55593 Computational Chemistry Basics for Organic Chemistry (3 ECTS). University Lecturer Juho Helaja Period Ii Tue, Fri 9-11, A122. Optionally in English.
- lab course with ORCA (quantum chemistry program) via Gabedit graphical user interface as main tools (shareware programs) in electronic computations of organic molecules and reactions
(+ selected Gaussian calculations (on CSC) via Gview graphical interface)
- theoretical basis is presented only in concise manner with lecture notes
- Introduction to computational chemistry course (Phys Chem. Vesa Hänninen) is recommended for background knowledge
- The primary aim of the course is to give information which specific chemical (molecular) properties are computationally straightforwardly accessible, provide tools for this purpose
- Additionally, some advanced research computations are exemplified
- lab works: Electronic structure computational methods (ab initio and dft-methods): Calculation of energy minima; Calculation of conformations; Reaction scanning; Finding transitions states (for Diels Alder, SN2); (pKa computations); Calculation NMR spectra; Calculation IR-spectra; UV-vis calculations; Natural orbital analysis (visualization); Charge density analysis (visualization)
- max 16 students
55594 Introduction to Chemical Biology (3 ECTS). Doc. Annamaria Lilienkampf, Period II
(12.-18.12. 2013, 9-16)
Recommended preceding/background studies: Organic Chemistry 1 (55521), Organic Chemistry 2 (55522), Biological Chemistry (55508)
- To give an introduction to chemical biology as a sub-discipline of chemistry and biology.
- Familiarise students with the basic methods and techniques used in chemical biology.
- Show students how they can apply their chemistry knowledge to solve biological problems.
After successfully completing the course, the students should be able to:
- Define chemical biology as a discipline and describe some relevant/current research areas
- Describe and apply the basic methods used in the synthesis/production and analysis of biomacromolecules e.g. DNA, proteins and peptides
- Describe basic bioconjugate techniques and understand the organic chemistry behind them
- Know basic methods used in cellular delivery
- Be able to design basic molecular probes
- Define what nanoparticles are and how they can be used in chemical biology
This course aims to establish a basic understanding of chemical biology as a research topic, especially in the context of organic chemistry. The course is structured so as to familiarise students with the wide range of topics and research methods, and give students an overview how they can apply their chemistry skills to biology based research problems.
- Lecture notes
- Research articles (references provided)
- World Wide Web (SciFinder, Web of Knowledge)
- Hermanson, Bioconjugate Techniques, Elsevier, 2008
- Invitrogen, The Molecular Probes® Handbook—A Guide to Fluorescent Probes and Labeling Technologies, 11 th Ed (available on-line)
One assignment in a form of a course presentation (15 min + 5 min questions) of a given/chosen research topic/article (100%). Active participation on other presentation sessions in form of questions and feedback. (No written examination.)
The course takes a very broad approach to chemical biology. It is aimed at providing the student with an overview of this relatively new, but rapidly growing research area. The course is mostly based on provided lecture notes. However, the students are also expected to engage in independent learning in their course assignment and to share their findings with their peers in a form of a course presentation. This intense course will run for 1 week (5 days) with 2-3 lectures (2-3 × 50min) each day. In addition, there will be small exercise sessions embedded into the lectures. The lectures are followed by a presentation day for the independent study later on the term (date and time to be agreed later). Significant study time is expected in preparation for the course assignment/presentation. Furthermore, the students are expected to actively participate in the discussions following each presentation.
Docent Annamaria Lilienkampf (firstname.lastname@example.org)
Professor Kristiina Wähälä (email@example.com)