Journal of Chemical Physics最新文献

Quantum-mechanical descriptions of luminescence, excitation energy transfer, and resonant dipole-dipole interactions are usually formulated in terms of transition dipoles from the 1-particle density matrix. However, transition dipoles cannot adequately capture the retardation and polariton effects for large entities. A previous study [M.-W. Lee and L.-Y. Hsu, Phys. Rev. A, 107, 053709 (2023)] showed that based on macroscopic quantum electrodynamics, the transition-current-density (TCD) approach not only enables the description of retardation effects but also accounts for the polariton effects arising from material structures and vacuum electromagnetic fields. Nevertheless, the quality of transition currents derived from ab initio calculations remains largely unexplored. In this study, we examine the numerical equivalence between transition dipoles derived from transition charge densities and those from TCDs for 1- and 2-electron systems, including H2+, HeH+, and H2. We further examine the continuity equation ∇ · Jnm = -iωnmρnm by comparing the transition charge density (ρnm) and the divergence of TCD (Jnm), for a transition between states n and m. Despite close agreement of transition dipole moments, we find substantial violations of the continuity equation. The deviations manifest as spurious oscillations in ∇ · Jnm due to the artifacts from the second-derivative features of the underlying Gaussian-type orbitals. To overcome this issue, we implement a reciprocal-space filtering technique that suppresses these non-physical oscillations, improving physical consistency for the TCD. Our study provides practical considerations for future calculations that require reliable transition currents.

Excited-state methods within the nuclear-electronic orbital (NEO) framework have the potential to capture vibrational, electronic, and vibronic transitions in a single calculation. In the NEO approach, specified nuclei, typically protons, are treated quantum mechanically at the same level of theory as the electrons. Affordable excited-state NEO methods, such as time-dependent density functional theory, are limited to capturing the subset of excitations with single-excitation character, whereas existing methods that capture the full spectrum are limited in applicability due to their high computational cost. Herein, we introduce the excited-state variant of NEO coupled cluster with approximate second-order doubles (NEO-CC2) and its scaled-opposite-spin variant with electron-proton correlation scaling (NEO-SOS'-CC2). We benchmark this method for positronium hydride, where the electrons and positron are treated quantum mechanically, and find that NEO-CC2 deviates from exact results, but NEO-SOS'-CC2 can achieve near-quantitative accuracy by increasing the electron-positron correlation. Benchmarking NEO-CC2 and NEO-SOS'-CC2 on four different triatomic molecules with a quantum proton, we find that NEO-CC2 captures qualitatively correct vibrational features such as overtones and combination bands, as well as mixed electron-proton double excitations. Electron-proton correlation scaling that increases the excited-state correlation relative to the ground-state correlation improves the accuracy across all the molecular systems tested. Quantitative accuracy is not achieved due to a combination of finite basis set effects and incomplete description of excited-state electron-proton correlation. Nevertheless, NEO-SOS'-CC2 can describe single and mixed protonic and electronic excitations with accuracy approaching that of much more computationally intensive methods.

Density functional theory (DFT) has transformed our ability to investigate and understand electronic ground states. In its original formulation, however, DFT is not suited to addressing (e.g.) degenerate ground states, mixed states with different particle numbers, or excited states. All these issues can be handled, in principle exactly, via ensemble DFT (EDFT). This Perspective provides a detailed introduction to and analysis of EDFT, in an in-principle exact framework that is constructed to avoid uncontrolled errors and inconsistencies that may be associated with ad hoc extensions of conventional DFT. In particular, it focuses on the "ensemblization" of both exact and approximate density functionals, a term that we coined to describe a rigorous approach that lends itself to the construction of novel approximations consistent with the general ensemble framework, yet applicable to practical problems where traditional DFT tends to fail or does not apply at all. In particular, symmetry considerations and ensemble properties are shown to enable each other in shaping a practical DFT-based methodology that extends beyond the ground state and, in doing so, highlights the need to look outside the standard ground state Kohn-Sham treatment.

