Simulation Of Electron Dynamics Research Articles

Multistate Reaction Coordinate Model for Charge and Energy Transfer Dynamics in the Condensed Phase.

Constructing multistate model Hamiltonians from all-atom electronic structure calculations and molecular dynamics simulations is crucial for understanding charge and energy transfer dynamics in complex condensed phases. The most popular two-level system model is the spin-boson Hamiltonian, where the nuclear degrees of freedom are represented as shifted normal modes. Recently, we proposed the general multistate nontrivial extension of the spin-boson model, i.e., the multistate harmonic (MSH) model, which is constructed by extending the spatial dimensions of each nuclear mode so as to satisfy the all-atom reorganization energy restrictions for all pairs of electronic states. In this work, we propose the multistate reaction coordinate (MRC) model with a primary reaction coordinate and secondary bath modes as in the Caldeira-Leggett form but in extended spatial dimensions. The MRC model is proven to be equivalent to the MSH model and offers an intuitive physical picture of the nuclear-electronic feedback in nonadiabatic processes such as the inherent trajectory of the reaction coordinate. The reaction coordinate is represented in extended dimensions, carrying the entire reorganization energies and bilinearly coupled to the secondary bath modes. We demonstrate the MRC model construction for photoinduced charge transfer in an organic photovoltaic caroteniod-porphyrin-C60 molecular triad dissolved in tetrahydrofuran as well as excitation energy transfer in a photosynthetic light-harvesting Fenna-Matthews-Olson complex. The MRC model provides an effective and robust platform for investigating quantum dissipative dynamics in complex condensed-phase systems since it allows a consistent description of realistic spectral density, state-dependent system-bath couplings, and heterogeneous environments due to static disorder in reorganization energies.

A multi-GPU implementation of Real-Time Time-Dependent Auxiliary Density Functional Theory for the investigation of nanosystems irradiations

We report a new Multi-GPU (Graphical Processor Unit) implementation of real-time time-dependent Auxiliary Density Functional Theory (DFT) for simulations of attosecond electronic dynamics in molecular systems subjected to strong perturbations. Our code relies on the Kohn-Sham formalism of DFT and has been implemented in the deMon2k Fortran code. We expand single-particle wave functions (i.e molecular orbitals) as linear combinations of Gaussian-type-orbitals centered on atoms. The density matrix propagation is carried out on GPU while the Kohn-Sham potential is operated on CPUs (Central Processor Unit) with the help of variationally fitted densities. We propose a parallelization strategy using the MAGMA/CUDA libraries to calculate the exponential of dense Hermitian matrices entering the mathematical definition of the propagator, here using Taylor expansions. We report performance benchmarks on water droplets and on fullerenes (C50 to C540). They show a clear advantage of GPU over CPU (using the Scalapack library). The benchmarks also show the benefit of using more than one GPU for systems comprised of up to more than 10,000 basis functions. There, a speed-up of almost 40 between pure 40 CPU and four 4 GPU is obtained. Attosecond electron dynamics simulation in molecular systems comprised of several thousands of electrons becomes amenable to routine simulations in our code. We assess the accuracy of the GPU implementation considering various applications, namely, the calculation of extreme UV absorption spectra with non-Hermitian dynamics, the response of C180 to an electric perturbation, and finally the irradiation of a DNA/protein complex by a 0.4 MeV proton. The results demonstrate the robustness of the implementation. This work also paves the way for future even more efficient implementations. Program SummaryProgram title: deMon2k-RT-TDDFTCPC Library link to program files: https://doi.org/10.17632/whwc5zkst5.1Developer's repository link: DOI: 10.5281/zenodo.8301468Licensing provisions: CeCILL Free Software License Agreement v2.1Programming language: FortranExternal routines/libraries: MPI, BLAS/LAPACK, CUDA, MAGMASupplementary material: User manual, installation instructions, test cases. Nature of problem: Electron dynamics within molecular systems is amenable to simulation with Real-Time Time-Dependent Density Functional Theory (RT-TD-DFT). The methodology consists in propagating on the attosecond time scale the single particle electronic wave functions on the underlying Kohn-Sham potential [1,2]. In deMon2k-RT-TDDFT, the propagation is coupled to the Auxiliary DFT framework for fast evaluation of the potential [3]. A remaining computational bottleneck is the matrix exponential calculation of the Hermitian Hamiltonian matrix. This task is achieved in deMon2k via diagolanization or expansions formulas (Taylor, Chebychev or Baker-Campbell-Hausdorff). The operation is cumbersome on central-processor-unit machines for large matrices (e.g. > 5000 × 5000), which corresponds to molecular systems comprising around 2,000 electrons. Alternatives are needed to overcome this bottleneck.Solution method: We propose to carry out the matrix exponentiation on graphical-processor-units thanks to the MAGMA[4]/CUDA libraries. The code permits a drastic reduction of the computational cost, opening the attosecond dynamic simulations of large molecular systems comprised thousands of electrons with controlled accuracy. The method is tested here for Taylor expansions. Additional comments including restrictions and unusual features: The code described in this article opens the realization of RT-TD-ADFT simulations. The code is linked to the Master version 6.1.6 of deMon2k (http://www.demon-software.com), which must be pre-installed by the user.

