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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Observation of a super-tetrahedral cluster of acetonitrile-solvated dodecaborate dianion via dihydrogen bonding

We launched a combined negative ion photoelectron spectroscopy and multiscale theoretical investigation on the geometric and electronic structures of a series of acetonitrile-solvated dodecaborate clusters, i.e., B 12 H 12 2- ·nCH 3 CN (n = 1–4). The electron binding energies of B 12 H 12 2- ·nCH 3 CN are observed to increase with cluster size, suggesting their enhanced electronic stability. B3LYP-D3(BJ)/ma-def2-TZVP geometry optimizations indicate each acetonitrile molecule binds to B 12 H 12 2- via a threefold dihydrogen bond (DHB) B3–H3 ⋮⋮⋮ H3C–CN unit, in which three adjacent nucleophilic H atoms in B 12 H 12 2- interact with the three methyl hydrogens of acetonitrile. The structural evolution from n = 1 to 4 can be rationalized by the surface charge redistributions through the restrained electrostatic potential analysis. Notably, a super-tetrahedral cluster of B 12 H 12 2- solvated by four acetonitrile molecules with 12 DHBs is observed. The post-Hartree–Fock domain-based local pair natural orbital- coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)] calculated vertical detachment energies agree well with the experimental measurements, confirming the identified isomers as the most stable ones. Furthermore, the nature and strength of the intermolecular interactions between B 12 H 12 2- and CH 3 CN are revealed by the quantum theory of atoms-in-molecules and the energy decomposition analysis. Ab initio molecular dynamics simulations are conducted at various temperatures to reveal the great kinetic and thermodynamic stabilities of the selected B 12 H 12 2- ·CH 3 CN cluster. The binding motif in B 12 H 12 2- ·CH 3 CN is largely retained for the whole halogenated series B 12 X 12 2- ·CH 3 CN (X = F–I). This study provides a molecular-level understanding of structural evolution for acetonitrile-solvated dodecaborate clusters and a fresh view by examining acetonitrile as a real hydrogen bond (HB) donor to form strong HB interactions.

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

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks

Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.

Shen, Runze [Univ. of Texas, Houston, TX (United S↗
DOE OSTI2022

Influence of the Molecular Structure on the Electrocatalytic Hydrogenation of Carbonyl Groups and H 2 Evolution on Pd

We investigated the electrocatalytic hydrogenation (ECH) of model aldehydes and ketones over carbon supported Pd in aqueous phase. We propose reaction mechanisms based on kinetic measurements and on spectroscopic and electrochemical characterization of the working catalyst. The reaction rates of ECH and of the H 2 evolution reaction (HER) vary with the applied electric potential following trends that strongly depend on the organic substrate. The intrinsic rates of hydrogenation and H 2 evolution are influenced, in opposing ways, by the sorption of the reacting organic substrate. Strong interactions, i.e., higher standard free energies of adsorption of the organic compound, induce high hydrogenation rates but decrease the overall currents. The fast hydrogenation kinetics produces a hydrogen-depleted environment that kinetically hinders the HER and the bulk phase transition of Pd to a H-rich bulk Pd hydride, which is triggered by the applied potential in the absence of reacting organic compounds. As consequence of strong organic-metal interactions, hydrogenation dominates at low overpotential. However, the coverages of organic substrates on the metal surface decrease and the rates of H 2 evolution surpass those of hydrogenation with increasingly negative electric potential. We determined the range of electric potential favoring hydrogenation on Pd and quantitatively deconvoluted the effects of the sorption of the organic compound, and of the rates of proton coupled electron transfers, on the kinetics of both ECH and HER. The results indicate that electrocatalysis offers hydrogenation pathways for polar molecules that are different and, in some cases, faster than those dominating in the absence of an external electric potential.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

How Accurate Can Crystal Structure Predictions Be for High-Energy Molecular Crystals?

Molecular crystals have shallow potential energy landscapes, with multiple local minima separated by very small differences in total energy. Predicting molecular packing and molecular conformation in the crystal generally requires ab initio methods of high accuracy, especially when polymorphs are involved. We used dispersion-corrected density functional theory (DFT-D) to assess the capabilities of an evolutionary algorithm (EA) for the crystal structure prediction (CSP) of well-known but challenging high-energy molecular crystals (HMX, RDX, CL-20, and FOX-7). While providing the EA with the experimental conformation of the molecule quickly re-discovers the experimental packing, it is more realistic to start instead from a naïve, flat, or neutral initial conformation, which reflects the limited experimental knowledge we generally have in the computational design of molecular crystals. By doing so, and using fully flexible molecules in fully variable unit cells, we show that the experimental structures can be predicted in fewer than 20 generations. Nonetheless, one must be aware that some molecular crystals have naturally hindered evolutions, requiring as many attempts as there are space groups of interest to predict their structures, and some may require the accuracy of all-electron calculations to discriminate between closely ranked structures. To save resources in this computationally demanding process, we showed that a hybrid xTB/DFT-D approach could be considered in a subsequent study to push the limits of CSP beyond 200+ atoms and for cocrystals.

