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Results for “electronic structure of atoms & molecules”

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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes

The metal centers in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.

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

Chiral population analysis: a real space visualization of X-ray circular dichroism

The microscopic understanding of probing and controlling molecular chirality is of considerable interest. Numerous spectroscopic techniques are capable of monitoring molecular asymmetry and its consequences, ranging from the infrared to the X-ray regime. Resonant X-rays have long been used to investigate local atomic sites within molecules thanks to the localized nature of core electronic transitions. These techniques can be used to determine the extent to which chirality is a local versus a delocalized property. However, how to systematically partition dichroic contributions from the point of view of electronic structure simulations remains an open question. Here, we introduce the concept of chiral population analysis that connects chirality to the atomic orbital picture. In analogy with Mulliken population analysis, which assigns charges to atomic orbitals, chiral populations allow the dichroic response to be distributed among the participating atomic orbitals. This decomposition can be further visualized in real space by representing it in terms of isosurface plots, providing an intuitive way to connect the dichroic response to its origins. Thus chiral population analysis can be particularly useful to assess the extent to which a given electronic transition is sensitive to chirality as a local or global feature of the molecular geometry.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Data for Photoenzymatic Stereoablative Enantioconvergence of γ-chiral Oximes via Hydrogen Atom Transfer

Producing enantioenriched molecules from racemic mixtures is essential for manufacturing. Traditional methods such as resolution, deracemization and enantioconvergent catalysis primarily involve separating or converting enantiomers without altering their structures, or functionalization of stereocentres at or proximal to functional groups. However, there are challenges in enantioselectively forging C–H bonds that are remote from functional groups via hydrogen atom transfer (HAT) with these methods. Here we introduce a strategy for the photoenzymatic stereoablative enantioconvergence of γ-chiral oximes using repurposed flavin-dependent ene-reductases. A photoinduced single-electron reduction of the γ-chiral oxime by an ene-reductase generates an iminyl radical, which then undergoes stereoablative 1,5-HAT at the γ-stereocentre. Subsequent chiral reconstruction through enzymatic HAT and spontaneous imine hydrolysis yields the γ-chiral ketone with high enantioselectivity. This work provides a robust method for remote stereoablative enantioconvergent HAT and broadens the synthetic utility of photobiocatalysis.

Bioproducts↗
DOE OSTI2025

Synergistic Density Functional Theory and Molecular Dynamics Approach to Elucidate PNIPAM–Water Interaction Mechanisms

This study employs Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations to investigate interactions between water molecules and Poly(N-isopropylacrylamide) (PNIPAM). DFT reveals preferential water binding sites, with enhanced binding energy observed in the linker zone. Quantum Theory of Atoms in Molecules (QTAIM) and electron localization function (ELF) analyses highlight the roles of hydrogen bonding and steric hindrance. MD simulations unveil temperature-dependent hydration dynamics, with structural transitions marked by changes in the radius of gyration (Rg) and the radial distribution function (RDF), aligning with DFT findings. Our work goes beyond prior studies by combining a DFT, QTAIM and MD simulations approach across different PNIPAM monomer-to-30mer structures. It introduces a systematic quantification of pseudo-saturation thresholds and explores water clustering dynamics with structural specificity, which have not been previously reported in the literature. These novel insights establish a more complete molecular-level picture of PNIPAM hydration behavior and temperature responsiveness, emphasizing the importance of amide hydrogen and carbonyl oxygen sites in hydrogen bonding, which weakens above the lower critical solution temperature (LCST), resulting in increased hydrophobicity and paving the way for understanding water sorption mechanisms, offering guidance for future applications such as dehumidification and atmospheric water harvesting.