Tuning ultrafast time-evolution of photo-induced charge-transfer states: A real-time electronic dynamics study in substituted indenotetracene derivatives.

Photo-induced charge transfer (CT) states are pivotal in many technological and biological processes. A deeper knowledge of such states is mandatory for modeling the charge migration dynamics. Real-time time-dependent density functional theory (RT-TD-DFT) electronic dynamics simulations are employed to explicitly observe the electronic density time-evolution upon photo-excitation. Asymmetrically substituted indenotetracene molecules, given their potential application as n-type semiconductors in organic photovoltaic materials, are here investigated. Effects of substituents with different electron-donating characters are analyzed in terms of the overall electronic energy spacing and resulting ultrafast CT dynamics through linear response (LR-)TD-DFT and RT-TD-DFT based approaches. The combination of the computational techniques here employed provided direct access to the electronic density reorganization in time and to its spatial and rational representation in terms of molecular orbital occupation time evolution. Such results can be exploited to design peculiar directional charge dynamics, crucial when photoactive materials are used for light-harvesting applications.

Deep learning model of hiss waves in the plasmasphere and plumes and their effects on radiation belt electrons

Hiss waves play an important role in removing energetic electrons from Earth’s radiation belts by precipitating them into the upper atmosphere. Compared to plasmaspheric hiss that has been studied extensively, the evolution and effects of plume hiss are less understood due to the challenge of obtaining their global observations at high cadence. In this study, we use a neural network approach to model the global evolution of both the total electron density and the hiss wave amplitudes in the plasmasphere and plume. After describing the model development, we apply the model to a storm event that occurred on 14 May 2019 and find that the hiss wave amplitude first increased at dawn and then shifted towards dusk, where it was further excited within a narrow region of high density, namely, a plasmaspheric plume. During the recovery phase of the storm, the plume rotated and wrapped around Earth, while the hiss wave amplitude decayed quickly over the nightside. Moreover, we simulated the overall energetic electron evolution during this storm event, and the simulated flux decay rate agrees well with the observations. By separating the modeled plasmaspheric and plume hiss waves, we quantified the effect of plume hiss on energetic electron dynamics. Our simulation demonstrates that, under relatively quiet geomagnetic conditions, the region with plume hiss can vary from L = 4 to 6 and can account for up to an 80% decrease in electron fluxes at hundreds of keV at L > 4 over 3 days. This study highlights the importance of including the dynamic hiss distribution in future simulations of radiation belt electron dynamics.

Time-dependent equation-of-motion coupled-cluster simulations with a defective Hamiltonian.

Simulations of laser-induced electron dynamics in a molecular system are performed using time-dependent (TD) equation-of-motion (EOM) coupled-cluster (CC) theory. The target system has been chosen to highlight potential shortcomings of truncated TD-EOM-CC methods [represented in this work by TD-EOM-CC with single and double excitations (TD-EOM-CCSD)], where unphysical spectroscopic features can emerge. Specifically, we explore driven resonant electronic excitations in magnesium fluoride in the proximity of an avoided crossing. Near the avoided crossing, the CCSD similarity-transformed Hamiltonian is defective, meaning that it has complex eigenvalues, and oscillator strengths may take on negative values. When an external field is applied to drive transitions to states exhibiting these traits, unphysical dynamics are observed. For example, the stationary states that make up the time-dependent state acquire populations that can be negative, exceed one, or even complex-valued.