42 ENGINEERING↗
DOE OSTI2022

Formation and Evolution of Metallocene Single-Molecule Circuits with Direct Gold-π Links

Single molecule circuits with group 8 metallocenes are formed without additional linker groups in Scanning Tunnelling Microscope-based break junction (STMBJ) measurements at cryogenic and room temperature conditions with gold (Au) electrodes. We investigate the nature of this direct gold-π binding motif and its affect on molecular conductance and persistence characteristics during junction evolution. The measurement technique under cryogenic conditions tracks molecular plateaus through the full cycle of extension and compression. Analysis reveals that junction persistence when the metal electrodes are pushed together correlates with whether electrodes are locally sharp or blunt, suggesting distinct scenarios for metallocene junction formation and evolution. The top and bottom surfaces of the "barrel" shaped metallocenes present the electron-rich π system of cyclopentadienyl rings which interacts with the gold electrodes in two distinct ways. An undercoordinated gold atom on a sharp tip forms a donor-acceptor bond to a specific carbon atom in the ring. However, a small, flat patch on a dull tip can bind more strongly to the ring as a whole through Van der Waals interactions. Density functional theory (DFT) based calculations of model electrode structures provide an atomic-scale picture of these scenarios, demonstrating the role of these bonding motifs during junction evolution and showing that the conductance is relatively independent of tip atomic-scale structure. Furthermore, the non-specific interaction of the cyclopentadienyl rings with the electrodes enables extended conductance plateaus, a mechanism distinct from that identified for the more commonly studied, rod-shaped organic molecular wires.

25 ENERGY STORAGE↗
DOE OSTI2025

Overcoming time and complexity limitations in molecular dynamics investigations of equilibrium melting

Abstract A hybrid Monte-Carlo molecular-dynamics method for determining solidus and liquidus compositions in multicomponent systems is presented that overcomes both the time limitations in conventional molecular dynamics that prevent the evolution of distinct solid and liquid compositions via diffusion and the complexity challenge that prevents use of thermodynamic assessment in systems of many components. This hybrid method is validated in the Cu–Ni system against an independent assessment of solidus and liquidus compositions based on the regular solution model. Strategies for efficient mapping of different phase diagrams, based on the thermodynamic parameter T 0 , the temperature at which two phases of the composition X 0 have equal free energies, are presented and then demonstrated for the copper-nickel fully miscible system and the gold–silicon eutectic system. A calculation of the solidus and liquidus sampled during the equilibrium melting of equiatomic CrMnFeCoNi is performed, indicating that this method has potential to be extended to the study of many component alloys.

Au-Si↗
DOE OSTI2022

Ancestral archaea expanded the genetic code with pyrrolysine

The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA Pyl ) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA Pyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA Pyl and reveal the emergence of tRNA Pyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA Pyl species with the more common G73-containing tRNA Pyl will enable future efforts to engineer PylRS systems for further genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗
DOE OSTI2021

Preface to Special Issue on Neutron Scattering for Catalysis

In the pursuit of understanding the chemical transformations of catalytic reactions and the structural evolution of catalysts at the molecular level, a suite of advanced experimental methods has been developed in the studies of catalysis science. Furthermore, among these methods, neutron scattering not only gives catalytic information that is highly complementary to other microscopic scattering techniques such as electrons (microscopy and diffraction) and photons from visible light to synchrotron X-rays, but also frequently provides unique insights into catalysis regarding the structure and chemical nature of light elements such as hydrogen and oxygen that are either not possible or difficult to study with other approaches.

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

The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase

Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. In this work we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD + reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the “aromatic box” that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.