The oxidative modification of tryptophan and tyrosine residues in proteins has been strongly associated with the onset and progression of neurodegenerative disorders, such as Alzheimer's disease and amyotrophic lateral sclerosis. Consequently, the identification of small molecules capable of repairing these oxidized residues is of considerable medicinal interest. In this study, the antioxidant activity of four hydroxy-2-pyridones against tyrosyl and tryptophanyl radicals was investigated in silico using density functional theory, with the aim of elucidating their structure-activity relationships at the molecular level. Thermochemical analyses were conducted to evaluate the most favorable repair pathways, focusing on formal hydrogen transfer (FHT) and single electron transfer (SET) processes. For exergonic reactions, kinetic parameters were determined within the quantum mechanics-based overall free radical scavenging activity (QM-ORSA) protocol, providing predictive data on radical-scavenging efficiency. The results indicate that three of the tested pyridones can repair the tyrosyl radical and that two of them react at rates comparable with the dityrosine formation, thereby competing with this deleterious pathway. In contrast, all four pyridones are able to reduce the tryptophanyl radical, although the calculated kinetics suggest that they may not efficiently suppress the Trp-Trp cross-linking in small peptides. Mechanistic analysis further revealed that FHT proceeds through proton-coupled electron transfer for tyrosyl radical repair, whereas tryptophanyl radical repair involves a proton-electron sequential transfer mechanism. These findings establish hydroxy-2-pyridones as promising scaffolds for the rational design of neuroprotective antioxidants and provide molecular insights that may guide the development of new therapeutic agents targeting oxidative stress.

Active matter swarms-collectives of self-propelled particles that can self-assemble, ferry microscopic cargo, or endow materials with dynamic properties-remain hard to steer. In crowded systems, tracking or controlling individual agents becomes challenging, so strategies must operate on macroscopic fields like particle density. Yet predicting how density evolves is difficult because of inter-agent interactions. For model-based feedback control methods-such as Model Predictive Control (MPC)-fast, accurate, and differentiable models are crucial. Detailed agent-based simulations are too slow, necessitating coarse-grained continuum models. However, constructing accurate closures-approximations that express the effects of unresolved microscopic states (e.g., agent positions) on continuum dynamics in terms of the modeled continuum fields (e.g., density)-is challenging for active matter swarms. We present a learning-for-control framework that learns continuum closures from agent simulations, demonstrated with active Brownian particles under a controllable external field. Our Universal Differential Equation (UDE) framework represents the continuum as an advection-diffusion equation. A neural operator learns the advection term, providing closure relations for microscopic effects such as self-propulsion, interactions, and external-field responses. This UDE approach, embedding universal function approximators in differential equations, ensures adherence to physical laws (e.g., conservation) while learning complex dynamics directly from data. We embed this learned continuum model into MPC for precise agent-simulation control. We demonstrate this framework's capabilities by dynamically exchanging particle densities between two groups and by simultaneously controlling particle density and mean flux to follow a prescribed sinusoidal profile. These results highlight the framework's potential to control complex active-matter dynamics, foundational for programmable materials.

The co-assembly of multiple nanoparticles ("fragmented cargo") and virus coat proteins is very sensitive both to the size of the nanocolloids and the stoichiometric ratio of nanoparticles to coat proteins, as recent experiments demonstrate. In addition, in a head-to-head competition, larger nanoparticles turn out to be preferentially encapsulated. In order to rationalize these findings, we investigate a simple mass-action model in which we allow for the co-existence of free nanoparticles and coat proteins, complexes consisting of a nanocolloid bound to a coat protein, and fully formed capsids consisting of a fixed number of coat proteins and a variable number of nanoparticles. In qualitative agreement with the experimental findings, we find (i) that there is a relatively narrow range of concentrations of nanocolloids that allows for the formation of appreciable numbers of partially filled capsids, and (ii) that the number of nanocolloids adsorbed on the inner wall of the capsid shell is typically well below the maximum number that fits on the wall facing the lumen. We attribute this to the impact of entropy that offsets the increase in binding free energy gain, which for smaller particles tends to be weaker.