Mechanistic photophysics of tellurium-substituted cytosine: Electronic structure calculations and nonadiabatic dynamics simulations.

Previously, the MS-CASPT2 method was performed to study the static and qualitative photophysics of tellurium-substituted cytosine (TeC). To get quantitative information, we used our recently developed QTMF-FSSH dynamics method to simulate the excited-state decay of TeC. The CASSCF method was adopted to reduce the calculation costs, which was confirmed to provide reliable structures and energies as those of MS-CASPT2. A detailed structural analysis showed that only 5% trajectories will hop to the lower triplet or singlet state via the twisted (S2 /S1 /T2 )T intersection, while 67% trajectories will choose the planar intersections of (S2 /S1 /T3 /T2 /T1 )P and (S2 /S1 /T2 /T1 )P but subsequently become twisted in other electronic states. By contrast, ~28% trajectories will maintain in a plane throughout dynamics. Electronic population revealed that the S2 population will ultrafast transfer to the lower triplet or singlet state. Later, the TeC system will populate in the spin-mixed electronic states composed of S1 , T1 and T2 . At the end of 300 fs, most trajectories (~74%) will decay to the ground state and only 17.4% will survive in the triplet states. Our dynamics simulation verified that tellurium substitution will enhance the intersystem crossings, but the very short triplet lifetime (ca. 125 fs) will make TeC a less effective photosensitizer.

Quantum simulation of exact electron dynamics can be more efficient than classical mean-field methods

Quantum algorithms for simulating electronic ground states are slower than popular classical mean-field algorithms such as Hartree–Fock and density functional theory but offer higher accuracy. Accordingly, quantum computers have been predominantly regarded as competitors to only the most accurate and costly classical methods for treating electron correlation. However, here we tighten bounds showing that certain first-quantized quantum algorithms enable exact time evolution of electronic systems with exponentially less space and polynomially fewer operations in basis set size than conventional real-time time-dependent Hartree–Fock and density functional theory. Although the need to sample observables in the quantum algorithm reduces the speedup, we show that one can estimate all elements of the k-particle reduced density matrix with a number of samples scaling only polylogarithmically in basis set size. We also introduce a more efficient quantum algorithm for first-quantized mean-field state preparation that is likely cheaper than the cost of time evolution. We conclude that quantum speedup is most pronounced for finite-temperature simulations and suggest several practically important electron dynamics problems with potential quantum advantage.

Adiabatic extraction of nonlinear optical properties from real-time time-dependent electronic-structure theory.

Real-time simulations of laser-driven electron dynamics contain information about molecular optical properties through all orders in response theory. These properties can be extracted by assuming convergence of the power series expansion of induced electric and magnetic multipole moments. However, the accuracy relative to analytical results from response theory quickly deteriorates for higher-order responses due to the presence of high-frequency oscillations in the induced multipole moment in the time domain. This problem has been ascribed to missing higher-order corrections. We here demonstrate that the deviations are caused by nonadiabatic effects arising from the finite-time ramping from zero to full strength of the external laser field. Three different approaches, two using a ramped wave and one using a pulsed wave, for extracting electrical properties from real-time time-dependent electronic-structure simulations are investigated. The standard linear ramp is compared to a quadratic ramp, which is found to yield highly accurate results for polarizabilities, and first and second hyperpolarizabilities, at roughly half the computational cost. Results for the third hyperpolarizability are presented along with a simple, computable measure of reliability.

Collision Induced Dissociation of Deprotonated Isoxazole and 3-Methyl Isoxazole via Direct Chemical Dynamics Simulations.

