DOCSLIB.ORG

University of Groningen Steps Towards De-Novo Life Monreal Santiago

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Groningen Steps Towards De-Novo Life Monreal Santiago University of Groningen Steps towards de-novo life Monreal Santiago, Guillermo DOI: 10.33612/diss.121581426 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2020 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Monreal Santiago, G. (2020). Steps towards de-novo life: compartmentalization and feedback mechanisms in synthetic self-replicating systems. University of Groningen. https://doi.org/10.33612/diss.121581426 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 27-09-2021 About the author Guillermo Monreal Santiago was born in 1992 in Madrid, Spain. He pursued his undergraduate studies at the Universidad Complutense de Madrid (UCM), where he received a Bachelor’s degree in Chemistry (2014) and a Masters de- gree in Organic Chemistry (2015). His undergraduate research projects consisted on the synthesis of biologically active b-aminoalcohols from enantioenriched O- acylated cyanohydrins (under the supervision of Christina Moberg, at KTH in Stockholm), and the synthesis of Fe-Fe polymetallic clusters bound to nucleobases as hydrogenase mimics (under the supervision of Mar Gómez Gallego and Miguel Ángel Sierra, in the bioorganometallic group at the UCM). He moved to Gronin- gen in 2015 to pursue a PhD in the group of Sijbren Otto, researching the com- bination of life-like properties with synthetic self-replicators emerging from dy- namic combinatorial libraries. The results of his PhD research are described in this thesis. List of publications [1] Matysiak, B. M.; Monreal Santiago, G.; Otto, S. Teaching an old compound new tricks: Reversible transamidation in maleamic acids. In preparation [2] Maity, S.; Ottelé, J.; Monreal Santiago, G.; Frederix, P. W.; Kroon, P. C.; Markovitch, O.; Stuart, M. C. A.; Marrink, S. J.; Otto, S.; Roos, W. H. Caught in the act: Mechanism of supramolecular polymerization driven self-replication visualized in real time. Submitted. [3] Monreal Santiago, G.; Liu, K.; Browne, W. R.; Otto, S. Emergence of light- driven protometabolism upon recruitment of a photocatalytic cofactor by a self-replicator. Nat. Chem. 2020, Accepted. Preprint – doi: 10.26434/chem- rxiv.10002122.v1. [4] Komaromy, D.; Tiemersma-Wegman, T.; Kemmink, J.; Portale, G.; Aalbers, F.; Mari´c,I.; Monreal Santiago, G.; Ottelé, J. O.; Sood, A.; Saggiomo, V.; Liu, B.; van der Meulen, P.; Otto, S. Controlling supramolecular plasticity through stoichiometry. ChemRxiv 2019, doi: 10.26434/chemrxiv.10117343.v1. [5] Bartolec, B.; Leonetti, G.; Li, J.; Smit, W.; Altay, M.; Monreal Santiago, G.; Yan, Y.; Otto, S. Emergence of compartments formed from unconventional surfactants in dynamic combinatorial libraries. Langmuir 2019, 35, 5787–5792. 183 [6] Malakoutikhah, M.; Schaeffer, G.; Monreal Santiago, G.; Yang, S.; Mari´c,I.; Otto, S. Cross-catalysis between self-replicators of different handedness. J. Syst. Chem. 2019, 7. [7] Cvrtila, I.; Fanlo-Virgós, H.; Schaeffer, G.; Monreal Santiago, G.; Otto, S. Re- dox control over acyl hydrazone photoswitches. J. Am. Chem. Soc. 2017, 139, 12459–12465. [8] Komáromy, D.; Stuart, M. C.; Monreal Santiago, G.; Tezcan, M.; Kras- nikov, V. V.; Otto, S. Self-assembly can direct dynamic covalent bond forma- tion toward diversity or specificity. J. Am. Chem. Soc. 2017, 139, 6234–6241. [9] Hertzberg, R.; Monreal Santiago, G.; Moberg, C. Synthesis of the β3- adrenergic receptor agonist Solabegron and analogous N-(2-Ethylamino)-β- amino alcohols from O-acylated cyanohydrins - expanding the scope of mi- nor enantiomer recycling. J. Org. Chem. 2015, 80, 2937–2941. 184.
