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At least 505 records · Page 28

Li1−xNiO2 Many-body DMC Benchmark Dataset

The dataset contains all numerical data generated in support of the manuscript “Many‑body Benchmark of Electronic Charge and Spin Densities for Li1–xNiO2​” (Journal of Chemical Theory and Computation, DOI: 10.1021/acs.jctc.5c02097, URL: https://pubs.acs.org/doi/10.1021/acs.jctc.5c02097). The materials included in this repository are: 1. Data files used to produce all figures and tables in the main manuscript and supporting information. 2. Benchmark density‑functional theory (DFT) datasets used for the charge‑ and spin‑density analyses. 3. Reference many‑body diffusion Monte Carlo (DMC) calculations and associated input/output files.

36 MATERIALS SCIENCE↗

Non-equilibrium plasma generation via nano-second multi-mode laser pulses

The formation and growth of plasma kernels generated via nano-second mode-beating laser pulses is investigated here via a non-equilibrium self-consistent computational model. Chemically reactive Navier–Stokes equations are used to describe the hydrodynamics, and non-equilibrium effects are taken into account with a two-temperature model. Inverse Bremsstrahlung and multiphoton ionization are included self-consistently in the model via a coupled solution of the plasma governing equations and the radiative transfer equation (that describes the laser beam propagation and attenuation). A self-consistent approach (despite carrying additional challenges) minimizes the empiricism and it allows for a more accurate description since it prevents both the utilization of artificial plasma seeds to trigger the breakdown and the implementation of tuning parameters to simulate the laser-energy deposition. The advantages of this approach are confirmed by the good agreement between the numerically predicted and the experimentally measured plasma boundary evolution and absorbed energy. This also holds true for the periodic plasma kernel structures that, as suggested by the experiments and confirmed by the simulations presented here, are connected to the modulating frequency.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules

Abstract We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the “Andes” cluster of the Oak Ridge Leadership Computing Facility (OLCF).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rotational excitation and de-excitation of magnesium mono-sulphide (MgS) by He collisions

ABSTRACT Magnesium mono-sulphide (MgS) plays a crucial role in astrochemical processes, particularly in the interstellar medium (ISM), where metal-sulphur chemistry influences molecular formation and evolution. This work presents a detailed study of the rotational excitation and de-excitation of MgS through collisions with helium (He) atoms, the second most abundant species in the ISM after hydrogen, which includes both atomic (H) and molecular forms (H2). The focus on MgS–He collisions arises from He's high abundance, chemical inertness, and simpler electronic structure, which make it well suited for quantum scattering calculations. These characteristics establish He as an ideal candidate for initial studies, providing fundamental data for future investigations involving H2. The study uses quantum scattering methods to calculate the collisional rate coefficients over a broad temperature range. These rates are critical for interpreting observational data on MgS and predicting its abundance in space. The interaction potential between MgS and He is calculated using the rigid rotor approximation and the Jacobi coordinate system, employing the CCSD(T)-F12a/aug-cc-pVTZ method for accurate two-dimensional potential energy surface. The study explores the anisotropic nature of the MgS–He interaction, which favours odd Δj rotational transitions at low collision energies. The inelastic cross-sections for rotational transitions involving up to 16 rotational levels of MgS were computed up to 1000 cm−1, enabling the calculation of rate coefficients up to 150 K for Δj = ±1, ±2, and ± 3 rotational transitions. The results show that Δj = 1 transitions dominate at low temperatures, while Δj = 2 transitions become more significant at higher temperatures. This study provides valuable data for interpreting future astrophysical observations of MgS. The findings also propose new rotational transitions for MgS detection in space, enhancing our ability to track and study this molecule in various cosmic environments.

Hendaoui, Hamza (ORCID:0000000218641872)↗

A first-principles study of hydrogen surface coverage on δ-Pu (100), (111), and (110) surfaces

Hydriding corrosion of plutonium leads to surface cracking, pitting, and ultimately structural failure. Laboratory experiments demonstrate that hydriding begins on the surface or near the subsurface of plutonium. However, there has not yet been a systematic evaluation of hydrogen surface coverage on plutonium. In this work, we compute the surface energies of the low facet surfaces of face-centered cubic δ-Pu. The adsorption free energies of expected hydrogen structures at low and high coverage are presented along with the likely progression for filling sites as the H 2 partial pressure increases. Implications for near-equilibrium pressure hydride nucleation and non-equilibrium millibar pressure hydriding are discussed.

