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<p>The Effective Fragment Potential (EFP) is a quantum-mechanical based model potential for
accurate calculations of non-covalent interactions between molecules. It can be coupled with ab
initio methods in so-called QM/EFP models to explore the electronic properties of extended
molecular systems by providing rigorous description of surrounding environments. The current
EFP formulation is, however, not well suited for large-scale simulations due to its inherent
limitation of representing effective fragments as rigid structures. The process of utilizing EFP
method for the molecular systems with flexible degrees of freedom entails multiple sets of
parameter calculations requiring intensive computational resources. This work presents
development of the EFP method for describing flexible molecular systems, so-called Flexible EFP.
To validate the applicability of the Flexible EFP method, extensive benchmark studies on the
amino acid interactions, binding energies, and electronic properties of flavin chromophore of the
cryptochrome protein have been demonstrated. In addition to methodological developments,
excitonic properties of the Fenna-Matthews-Olson (FMO) photosynthetic pigment-protein
complex are explored. In biological systems where intermolecular interactions span a broad range
from non-polar to polar and ionic forces, EFP is superior to the classical force fields. In the present
study, we demonstrate excellent performance of the QM/EFP model for predicting excitonic
interactions and spectral characteristics of the FMO wildtype complex. We characterize the key
factors for accurate modeling of electronic properties of bacteriochlrophyll a (BChl a)
photosynthetic pigments and suggest a robust computational protocol that can be applied for
modeling other photosynthetic systems. Developed computational procedures were also
successfully utilized to elucidate photostability and triplet dynamics in the FMO complex and
spectroscopic effects of single-point mutagenesis in FMO. A combination of polarizable EFP
molecular dynamics and QM/EFP vibrational frequency calculations were also applied to
understanding and interpreting structures and Raman spectroscopy of tert-butyl alcohol solutions.
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| Identifer | oai:union.ndltd.org:purdue.edu/oai:figshare.com:article/12739961 |
| Date | 31 July 2020 |
| Creators | Yongbin Kim (9187811) |
| Source Sets | Purdue University |
| Detected Language | English |
| Type | Text, Thesis |
| Rights | CC BY 4.0 |
| Relation | https://figshare.com/articles/thesis/DEVELOPMENT_AND_APPLICATION_OF_EFFECTIVE_FRAGMENT_POTENTIALS_FOR_BIO_MOLECULAR_SYSTEMS/12739961 |
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