Browse Articles
Discover research articles across all indexed journals
Random-phase approximation vs Møller–Plesset perturbation theory for many-body energy contributions of hydrogen-bonded molecular solids
The fragment-based approach is a promising strategy for applying correlated-wavefunction methods to lattice energies of molecular solids. A key requirement is the efficient inclusion of the long-distance and nonadditive contributions to the many-body expansion (MBE) of the lattice energy. This is especially important in crystals of polar molecules, where MBE converges slowly with distance. In this context, we compare the simplest coupled-cluster approach—the random-phase approximation (RPA)—against the well-established methodology of Møller–Plesset (MP) perturbation theory. Using the examples of solid ammonia, methanol, and formic acid, we show that the RPA with singles corrections based on the Kohn–Sham (KS) Perdew–Burke–Ernzerhof (PBE) orbitals yields near-benchmark accuracy for the two-body contributions. However, for any PBE-based variant of RPA, the three- and four-body contributions suffer from artifacts. For the nonadditive terms, the Hartree–Fock (HF) orbitals appear necessary. In fact, we find that the HF-based RPA with additional corrections recovers the nonadditive interactions about as accurately as the more expensive MP2.5 method. This is a departure from the typical KS-based RPA and an indication that the HF-based RPA can serve as an alternative to the usual MP methods in accurate approximations of the crystal lattice energy.
Isomer effects on neutral-loss dissociation channels of nitrogen-substituted PAH dications
We investigate two nitrogen-containing isomers of polycyclic aromatic hydrocarbons, quinoline and isoquinoline, of composition C9H7N in collisions with 7 keV O+ and 48 keV O6+ projectile ions. By employing ion–ion coincidence mass spectrometry, we determine branching ratios for H-loss, C2H2-loss, and HCN-loss dissociation channels of Q2+ and IQ2+. The overall contribution of HCN loss is found to be the dominant decay channel. A comparison with the results of a parallel experiment on naphthalene, the simplest PAH, reveals that HCN loss in both isomers has a higher propensity than the analogous C2H2 loss of naphthalene. The positional identity of the nitrogen atom in the two isomers mainly manifests in many-body fragmentation of their dications. Potential energy surfaces of Q2+ and IQ2+ are further computed to explore complete fragmentation mechanisms. Parent dications (Q2+ and IQ2+) are identified to isomerize via seven-membered ring structures before elimination of C2H2 and HCN. While prompt dissociation is the primary pathway, the dominant channel of each neutral-loss class also exhibits delayed fragmentation.
Pressure-induced phase transition of 3,4-dinitropyrazole by 2D hydrogen bonded networks
As a kind of energetic material, explosives would face an environment of high-pressure during initiation to detonation or under shock waves. Under such conditions, explosives would experience a phase transition and even directly decompose. Therefore, there is a need to achieve the high-pressure evolution of explosives. 3,4-dinitropyrazole (DNP), which has excellent energy and sensibility, can be used as a potential carrier of melt cast explosive to replace TNT. However, the structural evolution of DNP with the increase in pressure remains elusive. With the help of diamond anvil cell technology, in situ high-pressure angle-dispersive x-ray diffraction (ADXRD) and Raman spectra were performed to investigate the structural variations of DNP. Both ADXRD and Raman experiments indicated that the DNP experienced a phase transition in the pressure range between 6.1 and 9.2 GPa. After carefully analyzing the Hirshfeld surface, first-principles calculations, and Raman spectra, we suggested that the newly generated N–H⋯N hydrogen bonds should be responsible for these high-pressure changes. The DNP crystal packing patterns have been changed from 1D molecular tapes to 2D hydrogen bonded networks. This research systemically investigated the high-pressure structural changes of DNP and studied the evolution of weak intermolecular interactions, so it built the relationship between phase transition and weak intermolecular interactions.
