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Ab initio molecular dynamics calculations on non-stoichiometric QDs reveal that dynamic Se atoms influences optical modes and HOMO fluctuations to the greatest extent, thereby weaking photoluminescence in Se-rich QDs compared to Cd-rich QDs.
Temporal modulation of the quantum vacuum through fast motion of a neutral body or fast changes of its optical properties is known to promote virtual into real photons, the so-called dynamical Casimir effect. Empowering modulation protocols with spatial control could enable the shaping of spectral, spatial, spin, and entanglement properties of the emitted photon pairs. Space–time quantum metasurfaces have been proposed as a platform to realize this physics via modulation of their optical properties. Here, we report the mechanical analog of this phenomenon by considering systems in which the lattice structure undergoes modulation in space and in time. We develop a microscopic theory that applies both to moving mirrors with a modulated surface profile and atomic array meta-mirrors with perturbed lattice configuration. Spatiotemporal modulation enables motion-induced generation of co- and cross-polarized photon pairs that feature frequency-linear momentum entanglement as well as vortex photon pairs featuring frequency-angular momentum entanglement. The proposed space–time dynamical Casimir effect can be interpreted as induced dynamical asymmetry in the quantum vacuum.
Machine-learning potentials (MLPs) trained on data from quantum-mechanics based first-principles methods can approach the accuracy of the reference method at a fraction of the computational cost. To facilitate efficient MLP-based molecular dynamics and Monte Carlo simulations, an integration of the MLPs with sampling software is needed. Here, we develop two interfaces that link the atomic energy network (ænet) MLP package with the popular sampling packages TINKER and LAMMPS. The three packages, ænet, TINKER, and LAMMPS, are free and open-source software that enable, in combination, accurate simulations of large and complex systems with low computational cost that scales linearly with the number of atoms. Scaling tests show that the parallel efficiency of the ænet–TINKER interface is nearly optimal but is limited to shared-memory systems. The ænet–LAMMPS interface achieves excellent parallel efficiency on highly parallel distributed memory systems and benefits from the highly optimized neighbor list implemented in LAMMPS. We demonstrate the utility of the two MLP interfaces for two relevant example applications: the investigation of diffusion phenomena in liquid water and the equilibration of nanostructured amorphous battery materials.
We review the properties that have been predicted for MXenes and MXene analogs from computational simulation with a focus on structural and electronic properties, energy storage, and ion transport. Methods considered range from quantum mechanical approaches to classical molecular dynamics. We conclude by reviewing current limitations and outstanding questions for simulation and MXene properties that have been little explored to-date.
Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.
Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.
Electronically non-adiabatic effects play an important role in many chemical reactions. However, how these effects manifest in cold and ultracold chemistry remains largely unexplored. Here for the first time we present from first principles the non-adiabatic quantum dynamics of the reactive scattering between ultracold alkali-metal LiNa molecules and Li atoms. We show that non-adiabatic dynamics induces quantum interference effects that dramatically alter the ultracold rotationally resolved reaction rate coefficients. The interference effect arises from the conical intersection between the ground and an excited electronic state that is energetically accessible even for ultracold collisions. These unique interference effects might be exploited for quantum control applications such as a quantum molecular switch. The non-adiabatic dynamics are based on full-dimensional ab initio potential energy surfaces for the two electronic states that includes the non-adiabatic couplings and an accurate treatment of the long-range interactions. A statistical analysis of rotational populations of the Li2 product reveals a Poisson distribution implying the underlying classical dynamics are chaotic. The Poisson distribution is robust and amenable to experimental verification and appears to be a universal property of ultracold reactions involving alkali metal dimers.
We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.
