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At least 595 records · Page 33

All sources NASA NTRS DOE OSTI

DOE OSTI2024

Molecular insights into the in situ early-stage assembly of metal–organic frameworks on cellulose nanofibrils

The integration of metal–organic frameworks (MOFs) into renewable matrices, including those derived from cellulose, to create cellulose/MOF hybrids has attracted significant interest due to the synergistic combination of cellulosic biopolymer properties and MOFs' multifunctional features. The interfacial interactions between cellulose and MOF not only ensure stable bonding, but ultimately also determine the bulk physical properties of the macroscopic composites. However, the mechanistic understanding of the in situ assembly between the two materials remains unclear. In this study, we employ a combination study of synthesis, experimental characterization, and molecular dynamics simulations to explore the early-stage assembly of a cellulose/MOF hybrid. Our results revealed that the growth of MOF clusters on the 2,2,6,6-tetramethyl-1-piperidinyloxy oxidized cellulose nanofibrils (TOCNF) follows an inhomogeneous sequential transformation pathway. The carboxylates of TOCNF form coordination-like bonds with the metal ions, while the hydroxyl groups of TOCNF form hydrogen bonds with MOF ligands. These interactions provide the initial nucleation sites that mediate the growth of MOF clusters and also guide the assembly of larger MOF clusters onto the TOCNF substrate. In conclusion, the fundamental insights into the in situ assembly of MOF nanoparticles on cellulosic substrates are essential for the rational design of high-performance materials with tailored morphology and optimized properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Unlocking High Capacity and Reversible Alkaline Iron Redox Using Silicate-Sodium Hydroxide Hybrid Electrolytes

Alkaline iron (Fe) batteries are attractive due to the high abundance, low cost, and multiple valent states of Fe but show limited columbic efficiency and storage capacity when forming electrochemically inert Fe 3 O 4 on discharging and parasitic H 2 on charging. Herein, sodium silicate is found to promote Fe(OH) 2 /FeOOH against Fe(OH) 2 /Fe 3 O 4 conversions. Electrochemical experiments, operando X-ray characterization, and atomistic simulations reveal that improved Fe(OH) 2 /FeOOH conversion originates from (i) strong interaction between sodium silicate and iron oxide and (ii) silicate-induced strengthening of hydrogen-bond networks in electrolytes that inhibits water transport. Furthermore, the silicate additive suppresses hydrogen evolution by impairing energetics of water dissociation and hydroxyl de-sorption on iron surfaces. In conclusion, this new silicate-assisted redox chemistry mitigates H 2 and Fe 3 O 4 formation, improving storage capacity (199 mAh g -1 in half-cells) and coulombic efficiency (94 % after 400 full-cell cycles), paving a path to realizing green battery systems built from earth-abundant materials.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Ab initio Geochemistry of Hydrous Phases (Final Report)

Hydrous phases are among the most important Earth components. They are important for a broad suite of Earth processes, including the origin of life. From both thermodynamic and structural perspectives, however, they represent some of the most complex naturally occurring materials: their bonding often includes a combination of covalent solid, weak ionic, van der Waals, and hydrogen bonding, all within large unit cells. Most are solid solutions, and many are prone to variations in layer packing. Thermodynamic modeling of these materials is fundamental for understanding present and past natural processes, including those that shaped—and continue to shape—the structure and evolution of our planet. Yet, the thermodynamic properties of these materials at appropriate conditions are challenging to measure. To make significant progress and attain a deep understanding of these materials requires an atomistic theoretical approach.

36 MATERIALS SCIENCE↗

NASA NTRS1992

Concerted hydrogen atom exchange between three HF molecules

We have investigated the termolecular reaction involving concerted hydrogen exchange between three HF molecules, with particular emphasis on the effects of correlation at the various stationary points along the reaction. Using an extended basis, we have located the geometries of the stable hydrogen-bonded trimer, which is of C(sub 3h) symmetry, and the transition state for hydrogen exchange, which is of D(sub 3h) symmetry. The energies of the exchange reation were then evaluated at the correlated level, using a large atomic natural orbital basis and correlating all valence electrons. Several correlation treatments were used, namely, configration interaction with single and double excitations, coupled-pair functional, and coupled-cluster methods. We are thus able to measure the effect of accounting for size-extensivity. Zero-point corrections to the correlated level energetics were determined using analytic second derivative techniques at the SCF level. Our best calculations, which include the effects of connected triple excitations in the coupled-cluster procedure, indicate that the trimer is bound by 9 +/- 1 kcal/mol relative to three separate monomers, in excellent agreement with previous estimates. The barrier to concerted hydrogen exchange is 15 kcal/mol above the trimer, or only 4.7 kcal/mol above three separated monomers. Thus the barrier to hydrogen exchange between HF molecules via this termolecular process is very low.