08 HYDROGEN↗
DOE OSTI2023

Mass-selected ion–molecule cluster beam apparatus for ultrafast photofragmentation studies

We describe an apparatus for investigating the excited-state dissociation dynamics of mass-selected ion–molecule clusters by mass-resolving and detecting photofragment-ions and neutrals, in coincidence, using an ultrafast laser operating at high repetition rates. The apparatus comprises a source that generates ion–molecule clusters, a time-of-flight spectrometer, and a mass filter that selects the desired anions, and a linear-plus-quadratic reflectron mass spectrometer that discriminates the fragment anions after the femtosecond laser excites the clusters. The fragment neutrals and anions are then captured by two channeltron detectors. The apparatus performance is tested by measuring the photofragments: I – , CF 3 I – , and neutrals from photoexcitation of the ion–molecule cluster CF 3 I·I – using femtosecond UV laser pulses with a wavelength of 266 nm. Here, the experimental results are compared with our ground state and excited state electronic structure calculations as well as the existing results and calculations, with particular attention to the generation mechanism of the anion fragments and dissociation channels of the ion–molecule cluster CF 3 I·I – in the charge-transfer excited state.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
NASA NTRS1993

Imaging Genetic Molecules At Atomic Resolution

Proposed method of imaging informational polymeric biological molecules at atomic resolution enables determination of sequences of component monomers about 10 to the 3rd power to 10 to the 4th power times as fast as conventional methods do. Accelerates research on genetic structures of animals and plants. Also contributes significantly to imaging processes like scanning electron microscopy (SEM), atomic-force microscopy (AFM), and scanning tunneling microscopy (STM) in cases in which necessary to locate or identify small specimens on relatively large backgrounds and subtract background images to obtain images of specimens in isolation. V-grooves on silicon wafer laid out in square pattern, intersections of which marked to identify coordinates. Specimen molecules held in grooves for reproducible positioning and scanning by AFM or STM.

Coles, L. Stephen↗
DOE OSTI2021

Potential energy surfaces for high-energy N + O 2 collisions

Potential energy surfaces for high-energy collisions between an oxygen molecule and a nitrogen atom are useful for modeling chemical dynamics in shock waves. In the present work, we present doublet, quartet, and sextet potential energy surfaces that are suitable for studying collisions of O 2 ( 3 Σ$^{–}_{g}$) with N( 4 S) in the electronically adiabatic approximation. Two sets of surfaces are developed, one using neural networks (NNs) with permutationally invariant polynomials (PIPs) and one with the least-squares many-body (MB) method, where a two-body part is an accurate diatomic potential and the three-body part is expressed with connected PIPs in mixed-exponential-Gaussian bond order variables (MEGs). We find, using the same dataset for both fits, that the fitting performance of the PIP-NN method is significantly better than that of the MB-PIP-MEG method, even though the MB-PIP-MEG fit uses a higher-order PIP than those used in previous MB-PIP-MEG fits of related systems (such as N 4 and N 2 O 2 ). However, the evaluation of the PIP-NN fit in trajectory calculations requires about 5 times more computer time than is required for the MB-PIP-MEG fit.

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

Hexanitrato complexes and hybrid double perovskites of Am 3+ and Cm 3+

The synthesis and structures of the homoleptic hexanitrato complexes of Am(III) and Cm(III), [(CH 3 ) 4 N] 2 KAn(NO 3 ) 6 are reported. These compounds form a double perovskite structure type, A 2 B'BX 6 , crystallizing in the cubic space group $Fm$$\bar{3}$$m$. Furthermore, their electronic properties, as calculated using the Quantum Theory of Atoms in Molecules, are reported and compared to their lanthanide homologues Eu(III) and Gd(III).