Load more

Recommended publications
  • Towards Life Originating De-Novo
    Diplomarbeit Towards Life originating de-novo: Strategies how Compartmentalization could be induced by a synthetic Self-Replicator Ausgefuhrt¨ zum Zwecke der Erlangung des akademischen Grades der Diplom-Ingeneurin (Dipl.-Ing.) im Rahmen des Studiums Technische Chemie unter der Leitung von Univ.Prof. Dipl.-Ing. Dr. (tech) Johannes Frohlich¨ Institut fur¨ Angewandte Synthesechemie Technische Universitat¨ Wien und Prof. Dr. Sijbren Otto Stratingh Institut fur¨ Systemchemie Universitat¨ Groningen Eingereicht an der Technischen Universitat¨ Wien Institut fur¨ Angewandte Synthesechemie Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. von Anna-Patricia Wolf, BSc. 1302118 Wien, am 23. April 2020 Unterschrift Verfasserin Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. "Der Mensch braucht ein Ziel!" - Heinz Tauscher Die approbierte gedruckte Originalversion dieser Diplomarbeit ist an der TU Wien Bibliothek verfügbar. The approved original version of this thesis is available in print at TU Wien Bibliothek. DECLARATIONONOATH statutory declaration I declare that I have written this thesis independently, that I have not used other than the declared sources or resources, and that I have explicitly marked all material, which has been quoted either literally or by content from the used sources. eidesstattliche erklärung Ich erkläre an Eides statt, dass ich die vorliegende Arbeit selbstständig verfasst, andere als die angegebenen Quellen oder Hilfsmittel nicht benutzt und die den benutzten Quellen wörtlich und inhaltlich entnommenen Stellen als solche kenntlich gemacht habe.
    [Show full text]
  • Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
    OLEFIN METATHESIS IN PEPTIDOMIMETICS, DYNAMIC COMBINATORIAL CHEMISTRY, AND MOLECULAR IMPRINTING By TAMMY KARRIE CHENG LOW A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2006 The views expressed in this dissertation are those of the author and do not reflect the official policy or position of the United States Air Force, Department of Defense, or the U.S. Government. This dissertation is dedicated to my parents for their unconditional love and support. ACKNOWLEDGEMENTS My sincere gratitude goes out to the many individuals who have supported me throughout the years. I first like to thank the Air Force Academy for giving me the opportunity to pursue my Ph.D. I look forward to returning and working in a wonderful teaching environment. Special thanks go to Lt Col Ron Furstenau, a mentor and role model, who taught me a lot about being a good instructor and inspired me to teach. I would like to extend my sincere appreciation to my research advisor, Dr. Eric Enholm, for his support, patience, understanding, and invaluable help. He provided me all the necessary guidance to complete my dissertation, and allowed me the research freedom to develop my own ideas. Most importantly, he is a caring person who was always concerned for my family, especially during the monstrous hurricane season of 2004 in Florida. He has been a great advisor and I will never forget his encouragement and kindness. I would like to thank my committee members for their constructive feedback and advice.
    [Show full text]
  • Sijbren Otto Is Awarded a TA-NEWPOL Grant Highlights By
    116 March 2016 Sijbren Otto is awarded a TA-NEWPOL grant Sijbren Otto is awarded a 250.000 TA-NEWPOL grant. These grants aim at developing new polymer materials which meet the social and industrial need for sustainability and multifunctionali- ty. Self -synthesizing gels This research aims to develop new gels that form from simple building blocks. The build-up process can be controlled so that the gels have the desired structure and properties. The investiga- tors wish to apply the resulting materials as media for the growth of cells in three dimensions. Highlights by Prof. dr. Jan B.F.N.Engberts Three organic chemists from the Technical University of Munich wrote an interesting re- view about self-assembled supramolecular structures that can be used as catalysts for re- actions that occur via cationic transition states. Such catalysts are highly necessary since otherwise the cationic transition states may be attacked by counterions and/or solvent molecules. The supramolecular structures contain aromatic, hydrophobic reaction pockets and make it possible to perform cationic reactions outside the scope of standard solution chemistry. A number of such processes have been discussed in some detail. However, se- veral problems have still to be solved and a variety of new host structures have to be desig- ned and prepared. Such structures should be easily obtainable, tailored towards a particu- lar transformation and highly modifiable. Catti, L., Zhang, Q., Tiefenbacher, K., Synthesis 2016, 48, 313. SN2 nucleophilic substitution processes are significantly dependent on nucleophile, sol- vent and the leaving group. Physical-organic chemists from Institutes in Austria and Hun- gary argue that the role of the leaving group on the reaction dynamics has remained rather unclear.
