Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from <i>Synechococcus elongatus</i>, <i>Thermococcus vulcanus</i>, and <i>Rhodobacter sphaeroides</i>, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer

We present a computational analysis of the spin-density asymmetry in cation radical states of reaction center models from photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from inner pairs of (bacterio)chlorophyll a molecules in vacuum to large protein including up to about 2000 atoms. The calculated spin densities show a good agreement with available experimental results and were used to validate reaction center models reported in the literature. Here we demonstrate that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.<br>


2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer

We present a computational analysis of the spin-density asymmetry in cation radical states of reaction center models from photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from inner pairs of (bacterio)chlorophyll a molecules in vacuum to large protein including up to about 2000 atoms. The calculated spin densities show a good agreement with available experimental results and were used to validate reaction center models reported in the literature. Here we demonstrate that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.<br>


Author(s):  
Maximilian Theiß ◽  
Merten Grupe ◽  
Tilman Lamparter ◽  
Maria Andrea Mroginski ◽  
Rolf Diller

AbstractDeactivation processes of photoexcited (λex = 580 nm) phycocyanobilin (PCB) in methanol were investigated by means of UV/Vis and mid-IR femtosecond (fs) transient absorption (TA) as well as static fluorescence spectroscopy, supported by density-functional-theory calculations of three relevant ground state conformers, PCBA, PCBB and PCBC, their relative electronic state energies and normal mode vibrational analysis. UV/Vis fs-TA reveals time constants of 2.0, 18 and 67 ps, describing decay of PCBB*, of PCBA* and thermal re-equilibration of PCBA, PCBB and PCBC, respectively, in line with the model by Dietzek et al. (Chem Phys Lett 515:163, 2011) and predecessors. Significant substantiation and extension of this model is achieved first via mid-IR fs-TA, i.e. identification of molecular structures and their dynamics, with time constants of 2.6, 21 and 40 ps, respectively. Second, transient IR continuum absorption (CA) is observed in the region above 1755 cm−1 (CA1) and between 1550 and 1450 cm−1 (CA2), indicative for the IR absorption of highly polarizable protons in hydrogen bonding networks (X–H…Y). This allows to characterize chromophore protonation/deprotonation processes, associated with the electronic and structural dynamics, on a molecular level. The PCB photocycle is suggested to be closed via a long living (> 1 ns), PCBC-like (i.e. deprotonated), fluorescent species.


2005 ◽  
Vol 19 (15n17) ◽  
pp. 2538-2543 ◽  
Author(s):  
YI QUAN ZHANG ◽  
CHENG LIN LUO ◽  
ZHI YU

Magnetic coupling constants J for the complete structures of [ Gd(capro) 2( H 2 O )4 Cr(CN) 6]• H 2 O (capro represents caprolactam) (a) and trans-[ Fe(CN) 4(μ- CN )2 Gd ( H 2 O )4 (bpy) ]•4 H 2 O •1.5 bpy (b) have been calculated using hybrid density functional theory (DFT) B3LYP combined with a modified broken symmetry approach (BS). The calculated J value of -0.24 cm-1 for a is very close to the experimental -0.33 cm-1. They both show the antiferromagnetic interaction between Gd(III) and Cr(III) . For b, although the sign of the calculated J value of 4.24 cm-1 is different from that of the experimental -0.38 cm-1, the two values both show the weak magnetic coupling interaction between Gd(III) and Fe(III) . The spin density distributions are discussed on the basis of Mulliken population analysis. For complexes a and b, both transition metal ( Fe(III) or Cr(III) ) and rare earth Gd(III) display a spin polarization effect on the surrounding atoms, where a counteraction of the opposite polarization effects leads to a low spin density on the bridging ligand C1N1 . For the compounds Gd(III) - Cr(III) (a) and Gd(III) - Fe(III) (b) in the HS states, Cr(III) has stronger spin polarization influence on the bridging atoms than Fe(III) even causing the positive spin population on the bridging atom N1 .


2020 ◽  
Author(s):  
Dalvin D Méndez-Hernández ◽  
Amgalanbaatar Baldansuren ◽  
Vidmantas Kalendra ◽  
Philip Charles ◽  
Brian Mark ◽  
...  

