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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Reaction Chemistry at Discrete Organometallic Fragments on Black Phosphorus

Abstract Black phosphorus (bP) is a two‐dimensional van der Waals material unique in its potential to serve as a support for single‐site catalysts due to its similarity to molecular phosphines, ligands quintessential in homogeneous catalysis. However, there is a scarcity of synthetic methods to install single metal centers on the bP lattice. Here, we demonstrate the functionalization of bP nanosheets with molecular Re and Mo complexes. A suite of characterization techniques, including infrared, X‐ray photoelectron and X‐ray absorption spectroscopy as well as scanning transmission electron microscopy corroborate that the functionalized nanosheets contain a high density of discrete metal centers directly bound to the bP surface. Moreover, the supported metal centers are chemically accessible and can undergo ligand exchange transformations without detaching from the surface. The steric and electronic properties of bP as a ligand are estimated with respect to molecular phosphines. Sterically, bP resembles tri(tolyl)phosphine when monodentate to a metal center, and bis(diphenylphosphino)propane when bidentate, whereas electronically bP is a σ‐donor as strong as a trialkyl phosphine. This work is foundational in elucidating the nature of black phosphorus as a ligand and underscores the viability of using bP as a basis for single‐site catalysts.

Chemistry↗
DOE OSTI2023

Atomistic insight into the effects of electrostatic fields on hydrocarbon reaction kinetics

Reactive Molecular Dynamics (MD) and Density Functional Theory (DFT) computations are performed to provide insight into the effects of external electrostatic fields on hydrocarbon reaction kinetics. By comparing the results from MD and DFT, the suitability of the MD method in modeling electrodynamics is first assessed. Results show that the electric field-induced polarization predicted by the MD charge equilibration method is in good agreement with various DFT charge partitioning schemes. Then, the effects of oriented external electric fields on the transition pathways of non-redox reactions are investigated. Results on the minimum energy path suggest that electric fields can cause catalysis or inhibition of oxidation reactions, whereas pyrolysis reactions are not affected due to the weaker electronegativity of the hydrogen and carbon atoms. MD simulations of isolated reactions show that the reaction kinetics is also affected by applied external Lorentz forces and interatomic Coulomb forces since they can increase or decrease the energy of collision depending on the molecular conformation. In addition, electric fields can affect the kinetics of polar species and force them to align in the direction of field lines. These effects are attributed to energy transfer via intermolecular collisions and stabilization under the external Lorentz force. The kinetics of apolar species is not significantly affected mainly due to the weak induced dipole moment even under strong electric fields. The dynamics and reaction rates of species are studied by means of large-scale combustion simulations of n-dodecane and oxygen mixtures. Results show that under strong electric fields, the fuel, oxidizer, and most product molecules experience translational and rotational acceleration mainly due to close charge transfer along with a reduction in their vibrational energy due to stabilization. This study will serve as a basis to improve the current methods used in MD and to develop novel methodologies for the modeling of macroscale reacting flows under external electrostatic fields.

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

Diffusion Monte Carlo approaches for studying nuclear quantum effects in fluxional molecules

Abstract Diffusion quantum Monte Carlo (DMC) provides a powerful approach for obtaining the ground state energy and wave function of molecules, ions, and molecular clusters. The approach is uniquely well suited for studies of fluxional molecules, which undergo large amplitude vibrational motions even in their ground state. In contrast to the electronic structure problem, where the wave function must be antisymmetric with respect to exchange of any pair of electrons, the wave function for the ground vibrational state is nodeless. This greatly simplifies the application of DMC for vibrational problems. Because there is not a single potential function that can be used to describe the intramolecular and intermolecular interactions in all molecular systems, most methods that are used to describe nuclear quantum effects rely on a carefully chosen zero‐order description of the molecular vibrations. In contrast, DMC calculations can be performed in Cartesian coordinates, making the DMC algorithm easily transferable between different chemical systems. In this contribution, the theory that underlies DMC will be discussed along with important considerations for performing DMC calculations. Extensions for evaluating vibrationally excited states and molecular properties are also discussed. Insights that can be obtained from DMC calculations are illustrated in the context of the protonated water clusters. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Theoretical and Physical Chemistry > Spectroscopy

Chemistry↗
DOE OSTI2025

Real-Space Local Dynamics in 1,2,3-Triazole Using Inelastic Neutron Scattering

Enhancing proton transport in polymer electrolytes is crucial for advancing next-generation solid-state batteries, yet our understanding of proton conductivity in nonaqueous environments remains limited due to a lack of atomic-scale insights. Here, in this study, we investigated the atomic-scale dynamics of 1,2,3-triazole, a small molecule capable of dynamic hydrogen bonding, as a model system for proton hopping in nonaqueous environments. Using the real-space correlation function determined by the double Fourier transformation of inelastic neutron scattering spectra, we identified that the self-motion of protons and intermolecular dynamics occur on comparable time scales. Furthermore, we observed that the activation energy associated with the intermolecular dynamics matches the energy barrier for molecular rotations determined through Density Functional Theory calculations. These findings underscore the importance of controlling molecular dynamics at the atomic scale to control proton transport. Additionally, we demonstrated that intermolecular dynamics in systems involving protons can be studied using inelastic neutron scattering even without deuteration, thereby providing a broader avenue for studying atomic-scale dynamics in soft matter systems.

