scholarly journals A hybrid approach to simulation of electron transfer in complex molecular systems

2013 ◽  
Vol 10 (87) ◽  
pp. 20130415 ◽  
Author(s):  
Tomáš Kubař ◽  
Marcus Elstner
Keyword(s):  
Electron Transfer ◽  
Density Functional ◽  
Degrees Of Freedom ◽  
Hybrid Approach ◽  
Theoretical Description ◽  
Model Systems ◽  
Hole Transfer ◽  
Model Calculations ◽  
Hand Model ◽  
Quantum Mechanical Treatment

Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors.

scholarly journals Electron Transfer to CO2 during Adsorption at the Metal | Solution Interface

2019 ◽  
Author(s):  
Michal Bajdich ◽  
Meredith Fields ◽  
Leanne D. Chen ◽  
Robert B. Sandberg ◽  
Karen Chan ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Density Functional ◽  
Degrees Of Freedom ◽  
Adsorption Process ◽  
Density Functional Theory Calculations ◽  
High Rate ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Generalized Gradient Approximation ◽  
Solution Interface

<i>We estimate the rate of electron transfer to CO<sub>2</sub> at the Au(211)|water interface during adsorption in an electrochemical environment under negative potentials. Based on density functional theory calculations at the generalized gradient approximation, hybrid, and GW levels of theory, we find electron transfer to adsorbed *CO<sub>2</sub> to be very facile. This high rate of transfer is estimated by the energy distribution of the adsorbate-induced density of states as well as from the interaction between diabatic states representing neutral and negatively charged CO<sub>2</sub>. Up to 0.54 electrons is transferred to CO<sub>2</sub>, and this charge adiabatically increases with the bending angle to a lower limit of 140°. We conclude that this rate of electron transfer is extremely fast compared to the timescale of the nuclear degrees of freedom, that is, the adsorption process</i><br>

scholarly journals Facile Electron Transfer to CO2 during Adsorption at the Metal | Solution Interface

2019 ◽  
Author(s):  
Joseph Gauthier ◽  
Meredith Fields ◽  
Michal Bajdich ◽  
Leanne D. Chen ◽  
Robert B. Sandberg ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Density Functional ◽  
Degrees Of Freedom ◽  
Adsorption Process ◽  
Density Functional Theory Calculations ◽  
High Rate ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Generalized Gradient Approximation ◽  
Solution Interface

<i>We estimate the rate of electron transfer to CO2 at the Au (211)|water interface during adsorption in an electrochemical environment under reducing potentials. Based on density functional theory calculations at the generalized gradient approximation and hybrid levels of theory, we find electron transfer to adsorbed *CO2 to be very facile. This high rate of transfer is estimated by the energy distribution of the adsorbate-induced density of states as well as from the interaction between diabatic states representing neutral and negatively charged CO2. Up to 0.62 electrons are transferred to CO2, and this charge adiabatically increases with the bending angle to a lower limit of 137°. We conclude that this rate of electron transfer is extremely fast compared to the timescale of the nuclear degrees of freedom, that is, the adsorption process.</i><br>

Wechselwirkungen in Molekülkristallen, 175 [1, 2]. Kristallzüchtung und Strukturbestimmung von {Cäsium-tetraphenylimido- diphosphat}-Aggregaten mit unterschiedlicher lipophiler Umhüllung durch verschiedenartig Methyl-substituierte Phenylringe sowie relativistische DFT-Modellberechnungen zu Cäsium/Cäsium-Wechselwirkungen / Interaction in M olecular Crystals, 175 [1,2]. Crystal Growth and Structure Determination of {Cesium-tetraphenylimidodiphosphate} Aggregates with Differing Lipophilic Wrapping Due to Differently Methyl-Substituted Phenyl Rings, and Relativistic DFT-Model Calculations of Cesium/Cesium Interactions

2001 ◽  
Vol 56 (6) ◽  
pp. 483-511 ◽  
Author(s):  
Hans Bock ◽  
Erik Heigel ◽  
Zdenek Havlas
Keyword(s):  
Density Functional ◽  
Model Systems ◽  
Simplified Model ◽  
Functional Theory ◽  
Model Calculations ◽  
Polymeric Chains ◽  
Phenyl Rings ◽  
Dft Model ◽  
Potential Curves

