Nonadiabatic Molecular Dynamics Simulations Research Articles

Temperature Controlled Decay and Pendulum Dynamics of Green Fluorescent Protein (GFP) Chromophore.

The excited-state dynamics of the GFP chromophore, HBDI- (anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone), were investigated through a combination of theoretical nonadiabatic molecular dynamics (NAMD) simulations and femtosecond transient absorption spectroscopy (fs-TA). The NAMD simulations revealed that the primary dynamics in excited states involve the formation of a P-twisted intermediate (S1min,P), which undergoes pendulum-like oscillations with respect to ϕ = 90°. This motion serves as a reservoir for the excited-state population and the primary source of fluorescence. Rather than a direct channel from the major S1min,P, a coordinated pathway of S1min,P → S1min → S1min,I → S0 is responsible for the decay to the ground state, emphasizing the importance of planar intermediate (S1min) formation. The experimental fs-TA spectra confirmed these dynamics, revealing three distinct time scales (340-470 fs, 1.4 ps, and 8.3 ps), corresponding to the formation of S1min,P and its decay governed by the coordinated pathway. At low temperatures, the coordinated decay pathway is suppressed, leading to prolonged fluorescence lifetimes, consistent with low-temperature experimental results. This study presents a new model for the excited-state dynamics of GFP chromophore, suggesting that pendulum motion and the coordinated decay pathway play a crucial role in regulating fluorescence intensity.

Theoretical Insights into Ultrafast Separation of Photogenerated Charges in a Push-Pull Polarized Molecular Triad.

Herein, we propose a purely-organic donor-acceptor (D-A) molecular triad, with a light-absorbing polarized molecular wire (PMW) used as a central linkage, as a proof of concept for the possible future applications of the D-PMW-A arrangement in molecular photovoltaics. This work builds upon our earlier study on the PMW unit itself, which proved to be highly promising for the ultrafast photogeneration of free charge carriers. Quantum-chemical calculations performed for the D-PMW-A triad at a semi-empirical level of theory reveal a large electric dipole moment of the system, and show strong charge-transfer (CT) character of its lowest-energy excited electronic states, including the S1, which favours efficient dissociation of an exciton initially formed upon the absorption of light. The confirmation for this effect was found with nonadiabatic molecular dynamics simulations, revealing an ultrafast relaxation from higher, bright excited states to S1, completed on a subpicosecond timescale. The architecture of the proposed molecular triad enables its electronic coupling to the surrounding environment through chemical bonds, or noncovalent stacking interactions, which might open way for synthesis of a new class of D-PMW-A efficient molecular organic photovoltaic materials.

Photocarrier Dynamics of Two-Dimensional Aza-Fused Covalent Organic Frameworks as Bifunctional Photocatalysts toward Overall Water Splitting.

Designing high-efficiency bifunctional photocatalysts toward photoinduced overall water splitting is one of the most promising and challenging research directions for clean energy generation. By employing static electronic structure calculation and nonadiabatic molecular dynamics (NAMD) simulation, we herein established a recently synthesized two-dimensional (2D) aza-fused covalent organic framework (aza-COF) as a potential bifunctional photocatalyst toward overall water splitting reactions. Our calculated results reveal that the overpotentials for hydrogen evolution reaction and oxygen evolution reaction are only 0.06 and 0.31 V, respectively, at pH = 4. The dynamics of photoexcited charge carriers studied through NAMD simulation predicts the electron-hole recombination time (25.15 ns), and this confirms that the photogenerated electron and hole carriers migrate to the active sites for the occurrence of reaction before they recombine. Therefore, our results suggest that the 2D aza-COFs exhibit great potential as metal-free and single-material photocatalysts toward overall water splitting under visible light.

Self-passivation of Halide Interstitial Defects by Organic Cations in Hybrid Lead-Halide Perovskites: Ab Initio Quantum Dynamics.