Shinohara, Yuya [Oak Ridge National Laboratory (OR↗
NASA NTRS2016

Effect of Molecular Flexibility upon Ice Adhesion Shear Strength

Ice formation on aircraft surfaces effects aircraft performance by increasing weight and drag leading to loss of lift. Current active alleviation strategies involve pneumatic boots, heated surfaces, and usage of glycol based de-icing fluids. Mitigation or reduction of in-flight icing by means of a passive approach may enable retention of aircraft capabilities, i.e., no reduction in lift, while reducing the aircraft weight and mechanical complexity. Under a NASA Aeronautics Research Institute Seedling activity, the effect of end group functionality and chain length upon ice adhesion shear strength (IASS) was evaluated with the results indicating that chemical functionality and chain length (i.e. molecular flexibility) affected IASS. Based on experimental and modeling results, diamine monomers incorporating molecular flexibility as either a side chain or in between diamine functionalities were prepared, incorporated into epoxy resins that were subsequently used to fabricate coatings on aluminum substrates, and tested in a simulated icing environment. The IASS was found to be lower when molecular flexibility was incorporated in the polymer chain as opposed to a side chain.

Smith, Joseph G.↗
DOE OSTI2021

Interpretation of multiple solutions in fully iterative GF2 and GW schemes using local analysis of two-particle density matrices

Due to the presence of non-linear equations, iterative Green’s function methods can result in multiple different solutions even for simple molecular systems. In contrast to the wave-function methods, a detailed and careful analysis of such molecular solutions was not performed before. In this work, we use two-particle density matrices to investigate local spin and charge correlators that quantify the charge resonance and covalent characters of these solutions. When applied within the unrestricted orbital set, spin correlators elucidate the broken symmetry of the solutions, containing necessary information for building effective magnetic Hamiltonians. Based on GW and GF2 calculations of simple molecules and transition metal complexes, we construct Heisenberg Hamiltonians, four-spin-four-center corrections, and biquadratic spin–spin interactions. These Hamiltonian parameterizations are compared to previous wave-function calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1986

Dipole moments and transition probabilities of the a 3Sigma(+)g - b 3Sigma(+)u system of molecular hydrogen

Multiconfiguration variational calculations of the electronic wave functions of the a 3Sigma(+)g and b 3Sigma(+)u states of molecular hydrogen are presented, and the electric dipole transition moment between them (of interest in connection with stellar atmospheres and the UV spectrum of the Jovian planets) is obtained. The dipole moment is used to calculate the probabilities of radiative transitions from the discrete vibrational levels of the a 3Sigma(+)g state to the vibrational continuum of the repulsive b 3Sigma(+)u state as functions of the wavelength of the emitted photons. The total transition probabilities and radiative lifetimes of the levels v prime = 0-20 are presented.

Guberman, S.↗
DOE OSTI2024

Variations in proton transfer pathways and energetics on pristine and defect-rich quartz surfaces in water: Insights into the bimodal acidities of quartz

Hypothesis. Understanding the mechanisms of proton transfer on quartz surfaces in water is critical for a range of processes in geochemical, environmental, and materials sciences. The wide range of surface acidities (>9 pKa units) found on the ubiquitous mineral quartz is caused by the structural variations of surface silanol groups. Molecular scale simulations provide essential tools for elucidating the origin of site-specific surface acidities. Simulations. Here, we used density-functional tight-binding-based molecular dynamics combined with rare-event metadynamics simulations to probe the mechanisms of deprotonation reactions from ten representative surface silanol groups found on both pristine and defect-rich quartz (1 0 1) surfaces with Si vacancies. Findings. The results show that deprotonation is a highly dynamic process where both the surface hydroxyls and bridging oxygen atoms serve as the proton acceptors, in addition to water. Deprotonation of embedded silanols through intrasurface proton transfer exhibited lower pKa values with less H-bond participation and higher energy barriers, suggesting a new mechanism to explain the bimodal acidity observed on quartz surface. Defect sites, recently shown to comprise a significant portion of the quartz (1 0 1) surface, diversify the coordination and local H-bonding environments of the surface silanols, changing both the deprotonation pathways and energetics, leading to a wider range of pKa values (2.4 to 11.5) than that observed on pristine quartz surface (10.4 and 12.1).

