Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna-Matthews-Olson complex.

A trajectory surface hopping approach, which uses machine learning to speed up the most time-consuming steps, has been adopted to investigate the exciton transfer in light-harvesting systems. The present neural networks achieve high accuracy in predicting both Coulomb couplings and excitation energies. The latter are predicted taking into account the environment of the pigments.

Nonadiabatic Simulation of Exciton Dynamics in Organic Semiconductors Using Neural Network-Based Frenkel Hamiltonian and Gradients.

In this study, we present a multiscale method to simulate the propagation of Frenkel singlet excitons in organic semiconductors (OSCs). The approach uses neural network models to train a Frenkel-type Hamiltonian and its gradient, obtained by the long-range correction version of density functional tight-binding with self-consistent charges. Our models accurately predict site energies, excitonic couplings, and corresponding gradients, essential for the nonadiabatic molecular dynamics simulations.

Theory for nonlinear conductivity switching in semiconducting organic ferroelectrics.

In this work, the ferroelectric and semiconducting properties of the organic semiconducting ferroelectric benzotrithiophene tricarboxamide (BTTTA), and especially their nonlinear coupling, are theoretically investigated. BTTTA is an exponent of a small class of semiconducting organic ferroelectrics for which experiments have established a surprising polarization direction dependence of the bulk conductivity at finite fields. First, molecular dynamics (MD) simulations are used to investigate the occurrence and, under the influence of an external electric field, the inversion of the macroscopic electric dipole that forms along the axis of supramolecular columns of BTTTA.

GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting.

Initiation of development requires differential gene expression and metabolic adaptations. Here we show in the nematode-trapping fungus, Arthrobotrys flagrans, that both are achieved through a dual-function G-protein-coupled receptor (GPCR). A.

Dynamic Effects on Hole Transport in Amorphous Organic Semiconductors: a Combined QM/MM and kMC Study.

Small-molecule-based amorphous organic semiconductors (OSCs) are essential components of organic photovoltaics and organic light-emitting diodes. The charge carrier mobility of these materials is an integral and limiting factor in regard to their performance. Integrated computational models for the hole mobility, taking into account structural disorder in systems of several thousand molecules, have been the object of research in the past.

Correction: Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes.

Correction for 'Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes' by Beatrix M. Bold , , 2020, , 10500-10518, https://doi.org/10.

Disulfide bond reduction and exchange in C4 domain of von Willebrand factor undermines platelet binding.

Background: The von Willebrand factor (VWF) is a key player in regulating hemostasis through adhesion of platelets to sites of vascular injury. It is a large, multi-domain, mechano-sensitive protein that is stabilized by a net of disulfide bridges. Binding to platelet integrin is achieved by the VWF-C4 domain, which exhibits a fixed fold, even under conditions of severe mechanical stress, but only if critical internal disulfide bonds are closed.

Mechanism of proton-coupled electron transfer described with QM/MM implementation of coupled-perturbed density-functional tight-binding.

Coupled-perturbed equations for degenerate orbitals were implemented for third order density-functional tight binding, which allowed the use of Mulliken charges as reaction coordinates. The method was applied to proton-coupled electron transfer (PCET) reactions in a model system and thoroughly tested for QM and QM/MM setups (i.e.

Reduction pathway of glutaredoxin 1 investigated with QM/MM molecular dynamics using a neural network correction.

Glutaredoxins are small enzymes that catalyze the oxidation and reduction of protein disulfide bonds by the thiol-disulfide exchange mechanism. They have either one or two cysteines in their active site, resulting in different catalytic reaction cycles that have been investigated in many experimental studies. However, the exact mechanisms are not yet fully known, and to our knowledge, no theoretical studies have been performed to elucidate the underlying mechanism.

Efficient Surface Hopping Approach for Modeling Charge Transport in Organic Semiconductors.

The trajectory surface hopping (TSH) method is nowadays widely applied to study the charge/exciton transport process in organic semiconductors (OSCs). In the present study, we systematically examine the performance of two approximations in the fewest switched surface hopping (FSSH) simulations for charge transport (CT) in several representative OSCs. These approximations include (i) the substitution of the nuclear velocity scaling along the nonadiabatic coupling vector (NCV) by rescaling the hopping probability with the Boltzmann factor (Boltzmann correction (BC)) and (ii) a phenomenological approach to treat the quantum feedback from the electronic system to the nuclear system (implicit charge relaxation (IR)) in the OSCs.

Understanding excited state properties of host materials in OLEDs: simulation of absorption spectrum of amorphous 4,4-bis(carbazol-9-yl)-2,2-biphenyl (CBP).

4,4-Bis(carbazol-9-yl)-2,2-biphenyl (CBP) is widely used as a host material in phosphorescent organic light-emitting diodes (PhOLEDs). In the present study, we simulate the absorption spectra of CBP in gas and condensed phases, respectively, using the efficient time-dependent long-range corrected tight-binding density functional theory (TD-LC-DFTB). The accuracy of the condensed-phase absorption spectra computed using the structures obtained from classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) simulations is examined by comparison with the experimental absorption spectrum.

Unravelling the mechanism of glucose binding in a protein-based fluorescence probe: molecular dynamics simulation with a tailor-made charge model.