Halide interstitial defects severely hinder the optoelectronic performance of metal halide perovskites, making research on their passivation crucial. We demonstrate, using ab initio nonadiabatic molecular dynamics simulations, that hydrogen vacancies (Hv) at both N and C atoms of the methylammonium (MA) cation in MAPbI3 efficiently passivate iodine interstitials (Ii), providing a self-passivation strategy for dealing with the Hv and Ii defects simultaneously. Hv at the N site (Hv-N) introduces a defect state into the valence band, while the state contributed by Hv at the C site (Hv-C) evolves from a shallow level at 0 K to a deep midgap state at ambient temperature, exhibiting a high environmental activity. Both Hv-N and Hv-C are strong Lewis bases, capable of capturing and passivating Ii defects. Hv-C is a stronger Lewis base, bonds with Ii better, and exhibits a more pronounced passivation effect. The charge carrier lifetimes in the passivated systems are significantly longer than in those containing either Hv or Ii, and even in pristine MAPbI3. Our demonstration of the Hv and Ii defect self-passivation in MAPbI3 suggests that systematic control of the relative concentrations of Hv and Ii can simultaneously eliminate both types of defects, thereby minimizing charge and energy losses. The demonstrated defect self-passivation strategy provides a promising means for defect control in organic-inorganic halide perovskites and related materials and deepens our atomistic understanding of defect chemistry and charge carrier dynamics in solar energy and optoelectronic materials.

Suppressed nonradiative electron–hole recombination in bismuth halide perovskite Cs3Bi2Cl9: Time domain ab initio analysis

Time-domain density functional theory, coupled with non-adiabatic molecular dynamics simulations, was employed to explore the defect characteristics and the associated nonradiative recombination processes in the bismuth halide perovskite Cs3Bi2Cl9. Our findings indicate that Cs3Bi2Cl9 inherently exhibits p-type semiconductor behavior, with vacancies at the Cs and Bi sites acting as predominant shallow acceptor defects. Although Cl vacancy and interstitial Cl defects introduce trap states within the bandgap of Cs3Bi2Cl9, the by-defect electron–hole (e-h) recombination is substantially impeded, which is attributed to the remarkable local structural deformations associated with the BiCl63− octahedral compression around the defects, which further results in decoupling between the defect state and the band edge state. As a result, the enhanced delocalization of defect states leads to a notably small wave function overlap between defect states and band edge states, as well as weak nonadiabatic couplings dominated by low-frequency phonons. Our study offers crucial insights into the mechanism of defect-mediated e-h recombination in bismuth-based perovskites and provides guidelines for designing efficient optoelectronic devices based on these materials.

Photoinduced Nonadiabatic Dynamics of a Single-Walled Carbon Nanotube-Porphyrin Complex.

Single-walled carbon nanotubes (SWCNTs) have gained a lot of attention in the past few decades due to their promising optoelectronic properties. In addition, SWCNTs can form complexes that have good chemical stability and transport properties with other optical functional materials through noncovalent interactions. Elucidating the detailed mechanism of these complexes is of great significance for improving their optoelectronic properties. Nevertheless, simulating the photoinduced dynamics of these complexes accurately is rather challenging since they usually contain hundreds of atoms. To save computational efforts, most of the previous works have ignored the excitonic effects by employing nonadiabatic carrier (electron and hole) dynamics simulations. To properly consider the influence of excitonic effects on the photoinduced ultrafast processes of the SWCNT-tetraphenyl porphyrin (H2TPP) complex and to further improve the computational efficiency, we developed the nonadiabatic molecular dynamics (NAMD) method based on the extended tight binding-based simplified Tamm-Dancoff approximation (sTDA-xTB), which is applied to study the ultrafast photoinduced dynamics of the noncovalent SWCNT-porphyrin complex. In combination with statically electronic structure calculations, the present work successfully reveals the detailed microscopic mechanism of the ultrafast excitation energy transfer process of the complex. Upon local excitation on the H2TPP molecule, an ultrafast energy transfer process occurs from H2TPP (SWCNT-H2TPP*) to SWCNT (SWCNT*-H2TPP) within 10 fs. Then, two slower processes corresponding to the energy transfer from H2TPP to SWCNT and hole transfer from H2TPP to SWCNT take place in the 1 ps time scale. The sTDA-xTB-based electronic structure calculation and NAMD simulation results not only match the previous experimental observations from static and transient spectra but also provide more insights into the detailed information on the complex's photoinduced dynamics. Therefore, the sTDA-xTB-based NAMD method is a powerful theoretical tool for studying the ultrafast photoinduced dynamics in large extended systems with a large number of electronically excited states, which could be helpful for the subsequent design of SWCNT-based functional materials.

