We explore the capability of real-time time-dependent auxiliary density functional theory (RT-TD-ADFT) to capture photoionization of the nitrogen molecule when employed in combination with atomic Gaussian basis sets optimized for the continuum (AOC). The molecule is ionized by an ultrashort laser pulse in the near- and far off-resonant energy conditions. The dependence of the calculated amount of deposited energy and of emitted electrons on various sets of AOC is investigated. We find that for energies below a threshold of ∼25 eV, the simulations carried out with sufficiently angularly flexible AOC capture reasonably well the physics of the photoionization process, while AOC do not seem adequate to describe photoionization occurring at higher energies. We also find that accounting for exact exchange in the simulation moderately affects the results in the near-resonant situation, while it has a stronger impact on the appearance of the so-called molecular dipole instability a few fs after ionization in the far off-resonant case. Overall, this work paves the way for the evaluation of photoelectron spectra based on RT-TD-ADFT.
A widely used computational framework to calculate the membrane permeability coefficient of small molecules is the inhomogeneous solubility-diffusion (ISD) model. It requires two ingredients that can be calculated using molecular dynamics simulations: the potential of mean force, which is well-defined, and the position-dependent diffusivity, which is often problematic and challenging. Two methods (Woolf-Roux and Hummer) have been proposed to determine the position-dependent diffusivity profiles using biased umbrella sampling simulations. While both are constructed from similar time-correlation functions, they can disagree quantitatively. Here, a reconciliation of these methods is achieved through deep learning memory functions in the time domain. The diffusivity extracted through this analysis is shown to be in best agreement with the equilibrium counting permeability for the same membrane system compared to both the Woolf-Roux and Hummer diffusivities. The effect of memory on the rate of barrier crossing is assessed through numerical simulations of the generalized Langevin equation (GLE). The GLE is efficiently simulated via Markovian embedding, which relies on the positive, decaying exponential form of the memory functions extracted by deep learning. Our results based on the ISD permeability, the known permeability from equilibrium molecular dynamics, and the numerical GLE simulations indicate that memory effects most likely do not have a significant effect on the permeation of water.
Accurate prediction of inverted singlet-triplet gaps (ΔST < 0) remains a major challenge for conventional linear-response time-dependent density functional theory because the adiabatic exchange-correlation kernel fails to properly account for double-excitation effects. Although range-separated and double hybrid functionals partially improve the description of such systems, their performance strongly depends on the choice of the range-separation parameter (μ) and perturbative correlation fraction (ac). In the present study, we develop a dual-tuned range-separated double hybrid framework based on the LC-BLYP(D) functional, in which both μ and ac are determined using physically motivated electronic-structure descriptors. The range-separation parameter is obtained through a single-step tuning scheme derived from the electron localization function, while the perturbative correlation fraction is expressed as a function of the tuned μ∗ and the HOMO-LUMO overlap integral. The resulting framework simultaneously balances long-range Hartree-Fock exchange and MP2/CIS(D) correlation contributions, thereby improving the description of excited states possessing strong double-excitation character. The proposed methodology was validated using an extensive benchmark consisting of the original INVEST systems, 15 additional molecules exhibiting inverted singlet-triplet gaps, substituted azulene derivatives with conventional positive gaps, and a broad set of common molecular excitations. For weak-overlap INVEST chromophores such as substituted heptazines and pentaazaphenalene derivatives, the dual-tuned functional significantly reduces the absolute error relative to fixed-parameter approaches while consistently preserving the inverted excited-state ordering. Importantly, the method also maintains balanced performance for molecules with conventional positive singlet-triplet gaps and for ordinary valence excitation energies, demonstrating that the additional perturbative correlation does not artificially overstabilize singlet states.
Ultrafast decompression experiments on deeply supercooled water have been interpreted as showing long-lived coexistence of high- and low-density liquids. We reassess this interpretation by separating the timescales of pressure release, structural relaxation, crystallization, and heat exchange. The experimental trajectories are adiabatic, and under these conditions, the two fitted wide-angle x-ray scattering components cannot represent equilibrium HDL and LDL persisting along a common thermodynamic path. We show instead that the spectra are consistent with a responsive liquid fraction evolving during decompression together with a structurally lagged, HDA-like fraction produced by heterogeneous heating. This framework also rationalizes the fluence dependence and clarifies the distinct information contained in the small-angle x-ray scattering response. The analysis identifies which observables can provide decisive evidence for a first-order liquid-liquid transition and constrain the location of its critical point.
