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At least 541 records · Page 30

Molecular chemisorption of N 2 on IrO 2 (110)

We investigated the adsorption of N 2 on stoichiometric and O-rich IrO 2 (110) surfaces using temperature programmed desorption (TPD) experiments and density functional theory (DFT) calculations. TPD shows that N 2 desorbs predominantly from the stoichiometric-IrO 2 (110) surface in a well-defined peak at 270 K for N 2 coverages below about 0.5 ML, and that a shoulder centered near 235 K develops in the N 2 TPD traces as the coverage approaches saturation, indicating that adsorbed N 2 molecules become destabilized at high N 2 coverage. Experiments of N 2 adsorption onto O-rich IrO 2 (110) surfaces provide evidence that N 2 adsorbs exclusively on the coordinatively-unsaturated Ir atoms (Ircus) of the surface, and that pre-adsorbed O-atoms (“on-top” oxygen) stabilize adsorbed N 2 molecules, causing the main N 2 TPD peak to shift toward higher temperature with increasing oxygen coverage. Consistent with prior results, our DFT calculations predict that an N 2 molecule preferentially adsorbs into an upright configuration on an Ircus atom of the IrO 2 (110) surface and achieves a binding energy of about 100 kJ/mol. The computed binding energy agrees well with our experimental estimate of ~90 kJ/mol for low N 2 coverages on stoichiometric IrO 2 (110). Lastly, the DFT calculations also quantitatively reproduce the observed stabilization of N 2 by co-adsorbed on-top O-atoms and predict the destabilization of N 2 on IrO 2 (110) as the N 2 adlayer becomes crowded at high coverage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A density functional theory based comparative study of hybrid photoemissions from Cl@C 60 , Br@C 60 and I@C 60

Photoionization from atom-C 60 hybrid levels in halogen endofullerene molecules, Cl@C 60 , Br@C 60 and I@C 60 , are calculated using a linear response density functional method. Both the ordinary electron-configuration where the open shell halogen is at the center of C 60 and the stable configuration after the atom receives an electron from C 60 to form a closed shell anion are considered. Similar ground state hybridization is found for all three systems while, in general, a slight weakening of the effect is noticed after the electron transfer. At lower photon energies, cross sections of the outer hybrid levels attain identical shapes from enhancements driven by the C 60 plasmon resonances, while the higher energy emissions remain distinguishable from the differences in atomic responses. These results further show near insensitivity to the choice of a configuration. The inner hybrid cross sections in general exhibit similar overall structures, although differ in details between molecules. Furthermore, for these states the results significantly differ before and after the electron transfer – a feature that can be useful to experimentally determine the real configuration of the molecules via photoelectron spectroscopy.

74 ATOMIC AND MOLECULAR PHYSICS↗

Implementation of Perdew–Zunger self-interaction correction in real space using Fermi–Löwdin orbitals

Most widely used density functional approximations suffer from self-interaction error, which can be corrected using the Perdew–Zunger (PZ) self-interaction correction (SIC). We implement the recently proposed size-extensive formulation of PZ-SIC using Fermi–Löwdin Orbitals (FLOs) in real space, which is amenable to systematic convergence and large-scale parallelization. Here, we verify the new formulation within the generalized Slater scheme by computing atomization energies and ionization potentials of selected molecules and comparing to those obtained by existing FLOSIC implementations in Gaussian based codes. The results show good agreement between the two formulations, with new real-space results somewhat closer to experiment on average for the systems considered. We also obtain the ionization potentials and atomization energies by scaling down the Slater statistical average of SIC potentials. The results show that scaling down the average SIC potential improves both atomization energies and ionization potentials, bringing them closer to experiment. Finally, we verify the present formulation by calculating the barrier heights of chemical reactions in the BH6 dataset, where significant improvements are obtained relative to Gaussian based FLOSIC results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Molecular structure retrieval directly from laboratory-frame photoelectron spectra in laser-induced electron diffraction

