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At least 505 records · Page 28

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural incorporation into goethite fractionates rare earth elements

Up to 20% of rare earth elements (REEs) in ion adsorption deposits (IADs) are associated with iron oxide minerals, primarily goethite. Often termed “non-extractable”, goethite-hosted REEs are thought to be structurally incorporated into the mineral lattice. The large mismatch in size and charge density between REEs (ionic radius, r = 0.86–1.03 Å) and Fe 3+ (r = 0.65 Å), however, makes direct substitution energetically unfavorable. To determine REE compatibility with and incorporation into goethite on the atomic level, we used X-ray pair distribution function analysis (PDF) and LIII-edge extended X-ray absorption fine structure (EXAFS) spectroscopy. The compatibility of REEs with goethite and the precursor ferrihydrite (FH) is Lu ≥ Yb ≫ Dy > Nd for both phases. Nd and Dy primarily form secondary amorphous phases, with <30% Nd and Dy incorporated into goethite. In the FH precursor at pH 6.8, Yb and Lu assumed a local REE-OOH like structure with next nearest neighbor Fe. The Yb, Lu, and Nd-FH samples were also matured at ambient conditions for 100 days; despite the presence of only ∼5% goethite, Lu and Yb were 42% and 100% in goethite-like structural environments, respectively, whereas the PDF and EXAFS of Nd showed little evidence of any incorporation. Using ab initio molecular dynamics (AIMD) to model the EXAFS, we determined the presence of protonated Fe vacancies, edge-sharing with structural Lu and Yb, likely helped accommodate these REEs in the goethite structure. Incorporation into Fe oxyhydroxides thus potentially fractionates the REEs during weathering associated with formation of lateritic and ion adsorption deposits.

Mergelsberg, Sebastian T. [Pacific Northwest Natio↗

A Combined Crossed Molecular Beam and Theoretical Investigation of the Elementary Reaction of Tricarbon (C 3 (X 1 Σ g + )) with Diacetylene (C 4 H 2 (X 1 Σ g + )): Gas Phase Formation of the Heptatriynylidyne Radical ( l -C 7 H(X 2 Π))

An elucidation of the underlying formation pathways to acyclic hydrocarbons such as polyynes (C n H 2 ), cumulenes (C n H 2 ), and linear resonantly stabilized linear radicals (l-C n H) is indispensable to understand the hydrocarbon chemistry in extreme low and high temperature environments. In this study, we exploited the crossed molecular beam technique to investigate the reaction of tricarbon C 3 (X 1 Σ g + ) with diacetylene (butadiyne; HCCCCH; X 1 Σ g + ) at a collision energy of 47 ± 1 kJ mol ⁻1 . The experimental data were merged with ab initio calculations of the singlet C 7 H 2 potential energy surface (PES) revealing that the reaction is initiated via the formation of an initial van der Waals reactant complex in the entrance channel. Subsequent rearrangements lead to various carbene-type and cyclic intermediates via ring-opening, ring-closure, and hydrogen migration processes eventually forming acyclic C 7 H 2 isomers prior to their barrierless unimolecular decomposition to the most stable linear isomer, heptatriynylidyne (C 7 H, X 2 Π) in an overall endoergic reaction (+57 kJ mol ⁻1 ). The reaction exhibits strong similarities to the tricarbon – acetylene (C 3 – C 2 H 2 ). Furthermore, the significant energy threshold suggests that the tricarbon reaction with (poly)acetylenes forming resonantly stabilized linear radicals are open in high-temperature environments such as combustion flames and circumstellar envelopes of carbon stars and planetary nebulae as their descendants; however, these reactions are closed in low-temperature environments as in cold molecular clouds and hydrocarbon-rich atmospheres of planets and their moons such as in Titan.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Melting point of iron at high pressure: An assessment of uncertainties and effect of electronic temperature