Thermofield dynamics (TFD) is a powerful framework for accounting for thermal effects in a wave function setting and has been extensively used in physics and quantum optics. TFD relies on a duplicated state space and creates a correlated two-mode thermal state via a Bogoliubov transformation acting on the vacuum state. However, a very useful variant of TFD uses the vacuum state as the initial condition and transfers the Bogoliubov transformation into the propagator. This variant, referred to here as the inverse Bogoliubov transformation (iBT) variant, has recently been applied to vibronic coupling problems and coupled-oscillator Hamiltonians in a chemistry context, where the method is combined with efficient tensor network methods for high-dimensional quantum propagation. In the iBT-TFD representation, the mode expectation values are clearly defined and easy to calculate, but the thermalized reduced particle distributions, such as the reduced 1-particle densities or Wigner distributions, are highly non-trivial due to the Bogoliubov back-transformation of the original thermal TFD wave function. Here, we derive formal expressions for the reduced 1-particle density matrix (1-RDM) that use the correlations between the real and tilde modes encoded in the associated reduced 2-particle density matrix. We apply this formalism to define the 1-RDM and the Wigner distributions in the special case of a thermal harmonic oscillator. Moreover, we discuss several approximate schemes that can be extended to higher-dimensional distributions. These methods are demonstrated for the thermal reduced 1-particle density of an anharmonic oscillator.

Modeling optical spectra of pigment-protein complexes requires accurate treatment of both excitonic and vibronic interactions. While nonperturbative approaches, such as the hierarchical equations of motion, are, in principle, numerically exact, they are computationally demanding, making the use of approximate lineshape theories appealing. However, the biases introduced by these perturbative treatments still need assessment. Here, we systematically compare methods based on cumulant expansion and successive approximations against exact calculations. Using chlorophyll dimers in the water-soluble chlorophyll-binding protein and the CP29 light-harvesting complex as test systems, we analyze absorption spectra under varying coupling strengths. Our results show that vibronic renormalization of excitonic coupling can be captured by the partially Markovian complex Redfield (cR) theory, whereas fully non-Markovian approaches are essential for reproducing the intensities of vibronic sidebands. A model that treats electronic transitions involving high-frequency vibrational modes as localized recovers many of the non-Markov and non-secular effects. We extend our analysis to fluorescence spectra, which pose more difficulties because excitonic and vibrational states are entangled before emission. While non-Markovian methods still perform better for fluorescence, their performance in reproducing vibronic sidebands is less than satisfactory. Our results allow quantifying the errors made by approximate theories and define a reliability range for spectroscopic simulations.

The accurate prediction of ionization potentials (IPs) is central to understanding molecular reactivity, redox behavior, and spectroscopic properties. While vertical IPs can be accessed directly from electronic excitations at fixed nuclear geometries, the computation of adiabatic IPs requires nuclear gradients of the ionized states, posing a major theoretical and computational challenge, especially within correlated frameworks. Among the most promising approaches for IP calculations is the many-body Green's function GW method, which provides a balanced compromise between accuracy and computational efficiency. Furthermore, it is applicable to both finite and extended systems. Recent work has established formal connections between GW and coupled-cluster doubles (CCD) theory, leading to the first derivation of analytic GW nuclear gradients via a unitary CCD framework. In this work, we present an alternative, fully analytic formulation of GW nuclear gradients based on a modified version of the traditional equation-of-motion CCD formalism, enabling the inclusion of missing correlation effects in the traditional CCD methods.

Polarizable quantum mechanics/molecular mechanics (QM/MM) approaches based on fluctuating charges and dipoles [QM/FQ(Fμ)] are formulated within the state-specific vertical excitation model (VEM) to compute vertical excitation energies of solvated systems. This methodology overcomes the limitations of the widely used linear response (LR) approach. While LR can capture the dynamic response of the solvent to the QM transition density, it neglects the solvent reorganization that follows solute relaxation upon electronic excitation. In contrast, the VEM framework explicitly accounts for this effect. Benchmark calculations of vertical excitation energies using QM/FQ(Fμ) are reported for a representative set of solutes-acrolein, acetone, caffeine, p-nitroaniline, coumarin 153, doxorubicin, and betaine-30-comparing VEM with LR, corrected LR (cLR), and cLR2 schemes. The results reveal notable variations in solvent response, depending on the character of the electronic transition, and demonstrate that optimal accuracy can be achieved by selecting the most appropriate model for each specific system and excitation.