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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Four‐Electron Oxidative Addition of an N=N Double Bond at a Chromium Metallocyclopropene**

Abstract This report describes the synthesis of a pseudo‐tetrahedral chromium alkyne complex supported by a bidentate phosphinimide ligand and its reactivity with an azobenzene derivative. Characterization of the former by structural and computational methods reveals an unprecedented extent of alkyne activation by a formal chromium(II) center, suggesting that this complex is best described as a chromium(IV)‐metallocyclopropene. Exposure of this compound to 4,4′‐difluoroazobenzene results in the formation of a chromium(VI) diimido complex, which constitutes a rare 4‐electron oxidative addition of an N=N double bond. The isolation of a chromium(IV)‐hydrazido intermediate enabled mechanistic investigations of this challenging bond cleavage process. This work substantiates the notion that terminal phosphinimide ligands can engender first‐row transition metal ions with exceptional reactivity.

Chemistry↗
DOE OSTI2020

Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus

Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. Here, this integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structural and functional features of lysine acetylation of plant and animal tubulins

Abstract The study of the genome and the proteome of different species and representatives of distinct kingdoms, especially detection of proteome via wide‐scaled analyses has various challenges and pitfalls. Attempts to combine all available information together and isolate some common features for determination of the pathway and their mechanism of action generally have a highly complicated nature. However, microtubule (MT) monomers are highly conserved protein structures, and microtubules are structurally conserved from Homo sapiens to Arabidopsis thaliana . The interaction of MT elements with microtubule‐associated proteins and post‐translational modifiers is fully dependent on protein interfaces, and almost all MT modifications are well described except acetylation. Crystallography and interactome data using different approaches were combined to identify conserved proteins important in acetylation of microtubules. Application of computational methods and comparative analysis of binding modes generated a robust predictive model of acetylation of the ϵ‐amino group of Lys40 in α‐tubulins. In turn, the model discarded some probable mechanisms of interaction between elements of interest. Reconstruction of unresolved protein structures was carried out with modeling by homology to the existing crystal structure (PDBID: 1Z2B) from B. taurus using Swiss‐model server, followed by a molecular dynamics simulation. Docking of the human tubulin fragment with Lys40 into the active site of α‐tubulin acetyltransferase, reproduces the binding mode of peptidomimetic from X‐ray structure (PDBID: 4PK3).

Rayevsky, Alexey V.↗
DOE OSTI2022

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Atomistic‐Level Effects of Noncovalent Interactions and Crystalline Packing for Organic Material Structural Integrity upon Exposure to Gamma Radiation

Developing an atomistic understanding of ionizing radiation induced changes to organic materials is necessary for intentional design of greener and more sustainable materials for radiation shielding and detection. Cocrystals are promising for these purposes, but a detailed understanding of how the specific intermolecular interactions within the lattice upon exposure to radiation affect the structural stability of the organic crystalline material is unknown. This study evaluates atomistic-level effects of γ radiation on both single- and multicomponent organic crystalline materials and how specific noncovalent interactions and packing within the crystalline lattice enhance structural stability. Dose studies were performed on all crystalline systems and evaluated via experimental and computational methods. Changes in crystallinity were evaluated by p-XRD and free radical formation was analyzed via EPR spectroscopy. Type of intermolecular interactions and packing within the crystal lattice was delineated and related to the specific free radical species formed and the structural integrity of each material. Periodic DFT and HOMO-LUMO surface mapping calculations provided atomistic-level identifications of the most probable sites for the radicals formed upon exposure to γ radiation and relate intermolecular interactions and molecular packing within the crystalline lattice to experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Uncovering Multiple Metal-Metal Bonding in a Tetranuclear Fluoride Rhenium Cluster or the Curious Case of {[Ni(H 2 O) 6 ](NH 4 ) 4 }[Re 4 F 18 ]·4H 2 O

The compound {[Ni(H 2 O) 6 ](NH 4 ) 4 }[Re 4 F 18 ]·4H 2 O (1) has been isolated and characterized by single-crystal X-ray diffraction, Raman spectroscopy and computational methods. The compound 1 crystallizes in the triclinic space group P 1 (a = 6.6620(9) Å, b = 9.7121(13) Å, c = 11.2007(15) Å, α = 67.644(2)°, β = 83.827(2)°, γ = 84.366(2)°). In 1, the [Re 4 F 18 ] 6– anion is composed of four Re(III) atoms bridged by two µ-bridging fluorine atoms and two di-µ-bridging fluorine atoms. Furthermore, in [Re 4 F 18 ] 6– , the shortest Re–Re distance (i.e., 2.3631(6) Å) is characteristic of the presence of a Re=Re double bond; the Re–F distances range from 1.854(6) to 2.008(5) Å. Theoretical calculations confirm the presence of a weak Re=Re double bond; the Mayer–Mulliken bond order of the doubly bridged Re atoms is 1.8097 and the natural localized molecular orbital bond order is 1.8751. The Raman spectrum of 1 has been measured and shows a series of bands in the region 167–1449 cm –1 that have been attributed to Re–F and Ni–O stretches, Re 4 F 18 ring breathing and NH 4 + bending and libration modes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Advanced Nanomaterials for Nuclear Energy and Nanotechnology

The use of the latest engineered nanomaterials in nuclear energy systems has opened doors for improving the performance and safety of nuclear power. Nuclear nanotechnology (NNT) deals with the use of engineered nanomaterials for future nuclear energy applications. In this paper, the recent progress in research and benefits of using nanomaterials in different areas of nuclear energy like nuclear fuel extraction and fabrication, fission product capturing, creating robust reactor materials, radiation sensing and monitoring, and radioactive waste separation and spent nuclear fuel reprocessing are summarized. Ongoing research around the world in this field is reviewed, including experimental and computational methods.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

Abstract Host‐associated and environmental microbiomes play central roles in human health, biogeochemical cycling, response to ecosystem change, and agriculture. Scientific approaches that can reveal the functional activities that contribute to observed phenotypes are needed in microbiome research. Broad characterization of the functional activity of microbes within microbiomes is currently hampered by approaches that rely on inference of function from metagenomes or indirect measurements. Activity‐based protein profiling is uniquely positioned to overcome these challenges and reveal the protein‐level mechanisms associated with microbiome phenotypes. In this review we describe the progress made to date using ABPP in gut microbiome, plant‐microbe interaction, and soil microbiome research, and suggest how ABPP data can be coupled with advanced computational methods to enable phenotype prediction and bioengineering of microbiomes for applied purposes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Stress field and interaction forces between dislocations and precipitate distributions

A computational method is developed for calculation of the stress field and interaction forces between dislocations and precipitates of arbitrary shape and distribution. The internal stress generated by precipitates due to coherency strain is implemented within the discrete dislocation dynamics (DDD) framework. The s-version finite element method (s-FEM), which models a precipitate of arbitrary shape using a local mesh is used to calculate coherency stress fields. The method facilitates meshing precipitate volumes of arbitrary geometry, and multiple local meshes can be superimposed at various positions of the global mesh. Accuracy and convergence conditions of the method are established. For a single precipiate, the method is shown to be 3.5 times faster than a standard FEM calculation for the same accuracy, and the gain in speed increases with the number of precipitates. The CRSS of spherical precipitates is found to be higher than disk-shaped precipitates of the same volume fraction.

42 ENGINEERING↗
DOE OSTI2023

Dissecting the structural heterogeneity of proteins by native mass spectrometry

Abstract A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Crystal Chemistry of RE 6 Mg x Cd 23- x Pb [0.6(1) ≤ x ≤ 3.2(1); RE = La and Ce]. New Mixed-Metal Derivatives of the RE 6 Cd 23 T Phases ( T = Group 14/15/16 Element)

Synthesis and crystal structure determinations are reported for six quaternary phases with the general formula RE 6 Mg x Cd 23-x Pb [RE = La, Ce; 0.6(1) ≤ x ≤ 3.2(1)]. These compounds were prepared by high temperature reaction of the elements in sealed Nb tubes. As revealed by powder and single-crystal X-ray diffraction, their crystal structures are of the cubic Zr 6 Zn 23 Si system (cF120, Fm 3 m, Z = 4), itself an interstitially filled variant of the Th 6 Mn 23 structure type. Finally, rather than distributing equally across the entire Cd 23 sub-lattice, Mg displayed a tendency to accumulate at specific sites (most notably 4a); charge differences between sites within the sub-lattice, as revealed by computational methods, are the likeliest explanation.