36 MATERIALS SCIENCE↗

Toward Quantum Confinement in Graphitic Carbon Nitride-Based Polymeric Monolayers

raphitic carbon nitride (g-C 3 N 4 ) has garnered much attention due to its potential as an efficient metal-free photocatalyst. This study examines the evolution of properties in zero-dimensional quantum dots up to sizable clusters that mimic extended g-C 3 N 4 monolayers. We employ density functional theory to investigate systematically the structural, electronic, and optical properties of the g-C 3 N 4 -based melamine and heptazine building blocks using a “bottom-up” construction of polymeric monolayers. The results from our computations indicate that the melamine- and heptazine-based polymeric g-C 3 N 4 systems must be reduced to at least 2.74 and 4.00 nm, respectively, to observe an increase of its optical gap with a size reduction. The present study also examines the nature of the electronic transitions exhibited by g-C 3 N 4 -based monolayers through full natural transition orbital and density of state analyses. Furthermore, the most promising sites for water splitting and subsequent chemical doping studies are identified, which generally correspond to the nitrogen and carbon atoms, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗

Photoluminescence, photophysics, and photochemistry of the V B - defect in hexagonal boron nitride

Extensive photochemical and spectroscopic properties of the V B - defect in hexagonal boron nitride are calculated, concluding that the observed photoemission associated with recently observed optically detected magnetic resonance is most likely of (1) 3 E'' → (1) 3 A' 2 origin. Rapid intersystem crossing from the defect's triplet to singlet manifolds explains the observed short excited-state lifetime and very low quantum yield. New experimental results reveal smaller intrinsic spectral bandwidths than previously recognized, interpreted in terms of spectral narrowing and zero-phonon-line shifting induced by the Jahn-Teller effect. Different types of computational methods are applied to map out the complex triplet and singlet defect manifolds, including the doubly ionized formulation of the equation-of-motion coupled-cluster theory that is designed to deal with the open-shell nature of defect states, and mixed quantum-mechanics/molecular-mechanics schemes enabling 5763-atom simulations. Finally, two other energetically feasible spectral assignments from among the singlet and triplet manifolds are considered, but ruled out based on inappropriate photochemical properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Computational Study of Electron-Molecule Collisions Related to Low-Temperature Plasmas

Computational study of electron-molecule collisions not only complements experimental measurements, but can also be used to investigate processes not readily accessible experimentally. A number of ab initio computational methods are available for these types of calculations. Here we describe a recently developed technique, the finite element Z-matrix method, Analogous to the R-matrix, method, it partitions the space into regions and employs real matrix elements. However, unlike the implementation of the R-matrix method commonly used in atomic and molecular physics, the Z-matrix method is fully variational. In the present implementation, a mixed basis of finite elements and Gaussians is used to represent the continuum electron, thus offering full flexibility without imposing fixed boundary conditions. Numerical examples include the electron-impact dissociation of N2 via the metastable A3Su+ state, a process which may be important in the lower thermosphere, and the dissociation of the CF radical, a process of interest to plasma etching. To understand the dissociation pathways, large scale quantum chemical calculations have been carried out for all target states which dissociate to the lowest five limits in the case of N2, and to the lowest two limits in the case of CF. For N2, the structural calculations clearly show the preference for predissociation if the initial state is the ground X1 Sg+ state, but direct dissociation appears to be preferable if the initial state is the A3Su+ state. Multi-configuration SCF target functions are used in the collisional calculation.