The diatomic variational nuclear-motion program duo is extended to calculate hyperfine-resolved spectra of homonuclear diatomic molecules. The hyperfine interactions considered include five nuclear magnetic dipole terms and one nuclear electric quadrupole term. Nuclear-exchange symmetry is explicitly incorporated, and the final hyperfine-resolved parity-adapted Hamiltonian is constructed in a complete angular-momentum basis. After diagonalization of this Hamiltonian, hyperfine-resolved line lists can be generated using transition electric dipole and quadrupole moment curves. To validate the implementation, we apply the extended program to H2 and D2, as well as 14N2 and 14N2+, and compare the calculated results with those from previous experimental and theoretical work and from the perturbative program pgopher; good agreement is obtained in all cases.
Multicomponent carbonate electrolytes are central to next generation electrochemical energy storage devices, and the choice of electrode model strongly shapes their predicted interfacial behavior. This study compares the constant charge method (CCM) and constant potential method (CPM) for modeling electrified interfaces in such electrolytes. Molecular dynamic simulations are performed for 1 M LiPF6 in an ethylene carbonate:dimethyl carbonate:ethyl methyl carbonate ternary carbonate electrolyte sandwiched between two graphite electrodes. Results show that CCM and CPM give nearly identical interfacial structures at low and moderate polarization, with clear deviations emerging at ±1.35 V, equivalent to a 2.70 V cell voltage. This method-dependent response originates mainly from Li+ behavior at the negative electrode, where CCM promotes partial desolvation and contact-like adsorption, whereas CPM preserves solvent separated adsorption through dynamic charge redistribution and stronger interfacial solvent ordering. Meanwhile, PF6- distributions remain comparatively insensitive to electrode treatment. This study defines the polarization regime where CCM is sufficient and establishes when CPM is required to capture coupled Li+/solvent/electrode interactions in carbonate solvent-based energy storage electrolytes.
Cell-penetrating peptides translocate across a membrane via different mechanisms. In this work, we employ coarse-grained molecular dynamics simulations to study the effect of an external electric field, which mimics the transmembrane potential, on the stability of a mitochondrial membrane and the translocation of peptide(s) across it. In the absence of peptides, we observed that the membrane undulates under the applied field and develops a curvature promoted by the presence of cardiolipin, which further leads to the formation of a transient pore caused by the merging of the phospholipids from the upper leaflet into the lower leaflet. We also studied the translocation of two different mitomembrane-targeting peptides at various electric field intensities in which the integrity of the membrane was preserved. Under the applied field, we observed that the cationic residues of each peptide bound to the phosphate headgroups of lipids, gradually moving toward the membrane region where a transient pore forms at a critical field strength, followed by the translocation across the mitomembrane via this transient pore. Comparing systems containing single peptides with those containing ten peptides of each type, we found that the transport of multiple peptides across the mitomembrane requires lower field magnitudes, no more than two peptides translocate at a time, and the translocation time, once in the pore, is marginally higher for multiple peptides compared to a single peptide. Overall, the findings from this work enhance our understanding of the effect of the transmembrane potential on the transport of mitomembrane-targeting peptides.
We introduce a unified statistical framework for quantifying system-environment coupling by treating the interaction energy VSE as a stochastic variable. Using our proposed reference-particle decomposition, we derive exact, closed-form expressions for the mean and variance of VSE in terms of the single-particle density and correlation functions up to fourth order. These expressions are valid throughout all coupling regimes, from strongly coupled finite systems to the weak-coupling thermodynamic limit. They connect interaction-energy statistics directly to equilibrium structural information and provide a systematic route for evaluating coupling across open system-environment boundaries. We further show how the moment framework enters free energy constructions, including the Hamiltonian of mean force and the quasichemical-theory outer-shell contribution. When the relevant interaction-energy distribution is approximately Gaussian, the first two moments determine the corresponding second-cumulant free energy estimate. To validate our framework, we performed explicit Monte Carlo simulations of a Lennard-Jones system across a range of system sizes, generating reference distributions of the system-environment interaction energy VSE. We also performed independent empty-cavity Monte Carlo calculations to validate the quasichemical outer-shell specialization. We then applied our derived analytical formulas to predict these distributions and found excellent agreement in both the weak- and strong-coupling regimes. The results demonstrate that interaction-energy distributions and the associated thermodynamic contributions can be reconstructed from microscopic structural correlations.
