doctoral position in Prof. Andy Cooper’s group, where I first worked with porous polymeric materials. In 2014, I moved to London for a position in Imperial College London’s Department of Chemical Engineering in the Polymer and Composite Engineering group. There I started to explore other types of porous polymers, as well as investigating their application to several problems, such as energy storage, biomass treatment, and gas separation and storage. I was lucky to have great supervisors who were supportive of me establishing my own independent work. In 2017, I was awarded the Sir William Wakeham prize by Imperial for my research, which gave me the belief that I could pursue a career in academia. Finally, I was offered the role in Vienna just a few weeks ago! So, I am very excited to get that underway and to continue to explore my chosen research avenues.

What is the best piece of advice you have ever been given?

Tough question! Well, my dad always tells me that sometimes you must be a bit cheeky to get what you want – but I’m not sure how well that would go down with a review panel! I have had many great mentors in my academic life too, all of whom have given me advice that I will take forward. However, my PhD supervisor, Dr. Jonathan Weaver, not only taught me to face my demons head on but also assured me that I was able to. He taught me not to take life too seriously and that fostering happiness in all facets of your life was the key to success. Jon passed away at only 32 years old, before we could finish the PhD together, so his advice and guidance has become very special to me.

Why did you choose to publish in ChemComm?

I definitely envisioned the article as a Communication, a short proof of concept for this new approach to making hypercrosslinked polymers. I chose ChemComm as I know it has a great reputation and a broad readership, making it an ideal platform for me to report my work to researchers around the globe. Furthermore, this is the third article I have published in ChemComm (the first as an independent researcher) and the entire process has always been very smooth and transparent, so I was very happy to return.

Rob obtained his PhD from The University of Liverpool (UK) in 2013, before completing a short post-doctoral position in Prof. Andy Cooper’s group. In 2014 he moved to Imperial College London’s Department of Chemical Engineering, where he joined the Polymer and Composite Engineering group and began to build his independent research profile in the design and application of porous polymers. This year Rob was appointed as an Assistant Professor at the University of Vienna’s Institute of Materials Chemistry, marking the beginning of his independent academic career. Find Rob on Twitter: @robbiewoody

Read Rob’s #ChemComm1st article and others in our new collection ChemComm Milestones – First Independent Articles. Follow us on Twitter for the latest #ChemCommMilestones news.