Isoxazoles are an important class of organic compounds widely employed in synthesis and drug design. Fragmentation chemistry of the parent isoxazole molecule and its substituents has been the subject of several experimental and theoretical investigations. Collision induced dissociation (CID) of isoxazole and its substituents has been studied experimentally under negative ion conditions. Based on the observed reaction products, dissociation patterns were proposed. In the present work, we studied the dissociation chemistry of deprotonated isoxazole and 3-methyl isoxazole using electronic structure theory calculations and direct chemical dynamics simulations. Various deprotonated isomers of these molecules were activated by collision with an Ar atom, and the ensuing fractionation patterns were studied using on-the-fly classical trajectory simulations at the density functional B3LYP/6-31+G* level of electronic structure theory. A variety of reaction products and pathways were observed, and it was found that a nonstatistical shattering mechanism dominates the CID dynamics of these molecules. Simulation results are compared with experiments, and detailed atomic level dissociation mechanisms are presented.

Nanoscale and Real-Time Nuclear-Electronic Dynamics Simulation Study of Charge Transfer at the Donor-Acceptor Interface in Organic Photovoltaics.

Charge-transfer (CT) processes in donor-acceptor interfaces of organic photovoltaics have been challenging targets for computational chemistry owing to their nanoscale and ultrafast nature. Herein, we report real-time nuclear-electronic dynamics simulations of CT processes in a nanometer-scale donor-acceptor interface model composed of a donor poly(3-hexylthiophene-2,5-diyl) crystal and an acceptor [6,6]-phenyl-C61-butyric acid methyl ester aggregate. The simulations were realized using our original reduced-scaling computational technique, namely, patchwork-approximation-based Ehrenfest dynamics. The results illustrated the CT pathway with atomic resolution, thereby rationalizing the observed excitation-energy dependence of the quantity of CT. Further, nuclear motion, which is affected by the electronic dynamics, was observed to play a significant role in the CT process by modulating molecular orbital energies. The present study suggests that microscopic CT processes strongly depend on local structures of disordered donor-acceptor interfaces as well as coupling between nuclear and electronic dynamics.

Non-negligible roles of charge transfer excitons in ultrafast excitation energy transfer dynamics of a double-walled carbon nanotube.

Herein, we employed a developed linear response time dependent density functional theory-based nonadiabatic dynamics simulation method that explicitly takes into account the excitonic effects to investigate photoinduced excitation energy transfer dynamics of a double-walled carbon nanotube (CNT) model with different excitation energies. The E11 excitation of the outer CNT will generate a local excitation (LE) |out*〉 exciton due to its low energy, which does not induce any charge separation. In contrast, the E11 excitation of the inner CNT can generate four kinds of excitons with the LE exciton |in*〉 dominates. In the 500-fs dynamics simulation, the LE exciton |in*〉 and charge transfer (CT) excitons |out-in+〉 and |out+in-〉 are all gradually converted to the |out*〉 exciton, corresponding to a photoinduced excitation energy transfer, which is consistent with experimental studies. Finally, when the excitation energy is close to the E22 state of the outer CNT (∼1.05eV), a mixed population of different excitons, with the |out*〉 exciton dominated, is generated. Then, photoinduced energy transfer from the outer to inner CNTs occurs in the first 50fs, which is followed by an inner to outer excitation energy transfer that is completed in 400fs. The present work not only sheds important light on the mechanistic details of wavelength-dependent excitation energy transfer of a double-walled CNT model but also demonstrates the roles and importance of CT excitons in photoinduced excitation energy transfer. It also emphasized that explicitly including the excitonic effects in electronic structure calculations and nonadiabatic dynamics simulations is significant for correct understanding/rational design of optoelectronic properties of periodically extended systems.

Excited-state relaxation mechanisms of 2,2'-(1-phenyl-1H-1,2,4-triazole-3,5-diyl)diphenol: single- or double-proton transfer?

