scholarly journals Photoinduced hole hopping through tryptophans in proteins

2021 ◽  
Vol 118 (11) ◽  
pp. e2024627118
Author(s):  
Stanislav Záliš ◽  
Jan Heyda ◽  
Filip Šebesta ◽  
Jay R. Winkler ◽  
Harry B. Gray ◽  
...  
Keyword(s):  
Density Functional ◽  
Theoretical Work ◽  
Solvation Dynamics ◽  
Electron Hole ◽  
Functional Theory ◽  
Strongly Coupled ◽  
Field Fluctuations ◽  
Triplet Excited States ◽  
Experimental Kinetics ◽  
Suitable Technique

Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors controlling hopping speed and efficiency in two modified azurin constructs that include a rhenium(I) sensitizer, Re(His)(CO)3(dmp)+, and one or two tryptophans (W1, W2). Experimental kinetics investigations showed that the two closely spaced (3 to 4 Å) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from CuI to the photoexcited sensitizer. In our theoretical work, we found that time-dependent density-functional theory (TDDFT) quantum mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) trajectories of low-lying triplet excited states of ReI(His)(CO)3(dmp)+–W1(–W2) exhibited crossings between sensitizer-localized (*Re) and charge-separated [ReI(His)(CO)3(dmp•–)/(W1•+ or W2•+)] (CS1 or CS2) states. Our analysis revealed that the distances, angles, and mutual orientations of ET-active cofactors fluctuate in a relatively narrow range in which the cofactors are strongly coupled, enabling adiabatic ET. Water-dominated electrostatic field fluctuations bring *Re and CS1 states to a crossing where *Re(CO)3(dmp)+←W1 ET occurs, and CS1 becomes the lowest triplet state. ET is promoted by solvation dynamics around *Re(CO)3(dmp)+(W1); and CS1 is stabilized by Re(dmp•–)/W1•+ electron/hole interaction and enhanced W1•+ solvation. The second hop, W1•+←W2, is facilitated by water fluctuations near the W1/W2 unit, taking place when the electrostatic potential at W2 drops well below that at W1•+. Insufficient solvation and reorganization around W2 make W1•+←W2 ET endergonic, shifting the equilibrium toward W1•+ and decreasing the charge-separation yield. We suggest that multiscale TDDFT/MM/MD is a suitable technique to model the simultaneous evolution of photogenerated excited-state manifolds.

TIME DEPENDENT DENSITY FUNCTIONAL METHODS AND THEIR APPLICATION TO CHEMICAL PHYSICS

2004 ◽  
Vol 03 (01) ◽  
pp. 117-144 ◽  
Author(s):  
AKIRA YOSHIMORI
Keyword(s):  
Density Functional ◽  
Nonlinear Effects ◽  
Functional Method ◽  
Time Dependent ◽  
Solvation Dynamics ◽  
Chemical Physics ◽  
Functional Theory ◽  
Polar Liquids ◽  
Density Functional Methods ◽  
Functional Methods

This article reviews microscopic development of time dependent functional method and its application to chemical physics. It begins with the formulation of density functional theory. The time dependent extension is discussed after the equilibrium formulation. Its application is explained by solvation dynamics. In addition, it reviews studies of nonlinear effects on polar liquids and simple mixtures.

scholarly journals Structure and Properties of Chained Carbon: Recent Ab Initio Studies

2019 ◽  
Vol 5 (3) ◽  
pp. 56 ◽  
Author(s):  
Buntov ◽  
Zatsepin ◽  
Kitayeva ◽  
Vagapov
Keyword(s):  
Thermal Conduction ◽  
Density Functional ◽  
Theoretical Work ◽  
Static Properties ◽  
Functional Theory ◽  
Carbon Chains ◽  
Current State ◽  
Carbon Structures ◽  
Phonon Spectra ◽  
State Of Research

Carbon chains or carbyne-like structures represent the next generation of 1D materials whose properties can be tuned by the chain length, doping, and the type of termination. Currently inaccessible technology of the macroscopic carbyne synthesis and characterization makes theoretical work especially valuable. The state of the art methods being applied in the field are density functional theory and molecular dynamics. This paper provides a review of the current state of research on modeling linear carbon structures and related materials. We show that even though the “static” properties of carbon chains (mechanical strength, thermal conduction, band gaps, and phonon spectra) are extensively described, there are only a few simulations of the synthesis processes that constitute the next challenge in 1D research.