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

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗
DOE OSTI2024

The Radical Atom: Mechanosynthetic 3D Printing of an Atomically Precise SPM Tip

This research effort sought to overcome current limitations in scanning probe-based atomic manipulation to enable atomically precise manufacturing (APM). Previous theoretical and experimental works on atom by atom and molecule by molecule fabrication of precise structures are limited to essentially to two-dimensions. APM will enable a paradigm shift in 21st century manufacturing practices in which every single atom in a electronic chip, device or machine can be placed in an exact and predefined position in three-dimensions. By providing a general method for generating reproducible SPM tip structure, this project will drive forward the entire field of atomically precise scanning probe microscopy, opening the door to positional control of nearly arbitrary covalent chemistry. Such control could, for example, be used in applications such as novel 2.5 or 3D microchip fabrication. The creation of a unique manufacturing method through APM has the potential to impact technologies at the theoretical limits of performance, weight, and utility including: solid-state quantum and spintronic computing systems, high efficiency optical antenna, solar power systems, defect engineered materials and extremely efficient catalysts. Although this experiment focused on pick-and-place non-scalable APM, the better understanding of the chemistry is crucial to the eventual goal of scalable APM. To place individual atoms into a specified location is a seminal aspiration of researchers and engineers in the many fields and may have early premium applications in medical devices and microelectronics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

The DREAM Endstation at the Linac Coherent Light Source

Free-electron lasers (FEL), with their ultrashort pulses, ultrahigh intensities, and high repetition rates at short wavelength, have provided new approaches to Atomic and Molecular Optical Science. One such approach is following the birth of a photo electron to observe ion dynamics on an ultrafast timescale. Such an approach presents the opportunity to decipher the photon-initiated structural dynamics of an isolated atomic and molecular species. It is a fundamental step towards understanding single- and non-linear multi-photon processes and coherent electron dynamics in atoms and molecules, ultimately leading to coherent control following FEL research breakthroughs in pulse shaping and polarization control. A key aspect for exploring photoinduced quantum phenomena is visualizing the collective motion of electrons and nuclei in a single reaction process, as dynamics in atoms/ions proceed at femtosecond (10 –15 s) timescales while electronic dynamics take place in the attosecond timescale (10 –18 s). Here, we report on the design of a Dynamic Reaction Microscope (DREAM) endstation located at the second interaction point of the Time-Resolved Molecular and Optical (TMO) instrument at the Linac Coherent Light Source (LCLS) capable of following the photon–matter interactions by detecting ions and electrons in coincidence. The DREAM endstation takes advantage of the pulse properties and high repetition rate of LCLS-II to perform gas-phase soft X-ray experiments in a wide spectrum of scientific domains. With its design ability to detect multi-ions and electrons in coincidence while operating in step with the high repetition rate of LCLS-II, the DREAM endstation takes advantage of the inherent momentum conservation of reaction product ions with participating electrons to reconstruct the original X-ray photon–matter interactions. In this report, we outline in detail the design of the DREAM endstation and its functionality, with scientific opportunities enabled by this state-of-the-art instrument.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Localized High Concentration Electrolytes for High Voltage Lithium-Metal Batteries: Correlation between the Electrolyte Composition and Its Reductive/Oxidative Stability

We demonstrate a first-principles screening methodology as an effective tool to explore electrolyte formulations for the new generation of high energy density rechargeable batteries. We study the liquid structure and electronic properties in dilute electrolytes, high concentration electrolytes (HCE), and localized high concentration electrolytes (LHCE), with focus on electrolyte formulations based on lithium bis(fluorosulfonyl)imide (LiFSI), dimethyl carbonate (DMC), and bis(2,2,2-trifluoroethyl) ether (BTFE) as a diluent. We describe the solvation complexes in the dilute electrolyte and explore structural changes triggered by the increase in lithium salt concentration for HCEs and the diluent effects in LHCEs. In HCE formulations, there is a 4-fold coordination environment of lithium-ions as in the dilute electrolyte, but the number of lithium-ion interactions with O atoms from FSI- anions dominates. In these solutions, the ability of the FSI- anions to interact with multiple lithium-ions allows complex 3D network formation and influences the reductive/oxidative behavior of the electrolyte. Interestingly, in LHCEs, the BTFE diluent molecules do not change the 3D solution structure when diluting the HCE formulation from 5.49 to 3.83 M. However, there is a composition threshold where the structural and electronic behavior may change. We show that diluting the HCE electrolyte with BTFE down to 1.77 M breaks the three-dimensional solution structure into an island-like solvation complex. We relate these structural changes to the electronic properties of the electrolytes finding a causal relationship between the reductive/oxidative behavior and the lithium-oxygen interaction mechanisms in the solvated complexes. The coordination with lithium-ions lowers the electrolyte LUMO and HOMO levels: the higher is the number of interactions with lithium-ions, the more likely the solvent molecule, FSI- anion, or diluent molecule is to be reduced and the less likely it is to become oxidized. The evolution of the solvated ion structure in HCE and LHCE suggests a close connection to a corresponding change in the lithium-ion transport mechanisms for these electrolytes.