Triazole compounds are important organic systems with excellent electronic properties, which have diagnostic potential in the fields of organic electronics and organic photovoltaics. The important photophysical nature of these systems is the transformation between the enol and keto forms after excited-state proton transfer. In this study, the IR vibrational spectrum, ESIPT mechanism, and excited-state decay dynamics of 2,2'-(1-phenyl-1H-1,2,4-triazole-3,5-diyl)diphenol (ExPh) were explored using electronic structure calculations and non-adiabatic dynamics simulations. Two S1/S0 conical intersections with distinct proton transfer (ESIPT-I and ESIPT-II) involved were obtained. The associated two-dimensional S1 minimum-energy potential energy surface indicated that the dynamical roles of these two S1/S0 conical intersections in the S1 excited-state decay were quite different. The ESIPT-I reaction was more favorable to occur than the ESIPT-II process. Our dynamics simulations supported this hypothesis with the whole trajectories decaying to the ground state via the S1S0-1 conical intersection, which involved the ESIPT-I process. The ESIPT-Involved efficient deactivation pathway could be partially responsible for the decrease in fluorescence emission. These results and ESIPT mechanisms are helpful for understanding the decay pathways of similar systems.

Nature of the Ultrafast Interligands Electron Transfers in Dye-Sensitized Solar Cells.

Charge-transfer dynamics and interligand electron transfer (ILET) phenomena play a pivotal role in dye-sensitizers, mostly represented by the Ru-based polypyridyl complexes, for TiO2 and ZnO-based solar cells. Starting from metal-to-ligand charge-transfer (MLCT) excited states, charge dynamics and ILET can influence the overall device efficiency. In this letter, we focus on N34- dye ( [Ru(dcbpy)2(NCS)2]4-, dcbpy = 4,4'-dicarboxy-2,2'-bipyridine) to provide a first direct observation with high time resolution (<20 fs) of the ultrafast electron exchange between bpy-like ligands. ILET is observed in water solution after photoexcitation in the ∼400 nm MLCT band, and assessment of its ultrafast time-scale is here given through a real-time electronic dynamics simulation on the basis of state-of-the-art electronic structure methods. Indirect effects of water at finite temperature are also disentangled by investigating the system in a symmetric gas-phase structure. As main result, remarkably, the ILET mechanism appears to be based upon a purely electronic evolution among the dense, experimentally accessible, MLCT excited states manifold at ∼400 nm, which rules out nuclear-electronic couplings and proves further the importance of the dense electronic manifold in improving the efficiency of dye sensitizers in solar cell devices.

Aggregation of Charge Acceptors on Nanocrystal Surfaces Alters Rates of Photoinduced Electron Transfer.

Semiconductor nanocrystals (NCs) interfaced with molecular ligands that function as charge and energy acceptors are an emerging platform for the design of light-harvesting, photon-upconverting, and photocatalytic materials. However, NC systems explored for these applications often feature high concentrations of bound acceptor ligands, which can lead to ligand-ligand interactions that may alter each system's ability to undergo charge and energy transfer. Here, we demonstrate that aggregation of acceptor ligands impacts the rate of photoinduced NC-to-ligand charge transfer between lead(II) sulfide (PbS) NCs and perylenediimide (PDI) electron acceptors. As the concentration of PDI acceptors is increased, we find the average electron transfer rate from PbS to PDI ligands decreases by nearly an order of magnitude. The electron transfer rate slowdown with increasing PDI concentration correlates strongly with the appearance of PDI aggregates in steady-state absorption spectra. Electronic structure calculations and molecular dynamics (MD) simulations suggest PDI aggregation slows the rate of electron transfer by reducing orbital overlap between PbS charge donors and PDI charge acceptors. While we find aggregation slows electron transfer in this system, the computational models we employ predict ligand aggregation could also be used to speed electron transfer by producing delocalized states that exhibit improved NC-molecule electronic coupling and energy alignment with NC conduction band states. Our results demonstrate that ligand aggregation can alter rates of photoinduced electron transfer between NCs and organic acceptor ligands and should be considered when designing hybrid NC:molecule systems for charge separation.

Extracting Inelastic Scattering Cross Sections for Finite and Aperiodic Materials from Electronic Dynamics Simulations.