Ubiquitous to most molecular scattering methods is the challenge to retrieve bond distance and angle from the scattering signals since this requires convergence of pattern matching algorithms or fitting methods. This problem is typically exacerbated when imaging larger molecules or for dynamic systems with little a priori knowledge. Here, we employ laser-induced electron diffraction (LIED) which is a powerful means to determine the precise atomic configuration of an isolated gas-phase molecule with picometre spatial and attosecond temporal precision. We introduce a simple molecular retrieval method, which is based only on the identification of critical points in the oscillating molecular interference scattering signal that is extracted directly from the laboratory-frame photoelectron spectrum. The method is compared with a Fourier-based retrieval method, and we show that both methods correctly retrieve the asymmetrically stretched and bent field-dressed configuration of the asymmetric top molecule carbonyl sulfide (OCS), which is confirmed by our quantum-classical calculations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

ezAlign

The ezAlign is aimed at clustering coarse grain simulation to find common or uncommon occurrences and convert coarse (CG) grained coordinate and topology files to atomistic formats. We use a PointNet based approach to map individual frames of simulation to points in a latent space. These points are then clustered using a variety of clustering methods. Clusters are analyzed to associate them with states in the simulation. Frames can be chosen from these clusters based on proximity to cluster centers. ezAlign takes CG coordinate and topology files and converts and outputs their corresponding atomistic formats using an alignment and relaxation procedure. ezAlign is designed to convert complex, solvated biological systems including lipid membranes with drug-like molecules using GROMACS. A GROMACS checkpoint (.cpt) file is also outputted to enable continuation simulations that retain the equilibrated atomic velocities. Independent atomistic coordinates and topologies for every molecule must already be included in ezAlign/files. A number of commonly simulated biological molecules are currently provided.

Bennett, WilliamF.↗

Photothermal alternative to device fabrication using atomic precision advanced manufacturing techniques

The attachment of dopant precursor molecules to depassivated areas of hydrogen-terminated silicon templated with a scanning tunneling microscope (STM) has been used to create electronic devices with sub-nanometer precision, typically for quantum physics demonstrations, and to dope silicon past the solid-solubility limit, with potential applications in microelectronics and plasmonics. However, this process, which we call atomic precision advanced manufacturing (APAM), currently lacks the throughput required to develop sophisticated applications because there is no proven scalable hydrogen lithography pathway. Here, we demonstrate and characterize an APAM device workflow where STM lithography has been replaced with photolithography. An ultraviolet laser is shown to locally heat silicon controllably above the temperature required for hydrogen depassivation. STM images indicate a narrow range of laser energy density where hydrogen has been depassivated, and the surface remains well-ordered. A model for photothermal heating of silicon predicts a local temperature which is consistent with atomic-scale STM images of the photo-patterned regions. Finally, a simple device made by exposing photo-depassivated silicon to phosphine is found to have a carrier density and mobility similar to that produced by similar devices patterned by STM.

42 ENGINEERING↗

Coupled Cluster Study of the Heats of Formation of UF 6 and the Uranium Oxyhalides, UO 2 X 2 (X = F, Cl, Br, I, and At)

The atomization enthalpies of the U(VI) species UF6 and the uranium oxyhalides UO 2 X 2 (X=F, Cl, Br, I, At) were calculated using a composite relativistic Feller-Peterson-Dixon (FPD) approach based on scalar relativistic DKH3-CCSD(T) with extrapolations to the CBS limit. The inherent multideterminantal nature of the U atom was mitigated by utilizing the singly charged atomic cation in all calculations with correction back to the neutral asymptote via the accurate ionization energy of the U atom. The effects of SO coupling were recovered using full 4-component CCSD(T) with contributions due to the Gaunt Hamiltonian calculated using Dirac-Hartree-Fock. The final atomization enthalpy for UF 6 (752.2 kcal/mol) was within 2.5 kcal/mol of the experimental value, but unfortunately the latter carries a ±2.4 kcal/mol uncertainty that is predominantly due to the experimental uncertainty in the formation enthalpy of U atom. The analogous value for UO 2 F 2 (607.6 kcal/mol) was in nearly exact agreement with experiment, but the latter has a stated experimental uncertainty of ±4.3 kcal/mol. The FPD atomization enthalpy for UO 2 Cl 2 (540.4 kcal/mol) was within the experimental error limits of ±5.5 kcal/mol. FPD atomization energies for the non-U-containing molecules (used for reaction enthalpies) H 2 O and HX (X=F, Cl, Br, I, At) were within at most 0.3 kcal/mol of their experimental values where available. The FPD atomization enthalpies, together with FPD reaction enthalpies for two different reactions, were used to determine heats of formation for all species of this work with estimated uncertainties of ±4 kcal/mol. The calculated heat of formation for UF 6 (-511.0 kcal/mol) is within 2.5 kcal/mol of the accurately-known (±0.45 kcal/mol) experimental value.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cu Evolution over Bimetallic Cu‐Y/Beta Zeolite Under H 2 and Ethanol Atmospheres: Unveiling the Role of Diatomic Metal–Metal Interactions

