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At least 1,117 records · Page 62

GradDFT. A software library for machine learning enhanced density functional theory

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT: an endeavor with many open questions and technical challenges. In this work, we present GradDFT a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange–correlation energy functionals. GradDFT employs a pioneering parametrization of exchange–correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, GradDFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

Chemistry↗

Efficient formulation of multitime generalized quantum master equations: Taming the cost of simulating 2D spectra

Modern 4-wave mixing spectroscopies are expensive to obtain experimentally and computationally. In certain cases, the unfavorable scaling of quantum dynamics problems can be improved using a generalized quantum master equation (GQME) approach. However, the inclusion of multiple (light–matter) interactions complicates the equation of motion and leads to seemingly unavoidable cubic scaling in time. In this paper, we present a formulation that greatly simplifies and reduces the computational cost of previous work that extended the GQME framework to treat arbitrary numbers of quantum measurements. Specifically, we remove the time derivatives of quantum correlation functions from the modified Mori–Nakajima–Zwanzig framework by switching to a discrete-convolution implementation inspired by the transfer tensor approach. We then demonstrate the method’s capabilities by simulating 2D electronic spectra for the excitation-energy-transfer dimer model. In our method, the resolution of data can be arbitrarily coarsened, especially along the t2 axis, which mirrors how the data are obtained experimentally. Even in a modest case, this demands O(103) fewer data points. We are further able to decompose the spectra into one-, two-, and three-time correlations, showing how and when the system enters a Markovian regime where further measurements are unnecessary to predict future spectra and the scaling becomes quadratic. This offers the ability to generate long-time spectra using only short-time data, enabling access to timescales previously beyond the reach of standard methodologies.

Chemistry↗

Managing photon flux in a miniaturized photoionization detector

Miniaturized photoionization detectors (PIDs) are used in conjunction with gas chromatography systems to detect volatile compounds in gases by collecting the current from the photoionized gas analytes. PIDs should be inexpensive and compatible with a wide range of analyte species. One such PID is based on the formation of a He plasma in a dielectric barrier discharge (DBD), which generates vacuum UV (VUV) photons from excited states of He to photoionize gas analytes. There are several design parameters that can be leveraged to increase the ionizing photon flux to gas analytes to increase the sensitivity of the PID. To that end, the methods to maximize the photon flux from a pulsed He plasma in a DBD-PID were investigated using a two-dimensional plasma hydrodynamics model. The ionizing photon flux originated from the resonance states of helium, He(3P) and He(2 1 P), and from the dimer excimer He 2 *. While the photon flux from the resonant states was modulated over the voltage pulse, the photon flux from He 2 * persisted long after the voltage pulse passed. Several geometrical optimizations were investigated, such as using an array of pointed electrodes. However, increasing the capacitance of the dielectric enclosing the plasma chamber had the largest effect on increasing the VUV photon fluence to gas analytes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Laser pulse induced second- and third-harmonic generation of gold nanorods with real-time time-dependent density functional tight binding (RT-TDDFTB) method

In this paper, we investigate second- and third-harmonic generation processes in Au nanorod systems using the real-time time-dependent density functional tight binding method. Our study focuses on the computation of nonlinear signals based on the time dependent dipole response induced by linearly polarized laser pulses interacting with nanoparticles. We systematically explore the influence of various laser parameters, including pump intensity, duration, frequency, and polarization directions, on harmonic generation. We demonstrate all the results using Au nanorod dimer systems arranged in end-to-end configurations, and disrupting the spatial symmetry of regular single nanorod systems is crucial for second-harmonic generation processes. Furthermore, we study the impact of nanorod lengths, which lead to variable plasmon energies, on harmonic generation, and estimates of polarizabilities and hyper-polarizabilities are provided.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Interplay of coulomb and exciton–phonon coupling controls singlet fission dynamics in two pentacene polymorphs

Pentacene is an important model organic semiconductor in both the singlet exciton fission (SF) and organic electronics communities. We have investigated the effect of changing crystal structure on the SF process, generating multiple triplet excitons from an initial singlet exciton, and subsequent triplet recombination. Unlike for similar organic semiconductors that have strong SF sensitive to polymorphism, we find almost no quantitative difference between the kinetics of triplet pair (TT) formation in the two dominant polymorphs of pentacene. Both pairwise dimer coupling and momentum-space crystal models predict much faster TT formation from the bright singlet excited state of the Bulk vs ThinFilm polymorph, contrasting with the experiment. GW and Bethe–Salpeter equation calculations, including exciton–phonon coupling, reveal that ultrafast phonon-driven transitions in the ThinFilm polymorph compensate the intrinsically slower purely Coulomb-mediated TT formation channel, rationalizing the similarity in observed rates. Taking into account the influence of subtle structural distinctions on both the direct and phonon-mediated SF pathways reveals a predictive capability to these methods, expected to be applicable to a wide variety of molecular crystals.