Graphitic carbon nitride (GCN) has attracted significant attention due to its excellent performance in photocatalytic applications. Non-metal doping of GCN has been widely used to improve the efficiency of the material as a photocatalyst. Using a combination of time-domain density functional theory with nonadiabatic molecular dynamics, we study the charge carrier dynamics in oxygen and boron doped GCN systems. The reported simulations provide a detailed time-domain mechanistic description of the charge separation and recombination processes that are of fundamental importance while evaluating the photovoltaic and photocatalytic performance of the material. The appearance of smaller energy gaps due to the presence of dopant states improves the visible light absorption range of the doped systems. At the same time, the nonradiative lifetimes are shortened in the doped systems as compared to the pristine GCN. In the case of boron doped at a carbon (B–C–GCN), the charge recombination time is very long as compared to the other two doped systems owing to the smaller electron–phonon coupling strength between the valence band maximum and the trap state. The results suggest B–C–GCN as the most suitable candidate among three doped systems studied in this work for applications in photocatalysis. Finally, this work sheds light into the influence of dopants on quantum dynamics processes that govern GCN performance and, thus, guides toward building high-performance devices in photocatalysis.
Triplet-triplet annihilation (TTA) enables photon upconversion by combining two lower-energy triplet excitons to produce a higher-energy singlet exciton. This mechanism enhances light-harvesting efficiency for solar energy conversion and enables the use of lower-energy photons in bioimaging and photoredox catalysis applications. The magnetic modulation of such high-energy excitons presents an exciting opportunity to develop molecular quantum information technologies. While the spin dynamics of triplet exciton pairs are sensitive to external magnetic fields, the magnetic field effects (MFEs) associated with these pairs are generally limited by spin statistics to at most 10% at low fields (<1 Tesla), making them challenging to apply in technological advancements. In contrast, MFEs on spin-correlated radical pairs (SCRPs) can be significantly greater, surpassing those on triplet pairs. By using SCRPs-based molecular qubits as triplet sensitizers in the sensitized TTA scheme, we can magnetically modulate TTA and consequently, the delayed fluorescence of annihilators. In our current system, we have achieved more than 70% magnetic modulation of delayed fluorescence, effectively harnessing and even amplifying magnetic modulation within SCRPs to influence high-energy excitons. In conclusion, this work opens new opportunities for advancing spin-controlled chemical reactions and molecular quantum information technologies.
The nature of solid phases and cross-over of order–disorder phase transitions from two-dimensional (2D) layers to three-dimensional (3D) bulk in confined atomic systems remain largely unexplained. To this end, we consider noble gases and aluminum confined between graphene sheets at different pressures and temperatures. Using crystal structure search methods and molecular dynamics based on machine-learned potentials with quantum-mechanical accuracy, we identify structures of multilayer confined solids that deviate from simple close packing. Upon heating, we find that confined 2D monolayers melt according to the two-step continuous Kosterlitz–Thouless–Halperin–Nelson–Young theory. However, multilayer solids transition continuously into an intermediate layered-hexatic phase before melting discontinuously into an isotropic liquid. This intermediate phase persists at least up to 12 layers studied here. This change can be qualitatively understood based on the cross-over from 2D topological defects toward 3D ones during melting as the number of layers increases.
Advances in coherent light sources and development of pump–probe techniques in recent decades have opened the way to study electronic motion in its natural time scale. When an ultrashort laser pulse interacts with a molecular target, a coherent superposition of electronic states is created and the triggered electron dynamics is coupled to the nuclear motion. A natural and computationally efficient choice to simulate this correlated dynamics is a trajectory-based method where the quantum-mechanical electronic evolution is coupled to a classical-like nuclear dynamics. These methods must approximate the initial correlated electron–nuclear state by associating an initial electronic wavefunction to each classical trajectory in the ensemble. Different possibilities exist that reproduce the initial populations of the exact molecular wavefunction when represented in a basis. We show that different choices yield different dynamics and explore the effect of this choice in Ehrenfest, surface hopping, and exact-factorization-based coupled-trajectory schemes in a one-dimensional two-electronic-state model system that can be solved numerically exactly. Furthermore, this work aims to clarify the problems that standard trajectory-based techniques might have when a coherent superposition of electronic states is created to initialize the dynamics, to discuss what properties and observables are affected by different choices of electronic initial conditions and to point out the importance of quantum-momentum-induced electronic transitions in coupled-trajectory schemes.
