Literature Seminar "Systems Chemistry"
Intro: Systems Chemistry
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 underly the new discipline.
The teaching in chemistry, in particular in synthetic chemistry, relies on 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. This thinking has hindered much the development of complex chemical systems and the investigation of networks of chemical reactions. Therefore chemistry lags behind as far as the ideas are concerned that describe complex systems. Many other disciplines such as systems biology, climate research, sociology, kybernetics, ecosystem research already anticipated what chemists are about to learn.
Systems chemistry is therefore an extremely interesting and very new way to do chemistry. The seminar aims at showing this with a number of examples.
Organizational Matters
The seminar aims at the master level. For one talk given by you and your regular presence in at least 12 seminar sessions, you earn 3 credit points.
The talks will be graded according to the criteria described below. There will be no written or oral exam. The grade of your talk is the grade for this seminar.
If you wish to participate, please register with name, matriculation number, and a suggestion of the topic from the list below by email to
christoph
schalley-lab.de
Preparation meeting: Oct 18th, 2011, 12:30 pm,
Schalley group coffee room (Taku 3, 32.04)
I strongly encourage talks in English as a preparation for your future work, but would also accept talks in German. Each seminar talk should be ca. 30 minutes long and allow for a detailed discussion.
I offer help for the preparation of your seminars. In order to be able to help, it would be useful, if you would come and see me early on, at least two weeks before the seminar to discuss a concept for the talk. Approximately one week before the scheduled seminar, it would be advisable to briefly discuss your transparencies.
Tips for the Preparation of the Talks
Please make sure that you take into account the following points to make your seminar interesting and beneficial for all others. At the same time, they define a set of criteria for the grading.
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Be absolutely clear: Don't expect your audience to know too much about the topic. In view of the time, reduce the seminar to the really important arguments and concepts. Rather restrict yourselves to a good selection of important points and discuss them in greater detail than trying to make a superficial summery of everything. Choose really illustrative examples. Organize your talks clearly: What argument builds on which other one? How do I introduce each one of them at the appropriate moment? Direct the audience through your talk with (only a couple) of structuring remarks.
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Clarity should also be found in your transparencies: Large enough letter size (usually not below 14 pt), not too much text, easy to grasp graphics, if schematic cartoons help to reduce complexity, you can show a molecule, discuss its properties briefly and then explain the concept using cartoons. Nevertheless, don't forget that we are chemists and need to see how the molecules you discuss look like. A cartoon-only talk would not be sufficient!
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If you want to use a sheet of paper with short remarks to remind you of what you wanted to say, prepare it in a clear way so that you easily find your way through it. My suggestion would be to prepare the transparencies in a way that they also guide you through the talk.
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Use the appropriate scientific language. It is part of your science and you need to be able to use it actively and passively. Name the molecules and things on your transparency by their appropriate names. Reduce for example, IUPAC names to the functional group important in that particular moment. But don't say: "This thing here...", if the molecule can be easily given a more suitable name.
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Restrict yourselves to a small number of well-chosen examples. They should perfectly illustrate your points. Don't try to make the collection complete (even if that would match the Germans' need for "Gründlichkeit"). Your audience will be able to transfer the things learnt with the help of a well-chosen and well-explained example to others they encounter. A too large number of examples reduces the time for going into detail and makes the discussion superficial. You have then seen many examples without really understanding a single one ...
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Instead of printed handouts, I will collect your talks as pdf files and make them available on this internet page. Access will be password-protected and the password is made available only to the course participants. Make sure you have downloaded all material before the official end of the semester (Mar 1st or Sep 1st). After these dates, I will erase the pdfs to save space for other course materials for the following term.
Seminar Topics
I have added a few keywords for each topic (blue headlines) which hopefully make it easier for you to focus your talk. Also, you will find some access to literature concerning the topic. Nevertheless, these literature references are not comprehensive. So, please do your own literature search! The red headlines refer to short discussions, I will lead you through.
1. Introduction: Chemical Networks and Systems Chemistry
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Thought experiment: Buttons and Wires - or when Quantity becomes Quality
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Exploring Complex Networks: Non-Linear Dynamics
Non-linear dynamics and complex networks are almost ubiquitous in nature from chemistry (see below) to biology (the brain, food webs, ecosystems), and even to sociology (internet, human society). This talk should provide some introduction into the terminology used to describe complex networks on an abstract level and some insight into how complex networks work, what complications might emerge and how one could possibly control them. It might end with some ideas, how chemistry might be affected by complexity and how dealing with complex chemical systems might change our thinking on chemistry.
Literature:
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Chemical Networks: Evolution of Complex Mixtures
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What Systems Chemistry is About
This talk should provide an overview, what the central topics of systems chemistry are so that it is clear after the talk, how the topics of the seminar are interconnected.