Fluorophores linked to the glucose/galactose-binding protein (GGBP) are a promising class of glucose sensors with potential application in medical devices for diabetes patients. Several different fluorophores at different positions in the protein were tested experimentally so far, but a deeper molecular understanding of their function is still missing. In this work, we use molecular dynamics simulations to investigate the mechanism of glucose binding in the GGBP-Badan triple mutant and make a comparison to the GGBP wild-type protein.

Accurate Free Energies for Complex Condensed-Phase Reactions Using an Artificial Neural Network Corrected DFTB/MM Methodology.

Semiempirical methods like density functional tight-binding (DFTB) allow extensive phase space sampling, making it possible to generate free energy surfaces of complex reactions in condensed-phase environments. Such a high efficiency often comes at the cost of reduced accuracy, which may be improved by developing a specific reaction parametrization (SRP) for the particular molecular system. Thiol-disulfide exchange is a nucleophilic substitution reaction that occurs in a large class of proteins.

HAB79: A new molecular dataset for benchmarking DFT and DFTB electronic couplings against high-level ab initio calculations.

A new molecular dataset called HAB79 is introduced to provide ab initio reference values for electronic couplings (transfer integrals) and to benchmark density functional theory (DFT) and density functional tight-binding (DFTB) calculations. The HAB79 dataset is composed of 79 planar heterocyclic polyaromatic hydrocarbon molecules frequently encountered in organic (opto)electronics, arranged to 921 structurally diverse dimer configurations. We show that CASSCF/NEVPT2 with a minimal active space provides a robust reference method that can be applied to the relatively large molecules of the dataset.

Electrostatic interactions contribute to the control of intramolecular thiol-disulfide isomerization in a protein.

The roles of structural factors and of electrostatic interactions with the environment on the outcome of thiol-disulfide exchange reactions were investigated in a mutated immunoglobulin domain (I27*) under mechanical stress. An extensive ensemble of molecular dynamics trajectories was generated by means of QM/MM simulations for a total sampling of 5.7 μs.

O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism.

Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity.

Interplay of structural dynamics and electronic effects in an engineered assembly of pentacene in a metal-organic framework.

Charge carrier mobility is an important figure of merit to evaluate organic semiconductor (OSC) materials. In aggregated OSCs, this quantity is determined by inter-chromophoric electronic and vibrational coupling. These key parameters sensitively depend on structural properties, including the density of defects.

Geometry dependence of excitonic couplings and the consequences for configuration-space sampling.

Excitonic coupling plays a key role for the understanding of excitonic energy transport (EET) in, for example, organic photovoltaics. However, the calculation of realistic systems is often beyond the applicability range of accurate wavefunction methods so that lower-scaling semi-empirical methods are used to model EET events. In the present work, the distance and angle dependence of excitonic couplings of dimers of selected organic molecules are evaluated for the semi-empirical long-range corrected density functional based tight binding (LC-DFTB) method and spin opposite scaled second order approximate coupled cluster singles and doubles (SOS-CC2).

Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II.

Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged.

Analytical Time-Dependent Long-Range Corrected Density Functional Tight Binding (TD-LC-DFTB) Gradients in DFTB+: Implementation and Benchmark for Excited-State Geometries and Transition Energies.

The absorption and emission of light is a ubiquitous process in chemical and biological processes, making a theoretical description inevitable for understanding and predicting such properties. Although and DFT methods are capable of describing excited states with good accuracy in many cases, the investigation of dynamical processes and the need to sample the phase space in complex systems often requires methods with reduced computational costs but still sufficient accuracy. In the present work, we report the derivation and implementation of analytical nuclear gradients for time-dependent long-range corrected density functional tight binding (TD-LC-DFTB) in the DFTB+ program.

Improvement of d-d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+ model on nickel coordination compounds.

To improve the description of interactions among the localized d, f electrons in transition metals, we have introduced a ligand-field motivated contribution into the Density Functional Tight Binding (DFTB) model. Referred to as DFTB3+U, the approach treats the d, f electron repulsions with rotationally invariant orbital-orbital interactions and a Hartree-Fock model; this represents a major conceptual improvement over the original DFTB3 approach, which treats the d, f-shell interactions in a highly averaged fashion without orbital level of description. The DFTB3+U approach is tested using a series of nickel compounds that feature Ni(ii) and Ni(iii) oxidation states.

DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex.

Because of the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated with a combined quantum-classical description. To this end, Born-Oppenheimer molecular dynamics simulations have been employed in a quantum mechanics/molecular mechanics (QM/MM) fashion for the ground state followed by excitation energy calculations again in a QM/MM scheme for the Fenna-Matthews-Olson (FMO) complex. The self-consistent-charge density functional tight-binding (DFTB) method electrostatically coupled to a classical description of the environment was applied to perform the ground-state dynamics.

Charge and Exciton Transfer Simulations Using Machine-Learned Hamiltonians.

Quantum-mechanical simulations of charge and exciton transfer in molecular organic materials are a key method to increase our understanding of organic semiconductors. Our goal is to build an efficient multiscale model to predict charge-transfer mobilities and exciton diffusion constants from nonadiabatic molecular dynamics simulations and Marcus-based Monte Carlo approaches. In this work, we apply machine learning models to simulate charge and exciton propagation in organic semiconductors.