Catalysis in Extreme Field Environments: A Case Study of Strongly Ionized SiO2 Nanoparticle Surfaces.

High electric fields can significantly alter catalytic environments and the resultant chemical processes. Such fields arise naturally in biological systems but can also be artificially induced through localized nanoscale excitations. Recently, strong field excitation of dielectric nanoparticles has emerged as an avenue for studying catalysis in highly ionized environments, producing extreme electric fields. While the dynamics of laser-driven surface ion emission has been extensively explored, understanding the molecular dynamics leading to fragmentation has remained elusive. Here, we employ a multiscale approach performing nonadiabatic quantum molecular dynamics (NAQMD) simulations on hydrogenated silica surfaces in both bare and wetted environments under field conditions mimicking those of an ionized nanoparticle. Our findings indicate that hole localization drives fragmentation dynamics, leading to surface silanol dissociation within 50 fs and charge transfer-induced water splitting in wetted environments within 150 fs. Further insight into such ultrafast mechanisms is critical for the advancement of catalysis on the surface of charged nanosystems.

Unsupervised Machine Learning in the Analysis of Nonadiabatic Molecular Dynamics Simulation.

The all-atomic full-dimensional-level simulations of nonadiabatic molecular dynamics (NAMD) in large realistic systems has received high research interest in recent years. However, such NAMD simulations normally generate an enormous amount of time-dependent high-dimensional data, leading to a significant challenge in result analyses. Based on unsupervised machine learning (ML) methods, considerable efforts were devoted to developing novel and easy-to-use analysis tools for the identification of photoinduced reaction channels and the comprehensive understanding of complicated molecular motions in NAMD simulations. Here, we tried to survey recent advances in this field, particularly to focus on how to use unsupervised ML methods to analyze the trajectory-based NAMD simulation results. Our purpose is to offer a comprehensive discussion on several essential components of this analysis protocol, including the selection of ML methods, the construction of molecular descriptors, the establishment of analytical frameworks, their advantages and limitations, and persistent challenges.

Positional Isomerism of Aromatic Heterocyclic Spacer Cations in Two-Dimensional Dion-Jacobson Hybrid Perovskites.

Ligand engineering of aromatic heterocyclic cations in two-dimensional (2D) Dion-Jacobson (DJ) perovskites has been widely explored in recent years. In this study, how the positional isomers of aromatic heterocyclic cations tune the lattice of 2D perovskites, thereby influencing the transport and recombination dynamics of charge carriers, has been investigated through nonadiabatic molecular dynamics simulations. We demonstrate that the meta-substituted 3-(aminomethyl)pyridinium (3AMPY) cations greatly reduce the strength of electron-vibration coupling since the strong hydrogen-bonding network introduced by the changes in the arrangement of spacer cations significantly suppresses the structural thermal fluctuations. Compared to the para-substituted 4-(aminomethyl)pyridinium (4AMPY) cation, using the asymmetric 3AMPY as a spacer cation can achieve improved in-plane transport performance, enhanced thermal stability, and suppressed charge carrier recombination through weakening electron-vibration interactions. Our results explain the observed lifetime difference between the two types of DJ-phase perovskites in experiments and provide new guidance for optimizing the performance of perovskite devices.

Enhanced Carrier Lifetime and Mobility in Monolayer NbOI2.

The lifetime and mobility of hot carriers are critical parameters for assessing the performance of optoelectronic materials, as they directly impact the response speed and operational efficiency of devices. Combining first-principles calculations with nonadiabatic molecular dynamics (NAMD) simulations, we systematically investigated the electronic properties and carrier dynamics of monolayer NbOI2. Our findings indicate that, at room temperature, this material demonstrates a carrier lifetime of up to ∼13 ns and an electron mobility reaching as high as ∼9 × 103 cm2 V-1 s-1. The low Young's modulus makes it susceptible to deformation under external stress, and we found that the carrier lifetime extends to ∼40 ns under a 4% tensile strain, along with a significant increase in hole mobility. This study elucidates the carrier dynamics in monolayer NbOI2, facilitating its potential application in future flexible optoelectronic devices.