AbstractIn alkali-tetraphenylimidodiphosphate ion aggregates, the size of the cation determines the curvature of the ligand and, therefore, whether hexameric ellipsoidal clusters or polymeric chains are formed. To further characterize the ligand spatial requirements, the phenyl rings have been methylsubstituted in 4-, 3/5-, 3/4- or 2,3-positions, their conformations structurally analyzed and correlated with the van der Waals substituent profiles. In addition, relativistic density functional theory potential curves have been calculated for the Cs⊕ ··· Cs⊕interactions in simplified model systems.

scholarly journals Ultrafast electron and hole transfer in bulk heterojunctions of low-bandgap polymers

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Oleg V. Kozlov ◽  
Vlad G. Pavelyev ◽  
Hilde D. de Gier ◽  
Remco W. A. Havenith ◽  
Paul H.M. van Loosdrecht ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Energy Level ◽  
Charge Separation ◽  
Density Functional ◽  
Free Charge ◽  
Charge Generation ◽  
Hole Transfer ◽  
Low Bandgap ◽  
Transfer Processes ◽  
Energy Level Alignment

AbstractIn modern bulk heterojunction (BHJ) organic solar cells, blends of low-bandgap polymer and [70]PCBM acceptor are used in the active layer. In this combination, the polymer absorbs photons from the red and near-IR parts of the solar spectrum, while the blue and near-UV photons are harvested by [70]PCBM. As a result, both electron transfer from polymer to [70]PCBM and hole transfer from [70]PCBM to polymer are of utmost importance in free charge generation and have to be optimized simultaneously. Here we study electron and hole transfer processes in BHJ blends of two low-bandgap polymers, BTT-DPP and PCPDTBT, by ultrafast photoinduced spectroscopy (PIA). By tracking the PIA dynamics, we observed substantially different charge separation pathways in BHJs of the two polymers with [70]PCBM. From the photoinduced anisotropy dynamics, we demonstrated that in the PCPDTBT:[70]PCBM system both electron and hole transfer processes are highly efficient, while in the BTTBPP:[ 70]PCBM electron transfer is blocked due to the unfortunate energy level alignment leaving hole transfer the only pathway to free charge generation. Calculations at the density functional theory level are used to gain more insight into our findings. The presented results highlight the importance of the energy level alignment on the charge separation process.

scholarly journals Effects of co-adsorption on interfacial charge transfer in a quantum dot@dye composite

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Peng Cui ◽  
Yuan Xue
Keyword(s):  
Electron Transfer ◽  
Charge Transfer ◽  
Quantum Dot ◽  
Charge Separation ◽  
Density Functional ◽  
Co Adsorption ◽  
Hole Transfer ◽  
Interfacial Charge Transfer ◽  
Efficient Charge ◽  
Interfacial Charge

AbstractThe sensitive electronic environment at the quantum dot (QD)–dye interface becomes a roadblock to enhancing the energy conversion efficiency of dye-functionalized quantum dots (QDs). Energy alignments and electronic couplings are the critical factors governing the directions and rates of different charge transfer pathways at the interface, which are tunable by changing the specific linkage groups that connect a dye to the QD surface. The variation of specific anchors changes the binding configurations of a dye on the QD surface. In addition, the presence of a co-adsorbent changes the dipole–dipole and electronic interactions between a QD and a dye, resulting in different electronic environments at the interface. In the present work, we performed density functional theory (DFT)-based calculations to study the different binding configurations of N719 dye on the surface of a Cd33Se33 QD with a co-adsorbent D131 dye. The results revealed that the electronic couplings for electron transfer were greater than for hole transfer when the structure involved isocyanate groups as anchors. Such strong electronic couplings significantly stabilize the occupied states of the dye, pushing them deep inside the valence band of the QD and making hole transfer in these structures thermodynamically unfavourable. When carboxylates were involved as anchors, the electronic couplings for hole transfer were comparable to electron transfer, implying efficient charge separation at the QD–dye interface and reduced electron–hole recombination within the QD. We also found that the electronic couplings for electron transfer were larger than those for back electron transfer, suggesting efficient charge separation in photoexcited QDs. Overall, the current computational study reveals some fundamental aspects of the relationship between the interfacial charge transfer for QD@dye composites and their morphologies which benefit the design of QD-based nanomaterials for photovoltaic applications.

