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At least 721 records · Page 40

Non-Empirical and Self-Interaction Corrections for DFTB: Towards Accurate Quantum Simulations for Large Mesoscale Systems (Final Report)

This project was comprised of two complementary (but parallel) thrusts: (1) implementing massively-parallelized computing hardware (with new computational hardware that may replace GPUs) in the density functional tight binding (DFTB) approach and (2) developing new capabilities in DFTB to calculate the electronic structure and dynamics of large chemical systems. While classical molecular dynamics can handle hundreds of thousands of atoms, it cannot provide a first-principles based description of chemical systems at the quantum level. At the other extreme, conventional Kohn-Sham DFT methods can probe the true quantum mechanical nature of chemical systems; however, these methods cannot tackle the large sizes and length scales relevant to dynamics simulations of realistic systems. The DFTB formalism utilized in this project provides a viable approach for probing these large systems at a quantum mechanical level of detail. However, to utilize the DFTB approach for accurate calculations of electronic properties, it is crucial to incorporate quantum-based corrections in DFTB since exchange-correlation effects can still remain very strong in these large systems. At the same time, enhancing the computational efficiency of DFTB is also essential since optimal computational performance is required for addressing the large size scales associated with realistic chemical systems. As such, the new non-empirical corrections and computing hardware enhancements implemented in this project will enable accurate and computationally efficient approaches to directly probe electronic properties in these large, complex systems.

36 MATERIALS SCIENCE↗

Visualizing Anisotropic Oxygen Diffusion in Ceria under Activated Conditions

Oxygen reactivity plays a key role in the performance of ceria-based catalysts. Aberration-corrected transmission electron microscopy and molecular dynamics simulations were used to study the oxygen atom diffusion in ceria under activated conditions. Reactive oxygen atom and its real-time diffusion were visualized. Additionally, the interplay between cerium and oxygen atoms originating from a Coulomb interaction was revealed by the out-of-plane buckling of cerium atoms associated with oxygen transport. Anisotropic oxygen atom diffusion that depends on crystal orientations was discovered, demonstrating a preferential [001] crystallographic diffusion pathway. These findings reveal prospects for applications of anisotropic orientation-relevant fluorite-structured oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electron-beam-driven chemical processes during liquid phase transmission electron microscopy

Liquid phase (or liquid cell) transmission electron microscopy (LP-TEM) has been established as a powerful tool for observing dynamic processes in liquids at nanometer to atomic length scales. However, the simple act of observation using electrons irreversibly alters the nature of the sample. A clear understanding of electron beam-driven processes during LP-TEM is required to interpret in situ observations and utilize the electron beam as a stimulus to drive nanoscale dynamic processes. In this review, we discuss recent advances toward understanding, quantifying, mitigating, and harnessing electron beam-driven chemical processes occurring during LP-TEM. We will highlight progress in several research areas, including modeling electron beam-induced radiolysis near interfaces, electron beam-induced nanocrystal formation, and radiation damage of soft materials and biomolecules.

Woehl, Taylor J.↗

Large-Scale, GPU-Enhanced DFTB Approaches for Probing Multi-Component Alloys

The major goals of the project are to develop and apply GPU-enhanced density functional theory tight binding (DFTB) calculations for efficient simulations of structural materials of alloy systems. The figure below depicts the GPU algorithmic developments on the left that will be carried out, and the solid-state structures on the right are representative of the complex alloys that can be computed with the GPU-enhanced DFTB approach. The methodology and tools developed in this project encompass accurate intermolecular potentials and GPU enhancements to the density functional tight binding (DFTB) approach for high-throughput ab initio molecular dynamics calculations of multi-component alloys at elevated temperatures. While classical molecular dynamics can handle hundreds of thousands of atoms, it cannot provide a first-principles based description of large, multi-component alloys at the predictive quantum level. At the other extreme, conventional Kohn-Sham DFT methods can probe the true quantum nature of chemical systems; however, these methods cannot tackle the large sizes relevant to these multi-component systems. The DFTB-based ab initio molecular dynamics approach (coupled with our in-house GPU capabilities for enhanced speed) used in this project provides a viable approach for probing these large systems at a quantum level of detail that is significantly faster than current first-principle methods Collectively, the capabilities developed in this project directly respond to DOE HBCU-OMI, AOI 2-1 initiatives by (1) enabling accurate and efficient predictions and (2) bringing a fundamental understanding of structural interactions in these complex systems at elevated temperatures.