Literature:
2. Self-Assembly: Creating Complex Mixtures under Thermodynamic Control
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Conways Game of Life
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Metallosupramolecular Chemistry: Helicates, Grids, Polygons and Polyeders
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 Aapproach
Literature:
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Reactivity Modulation in Container Molecules
Encapsulation of molecules in metallosupramolecular containers can alter their reactivity significantly. Discuss a couple of examples in greater detail with respect to the origin of the alterations through guest inclusion.
Literature:
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Cascading Transformations in Dynamic Self-Assembled Systems
Through changes in the system - e.g. by adding new compounds - the system as a whole changes, often in a predictable way, if the behavior of the components is well studied. This talk focuses on a few illustrative examples for the adaptability of the systems under study.
Literature:
3. Dynamic Combinatorial Chemistry: Amplification through Templation
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Langtons Ant
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This talk reports about the background for this chapter in the seminar: What is the classical combinatorial chemistry approach to drug development. How is it different from classical strategies? What does the term combinatorial library describe? How can these libraries be made with the mix-and-split algorithm?
Literature:
- G. Jung, Combinatorial Chemistry, Wiley-VCH, Weinheim 1999
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Dynamic Combinatorial Libraries: Reversible Covalent Chemistry
Based on the preceding talk on combinatorial chemistry, this talk reports the approach to use reversible covalent bonds to make dynamic combinatorial libraries whose composition can change, when an appropriate template is added. How can good receptors be made with this approach?
Literature:
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Boundary Conditions for Template-Mediated Amplification in Dynamic Combinatorial Libraries
DCLs can change their constitution, when templates are added that induce the formation of a certain library member, which binds better to the template than others. Is this a general phenomenon? What are the limitations of the dynamic combinatorial approach? Is the best binder always amplified the most or does this depend on the conditions?
Literature:
4. Self-Sorting Phenomena in Complex Supramolecular Systems
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The Brazil Nut Effect - Why is the Thickest Stuff Always on Top?
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Self-Sorting: Terms and Definitions
Complex Supramolecular Mixtures may undergo self-sorting processes, if some components exhibit preferences for binding particular others with selectivity. The terms narcissistic and social self-sorting should be defined. There are two different types of social self-sorting that should be distinguished. Also, the difference between thermodynamic and kinetic self-sorting and the concept of integrative self-sorting which leads to the construction of larger supramolecular architecture are topics of this talk. What are the factors that govern self-sorting processes?
Literature:
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Chiral self-sorting processes may have had an impact on the development of a homochiral world (see below). Therefore, chiral self-sorting is a highly interesting phenomenon in the context of the present seminar. Provide examples for chiral self-sorting in this talk and discuss, what the origin of the self-sorting is in them.
Literature:
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Changing Network Topologies in DCLs through Self-Sorting
Self-Sorting may be used to change the topology of dynamic combinatorial libraries in that the self-sorting prevents some interactions between members of the library. Please discuss the paper given here in detail!
Literature:
5. Self-Replicating Molecules
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Feedback Loops: The "pork cycle" and the Lotka-Volterra Rules
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Small molecules with suitable structure and binding properties can act as templates for their own generation. Therefore, autocatalysis is realized so that self-replication is possible even for very simple molecules. The talk shows examples for self-replicating molecules and discusses the kinetics of self-replication.
Literature:
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Integrating Replicators in Dynamic Covalent Systems
Complex reactivity networks evolve, when self-replicating molecules are integrated into dynamically covalent systems. At the same time, this means to merge thermodynamically controlled systems (the DCLs) with kinetically controlled systems (the replicators). Interesting properties emerge. Maybe it is best, if you chose very few illustrative examples and discuss them in detail, so that every participant understands the idea behind it.
Literature:
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Of Figs and Wasps
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Error Correction and Symbiosis in Autocatalytic Peptide Networks
Not only oligonucleotides and small model molecules can replicate. Self-replicating peptides are also known. This talk introduces the principles according to which peptides self-replicate and describes phenomena such as error correction and symbiosis that can occur in networks of autocatalytic peptides.
Literature:
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Building Logic into Peptide Networks
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:
6. Self-Organization in Chemistry: Oszillating Reactions
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Granular Media and Non-Newtonian Liquids: Sand-Sorting and the Funny Shampoo
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The Belousov-Zhabotinski Reaction
Autocatalysis and feedback loops are an important topic in the Belusov-Zhabotinski reaction. As long as chemical energy generated through the individual steps of this reaction flows through the system, patterns are created. When all reactants are consumed and the energy flow stops, the patterns are destroyed through diffusion. This reaction is a great chemical example for pattern generation in open systems. If you like, we can include a demonstration of this reaction on an overhead projector. I need to know that early enough, though.