Understanding the dynamic evolution of Cu species under varying environmental conditions is critical for addressing challenges related to the activity and the stability of copper‐based catalysts in thermo‐, photo‐, and electrocatalysis. However, metal–metal interactions between dual single atoms and their effects on Cu evolution after exposure to different environmental molecules remain underexplored. Herein, we synthesized bimetallic Cu‐Y/Beta catalysts with dual single‐atom Cu and Y sites and monometallic Cu‐Beta catalysts with isolated Cu sites in dealuminated Beta zeolites. By varying Cu and Y compositions, diatomic interactions were studied under H 2 and ethanol atmospheres. With 6 wt% Y loading, approximately 0.4 wt% of Cu species in Cu‐Y/Beta remained partially oxidized as Cu(I) after reduction in pure H 2 at 350 °C, in contrast to the full transition to metallic Cu observed in Cu‐Beta. Combining X‐ray absorption spectroscopy with kinetic studies revealed that metallic Cu became the predominant species after reduction with H 2 as Cu loading increased from 0.4 to 1.7 wt%, quadrupling the initial ethanol dehydrogenation rate and demonstrating the dominant role of Cu(0) sites. In conclusion, scanning transmission electron microscopy and density functional theory simulations indicated spatial proximity between dual single‐atom Cu and Y sites and elucidated Cu speciation controlled by diatomic interactions.

Copper↗

Tunable Magnetic Coupling in Graphene Nanoribbon Quantum Dots

Abstract Carbon‐based quantum dots (QDs) enable flexible manipulation of electronic behavior at the nanoscale, but controlling their magnetic properties requires atomically precise structural control. While magnetism is observed in organic molecules and graphene nanoribbons (GNRs), GNR precursors enabling bottom‐up fabrication of QDs with various spin ground states have not yet been reported. Here the development of a new GNR precursor that results in magnetic QD structures embedded in semiconducting GNRs is reported. Inserting one such molecule into the GNR backbone and graphitizing it results in a QD region hosting one unpaired electron. QDs composed of two precursor molecules exhibit nonmagnetic, antiferromagnetic, or antiferromagnetic ground states, depending on the structural details that determine the coupling behavior of the spins originating from each molecule. The synthesis of these QDs and the emergence of localized states are demonstrated through high‐resolution atomic force microscopy (HR‐AFM), scanning tunneling microscopy (STM) imaging, and spectroscopy, and the relationship between QD atomic structure and magnetic properties is uncovered. GNR QDs provide a useful platform for controlling the spin‐degree of freedom in carbon‐based nanostructures.

36 MATERIALS SCIENCE↗

Exploring the Role of Inorganic and Organic Interfaces on CO 2 and CH 4 Partitioning: Case Study of Silica, Illite, Calcite, and Kerogen Nanopores on Gas Adsorption and Nanoscale Transport Behaviors

The adsorption, partitioning, and diffusion of CO 2 and CH 4 in organic–inorganic pores composed of kerogen with silica, illite, or calcite are studied using density functional theory and classical molecular dynamics simulations. The adsorption and partitioning behavior of CO 2 and CH 4 molecules is found to be a function of chemistry of the solid interface, pore size, and surface area. CO 2 molecules are preferentially adsorbed compared to CH 4 molecules on silica, illite, calcite, and kerogen surfaces due to significant contributions of electrostatic interactions with the atoms of the associated surfaces. CO 2 and CH 4 molecules display higher adsorption energy on calcite and silica compared to those on illite and kerogen because of enhanced interactions with the positively charged calcium ions on the calcite surface and the hydroxyl group (-OH) on the silica surface. Enhanced internal nanopores and the availability of adsorption active sites in illite and kerogen matrices aid in higher partitioning of the gas molecules into these pores. CO 2 has a significant influence on the clustering and swelling of kerogen fragments compared to CH 4 . Higher CO 2 adsorption on inorganic and kerogen surfaces results in lower overall self-diffusivities compared to CH 4 . This study illustrates surface and pore size controls on the adsorption, partitioning, and self-diffusivities of CO 2 and CH 4 at conditions relevant for subsurface energy applications. The chemistry of the surfaces along with the availability of internal pores and active adsorption sites influences the adsorption behavior of gases. Our results suggest that CO 2 stored in depleted gas reservoirs may preferentially inhabit nanoconfined pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanism and kinetics of the oxidation of 1,3-butadien-1-yl (n-C 4 H 5 ): a theoretical study

