QM/MM methods for biomolecular systems.
To model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region and an MM treatment for the surroundings, enabling the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis
P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations.
- S. Shaik, Shimrit Cohen, Yong Wang, Hui Chen, Devesh Kumar, W. Thiel
- PhysicsChemical Reviews
- 10 February 2010
This work confirms that setup issues can be resolved in a consistent manner if proper care is exercised and generates a common setup that gives QM/MM results for P450cam which are generally consistent with those obtained previously with individual setups.
DL-FIND: an open-source geometry optimizer for atomistic simulations.
- J. Kästner, J. M. Carr, T. Keal, W. Thiel, A. Wander, P. Sherwood
- Computer ScienceJournal of Physical Chemistry A
- 29 July 2009
A geometry optimizer, called DL-FIND, to be included in atomistic simulation codes, that can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalizedinternal coordinates, and also functions of more variables independent of atomic structures.
Benchmarks for electronically excited states: CASPT2, CC2, CCSD, and CC3.
- M. Schreiber, Mario R Silva-Junior, S. Sauer, W. Thiel
- ChemistryJournal of Chemical Physics
- 7 April 2008
A benchmark set of 28 medium-sized organic molecules is assembled that covers the most important classes of chromophores including polyenes and other unsaturated aliphatic compounds, aromatic…
Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes.
QM/MM Methods for Biological Systems
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus on biomolecular…
Photochemical steps in the prebiotic synthesis of purine precursors from HCN.
cis-2,3-diaminomaleonitrile (cis-DAMN, 1), which may be converted photochemically into an imidazole intermediate (4amino-1H-imidazole-5-carbonitrile, AICN, 2). Although this reaction has been…
Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters