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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

DFT-Based Calculation of Molecular Hyperpolarizability and SFG Intensity of Symmetric and Asymmetric Stretch Modes of Alkyl Groups

Vibrational sum frequency generation (SFG) spectroscopy has been extensively used for obtaining structural information of molecular functional groups at two-dimensional (2D) interfaces buried in the gas or liquid medium. Although the SFG experiment can be done elegantly, interpreting the measured intensity in terms of molecular orientation with respect to the lab coordinate is quite complicated. One of the main reasons is the difficulty of determining the hyperpolarizability tensors of even simple molecules that govern their SFG responses. The single-bond polarizability derivative (SBPD) model has been proposed to estimate the relative magnitude of SFG-active hyperpolarizability by assuming that the perturbation associated to each vibration is negligible. In this study, density functional theory (DFT) was used to calculate the polarizability and dipole derivative tensors of the CH 3 stretch mode of CH 3 I, CH 3 CH 2 I, CH 3 OH, CH 3 CH 2 OH. Then, the hyperpolarizability tensors of symmetric and asymmetric vibration modes were calculated considering the Boltzmann distribution of representative conformers, which allowed theoretical calculation of their SFG intensities at all polarization combinations as a function of the tilt angle of the CH 3 group with respect to the surface normal direction. Then the ratios of the calculated SFG intensities for the CH 3 peaks used in experimental studies for the CH 3 tilt angle determination were compared. This comparison clearly showed the effect of vibrational coupling among neighboring functional groups. As a result, this study presents new parameters that can be used in determining the average tilt angle of the CH 3 group at the 2D interface with SFG measurements as well as limitations of the method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1997

Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set expansion, it is comparable in accuracy to the MP2 method (better than Hartree Fock, but less accurate than more extensive electron correlation methods such as MP4 or CCSD). However, for systems with large numbers of basis functions it more efficient than any other methods that include electron correlation effects. In this presentation we show the results of DFT calculations for the reaction of benzyne with naphthalene, C60, and nanotube models. We compare energies for [2+2] and [2+4] cycloaddition products. The preferred products for the naphthalene and C60 reactions have been determined by experiment and, thus, these cases serve as a validation of our quantum chemical approach. We also compare the DFT and Brenner potential results. Finally we can predict the likelihood of reaction between benzyne and nanotubes.

Jaffe, Richard↗
DOE OSTI2020

Phonon Spectroscopy in Antimony and Tellurium Oxides

α-Sb 2 O 3 (senarmontite), β-Sb 2 O 3 (valentinite), and α-TeO 2 (paratellurite) are compounds with pronounced stereochemically active Sb and Te lone pairs. The vibrational and lattice properties of each have been previously studied but often lead to incomplete or unreliable results due to modes being inactive in infrared or Raman spectroscopy. Here in this paper, we present a study of the relationship between bonding and lattice dynamics of these compounds. Mössbauer spectroscopy is used to study the structure of Sb in α-Sb 2 O 3 and β-Sb 2 O 3 , whereas the vibrational modes of Sb and Te for each oxide are investigated using nuclear inelastic scattering, and further information on O vibrational modes is obtained using inelastic neutron scattering. Additionally, vibrational frequencies obtained by density functional theory (DFT) calculations are compared with experimental results in order to assess the validity of the utilized functional. Good agreement was found between DFT-calculated and experimental density of phonon states with a 7% scaling factor. The Sb–O–Sb wagging mode of α-Sb 2 O 3 whose frequency was not clear in most previous studies is experimentally observed for the first time at ~340 cm -1 . Softer lattice vibrational modes occur in orthorhombic β-Sb 2 O 3 compared to cubic α-Sb 2 O 3 , indicating that the antimony bonds are weakened upon transforming from the molecular α phase to the layer-chained β structure. The resulting vibrational entropy increase of 0.45 ± 0.1 kB/Sb 2 O 3 at 880 K accounts for about half of the α–β transition entropy. The comparison of experimental and theoretical approaches presented here provides a detailed picture of the lattice dynamics in these oxides beyond the zone center and shows that the accuracy of DFT is sufficient for future calculations of similar material structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Kinetic Study of Polyvinyl Chloride Pyrolysis with Characterization of Dehydrochlorinated PVC

In this paper, we study the kinetics of polyvinyl chloride (PVC) decomposition using a combination of experimental and computational approaches. Here, we develop a simplified kinetic model that contains only two steps: dehydrochlorination of PVC and further decomposition of the PVC residue. The model is consistent with density functional theory (DFT) calculations and experimental data. Dehydrochlorination is an autocatalytic reaction that starts with a tertiary chloride (Cl) and generates hydrogen chloride (HCl) and benzene as the main products. Benzene and HCl formation rates showed similar trends, indicating that HCl likely catalyzes a homolytic carbon-carbon (C-C) bond cleavage, which gives rise to benzene and an aliphatic fragment. We characterized the structure of dehydrochlorinated PVC (PVC residue) by using thermal gravimetric analysis (TGA), Fourier-transform infrared spectroscopy (FTIR), and nuclear magnetic resonance spectroscopy (NMR). FTIR and NMR results indicate that the PVC residue contains 20% quaternary carbon content, indicating a high concentration of cross-linked molecules. We predict that the most probable structure in the cross-linked centers of the PVC residue is cyclohexadiene, which is supported by DFT calculations, FTIR, and NMR.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Cluster Expansion Analysis of Atomic Order in Li-Ion Battery Cathode Material LiCo y Ni 1-y O 2

A modified cluster-expansion treatment was developed recently to analyze atomic order in LiCo y Ni 1-y O 2 , a model cathode material for Li-ion batteries. In this treatment, referred to as a “spin-atom” cluster expansion, the occupant of a lattice site is identified by its spin state as well as its atomic species. Further, Effective Cluster Interaction (ECI) coefficients are derived from a large training data set (i.e., the set of atomic arrangements for which DFT calculations are performed) which is filtered by an anomaly detection algorithm to eliminate poorly converged DFT calculations. The cluster expansion incorporates Li-Ni (LN) exchange as well as intralayer Co-Ni (CN) exchange. Monte Carlo simulations based on the cluster expansion were applied to the Ni-rich part of the phase diagram. The simulations predict a miscibility gap between y = 0.05 and y = 0.65.

25 ENERGY STORAGE↗
DOE OSTI2025

Engineering PdAu/CeO 2 Alloy/Oxide Interfaces for Selective Methane‐to‐Methanol Conversion with Water

The direct conversion of methane-to-methanol remains a critical challenge in methane valorization. In this study, we unveil the crucial role of PdAu/CeO 2 catalysts in enabling selective methane transformation under mild conditions, using only water as the sole oxidant. Through a combination of experimental techniques, including XPS and catalytic testing, alongside density functional theory (DFT) calculations, we demonstrate that a Pd 0.3 Au 0.7 /CeO 2 catalyst, which predominantly exposes isolated Pd atoms, achieves remarkable methanol selectivity (∼80%) at 500 K with a 1:1 methane-to-water ratio. While Pd/CeO 2 efficiently activates methane, its tendency for overreaction leads to complete methanol decomposition, thereby limiting selectivity. Alloying Pd with Au on ceria mitigates this over-reactivity, preventing methanol degradation while maintaining sufficient catalytic activity. The PdAu/CeO 2 composite exhibits a synergistic effect: Pd in contact with the ceria support facilitates methane activation and water dissociation, while Au fine-tunes reactivity to promote methanol formation. DFT calculations confirm that isolated Pd sites at the PdAu/CeO 2 interface play a key role in balancing activity and selectivity. This work underscores the importance of alloy/oxide interfaces in controlling selective methane conversion with water and offers valuable insights for designing highly efficient catalysts for methanol synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Product-promoted acetylene cyclotrimerization to benzene on Ag(111)

Acetylene cyclotrimerization to benzene on Ag(111) has recently been found to be 100% selective. However, it requires monolayer coverages, limiting its practical application due to the high pressure required to attain this surface coverage of acetylene near room temperature. Here, we show that co-adsorbed benzene, the reaction product, promotes cyclotrimerization at submonolayer acetylene coverages without compromising the 100% selectivity of Ag(111) via temperature-programmed desorption experiments. Scanning tunneling microscopy and density functional theory (DFT) calculations elucidate the origin of this effect whereby attractive acetylene–benzene interactions locally compress acetylene domains. DFT calculations further illustrate how co-adsorbed benzene reduces the transition-state energy for formation of the key C 4 intermediate, making cyclotrimerization competitive with desorption. Together, these findings reveal how product-reactant interactions can enhance C–C coupling.

Acetylene cyclotrimerization↗
DOE OSTI2019

Quasicubic model for metal halide perovskite nanocrystals

In this work, we present an analysis of quantum confinement of carriers and excitons, and exciton fine structure, in metal halide perovskite (MHP) nanocrystals (NCs). Starting with coupled-band k · P theory, we derive a nonparabolic effective mass model for the exciton energies in MHP NCs valid for the full size range from the strong to the weak confinement limits. We illustrate the application of the model to CsPbBr 3 NCs and compare the theory against published absorption data, finding excellent agreement. We then apply the theory of electron-hole exchange, including both short- and long-range exchange interactions, to develop a model for the exciton fine structure. We develop an analytical quasicubic model for the effect of tetragonal and orthorhombic lattice distortions on the exchange-related exciton fine structure in CsPbBr 3 , as well as some hybrid organic MHPs of recent interest, including formamidinium lead bromide (FAPbBr 3 ) and methylammonium lead iodide (MAPbI3). Testing the predictions of the quasicubic model using hybrid density functional theory (DFT) calculations, we find qualitative agreement in tetragonal MHPs but significant disagreement in the orthorhombic modifications. Moreover, the quasicubic model fails to correctly describe the exciton oscillator strength and with it the long-range exchange corrections in these systems. Introducing the effect of NC shape anisotropy and possible Rashba terms into the model, we illustrate the calculation of the exciton fine structure in CsPbBr 3 NCs based on the results of the DFT calculations and examine the effect of Rashba terms and shape anisotropy on the calculated fine structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Conjugation in Isomeric Cyclosilane Thioethers

Conjugation in thioether-functionalized cyclosilanes depends on both conformation and connectivity. Borane-catalyzed dehydrocoupling of thiophenols with partially hydrogenated cyclosilanes proceeded with high chemoselectivity for Si–H bonds in the presence of Si–Si bonds. Isomeric 1,3- and 1,4-functionalized cyclosilanes afforded isomeric cyclosilane thioethers that also differed in preference for chair or twist-boat conformations as demonstrated by both X-ray crystal structures and density functional theory (DFT) calculations. Here, the confounding effects of different conformations and connectivity could be distinguished with time-dependent DFT (TD-DFT) calculations and validated with experimentally obtained UV–vis spectra.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Examination of Replicate Syntheses of Metal Organic Frameworks as a Window into Reproducibility in Materials Chemistry

Replicate experiments are a useful tool in understanding the repeatability of scientific measurements. In 2019, a systematic search for replicate syntheses of a collection of 130 metal–organic frameworks (MOFs) found that 89% of these materials had no reported replicate syntheses apart from the original publications identifying the material (Agrawal, M. Proc. Natl. Acad. Sci. U.S.A. 2020, 117, 877−88210.1073/pnas.1918484117). A potential weakness of that search was that only 5–11 years had elapsed since the original publication of each material. Here, this analysis is extended to all publications 11–17 years after the original publication. Although this extended time period identifies more repeat syntheses, 83% of the materials still have no reported replicate syntheses. We also consider how appropriately selected Density Functional Theory (DFT) calculations can provide corroboration for the experimentally reported crystal structures. By using data from previous high-throughput DFT studies, corroborating evidence from DFT was available for 17% of the 130 structures for which no replicate syntheses are available. In total, approximately 1/3 of the 130 MOFs have data associated with replicate synthesis experiments and/or directly corroborating DFT calculations.

Sholl, David S. [Oak Ridge National Laboratory (OR↗
DOE OSTI2020

First-principles study of intrinsic point defects and Xe impurities in uranium monocarbide