14 SOLAR ENERGY↗

Noncollinear polar magnet Fe 2 (SeO 3 ) 3 (H 2 O) 3 with inequivalent Fe 3+ sites

The emergence of novel magnetic states becomes more likely when the inversion symmetry of the crystal field, relative to the center between two spins, is broken. We propose that placing magnetic spins in inequivalent sites in a polar lattice can promote a realization of nontrivial magnetic states and associated magnetic properties. To test our hypothesis, we study Fe 2 (SeO 3 )(H 2 O) 3 as a model system that displays two distinct Fe(1) and Fe(2) magnetic sites in a polar structure (R3c space group). At low fields μ 0 H≤ 0.06 T, the material undergoes an antiferromagnetic ordering with T N1 = 77 K and a second transition at T N2 ≈ 4 K. At μ 0 H≥ 0.06 T and 74 K ≤T≤ 76 K, a positive entropy change of ∼0.12 mJ mol −1 K −1 can be associated with a metamagnetic transition to possibly nontrivial spin states. At zero field, Fe(1) is nearly fully ordered at T≈ 25 K, while Fe(2) features magnetic frustration down to T = 4 K. The magnetic ground state, a result corroborated by single-crystal neutron diffraction and 57 Fe Mössbauer spectroscopy, is a noncollinear antiparallel arrangement of ferrimagnetic Fe(1)–Fe(2) dimers along the c-axis. The results demonstrate that placing distinct magnetic sites in a polar crystal lattice can enable a new pathway to modifying spin, orbital, and lattice degrees of freedom for unconventional magnetism.

Crystal lattices↗

Extending Badger's rule. I. The relationship between energy and structure in hydrogen bonds

Here, we derive a new expression for the strength of a hydrogen bond (V HB ) in terms of the elongation of the covalent bond of the donor fragment participating in the hydrogen bond (Δr HB ) and the intermolecular coordinates R (separation between the heavy atoms) and θ (deviation of the hydrogen bond from linearity). The expression includes components describing the covalent D–H bond of the hydrogen bond donor via a Morse potential, the Pauli repulsion, and electrostatic interactions between the constituent fragments using a linear expansion of their dipole moment and a quadratic expansion of their polarizability tensor. We fitted the parameters of the model using ab initio electronic structure results for six hydrogen bonded dimers, namely, NH 3 –NH 3 , H 2 O–H 2 O, HF–HF, H 2 O–NH 3 , HF–H 2 O, and HF–NH 3 , and validated its performance for extended parts of their potential energy surfaces, resulting in a mean absolute error ranging from 0.07 to 0.31 kcal/mol. The derived expression describes the energy–structure relationship in terms of a single structural parameter, namely, the elongation of the donor’s covalent bond (Δr HB ), and suggests the novel relationship of 8.0 kcal/mol pm −1 (or 0.8 kcal/mol per 0.001 Å elongation). This structural parameter is easily obtained from theory and can serve as the single descriptor of the strength of individual hydrogen bonds.

Santis, Garrett D. [Univ. of Washington, Seattle, ↗

Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures

It is essential that mesoscopic simulations of reactive systems reproduce the correct statistical distributions at thermodynamic equilibrium. By considering a compressible fluctuating hydrodynamics (FHD) simulation method of ideal gas mixtures undergoing reversible reactions described by the chemical Langevin equations, we show that thermodynamic consistency in reaction rates and the use of instantaneous temperatures for the evaluation of reaction rates is required for fluctuations for the overall system to be correct. We then formulate the required properties of a thermodynamically consistent reaction (TCR) model. As noted in the literature, while reactions are often discussed in terms of forward and reverse rates, these rates should not be modeled independently because they must be compatible with thermodynamic equilibrium for the system. Using a simple TCR model where each chemical species has constant heat capacity, we derive the explicit condition that the forward and reverse reaction rate constants must satisfy in order for the system to be thermodynamically consistent. We perform equilibrium and non-equilibrium simulations of ideal gas mixtures undergoing a reversible dimerization reaction to measure the fluctuational behavior of the system numerically. We confirm that FHD simulations with the TCR model give the correct static structure factor of equilibrium fluctuations. For the statistically steady simulation of a gas mixture between two isothermal walls with different temperatures, we show using the TCR model that the temperature variance agrees with the corresponding thermodynamic-equilibrium temperature variance in the interior of the system, whereas noticeable deviations are present in regions near walls, where chemistry is far from equilibrium.