Abstract The double photoionization of a molecule by one photon ejects two electrons and typically creates an unstable dication. Observing the subsequent fragmentation products in coincidence can reveal a surprisingly detailed picture of the dynamics. Determining the time evolution and quantum mechanical states involved leads to deeper understanding of molecular dynamics. Here in a combined experimental and theoretical study, we unambiguously separate the sequential breakup via D + + OD + intermediates, from other processes leading to the same D + + D + + O final products of double ionization of water by a single photon. Moreover, we experimentally identify, separate, and follow step by step, two pathways involving the b 1 Σ + and a 1 Δ electronic states of the intermediate OD + ion. Our classical trajectory calculations on the relevant potential energy surfaces reproduce well the measured data and, combined with the experiment, enable the determination of the internal energy and angular momentum distribution of the OD + intermediate.
Significance Monitoring the real-space motion of the electrons directly involved in ultrafast molecular dynamics is a challenging goal, hindered by the strong contributions of the remaining inactive electrons. Molecular quantum coherences can provide a direct window into elementary electronic dynamics, but they could not be separately imaged so far. Here, we demonstrate a time- and frequency-resolved X-ray diffraction technique, which can employ existing stochastic X-ray pulses to separately image the coherence contributions. The technique can selectively follow the relevant electrons involved in the ultrafast dynamics and identify the confined molecular regions covered by their motion. It enables readily feasible measurements and can be straightforwardly extended to full three-dimensional imaging via X-ray and electron diffraction.
Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.
Diamond is a promising material for multiple applications in quantum information processing and sensing as well as applications in microelectronics. However, diamond devices can be limited by surface defects that compromise charge stability and spin coherence, among others. Improved strategies in plasma etching of diamond could play an important role in minimizing or eliminating these defects. In this work, we explore plasma-assisted atomic scale etching of diamond using argon ions (Ar + ), hydrogen ions (H + ) and hydrogen atoms (H). We employ classical molecular dynamics (MD) simulations and test several interatomic potentials based on the Reactive Empirical Bond Order (REBO) form with comparisons to a variety of published experimental results. We performed MD simulations of low-energy hydrogen ($\leqslant$50 eV) and argon ( $\leqslant$200 eV) ion bombardment of diamond surfaces. Ar + bombardment can be used to locally smooth initially rough diamond surfaces via the formation of an amorphous C layer, the thickness of which increases with argon ion energy. Subsequent exposure with hydrogen ions (or fast neutrals) will selectively etch this amorphous C layer, leaving the underlying diamond layer mostly intact if the H energy is maintained below about 10 eV. The simulations suggest that combining Ar + smoothing with selective, near threshold energy H removal of amorphous C can be an effective strategy for diamond surface engineering, leading to more reliable and sensitive diamond color center devices.
When the interaction between a molecular system and confined light modes in an optical or plasmonic cavity is strong enough to overcome the dissipative process, hybrid light-matter states (polaritons) become the fundamental excitations in the system. The mixing between the light and matter characters modifies the photophysical and photochemical properties. Notably, it was reported that these polaritons can be employed to control photochemical reactions, charge and energy transfer, and other processes. In addition, according to recent studies, vibrational strong coupling can be employed to resonantly enhance the thermally-activated chemical reactions. In this work, a theoretical model and an efficient numerical method for studying the dynamics of molecules strongly interacting with quantum light are developed based on nonadiabatic excited-state molecular dynamics. The methodology was employed to study the cis-trans photoisomerization of a realistic molecule in a cavity. Numerical simulations demonstrate that the photochemical reactions can be controlled by tuning the properties of the cavity. In the calculated example, the isomerization is suppressed when polaritonic states develop a local minimum on the lower polaritonic state. Moreover, the observed reduction of isomerization is tunable via the photon energy and light-molecule coupling strength. However, the fluctuation in the transition dipole screens the effect of light-matter, which makes it harder to tune the photochemical properties via the coupling strength. These insights gained from this study suggest quantum control of photochemical reactions is possible by specially designed photonic or plasmonic cavities.