An accurate calculation of the melting point of iron at various pressures in the Earth's core is important for understanding the core structure, geodynamo, and the Earth's history. Previous studies have assessed the melt line of iron at these extreme conditions using various experimental measurement techniques as well as both ab initio and classic molecular dynamics simulations. However, experimental measurements have uncertainties up to several hundred Kelvin, and inconsistencies remain among simulation results. Here in this work, we propose an iterative framework that couples density functional theory (DFT) calculations and molecular dynamics simulations performed using an ensemble of interatomic potentials to assess the effect of electronic temperature on the melting point. We systematically validate the potentials by comparing lattice constants and phonon dispersion curves at 0 K and enthalpy differences between liquid and HCP, FCC, BCC phases of iron close to the melt line at 300 GPa with DFT. Our results show that HCP iron melts at 6144 K (at 300 GPa), BCC phase is thermodynamically unstable, and FCC is metastable at this temperature. The melting points of FCC and BCC phases at 300 GPa are 5858 and 5647 K, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Association Kinetics for Perfluorinated n -Alkyl Radicals

Radical-radical reaction channels are important in the pyrolysis and oxidation chemistry of perfluoroalkyl substances (PFAS). In particular, unimolecular dissociation reactions within unbranched n-perfluoroalkyl chains, and their corresponding reverse barrierless association reactions, are expected to be significant contributors to the gas-phase thermal decomposition of families of species such as perfluorinated carboxylic acids and perfluorinated sulfonic acids. Unfortunately, experimental data for these reactions are scarce and uncertain. Furthermore, obtaining reliable theoretical predictions for such reactions is a laborious and computationally intensive task. Here, in this work, the chemical kinetics of the various association/decomposition reactions producing/decomposing the C 2 -C 4 series of unbranched n-perfluoroalkanes (C 2 F 6 , C 3 F 8 , and C 4 F 10 ) are examined using state-of-the-art ab initio transition-state-theory-based master-equation calculations. The variable-reaction-coordinate transition-state theory (VRC-TST) formalism is employed in computing the microcanonical and canonical rates for the association reactions. Reaction thermochemistry is obtained via composite quantum chemistry calculations and the laddering of error-canceling reaction schemes via a connectivity-based hierarchy approach employing ANL1/ANL0-style reference energies. Lennard-Jones collision model parameters for the considered systems were estimated by a direct dynamics approach, and collisional energy transfer parameters were obtained from analogies to systems of similar size and heavy-atom connectivity. A one-dimensional master equation approach was used to convert the microcanonical rate coefficients from the VRC-TST analysis into temperature- and pressure-dependent rate constants for the association reactions and the reverse dissociation reactions. The data are reported in standardized formats for usage in comprehensive chemical kinetic models for PFAS thermal destruction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge-density-wave quantum critical point under pressure in 2 H -TaSe 2

The presence of a quantum-critical point (QCP) at which a nearby ordered phase is suppressed to zero temperature is often invoked to explain emergent quantum phases, e.g. superconductivity. Yet, identifying a QCP and establishing its correlation with superconductivity remains challenging. Materials featuring charge-density-wave (CDW) order and superconductivity offer a clear scenario as both states can be associated with electron-phonon coupling. Here, we uncover a CDW-QCP and demonstrate its interrelation with superconductivity in the prototypical transition-metal dichalcogenide 2 H -TaSe 2 . We determine the evolution of the CDW state up to and beyond its suppression at the critical pressure p c = 19.9(1) GPa by means of X-ray diffraction and inelastic X-ray scattering measurements providing a full crystallographic refinement of the commensurate CDW superstructure. The pressure-induced CDW-QCP in close vicinity to the maximum superconducting transition temperature. Ab-initio lattice dynamical calculations corroborate that 2 H -TaSe 2 features order-parameter fluctuation enhanced superconductivity and can serve as a paradigm to investigate superconductivity near a CDW-QCP.

critical phenomena↗

A numerical study of the meso-structure variability in the compaction process of prepreg platelet molded composites

Compaction deformations in a thermoplastic composite system molded from chopped prepreg platelets were analyzed to obtain statistical distributions of local distortions that define the final consolidated meso-structure. This study provides an insight into and allows quantification of the intrinsic geometric variability of the composite meso-structure that controls the variability of the effective composite mechanical properties. A two-phase viscoelastic finite element model was utilized to treat the behavior of molten prepreg platelets, which were assumed to be incompressible and inextensible in the fiber direction during processing. A two-step simulation procedure with discretely modeled platelets and platelet-to-platelet contacts is proposed. The analysis begins with a drop simulation of the uncontrolled material deposition followed by a 3D finite element analysis of the preform compaction and bulk material flow. The proposed model provides a method for generating a composite meso-structure ab initio starting from a statistical sampling of the initial conditions for platelet deposition. The predicted platelet thickness distribution, intra-platelet fiber waviness and out-of-plane platelet undulations were found to be in good agreement with experimental measurements. An estimate of the volume of resin pockets was inferred from the compaction simulation.