<p>Light-driven water oxidation in algae, cyanobacteria, and higher plants generates dioxygen that supports life on Earth. The water-oxidation reaction is catalyzed by the oxygen-evolving complex (OEC) in photosystem II (PSII) that is comprised of the tetranuclear manganese calcium-oxo (Mn<sub>4</sub>CaO<sub>5</sub>) cluster, with participation of the redox-active tyrosine residue (Y<sub>Z</sub>) and a hydrogen-bonded network of amino acids and water molecules. Y<sub>Z</sub> mediates successive proton-coupled electron transfer (PCET) reactions that are essential for the oxidation of water to dioxygen at the Mn<sub>4</sub>CaO<sub>5</sub> cluster. It has been proposed that the strong hydrogen bond between Y<sub>Z</sub> and and its conjugate base, D1-His190, likely renders Y<sub>Z</sub> kinetically and thermodynamically competent leading to highly efficient water oxidation.<sup>1</sup> However, a detailed understanding of PCET at Y<sub>Z</sub> remains elusive due to the transient nature of its intermediate states. In this study, we utilize a combination of high-resolution two-dimensional (2D) <sup>14</sup>N hyperfine sublevel correlation (HYSCORE) spectroscopy and density functional theory (DFT) methods to investigate the electronic structure of a bioinspired artificial photosynthetic reaction center, benzimidazole-phenol porphyrin (BiP–PF<sub>10</sub>), that mimics the PCET process at the Y<sub>Z</sub> residue of PSII. The results of these studies underscore the importance of proximal water molecules and charge delocalization on the electronic structure of the artificial reaction center.</p>


2020 ◽  
Author(s):  
Dalvin D Méndez-Hernández ◽  
Amgalanbaatar Baldansuren ◽  
Vidmantas Kalendra ◽  
Philip Charles ◽  
Brian Mark ◽  
...  

<p>Light-driven water oxidation in algae, cyanobacteria, and higher plants generates dioxygen that supports life on Earth. The water-oxidation reaction is catalyzed by the oxygen-evolving complex (OEC) in photosystem II (PSII) that is comprised of the tetranuclear manganese calcium-oxo (Mn<sub>4</sub>CaO<sub>5</sub>) cluster, with participation of the redox-active tyrosine residue (Y<sub>Z</sub>) and a hydrogen-bonded network of amino acids and water molecules. Y<sub>Z</sub> mediates successive proton-coupled electron transfer (PCET) reactions that are essential for the oxidation of water to dioxygen at the Mn<sub>4</sub>CaO<sub>5</sub> cluster. It has been proposed that the strong hydrogen bond between Y<sub>Z</sub> and and its conjugate base, D1-His190, likely renders Y<sub>Z</sub> kinetically and thermodynamically competent leading to highly efficient water oxidation.<sup>1</sup> However, a detailed understanding of PCET at Y<sub>Z</sub> remains elusive due to the transient nature of its intermediate states. In this study, we utilize a combination of high-resolution two-dimensional (2D) <sup>14</sup>N hyperfine sublevel correlation (HYSCORE) spectroscopy and density functional theory (DFT) methods to investigate the electronic structure of a bioinspired artificial photosynthetic reaction center, benzimidazole-phenol porphyrin (BiP–PF<sub>10</sub>), that mimics the PCET process at the Y<sub>Z</sub> residue of PSII. The results of these studies underscore the importance of proximal water molecules and charge delocalization on the electronic structure of the artificial reaction center.</p>


Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3537 ◽  
Author(s):  
Giovanna Bruno ◽  
Giovanni Macetti ◽  
Leonardo Lo Presti ◽  
Carlo Gatti

Despite its role in spin density functional theory and it being the basic observable for describing and understanding magnetic phenomena, few studies have appeared on the electron spin density subtleties thus far. A systematic full topological analysis of this function is lacking, seemingly in contrast to the blossoming in the last 20 years of many studies on the topological features of other scalar fields of chemical interest. We aim to fill this gap by unveiling the kind of information hidden in the spin density distribution that only its topology can disclose. The significance of the spin density critical points, the 18 different ways in which they can be realized and the peculiar topological constraints on their number and kind, arising from the presence of positive and negative spin density regions, is addressed. The notion of molecular spin graphs, spin maxima (minima) joining paths, spin basins and of their valence is introduced. We show that two kinds of structures are associated with a spin–polarized molecule: the usual one, defined through the electron density gradient, and the magnetic structure, defined through the spin density gradient and composed in general by at least two independent spin graphs, related to spin density maxima and minima. Several descriptors, such as the spin polarization index, are introduced to characterize the properties of spin density critical points and basins. The study on the general features of the spin density topology is followed by the specific example of the water molecule in the 3B1 triplet state, using spin density distributions of increasing accuracy.


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