Photocatalytic overall water splitting Z-schemes for hydrogen production with the X@CTF-0/β-Sb (X = S, Se) heterostructures

The covalent triazine framework (CTF-0) is believed to possess the potential to serve as a photocatalyst for overall water splitting, but its large bandgap constrains the solar-to-hydrogen (STH) efficiency. Here, we demonstrate that the STH efficiency can be boosted by constructing the CTF-0/β-Sb heterostructure and manipulating the band gap by the doped S or Se atoms in the CTF-0 monolayer. The electronic, optical, and thermodynamic properties are calculated to justify the photocatalytic Z-scheme for overall water splitting, and the interlayer transfers of the photogenerated carriers are investigated using non-adiabatic molecular dynamics simulations to understand the photocatalytic activity of the carriers. The electronic properties indicate that the band alignments hold a staggered character and there is a built-in electric field from the β-Sb to the CTF-0 monolayers in the heterostructures, which supports the photogenerated carriers to perform photocatalytic overall water splitting with Z-scheme and STH efficiencies of 13.28 % and 12.17 % can be achieved for the S@CTF-0/β-Sb and Se@CTF-0/β-Sb heterostructures. Moreover, the STH efficiencies remain increasing within 4 % biaxial strains, regardless of the tensile and compressive ones, implying that no need to worry about the effect of the smaller deformations on the photocatalytic performance in the preparation. Nonadiabatic molecular dynamics simulations show that the photocatalytic activities of the photogenerated carriers in the S@CTF-0/β-Sb are better protected in comparison with those in the Se@CTF-0/β-Sb heterostructures. However, the recombination times indicate that the latter can exert a better photocatalytic performance. Therefore, both the S@CTF-0/β-Sb and Se@CTF-0/β-Sb heterostructures are promising candidates for overall water-splitting for hydrogen production.

Polyacid-Modulated Carrier Dynamic Behavior at the Interface of 0D/2D Heterojunctions.

Heterojunctions formed by polyoxometalates and 2D materials draw attention owing to their remarkable photoelectric and catalytic properties. However, the intrinsic mechanisms of polyoxometalates regulating the heterojunction photoelectric properties are unclear. Herein, we constructed two types of heterojunctions by integrating polyoxometalates (Keggin-type H3PW12O40 and Lindqvist-type H2W6O19) on g-C3N4 monolayers, exploring photoexcited carrier dynamics in these heterojunctions by ab initio calculations combined with nonadiabatic molecular dynamics (NAMD) simulations. Our results show that electrons and holes in H3PW12O40 on g-C3N4 monolayers relax within 583 and 760 fs, respectively. The electron-hole recombination occurs at 342 fs, faster than carrier separation, aligning with the behavior of Z-type heterojunctions. Contrarily, the H2W6O19/g-C3N4 heterojunction exhibits the typical characteristics of type II heterojunctions, with a long photogenerated carrier lifetime reaching 652 fs. These findings show tunable band alignment in polyoxometalate-supported systems by modulating polyoxometalate type, influencing hot electron dynamics, and guiding 0D/2D heterojunction design.

Controlling Ultrafast Magnetization Dynamics via Coherent Phonon Excitation in a Ferromagnet Monolayer.

Exploring ultrafast magnetization control in 2D magnets via laser pulses is established, yet the interplay between spin dynamics and the lattice remains underexplored. Utilizing real-time time-dependent density functional theory (rt-TDDFT) coupled with Ehrenfest dynamics and nonadiabatic molecular dynamics (NAMD) simulations, we systematically investigate the laser-induced spin-nuclei dynamics with pre-excited A1g and E2g coherent phonons in the 2D ferromagnet Fe3GeTe2 (FGT) monolayer. Selective pre-excitation of coherent phonons under ultrafast laser irradiation significantly alters the local spin moment of FGT, consequently inducing additional spin loss attributed to the nuclear motion-induced asymmetric interatomic charge transfer. Excited spin-resolved charge undergoes a bidirectional spin-flip between spin-down and spin-up states, characterized by a subtle change in the spin moment within approximately 100 fs, followed by unidirectional spin-flip, which will further contribute to the spin moment loss of FGT within tens of picoseconds. Our results shed light on the coupling of coherent phonons with magnetization dynamics in 2D limit.