Accurate prediction of solubility is crucial in various fields, including pharmaceuticals, environmental chemistry, and materials science. In this study, we demonstrate the application of Adaptive Force Matching (AFM) to predict the solubility of molecular liquids in water. By developing high-quality force fields using AFM, we accurately compute the free energy of vaporization and hydration, which are essential components for predicting solubility. Our results show that AFM models can reliably predict the solvation free energy of selected small molecules, exhibiting a deviation of <1.3 kJ/mol from experimental references for cyclohexene, isopentane, and n-butanol. Although a slightly larger error is observed for n-octanol, which was developed by borrowing AFM parameters from other molecules, the deviation remains comparable to commonly accepted chemical accuracy. This study highlights the potential of AFM as a powerful tool for predicting solubility, enabling the design and development of new materials and molecules with tailored properties.
Accurate prediction of activation barriers is essential for reliable mechanistic modeling of copper-catalyzed carbon conversion reactions yet remains challenging for conventional density functional theory. Here, we evaluate a hybrid PBE-D3/M06 approach for reaction kinetics on low-index Cu(100), Cu(110), and Cu(111) surfaces. Benchmarking against experimental barriers for seven representative elementary reactions shows that PBE-D3/M06 achieves near-chemical accuracy, with a mean absolute error and root mean square error of 0.06 eV, substantially outperforming PBE and RPBE. The method also reproduces embedded CASPT2 trends for C-C coupling on Cu(111), correctly identifying COH*-CHO* coupling as both kinetically and thermodynamically preferred. Applied to CO2 hydrogenation to methanol on Cu(111), PBE-D3/M06 indicates that the formate-mediated pathway is favored, with HCOOH* hydrogenation as the rate-determining step. This work suggests that PBE-D3/M06 is a promising framework for modeling elementary steps in copper-catalyzed carbon chemistry.
Microbial rhodopsins are photoreceptive membrane proteins that utilize retinal as a chromophore to absorb light and drive diverse photochemical functions. Recent studies have revealed that some microbial rhodopsins bind carotenoids in addition to retinal. The bound carotenoids may function as light-harvesting antennas in vivo by absorbing light in spectral regions where retinal absorbs less efficiently and transferring the excitation energy to the retinal chromophore. Here, we employed resonance Raman spectroscopy with excitation wavelengths from 440 to 600 nm to investigate the retinal and carotenoid chromophores in the complex of Gloeobacter rhodopsin (GR) and canthaxanthin (CAN). We found that the binding of one chromophore to the protein affects the π-conjugated system of the other chromophore, indicating mutual perturbation between retinal and CAN. We also observed excitation-wavelength-dependent shifts in the ν(C=C) vibrational bands of both retinal and CAN, providing evidence for structural inhomogeneity of the chromophores. Model calculations supported the presence of multiple substates within the ensemble. These findings provide new spectroscopic insights into interchromophore interactions and structural heterogeneity in the GR-CAN complex. Moreover, this study demonstrates that variation of the resonance Raman excitation wavelength provides a structurally sensitive means of probing intrinsic inhomogeneity within ensembles of protein-bound chromophores.
Using the Lifshitz theory of the van der Waals and Casimir forces, we calculate the Casimir free energy of thin peptide films deposited on silicon substrates. The Casimir free energy is found as a function of film thickness for different fractions of water in the film, in the presence of either nonmagnetic or magnetic nanoparticles, and under the impact of irradiation of a silicon substrate with laser pulses or dopants resulting in the dielectric-to-metal phase transition. It is shown that for dielectric silicon, there is a borderline value of the film thickness such that the Casimir free energy is negative and contributes to the film stability for thicker films but is positive and makes the film less stable for thinner ones. According to our results, the borderline value of peptide film thickness decreases with increasing volume fractions of water and nanoparticles in the film. This decrease is more pronounced for the magnetic nanoparticles and becomes stronger with increasing their radius. The borderline value of peptide film thickness is found as a function of the fraction of water in the film. If the silicon substrate is in a metallic state, the Casimir free energy of the peptide coating is always positive, which makes it less stable. Possible applications of the obtained results in organic electronics and biomedicine are discussed.
We derive the stress tensor of a flexible polymer solution within the Gaussian-chain self-consistent field theory (SCFT) without invoking the ground-state dominance (GSD) approximation. Starting from a covariant formulation of the single-chain partition function in a background metric, we obtain the symmetric stress tensor expressed through the full Edwards propagators. The result contains the local interaction pressure, the ideal translational pressure of chains, and a conformational contribution originating from the metric dependence of the Edwards operator. It provides the local counterpart of earlier global stress formulas in polymer SCFT and gives a thermomechanical generalization of the GSD conformational stress. We demonstrate that the GSD conformational stress tensor-previously used in studies of capillary-induced self-coacervation and confined polyelectrolytes-is recovered exactly as the lowest-mode limit. The derived stress tensor is applied to a slit geometry to obtain the disjoining pressure, providing a framework for mechanical calculations in confined polymer systems beyond the GSD regime. For ideal chains between hard repulsive walls, we show that the local stress reproduces the exact depletion pressure and that higher Edwards modes become essential in wide pores, where the GSD approximation fails to recover the correct bulk limit.