    [Show full text]
  • Famelabnl Audience Award Goes to Groningen!
    136 May 2018 FameLabNL audience award goes to Groningen! Photo courtesy of Joost Weddepohl Last week the national final of FameLab was held in Utrecht. FameLab is the big- gest science communication competition in the world. The idea behind FameLab is that young scientists (students, PhD’s, postdocs and starting professors) have to present a scientific topic to an audience of laymen in under 3 minutes without using powerpoint. This year the audience award was awarded to Marcel Eleveld, who gave a presen- tation about the Eigen paradox of the origin of life (“Machinery for accurate (molecular) self-replication needs a lot of information to be encoded - but how do you obtain such machinery before the associated information can be accurately co- pied?”). Marcel is a Nanoscience master student who is working in the group of Sijbren Otto. The jury award was awarded to Jair Santanna (assistant professor at the TU Twen- te) who spoke about DDoS attacks and how they can be prevented. Stratingh Institute for Chemistry Newsletter nr 136 - May 2018 1 Sijbren Otto wins prestigious Royal Society of Chemistry Award Professor of Systems Chemistry Sijbren Otto is the 2018 re- cipient of the Royal Society of Chemistry (UK) Supramole- cular Chemistry Award. This biennial award is in recogni- tion of Otto’s contribution to the science of molecular net- works and systems chemistry. The main theme of his cur- rent work is chemical evolution. As recipient of the award, Otto will give a number of lectures in Britain. ‘I feel very honoured to receive this award’, says Otto.
    [Show full text]
  • University of Groningen a Systematic Study of Ligand Effects on a Lewis
    University of Groningen A systematic study of ligand effects on a Lewis-acid-catalyzed Diels-Alder reaction in water. Water-enhanced enantioselectivity Otto, S.; Engberts, J.B.F.N. Published in: Journal of the American Chemical Society DOI: 10.1021/ja984273u IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 1999 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Otto, S., & Engberts, J. B. F. N. (1999). A systematic study of ligand effects on a Lewis-acid-catalyzed Diels-Alder reaction in water. Water-enhanced enantioselectivity. Journal of the American Chemical Society, 121(29), 6798 - 6806. https://doi.org/10.1021/ja984273u Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 20-01-2020 6798 J. Am. Chem. Soc. 1999, 121, 6798-6806 A Systematic Study of Ligand Effects on a Lewis-Acid-Catalyzed Diels-Alder Reaction in Water.
    [Show full text]
  • University of Groningen Diels–Alder Reactions in Water Otto, Sijbren
    University of Groningen Diels–Alder reactions in water Otto, Sijbren; Engberts, Jan B.F.N. Published in: Pure and Applied Chemistry DOI: 10.1351/pac200072071365 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2000 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Otto, S., & Engberts, J. B. F. N. (2000). Diels–Alder reactions in water. Pure and Applied Chemistry, 72(7), 1365-1372. https://doi.org/10.1351/pac200072071365 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.
    [Show full text]
  • Charalampos Pappas, Ph.D. Curriculum Vitae and Publication List
    Charalampos Pappas, Ph.D. Curriculum vitae and publication list Charalampos Pappas, Ph.D. University of Freiburg Cluster of Excellence Living, Adaptive and Energy-Autonomous Materials Systems (livMatS) Georges-Kohler-Allee 105 D-79110 Freiburg Phone: +49 01627608434 E-mail: [email protected] Current position University of Freiburg since 10/2020 Junior Research Group Leader Education University of Strathclyde, Glasgow 01/2013-01/2016 Ph.D., Department of Pure and Applied Chemistry Ph.D. Thesis: Supramolecular Systems Chemistry Using Peptides University of Ioannina 09/2010-11/2012 M.Sc., Department of Chemistry and Biochemistry University of Ioannina 09/2005-03/2010 B.Sc., Department of Chemistry and Biochemistry Degree of excellence Research experience University of Groningen 10/2016-10/2020 Stratingh Institute for Chemistry Postdoctoral Marie Skłodowska Curie Fellow with Prof. Sijbren Otto Developed a new research direction on the autonomous emergence of folded macromolecules having the size and complexity of a protein, yet produced from a single monomer. Engineered the spontaneous formation of self-replicating and folded structures using dynamic combinatorial chemistry. City University of New York (CUNY) 01/2016-08/2016 Advanced Science Research Centre (ASRC) Postdoctoral Researcher with Prof. Rein Ulijn Design and fabrication of active soft nanostructures through (bio)catalytic self-assembly. Developed dynamic peptide libraries for the discovery of highly ordered supramolecular nanomaterials based on minimalistic motifs. University of Strathclyde, Glasgow 01/2013-09/2014 Department of Pure and Applied Chemistry Graduate Researcher, with Prof. Rein Ulijn 1 Charalampos Pappas, Ph.D. Curriculum vitae and publication list City University of New York (CUNY) Advanced Science Research Centre (ASRC) 09/2014-01/2016 Graduate Researcher, with Prof.