anions, molecules, oxygen, solvents, electrolytes↗
DOE OSTI2024

Runtime performance of a GAMESS quantum chemistry application offloaded to GPUs

Summary Computational chemistry is at the forefront of solving urgent societal problems, such as polymer upcycling and carbon capture. The complexity of modeling these processes at appropriate length and time scales is mainly manifested in the number and types of chemical species involved in the reactions and may require models of several thousand atoms and large basis sets to accurately capture the chemical complexity and heterogeneity in the physical and chemical processes. The quantum chemistry package General Atomic and Molecular Electronic Structure System (GAMESS) has a wide array of methods that can efficiently and accurately treat complex chemical systems. In this work, we have used the GAMESS Effective Fragment Molecule Orbital (EFMO) method for electronic structure calculation of a challenging mesoporous silica nanoparticle (MSN) model surrounded by about 4700 water molecules to investigate the strong scaling and GPU offloading on hybrid CPU‐GPU nodes. Experiments were performed on the Perlmutter platform at the National Energy Research Scientific Computing Center. Good strong scaling and load balancing have been observed on up to 88 hybrid nodes for different settings of the execution parameters for the calculation considered here. When GPUs are oversubscribed by offloading work from multiple CPU processes, using the NVIDIA multi‐process service (MPS) has consistently reduced time to solution and energy consumed. Additionally, for some configuration parameter settings, oversubscription with MPS improved performance by up to 5.8% over the case without oversubscription.

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

Improved accuracy and transferability of molecular-orbital-based machine learning: Organics, transition-metal complexes, non-covalent interactions, and transition states

We report molecular-orbital-based machine learning (MOB-ML) provides a general framework for the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. The application of Nesbet’s theorem makes it possible to recast a typical extrapolation task, training on correlation energies for small molecules and predicting correlation energies for large molecules, into an interpolation task based on the properties of orbital pairs. We demonstrate the importance of preserving physical constraints, including invariance conditions and size consistency, when generating the input for the machine learning model. Numerical improvements are demonstrated for different datasets covering total and relative energies for thermally accessible organic and transition-metal containing molecules, non-covalent interactions, and transition-state energies. MOB-ML requires training data from only 1% of the QM7b-T dataset (i.e., only 70 organic molecules with seven and fewer heavy atoms) to predict the total energy of the remaining 99% of this dataset with sub-kcal/mol accuracy. This MOB-ML model is significantly more accurate than other methods when transferred to a dataset comprising of 13 heavy atom molecules, exhibiting no loss of accuracy on a size intensive (i.e., per-electron) basis. It is shown that MOB-ML also works well for extrapolating to transition-state structures, predicting the barrier region for malonaldehyde intramolecular proton-transfer to within 0.35 kcal/mol when only trained on reactant/product-like structures. Finally, the use of the Gaussian process variance enables an active learning strategy for extending the MOB-ML model to new regions of chemical space with minimal effort. We demonstrate this active learning strategy by extending a QM7b-T model to describe non-covalent interactions in the protein backbone–backbone interaction dataset to an accuracy of 0.28 kcal/mol.