Efficient 13C–13C correlations obtained by AL FRESCO mixing schemes under any arbitrary MAS spinning rates
An efficient chirp pulse-based mixing technique, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), is introduced for establishing broadband two-dimensional (2D) 13C–13C dipolar correlations in uniformly 13C-labeled protein samples. AL FRESCO utilizes a single or a series of frequency-swept (chirped) pulses applied to homonuclear spin pairs (e.g., 13Cs, 15Ns, or 1Hs) to mediate homonuclear correlations under magic-angle spinning (MAS). Originally developed for ultrafast MAS, we demonstrate that AL FRESCO performs robustly across a wide range of MAS rates. The AL FRESCO method exhibits strong immunity to dipolar truncation, allowing efficient recoupling of long-range interactions even in the presence of dominant short-range dipolar couplings and regardless of the chemical shift difference between the recoupled sites. A distinctive feature of AL FRESCO is its use of weak radiofrequency (rf) fields (5–20 kHz), independent of the MAS rate, significantly reducing sample heating and enabling extended mixing times (>1 s). This facilitates the observation of long-range correlations that are often inaccessible using conventional recoupling techniques under ultrafast MAS rates. The effectiveness of the method is governed by key parameters such as rf amplitude and envelope shape, dwell time (Δt), and sweep bandwidth. Numerical simulations and average Hamiltonian theory offer insight into the recoupling mechanism. Experimental validation was carried out via 2D 13C–13C correlation spectroscopy at fast, moderate, and slow MAS rates using three different protein systems: uniformly 13C,15N-labeled transthyretin, selectively 13C-[T,W]-labeled CrgA, and uniformly 13C,15N-labeled GB1.
Shaping the aggregates of discotic particles with directional pair interactions
Aggregation processes in systems of planar macromolecules and colloids drive a broad range of phenomena in natural systems and soft materials. Depending on the chemical architecture, intermolecular interactions in these systems may favor different relative pair orientations, such as stacking face–face or percolating edge–edge arrangements. In this work, we employ a versatile coarse-grained interaction model for disk-like particles to provide a general framework to rationalize the thermotropic formation of aggregates and predict the topology of the resulting suprastructures. Monte Carlo and Brownian dynamics simulations show that, with appropriate tuning of the interactions, discotics spontaneously nucleate into clusters with globular, planar, or stacked geometries, leading to materials with specific internal order and associated physicochemical properties.
Simulating decoherence of two coupled spins using the generalized cluster correlation expansion
We simulate the coherence of two coupled electron spins interacting with a bath of nuclei using the generalized cluster correlation expansion method. An exchange interaction between the electrons facilitates a family of entangling gates that can be spoiled by nuclear-induced dephasing. Consequently, we study the dephasing of the coherent two-electron system by characterizing the T2 and T2* of the two-electron reduced density matrix for various system parameters in the range mimicking magnetic molecules, including magnetic field strength and orientation, exchange interaction strength, distance between the two spins, minimum distance between electron and nuclei and between nuclei, and nuclei density. We find the optimal regime for each parameter in which the coherence time is maximized and provide a physical understanding of it.
The reactivity of Ta <i>n</i> + clusters with NO molecules: N–O bond dissociation and NO <i>x</i> conversion
Nitric oxides are primary contributors to air pollution. Examining their chemical transformations is crucial for developing effective clean air strategies. In this study, we studied the reactions between cationic tantalum clusters Tan+ (n = 1–16) and NO, utilizing our customized laminar flow tube reactor coupled with a tandem quadrupole mass spectrometer. The experimental results indicate that the reaction pathways of Tan+ clusters vary with cluster size: for smaller tantalum clusters Tan+ (n ≤ 5), the reaction products are mainly composed of TanN+ and TanO+, suggesting direct N–O dissociation or bimolecular reaction to release N2O or NO2 mediated by small metal clusters. In contrast, the larger clusters Tan≥6+ exhibit a range of reaction products, facilitated by the favorable adsorption of multiple molecules to generate the Tan(NO)m+ and TanO(NO)m+ series. Theoretical calculations reveal that the energetics and reaction dynamics differ among Tan+ clusters of varying sizes. This study clarifies the substantial size effect of the Tan+ clusters in reactions with nitric oxide and underscores the importance of small Ta clusters for NO elimination and NOx conversion.
Quantum dynamics of electron transfer in single-molecule systems coupled to polaritons: A macroscopic quantum electrodynamics approach
Controlling electron transfer and related chemical processes through polaritons has emerged as a promising direction in chemical physics. We present a general framework for electron transfer in molecules strongly coupled to polaritons. The theory is formulated within macroscopic quantum electrodynamics, a quantization scheme for electromagnetic fields in non-homogeneous, dispersive, and lossy media. To capture both molecular and dielectric contributions, our formulation incorporates two baths: molecular vibrations and a dielectric-photonic continuum that generates polaritons. This formulation is then transformed into a numerically tractable form that can be naturally combined with methods such as the pseudomode approach or the hierarchical equations of motion. Using a molecule above a plasmonic surface as an example, we show that the framework captures accurate dynamics across light–matter coupling regimes, thereby providing a powerful tool for investigating polariton-mediated electron transfer.