36 MATERIALS SCIENCE↗

Phase-field modeling of dislocation–interstitial interactions

The mechanical behavior of body-centered cubic (BCC) materials can be dramatically affected by the presence of interstitial solute atoms. Here we present a new phase-field dislocation dynamics formulation to include the diffusion of interstitials. Short-range interactions are accounted for by a concentration-dependent lattice energy, and long-range interactions are accounted for by modifications to the elastic energy. The interstitial diffusion law introduces gradients that require methods for minimizing Gibbs oscillations, which is done via a modified Green’s function. The formulation is general to any solute-solvent system and is applied here to Nb-O as a model system, whose interstitial parameters are obtained from ab initio calculations. The effect of O on the core structures of Nb edge and screw dislocations is calculated. The diffusion of O to form interstitial atmospheres around dislocation cores is simulated, as well as the critical stresses required for dislocations to break away or cross slip from these atmospheres. Future applications of the method to simulate complex interstitial embrittlement mechanisms are discussed.

36 MATERIALS SCIENCE↗

The Role of Cation Coordination in the Electrical and Optical Properties of Amorphous Transparent Conducting Oxides

Amorphous oxide semiconductor materials have demonstrated numerous advantages without compromise of electrical properties as compared to their crystalline counterparts, yet understanding of the fundamental principles allowing this has remained elusive. To study the origins of enhanced optoelectronic properties, we apply high-throughput, combinatorial sputtering, structural and spectral mapping, and computationally intensive ab initio molecular dynamics simulations with density functional theory to a ternary, post-transition metal oxide system, namely, zinc tin oxide. The deposited thin films exhibit a high figure of merit, achieving carrier densities in the range of 1019 to 1020 cm–3 and carrier mobilities up to 35 cm2/Vs. These results highlight the role of local distortions and cation coordination in determining the microscopic origins of carrier generation and transport. In particular, we identify the strong likelihood of Sn undercoordination in both Zn-poor and Zn-rich phases leading to the high carrier concentrations observed. This not only diverges from the still widespread historical indictment of oxygen vacancies controlling carrier population in crystalline oxides but also provides a comprehensive framework to describe the unique structure–property relationships using specific structural and electronic descriptors in disordered phase materials.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,M↗

Applications of the modified Hulthén-Kohn method for bound and scattering states

We adapt the Hulthén–Kohn method suggested by Efros [Phys. Rev. C 99, 034620 (2019)] for calculating various observables in the continuum and discrete spectrum using two-body interactions in single- and coupled channel systems. We explore the convergence of phase shifts and wave functions as well as the location of S-matrix poles which enables obtaining both resonance and bound state parameters. We find that employing a harmonic oscillator basis, together with an interaction smoothing scheme introduced by Gyarmati et al. [Nucl. Phys. A 326, 119 (1979)], and adopting approximate bound-state solutions for the short-range components of basis wave functions lead to good convergence even with restricted oscillator quanta accessible for modern no-core shell model codes. The adapted Efros method will facilitate ab initio many-body nuclear structure applications.

Nuclear reactions↗

Doping topological Dirac semimetal with magnetic impurities: Electronic structure of Mn-doped Cd 3 ⁢As 2

The prospect of transforming a Dirac topological semimetal (TSM) into a Weyl TSM phase, following doping by magnetic impurities, is central to TSM applications. The magnetic field from polarized 𝑑 levels of magnetic impurities produces a field with a sharp local structure. To what extent magnetic impurities act in the same manner as an applied field and what are the effects of such a field on the electronic structure of a Dirac TSM are the subject of this paper. We present electronic structure calculations of bulk Cd 3 ⁢As 2 with substitutional doping of Mn impurities in the dilute alloy range. Quasiparticle 𝐺⁡𝑊 (QS⁢𝐺⁡𝑊) ab initio electronic structure calculations are used in conjunction with 𝑘 · 𝑝 model Hamiltonian calculations. As expected, we observe the splitting of the Dirac points into pairs of Weyl points following the doping with Mn. We also show that the electronic structure of Mn-doped Cd 3⁢ As 2 can be emulated by the electronic structure of pristine Cd 3⁢ As 2 with an appropriate external magnetic field. Some properties of the conductivity of bulk Cd 3 ⁢As 2 for different magnetic field orientations are also investigated. Our results inform future opportunities for unique device functionality based on band structure tuning not found in conventional magnetic Weyl TSM.

