@article{shrestha_virgil_jakubikova_2016, title={Electronic Absorption Spectra of Tetrapyrrole-Based Pigments via TD-DFT: A Reduced Orbital Space Study}, volume={120}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.6b04797}, abstractNote={Tetrapyrrole-based pigments play a crucial role in photosynthesis as principal light absorbers in light-harvesting chemical systems. As such, accurate theoretical descriptions of the electronic absorption spectra of these pigments will aid in the proper description and understanding of the overall photophysics of photosynthesis. In this work, time-dependent density functional theory (TD-DFT) at the CAM-B3LYP/6-31G* level of theory is employed to produce the theoretical absorption spectra of several tetrapyrrole-based pigments. However, the application of TD-DFT to large systems with several hundreds of atoms can become computationally prohibitive. Therefore, in this study, TD-DFT calculations with reduced orbital spaces (ROSs) that exclude portions of occupied and virtual orbitals are pursued as a viable, computationally cost-effective alternative to conventional TD-DFT calculations. The effects of reducing orbital space size on theoretical spectra are qualitatively and quantitatively described, and both conventional and ROS results are benchmarked against experimental absorption spectra of various tetrapyrrole-based pigments. The orbital reduction approach is also applied to a large natural pigment assembly that comprises the principal light-absorbing component of the reaction center in purple bacteria. Overall, we find that TD-DFT calculations with proper and judicious orbital space reductions can adequately reproduce conventional, full orbital space, TD-DFT results of all pigments studied in this work.}, number={29}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Shrestha, Kushal and Virgil, Kyle A. and Jakubikova, Elena}, year={2016}, month={Jul}, pages={5816–5825} }
 @article{shrestha_jakubikova_2015, title={Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method}, volume={119}, ISSN={["1089-5639"]}, DOI={10.1021/acs.jpca.5b05644}, abstractNote={Light-harvesting antennas are protein-pigment complexes that play a crucial role in natural photosynthesis. The antenna complexes absorb light and transfer energy to photosynthetic reaction centers where charge separation occurs. This work focuses on computational studies of the electronic structure of the pigment networks of light-harvesting complex I (LH1), LH1 with the reaction center (RC-LH1), and light-harvesting complex II (LH2) found in purple bacteria. As the pigment networks of LH1, RC-LH1, and LH2 contain thousands of atoms, conventional density functional theory (DFT) and ab initio calculations of these systems are not computationally feasible. Therefore, we utilize DFT in conjunction with the energy-based fragmentation with molecular orbitals method and a semiempirical approach employing the extended Hückel model Hamiltonian to determine the electronic properties of these pigment assemblies. Our calculations provide a deeper understanding of the electronic structure of natural light-harvesting complexes, especially their pigment networks, which could assist in rational design of artificial photosynthetic devices.}, number={33}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Shrestha, Kushal and Jakubikova, Elena}, year={2015}, month={Aug}, pages={8934–8943} }
 @article{shrestha_gonzalez-delgado_blew_jakubikova_2014, title={Electronic Structure of Covalently Linked Zinc Bacteriochlorin Molecular Arrays: Insights into Molecular Design for NIR Light Harvesting}, volume={118}, ISSN={["1520-5215"]}, DOI={10.1021/jp507749c}, abstractNote={Pigment-based molecular arrays, especially those based on porphyrins, have been extensively studied as viable components of artificial light harvesting devices. Unlike porphyrins, bacteriochlorins absorb strongly in the NIR, yet little is known of the applicability of covalently linked bacteriochlorin-based arrays in this arena. To lay the foundation for future studies of excited state properties of such arrays, we present a systematic study of the ground state electronic structure of zinc bacteriochlorin (ZnBC) molecular arrays with various linkers and linker attachment sites (meso vs β) employing density functional theory in combination with the energy-based fragmentation (EBF) method, and the EBF with molecular orbitals (EBF-MO) method. We find that the level of steric hindrance between the ZnBC and the linker is directly correlated with the amount of ground sate electronic interactions between the ZnBCs. Low steric hindrance between the ZnBC and the linker found in alkyne-linked arrays results in strongly interacting arrays that are characterized by a decrease in the HOMO-LUMO energy gaps, large orbital energy dispersion in the frontier region, and low ZnBC-linker rotational barriers. In contrast, sterically hindered linkers, such as aryl-based linkers, result in weakly interacting arrays characterized by increased orbital energy degeneracy in the frontier region and high ZnBC-linker rotational barriers. For all linkers studied, the level of steric hindrance decreases when the ZnBCs are linked at the β position. Hence, ZnBC arrays that exhibit strong, weak, or intermediate ground-state electronic interactions can be realized by adjusting the level of steric hindrance with a judicious choice of the linker type and linker attachment site. Such tuning may be essential for design of light harvesting arrays with desired spectral properties.}, number={42}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Shrestha, Kushal and Gonzalez-Delgado, Jessica M. and Blew, James H. and Jakubikova, Elena}, year={2014}, month={Oct}, pages={9901–9913} }
 @article{tsuchiya_shrestha_jakubikova_2013, title={Orbital Analysis and Excited-State Calculations in an Energy-Based Fragmentation Method}, volume={9}, ISSN={["1549-9626"]}, DOI={10.1021/ct400025a}, abstractNote={Covalently bound molecular arrays composed of porphyrins or related pigments have gained a lot of interest as components of artificial light-harvesting systems and molecular photonic devices. The large size of these arrays, however, makes their theoretical investigation employing the ab initio or density functional methodologies difficult. Energy-based fragmentation methods (EBF) represent a set of conceptually simple approaches to theoretical investigation of large systems and were therefore chosen as a tool to study these systems. Here a new approach to EBF, EBF-MO, is introduced that enables one to obtain orbitals and orbital energies and to perform population analysis and excited-state calculations of large systems composed of hundreds of atoms. This approach was implemented into a parallel program, JETT, and the benchmark calculations have shown its accuracy and applicability to the ground- and excited-state calculations of systems containing transition metals and extended π-conjugation. EBF-MO was then applied to the density functional theory (DFT) and the time-dependent density functional theory (TDDFT) calculations of ground- and excited-state properties of a porphyrin-based molecular photonic wire composed of 472 atoms and 4265 basis functions at the B3LYP/LANL08,6-31G* level. The TDDFT calculations have revealed the character of the excited states, and the unidirectionality of the excitation energy transfer across the array relevant to its signal transfer function. The computational approaches introduced here have widened the applicability of the ab initio and density functional methodologies to calculations of extended systems such as natural and artificial light-harvesting systems and molecular photonic devices.}, number={8}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, author={Tsuchiya, Takashi and Shrestha, Kushal and Jakubikova, Elena}, year={2013}, month={Aug}, pages={3350–3363} }