Takudrei

Lecture Course "Systems Chemistry"

Course No. 21 234

 


Quicklink: Seminar schedule - Materials for Download


 

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 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. 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, cybernetics, ecosystem research already anticipated what chemists are about to learn.

Systems chemistry is therefore an extremely interesting and very new way to do - and to think - chemistry. The lecture course aims at demonstrating the intriguing emergent properties with a number of quite recent examples from the forefront of chemical research.

 

Organizational Matters

The course aims at the master level and is organized a bit aside of the well-trodden paths of lecture course & seminars/exercises. The major part of it consists of talks done by the participants on a topic selected from those below. For one talk given by you and regular/active presence plus a passed oral exam you earn 5 credit points.

The course finishes with a ca. 30 min oral exam. The grade of this exam 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

c.schalley@fu-berlin.de

Start date: Wed, Oct 15th, 2014, 13:00 pm (preparation meeting)
OC conference room (Taku 3, 31.09)

The course itself is scheduled Wednesdays, 9-12 in room 31.09.

Talks should be given in English as a preparation for your future work. Each seminar talk should be ca. 30-40 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, better three 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.

  • 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.

  • 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!

  • 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.

  • 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.

  • 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 ...

  • 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.

Chapter 1 - Introduction: Chemical Networks and Systems Chemistry

  • Thought experiment: Buttons and Wires - or when Quantity becomes Quality

  • 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:

 

 

Chapter 2 - Self-Assembly: Creating Complex Mixtures under Thermodynamic Control

 

 

 

Chapter 3 - Dynamic Combinatorial Chemistry: Amplification through Templation

  • Langtons Ant

  • Combinatorial Chemistry

    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

 

 

 

Chapter 4 - Self-Sorting Phenomena in Complex Supramolecular Systems

 

 

 

Chapter 5 - Self-Replicating Molecules

 

 

 

 

Chapter 6 - Self-Organization in Chemistry: Oszillating Reactions

 

 

  • 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:

 

Chapter 7 - The Origin of Homochirality and its Importance for the Development of Life

  • An Indeterministic World? Symmetry Breaking in NaClO3 and KClO3 Crystallization Experiments

  • Origin of Homochirality

    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.

 

 

 

 

 

 

Chapter 8 - From Chemical Models of Homeostasis and Autopoiesis to Protocells

 

 

Chapter 9 - Functional and Stimuli-Responsive Materials

 

  • 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.