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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Self-Assembly of Silica Nanoparticles at Water–Hydrocarbon Interfaces: Insights from In Operando Small-Angle X-ray Scattering Measurements and Molecular Dynamics Simulations

To achieve tunable controls on the interactions of siliceous materials in subsurface environments bearing water and hydrocarbons, it is essential to determine the influence of hydrocarbon–water interfaces on the self-assembly of the silica particles. The hydrophilic silica particle have a tendency to aggregate on the water front of the interface. Self-assembly of silica nanoparticles proceeds via the migration of these nanoparticles to the water–hydrocarbon interface followed by aggregation at the interface. Fractal-like morphologies of assembled silica nanoparticles at water–hydrocarbon interfaces are observed. Rapid assembly of the hydrophilic silica nanoparticles at water–hydrocarbon interfaces corresponds to an overall reduction in the surface tension of water–toluene and water–heptane systems. These studies demonstrate the silica aggregation that is the precursor of silica polymerization, or nucleation and growth is influenced by the presence of hydrocarbons in subsurface geologic environments. These insights were derived from in operando ultrasmall and small-angle X-ray scattering (USAXS/SAXS) measurements, cryo-scanning electron microscopy (Cryo-SEM) imaging, and classical molecular dynamics simulations. As a result, these studies are intended to inform current and future efforts aimed at tuning silica reactivity in subsurface geologic environments to enhance permeability, the design and use of silica-based proppants to enhance fractures, and the development of effective strategies to control silica-based scaling behavior in subsurface reservoirs.

42 ENGINEERING↗
DOE OSTI2020

Nonadiabatic Excited-State Molecular Dynamics for Open-Shell Systems

Nonadiabatic Molecular Dynamics (NAMD) of excited states has been widely used in the simulation of photoinduced phenomena. However, the inability to treat bond breaking and forming processes with single-reference electronic structure methods limits their application in photochemistry for extended molecular systems. In this work, the extension of excited-state NAMD for open-shell systems is developed and implemented in the NEXMD software. We present the spin-unrestricted CIS and TDSCF formalism for the ground and excited states, analytical derivatives, and nonadiabatic derivative couplings for the respective potential energy surfaces. Next, this methodology is employed to study the photochemical reaction of three model molecules. The results demonstrate the advantage of the open-shell approach in modeling photochemical reactions, especially involving bond breaking processes. We find that the open-shell method lowers the reaction barrier at the bond-breaking limits resulting in larger calculated photochemical quantum yields compared to the respective closed-shell results. We also address problems related to spin contamination in the open-shell method, especially when molecular geometries are far from equilibrium.

36 MATERIALS SCIENCE↗
NASA NTRS1975

Quantum chemical study of relative reactivities of a series of amines and nitriles - Relevance to prebiotic chemistry

Using the Iterative Extended Huckel Theory (IEHT) calculations of the electron distribution and orbital energies of a series of thirteen amines, nitriles and amino-nitriles relevant to prebiotic and cosmo-chemistry have been carried out. Ground state properties such as the energy and nature of the highest occupied (HOMO) and lowest empty (LEMO) molecular orbitals, net atomic charges and number of nonbonding electrons have been identified as criteria for correlating the relative nucleophilicity of amine and nitrile nitrogens and the electrophilicity of nitrile and other unsaturated carbon atoms. The results of such correlations can be partially verified by known chemical behavior of these compounds and are used to predict and understand their role in prebiotic organic synthesis.

Loew, G. H.↗
DOE OSTI2026

Generative modeling enables molecular structure retrieval from Coulomb explosion imaging

Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to tackle this challenging task is Coulomb explosion imaging, which benefited decisively from recently emerging high-repetition-rate X-ray free-electron laser sources. With this technique, information on the molecular structure is inferred from the momentum distributions of the ions produced by the rapid Coulomb explosion of molecules. Retrieving molecular structures from these distributions poses a highly non-linear inverse problem that remains unsolved for molecules consisting of more than a few atoms. Here, we address this challenge using a diffusion-based Transformer neural network. We show that the network reconstructs unknown molecular geometries from ion-momentum distributions with a mean absolute error below one Bohr radius, which is half the length of a typical chemical bond.