Here, ab initio CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311G(d,p) calculations of the C 4 H 5 O 2 potential energy surface have been combined with Rice–Ramsperger–Kassel–Marcus Master Equation (RRKM-ME) calculations of temperature- and pressure-dependent rate constants and product branching ratios to unravel the mechanism and kinetics of the n-C 4 H 5 + O 2 reaction. The results indicate that the reaction is fast, with the total rate constant being in the range of 3.4–5.6 × 10 –11 cm 3 molecule –1 s –1 . The main products include 1-oxo-n-butadienyl + O and acrolein + HCO, with their cumulative yield exceeding 90% at temperatures above 1500 K. Two conformers of 1-oxo-n-butadienyl + O are formed via a simple mechanism of O 2 addition to the radical site of n-C 4 H 5 followed by the cleavage of the O–O bond proceeding via a van der Waals C 4 H 5 O∙∙∙O complex. Alternatively, the pathways leading to acrolein + HCO involve significant reorganization of the heavy-atom skeleton either via formal migration of one O atom to the opposite end of the molecule or its insertion into the C1–C2 bond. Not counting thermal stabilization of the initial peroxy adducts, which prevails at low temperatures and high pressures, all other products share a minor yield of under 5%. Rate constants for the significant reaction channels have been fitted to modified Arrhenius expressions and are proposed for kinetic modeling of the oxidation of aromatic molecules and 1,3-butadiene. As a secondary reaction, n-C 4 H 5 + O 2 can be a source for the formation of acrolein observed experimentally in oxidation of the phenyl radical at low combustion temperatures, whereas another significant (secondary) product of the C 6 H 5 + O 2 reaction, furan, could be formed through unimolecular decomposition of 1-oxo-n-butadienyl. Both the n-C 4 H 5 + O 2 reaction and unimolecular decomposition of its 1-oxo-n-butadienyl primary product are shown not to be a substantial source of ketene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Measurements and kinetic modeling of O 2 vibrational kinetics in O 2 –Ar mixtures partially dissociated by a Ns pulse discharge

Vibrational kinetics of O 2 is studied during the O atom recombination in an O 2 –Ar mixture, partially dissociated by a burst of ns discharge pulses in a heated plasma flow reactor. The time-resolved temperature in the discharge afterglow is determined by Rayleigh scattering. Time-resolved O atom number density is measured by ps Two-Photon absorption Laser Induced Fluorescence, calibrated in xenon. Time-resolved vibrational level populations of molecular oxygen, O 2 (v= 8–20), are measured by ps Laser Induced Fluorescence (LIF), with the absolute calibration by NO LIF. Time-resolved ozone number density is monitored by broadband UV absorption. The results are compared with the predictions of a state-specific kinetic model. The experimental data indicate a rapid initial decay of O 2 (v) populations generated by electron impact in the discharge, due to the vibration-translation (V–T) relaxation by O atoms. This is followed by a slower population reduction, on the time scale much longer compared to that for V–T relaxation or vibration-vibration (V–V) exchange. Both O atoms and the O 2 (v) populations decay on the same time scale, indicating that chemical reactions initiated by the O atom recombination result in the generation of vibrationally excited O 2 molecules. These trends are reproduced by the kinetic model, which shows that the reaction of O atoms with ozone is the dominant pathway of O 2 (v) generation at the present conditions. The predicted relative O 2 (v) populations are close to the experimental results, but absolute number densities differ from the experimental data. This is likely due to uncertainties in the absolute calibration of LIF measurements and in the spectroscopic model used in the data reduction. The present work demonstrates the capability for the absolute, time-resolved measurements of vibrationally excited O 2 in recombining gas flows, to quantify the energy partition in the recombination reactions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fractional occupation numbers and self-interaction correction-scaling methods with the Fermi-Löwdin orbital self-interaction correction approach

In this work, we present a new assessment of the Fermi-Löwdin orbital self-interaction correction (FLO-SIC) approach with an emphasis on its performance for predicting energies as a function of fractional occupation numbers (FONs) for various multielectron systems. Our approach is implemented in the massively parallelized NWChem quantum chemistry software package and has been benchmarked on the prediction of total energies, atomization energies, and ionization potentials of small molecules and relatively large aromatic systems. Within our study, we also derive an alternate expression for the FLO-SIC energy gradient expressed in terms of gradients of the Fermi-orbital eigenvalues and revisit how the FLO-SIC methodology can be seen as a constrained unitary transformation of the canonical Kohn–Sham orbitals. Finally, we conclude with calculations of energies as a function of FONs using various SIC-scaling methods to test the limits of the FLO-SIC formalism on a variety of multielectron systems. We find that these relatively simple scaling methods do improve the prediction of total energies of atomic systems as well as enhance the accuracy of energies as a function of FONs for other multielectron chemical species.

fractional occupation number↗

Atomic-Scale Corrugations in Crystalline Polypeptoid Nanosheets Revealed by Three-Dimensional Cryogenic Electron Microscopy