scholarly journals Facile Electron Transfer to CO2 during Adsorption at the Metal | Solution Interface

2019 ◽  
Author(s):  
Joseph Gauthier ◽  
Meredith Fields ◽  
Michal Bajdich ◽  
Leanne D. Chen ◽  
Robert B. Sandberg ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Density Functional ◽  
Degrees Of Freedom ◽  
Adsorption Process ◽  
Density Functional Theory Calculations ◽  
High Rate ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Generalized Gradient Approximation ◽  
Solution Interface

<i>We estimate the rate of electron transfer to CO2 at the Au (211)|water interface during adsorption in an electrochemical environment under reducing potentials. Based on density functional theory calculations at the generalized gradient approximation and hybrid levels of theory, we find electron transfer to adsorbed *CO2 to be very facile. This high rate of transfer is estimated by the energy distribution of the adsorbate-induced density of states as well as from the interaction between diabatic states representing neutral and negatively charged CO2. Up to 0.62 electrons are transferred to CO2, and this charge adiabatically increases with the bending angle to a lower limit of 137°. We conclude that this rate of electron transfer is extremely fast compared to the timescale of the nuclear degrees of freedom, that is, the adsorption process.</i><br>

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

Excitonic Coupled-cluster Theory: Part I, General Formalism

2017 ◽  
Author(s):  
Yuhong Liu ◽  
Anthony Dutoi
Keyword(s):  
Electron Correlation ◽  
Degrees Of Freedom ◽  
Model Systems ◽  
Coupled Cluster ◽  
Effective Hamiltonian ◽  
Coupled Cluster Theory ◽  
Cluster Theory ◽  
Companion Article ◽  
High Level ◽  
Fragment Interaction

<div> <div>A shortcoming of presently available fragment-based methods is that electron correlation (if included) is described at the level of individual electrons, resulting in many redundant evaluations of the electronic relaxations associated with any given fluctuation. A generalized variant of coupled-cluster (CC) theory is described, wherein the degrees of freedom are fluctuations of fragments between internally correlated states. The effects of intra-fragment correlation on the inter-fragment interaction is pre-computed and permanently folded into the effective Hamiltonian. This article provides a high-level description of the CC variant, establishing some useful notation, and it demonstrates the advantage of the proposed paradigm numerically on model systems. A companion article shows that the electronic Hamiltonian of real systems may always be cast in the form demanded. This framework opens a promising path to build finely tunable systematically improvable methods to capture precise properties of systems interacting with a large number of other systems. </div> </div>

Excitonic Coupled-cluster Theory: Part I, General Formalism

2017 ◽  
Author(s):  
Yuhong Liu ◽  
Anthony Dutoi
Keyword(s):  
Electron Correlation ◽  
Degrees Of Freedom ◽  
Model Systems ◽  
Coupled Cluster ◽  
Effective Hamiltonian ◽  
Coupled Cluster Theory ◽  
Cluster Theory ◽  
Companion Article ◽  
High Level ◽  
Fragment Interaction

<div> <div>A shortcoming of presently available fragment-based methods is that electron correlation (if included) is described at the level of individual electrons, resulting in many redundant evaluations of the electronic relaxations associated with any given fluctuation. A generalized variant of coupled-cluster (CC) theory is described, wherein the degrees of freedom are fluctuations of fragments between internally correlated states. The effects of intra-fragment correlation on the inter-fragment interaction is pre-computed and permanently folded into the effective Hamiltonian. This article provides a high-level description of the CC variant, establishing some useful notation, and it demonstrates the advantage of the proposed paradigm numerically on model systems. A companion article shows that the electronic Hamiltonian of real systems may always be cast in the form demanded. This framework opens a promising path to build finely tunable systematically improvable methods to capture precise properties of systems interacting with a large number of other systems. </div> </div>

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