Ground-and excited-state fragmentation dynamics of doubly ionized OCS: A theoretical study
We investigated fragmentation dynamics of OCS2+ after photoinduced double ionization by combining static potential energy surface (PES) analysis with ab initio molecular dynamics (AIMD) and surface-hopping AIMD (SH-AIMD). In the ground state, AIMD shows that the isomerization pathway from OCS2+ to COS2+, although accessible on the static PES, is dynamically hidden. Trajectories rarely follow it because it requires unrealistically high bending excitation, whereas S+ dissociation proceeds without such a constraint. Consequently, energy released upon ionization is funneled more efficiently into dissociation, favoring S+ dissociation over isomerization. For excited states, SH-AIMD trajectories launched from the lowest triplet 3Π states and the 23Δ state reproduce the observed fragmentation: predominant S+ dissociation with minor O+ formation. The isomerization process leading to the COS2+ structure was not observed in the simulations. These results are consistent with experimental observations. Notably, for the O+ channel, we likely achieve the first AIMD reproduction of the experimental appearance threshold using only triplet states and no external laser fields. This indicates that vibronic coupling via bending motion is essential to enable O+ release, although its probability remains small relative to S+ dissociation. Overall, fragmentation in OCS2+ is governed by the interplay of vibronic coupling and dynamical effects: bending vibrations can facilitate O+ release, whereas isomerization to COS2+ is dynamically suppressed by the requirement of extreme bending excitation. The high density of states in the excited manifold further underscores the strongly nonadiabatic character of OCS2+. Our results connect static PES features with trajectory-based dynamics, offering new insight into selective fragmentation in polyatomic dications.
The geometry of the classical action in phase space
We present a geometric representation in phase space of the classical action. Specifically, we find three seemingly unrelated interpretations for the action as the sum of signed areas of shapes in phase space. By using the Poincaré–Cartan integral invariants in extended phase space, we are able to show the equivalence between all three. As a concrete example, we consider the 1D harmonic oscillator, but the results are general for arbitrary potentials and numbers of dimensions.
Inferring intermediate states by leveraging the many-body Arrhenius law
Metastable states appear as long-lived intermediate states in various natural transport phenomena, which are governed by energy landscapes. As such, these intermediate metastable states dominate the system’s dynamics at coarse grained times. Moreover, they can strongly influence the overall pathways through which the energy landscape is explored. Therefore, quantifying these metastabilities is crucial for uncovering the key details of the underlying landscape. Here, we introduce a robust method based on a generalized many-body Arrhenius law to identify metastable states in escape problems involving interacting particles with excluded volume. Experimental platforms such as colloidal transport or macromolecular translocation through biological pores can offer promising settings to validate our predictions.
Hierarchical equations of motion solved with the multiconfigurational Ehrenfest ansatz
Being a numerically exact method for the simulation of dynamics in open quantum systems, the hierarchical equations of motion (HEOM) approach still suffers from the curse of dimensionality. In this study, we propose a novel multiconfigurational Ehrenfest (MCE)-HEOM method, which introduces the MCE ansatz to the second quantization formalism of HEOM. Here, the MCE equations of motion are derived from the time-dependent variational principle in a composed Hilbert–Liouville space, and each MCE coherent-state basis can be regarded as having an infinite hierarchical tier such that the truncation tier of auxiliary density operators in MCE-HEOM can also be considered to be infinite. As demonstrated in a series of representative spin-boson models, our MCE-HEOM significantly reduces the number of variational parameters and could efficiently handle the strong non-Markovian effect, which is difficult for conventional HEOM due to the requirement of a very deep truncation tier. MCE-HEOM is further applied to the 7-site Fenna–Matthews–Olson complex to study energy transfer in photosynthesis, and the results indicate that multi-site and multi-bath cases can also be accurately described with high efficiency. Compared to MCE, MCE-HEOM reduces the number of effective bath modes and circumvents the initial sampling for finite temperatures, eventually resulting in a significant reduction in computational cost.