Based on density functional theory (DFT) calculations, we perform an extensive investigation of intrinsic point defects and Xe impurities in uranium monocarbide (UC). The DFT calculations involve both the conventional generalized gradient approximation (GGA) and the GGA+U approach with the Hubbard parametric term (U), using up to 5×5×5 supercells. GGA calculations for the formation energy of intrinsic defects demonstrate the significant effect of using larger supercells than in previous studies. Results confirm that the ⟨111⟩ and ⟨100⟩ dumbbell interstitials are the most stable interstitial configurations for U and C, respectively. The interstitial mechanisms are favored for self-diffusion of both uranium and carbon and diffusion of Xe under equilibrium conditions. Calculations also reveal that the Xe substitutional defect at the C lattice site tends to adopt an off-site configuration, which can be interpreted as a Xe interstitial–C vacancy complex. We also utilize GGA+U to assess the impact of effective U parameter (Ueff) on the results. Moreover, we introduce a method to estimate the carbon chemical potential by fitting the phase diagram composition data and propose a selection Ueff=1.25 eV based on the experimental Xe diffusion activation energy. With this approach, GGA+U calculations reproduce the available experimental data for the formation energy of the carbon Frenkel pair and can explain the stepwise recovery of intrinsic properties and burst Xe release behavior in UC observed in annealing experiments.

Huang, Gui-Yang (ORCID:0000000301447376)↗
DOE OSTI2026

Investigating the electrical transport properties and electronic structure of Zr 2 ⁢CuSb 3

The checkerboard lattice has been proposed to host topological flat bands as a result of destructive interference among its various electronic hopping terms. However, it has proven challenging to realize experimentally due to the difficulty of isolating this structure from any significant out-of-plane bonding while maintaining structural integrity. Here, in this study, single crystals of Zr 2 CuSb 3 , a potential candidate for the checkerboard lattice, were synthesized using the solution (self-flux) method, and their structure was confirmed via x-ray diffraction. Electrical-transport measurements indicate metallic behavior with electron-dominated carriers. Angle-resolved photoemission spectroscopy reveals multiple electron pockets and significant k z broadening due to its large c axis and low dispersion features in k z . Density-functional theory (DFT) calculations further disentangle the contributions from each high-symmetry plane, providing a comprehensive characterization of electronic behavior. The DFT calculations were then used to determine the orbital contributions of the bands and detect the out-of-plane bonding which prevented the flat bands from forming.

Downey, Eoghan [Univ. of Michigan, Ann Arbor, MI (↗
DOE OSTI2026

Controllable Formation of Threefold-Coordinated Oxygen in Graphene by Low-Energy Ion Implantation

The atomically precise engineering of impurities in graphene and the understanding of their structural and carrier-dependent electronic properties at the nanoscale are crucial for advancing graphene-based nanoelectronics, catalysis, and energy technologies. Here, we demonstrate controllable incorporation of the elusive 3-fold-coordinated O substitutions into graphene using low-energy O + ion implantation under ultrahigh-vacuum conditions. By combining high-resolution scanning tunneling microscopy and spectroscopy (STM/S), bond-resolved noncontact atomic force microscopy techniques, and density functional theory (DFT) calculations, we resolve both the structural and electronic properties of the O-related defects. The STM/S measurements, corroborated by DFT calculations, uncover a characteristic impurity state that is energetically pinned to the Dirac point across different charge-carrier doping regimes. Molecular dynamics simulations further reveal the distribution of implantation-induced configurations and identify the formation of 3-fold-coordinated O dopants. Furthermore, this work provides a viable route to incorporate 3-fold-coordinated O dopants and opens new opportunities for controlled defect engineering in graphene.

3-fold-coordinated oxygen↗
DOE OSTI2021

Spectroscopic and computational investigations of organometallic complexation of group 12 transition metals by methanobactins from Methylocystis sp. SB2

Methanotrophic bacteria catalyze the aerobic oxidation of methane to methanol using Cu-containing enzymes, thereby exerting a modulating influence on the global methane cycle. To facilitate the acquisition of Cu ions, some methanotrophic bacteria secrete small modified peptides known as “methanobactins,” which strongly bind Cu and function as an extracellular Cu recruitment relay, analogous to siderophores and Fe. In addition to Cu, methanobactins form complexes with other late transition metals, including the Group 12 transition metals Zn, Cd, and Hg, although the interplay among solution-phase configurations, metal interactions, and the spectroscopic signatures of methanobactin-metal complexes remains ambiguous. In this study, the complexation of Zn, Cd, and Hg by methanobactin from Methylocystis sp. strain SB2 was studied using a combination of absorbance, fluorescence, extended x-ray absorption fine structure (EXAFS) spectroscopy, and time-dependent density functional theory (TD-DFT) calculations. We report changes in sample absorbance and fluorescence spectral dynamics, which occur on a wide range of experimental timescales and characterize a clear stoichiometric complexation dependence. Mercury L3-edge EXAFS and TD-DFT calculations suggest a linear model for Hg--S coordination, and TD-DFT suggests a tetrahedral model for Zn 2+ and Cd 2+ . We observed an enhancement in the fluorescence of methanobactin upon interaction with transition metals and propose a mechanism of complexation-hindered isomerization drawing inspiration from the wild-type Green Fluorescent Protein active site. Collectively, our results represent the first combined computational and experimental spectroscopy study of methanobactins and shed new light on molecular interactions and dynamics that characterize complexes of methanobactins with Group 12 transition metals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Density functional thermodynamic description of spin, phonon and displacement degrees of freedom in antiferromagnetic-to-paramagnetic phase transition in YNiO 3