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

Modeling an S N 2 Reaction Mechanism for Hydrolysis of Siloxane Linkages with Density Functional Theory under Basic Conditions and Implications for Dissolution of Quartz

An extended silicate molecular cluster was used to perform density functional theory calculations to determine if an S N 2 mechanism, where OH – attacks a Q 1 Si coupled with Na + charge balancing an adjacent siloxane bridging O atom, could explain the observed energy of activation of quartz dissolution under basic conditions.

chemical calculations↗
DOE OSTI2021

Effect of Fluoroethylene Carbonate Additives on the Initial Formation of the Solid Electrolyte Interphase on an Oxygen-Functionalized Graphitic Anode in Lithium-Ion Batteries

The formation of a solid electrolyte interphase (SEI) at the electrode/electrolyte interface substantially affects the stability and lifetime of lithium-ion batteries (LIBs). One of the methods to improve the lifetime of LIBs is by the inclusion of additive molecules to stabilize the SEI. To understand the effect of additive molecules on the initial stage of SEI formation, in this work we compare the decomposition and oligomerization reactions of a fluoroethylene carbonate (FEC) additive on a range of oxygen-functionalized graphitic anodes to those of an ethylene carbonate (EC) organic electrolyte. A series of density functional theory (DFT) calculations augmented by ab initio molecular dynamics (AIMD) simulations reveal that EC decomposition on an oxygen-functionalized graphitic ($11\bar{2}0$) edge facet through a nucleophilic attack on an ethylene carbon site (C E ) of an EC molecule (S2 mechanism) is spontaneous during the initial charging process of LIBs. However, decomposition of EC through a nucleophilic attack on a carbonyl carbon (C C ) site (S1 mechanism) results in alkoxide species regeneration that is responsible for continual oligomerization along the graphitic surface. In contrast, FEC prefers to decompose through an S1 pathway, which does not promote alkoxide regeneration. Including FEC as an additive is thus able to suppress alkoxide regeneration and results in a smaller and thinner SEI layer that is more flexible toward lithium intercalation during the charging/discharging process. In addition, we find that the presence of different oxygen functional groups at the surface of graphite dictates the oligomerization products and the LiF formation mechanism in the SEI.

25 ENERGY STORAGE↗
DOE OSTI2023

An analytic and complete equation of state for condensed phase materials

Analytic equations of state (EOS) are intended to reproduce theoretical and experimental data in a single phase portion of the thermodynamic space. We devise a complete and thermodynamically consistent model with four distinct features: (1) a reference isotherm that remains thermodynamically stable, (2) a flexible specific heat model based on a fourth-order rational polynomial, (3) a Grüneisen parameter that depends on specific volume and temperature, and (4) pressure and internal energy functions that can be inverted analytically in temperature. The model aims to improve the accuracy of existing equations of state while remaining computationally efficient. To demonstrate its features, we include calibrations for single-crystal pentaerythritol tetranitrate (PETN), liquid nitromethane (NM), and hexagonal close-packed beryllium (Be) metal. The parameter optimization uses the specific heat capacity, Grüneisen parameter, and static compression curves obtained from density functional theory for the crystalline solids and molecular dynamics simulations for liquid NM. We also present a velocity autocorrelation function that yields accurate phonon densities of states for the EOS calibration from the molecular dynamics trajectories. Each of the three calibrations is constrained to enforce the ambient state from experimental measurements and validated against experimental Hugoniot data from multiple sources. We also include one-dimensional hydrodynamic simulations of the isentropic compression experiments for beryllium conducted at the Z facility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

19-LW-045 Full Length Final Report. Molecular Mechanisms of Bacterial Pathogenesis: Waging the Arms Race with Superbugs

As the current global pandemic makes abundantly clear, we need a better understanding of infectious disease to safeguard human health, the economy and global security. Modern omics techniques hold the promise of providing a comprehensive understanding of the molecular mechanisms of life, including causes of pathogenesis from infectious disease at the molecular level, but we there is a serious gap in annotation of gene function. For as much as half of the genes and gene products encoded in genomes the molecular and/or cellular function is unknown or only partially understood. Recent innovations in fluorescence microscopy for live cell imaging and genetic engineering make it possible to determine the temporal correlation between molecular events, such as a gene being expressed due to host-pathogen interaction, and cellular events, such as bacterial invasion of immune cells. This is turn allows us to gain new insight as to the molecular and cellular role of individual genes and will enable the discovery and validation of new molecular mechanisms essential for infectious disease. Knowing the molecular mechanisms of disease processes will provide new therapeutic targets or novel countermeasure strategies. We aimed to develop a lattice light sheet fluorescence microscope as a unique resource at LLNL for long time course live cell imaging experiments; to develop the reagents and cell lines needed to monitor molecular events during the course pathogenic bacteria infecting mammalian immune cells; and to demonstrate that we could capture molecular events during an infection. We fully commissioned the LLNL lattice light sheet microscope and conducted initial proof of principle imaging experiments on mammalian immune cells and pathogenic bacteria. It is clear from the experience gained that long time course live cell imaging has tremendous potential to help elucidate molecular mechanisms of host-pathogen interactions and to help annotate gene function, which would establish a basis for new countermeasures. It is also clear that if live cell imaging is to realize its full potential new data processing and analysis tools will need to be developed to facilitate analysis of molecular events within cells; new sample chambers and stages could facilitate studies with a wider range of cell and tissue types; and alternative molecular tagging methods need to be explored to enable more facile engineering of cells labeled with molecular specificity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