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

Understanding the effect of crystal anisotropy on grain growth, texturing and transport via the orthorhombic ?-U system [Slides]

The alpha phase of uranium exhibits the orthorhombic crystal structure, resulting in significant physical property anisotropy. These complex properties make the material challenging to work with in engineering settings but provide a rich arena to investigate the fundamental, multi-scale effects of anisotropy on physical behaviors such as grain growth and microstructure evolution under irradiation. We apply molecular dynamics and phase field modeling to study mass transport and grain growth in alpha-uranium. We characterize the mobilities of crystalline defects and the interfacial energy, and We find that the grain boundary energy is highly variable depending on the interface structure and that the relative rates of defect transport change with temperature. We also find that anisotropic thermal expansion has a significant impact on grain growth kinetics and texture development. Our results are used to explain experimental observations and to provide a basis for further hypotheses into the complex physical behavior of alpha-uranium.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Evolutionary Origins of Metabolic Reprogramming in Cancer

Metabolic changes that facilitate tumor growth are one of the hallmarks of cancer. These changes are not specific to tumors but also take place during the physiological growth of tissues. Indeed, the cellular and tissue mechanisms present in the tumor have their physiological counterpart in the repair of tissue lesions and wound healing. These molecular mechanisms have been acquired during metazoan evolution, first to eliminate the infection of the tissue injury, then to enter an effective regenerative phase. Cancer itself could be considered a phenomenon of antagonistic pleiotropy of the genes involved in effective tissue repair. Cancer and tissue repair are complex traits that share many intermediate phenotypes at the molecular, cellular, and tissue levels, and all of these are integrated within a Systems Biology structure. Complex traits are influenced by a multitude of common genes, each with a weak effect. This polygenic component of complex traits is mainly unknown and so makes up part of the missing heritability. Here, we try to integrate these different perspectives from the point of view of the metabolic changes observed in cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Kinetically Controlled Formation of Semi-crystalline Conjugated Polymer Nanostructures

Conjugated polymer (CP) materials that are considered as an attractive choice for various electronic and optoelectronic applications possess highly heterogeneous complex structures that can span several orders of magnitude in length scale. This is due to the intricate coupling effects of weak secondary interactions and entropic forces that determine molecular organization in bulk polymer materials. Understanding the influence of molecular interactions on the emergence and evolution of nano- and microscale structures is of paramount importance to the guided design and development of condensed CP materials. Such understanding is even more critical for the rational design of hierarchical systems away from equilibrium, where weak molecular interactions can guide the system along competing kinetic pathways toward local energy minima and metastable architectures. In this work, we studied a promising concept for accessing various kinetically stabilized semi-crystalline CP nanostructures that are formed in the process of controlled chain-growth Kumada catalyst-transfer polymerization initiated by a small-molecule catalytic species which can exist in equilibrium between free and aggregated states. Specifically, we chose a small-molecule perylenedicarboximide (PDCI) polymerization catalytic initiator which has a strong tendency toward reversible supramolecular assembly–disassembly that can be controlled by temperature. Addition of a thiophene monomer to a solution of the PDCI initiator starts the chain-growth polymerization process, which produces distinct nanoscale semi-crystalline polythiophene structures formed under predominant kinetic control. Furthermore, we demonstrated that, depending on the reaction temperature (which affects the fine balance between the position of PDCI assembly–disassembly equilibrium, rate of polymerization, and solvent–solute interactions for the growing polythiophene chains), a range of kinetically trapped hierarchically organized semi-crystalline CP systems with substantially varying optoelectronic properties could be obtained. In addition to spectroscopic and electron microscopic studies, in order to better reveal the structural aspects of the generated polymer nanoscale systems, we carried out a series of X-ray diffraction and neutron scattering experiments which indicated complex hierarchical organization in these kinetically stabilized CP assembled materials. We expect that this in situ polymerization-based approach can lead to a general way to expand access to various semi-crystalline CP nanostructured materials with broadly tunable electronic and optical properties.

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

Evolution of Metastable Structures at Bimetallic Surfaces from Microscopy and Machine-Learning Molecular Dynamics

The restructuring of interfaces plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different compositions and morphologies at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of long-time scale restructuring of Pd deposited on Ag using microscopy, spectroscopy, and novel simulation methods. By developing and performing accelerated machine-learning molecular dynamics followed by an automated analysis method, we discover and characterize previously unidentified surface restructuring mechanisms in an unbiased fashion, including Pd-Ag place exchange and Ag pop-out as well as step ascent and descent. Remarkably, layer-by-layer dissolution of Pd into Ag is always preceded by an encapsulation of Pd islands by Ag, resulting in a significant migration of Ag out of the surface and a formation of extensive vacancy pits within a period of microseconds. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. We report our approach is broadly applicable to complex multimetallic systems and enables the previously intractable mechanistic investigation of restructuring dynamics at atomic resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