20 FOSSIL-FUELED POWER PLANTS↗

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern↗

High-temperature ion-thermal behavior from average-atom calculations

Atom-in-jellium calculations of the Einstein frequency were used to calculate the mean displacement of an ion over a wide range of compression and temperature. Expressed as a fraction of the Wigner-Seitz radius, the displacement is a measure of the asymptotic freedom of the ion at high temperature, and thus of the change in heat capacity from six to three quadratic degrees of freedom per atom. A functional form for free energy was proposed based on the Maxwell-Boltzmann distribution as a correction to the Debye free energy, with a single free parameter representing the effective density of potential modes to be saturated. Finally, this parameter was investigated using molecular dynamics simulations, and found to be ~0.2 per atom. In this way, the ion-thermal contribution can be calculated for a wide-range equation of state (EOS) without requiring a large number of molecular dynamics simulations. Example calculations were performed for carbon, including the sensitivity of key EOS loci to ionic freedom.

74 ATOMIC AND MOLECULAR PHYSICS↗

Comment on broadening of water microwave lines by collisions with helium atoms

Earlier theoretical descriptions of interaction forces and collision dynamics in the H2O-He system (Palma et al., 1988; Green et al., 1991) are improved by calculating the interaction at additional orientations and by including diffuse functions in the molecular orbital expansion basis set. The improvements make substantial changes to the potential energy surface, but make only small changes in predicted microwave pressure broadening coefficients. The qualitative temperature dependence and relative widths of different lines appear to be converged with respect to successive improvements to the theoretical description of this system. Remaining discrepancies with available data must reflect problems with the experimental values.

Maluendes, Sergio↗

Aliovalent Doping of CeO 2 Improves the Stability of Atomically Dispersed Pt

Atomically dispersed supported catalysts hold considerable promise as catalytic materials. The ability to employ and stabilize them against aggregation in complex process environments remains a key challenge to the elusive goal of 100% atom utilization in catalysis. In this work, using a Gd-doped ceria support for atomically dispersed surface Pt atoms, we establish how the combined effects of aliovalent doping and oxygen vacancy generation provide dynamic mechanisms that serve to enhance the stability of supported single atom configurations. Using correlated, in situ X-ray absorption, photoelectron and vibrational spectroscopies for analysis of the samples on the two types of support (with and without Gd doping), we establish that the Pt atoms locate proximal to Gd dopants, forming a speciation that serves to enhance the thermal stability of Pt atoms against aggregation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energy Transfer Mechanisms in Large Low-Bandgap Polymers from Time-Resolved Experiments and Nonadiabatic Molecular Dynamics Calculations

Conjugated polymers offer unprecedented chemical tunability for modulating energy transfer in a multitude of infrared light applications. In this work, we use a combination of time-resolved spectroscopic experiments and nonadiabatic molecular dynamics calculations to probe the photochemistry and nonradiative transitions in a recently synthesized narrow bandgap donor–acceptor conjugated polymer based on alternating cyclopentadithiophene and electronegative benzothiadiazole heterocycles. Using large-scale semi-empirical nonadiabatic molecular dynamics, which can treat a large 260-atom hexamer, we calculate an S 5 → S 1 lifetime of 34.75 fs, which is consistent with our time-resolved spectroscopic data. Our simulations suggest that vibronic motions of the central carbons in the cyclopentadithiophene functional groups are predominantly involved in the nonradiative transitions, and the excitation becomes more localized on a monomer fragment over time. The combined use of time-resolved experiments and nonadiabatic molecular dynamics calculations in this work provides mechanistic insight into chemical functionalities that can be tuned to enhance energy transfer in other prospective low-bandgap polymer materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic-Scale Insights into Carbon Dissolution in α-, γ-, and θ-Al 2 O 3 : Phase-dependent Transport Dynamics from First-Principles Calculations

α-Al 2 O 3 exhibits superior carburizing corrosion resistance compared to metastable γ-Al 2 O 3 and θ-Al 2 O 3 phases in high-temperature CO 2 environments, yet its atomic-scale origins remain unclear. Using first-principles density functional theory, we systematically investigate carbon dissolution and diffusion in α-Al 2 O 3 , γ-Al 2 O 3 , and θ-Al 2 O 3 , including the effects of oxygen (O) and aluminum (Al) vacancies. Our results show that α-Al 2 O 3 consistently exhibits higher carbon solution enthalpies than γ-Al 2 O 3 and θ-Al 2 O 3 in both pristine and defective structures, indicating lower intrinsic carbon solubility in α-Al 2 O 3 . Vacancies significantly enhance carbon incorporation: O vacancies reduce solution enthalpy, while Al vacancies further amplify this effect, with a strong preference for carbon at Al vacancy sites. Carbon diffusion barriers are also highest in α-Al 2 O 3 , reflecting slower carbon mobility. Al vacancies increase diffusion barriers across all phases, while O vacancies raise barriers in α- and γ-Al 2 O 3 but slightly lower them in θ-Al 2 O 3 . These results reveal a dual mechanism behind the carburizing resistance of α-Al 2 O 3 : reduced carbon solubility and elevated diffusion barriers. Furthermore, this work provides atomic-scale insights to guide the design of alumina-based materials with improved carburizing resistance through phase selection and defect engineering.

