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Extending the capabilities of polarizable embedding through damped linear response theory
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

One of the greater challenges of modern quantum chemistry is to meet the growing demands of a detailed description of macro molecules, such as proteins and RNA/DNA. The size of such systems make it an almost impossible task to, from first principle calculations, obtain any detailed information regarding electronic structure. This thesis is focused on development of new computational tools for investigation of electronic transitions within large molecular systems. Central to this is the polarizable embedding (PE) model. For many of these systems electronic transitions are localized to one or a few active sites which in turn will be described by accurate quantum chemical methods. The remaining part of the system, defining the environment, is then treated at a lower level using a classical electrostatic approach. The environment is further incorporated into the Hamiltonian describing the quantum region in an effective manner.

The work presented in this thesis covers extensions to the PE model both in the quantum region and in the environmental description. The former, starts by combining the PE model with a damped linear response formalism. This coupling enables the study of electronic processes near resonance and in any frequency range desirable thus covering all from core hole transitions to valence transitions. Another important aspect of this work is the coupling of PE to a polarizable continuum model which allows for inclusion of bulk solvent  effects in an effective manner. In addition to these extensions we have further considered alternative ways of acquiring parameters used in the construction of the embedding potential. This is essential for accurate embedding calculations as the embedding potential enters directly in the wave function optimization.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2016. , 53 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1765
National Category
Chemical Sciences Physical Chemistry
Identifiers
URN: urn:nbn:se:liu:diva-127496ISBN: 978-91-7685-763-2 (Print)OAI: oai:DiVA.org:liu-127496DiVA: diva2:924315
Public defence
2016-05-27, Planck, Fysikhuset, Campus Valla, Linköping, 10:15 (English)
Opponent
Supervisors
Available from: 2016-04-28 Created: 2016-04-28 Last updated: 2016-05-25Bibliographically approved
List of papers
1. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental Theoretical Case Study of the AT Homo-Oligonucleotide
Open this publication in new window or tab >>DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental Theoretical Case Study of the AT Homo-Oligonucleotide
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2015 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 3, 355-359 p.Article in journal (Refereed) Published
Abstract [en]

A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment.

Place, publisher, year, edition, pages
American Chemical Society, 2015
National Category
Physical Sciences
Identifiers
urn:nbn:se:liu:diva-115321 (URN)10.1021/jz502696t (DOI)000349137400009 ()
Note

Funding Agencies|Swedish Research Council [621-2014-4646]; FNRS (Belgium) [2.4615.11-BINDER]

Available from: 2015-03-13 Created: 2015-03-13 Last updated: 2016-04-28
2. Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method
Open this publication in new window or tab >>Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method
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2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 3, 1164-1171 p.Article in journal (Refereed) Published
Abstract [en]

We present a combination of the polarizable embedding (PE) scheme with the complex polarization propagator (CPP) method with the aim of calculating response properties including relaxation for large and complex systems. This new approach, termed PE-CPP, will benefit from the highly advanced description of the environmental electrostatic potential and polarization in the PE method as well as the treatment of near-resonant effects in the CPP approach. The PE-CPP model has been implemented in a Kohn-Sham density functional theory approach, and we present pilot calculations exemplifying the implementation for the UV/vis and carbon K-edge X-ray absorption spectra of the protein plastocyanin. Furthermore, technical details associated with a PE-CPP calculation are discussed.

Place, publisher, year, edition, pages
American Chemical Society, 2014
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-106098 (URN)10.1021/ct400946k (DOI)000332913500026 ()
Available from: 2014-04-25 Created: 2014-04-24 Last updated: 2016-04-28

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