First-principles study on codoping effect to enhance photocatalytic activity of anatase TiO2

2017 ◽  
Vol 31 (06) ◽  
pp. 1750036
Author(s):  
Yujie Bai ◽  
Qinfang Zhang ◽  
Fubao Zheng ◽  
Yun Yang ◽  
Qiangqiang Meng ◽  
...  
Keyword(s):  
Visible Light ◽  
First Principles ◽  
Electronic Structures ◽  
Density Functional ◽  
Energy Gap ◽  
Density Functional Theory Calculations ◽  
Band Edge ◽  
Electron Hole ◽  
Functional Theory ◽  
Rich Condition

Codopant is an effective approach to modify the bandgap and band edge positions of transition metal oxide. Here, the electronic structures as well as the optical properties of pristine, mono-doped (N/P/Sb) and codoped (Sb, N/P) anatase TiO2 have been systematically investigated based on density functional theory calculations. It is found that mono-doped TiO2 exhibits either unoccupied or partially occupied intermediate state within the energy gap, which promotes the recombination of electron-hole pairs. However, the presence of (Sb, N/P) codopant not only effectively reduces the width of bandgap by introducing delocalized occupied intermediate states, but also adjusts the band edge alignment to enhance the hydrogen evolution activity of TiO2. Moreover, the optical absorption spectrum for (Sb, N/P) codoped TiO2, which is favored under oxygen-rich condition, demonstrates the improvement of its visible light absorption. These findings will promote the potential application of (Sb, N/P) codoped TiO2 photocatalysis for water splitting under visible light irradiation.

scholarly journals A Theoretical Evaluation of the Efficiencies of Metal-Free 1,3,4-Oxadiazole Dye-Sensitized Solar Cells: Insights From Electron-Hole Separation Distance Analysis.

2021 ◽  
Author(s):  
Louis-Charl Coetzee ◽  
Adedapo Adeyinka ◽  
Nomampondo Magwa
Keyword(s):  
Density Functional Theory ◽  
Solar Cells ◽  
Density Functional ◽  
Dye Sensitized Solar Cells ◽  
Separation Distance ◽  
Electron Hole ◽  
Functional Theory ◽  
Metal Free ◽  
Dye Sensitized ◽  
Sensitized Solar Cells

Abstract Herein, some novel metal-free 1,3,4-oxadiazole compounds O1-O7 were evaluated for Photovoltaic properties using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations to determine if they can serve as metal-free organic dyes for the use of dye-sensitized solar cells (DSSCs). To understand the trends in the relative efficiencies of the investigated compounds as dyes in DSSCs, their electron contributions, hole contributions, and electron-hole overlaps for each respective atom and fragment within the molecule were analyzed with a particular focus on the electron densities on the anchoring segments. As transition density matrices (TDM) provide details for the departure of each electron from its corresponding hole during excitations, which results in charge transfer (CT), the charge separation distance (Δr) between the electron and its corresponding hole was studied as well as the degree of electron-hole overlap (Ʌ). The latter, single-point excitation energy of each electron, the percentage electron contribution to the anchoring segments of each compound, the incident-photon-conversion-efficiency (IPCE), charge recombination, light harvesting efficiency (LHE) electron injection (Φinj) and charge collection efficiency (ncollect) were then compared to Δr to determine whether the expected relationships hold. Moreover, parameters such as diffusion constant (Dπ) and electron lifetime (t), amongst others, were also used to describe electron excitation processes. Since IPCE is the key parameter in determining the efficiency, O3 was found to be the best dye due to its highest value.

scholarly journals First Principles Study on Electronic and Optical Properties of Quinary Copper-based Sulfides and Selenides Cu2HgGe(S1-xSex)4