Photocatalytic water splitting and charge carrier dynamics of Janus PtSSe/ζ-phosphorene heterostructure

On the basis of first-principles calculations and non-adiabatic molecular dynamics (NAMD) simulations, we explore the photocatalytic water splitting properties of PtSSe/ζ-Phosphorene heterostructure. This heterostructure possess semiconducting nature with high carrier mobility (≈ 103 cm2V− 1s− 1). The calculated high value of electron-hole recombination rate as compared to electron transfer rate and hole transfer rate, establish the Type-II mechanism more favorable for PtSSe/ζ-Phosphorene heterostructure. Further, the calculated value of solar-to-hydrogen (STH) conversion efficiency of PtSSe/ζ-Phosphorene exceeds to 10%, which makes it the potential candidate for commercial production of hydrogen for industrial use. STH conversion efficiency is further tunable on rotating one monolayer over other with specific angles in the heterostructure. Our study demonstrates PtSSe/ζ-Phosphorene heterostructure to be efficient Type II-scheme photocatalyst for water splitting.

Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach.

Unraveling the reaction pathway of photoinduced reactions poses a great challenge owing to its complexity. Recently, graph theory-based machine learning combined with nonadiabatic molecular dynamics (NAMD) has been applied to obtain the global reaction coordinate of the photoisomerization of azobenzene. However, NAMD simulations are computationally expensive as they require calculating the nonadiabatic coupling vectors at each time step. Here, we showed that ab initio molecular dynamics (AIMD) can be used as an alternative to NAMD by choosing an appropriate initial condition for the simulation. We applied our methodology to determine a plausible global reaction coordinate of retinal photoisomerization, which is essential for human vision. On rank-ordering the internal coordinates, based on the mutual information (MI) between the internal coordinates and the HOMO energy, NAMD and AIMD give a similar trend. Our results demonstrate that our AIMD-based machine learning protocol for retinal is 1.5 times faster than that of NAMD to study reaction coordinates.

Arsenene/Ti2CO2 Heterojunction as a Promising Z‐Scheme Photocatalyst for Overall Water Splitting

AbstractIn order to address imminent energy and environmental challenges, photocatalytic water splitting emerges as a promising way for harnessing solar radiation to generate clean chemical energy. 2D arsenene (β‐As) has notable catalytic activity in hydrogen production. Based on first principles calculations and non‐adiabatic molecular dynamics (NAMD) simulations, the β‐As/Ti2CO2 heterojunction is predicted to be a promising Z‐scheme photocatalyst for overall solar water splitting. It has a desirable energy band structure with the valence band maximum of Ti2CO2 and the conduction band minimum of β‐As well below and above the redox potentials of H2O. Both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) can proceed spontaneously under light irradiation. NAMD simulations confirm that it is a Z‐scheme photocatalyst with fast electron–hole combination dynamics. Instead of by intrinsic electric field, such a fast electron–hole combination is driven by a large nonadiabatic coupling. The heterojunction exhibits strong optical absorption in the visible and ultraviolet regions. The estimated solar‐to‐hydrogen (STH) efficiency limit of β‐As/Ti2CO2 reaches 32%, which is the highest among all β‐As based junctions reported in the literature. These results suggest that β‐As/Ti2CO2 is a promising photocatalyst for achieving overall water splitting.

Photoinduced Negative Differential Resistance at a Graphene/Silicon Interface: A Nonadiabatic Quantum Molecular Dynamics Study.

The oscillatory retinal neuron (ORN) is a promising technology for achieving in-sensor cognitive image computing without external power. While its operation is based on photoinduced negative differential resistance (NDR) at a graphene/silicon interface to directly convert the incident optical signal into voltage oscillations, the optoelectronic mechanism of the NDR remains elusive. Here, nonadiabatic quantum molecular dynamics simulations show that the interplay of band alignment and charge transfer rates of photoexcited carriers at varying applied voltages gives rise to NDR at a graphene/silicon interface under illumination. Such intrinsic NDR at an interface, along with extrinsic circuit-level factors, could enable the much needed rational design of desired image computing functionality of ORN devices in the era of ubiquitous AI on edge devices.

