Overview

QM/MM Methods Applied to Reaction Mechanisms in Enzymes

February 4.  Update:
The papers and weeks are now assigned (randomly):
Feb 17: Erik presents the Gao paper
Feb 24: Martin presents the Friesner paper
March 10: Janus presents the Thiel paper
March 17: Kasper presents the Cui paper
March 24: Casper presents the Mulholland paper
March 31: Anders presents the Ryde paper

What: The course focuses on QM/MM methodologies that have been used recently to study reaction mechanisms in enzymes. The focus is on the methods, not the enzymes.
With the exception of the first week, where I introduce some concepts common to all QM/MM methods, the course consists of weekly student presentations of a particular QM/MM method application, picked from the list below, with plenty of discussion.

ECTS: 7.5 with a possible 2.5 ECTS extra credit.  The course is graded pass/fail

When: blok 3 (uge 5-13), Thursday afternoons from 14:00 to 16:00

Where: C506 (5th floor, C Building, H.C. Ørsted Institute, Universitetsparken 5)

Who: The course is organized by Jan Jensen.  If you are interested in attending the course send me an email.

Prerequisite: The UC Computational Chemistry course or equivalent

More info:
QM/MM is a relatively new field, and the software and methodology is still maturing.  Therefore there are still roughly as many QM/MM methods as there are QM/MM developers, and most state-of-the-art QM/MM studies are often performed by the developers themselves.  Some of the most established groups in the area of QM/MM enzymology are listed here together with a recent application-paper that will be discussed during the course:

Review papers:
Review of QM/MM by Adrian Mulholland
Review by Gao, Karplus, and Truhlar

Recent applications of
The Adrian Mulholland approach: paper 
The Walter Thiel approach: paper
The Rich Friesner approach: paper
The Weitao Yang approach: paper
The Qiang Cui approach: paper
The Jiali Gao approach: paper
The Ulf Ryde approach: paper

Note that presenting the method used in each paper will require you to summarize several other methodology papers from the group:

What is the QM region and what level of theory is used for the QM region?
What force field is used?
How is the covalent boundary treated?
Are any constraints applied to the structure?
How are the reaction barriers computed?
How are dynamical and entropic effects computed?
How is solvation incorporate in the model?