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

Smoky Mountain Data Challenge 2021: An Open Call to Solve Scientific Data Challenges Using Advanced Data Analytics and Edge Computing

The 2021 Smoky Mountains Computational Sciences and Engineering Conference enlists scientists from across Oak Ridge National Laboratory (ORNL) and industry to be data sponsors and help create data analytics and edge computing challenges for eminent datasets in a variety of scientific domains. This work describes the significance of each of the eight datasets and their associated challenge questions. The challenge questions for each dataset were required to cover multiple difficulty levels. An international call for participation was sent to students, asking them to form teams of up to six people and apply novel data analytics and edge computing methods to solve these challenges.

Devineni, Pravallika↗
DOE OSTI2024

Stable vacua with realistic phenomenology and cosmology in heterotic M-theory satisfying Swampland conjectures

We recently described a protocol for computing the potential energy in heterotic M-theory for the dilaton, complex structure and Kähler moduli. This included the leading order non-perturbative contributions to the complex structure, gaugino condensation and worldsheet instantons assuming a hidden sector that contains an anomalous U(1) structure group embedded in E8. In this paper, we elucidate, in detail, the mathematical and computational methods required to utilize this protocol. These methods are then applied to a realistic heterotic M-theory model, the B – L MSSM, whose observable sector is consistent with all particle physics requirements. Within this context, it is shown that the dilaton and universal moduli can be completely stabilized at values compatible with every phenomenological and mathematical constraint — as well as with ΛCDM cosmology. We also show that the heterotic M-theory vacua are consistent with all well-supported Swampland conjectures based on considerations of string theory and quantum gravity, and we discuss the implications of dark energy theorems for compactified theories.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Nuclear-Physical Foundation of Atomic Energy

The current status of the nuclear database used for engineering calculations in the field of nuclear energy is reported. It is shown that the nuclear database and its attendant computational methods, stabilization, and transmission to the next generation of specialists who will have to solve the problems of the future development of nuclear power must be improved and updated.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2018

FT-IR and Raman Spectroscopy and Computation of 5-Methylfurfural

5-Methylfurfural (5MF) was studied by vibrational (IR and Raman) spectroscopy and computational methods (DFT/B3LYP&MP2). FT-IR and FT-Raman spectra in KBr (at room temperature) were collected. The Gaussian 09 and Spartan 08 programs were used for conformational analysis and calculations of molecular structure, torsional barrier, and vibrational spectral data for the 5MF molecule. The obtained results were used in the analysis of experimental vibrational spectra of 5MF molecule.

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

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Theoretical Studies on Magnetic Structures, Hysteresis Loops and Size Effects of a Pair of Frustrated Double-Walled Nanotubes

We propose a theoretical quantum model and derive a set of analytic formulas to study the physical properties of a pair of double-walled magnetic nanotubes. The Heisenberg exchange parameters between the two walls of the nanotubes are assumed to differ only in sign. Thus, in the absence of external magnetic field, our calculated macroscopic properties of this pair of nanotubes are almost precisely identical, exhibiting fascinating duality of the nanosystems and demonstrating the correctness of our theoretical model. The two spin systems are all frustrated, so that sudden changes in the macroscopic properties are observed around T{sub M2} that is well below the transition temperature T{sub M1}. However, only the inner shell consisting of smaller A-type spins has been obviously affected. In the temperature range T{sub M2} < T < T{sub M1}, this shell becomes semi-antiferromagnetic and its magnetization is considerably suppressed, whereas as temperature falls below T{sub M2} the shell gradually restores its ferromagnetic nature. The longitudinal hysteresis behavior of such a double-waled nanotube is ferromagnetic-like below T{sub M2}, but antiferromagnetic-like in the temperature interval T{sub M2} < T < T{sub M1}. Moreover, we find that the diameter of the nanotube has seemly no effects on its physical properties, whereas its length does affects the two temperatures slightly, and also its spin configuration at very low temperatures if the tube is sufficiently long. More importantly, the theoretical results presented in this paper can be precisely reproduced with the quantum computational method we develop in recent years, justifying the validity of the numerical approach once again.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