36 MATERIALS SCIENCE↗

Microscopic force driving the photoinduced ultrafast phase transition: Time-dependent density functional theory simulations of IrTe 2

Photoinduced phase transitions can have complex and intriguing behaviors more than material ground-state dynamics. Understanding the underlying mechanism can help us to design new ways to manipulate the materials. A variety of mechanisms has been proposed to explain the photoinduced phase transitions of IrTe 2 , but a consensus has yet to be reached. Here, we study the photo-induced phase transitions of IrTe 2 by performing the real-time time-dependent density functional theory (rt-TDDFT) simulations in combination with the occupation constrained DFT method. We reveal that the microscopic driving force for the photo-induced phase transitions arises from the tendency to lower the energy levels occupied by the excited carriers, through the increase or decrease of the associated atomic pair distances, depending on whether the newly occupied states are antibonding or bonding states, respectively. The geometric constraints between different bonds represented by the Poisson ratio can bring together different tendencies from different atomic pairs, thus forming a complex intriguing dynamic picture depending on the intensity of the excitation. Furthermore, we also find that phonons don't play a primary role, but can assist the phase transition. These findings imply that one can control the structural phase transitions by selectively exciting photocarriers into designated atomic states using appropriate photon sources.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Simulation of 24,000 Electron Dynamics: Real-Time Time-Dependent Density Functional Theory (TDDFT) with the Real-Space Multigrids (RMG)

Here, we present the theory, implementation, and benchmarking of a real-time time-dependent density functional theory (RT-TDDFT) module within the RMG code, designed to simulate the electronic response of molecular systems to external perturbations. Our method offers insights into nonequilibrium dynamics and excited states across a diverse range of systems, from small organic molecules to large metallic nanoparticles. Benchmarking results demonstrate excellent agreement with established TDDFT implementations and showcase the superior stability of our time integration algorithm, enabling long-term simulations with minimal energy drift. The scalability and efficiency of RMG on massively parallel architectures allow for simulations of complex systems, such as plasmonic nanoparticles with thousands of atoms. Future extensions, including nuclear and spin dynamics, will broaden the applicability of this RT-TDDFT implementation, providing a powerful toolset for studies of photoactive materials, nanoscale devices, and other systems where real-time electronic dynamics is essential.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Auroral zone effects on hydrogen geocorona structure and variability

The effect of diurnal and magnetospheric modulations on the structure of the hydrogen geocorona is analyzed on the basis of recent observations. Particular attention is given to the enhancement of neutral escape by plasma effects, including the recently observed phenomenon of low-altitude ion acceleration. It is found that, while significant fluxes of neutral H should be produced by transverse ion acceleration in the auroral zone, the process is probably insufficient to account for the observed polar depletion of hydrogen atoms. Analysis of recent exospheric temperature measurements from the Dynamics Explorer-2 satellite suggest that neutral heating in and near the high latitude cusp may be the major contributor to depleted atomic hydrogen densities at high latitudes. Altitude profiles of the production rates for escaping neutral hydrogen atoms during periods of maximum, minimum, and typical solar activity are provided.

Moore, T. E.↗

Atomic-scale mechanism of carbon nucleation from a deep crustal fluid by replica exchange reactive molecular dynamics simulation

Here we present a mechanistic model of carbon nucleation and growth from a fluid at elevated temperature (T) and pressure conditions, typical of those found in the shallow Earth’s lithosphere. Our model uses a replica exchange reactive molecular dynamics framework in which molecular configurations are swapped between adjacent T replica at regular intervals according to underlying statistical mechanics. This framework allows predicting complex molecular structures and thermodynamics while remaining computationally efficient. Here we simulate the reactivity of an unstable mixture of CO 2 and CH 4 at 1000 K and 1 GPa. We find that the path to thermodynamic equilibrium is initially entropy-driven, producing a diversity of short-lived species, including various alcohols with intermediate carbon oxidation states. Cyclic and polycyclic radicals that are sometimes resonance-stabilized form next and set the stage for carbon nucleation. The carbon exsolution process releases abundant water, is exothermic and starts with the nucleation of a large aggregate of hydrogenated graphene flakes from covalently bonded polycyclic units. The carbon backbone of this nucleus subsequently grows into a hydrogen-depleted fullerene-like structure, before evolving toward a partially bilayered graphene layer. Overall, our results show that the mechanism of graphitic C formation is certainly not bimolecular, and that it may involve a combination of key condensation and radical chain reactions. This will help understand the isotopic, and reactive characteristics of carbon-bearing fluids during their upward transit through the Earth’s mantle and crust. Moreover, the mechanistic insights outlined here present intriguing similarities with the process of soot and interstellar dust formation, which suggests that the widespread distribution of abiotic polyaromatic and graphitic material on Earth and beyond may reflect the prevalence of a fundamental chemical pathway.