Polimeno, Matteo [University of California, Merced↗

Accurate noncovalent interactions in atomistic systems via quantum Drude oscillators

Accurately modeling polarization and van der Waals (vdW) interactions in atomistic systems typically requires high-level quantum-mechanical methods that are computationally expensive, hence limited in applicability. To address this challenge, efficient yet physically grounded models are needed—ones that not only enable accurate predictions but also provide insight into how noncovalent interactions scale in complex molecular and material systems. This review highlights the quantum Drude oscillator (QDO) model, a physically motivated and computationally efficient framework that captures the essential features of electronic response, including polarization and dispersion forces, across a wide range of chemical and material systems. We discuss how the QDO model quantitatively reproduces the polarization response of many-electron atoms and how key components of noncovalent interactions—exchange-repulsion, polarization, and dispersion—emerge naturally in QDO dimers. Furthermore, the model provides predictive scaling laws that elucidate trends in polarizability and dispersion across the periodic table and in molecular assemblies. By uniting interpretability, accuracy, and efficiency, the QDO model offers a versatile approach for modeling noncovalent interactions in systems ranging from isolated molecules to complex condensed phases and nanostructured materials.

Khabibrakhmanov, Almaz [Univ. of Luxembourg, Luxem↗

Evidence for Ga clusters in β-Ga 2 O 3 from Raman spectroscopy and density functional theory

Monoclinic gallium oxide (β-Ga 2 O 3 ) single crystals have a Raman mode at ∼250 cm −1 that is strongly correlated with free-electron density. Prior work attributed this peak to an electronic excitation of a shallow donor impurity band. However, heavily n-type thin films grown by metalorganic chemical vapor deposition or molecular beam epitaxy do not have the peak. In the present work, an alternate model is proposed: the 250 cm −1 Raman peak arises from Ga clusters, defined as two or more Ga atoms that form Ga–Ga bonds. Raman mapping reveals variations in the frequency that are consistent with a distribution of cluster sizes. The intensity of the peak decreases as the temperature is raised, attributed to melting of the Ga clusters. First-principles calculations indicate that the 250 cm −1 mode is due to Ga–Ga bond-stretching vibrations. As the Fermi energy is raised, the formation of Ga–Ga dimers becomes energetically favorable, explaining the correlation between n-type conductivity and the appearance of the Raman peak.

36 MATERIALS SCIENCE↗

Efficient Berry phase calculation via adaptive variational quantum computing approach

We present an adaptive variational quantum algorithm to estimate the Berry phase accumulated by a nondegenerate ground state under cyclic, adiabatic evolution of a time-dependent Hamiltonian. Our method leverages cyclic adiabatic evolution of the Hamiltonian and employs adaptive variational quantum algorithms for state preparation and evolution, optimizing circuit efficiency while maintaining high accuracy. We benchmark our approach on dimerized Fermi–Hubbard chains with four sites, demonstrating precise Berry phase simulations in both noninteracting and interacting regimes. Our results show that circuit depths reach up to 106 layers for noninteracting systems and increase to 279 layers for interacting systems due to added complexity. In addition, we demonstrate the robustness of our scheme across a wide range of parameters governing adiabatic evolution and variational algorithms. These findings highlight the potential of adaptive variational quantum algorithms for advancing quantum simulations of topological materials and computing geometric phases in strongly correlated systems.

Mootz, Martin [Ames Laboratory (AMES), Ames, IA (U↗

Prospects for detecting UF6 hydrolysis intermediates by mass spectrometry, resonance Raman, and NQR spectroscopy

Simulations are performed to consider several spectrometric and spectroscopic candidates for elucidating the mechanism of the hydrolysis of uranium hexafluoride (UF6). This study is among the first to benchmark the def-mTZVP basis sets for actinide-containing molecules, and it is shown to be a suitable basis set for surveying geometrical structures and vibrational spectra when used in conjunction with density functional theory. An experiment is proposed coupling mass spectrometric ion selection with vibrational spectroscopy, and supporting infrared and Raman spectral simulations demonstrate that ionization blue-shifts bands and can change their qualitative features. Ultraviolet resonance Raman is shown to have good prospects for discriminating U–O–U bridged intermediates, evidence for which was observed recently [L. E. McNamara et al., J. Phys. Chem. A 130, 775–786 (2026)]. As a more speculative approach, we also consider the prospect of addressing 233U or 235U nuclei by quadrupole resonance (NQR) spectroscopy for assigning early stage intermediate complexes. In doing so, we provide a first order-of-magnitude estimate for the collision-induced NQR signal for the UF6 dimer, which is of interest for the interpretation of a fast decoherence time observed in liquid-phase nuclear magnetic resonance. Having provided critical insights into the formation and stability of UF6 hydrolysis intermediates in previous studies, this computational spectroscopy survey is expected to help guide and expedite future laboratory campaigns.