36 MATERIALS SCIENCE↗

Acceptor and compensating donor doping of single crystalline SnO (001) films grown by molecular beam epitaxy and its perspectives for optoelectronics and gas-sensing

(La and Ga)-doped tin monoxide [stannous oxide, tin (II) oxide, SnO] thin films were grown by plasma-assisted and suboxide molecular beam epitaxy with dopant concentrations ranging from ≈ 5 × 10 18 to 2 × 10 21 cm -3 . In this concentration range, the incorporation of Ga into SnO was limited by the formation of secondary phases observed at 1.2 × 10 21 cm -3 Ga, while the incorporation of La showed a lower solubility limit. Transport measurements on the doped samples reveal that Ga acts as an acceptor and La as a compensating donor. While Ga doping led to an increase in the hole concentration from 1 × 10 18 -1 × 10 19 cm -3 for unintentionally doped (UID) SnO up to 5 × 10 19 cm -3 , La-concentrations well in excess of the UID acceptor concentration resulted in semi-insulating films without detectable n-type conductivity. Ab initio calculations qualitatively agree with our dopant assignment of Ga and La and further predict In Sn to act as an acceptor as well as Al Sn and B Sn as donors. These results show the possibilities of controlling the hole concentration in p-type SnO, which can be useful for a range of optoelectronic and gas-sensing applications.

36 MATERIALS SCIENCE↗

Signatures of van Hove singularities in the anisotropic in-plane optical conductivity of the topological semimetal Nb 3 ⁢SiTe 6

In this work, we present a temperature-dependent infrared spectroscopy study on the layered topological semimetal Nb 3 ⁢SiTe 6 combined with density-functional theory calculations of the electronic band structure and optical conductivity. Our results reveal an anisotropic behavior of the in-plane (ac-plane) optical conductivity, with three pronounced excitations located at around 0.15, 0.28, and 0.41 eV for the polarization of the incident radiation along the c axis. These excitations are well reproduced in the theoretical spectra. Based on the ab initio results, the excitations around 0.15 and 0.28 eV are interpreted as fingerprints of van Hove singularities in the electronic band structure and compared to the findings for other topological semimetals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

CrI 3 revisited with a many-body ab initio theoretical approach

CrI 3 has recently been shown to exhibit low-dimensional, long-range magnetic ordering from few layers to single layers of CrI 3 . The properties of CrI 3 bulk and few layered systems are uniquely defined by a combination of short-range intralayer and long-range interlayer interactions; including strong correlations, exchange and spin orbit coupling. Unfortunately, both the long-range van der Waals interactions, which are driven by dynamic, many-body electronic correlations and the competing strong intralayer correlations, present a formidable challenging for the local or semi local mean-field approximations employed in workhorse electronic structure approaches like density functional theory. In this work, we employ a sophisticated many-body approach that can simultaneously describe long- and short-range correlations. Herein, we establish that the fixed-node diffusion Monte Carlo (FNDMC) method reproduces the experimental interlayer separation distance of bulk CrI 3 for the high-temperature, monoclinic phase, with a reliable prediction of the interlayer binding energy. We subsequently employed, the FNDMC results to benchmark the accuracy of several density functional theory exchange-correlation approximations.

36 MATERIALS SCIENCE↗

The critical role of intrinsic defects and many-body interactions on the stability of MnBi2Te4