Artificial Intelligence (cs.AI)↗
DOE OSTI2025

P-Type Doping of Mixed Tin–Lead Halide Perovskites Using Electron Transfer to Mo(tfd-COCF3) 3 and F 4 TCNQ

Mixed tin-lead halide perovskites are emerging as promising candidates to address the toxicity issues of lead-based perovskites and to provide additional bandgap tunability for optoelectronic applications. Electron-transfer doping offers a prospective pathway to modulate electronic properties of metal-halide perovskites, while not disturbing the underlying crystal structure. However, limited research exists comparing molecular dopants for these systems. Here, our study investigates the p-type electron-transfer doping of the mixed tin-lead halide perovskite MAPb 0.5 Sn 0.5 I 3 (MA = methylammonium) using a sequential deposition approach (perovskite film followed by dopant incorporation) and the molecular dopants F 4 TCNQ and Mo(tfd-COCF 3 ) 3 . Up to 3 orders of magnitude higher carrier density and up to 2 orders of magnitude greater conductivity are achieved relative to the undoped samples, with F 4 TCNQ and Mo(tfd-COCF 3 ) 3 demonstrating similar doping efficiencies (associated with the ratio of mobile charges added to the number of dopant molecules incorporated) of 0.031(3) % and 0.024(3) %, respectively. Differences in the doping effectiveness for a given molarity doping solution likely follow from variations in dopant incorporation within the film during the spin coating deposition step.

14 SOLAR ENERGY↗
NASA NTRS1981

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

Kahn, L. R.↗
DOE OSTI2021

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2011

A Laboratory and Theoretical Study of Silicon Hydroxide SiOH

The rotational spectrum of the triatomic free radical SiOH in its X 2A' ground electronic state has been observed in a supersonic molecular beam by Fourier transform microwave spectroscopy. The fundamental (10,1 yields 00,0) transition has been detected for normal SiOH and for three rare isotopic species: (30)SiOH, Si(18)OH, and SiOD. The same transition has also been observed in two of three excited vibrational states, v2 and v3, for the most abundant species. Precise spectroscopic constants, including those that describe the effective spin doubling and hydrogen hyperfine structure, have been derived for each isotopic species or vibrational state. To complement the laboratory work, theoretical calculations of the structure, dipole moment, and energies of the X 2A' and low-lying 1 2A'' states have also been undertaken at the coupled cluster level of theory. In agreement with theoretical predictions, we conclude from the hyperfine constants that SiOH is a best described as a pi-type radical, with the unpaired electron localized on a p orbital on the silicon atom. Assuming a bond angle of 118.5 deg, the Si-O bond length is 1.647(2) Angstroms and the O-H bond length is 0.969(4) Angstrom.

McCarthy, M. C.↗
DOE OSTI2024

Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst

Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex that captures sunlight and converts it into chemical energy with near unity quantum efficiency, which generates low potential reducing equivalents for metabolism. Realizing and understanding the molecular basis for an approach that utilizes those electrons and stores solar energy as a fuel is therefore appealing. Here, we report the 2.27-Å global resolution cryo-EM structure of a photosystem I complex with bound platinum nanoparticles that catalyzes light-driven H 2 production. The platinum nanoparticle binding sites and possible stabilizing interactions are described. Overall, the investigation reveals a direct structural look at a photon-to-fuels photosynthetic biohybrid system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Competing Radical and Molecular Channels in the Unimolecular Dissociation of Methylformate

The thermal dissociation of methylformate has been characterized by numerous experimental and theoretical studies that all seem to agree that the lowest energetically accessible process is a 3-center H-atom transfer that leads to the molecular products CH3OH 3 OH + CO. However, these literature studies seem to be at odds with regards to the role of other competing molecular eliminations and bond-fission processes and therefore a complete and resolved mechanistic picture of methylformate thermal dissociation still eludes us. In this work, we have performed high-level electronic structure theory calculations to characterize the energetics of other overlooked molecular and radical processes that can originate on the complex CH3OCHO 3 OCHO potential energy surface (PES). The present calculations do indeed confirm that the lowest energy process accessible on this PES is molecular elimination to form CH3OH 3 OH + CO. However, unlike prior theoretical studies, the present calculations reveal that the second lowest energy process is a 5-center concerted elimination process that leads to the direct formation of H2 2 + CH2O 2 O + CO. We also note that HCO2 2 from the lowest-lying bond fission has two energetically comparable electronic states (of 2 B 2 and 2 A 1 symmetry). Furthermore, the barrier for H-atom migration of CH3OCHO 3 OCHO to form the carbene (CH3OCOH) 3 OCOH) is similar to that for the direct 4-center elimination process leading to CH2O 2 O + CH2O 2 O characterized in prior literature studies. Radical and molecular pathways to CH3 3 + HOCO and CH4 4 + CO2 2 can also be facilitated from this carbene. Master equation calculations were performed to characterize the competition between the various molecular and radical processes on this more elaborate CH3OCHO 3 OCHO PES. The results of the present theoretical analyses were used to resolve outstanding questions on the role of secondary radical- initiated reactions in characterizing prior literature experimental studies.

