Theoretical Methods
4
Marius Wanko and Angel Rubio
Abstract
The description of the electronic structure of molecules in the excited state is
usually more involved than the calculation of ground-state properties. The
development of approaches to calculate optical properties of chromophores,
including their specific interactions with a complex environment is a very active
field of research. This chapter gives an overview of quantum mechanical
methods and schemes to integrate them into a multi-scale description of
extended systems that contain an optically active center. Special attention is
paid to the problems and limitations of quantum methods that are commonly
used to describe excited-state properties of biological chromophores.
4.1
Introduction
There are two main goals in computational modelling of biochromophores and their
characterisation in terms of theoretical spectroscopy. The first is to propose atomistic structural models where structural information from experiments is limited.
Often it is difficult to produce 3D crystals of the active state of proteins, in
particular of mutants that prohibit oligomerisation. Short-lived intermediates that
cannot be trapped thermally can be identified from time-resolved spectroscopy, but
structural information from these experiments is limited and the interpretation
ambiguous. Lacking hydrogen atoms and mobile waters, x-ray crystallographic
structures often lack information about the protonation state of titratable amino acid
residues and their role in hydrogen-bonded networks (HBN) and electrostatic
interactions. All these issues are readily addressed by computational approaches
M. Wanko (*) • A. Rubio
Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de Fı ´sica
de Materiales, Centro de Fı ´sica de Materiales CSIC-UPV/EHU-MPC and DIPC, Universidad del
Paı ´s Vasco, Av. Tolosa 72, 20018 San Sebastia ´n, Spain
e-mail: marius.wanko@gmail.com; angel.rubio@ehu.es
S. Brøndsted Nielsen and J.A. Wyer (eds.), Photophysics of Ionic Biochromophores,
Physical Chemistry in Action, DOI 10.1007/978-3-642-40190-9_4,
# Springer-Verlag Berlin Heidelberg 2013
45
4
Marius Wanko and Angel Rubio
Abstract
The description of the electronic structure of molecules in the excited state is
usually more involved than the calculation of ground-state properties. The
development of approaches to calculate optical properties of chromophores,
including their specific interactions with a complex environment is a very active
field of research. This chapter gives an overview of quantum mechanical
methods and schemes to integrate them into a multi-scale description of
extended systems that contain an optically active center. Special attention is
paid to the problems and limitations of quantum methods that are commonly
used to describe excited-state properties of biological chromophores.
4.1
Introduction
There are two main goals in computational modelling of biochromophores and their
characterisation in terms of theoretical spectroscopy. The first is to propose atomistic structural models where structural information from experiments is limited.
Often it is difficult to produce 3D crystals of the active state of proteins, in
particular of mutants that prohibit oligomerisation. Short-lived intermediates that
cannot be trapped thermally can be identified from time-resolved spectroscopy, but
structural information from these experiments is limited and the interpretation
ambiguous. Lacking hydrogen atoms and mobile waters, x-ray crystallographic
structures often lack information about the protonation state of titratable amino acid
residues and their role in hydrogen-bonded networks (HBN) and electrostatic
interactions. All these issues are readily addressed by computational approaches
M. Wanko (*) • A. Rubio
Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de Fı ´sica
de Materiales, Centro de Fı ´sica de Materiales CSIC-UPV/EHU-MPC and DIPC, Universidad del
Paı ´s Vasco, Av. Tolosa 72, 20018 San Sebastia ´n, Spain
e-mail: marius.wanko@gmail.com; angel.rubio@ehu.es
S. Brøndsted Nielsen and J.A. Wyer (eds.), Photophysics of Ionic Biochromophores,
Physical Chemistry in Action, DOI 10.1007/978-3-642-40190-9_4,
# Springer-Verlag Berlin Heidelberg 2013
45