Lutz, Jesse J. [Center for Computing Research, San↗

High-throughput studies of novel magnetic materials in borides

Borides are a versatile material family with various properties for valuable applications. Conventional magnetism, such as ferromagnetism and antiferromagnetism in borides, have been extensively studied. However, research on unconventional magnetism in borides where quantum effects are dominant is scarce. Here, we implement a high-throughput workflow combining first-principles calculations, materials prediction, and magnetic properties calculations to discover novel magnetism and magnetic materials in borides. Successfully applying the workflow, we report three families of novel magnetic borides, including two families of borides exhibiting quantum magnetism. One is a family of dimerized quantum magnets among YCrB 4 -type borides, which provides a rare platform for studying the spin-gap quantum critical point. The other is a family of altermagnets among FeMo2B 2 -type borides, extending the magnetic orderings exhibited by borides beyond conventional ferromagnetism and antiferromagnetism. We also predict a family of magnetic laminate transition metal borides, known as the MAB phases, in the AlFe 2 B 2 -type family, which provide pure-phase or alloying candidates for studying magnetocaloric materials and the associated magnetic transitions. The workflow is expected to be used in further studies of novel magnetism and magnetic materials.

36 MATERIALS SCIENCE↗

TDP-43 α-helical structure tunes liquid–liquid phase separation and function

Liquid–liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. The RNA-binding protein TDP-43 is present in several MLOs, undergoes LLPS, and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some ALS-associated mutations in TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes upon dimerization of TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix–helix interaction, which are removed in part by variants at these positions, including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase-separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a minigene assay. Therefore, the TDP-43 helical region serves as a short but uniquely tunable module where application of biophysical principles can precisely control assembly and function in cellular and synthetic biology applications of LLPS.

60 APPLIED LIFE SCIENCES↗

Ring currents modulate optoelectronic properties of aromatic chromophores at 25 T

The properties of organic molecules can be influenced by magnetic fields, and these magnetic field effects are diverse. They range from inducing nuclear Zeeman splitting for structural determination in NMR spectroscopy to polaron Zeeman splitting organic spintronics and organic magnetoresistance. A pervasive magnetic field effect on an aromatic molecule is the aromatic ring current, which can be thought of as an induction of a circular current of π-electrons upon the application of a magnetic field perpendicular to the π-system of the molecule. While in NMR spectroscopy the effects of ring currents on the chemical shifts of nearby protons are relatively well understood, and even predictable, the consequences of these modified electronic states on the spectroscopy of molecules has remained unknown. In this work, we find that photophysical properties of model phthalocyanine compounds and their aggregates display clear magnetic field dependences up to 25 T, with the aggregates showing more drastic magnetic field sensitivities depending on the intermolecular interactions with the amplification of ring currents in stacked aggregates. These observations are consistent with ring currents measured in NMR spectroscopy and simulated in time-dependent density functional theory calculations of magnetic field-dependent phthalocyanine monomer and dimer absorption spectra. Here, we propose that ring currents in organic semiconductors, which commonly comprise aromatic moieties, may present new opportunities for the understanding and exploitation of combined optical, electronic, and magnetic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A cocrystal structure of dengue capsid protein in complex of inhibitor

Dengue virus (DENV) was listed as a top 10 public health threat by the World Health Organization in 2019. No clinically approved anti-DENV drug is currently available. Here we report the high-resolution cocrystal structure (1.5 Å) of the DENV-2 capsid protein in complex with an inhibitor that potently suppresses DENV-2 but not other DENV serotypes. The inhibitor induces a “kissing” interaction between two capsid dimers. The inhibitor-bound capsid tetramers are assembled inside virions, resulting in defective uncoating of nucleocapsid when infecting new cells. Resistant DENV-2 emerges through one mutation that abolishes hydrogen bonds in the capsid structure, leading to a loss of compound binding. Structure-based analysis has defined the amino acids responsible for the inhibitor’s inefficacy against other DENV serotypes. The results have uncovered an antiviral mechanism through inhibitor-induced tetramerization of the viral capsid and provided essential structural and functional knowledge for rational design of panserotype DENV capsid inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization and engineering of a two-enzyme system for plastics depolymerization

Significance Deconstruction of recalcitrant polymers, such as cellulose or chitin, is accomplished in nature by synergistic enzyme cocktails that evolved over millions of years. In these systems, soluble dimeric or oligomeric intermediates are typically released via interfacial biocatalysis, and additional enzymes often process the soluble intermediates into monomers for microbial uptake. The recent discovery of a two-enzyme system for polyethylene terephthalate (PET) deconstruction, which employs one enzyme to convert the polymer into soluble intermediates and another enzyme to produce the constituent PET monomers (MHETase), suggests that nature may be evolving similar deconstruction strategies for synthetic plastics. This study on the characterization of the MHETase enzyme and synergy of the two-enzyme PET depolymerization system may inform enzyme cocktail-based strategies for plastics upcycling.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis for autophagy inhibition by the human Rubicon–Rab7 complex

Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7–GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7–GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab–effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.

60 APPLIED LIFE SCIENCES↗