Chemical Kinetics↗
DOE OSTI2026

Ab Initio Polariton Spectra of ZnTPP Molecules Collectively Coupled Inside an Optical Cavity

Exciton-polaritons are quasi-particles formed by the quantum mechanical hybridization of electronic and photonic excitations. Despite extensive investigations, a fundamental understanding of molecular polariton spectra and the polariton delocalization from an ab initio theoretical perspective remains elusive. We simulate experimentally measured linear transmission spectroscopy of many Zinc(II) tetraphenylporphyrin (ZnTPP) molecules collectively coupled to a cavity from first principles. Our theoretical approach incorporates many low-lying electronic excitations in ZnTPP molecules, as well as collective light-matter couplings between ZnTPP and the quantized radiation modes, both of which are shown to be the key to accurately recovering the experimental spectra. We further analyzed to what extent the polariton and dark states are delocalized over many molecules, for the first time, using fully ab initio descriptions of the molecules. We finally investigate the line width as a function of detuning, providing new theoretical insights into the experimentally observed motional narrowing behavior. Our work presents first-ofits- kind theoretical studies on molecular polariton spectra, offering a new perspective on molecular polariton formation in realistic ab initio molecular systems whose rich, many-state nature provides spectral features enabled by the high density of electronic states beyond simple quantum optics models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Determining the Ensemble N -Representability of Reduced Density Matrices

The N-representability problem for reduced density matrices remains a fundamental challenge in electronic structure theory. Following our previous work that employs a unitary-evolution algorithm based on an adaptive derivative-assembled pseudo-Trotter variational quantum algorithm to probe pure-state N-representability of reduced density matrices [J. Chem. Theory Comput. 2024, 20, 9968], in this work we propose a practical framework for determining the ensemble N-representability of a p-body matrix. This is accomplished using a purification strategy that embeds an ensemble state into a pure state defined on an extended Hilbert space, such that the reduced density matrices of the purified state reproduce those of the original ensemble. By iteratively applying variational unitaries to an initial purified state, the proposed algorithm minimizes the Hilbert-Schmidt distance between its p-body reduced density matrix and a specified target p-body matrix, which serves as a measure of the N-representability of the target. This methodology facilitates both error correction of defective ensemble reduced density matrices and quantum-state reconstruction on a quantum computer, offering a route for density-matrix refinement. We validate the algorithm with numerical simulations on systems of two, three, and four electrons in both simple models as well as molecular systems at finite temperature, demonstrating its robustness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1992

Chemical characterization of selected LDEF polymeric materials

The chemical characterization of selected polymeric materials which received exposure on the LDEF is reported. The specimens examined include silvered fluorinated ethylene propylene (FEP) teflon thermal blanket material, polysulfone matrix resin/graphite fiber reinforced composites, and several high performance polymer films. These specimens came from numerous LDEF locations and, thus, received different environmental exposures. The results of infrared, thermal, x ray photoelectron, and various solution property analyses have shown no significant change at the molecular level in the polymer that survived exposure. However, scanning electron and scanning tunneling microscopies show resin loss and a texturing of the surface of some specimens which resulted in a change in optical properties. The potential effect of a silicon containing molecular contamination on these materials is addressed. The possibility of continued post-exposure degradation of some polymeric films is also proposed.

Young, Philip R.↗
DOE OSTI2021

Element-specific investigations of ultrafast dynamics in photoexcited Cu2ZnSnS4 nanoparticles in solution

Ultrafast, light-induced dynamics in copper–zinc–tin–sulfide (CZTS) photovoltaic nanoparticles are investigated through a combination of optical and x-ray transient absorption spectroscopy. Laser-pump, x-ray-probe spectroscopy on a colloidal CZTS nanoparticle ink yields element-specificity, which reveals a rapid photo-induced shift of electron density away from Cu-sites, affecting the molecular orbital occupation and structure of CZTS. We observe the formation of a stable charge-separated and thermally excited structure, which persists for nanoseconds and involves an increased charge density at the Zn sites. Combined with density functional theory calculations, the results provide new insight into the structural and electronic dynamics of CZTS absorbers for solar cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structural insights into transcriptional regulation by the helicase RECQL5

Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Post-Marcus Theory and Simulation of Interfacial Charge Transfer Dynamics in Organic Semiconducting Materials (Final Report)

The research program developed, validated and applies predictive computational protocols for calculating charge transfer (CT) rates in complex molecular systems, including molecular dyads and triads in liquid solution and solid-state organic semiconducting (OSC) materials. We have established a transformative computational scheme that goes beyond widely used simplifications, to achieve realistic descriptions of CT processes. The approach properly addresses the contribution of molecular environment at ambient conditions to CT processes. Our approach achieves unique insight on investigated CT processes in relevant experimental efforts. The collaborative team included three principal investigators (PIs), with complimentary expertise in classical molecular dynamics simulations and data science (Cheung), state-of-the-art electronic structure calculations (Dunietz), and cutting-edge theory and simulation techniques for modeling energy, charge and coherence transfer dynamics in molecular systems (Geva).

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

The Generality of the GUGA MRCI Approach in COLUMBUS for Treating Complex Quantum Chemistry

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