Huo, Winifred M.↗

Understanding the Electronic Behavior of f-Element Intermetallics

Due to their partially filled f-orbitals, lanthanide and actinide intermetallic materials exhibit intriguing electronic, structural, and magnetic properties. These materials provide a unique platform to explore exotic magnetic and quantum phenomena that arise from their strongly correlated f-electrons, offering insights into f-electron behavior. Incorporating light elements such as boron and carbon can significantly impact the electronic, chemical, and physical properties of these materials, with varying influence between lanthanides and actinides due to the more localized f-electrons in lanthanides. In this work, lanthanide-based intermetallic single crystals containing light atoms were synthesized using the molten metal flux growth method. In this method, one or more low-melting metals such as aluminum, gallium, tin, and bismuth are used in excess as the reaction medium. This solution-state approach allows for lower reaction temperatures compared to solid-state reactions and enables the isolation of kinetic products rather than thermodynamically stable compounds. The synthesized crystals were analyzed using an extensive array of analytical and computational characterization techniques, including single crystal X-ray diffraction, scanning electron microscopy, energy-dispersive spectroscopy, magnetization measurements, and density functional theory calculations. These analyses provided detailed insights into the structural and magnetic properties of the synthesized materials.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗

Structural and Spectroscopic Properties of Butanediol-Modified Boehmite Materials

Glycoboehmite (GB) materials are synthesized by a solvothermal reaction to form layered aluminum oxyhydroxide (boehmite) modified by intercalated butanediol molecules. These hybrid materials offer a platform to design materials with potentially novel sorption, wetting, and catalytic properties. Several synthetic methods have been used, resulting in different structural and spectroscopic properties, but atomistic detail is needed to determine the interlayer structure to explore the synthetic control of GB materials. Here, in this study, we use classical molecular dynamics (MD) simulations to compare the structural properties of GB interlayers containing chemisorbed butanediol molecules as a function of diol loading. Accompanying quantum (density functional theory, DFT) static calculations and MD simulations are used to validate the classical model and compute the infrared spectra of various models. Classical MD results reveal the existence of two unique interlayer environments at higher butanediol loading, corresponding to smaller (cross-linked) and expanded interlayers. DFT-computed infrared spectra reveal the sensitivity of the aluminol O–H stretch frequencies to the interlayer environment, consistent with the spectrum of the synthesized material. Insight from these simulations will aid in the characterization of the newly synthesized GB materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Generalized Approach to Photon Avalanche Upconversion in Luminescent Nanocrystals

Photon avalanching nanoparticles (ANPs) exhibit extremely nonlinear upconverted emission valuable for subdiffraction imaging, nanoscale sensing, and optical computing. Avalanching has been demonstrated with Tm 3+ -, Pr 3+ -, or Nd 3+ -doped nanocrystals, but their emission is limited to a few wavelengths and materials. Here, we utilize Gd 3+ -assisted energy migration to tune the emission wavelengths of Tm 3+ -sensitized ANPs and generate highly nonlinear emission from Eu 3+ , Tb 3+ , Ho 3+ , and Er 3+ ions. The upconversion intensities of these spectrally discrete ANPs scale with nonlinearity factor s = 10-17 under 1064 nm excitation at power densities as low as 7 kW cm -2 . This strategy for imprinting avalanche behavior on remote emitters can be extended to fluorophores adjacent to ANPs, as here we demonstrate with CdS/CdSe/CdS core/shell/shell quantum dots. ANPs with rationally designed energy transfer networks provide the means to transform conventional linear emitters into a highly nonlinear ones, expanding the use of photon avalanching in biological, chemical, and photonic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward the Observation of Dimagnesocene

We have examined the electronic structure of C 5 H 5 MgMgC 5 H 5 , or dimagnesocene, using high-level coupled-cluster techniques. This research is suitable in light of the remarkable synthesis of the valence-isoelectronic diberyllocene by Boronski, Crumpton, Wales, and Aldridge. The Mg–Mg bond distance is predicted to be 2.758 Å, and the Mg–Mg bond dissociation energy is predicted to be 51.8 kcal/mol. Unique aspects to the present research is our characterization of the ionization energy and the electron affinity of this molecule, the energy of dissociation into two neutral cyclopentadienyl magnesium radicals, the determination of the neutral structure at the CCSD(T)/cc-pVTZ level, and the computation of the Raman intensities at the MP2/cc-pVDZ level. Apart from mass spectroscopy, the simplest means of experimental detection is gas-phase or matrix-isolated infrared spectroscopy, in which the A 2 ″ peak at 801 cm –1 should be the most prominent, with an intensity of 581 km/mol.