Komornicki, Andrew↗

DOE OSTI2024

Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum

Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Takayesu, Allen↗

DOE OSTI2024

Subnanometer Scale Mapping of Hydrogen Doping in Vanadium Dioxide

Hydrogen donor doping of correlated electron systems such as vanadium dioxide (VO 2 ) profoundly modifies the ground state properties. The electrical behavior of H x VO 2 is strongly dependent on the hydrogen concentration; hence, atomic scale control of the doping process is necessary. It is however a nontrivial problem to quantitatively probe the hydrogen distribution in a solid matrix. As hydrogen transfers its sole electron to the material, the ionization mechanism is suppressed. Here in this study, a methodology mapping the doping distribution at subnanometer length scale is demonstrated across a H x VO 2 thin film focusing on the oxygen-hydrogen bonds using electron energy loss spectroscopy (EELS) coupled with first-principles EELS calculations. The hydrogen distribution was revealed to be nonuniform along the growth direction and between different VO 2 grains, calling for intricate hydrogenation mechanisms. Our study points to a powerful approach to quantitatively map dopant distribution in quantum materials relevant to energy and information science

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Ab Initio Structures and Energetics of Hydrated Flat and Terrace-Step Surfaces of Forsterite (Mg 2 SiO 4 )

Forsterite (Mg 2 SiO 4 ), a model divalent metal silicate mineral, has been extensively studied in the context of mineral carbonation. Although dissolution is a key step in this process, the mechanisms by which forsterite dissolves under high CO 2 conditions remain poorly understood. Atomistic simulations could aid in exploring these mechanisms, but it is essential first to understand the structures and energetics of the relevant forsterite surfaces. We present an ab initio study of the structure and surface energy at 0 K of the flat $(010), (110), (001), (111), (021), (101)$ and $(120)$ faces of forsterite using the density functional PBE Hamiltonian and a plane-wave basis set. Dry surfaces became stabilized upon hydration through the formation of bonds between surface Mg and O from water, as well as by the formation of hydrogen bonds. According to surface energy values, the stability order of the hydrated forsterite faces was found to be $(120) < (101) < (021) < (111) < (001) < (110) < (010)$. We also investigated the energetics of the terrace-step $(0\bar{41})$ surface as a model site for forsterite dissolution. Among all the facets, the $(0\bar{41})$ surface is the least stable termination in water. Hydration of Mg atoms on the $(0\bar{41})$ surface increases their susceptibility to dissolution. The presence of a step and its hydration destabilizes the terraces, making step retreat more likely than a dissolution front advancing along the [010] direction. This research will support future simulations to investigate forsterite dissolution in water under CO 2 -rich conditions.

PBE Hamiltonian↗

DOE OSTI2023

Time-resolved crystallography captures light-driven DNA repair

Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme’s catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3′ thymine ejected first, followed by the 5′ base.

Science & Technology - Other Topics↗

DOE OSTI2025

Understanding CO 2 adsorption on the surfaces of SrO and its hydroxylated variants Sr(OH) 2 · n H 2 O ( n = 0, 1, 8)

