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Theoretical Description of Electronic Transitions in Large Molecular Systems in the Optical and X-Ray Regions
Department of Physics, Chemistry and Biology, University of Southern Denmark, Denmark.ORCID iD: 0000-0002-0246-3995
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The size and conformational complexity of proteins and other large systems represent major challenges for today's methods of quantum chemistry.This thesis is centered around the development of new computational tools to gain molecular-level insight into electronic transitions in such systems. To meet this challenge, we focus on the polarizable embedding (PE) model, which takes advantage of the fact that many electronic transitions are localized to a smaller part of the entire system.This motivates a partitioning of the large system into two regions that are treated at different levels of theory:The smaller part directly involved in the electronic process is described using accurate quantum-chemical methods, while the effects of the rest of the system, the environment, are incorporated into the Hamiltonian of the quantum region in an effective manner.

This thesis presents extensions of the PE model with theaim of expanding its range of applicability to describe electronic transitions in large molecular systemsin the optical and X-ray regions. The developments cover both improvements with regardto the quantum region as well as the embedding potential representing the environment.Regarding the former, a damped linear response formulation has been implemented to allow for calculations of absorption spectra of large molecular systems acrossthe entire frequency range. A special feature of this development is its abilityto address core excitations that are otherwise not easily accessible.Another important development presented in this thesis is the coupling of the PE model to a multi-configuration self-consistent-field description of the quantum region and its further combination with response theory. In essence, this extends the PE model to the study of electronic transitions in large systems that are prone to static correlation --- a situation that is frequently encountered in biological systems. In addition to the direct environmental effects on the electronic structure of the quantum region, another important component of the description of electronic transitions in large molecular systems is an accurate account of the indirect effects of the environment, i.e., the geometrical distortions in the quantum region imposed by the environment. In thisthesis we have taken the first step toward the inclusion of geometry distortions in the PE frameworkby formulating and implementing molecular gradients for the quantum region.

To identify critical points related to the environment description, we perform a theoretical analysis of the PE model starting from a full quantum-mechanicaltreatment of a composite system. Based on this, we present strategies for an accurate yet efficient construction of the embedding potentialcovering both the calculation of ground state and transition properties. The accurate representation of the environment makes it possible to reduce the size of the quantum region without compromising the overall accuracy of the final results. This further enables use of highly accurate quantum-chemical methods despite their unfavorable scaling with the size of the system.

Finally, some examples of applications will be presented to demonstrate how the PE model may be applied as a tool to gain insight into and rationalize the factors influencing electronic transitions in large molecular systems of increasing complexity.

Place, publisher, year, edition, pages
Odense: University Library of Southern Denmark, Denmark , 2015. , p. 105
Keywords [en]
Polarizable embedding, multiscale modeling, localized electronic transitions, response theory, QM/MM, damped linear response, non-dipolar effects, light-matter interactions, multipole expansion, embedding potentials, local field effects, fluorescent proteins, computational chemistry, MCSCF
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
URN: urn:nbn:se:kth:diva-201156OAI: oai:DiVA.org:kth-201156DiVA, id: diva2:1072871
Public defence
2015-12-22, Campusvej 55, Odense, Denmark, 10:00 (English)
Opponent
Supervisors
Note

The dissertation was awarded the best PhD thesis prize 2016 by the Danish Academy of Natural Sciences.

QC 20170209

Available from: 2017-02-09 Created: 2017-02-09 Last updated: 2017-02-09Bibliographically approved

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