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Pham Dinh Khang ◽  
Vo Duy Dat ◽  
Dang Phuc Toan ◽  
Vu Van Tuan
Keyword(s):  
Optical Properties ◽  
Band Gap ◽  
Density Functional ◽  
Hybrid Functional ◽  
Electron Hole ◽  
Functional Theory ◽  
Electronic And Optical Properties ◽  
Pair Separation ◽  
Electron Hole Pair ◽  
Band Transition

Electronic and optical properties of Cu2HgGe(S1-xSex)4 compounds (x = 0, 0.25, 0.5, 0.75, and 1) were revealed by density functional theory (DFT), in which the Heyd-Scuseria-Ernzerhof hybrid functional was used. Dependence of band gap on the Se constituent in Cu2HgGe(S1-xSex)4 was reported. The substitution of Se element basically cause a slightly lattice expansion and minor change of the band gap. Meanwhile, the overlap of Cu and S/Se states becomes more dense leading to better electron/hole pair separation and inter-band transition of photo-excited electrons. The Cu2HgGe(S0.75Se0.25)4 compound was predicted to be very promising absorber due to the low band gap, high absorption rate, and low reflectivity in the incoming light energy range from 0 eV to 2 eV.    

scholarly journals Graphdiyne based metal atomic catalysts for synthesizing ammonia

2020 ◽  
Author(s):  
Huidi Yu ◽  
Yurui Xue ◽  
Lan Hui ◽  
Chao Zhang ◽  
Yan Fang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electron Transfer ◽  
Density Functional ◽  
Reaction Pathway ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Faradaic Efficiency ◽  
Nitrogen Reduction ◽  
Strongly Coupled ◽  
Neutral Media

Abstract Exploring new catalysts for nitrogen reduction at ambient pressures and temperatures with ultrahigh ammonia (NH3) yield and selectivity is still a giant challenge. In this work, atomic catalysts with separated Pd atoms on graphdiyne (Pd-GDY) have been synthesized and show fascinating electrocatalytic properties for nitrogen reduction. Outstandingly, the catalyst shows the highest average NH3 yield of 4.45 ± 0.30 mgNH3 mgPd−1 h−1, almost tens of orders larger than previously reported ones, and 100% reaction selectivity in neutral media. And Pd-GDY exhibits almost no decreases in the NH3 yield and Faradaic efficiency. Density functional theory calculations show that the reaction pathway prefers to perform at the (Pd, C1, C2) active area due to the strongly coupled (Pd, C1, C2) which elevates the selectivity via enhanced electron-transfer. By adjusting the p-d coupling accurately, the reduction of self-activated nitrogen is promoted by anchoring atom selection, and the side effects are minimized.

Theoretical Study of Structural, Elastic Properties and Phase Transitions of Cu2ZnSnS4

2014 ◽  
Vol 1058 ◽  
pp. 113-117 ◽  
Author(s):  
Yi Feng Zhao ◽  
Zu Ming Liu ◽  
De Cong Li
Keyword(s):  
Phase Transitions ◽  
Elastic Properties ◽  
Density Functional ◽  
Theoretical Work ◽  
Structure Stability ◽  
Ground State Structure ◽  
Preparation Technology ◽  
Functional Theory ◽  
Unstable Phase ◽  
Total Energies

The total energy, the electronic properties, phase transitions, and elastic properties of Cu2ZnSnS4(CZTS) in the three structures are investigated by first-principles calculations based on density functional theory. Results show that the total energies of stannite (ST) and primitive-mixed CuAu (PMCA) structures are higher than that of kesterite-type (KS), and the KS is the ground state structure. Relationships between enthalpy and pressure of the KS, ST and PMCA structure of CZTS are also investigated at 0 K, since the pressure can have profound impacts on the electronic structure, possible phase transitions and structure stability. And results also show that KS structure is always the most stable; ST is the second; and the PMCA structure is the most unstable; phase transitions of three structures could not occur in high pressure. The high ratios of shear modulus to bulk modulus (G/B) indicate that CZTS compounds in three types have ductile behaviors. The Poisson ratios for the three structures are from 0.27 to 0.31, which again proves that all structures of CZTS have better plasticity. The results can increase more hints about further research directions, and these effects can play an important role in future experimental preparation technology and theoretical work of CZTS materials.

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