Related Experiment Video
Updated: Jun 1, 2026
08:04
Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
Published on: May 27, 2020
A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals:
Yukio Kawashima1, Haruyuki Nakano, Jaewoon Jung
1Department of Chemistry, Graduate School of Sciences, Kyushu University, Fukuoka 812-8581, Japan.
Physical Chemistry Chemical Physics : PCCP
|May 21, 2011
Summary
The generalized hybrid orbital (GHO) method enhances quantum mechanical/molecular mechanical (QM/MM) excited state calculations. This new approach accurately predicts electronic excitation energies for biomolecules like bacteriorhodopsin.
Area of Science:
- Computational Chemistry
- Quantum Mechanics
- Molecular Mechanics
- Spectroscopy
Background:
- Accurate calculation of electronic excited states is crucial for understanding photochemical processes in biological systems.
- Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are essential for modeling large biomolecules, but their application to excited states presents challenges.
- The second-order approximate coupled cluster singles and doubles (CC2) method is a robust approach for excited state calculations.
Purpose of the Study:
- To implement and assess the generalized hybrid orbital (GHO) method at the CC2 level for QM/MM excited state calculations.
- To evaluate the accuracy of the GHO-CC2 method for predicting the first singlet excited states of aromatic amino acids and bacteriorhodopsin.
- To investigate the influence of QM/MM partitioning on excited state properties.
Main Methods:
- Derivation and implementation of the linear response CC2 function within the GHO scheme.
- Application of the GHO-CC2 method to phenylalanine, tyrosine, tryptophan, and bacteriorhodopsin.
- Comparison of GHO-CC2 results with full QM CC2 calculations and experimental data.
Main Results:
- GHO-CC2 calculations for aromatic amino acids showed excellent agreement with full QM CC2 results.
- Calculated excitation energies for bacteriorhodopsin and its all-trans retinal chromophore accurately reproduced experimental environmental shifts.
- The GHO method demonstrated good agreement with experimental data for bacteriorhodopsin's environmental shift.
Conclusions:
- The GHO method, when combined with CC2, provides a reliable and accurate approach for QM/MM excited state calculations.
- This implementation enables efficient and accurate modeling of electronic excited states in complex biological systems.
- The study highlights the importance of QM/MM partitioning in elucidating quantum effects on excited states.
Related Concept Videos
03:24Hybridization of Atomic Orbitals I
The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
03:35Hybridization of Atomic Orbitals II
sp3d and sp3d 2 Hybridization
02:35Molecular Orbital Theory I
Overview of Molecular Orbital Theory
02:38Valence Bond Theory and Hybridized Orbitals
According to valence bond theory, a covalent bond results when: (1) an orbital on one atom overlaps an orbital on a second atom, and (2) the single electrons in each orbital combine to form an electron pair. The strength of a covalent bond depends on the extent of overlap of the orbitals involved. Maximum overlap is possible when the orbitals overlap on a direct line between the two nuclei.
A σ bond (single bond in a Lewis structure) is a covalent bond in which the electron density is...
A σ bond (single bond in a Lewis structure) is a covalent bond in which the electron density is...
03:51Molecular Orbital Theory II
Molecular Orbital Energy Diagrams
02:45The Quantum-Mechanical Model of an Atom
Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing hydrogen spectra. Schrödinger...