Fullerene Machines

Fullerenes possess remarkable properties and many investigators have examined the mechanical, electronic and other characteristics of carbon SP2 systems in some detail. In addition, C-60 can be functionalized with many classes of molecular fragments and we may expect the caps of carbon nanotubes to have a similar chemistry. Finally, carbon nanotubes have been attached to t he end of scanning probe microscope (Spill) tips. Spills can be manipulated with sub-angstrom accuracy. Together, these investigations suggest that complex molecular machines made of fullerenes may someday be created and manipulated with very high accuracy. We have studied some such systems computationally (primarily functionalized carbon nanotube gears and computer components). If such machines can be combined appropriately, a class of materials may be created that can sense their environment, calculate a response, and act. The implications of such hypothetical materials are substantial.

Globus, Al↗
DOE OSTI2022

MOF-enabled confinement and related effects for chemical catalyst presentation and utilization

A defining characteristic of nearly all catalytically functional MOFs is uniform, molecular-scale porosity. MOF pores, linkers and nodes that define them, help regulate reactant and product transport, catalyst siting, catalyst accessibility, catalyst stability, catalyst activity, co-catalyst proximity, composition of the chemical environment at and beyond the catalytic active site, chemical intermediate and transition-state conformations, thermodynamic affinity of molecular guests for MOF interior sites, framework charge and density of charge-compensating ions, pore hydrophobicity/hydrophilicity, pore and channel rigidity vs. flexibility, and other features and properties. Collectively and individually, these properties help define overall catalyst functional behaviour. Here, this review focuses on how porous, catalyst-containing MOFs capitalize on molecular-scale confinement, containment, isolation, environment modulation, energy delivery, and mobility to accomplish desired chemical transformations with potentially superior selectivity or other efficacy, especially in comparison to catalysts in homogeneous solution environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Modeling Liquid Water by Climbing up Jacob’s Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials

Within the framework of Kohn–Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob’s ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric–isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Detection of translational noncrystallographic symmetry in Patterson functions

Detection of translational noncrystallographic symmetry (TNCS) can be critical for success in crystallographic phasing, particularly when molecular-replacement models are poor or anomalous phasing information is weak. If the correct TNCS is detected then expected intensity factors for each reflection can be refined, so that the maximum-likelihood functions underlying molecular replacement and single-wavelength anomalous dispersion use appropriate structure-factor normalization and variance terms. Here, an analysis of a curated database of protein structures from the Protein Data Bank to investigate how TNCS manifests in the Patterson function is described. These studies informed an algorithm for the detection of TNCS, which includes a method for detecting the number of vectors involved in any commensurate modulation (the TNCS order). The algorithm generates a ranked list of possible TNCS associations in the asymmetric unit for exploration during structure solution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nonintuitive Surface Self-Assembly of Functionalized Molecules on Ag(111)

The fabrication of nanomaterials involves selfordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on the functional groups alone does not provide a comprehensive picture. Especially at interfaces, processes that govern self-ordering are complex and involve various physical and chemical effects, often leading to unexpected structures, as we showcase here on the example of a homologous series of quinones on Ag(111). Naively, one could expect that such quinones, which all bear the same functionalization, form similar motifs. In salient contrast, our joint theoretical and experimental study shows that profoundly different structures are formed. Using a machine-learning-based structure search algorithm, we find that this is due to a shift of the balance of three antagonizing driving forces: adsorbate-substrate interactions governing adsorption sites, adsorbate-adsorbate interactions favoring close packing, and steric hindrance inhibiting certain otherwise energetically beneficial molecular arrangements. The theoretical structures show excellent agreement with our experimental characterizations of the organic/ inorganic interfaces, both for the unit cell sizes and the orientations of the molecules within. The nonintuitive interplay of similarly important interaction mechanisms will continue to be a challenging aspect for the design of functional interfaces. With a detailed examination of all driving forces, we are, however, still able to devise a design principle for self-assembly of functionalized molecules.

structure prediction↗