    [Show full text]
  • Controlling the Phase of Light by Nanostructuring of Materials by David Barth a Dissertation Submitted in Partial Satisfaction O
    Controlling the Phase of Light by Nanostructuring of Materials by David Barth A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Engineering { Mechanical Engineering in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Xiang Zhang, Chair Professor Lydia Sohn Professor Laura Waller Summer 2017 Controlling the Phase of Light by Nanostructuring of Materials Copyright 2017 by David Barth 1 Abstract Controlling the Phase of Light by Nanostructuring of Materials by David Barth Doctor of Philosophy in Engineering { Mechanical Engineering University of California, Berkeley Professor Xiang Zhang, Chair The previous century was defined to a major extent by the digital revolution, which ushered in the information age. This rapid proliferation and improvement of electronic technology continues to have far-reaching effects on human existence. Similarly, advances in photonics have the potential to lead to technology that drastically changes our lives. So far, the vast potential of photonics, and especially nanophotonics, has not resulted in such sweeping societal change. While the laser, LED, and photovoltaic cell serve important, and increasing, functions, technological advances in photon control at the nanoscale are required for the full potential of photonics for computing, medicine, and energy to be realized. In this dissertation, we examine some methods and devices that can address these needs in photonics, particularly by exploiting the refractive index of materials, the phase of light, and the relation between the two. The first chapter focuses on controlling the refractive index of silicon by inducing spatially varying porosity. This technique enables the fabrication of gradient index devices that can control light's propagation through the device to a degree that is not possible with traditional optical elements.
    [Show full text]
  • Emergence and Evolution of Complex Chemical Systems Is a Network Comprising More Than 90 European Research Groups
    • COST Action CM1304 - Emergence and Evolution of Complex Chemical Systems is a network comprising more than 90 European research groups. It has sparked invaluable collaborations that have helped advance the emerging field of systems chemistry Systems Chemistry The next big frontier Professor Sijbren Otto introduces us to systems chemistry, explaining why this field is so important and highlighting the role of his work on the emergence and evolution of chemical systems in addressing some of society’s major scientific challenges Could you briefly simply too difficult to study mixtures of It is still early days in the field and predicting introduce the molecules. However, with the recent rapid concrete applications is notoriously field of systems development in analytical equipment this difficult. Yet I am convinced that, given the chemistry? situation has now changed. Also, mixtures of fundamentally new approach to chemistry, molecules have become tractable, opening such applications will emerge. The most The field of systems up the new discipline of systems chemistry. likely will be in the interface with life. As chemistry deals a significant part of systems chemistry is with complex chemical systems that show Can you discuss the advantages and about making chemical systems that operate properties that go beyond the sum of its disadvantages of employing a bottom-up based on the organisational principles of components. Such emergent properties are approach within systems chemistry research? living systems, their interfacing with living commonly found in systems that have many systems is likely to be more efficient than the components that interact with each other. For The bottom-up strategy is second nature to rather blunt approach taken in, for example, example, the dynamics and characteristics of chemists, who are used to building bigger pharmaceutics, that relies on drugs with a a society come about from the interactions systems from smaller components.