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

Automated Construction of Artificial Lattice Structures with Designer Electronic States

Manipulating matter with a scanning tunneling microscope (STM) enables the creation of atomically defined artificial structures that host designer quantum states. However, the time-consuming nature of the manipulation process, coupled with the sensitivity of the STM tip, constrains the exploration of diverse configurations and limits the size of the designed features. In this study, we present a reinforcement learning (RL)-based framework for creating artificial structures by spatially manipulating carbon monoxide (CO) molecules on a copper substrate by using the STM tip. The automated workflow combines molecule detection and manipulation, employing deep-learning-based object detection to locate CO molecules and linear assignment algorithms to allocate these molecules to designated target sites. We initially perform molecule maneuvering based on randomized parameter sampling for sample bias, tunneling current set point, and manipulation speed. This data set is then structured into an action trajectory used to train an RL agent. The model is subsequently deployed on the STM for real-time fine-tuning of the manipulation parameters during structure construction. Our approach incorporates path-planning protocols coupled with active drift compensation to enable atomically precise fabrication of structures with significantly reduced human input while realizing larger-scale artificial lattices with the desired electronic properties. Furthermore, using our approach, we demonstrate the automated construction of an extended artificial graphene lattice and confirm the existence of a characteristic Dirac point in its electronic structure. Further challenges regarding the RL-based structural assembly scalability are discussed.

Algorithms↗
NASA NTRS1990

Electronic and molecular structure of carbon grains

Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

Almloef, Jan↗
DOE OSTI2024

Recent progress in realizing novel one-dimensional polymorphs via nanotube encapsulation

Encapsulation of various materials inside nanotubes has emerged as an effective method in nanotechnology that facilitates the formation of novel one-dimensional (1D) structures and enhances their functionality. Because of the effects of geometrical confinement and electronic interactions with host nanotubes, encapsulated materials often exhibit low-dimensional polymorphic structures that differ from their bulk forms. These polymorphs exhibit unique properties, including altered electrical, optical, and magnetic behaviors, making them promising candidates for applications in electronics, energy storage, spintronics, and quantum devices. This review explores recent advancements in the encapsulation of a wide range of materials such as organic molecules, elemental substances, metal halides, metal chalcogenides, and other complex compounds. In particular, we focus on novel polymorphs formed through the geometrical confinement effect within the nanotubes. The atomic structure, other key properties, and potential applications of these encapsulated materials are discussed, highlighting the impact of nanotube encapsulation on their functionalities.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Bond Length Alternation and Internal Dynamics in Model Aromatic Substituents of Lignin

In this report broadband microwave spectra were recorded over the 2-18 GHz frequency range for a series of four model aromatic components of lignin; namely, guaiacol (ortho-methoxy phenol, G), syringol (2,6-dimethoxy phenol, S), 4-methyl guaiacol (MG), and 4-vinyl guaiacol (VG), under jet-cooled conditions in the gas phase. Using a combination of 13 C isotopic data and electronic structure calculations, distortions of the phenyl ring by the substituents on the ring are identified. In all four molecules, the r C(1)-C(6) bond between the two substituted C-atoms lengthens, leading to clear bond alternation that reflects an increase in the phenyl ring resonance structure with double bonds at r C(1)-C(2) , r C(3)-C(4) and r C(5)-C(6) . Syringol, with its symmetric methoxy substituents, possesses a microwave spectrum with tunneling doublets in the a-type transitions associated with H-atom tunneling. These splittings were fit to determine a barrier to hindered rotation of the OH group of 1975 cm -1 , a value nearly 50% greater than that in phenol, due to the presence of the intramolecular OH…OCH 3 H-bonds at the two equivalent planar geometries. In 4-methyl guaiacol, methyl rotor splittings are observed and used to confirm and refine an earlier measurement of the three-fold barrier V 3 = 67 cm -1 . Finally, 4-vinyl guaiacol shows transitions due to two conformers differing in the relative orientations of the vinyl and OH groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