On the interconnection between products formed by dissociative electron attachment to gas-phase abscisic acid and its microbial (but not plants) metabolic pathways
Low-energy (0–14 eV) electron-driven processes in a racemic mixture of the chiral abscisic acid (ABA) molecules are studied using dissociative electron attachment (DEA) spectroscopy under gas-phase conditions. DFT calculations are employed to understand the electronic structure of the ABA molecule to assign the experimental findings. The lowest two normally empty π* molecular orbitals of ABA are predicted to lie in a bound region, whereas the vertical electron attachment energy to occupy the π3* LUMO+2 orbital is estimated to be 1.33 eV. The long-lived (90 μs) parent molecular negative ions are formed by thermal electron attachment via vibrational Feshbach resonance. The adiabatic electron affinity of the ABA molecule is experimentally estimated to be about 0.9 eV. With very few exceptions, the fragmentation of ABA by resonance electron attachment occurs at thermal electron energy, the dominant decay being associated with the formation of the 4-oxoisophorone negative ion (m/z = 152) and the isomeric form of the sorbic acid molecule as a neutral counterpart. The structure of ABA microbial metabolites coincides with that of the DEA products with m/z = 152, 204, and 220 and of the neutral species generated as a counterpart of the m/z = 111 negative ions. The likely relation of these findings to electron-triggered biological processes is briefly discussed in the framework of electron donation to ABA from the microbial nanowires.
Comparative analysis of liquid and gel platelet rich plasma from apheresis and buffy coat in wound healing
Episodic-like memory in a simulation of cuttlefish behavior
Abstract Episodic memory involves remembering the what, when, and where components of an event. It has been observed in humans, other vertebrates, and the invertebrate cuttlefish. In clever behavioral experiments, cuttlefish have been shown to have episodic-like memory, where they demonstrate the ability to remember when and where a preferred food source will appear. The present work replicates this behavior with a parsimonious model of episodic memory. To further test this model and explore episodic-like memory, we introduce a predator-prey scenario in which the agent must remember what creatures (e.g. predator, desirable prey, or less desirable prey) appear at a given time and region of the model environment. This simulates similar situations that cuttlefish face in the wild. They will typically hide when predators are in the area, and hunt for prey when available. When the memory model is queried for an action (e.g., hunt or hide), the cuttlefish agent hunts for preferred food, like shrimp, when available, and hides at other times when a predator appears. When the memory model is queried for a place, the cuttlefish agent acts opportunistically, seeking less-preferred food (e.g., crabs) if it is located farther from a predator. These differences show how behavior can be altered depending on how memory is accessed. Querying the model over time might mimic mental time travel, a hallmark of episodic memory. Although developed with cuttlefish in mind, the model shares similarities with the hippocampal indexing theory and captures aspects of vertebrate episodic memory. This suggests that the underlying mechanisms supporting episodic-like behavior in the present model may be an example of convergent cognitive evolution.
Correlation between serum endocrine hormone levels and malignancy degree of prolactinoma and their predictive value for patient prognosis
Computational study of metal doped coronene quantum dots for formaldehyde sensing and adsorption in medical and environmental applications
Abstract In this study, the ability of pure and aluminum- and zinc-doped coronene as dual-purpose adsorbent/sensor platforms for formaldehyde (FA) detection in environmental and biomedical applications was computationally studied. All molecular structures were optimized individually and in combination with FA using density functional theory (DFT) at the B97D/6-311 + G(d) level of theory in the gas and water phases, and validated using WB97XD calculations. Analyses included geometric optimization, coherence energy, IR and UV spectra (TD-DFT), MEP mapping, HOMO-LUMO distributions, DOS plots, reactivity descriptors, dipole moment and polarizability, adsorption energy, recovery time, and electrical conductivity. Intermolecular interactions were analyzed using the theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses. Among all structures, Al.Coronene@FA exhibited the strongest sensing ability with the highest adsorption energy of − 39.57 kcal/mol (water phase) and − 44.43 kcal/mol (gas phase), along with an extremely long recovery time of 1.08 × 10 13 s (water) and 3.93 × 10 16 s (gas). This was paired with the highest electrical conductivity of 2.85 × 10 9 A m − 2 (water), confirming a strong charge-transfer mechanism. Conversely, Zn.Coronene@FA showed moderate adsorption (− 6.16 kcal/mol) and fast recovery time (3.34 × 10 − 12 s), making it favorable for reusable sensing platforms. Optical studies revealed pronounced redshifts in λmax upon FA adsorption, particularly for Al.Coronene@FA with λmax = 579 nm and 694 nm (water phase), indicating excellent colorimetric detection capability. Overall, the combination of strong adsorption ability, high electrical conductivity, significant spectral shifts, and charge transfer indicates Al-doped coronene is a highly promising material for formaldehyde sensing, whereas Zn-doped coronene is better suited for rapid-response reusable sensors. These computational results establish a reliable foundation for developing coronene-based sensing and adsorption platforms for environmental and biomedical applications.