Tunable Ultrafast Charge Transfer across Homojunction Interface.

Charge transfer at heterojunction interfaces is a fundamental process that plays a crucial role in modern electronic and photonic devices. The essence of such charge transfer lies in the band offset, making charge transfer uncommon in a homojunction. Recently, sliding ferroelectricity has been proposed and confirmed in two-dimensional van der Waals stacked materials such as bilayer boron nitride. During the sliding of these layers, the band alignment shifts, creating conditions for charge separation at the interface. We employ ab initio nonadiabatic molecular dynamics simulations to elucidate the excited state carrier dynamics in bilayer boron pnictides. We propose that, akin to ferroelectric polarization flipping, the precise modulation of the distribution of excited state carriers can also be reached by sliding. Our results demonstrate that sliding induces a reversal of the frontier orbital distribution on the upper and lower layers, facilitating a robust interlayer carrier transfer. Notably, the interlayer carrier transfer is more pronounced in boron phosphide than in boron nitride, attributed to strong electron scattering in momentum space in boron nitride. We propose this novel method to manipulate carrier distribution and dynamics in a homojunction exhibiting sliding ferroelectricity, in general, paving a new way for developing advanced electronic and photonic devices.

Nonadiabatic Exciton Dynamics and Energy Gradients in the Framework of FMO-LC-TDDFTB.

We introduce a novel methodology for simulating the excited-state dynamics of extensive molecular aggregates in the framework of the long-range corrected time-dependent density-functional tight-binding fragment molecular orbital method (FMO-LC-TDDFTB) combined with the mean-field Ehrenfest method. The electronic structure of the system is described in a quasi-diabatic basis composed of locally excited and charge-transfer states of all fragments. In order to carry out nonadiabatic molecular dynamics simulations, we derive and implement the excited-state gradients of the locally excited and charge-transfer states. Subsequently, the accuracy of the analytical excited-state gradients is evaluated. The applicability to the simulation of exciton transport in organic semiconductors is illustrated on a large cluster of anthracene molecules. Additionally, nonadiabatic molecular dynamics simulations of a model system of benzothieno-benzothiophene molecules highlight the method's utility in studying charge-transfer dynamics in organic materials. Our new methodology will facilitate the investigation of excitonic transfer in extensive biological systems, nanomaterials, and other complex molecular systems consisting of thousands of atoms.

Nonadiabatic Molecular Dynamics Simulations Provide Evidence for Coexistence of Planar and Nonplanar Intramolecular Charge Transfer Structures in Fluorazene.

Fluorazene is a model compound for photoinduced intramolecular charge transfer (ICT) between aromatic moieties. Despite intensive studies, both spectroscopic and theoretical, a complete model of its photophysics is still lacking. Especially controversial is the geometry of its ICT structure, or structures. In order to fill in the gaps in the state of knowledge on this important model system, in the present study I report the results of nonadiabatic molecular dynamics (NAMD) simulations of its photorelaxation process in acetonitrile solution. To afford a direct comparison to spectroscopic data, I use the simulation results as the basis for the calculation of the transient absorption (TA) spectrum. The NAMD simulations provide detailed information on the sequence of events during the excited-state relaxation of the title compound. Following initial photoexcitation into the bright S2 state, the molecule undergoes rapid internal conversion into the S1 state, leading to the locally excited (LE) structure. The LE structure, in turn, undergoes isomerization into a population of ICT structures, with geometries ranging from near-planar to markedly nonplanar. The LE → ICT isomerization reaction is accompanied by the decay of the characteristic excited-state absorption band of the LE structure near 2 eV. The anomalous fluorescence emission band of fluorazene is found to originate mainly from the near-planar ICT structures, in part because they dominate the overall population of ICT structures. Thus, the planar ICT (PICT) model appears to be the most appropriate description of the geometry of the ICT structure of fluorazene.