Literature:
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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:
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Directional Transport through Oscillating Reactions in Gels
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:
7. The Origin of Homochirality and its Importance for the Development of Life
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An Indeterministic World? Symmetry Breaking in NaClO3 and KClO3 Crystallization Experiments
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Biotic and Abiotic Theories, statistical fluctuations with autocatalystic amplification, chirality through non-symmetric processes on elementary particle level? There are quite many potential explanations for the development of homochirality. The talk should first provide a breakdown of the three different steps involved (1. symmetry breaking, 2. chiral amplification of one particular type of molecule and 3. chirality transfer to other types of molecules) and then discuss the different theories for symmetry breaking.
- W.A. Bonner, Top. Stereochem. 1988, 18, 1 (see me for a printed copy)
- R.A. Hegstrom, D.K. Kondepudi, Spektrum der Wissenschaft 1990, 56
- M. Avalos, R. Babiano, P. Cintas, J.L. Jimenez, J.C. Palacios, Chem. Commun. 2000, 887
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Deracemization of a Dynamic Combinatorial Library
The talk describes the deracemization of a dynamic library by chiral analytes/templates.
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The Serine Octamer: Strong Homochiral Preference
Although so far only detected by mass spectrometry, the serine octamer appears to be a quite stable "magic-number" species with a large preference for homochirality. The talk should discuss its potential importance for the amplification and chirality transfer steps. Also, the evidence for a zwitterionic structure should be discussed in order to demonstrate how gas-phase experiments can lead to structure assignment.
- S.C. Nanita, R.G. Cooks, Angew. Chem. Int. Ed., 2006, 45, 554
- Z. Takats, S.C. Nanita, R.G. Cooks, Angew. Chem. Int. Ed., 2003, 42, 3521
- C.A. Schalley, P. Weis, Int. J. Mass Spectrom. 2002, 221, 9
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Symmetry Breaking as a General Phenomenon: From Astrophysics to Weather Phenomena
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Spontaneous Symmetry Breaking in Asymmetric Mannich and Aldol Reactions
The serine octamer already demonstrated that non-covalent interactions may play a significant role for chiral amplicfication. In solution, Mannich and aldol reactions are known in which spontaneous symmetry breaking is induced by hydrogen bonding. The talk provides details on the mechanism how this works.
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Asymmetric Autocatalysis: The Soai Reaction
The Soai reaction has attracted a lot of attention because it is an autocatalysis able of amplifying chirality. The talk should discuss it in detail with respect to the mechanism and the consequences for the development of homchirality.
- D.G. Blackmond, Proc. Natl. Acad. Sci. USA, 2004, 101, 5732
- K. Soai, T. Shibata, I. Sato, Acc. Chem. Res. 2000, 33, 382
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Chiral Self-Replicating Systems
Minimal model self-replicators can also amplify chirality when a chiral template is formed from achiral precursors. The talk describes in detail examples for this finding.
- V.C. Allen, D. Philp, N. Spencer, Org. Lett., 2001, 3, 727
- A. Diekmann, S. Beniken, C.D. Lorenz, N.L. Doltsinis, G. von Kiedrowski, Chem. Eur. J., 2011, 17, 468
8. From Chemical Models of Homeostasis and Autopoiesis to Protocells
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In brief: Niklas Luhmann's System Theory
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Chemical Models of 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.
- H.R. Maturana, F.J. Varela, Der Baum der Erkenntnis, Goldmann, München 1990 (English original: The Tree of Knowlege, Shambala, Boston 1987.
- H.H. Zepik, E. Blöchliger, P.L. Luisi, Angew. Chem. Int. Ed. 2001, 40, 199
- P. Stano, P.L. Luisi, Chem. Commun. 2010, 46, 3639
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Discuss the attempts to synthesize simple protocells that can evolve. How far have chemists already gone? What is left to do?
9. Functional and Stimuli-Responsive Materials
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Shape-Memory Polymers
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How can polymers be converted into nanomaterials that undergo triggered changes of their properties? What are suitable external triggers for which purpose? What functions can be realized?
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Stimuli-Responsive Supramolecular Gels
Supramolecular gels are gels that are not made from polymers, but from small molecules that interact non-covalently and then create a fiber structure with solvent-filled holes inside. This talk should describe how these gels can be made stimuli-responsive and what external stimuli can be used to mediate the transition between the gel state and the sol state.
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Organic/inorganic hybrid materials can be turned into dynamic interactive systems defined by networks of exchanging reversibly connected objects. How is adaptibility achieved? Please do not create too much overlap with the preceding talk on gels.
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Putting Things Together: Mechanosensitive Self-Replication Driven by Self-Organization
This final example in the seminar series combines almost all aspects that we have discussed. It comprises dynamic combinatorial libraries of disulfides that can form a supramolecular superstructure. Autocatalysis is involved in an unexpected way and the system reacts to mechanical stimuli - in different ways depending of how the system is treated. It would be great, if you could not only present this example, but at the same time draw conclusions about the seminar series and show how things fall into place in this system.