Intrinsic antisite defects pose a major challenge to understanding and predicting the exotic properties of the layered topological magnetic insulator MnBi2Te4 (MBT). In this work, we study the origin of the abundance of intrinsic defects in MBT, including many-body defect–defect interactions and many-body electronic correlations. Until now, ab initio methods have struggled to explain thermodynamic stability and properties influenced by defect behavior in MBT. We model native Mn–Bi antisite defects in MBT at finite temperatures using a cluster expansion that includes defect–defect interactions. To overcome the limitations of conventional density functional theory (DFT), we introduce a hybrid approach that incorporates high-accuracy quantum Monte Carlo (QMC) calculations, introducing missing correlations. This strategy allows for accurate estimation of defect energetics and finite-temperature properties. We compute the configurational free energy, defect concentration, and configurational heat capacity, revealing a second-order order–disorder phase transition near the experimental synthesis temperature. Our study provides the first theoretical insight into the thermodynamics of intrinsic defects in MBT. The negative free energy relative to pristine MBT at synthesis temperatures indicates that Mn–Bi antisite formation is thermodynamically spontaneous. We also present a broadly applicable general framework for correcting low-level theoretical theories using highly accurate many-body corrections from QMC.

Ghaffar, Abdul [ORNL] (ORCID:0000000241190168)↗

First principles free energy model with dynamic magnetism for δ -plutonium

We present an ab initio free energy model derived from a fully relativistic density functional theory (DFT) electronic structure with dynamic magnetism for δ -plutonium (face-centered cubic, fcc). The DFT model is extended with orbital-orbital interaction in a parameter free orbital polarization (OP) mechanism consistent with previous modeling of plutonium. Gibbs free energy is built from components associated with the temperature dependence of the electronic structure and the corresponding electronic entropy, lattice vibrations within an anharmonic lattice dynamics model, and dynamical fluctuations of the magnetization density, i.e. magnetic fluctuations. The fluctuation model consists of transverse and longitudinal modes driven by temperature induced excitations of the DFT + OP electronic structure. The ab initio model thus incorporates fluctuating states beyond the electronic ground state. Thanks to the dynamic magnetism, the theory predicts excellent thermodynamic properties and a Gibbs free energy in accord with CALPHAD and semi-empirical modeling developed from the thermodynamic observables. The magnetic fluctuations further explain anomalous behaviors of the thermal expansion in plutonium. Specifically, a thermal expansion for the δ -plutonium system turning from positive to negative at temperatures above room temperature, a tendency for gallium to reduce and remove the negative thermal expansion depending on composition, and a positive thermal expansion for the high temperature ϵ phase.

dynamic↗

Moiré Kanamori-Hubbard model for transition metal dichalcogenide homobilayers

Ab initio and continuum model studies predicted that the Γ valley transition metal dichalcogenide (TMD) homobilayers could simulate the conventional multiorbital Hubbard model on the moiré honeycomb lattice. Here, in this work, we perform the Wannierization starting from the continuum model and show that a more general moiré Kanamori-Hubbard model emerges, beyond the extensively studied standard multiorbital Hubbard model, which can be used to investigate the many-body physics in the Γ valley TMD homobilayers. Using the unrestricted Hartree-Fock and Lanczos techniques, we study these half-filled multiorbital moiré bands. By constructing the phase diagrams we predict the presence of an antiferromagnetic state and in addition we found unexpected and dominant states, such as a S = 1 ferromagnetic insulator and a charge density wave state. Our theoretical predictions made using this model can be tested in future experiments on the Γ valley TMD homobilayers.

2-dimensional systems↗

Revisiting Competitive Adsorption of Small Molecules in the Metal–Organic Framework Ni-MOF-74

To precisely evaluate the potential of metal-organic frameworks (MOFs) for gas separation and purification applications, it is crucial to understand how various molecules competitively adsorb inside MOFs. In this paper, we combine in situ infrared spectroscopy with ab initio calculations to investigate the mechanisms associated with co-adsorption of a number of small molecules including CO, NO, and CO 2 inside the prototypical framework Ni-MOF-74. Surprisingly, we find that the displacement of CO bound inside Ni-MOF-74 (binding energy of 53 kJ/mol) is readily driven by CO 2 exposure, even though CO 2 has a noticeably weaker binding energy of only 41 kJ/mol; meanwhile, the significantly more strongly binding NO molecule (90 kJ/mol) is not able to easily displace bound CO inside Ni-MOF74. These results show that single-phase binding energies of a molecule inside the MOF cannot completely describe their interaction with the MOF in the presence of other guest molecules. Here, we unveil a number of crucial factors such as the kinetic barrier, partial pressure, secondary binding sites, and guest-host/lateral interactions that control the co-adsorption process and combined with the binding energy are better descriptors of the behavior and adsorption of gas mixtures inside MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