Datorbaserad analys av enzymdesign för Diels-Alder reaktioner
Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesisAlternative title
In Silico Investigation of Enzyme Design Methods for Diels Alder Reactions (English)
This thesis has been focused around the Diels Alder reaction with the goal to design an enzyme catalyzed reaction pathway. To achieve this goal computer aided enzyme design was utilized. Common traditional methods of computational chemistry (B3LYP, MP2) do not do well when calculating reaction barriers or even reaction energies for the Diels Alder reaction. New calcu- lation methods were developed and tested. This was the focus of the first part of the thesis, by choosing a small system, extensive and heavy calculations could be done with CBS-QB3. Then by benchmarking faster methods of calculation (SCS-MP2, M06-2X) against the results, they could be graded by efficiency and cost. This was done anticipating that the same accuracy could be applied to larger systems where CBS-QB3 cannot be used.
In the second part activating groups were investigated for both the diene and the dienophile, along with their effects on reaction rates. A qualitative analysis was done. This is important not only for the uncatalyzed reaction, but also interesting when searching for possible substrates for the enzyme reaction.
In the last part the thesis presents a designed enzyme that catalyzes Diels Alder in silico using ∆5−3−Keto steroid isomerase. Using empirical calculations, the enzyme was scanned for catalytic activity. The catalytic effect was then showed with ab initio Quantum chemical calculations.
Place, publisher, year, edition, pages
2011. , 27 p.
Diels-Alder, Enzyme Design, Quantum Chemistry, Density Functional Theory (DFT), Protein Docking
IdentifiersURN: urn:nbn:se:kth:diva-34153OAI: oai:DiVA.org:kth-34153DiVA: diva2:419586
Subject / course
Chemical Science and Engineering
Master of Science in Engineering - Chemical Science and Engineering
UppsokPhysics, Chemistry, Mathematics