bond cleavage↗

Scaling Properties of Algorithms in Nanotechnology

At the present time, several technologies are pressing the limits of microminiature manufacturing. In semiconductor technology, for example, the Intel Pentium Pro (which is used in the Department of Energy's ASCI 'red' parallel supercomputer system) and the DEC Alpha 21164 (which is used in the CRAY T3E) both are fabricated using 0.35 micron process technology. Recently Texas Instruments (TI) announced the availability of 0.25 micron technology chips by the end of 1996 and plans to have 0.18 micron devices in production within two years. However, some significant challenges lie down the road. These include the skyrocketing cost of manufacturing plants, the 0.1 micron foreseeable limit of the photolithography process, quantum effects, data communication bandwidth limitations, heat dissipation, and others. Some related microminiature technologies include micro-electromechanical systems (MEMS), opto-electronic devices, quantum computing, biological computing, and others. All of these technologies require the fabrication of devices whose sizes are approaching the nanometer level. As such they are often collectively referred to with the name 'nanotechnology'. Clearly nanotechnology in this general sense is destined to be a very important technology of the 21st century. The ultimate dream in this arena is 'molecular nanotechnology', in other words the fabrication of devices and materials with most or all atoms and molecules in a pre-programmed position, possibly placed there by 'nano-robots'. This futuristic capability will probably not be achieved for at least two decades. However, it appears that somewhat less ambitious variations of molecular nanotechnology, such as devices and materials based on 'buckyballs' and 'nanotubes' may be realized significantly sooner, possibly within ten years or so. Even at the present time, semiconductor devices are approaching the regime where quantum chemical effects must be considered in design.

Saini, Subhash↗

Association Mechanisms of Unsaturated C2 Hydrocarbons with Their Cations: Acetylene and Ethylene

The ion-molecule association mechanism of acetylene and ethylene with their cations is investigated by ab initio quantum chemical methods to understand the structures, association energies, and the vibrational and electronic spectra of the products. Stable puckered cyclic isomers are found as the result of first forming less stable linear and bridge isomers. The puckered cyclic complexes are calculated to be strongly bound, by 87, 35 and 56 kcal/mol for acetylene-acetylene cation, ethylene-ethylene cation and acetylene-ethylene cation, respectively. These stable complexes may be intermediates that participate in further association reactions. There are no association barriers, and no significant inter-conversion barriers, so the initial linear and bridge encounter complexes are unlikely to be observable. However, the energy gap between the bridged and cyclic puckered isomers greatly differs from complex to complex: it is 44 kcal/mol in C4H4 +, but only 6 kcal/mol in C4H8 +. The accurate CCSD(T) calculations summarized above are also compared against less computationally expensive MP2 and density functional theory (DFT) calculations for structures, relative energies, and vibrational spectra. Calculated vibrational spectra are compared against available experiments for cyclobutadiene cation. Electronic spectra are also calculated using time-dependent DFT.

ethylene↗

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron–oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

59 BASIC BIOLOGICAL SCIENCES↗

State-to-State Internal Energy Relaxation Following the Quantum-Kinetic Model in DSMC

A new model for chemical reactions, the Quantum-Kinetic (Q-K) model of Bird, has recently been introduced that does not depend on macroscopic rate equations or values of local flow field data. Subsequently, the Q-K model has been extended to include reactions involving charged species and electronic energy level transitions. Although this is a phenomenological model, it has been shown to accurately reproduce both equilibrium and non-equilibrium reaction rates. The usefulness of this model becomes clear as local flow conditions either exceed the conditions used to build previous models or when they depart from an equilibrium distribution. Presently, the applicability of the relaxation technique is investigated for the vibrational internal energy mode. The Forced Harmonic Oscillator (FHO) theory for vibrational energy level transitions is combined with the Q-K energy level transition model to accurately reproduce energy level transitions at a reduced computational cost compared to the older FHO models.

Liechty, Derek S.↗

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin’s isoalloxazine ring in the diagnostic 1450–1750 cm−1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