Takudrei

Molecular Diversity - When Molecules Network

Course No. 21 234

Introduction: Systems Chemistry & Molecular Diversity

In 2005, the term "Systems Chemistry" appeared in a conference on Prebiotic Chemistry and Early Evolution. This new field of chemical research has its roots in a number of different areas such as dynamic combinatorial chemistry, self-assembly and self-organization, research on prebiotic chemistry, minimal self-replicating molecules and others. The idea of the seminar is to provide a sketch of the different ideas that underlay the new discipline.

The leading paradigm in chemistry so far, in particular in synthetic chemistry, has been the preparation of pure compounds. A pharmacologically active compound almost always needs to be pure in order to get approval for its use as a drug. Also, it is synthetically useful to work with pure compounds as reactants as otherwise unseparably complex product mixtures form. Finally, the analytical characterization of complex mixtures is still no trivial task - despite of all progress made in separation techniques and instrumental analytics. This paradigm of the pure compound has hindered the development of complex chemical systems and the investigation of networks of chemical reactions. However, such complex mixtures can be highly interesting not only from a fundamental point of view, when the molecules involved form reactivity networks. Thus, a simple mixtures of unreacting molecules is probably not very interesting, but as soon as chemical reaction networks incorporating feedback loops and elements of non-linearity form, new, often unexpected and unpredicted so-called emergent properties arise as properties of the whole chemical system. None of the components alone has these properties, but the whole system does.

Systems chemistry is therefore an extremely interesting and very new way to do - and to think - chemistry. Beyond the fundamental insight that we can get, new materials can be developed as well as chemical systems able to adapt, react upon the action of external stimuli, and sometimes evolve. The lecture course aims at demonstrating the intriguing emergent properties with a number of quite recent examples from the forefront of chemical research.

 

The Team

The course is organized by a team of six people: Beate Koksch and Christoph Schalley, Hendrik Schröder and Dorian Mikolajczak (Ph.D. students), Elena Petersen and Anthony Krause (students).

 

The Format

As learining profits from it, the course aims at maximum activity of the participants and thus does not use the traditional lecture course format.Each three-hour block is prepared and presented by a group of participants. The members of the groups take different roles. In the beginning, one member provides the course with an introduction into the topic in order to prepare the background (30 min). This is followed by the presentation of a "quickie" (20 min), which can be a brief thought experiment, a demonstration experiment, a simulation etc. Many "quickies" connect to disciplines outside chemistry to provide a glimpse of emergence in other fields. After the quicky, one particular highlight paper is discussed. One member of the group takes the role of the scientist presenting his results on a conference (30 min). The task is to convince the audience of the research described in the paper. This is meant to be a detailed discussion bringing together not only the results, but also a description of the experiments that lead to the results. Another member of the group takes the role of the opponent or reviewer. His/her task is to find the weak points in the paper and to bring up doubts - just like an expert reviewer who is asked by the journal editor to evaluate a submitted manuscript. The whole group joins in this discussion of the highlight paper (30 min). At the end, the group summarizes the most important messages learnt (20 min).

In addition, two talks of experts from other disciplins (sociology and biology) aim at looking beyond the horizon of chemistry to make clear the self-organization of systems follow similar rules as we find them for chemical systems. The participation at these scientific talks is mandatory for all participants.

Finally, each group has the task to prepare a short video explaining in a well-understandable and creative way their topic to a broader audience. The videos will be uploaded to a Youtube channel to make them available to a broader public. The aim of this element is to strengthen the participants ability to explain science to people outside the field. Some limited video equipment is available, but in most cases, simple equipment will probably be sufficient.

The course language will be English and thus the presentations should also be in English.

The whole team offers help for the preparation of your presentations. Below, you will find the names of the persons responsible for each course date. Our two student tutors, Elena and Anthony, will help with the preparation of quickies and videos.

 

Schedule & Dates

The course takes place: Wednesdays, 2:00 - 5:00 pm, seminar room 31.09, Takustr. 3. Please note that the two talks by external experts will be given in different rooms and at different dates. Participation in these two talks is mandatory.