58 GEOSCIENCES↗

Validating continuum theory for Cottrell atmosphere solute drag by molecular dynamics simulations

When a dislocation moves through a field of mobile solute atoms, solutes segregate to the dislocation and form Cottrell atmospheres which exert solute drag forces. Over the last 70 years, continuum theory has been used extensively to estimate these drag forces and their dependence on the dislocation velocity, however few prior works have validated the accuracy of continuum theories. Here, in this work, molecular dynamics (MD) simulations of dislocation motion in face-centered cubic Ni containing interstitial H atoms were performed in order to test the accuracy of continuum theory predictions. Our results demonstrate that continuum theory provides an accurate estimate of the solute drag force for velocities below the critical velocity at which the solute drag force is maximized. Above the critical velocity, continuum theory systematically deviates from MD. Additional analysis reveals that this deviation results from the multi-valued and unstable nature of solute drag under load control, and also from the transition to random solute drag which occurs at high velocities.

Dislocations↗

Structural and Dynamic Analysis of Sulphur Dioxide Adsorption in a Series of Zirconium-Based Metal–Organic Frameworks

We report reversible high capacity adsorption of SO 2 in robust Zr-based metal–organic framework (MOF) materials. Zr-bptc (H 4 bptc=biphenyl-3,3',5,5'-tetracarboxylic acid) shows a high SO 2 uptake of 6.2 mmol g -1 at 0.1 bar and 298 K, reflecting excellent capture capability and removal of SO 2 at low concentration (2500 ppm). Dynamic breakthrough experiments confirm that the introduction of amine, atomically-dispersed Cu II or heteroatomic sulphur sites into the pores enhance the capture of SO 2 at low concentrations. The captured SO 2 can be converted quantitatively to a pharmaceutical intermediate, aryl N-aminosulfonamide, thus converting waste to chemical values. In situ X-ray diffraction, infrared micro-spectroscopy and inelastic neutron scattering enable the visualisation of the binding domains of adsorbed SO 2 molecules and host–guest binding dynamics in these materials at the atomic level. Refinement of the pore environment plays a critical role in designing efficient sorbent materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Comparison of Solid Electrolyte Interphase Formation and Evolution on Highly Oriented Pyrolytic and Disordered Graphite Negative Electrodes in Lithium–Ion Batteries

The presence and stability of solid electrolyte interphase (SEI) on graphitic electrodes is vital to the performance of lithium-ion batteries (LIBs). However, the formation and evolution of SEI remain the least understood area in LIBs due to its dynamic nature, complexity in chemical composition, heterogeneity in morphology, as well as lack of reliable in situ/operando techniques for accurate characterization. In addition, chemical composition and morphology of SEI are not only affected by the choice of electrolyte, but also by the nature of the electrode surface. While introduction of defects into graphitic electrodes has promoted their electrochemical properties, how such structural defects influence SEI formation and evolution remains an open question. In this work, utilizing nondestructive operando electrochemical atomic force microscopy (EChem-AFM) the dynamic SEI formation and evolution on a pair of representative graphitic materials with and without defects, namely, highly oriented pyrolytic and disordered graphite electrodes, are systematically monitored and compared. Complementary to the characterization of SEI topographical and mechanical changes during electrochemical cycling by EChem-AFM, chemical analysis and theoretical calculations are conducted to provide mechanistic insights underlying SEI formation and evolution. The results provide guidance to engineer functional SEIs through design of carbon materials with defects for LIBs and beyond.

25 ENERGY STORAGE↗

Dynamic Ligand Surface Chemistry of Excited PbS Quantum Dots

The ligand shell around colloidal quantum dots mediates the electron and energy transfer processes that underpin their use in optoelectronic and photocatalytic applications. In this work, we show that the surface chemistry of carboxylate anchoring groups of oleate ligands passivating PbS quantum dots undergoes significant changes when the quantum dots are excited to their excitonic states. Additionally, we directly probe the changes of surface chemistry using time-resolved mid-infrared spectroscopy that records the evolution of the vibrational frequencies of carboxylate groups following excitation of the electronic states. The data reveal a reduction of the Pb-O coordination of carboxylate anchoring groups to lead atoms at the quantum dot surfaces. The dynamic surface chemistry of the ligands may increase their surface mobility in the excited state and enhance the ability of molecular species to penetrate the ligand shell to undergo energy and charge transfer processes that depend sensitively on distance.

36 MATERIALS SCIENCE↗