Explicit time-dependent electronic structure theory methods are increasingly prevalent in the areas of condensed matter physics and quantum chemistry, with the broad-band optical absorptivity of molecular and small condensed-phase systems nowadays routinely studied with such approaches. In this paper, it is demonstrated that electronic dynamics simulations can similarly be employed to study cross sections for the scattering-induced electronic excitations probed in nonresonant inelastic X-ray scattering and momentum-resolved electron energy loss spectroscopies. A method is put forth for evaluating the electronic dynamic structure factor, which involves the application of a momentum boost-type perturbation and transformation of the resulting reciprocal space density fluctuations into the frequency domain. Good agreement is first demonstrated between the dynamic structure factor extracted from these electronic dynamics simulations and the corresponding transition matrix elements from linear response theory. The method is then applied to some extended (quasi)one-dimensional systems, for which the wave vector becomes a good quantum number in the thermodynamic limit. Finally, the dispersion of many-body excitations in a series of hydrogen-terminated graphene flakes (and twisted bilayers thereof) is investigated to highlight the utility of the presented approach for capturing morphology-dependent effects in the inelastic scattering cross sections of nanostructured and/or noncrystalline materials.

Machine learning for enhanced semiconductor characterization from time-resolved photoluminescence

<h2>Summary</h2> To enhance the accuracy and effectiveness of optoelectronic characterization, Bayesian inference has been applied to the statistical analysis of time-resolved photoluminescence (TRPL) data with large-scale graphics-processing unit (GPU)-based simulations of electron dynamics. A simulated TRPL dataset, derived from a CH₃NH₃PbI_3-xCl_x perovskite absorber, was used as a case study. From a power scan, Bayesian inference extracts values of the (ambipolar) carrier mobility, free-carrier density, radiative recombination rate, and the overall lifetime of the nonradiative recombination processes. Analysis of the experimental TRPL data yields similar parameter values. The independent contributions of bulk and surface recombination can be distinguished via the introduction of an additional sample thickness. Further experiments separate the front and back surface recombination velocities and can distinguish the electron and hole mobilities. Ultimately, Bayesian inference enables a significant increase in the information yield from TRPL measurements.

Optical response of hydrogenated amorphous silicon: investigation with electronic dynamics simulations

Optical response of hydrogenated amorphous silicon: investigation with electronic dynamics simulations

Multiscale Modeling of Ion Dynamics in Memristive Elements

A multiscale computational scheme is proposed for ion dynamics that allows modeling based on primary information—data on the chemical composition of the material and its crystal structure. The scheme includes quantum mechanical and molecular dynamics modeling as well as Monte Carlo simulation of ion and electron dynamics taking into account the real crystal structure. Approbation of the proposed approach is carried out on a silicon oxide memristive element. The results of computational experiments are presented that demonstrate the stages of growth and destruction of a conductive filament under the action of a time-varying voltage.

Synthesis and characterization of a novel colorimetric and fluorometric probe “Turn-on” for the detection of Cu2+ of derivatives rhodamine

A new Rhodamine-based “Turn On” fluorescent probe (E)- 3′,6′-bis(diethylamino)-2-((2,5-dimethoxybenzylidene)amino)spiro[isoindoline-1,9′-xanthen]-3-one (WGB) was synthesized. Results show that WGB is selective for Cu2+ cations, forming a WGB-Cu2+ complex in a 2:1 stoichiometry, confirmed through density functional theory (DFT) electronic structure calculations and reactive molecular dynamics (MD) simulations. Theoretical calculations agreed with the experimental data. The detection limit of WGB-Cu+2 complex is 6.76 × 10-8 M. Preliminary studies employing epifluorescence microscopy demonstrate that Cu2+ can be imaged in neuroblastoma SH-SY5Y cells treated with WGB.

Computational Investigations of Metal-Organic Frameworks as Sorbents for BTEX Removal.

Sequestration of aromatic volatile organic compounds (VOCs) via metal-organic frameworks (MOFs) as sorbents is a viable means of environmental preservation. In this investigation, we shed light on the key features associated with MOFs that govern the selective uptake of a subclass of VOCs containing benzene, toluene, ethylbenzene, and xylenes (BTEX). We investigate, through a multistep computational framework including ab initio electronic structure and classical molecular dynamics simulations, the energetic and dynamical properties associated with BTEX capture in three MOFs: HKUST-1, ZIF-8, and MIL-53. Our work demonstrates the importance of considering both static and dynamical properties upon introduction of guest molecules in such computational investigations. We elucidate the key geometric factors associated with efficient capture of BTEX compounds and highlight possible postsynthetic modifications that can be used to produce next generation sorbents for BTEX capture.