This work herein demonstrates a direct density functional description of the finite-temperature thermodynamic properties of solids exhibiting phase transitions through positional and spin symmetry breaking degrees of freedom. A classic example addressed here is the rare-earth (R) nickelates RNiO 3 where the ground state is characterized by crystallographic and magnetic (e.g., antiferromagnetic) long-range order (LRO), whereas the higher temperature paramagnetic phase manifests a range of local spin and positional symmetry breaking motifs with short-range order (SRO). Unlike time-dependent simulations of spin and positional degrees of freedom, in the present work, phases are described via a superposition of static configurations constructed by populating a periodic base lattice supercell allowing for the formation of energy lowing distribution of positional and spin local motifs. The thermal populations of the configurations in such a superposition phase are obtained from the energy-minimized Density Functional Theory (DFT)-calculated partition functions at different temperatures. This approach offers flexible inclusion of different physical contributions to the free energy, such as elastic, electronic and phonon free energies, all obtained from the same underlying DFT total energy calculations of periodic structures. The thermodynamic and magnetic properties of both LRO and SRO crystallographic and spin phases, including antiferromagnetic (AFM) to paramagnetic (PM) Néel phase transition in YNiO3 are studied. Including spin and phonon contributions, we find a DFT-calculated Néel temperature to be 144 K in satisfactory agreement with the experimental value of 145 K; whereas omitting the phonon contribution, one obtains a Néel temperature of 81 K. We present phonon contributions to the DFT-calculated temperature-dependent SRO, heat capacities, and the polymorphous distribution of nonzero local magnetic moments in the PM phase. This approach thus extends to finite temperatures the symmetry-broken DFT description of both the AFM and PM phases, demonstrating that a thermodynamic superposition approach based on symmetry broken configurations evaluated by a mean-field like DFT is sufficient to obtain a consistent description of the thermal physics of the AFM, PM phases and their interconversion in 3d oxides illustrated by YNiO 3 .

36 MATERIALS SCIENCE↗
DOE OSTI2023

Kβ X-ray Emission Spectroscopy of Cu(I)-Lytic Polysaccharide Monooxygenase: Direct Observation of the Frontier Molecular Orbital for H 2 O 2 Activation

Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped “His-brace” configuration including the N-terminal histidine and its amine group as ligands. Here, this study explicitly investigates the electronic structure of the d 10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H 2 O 2 O–O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H 2 O 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Electronic Structures and Magnetism of Zr-, Th-, and U-based Metal-Organic Frameworks (MOFs) by Density Functional Theory

Metal-organic frameworks (MOFs) have recently gained wide interest as candidate materials for nuclear waste immobilization. While the fundamental thermodynamic properties, such as the substitution energies determine the favorability of radionuclide sequestration by utilization of a MOF matrix, the studies of MOF electronic structure reveal the role of d-, and/or f-electrons on changes in physical properties of actinide-containing materials. We use density functional theory (DFT) calculations to investigate the electronic structures of Zr-, Th-, and U-MOFs, including their electronic band structures and, where appropriate, their magnetic properties. We employ various DFT methods including DFT+U, collinear spin-polarization, spin-orbit coupling, and different flavors of exchange-correlation functionals to assess the robustness to the specific exchange-correlation functional. Unlike the Zr-, and Th-MOFs, the U-MOF is found to be sensitive to electron localization and spin; hence we explore the magnetic structure of the U-MOF in further detail.

Metal-Organic Framework, MOF, Actinides, DFT↗