Local hybrid exchange-correlation (LH XC) functionals incorporate position-dependent exact exchange but are often limited by computational cost and self-consistent field (SCF) convergence challenges. In this study, we examine the performance of a testbed LH XC functional within the contracted plane wave basis function framework, which enables the evaluation of the exact exchange energy density with minimal additional overhead. Calculations on diamond supercells show that SCF convergence is robust and that the cost of forming the non-local contributions is approximately twice that of analogous global hybrid calculations. When combined within a practical SCF optimization protocol, the results indicate that calculations using LH XC functionals incur only a modest increase in total cost relative to those using global hybrid functionals, demonstrating that this approach is computationally viable.
We employ a Non-Coulombic Non-Orthogonal Configuration Interaction (NC-NOCI) approach to study the confinement of three fermionic helium atoms, 3He, inside a C60 fullerene, with the aim of elucidating how encapsulation affects their spatial distribution and energy-level structure. To interpret the NC-NOCI results, we use a reference Hamiltonian that separates translational, rotational, and vibrational degrees of freedom, which allows us to distinguish (via symmetry arguments) the system's spin isomers, corresponding to doublet and quartet states. The results indicate that, under confinement, the 3He atoms behave collectively as an oblate symmetric rotor consistent with the global Ih symmetry of the 3He3@C60 endohedral fullerene. The NC-NOCI calculations show that the doublet state lies lower in energy than the quartet; moreover, the effect of the C60 cage is not strong enough to force the fermionic helium atoms to form a shell structure. This can be attributed to the very small energy differences between spin-isomer states, on the order of 2 cm-1.
Fluid motion is ubiquitous in solidification, yet its atomistic influence on the immediate solid-liquid interfacial region remains difficult to quantify. Here, we develop an atomistic simulation framework for maintaining solid-liquid coexistence interfaces under imposed tangential melt flow. The protocol combines equilibrated FCC(100) crystal-melt coexistence systems with a flow boundary condition, profile-unbiased thermostatting, and solid-phase momentum control, allowing the imposed flow, thermal fluctuations, and solid reference frame to be treated separately. The method is demonstrated for a Lennard-Jones (LJ) model system and an embedded-atom-method Ni system. For each system, dynamically stable flowing coexistence states are identified at three imposed flow velocities by requiring statistically stationary interfaces with no sustained melting, crystallization, overheating, or rigid translation of the solid. Fine-grained density, velocity, and temperature profiles show that the two phases remain distinguishable, the imposed flow is measurable through a central-liquid plateau velocity, and the streaming-velocity-subtracted kinetic temperature remains controlled. The flowing interfaces reveal a measurable flow dependence of liquid-side interfacial layering. For both LJ and Ni FCC(100) interfaces, the liquid-side density-maximum spacing dm increases over the sampled velocity range, indicating that tangential flow further modifies the known equilibrium spacing relaxation of FCC(100) interfacial liquids. In the LJ system, this increase occurs together with a decrease in the coarse-grained density width δρ, showing that flow can sharpen the mean density transition while relaxing the wavelength of liquid-side density oscillations. These results establish an atomistic platform for studying flow-modulated density layering, interfacial structure, and nonequilibrium response at crystal-melt interfaces.
Organic and main-group triradicals have potential applications in molecular magnetism and quantum information science, but the factors that determine whether a triangular triradical adopts a high-spin quartet or spin-frustrated doublet ground state remain poorly understood. Here, we present a multireference computational investigation of four triangular triradicals, including two experimentally characterized species and two rationally designed variants. The first experimentally characterized system is a triaza[4]triangulene triradical with a robust quartet ground state. The second is a boron-triptycene triangular triradical with a doublet ground state commonly attributed to Jahn-Teller distortion, although our computations reveal that the spin-frustrated doublet state is already strongly stabilized in the near-symmetric geometry. This provides quantitative evidence that triangular triradicals can remain spin-frustrated even in the absence of Jahn-Teller distortion, with subsequent distortions only amplifying rather than causing the low-spin ground state. The intrinsic electronic spin frustration of the triangular scaffold primarily determines the spin-state ordering, while vibrational modulation of magnetic exchange interactions governs the dynamic stability and thermal susceptibility of the spin manifold. By performing exchange-vibronic coupling analysis for triradical doublet-quartet energy gaps, ΔED-Q, through mode-resolved d(ΔED-Q)/dQi gradients and the resulting total thermal fluctuations, σtot, we identify symmetry-breaking vibrational modes whose thermal population strongly modulates these energy gaps. Mechanistic insights from this framework guide the rational design of the two additional triradicals with dramatically reduced doublet-quartet gaps, further validated for 19 additional systems. Our work establishes a design framework for tuning magnetic properties in triangular organic triradicals.
