Course detail
Supramolecular systems
FCH-MCO_SKOAcad. year: 2009/2010
Theoretical background of supramolecular chemistry, concept and terminology, overview of the most popular applications, theory of supramolecular design and simulations, background of statistical themodynamics.
Language of instruction
Czech
Number of ECTS credits
4
Mode of study
Not applicable.
Guarantor
Learning outcomes of the course unit
Basic definitions and concepts in supramolecular chemistry.
Overview of fundamental interactions and their applications in molecular simulations.
Computational experience for simulations of simple systems.
Overview of fundamental interactions and their applications in molecular simulations.
Computational experience for simulations of simple systems.
Prerequisites
Organic chemistry, Biochemistry and Physical chemistry knowledge.
Co-requisites
Not applicable.
Planned learning activities and teaching methods
Teaching methods depend on the type of course unit as specified in the article 7 of BUT Rules for Studies and Examinations. The first part will be presented by Dr. Kučerík, second one by Dr. Janeček.
Assesment methods and criteria linked to learning outcomes
Exam: oral
Course curriculum
Concept and definition - clasification of supramolecular host-guest systems; receptors, coordination, key-lock analogy, chelate and macrocyclic effect; preorganisation and complementarity; thermodynamic and kinetic selectivity; nature of supramolecular interactions; supramolecular host design
Supramolecular chemistry of biological systems - alkali metal cations in biochemistry (membrane potenial and transport); rhodopsin A - a supramolecular pigment; porphyrines and other macrocycles, neurotransmiters and hormones; biochemical self-assembled systems.
Synthetic ionophores - crown ethers and analogues; solution behaviour; selectivity of complexation; preorganisation and complementarity; soft ligands and metal cations; heterocrowns; completion of organic cations; chiral barriers. Alkalides. Calixarenes. Siderophores.
Binding of anions. Biological anionic receptors. Receptors (neutral, organometalic, guanidinium-like). Anticrowns.
Binding of neutral molecules - clathrates, hydrates. Zeolites. Organic hosts (urea clathrates, tetraphenylene, "hexahost" strategy). Intracavity complexes of neutral molecules - solution and solid-state binding (cyclodextrines, cyclophanes). Fullerenes.
Crystal engineering. Concept. Structure prediction, crystalographic databases. Crystalography vs. non-covalent interactions. Akward shapes and mismatch. Mixed crystals.
Basics of statistical thermodynamics - postulates, statistical ensembles, Boltzmann distribution, partition functions in canonical and grand-canoniucal ensembles, relations between thermodynamical properties and partition functions, factorization of partition functions.
Statistical-thermodynamical description of ideal gas and diluted systems, virial expansion. Ideal crystal.
Structural theories of fluids - correlation functions, Strukturní teorie tekutin - distribuční funkce, Ornstein-Zernike equation, relation between correlation functions and thermodynamic properties.
Debye-Hueckel theory for electrolytes - primitive model, presumptions and limitations of DH approach, thermodynamical properties; Bjerrum theory for ionic association.
Molecular simulations - Monte Carlo algorythm in various ensembles, Metropolis criterion; molecular dynamics, temperature and pressure coupling. Simulations of coarse-grained models.
Selected applications of molecular simulations.
Supramolecular chemistry of biological systems - alkali metal cations in biochemistry (membrane potenial and transport); rhodopsin A - a supramolecular pigment; porphyrines and other macrocycles, neurotransmiters and hormones; biochemical self-assembled systems.
Synthetic ionophores - crown ethers and analogues; solution behaviour; selectivity of complexation; preorganisation and complementarity; soft ligands and metal cations; heterocrowns; completion of organic cations; chiral barriers. Alkalides. Calixarenes. Siderophores.
Binding of anions. Biological anionic receptors. Receptors (neutral, organometalic, guanidinium-like). Anticrowns.
Binding of neutral molecules - clathrates, hydrates. Zeolites. Organic hosts (urea clathrates, tetraphenylene, "hexahost" strategy). Intracavity complexes of neutral molecules - solution and solid-state binding (cyclodextrines, cyclophanes). Fullerenes.
Crystal engineering. Concept. Structure prediction, crystalographic databases. Crystalography vs. non-covalent interactions. Akward shapes and mismatch. Mixed crystals.
Basics of statistical thermodynamics - postulates, statistical ensembles, Boltzmann distribution, partition functions in canonical and grand-canoniucal ensembles, relations between thermodynamical properties and partition functions, factorization of partition functions.
Statistical-thermodynamical description of ideal gas and diluted systems, virial expansion. Ideal crystal.
Structural theories of fluids - correlation functions, Strukturní teorie tekutin - distribuční funkce, Ornstein-Zernike equation, relation between correlation functions and thermodynamic properties.
Debye-Hueckel theory for electrolytes - primitive model, presumptions and limitations of DH approach, thermodynamical properties; Bjerrum theory for ionic association.
Molecular simulations - Monte Carlo algorythm in various ensembles, Metropolis criterion; molecular dynamics, temperature and pressure coupling. Simulations of coarse-grained models.
Selected applications of molecular simulations.
Work placements
Not applicable.
Aims
He aim is to provide the basic awareness on supramolecular chemistry, molecular simulations and applications.
Specification of controlled education, way of implementation and compensation for absences
not
Recommended optional programme components
Not applicable.
Prerequisites and corequisites
Not applicable.
Basic literature
Ariga K., Kunitake T.: Supramolecular chemistry: fundamentals and applications: advanced textbook. Springer, Berlin 2005. (CS)
Lehn J. - M.: Supramolecular chemistry. Wiley-VCH, Weinheim 1995. (CS)
Schalley, C.: Analytical Methods in Supramolecular Chemistry. Wiley-VCH Verlag 2007 (CS)
Lehn J. - M.: Supramolecular chemistry. Wiley-VCH, Weinheim 1995. (CS)
Schalley, C.: Analytical Methods in Supramolecular Chemistry. Wiley-VCH Verlag 2007 (CS)
Recommended reading
Steed J. W., Atwood J. L.: Supramolecular chemistry. John Wiley & Sons Ltd, Chichester 2000. (CS)
Classification of course in study plans