1
Chapter 1
Hybrid QM/MM Methods: Treating Electronic
Phenomena in Very Large Molecular Systems
Antonio Monari and Xavier Assfeld
© Springer Science+Business Media Dordrecht 2014
L. Gorb et al. (eds.), Application of Computational Techniques in Pharmacy and Medicine,
Challenges and Advances in Computational Chemistry and Physics 17,
DOI 10.1007/978-94-017-9257-8_1
X. Assfeld () · A. Monari
Université de Lorraine, Théorie-Modélisation-Simulation, SRSMC UMR 7565,
Vandœuvre-lès-Nancy, 54506 France
e-mail: xavier.assfeld@univ-lorraine.fr
A. Monari
e-mail: antonio.monari@univ-lorraine.fr
Abstract Hybrid methods, combining the accuracy of Quantum Mechanics and the
potency of Molecular Mechanics, the so-called QM/MM methods, arise from the
desire of theoretician chemists to study electronic phenomena in large molecular
systems. In this contribution, a focus, on the Physics and Chemistry on which theses
methods are based on, is given. The advantages, flaws, and limitations of each type
of methods are exposed. A special emphasis is put on the Local Self-Consistent
Field method, developed in our group. The latest developments are detailed and
illustrated by chosen examples.
1.1 Introduction
Except some very specific experiments dealing with gas phase with very low pressure, or some particular media (interstellar space, high atmosphere, …), chemists
encounter molecules in interaction with their surroundings. In fact, most of chemical or biochemical reactions take place in solution or involve macromolecules.
The role of the surroundings is crucial. For example, some chemical reactions, like
ethylene bromination, are quasi unfeasible in gas phase, very slow in apolar solvents, but instantaneous in water [1]. In the same vein, most biochemical reactions
wouldn’t be possible if not catalyzed by enzymes [2]. In addition to the role played
in enzymatic catalysis, the environment is also crucial to modify, to precisely tune
or to induce the response to light in photo-active systems. A paradigmatic example
being for instance the role played by opsin protein in assuring an ultra-fast highly
efficient photo isomerization of retinal chromophore in vision process [3, 4]. The
precise understanding and tuning of light-induced responses in complex biosystems
Chapter 1
Hybrid QM/MM Methods: Treating Electronic
Phenomena in Very Large Molecular Systems
Antonio Monari and Xavier Assfeld
© Springer Science+Business Media Dordrecht 2014
L. Gorb et al. (eds.), Application of Computational Techniques in Pharmacy and Medicine,
Challenges and Advances in Computational Chemistry and Physics 17,
DOI 10.1007/978-94-017-9257-8_1
X. Assfeld () · A. Monari
Université de Lorraine, Théorie-Modélisation-Simulation, SRSMC UMR 7565,
Vandœuvre-lès-Nancy, 54506 France
e-mail: xavier.assfeld@univ-lorraine.fr
A. Monari
e-mail: antonio.monari@univ-lorraine.fr
Abstract Hybrid methods, combining the accuracy of Quantum Mechanics and the
potency of Molecular Mechanics, the so-called QM/MM methods, arise from the
desire of theoretician chemists to study electronic phenomena in large molecular
systems. In this contribution, a focus, on the Physics and Chemistry on which theses
methods are based on, is given. The advantages, flaws, and limitations of each type
of methods are exposed. A special emphasis is put on the Local Self-Consistent
Field method, developed in our group. The latest developments are detailed and
illustrated by chosen examples.
1.1 Introduction
Except some very specific experiments dealing with gas phase with very low pressure, or some particular media (interstellar space, high atmosphere, …), chemists
encounter molecules in interaction with their surroundings. In fact, most of chemical or biochemical reactions take place in solution or involve macromolecules.
The role of the surroundings is crucial. For example, some chemical reactions, like
ethylene bromination, are quasi unfeasible in gas phase, very slow in apolar solvents, but instantaneous in water [1]. In the same vein, most biochemical reactions
wouldn’t be possible if not catalyzed by enzymes [2]. In addition to the role played
in enzymatic catalysis, the environment is also crucial to modify, to precisely tune
or to induce the response to light in photo-active systems. A paradigmatic example
being for instance the role played by opsin protein in assuring an ultra-fast highly
efficient photo isomerization of retinal chromophore in vision process [3, 4]. The
precise understanding and tuning of light-induced responses in complex biosystems