Using intense femtosecond soft x-ray pulses above the sulfur 2p edge produced by the Free-electron LASer in Hamburg (FLASH), we investigate the multiple ionization and fragmentation dynamics of CS2. We focus on the three-ion fragmentation pathways of CS2 polycations with total charges of +4 to +10, which can only be reached through absorption of multiple x-ray photons. By coupling three-dimensional velocity map imaging with covariance analysis, we determine the relative momentum distribution of all ions produced in each fragmentation channel at high ion count rates per shot. Deviations between these measured relative ion momentum distributions and those predicted by classical Coulomb explosion simulations, assuming an instantaneous charge buildup, grow with increasing total charge state, indicative of nuclear motion during the multiple ionizations that occur within the x-ray pulse duration-as confirmed by comparison with the main fragmentation channel of the trication, which can be formed following single-photon interaction. These dynamics can be modeled using a gradual charge buildup picture of sequential single-photon single-ionization events occurring during the pulse, following the initial core ionization. Our study underscores the importance of complete and channel-resolved measurements, the advances enabled by covariance analysis in high-count-rate experiments, and the critical role of charge buildup and nuclear dynamics during the x-ray free-electron laser pulse in Coulomb explosion imaging. The impacts of this nuclear motion can be controlled and minimized by utilizing shorter x-ray pulses, as will be of great importance in using time-resolved x-ray Coulomb explosion to probe the fastest dynamics in molecular photochemistry.
The growth of metal nanoparticles in solution has been the subject of many experimental and theoretical investigations due to the great and varied utility of these particles. While previous studies have focused on very small nanoclusters and nanometer-sized particles, the intermediate steps of the growth mechanism, where few atom clusters reach their critical nucleation radius, is less well understood. We extend our recently developed PathTree method for mapping metal nanocluster growth mechanisms to include Monte Carlo propagation and generation-by-generation growth based on a dynamical reservoir of reacting species, and we apply this to study the growth of Ag nanoclusters up to 19 atoms in water. Of particular interest is the growth of these clusters under plasma-driven solution electrolysis conditions, where there is a source of solvated electrons to reduce the otherwise cationic Ag nanoclusters. We examine the effects of this reduction, the subsequent anion formation on the thermodynamically favored growth reactions using the Monte Carlo style reaction propagation and the reaction reservoir, and the effects of temperature on the Ag growth mechanism.
A systematic many-body expansion (MBE) analysis is presented for 1169 (H2O)4-23 cluster structures at the B3LYP-D3(BJ)/def2-TZVP level, with full enumeration of all monomer, dimer, and trimer subsystems. The per-molecule interaction energy converges toward the large-cluster limit following finite-size scaling governed by the evolution of surface-to-interior molecular coordination. While the individual 2B and 3B fractional contributions require second-order c/n2 corrections, the total energy converges to a simpler functional form concealing a nontrivial redistribution between pairwise and cooperative interactions. Machine-learning information decomposition reveals a hierarchical descriptor structure: pairwise interactions require explicit hydrogen orientational information beyond O⋯O distances, whereas 3B cooperativity is predominantly encoded within the pairwise interaction landscape itself, with orientational refinement contributing only marginally. Further analysis indicates that the remaining variance arises primarily from hydrogen-bond directionality: classifying chain trimers according to their directed donor-relay topology nearly perfectly separates cooperative from anti-cooperative configurations, increasing the out-of-fold R2 from 0.808 to 0.917. Machine learning models constructed from these local descriptors reproduce the finite-size scaling relations and extrapolated large-cluster asymptotes (R2 ≥ 0.985). Cross-method validation against coupled-cluster single double triple-level many-body potentials and explicit delta corrections indicates that the scaling forms and the descriptor hierarchy are transferable across methods, while the quantitative MBE ratios remain method-dependent. These results demonstrate that the energetic evolution of water clusters is governed primarily by transferable local interaction patterns, suggesting a route toward size-transferable interaction models based on limited structural descriptors and low-order energy decompositions.