Wed Oct 18, 2017:
Session 1 - Introduction & Organizational Matters

Fri, Nov 03, 2017, 2:00 pm, seminar room 12.12, Takustr. 3
Prof. Dr. em. Margot Berghaus (Sociology, Hamburg):
"Niklas Luhmann beobachtet"

Wed Nov 08, 2017: Group 1
Session 2 - Self-Assembly under Thermodynamic Control

Wed Nov 15, 2017: Group 2
Session 3 - Mesoscale Self-Assembly and Mesoscale Self-Organization

Wed Nov 22, 2017: Group 3
Session 4 - Self-Sorting

Wed Nov 29, 2017: Group 4
Session 5 - Self-Replicating Molecules

Wed Dec 06, 2017: Group 5
Session 6 - Dynamic Combinatorial Chemistry

Wed Dec 13, 2017: Group 6
Session 7 - Nanoscale Motion

Wed Jan 10, 2018: Group 7
Session 8 - Oscillating Reactions

Wed Jan 17, 2018: Group 8
Session 9 - Transport & Quorum Sensing in Oscillating Reactions

Fri, Jan 19, 2018, 1:00 pm, seminar room 26.07, Takustr. 3
Prof. Dr. Britta Tietjen (Biology, FU Berlin):
"The More the Merrier? The Role of Biodiversity in Stabilising Ecosytems"

Wed Jan 24, 2018: Group 9
Session 10 - Homochirality & Life

Wed Jan 31, 2018: Group 10
Session 11 - Synthesizing Life

Wed Feb 07, 2018:
Session 12 - Summary & Conclusions

Wed Jan 31, 2018:
Session 13 - Videos

 

Grading

The quality of the presentations and the videos will be the basis for grading.

 

Seminar Topics

Please find the topics for each of the course dates. Some keywords are provided for your orientation and some introductory literature is linked so that you have an entry into the topic. Please make sure that you do a literature search nevertheless as more recent work might have appeared meanwhile. For the literature searches, I recommend to use the Scientific Citation Index as it also allows to search for newer papers that cite a particular one. You can thus do backward as well as forward searches. Access is free from FU computers or your own computer, if you use your VPN connection.

 

Session 1 - Molecular Diversity in Nature - An Intro to Chemical Systems

Beate Koksch, Christoph Schalley

 

Session 2 - Self-Assembly under Thermodynamic Control

Group 1 - Supervisor: Christoph Schalley

  • Background (30 min): Metallo-supramolecular Self-Assembly

    The principles of self-assembly illustrated by metallosupramolecular complexes such as helicates, grids, polygons, and polyeders/cages are the topic of this talk. Please discuss the general points such as error correction and reversibility as well as the three approaches to metallosupramolecular complexes including their advantages and disadvantages: Directional-Bonding Approach, Symmetry-Interaction Approach, Weak-Link Approach

    Literature:

    Review: B.J. Holliday, C.A. Mirkin, Angew. Chem. Int. Ed. 2001, 40, 2022

  • Quickie (20 min): Buttons and Wires - or when Quantity becomes Quality

 

Session 3 - Mesoscale Self-Assembly and Mesoscale Self-Organization

Group 2 - Supervisor: Christoph Schalley

  • Highlight (30 min): Dynamic Self-Organization of Magnetic Particles

    While self-assembly (also meso-scale self-assembly) occurs in equilibrium, this highlight reports an example, in which magnetic particles organize into patterns only when rotating. This is a driven self-organization process which requires a constant flow of energy. The difference between self-assembly (static) and self-organization (dynamic) should be discussed.

    Literature:

    Highlight: B.A. Grzybowski, H.A. Stone, G.M. Whitesides, Nature 2000, 405, 1033

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 4 - Self-Sorting

Group 3 - Supervisor: Hendrik Schröder

  • Highlight (30 min): Integrative Self-Sorting: Kinetic Path Selection in Self-Assembly

    Beyond simple self-recognition, integrative self-sorting is a strategy to program the precise positions of many different building blocks in larger assemblies. The highlight aims at showing that such processes proceed through well-defined pathways rather than through complex mixtures of intermediates, because of the different barriers that occur during the assembly process. Kinetic path selection is thus the result.

    Literature:

    Highlight: W. Jiang et al., J. Am. Chem. Soc. 2010, 132, 2309
    also, see: W. Jiang, C.A. Schalley, Proc. Natl. Acad. Sci. USA 2009, 106, 10425

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 5 - Self-Replicating Molecules

Group 4 - Supervisor: Dorian Mikolajczak

  • Highlight (30 min): Logic Gate Sensors Based on Self-Replication

    Catalytic networks of self-replicating peptides can be used to construct chemical systems to perform Boolean logic operations. This talk describes how logic gates are constructed from such networks.

    Literature:

    Highlight: G. Ashkenasy et al., Isr. J. Chem. 2011, 51, 106

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 6 - Dynamic Combinatorial Chemistry

Group 5 - Supervisor: Christoph Schalley

  • Highlight (30 min): Mechanosensitive Dynamic Libraries

    The highlight is about a very simple dynamic library, in which macrocycles form. The ring sizes depend on the mode of agitation and shaking leads reproducibly to another ring size than stirring. This mechanosensitivity should be explained in terms of the lessons learnt about systems chemistry so far.

    Literature:

    Highlight: J.M.A. Carnall, et al., Science 2010, 327, 1502

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 7 - Nanoscale Motion

Group 6 - Supervisor: Hendrik Schröder

  • Highlight (30 min): Supramolecular polymers: Transport along Gradients

    Salt gradients can be used to provide a direction to the growth of supramolecular polymers. When energy is dissipated, such directional growth is capable of realizing the transport of small particles.

    Literature:

    Highlight: L. Cera et al., Adv. Mater. 2017, 29, 1604430

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 8 - Oscillating Reactions

Group 7 - Supervisor: Dorian Mikolajczak

  • Highlight (30 min): Viscosity Oscillations in Polymers

    Incorporating the BZ reaction into polymers can cause rhythmic viscosity changes. This talk should prepare the audience by giving some background on polymers and viscosity measurements and then discuss in detail how the BZ reaction causes viscosity oscillations as a macroscopic "ensemble" effect of the system.

    Literature:

    Highlight: T. Ueno, K. Bundo, Y. Akagi, T. Sakai, R. Yoshida, Soft Matter 2010, 6, 6072

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 9 - Transport & Quorum Sensing in Oscillating Reactions

Group 8 - Supervisor: Christoph Schalley

  • Background (30 min): Oscillating Reactions to Drive Transport

    The oscillations in the BZ reaction are driven by a flow of energy: Chemical energy is dissipated into heat in this process. This gradient can be used to drive unidirectional processes such as the transport of particles on the surface of gels. Before you describe the transport phenomena, make sure that everyone has understood, what a gel is and what "swelling" is. Then explain the transport phenomenon on a molecular level.

    Literature:

    Review: R. Yoshida, Adv. Mater. 2010, 22, 3463

  • Quickie (20 min): Quorum Sensing in Biology

  • Highlight (30 min): Quorum Sensing in Chemical Systems

    Oscillating reactions can be performed on particles, when the redox catalyst is fixed to these. Each particle has its own "blinking" frequence. However, when a critical group size in an ensemble of particles is reached, the blinking occurs in a cooperative fashion.

    Literature:

    Highlight: A.F. Taylor et al., Science, 2009, 323, 614
    also, see: M.R. Tinsley et al., Phys. Rev. Lett. 2009, 102, 158301

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 10 - Homochirality and Life

Group 9 - Supervisor: Beate Koksch

  • Highlight (30 min): Chiral Self-Replication and Asymmetric Autocatalysis

    Minimal model self-replicators can amplify chirality when a chiral template is formed from achiral precursors. The talk describes in detail examples for this finding.

    Literature:

    Highlight: V.C. Allen, D. Philp, N. Spencer, Org. Lett. 2001, 3, 727

  • Discussion with Opponent and Audience (30 min)

  • Lessons Learnt (20 min)

 

Session 11 - Synthesizing Life

Group 10 - Supervisor: Beate Koksch

  • Background (30 min): Homeostasis and Autopoiesis

    If one accepts vesicles as minimal models for cells, coupling simple reactions to the formation and degradation of the membrane-forming components with the growth and division of the vesicles. It would be good to first carefully introduce the terms homeostasis and autopoiesis - e.g. by recurring to the concepts of Francisco Varela and Humberto Maturana. In view of the following talk, please restrict this one to laying the foundation and providing few and simple examples.

    Literature:

    Review: P. Stano, P.L. Luisi, Chem. Commun. 2010, 46, 3639
    Review: J.W. Szostak, D.P. Bartel, P.L. Luisi, Nature, 2001, 409, 387
    Review: P. Walde, BioEssays, 2010, 32, 296

  • Quickie (20 min): The Pink Panther - How We Listen to Music

 

Session 12 - Summary & Conclusions

Beate Koksch, Christoph Schalley

  

Session 13 - Video Presentation and Final Discussion

Beate Koksch, Christoph Schalley