Amphiphilic molecules that can crystallize often form molecularly thin nanosheets in aqueous solutions. The possibility of atomic-scale corrugations in these structures has not yet been recognized. We have studied the self-assembly of amphiphilic polypeptoids, a family of bio-inspired polymers that can self-assemble into various crystalline nanostructures. Atomic-scale structure of the crystals in these systems has been inferred using both X-ray diffraction and electron microscopy. We use cryogenic electron microscopy to determine the in-plane and out-of-plane structures of a crystalline nanosheet. Data were collected as a function of tilt angle and analyzed using a hybrid single-particle crystallographic approach. The analysis reveals that adjacent rows of peptoid chains, which are separated by 4.5 Å in the plane of the nanosheet, are offset by 6 Å in the direction perpendicular to the plane of the nanosheet. These atomic-scale corrugations lead to a doubling of the unit cell dimension from 4.5 to 9 Å. Our work provides an alternative interpretation for the observed Å X-ray diffraction peak often reported in polypeptoid crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding atom probe’s analytical performance for iron oxides using correlation histograms and ab initio calculations

Abstract Field evaporation from ionic or covalently bonded materials often leads to the emission of molecular ions. The metastability of these molecular ions, particularly under the influence of the intense electrostatic field (10 10 Vm −1 ), makes them prone to dissociation with or without an exchange of energy amongst them. These processes can affect the analytical performance of atom probe tomography (APT). For instance, neutral molecules formed through dissociation may not be detected at all or with a time of flight no longer related to their mass, causing their loss from the analysis. Here, we evaluated the changes in the measured composition of FeO, Fe 2 O 3 and Fe 3 O 4 across a wide range of analysis conditions. Possible dissociation reactions are predicted by density-functional theory calculations considering the spin states of the molecules. The energetically favoured reactions are traced on to the multi-hit ion correlation histograms, to confirm their existence within experiments, using an automated Python-based routine. The detected reactions are carefully analyzed to reflect upon the influence of these neutrals from dissociation reactions on the performance of APT for analysing iron oxides.

74 ATOMIC AND MOLECULAR PHYSICS↗

QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules

Quantitative structure–odor relationships are critically important for studies related to the function of olfaction. Current literature data sets contain expert-labeled molecules but lack feature data. This paper introduces QuantumScents, a quantum mechanics augmented derivative of the Leffingwell data set. QuantumScents contains 3.5k structurally and chemically diverse molecules ranging from 2 to 30 heavy atoms (CNOS) and their corresponding 3D coordinates, total PBE0 energy, molecular dipole moment, and per-atom Hirshfeld charges, dipoles, and ratios. The authors demonstrate that Hirshfeld charges and ratios contain sufficient information to perform molecular classification by training a Message Passing Neural Network with chemprop (Heid, E.; et al. ChemRxiv, 2023, DOI: 10.26434/chemrxiv-2023-3zcfl) to predict scent labels. Finally, the QuantumScents data set is freely available on Zenodo along with the authors’ code, example models, and data set generation workflow (https://zenodo.org/doi/10.5281/zenodo.8239853).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct momentum imaging of charge transfer following site-selective ionization

We study ultrafast charge rearrangement in dissociating 2-iodopropane (2-C 3 H 7 I) using site-selective core-ionization at the iodine atom. Clear signatures of electron transfer between the neutral propyl fragment and multiply charged iodine ions are observed in the recorded delay-dependent ion momentum distributions. The detected charge transfer pathway is only favorable within a small (few angstrom), charge-state-dependent spatial window located at C-I distances longer than that of the neutral ground-state molecule. Lastly, these results offer new insights into the physics underpinning charge transfer in isolated molecules and pave the way for a new class of time-resolved studies.

74 ATOMIC AND MOLECULAR PHYSICS↗

Method for conversion of diols to olefin products

A method for converting a diol in solution to an olefin fraction, the method comprising: (i) reacting a diol of the formula HO—R—OH in solution with a carbonyl-containing molecule of the formula: in the presence of an acid catalyst to result in a dioxolane molecule of the formula: wherein R is a hydrocarbon linker containing 1-12 carbon atoms, and R 1 and R 2 are independently selected from hydrogen atom and hydrocarbon groups containing 1-12 carbon atoms, wherein R 1 and R 2 optionally interconnect; (ii) removing the dioxolane molecule from the solution by phase separation; and (iii) contacting the dioxolane molecule with a metal-loaded zeolite at a temperature of 100-500° C. to convert the dioxolane molecule to an olefin fraction.

Li, Zhenglong↗