    [Show full text]
  • The Essence of Systems Chemistry
    life Essay The Essence of Systems Chemistry Peter Strazewski Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France; [email protected]; Tel.: +33-472-448-234 Received: 18 April 2019; Accepted: 25 June 2019; Published: 11 July 2019 Abstract: Systems Chemistry investigates the upkeep of specific interactions of an exceptionally broad choice of objects over longer periods of time than the average time of existence of the objects themselves. This maintenance of a dynamic state focuses on conditions where the objects are thermodynamically not very stable and should be rare or virtually inexistent. It does not matter whether they are homochirally enriched populations of chiral molecules, a specific composition of some sort of aggregate, supramolecules, or even a set of chemically relatively unstable molecules that constantly transform one into another. What does matter is that these specific interactions prevail in complex mixtures and eventually grow in numbers and frequency through the enhancing action of autocatalysis, which makes such systems ultimately resemble living cells and interacting living populations. Such chemical systems need to be correctly understood, but also intuitively described. They may be so complex that metaphors become practically more important, as a means of communication, than the precise and correct technical description of chemical models and complex molecular or supramolecular relations. This puts systems chemists on a tightrope walk of science communication, between the complex reality and an imaginative model world. This essay addresses, both, scientists who would like to read “A Brief History of Systems Chemistry”, that is, about its “essence”, and systems chemists who work with and communicate complex life-like chemical systems.
    [Show full text]
  • Nanoseminar Series 2021
    nanoSeminar Series 2021 Institute for Materials Science Dr. Charalampos Pappas Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg “Systems Chemistry: Steps towards Life-like Systems” Thursday, April 29th 2021 9:00 – 10:00 Normal: Seminar Room 115, Hallwachsstr. 3 (HAL) Pandemic version: https://tinyurl.com/nanoSeminar-GA Living systems possess overwhelming molecular complexity that largely results from combinations of just twenty amino acids that are found across all life forms. It is increasingly clear that structure and functionality may be observed in much simpler combinations of amino acids in short peptides. Thus, beyond their role as the molecular building blocks of life, amino acids may be ideally suited as building blocks for adaptive nanotechnology. Inspired by living systems, where molecular assemblies perform tasks that exceed the functionality of their basic constituents, systems chemistry focusses on connectedness, interactivity and patterns. The use of mixtures of interacting molecules that continuously exchange chemical information, leads to emergent properties, properties that only originate when parts assemble together. This network concept contrasts with the more traditional reductionist approach and has empowered soft matter systems with the abilities to replicate to compartmentalize and to adapt in response to chemical and physical signals from the environment. Herein, we demonstrate the use of a systems chemistry pathway towards the discovery of adaptive and active materials based on the building blocks of life. nanoSeminar Series 2021 Institute for MaterialsInstitute Science for Materials and Nanotechnology Science Dr. Charalampos Pappas Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg Charalampos (Babis) Pappas received his M.Sc.
    [Show full text]
  • CNN – 37 Systems Chemistry (Syst.Chem., SC)-I
    Available online at www.joac.info ISSN: 2278-1862 Journal of Applicable Chemistry 2021, 10 (1): 70-107 (International Peer Reviewed Journal) CNN – 37 Systems Chemistry (Syst.Chem., SC)-I Information Source ACS.org ; sciencedirect.com K. Somasekhara Rao, R. Sambasiva Rao, Dept. of Chemistry, School of Chemistry, Acharya Nagarjuna Univ., Andhra University, Dr. M.R.Appa Rao Campus, Visakhapatnam 530 003, India Nuzvid-521 201, India KLab rsr.chem1979 I. Object oriented terminology (OOT) for Syst.Chem II. Select Research Titles(2000 to2020) in Syst.Chem AAACNN Systems Chemistry 70 I . Most-fascinating questions over the last hundred years Life ? What is really (what we call) life ? Did life originate only onceby accident ? ! Is it possible to define life scientifically in terms of strictly chemical and biological criteria ! The principle “I know it when I see it’’ ! Is not at all satisfactory with respect to life/Consciousness ? ? Where, When, How and from what did life emerge on our mother Earth ? Did life arrive here from some extra-terrestrial source instead ? Is it the probable outcome of chemical evolution, which has frequently occurred elsewhere in the universe ? Which property of living beings came first ? Their ability to reproduce and transmit information to progeny ? Their metabolic capacity ? Their compartmentalization as individual entities Conditions ? What are theset of sufficient conditions that could generate an ‘‘organism’’that we would agree to call it as ‘‘living” ? Chemists are less or at least no better equipped to answer
    [Show full text]