Strontium oxide (SrO) is a promising material for CO 2 capture through a reversible cycle of carbonation and calcination, where SrO reacts with CO 2 to form SrCO 3 and can be regenerated by calcination. In the presence of moisture, SrO forms strontium hydroxide and its hydrates (Sr(OH) 2 ·nH 2 O). Here, this study, which employs density functional theory, investigates the CO 2 adsorption mechanism of these processes on various crystal surfaces, including SrO, Sr(OH) 2 , Sr(OH) 2 ·1H 2 O, and Sr(OH) 2 ·8H 2 O. A significant finding is that the interaction of CO 2 with these surfaces leads to carbonate/bicarbonate formation via electron transfer, with notable differences in CO 2 orientation and bond characteristics between SrO surfaces and its hydroxylated surfaces. To explore the effects of moisture on CO 2 adsorption, H 2 O adsorption on these stable surfaces was investigated. The results showed that H 2 O reacts with the SrO (100) surface to form hydroxyl (OH) groups while it bonds with the surfaces of Sr(OH) 2 ·nH 2 O (n = 0, 1, 8) with hydrogen bonding. A small amount of H 2 O can enhance CO2 adsorption while a large amount of H 2 O could decrease the capability of CO 2 adsorption.

CO2 capture↗

DOE OSTI2022

Breaking covalent bonds in the context of the many-body expansion (MBE). I. The purported “first row anomaly” in XH n (X = C, Si, Ge, Sn; n = 1–4)

We present a new, novel implementation of the Many-Body Expansion (MBE) to account for the breaking of covalent bonds, thus extending the range of applications from its previous popular usage in the breaking of hydrogen bonds in clusters to molecules. A central concept of the new implementation is the in situ atomic electronic state of an atom in a molecule that casts the one-body term as the energy required to promote it to that state from its ground state. The rest of the terms correspond to the individual diatomic, triatomic, etc., fragments. Its application to the atomization energies of the XH n series, X = C, Si, Ge, Sn and n = 1–4, suggests that the (negative, stabilizing) 2-B is by far the largest term in the MBE with the higher order terms oscillating between positive and negative values and decreasing dramatically in size with increasing rank of the expansion. The analysis offers an alternative explanation for the purported “first row anomaly” in the incremental H n–1 X–H bond energies seen when these energies are evaluated with respect to the lowest energy among the states of the XH n molecules. Due to the “flipping” of the ground/first excited state between CH 2 ( 3 B 1 ground state, 1 A 1 first excited state) and XH 2 , X = Si, Ge, Sn ( 1 A 1 ground state, 3 B 1 first excited state), the overall picture does not exhibit a “first row anomaly” when the incremental bond energies are evaluated with respect to the molecular states having the same in situ atomic states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1980

Modelling of DNA-protein recognition

Computer model-building procedures using stereochemical principles together with theoretical energy calculations appear to be, at this stage, the most promising route toward the elucidation of DNA-protein binding schemes and recognition principles. A review of models and bonding principles is conducted and approaches to modeling are considered, taking into account possible di-hydrogen-bonding schemes between a peptide and a base (or a base pair) of a double-stranded nucleic acid in the major groove, aspects of computer graphic modeling, and a search for isogeometric helices. The energetics of recognition complexes is discussed and several models for peptide DNA recognition are presented.

Rein, R.↗

NASA NTRS1992

Concerted hydrogen atom exchange between three HF molecules

The termolecular reaction involving concerted hydrogen-atom exchange between three HF molecules was investigated with particular attention given to the effects of correlation at the various stationary points along the reaction. Using large segmented Gaussian basis sets to locate the (HF)3 stationary points at the SCF level, the geometries of the stable hydrogen-bonded trimer, which is of C(3h) symmetry, were located, together with the transition state for hydrogen exchange, which is of D(3h) symmetry. Then, using a large atomic natural orbital basis and correlating all valence electrons, the energetics of the exchange reaction were evaluated at the correlated level.

Komornicki, Andrew↗

DOE OSTI2020

Au 3 -to-Ag 3 coordinate-covalent bonding and other supramolecular interactions with covalent bonding strength

An efficient strategy for designing charge-transfer complexes using coinage metal cyclic trinuclear complexes (CTCs) is described herein. Due to opposite quadrupolar electrostatic contributions from metal ions and ligand substituents, [Au(m-Pz-(i-C 3 H7) 2 )] 3 ∙[Ag(m-Tz-(n-C 3 F 7 ) 2 )] 3 (Pz = pyrazolate, Tz = triazolate) has been obtained and its structure verified by single crystal X-ray diffraction – representing the 1st crystallographically-verified M 3 @M' 3 stacked adduct of monovalent coinage metal CTCs. Abundant supramolecular interactions with aggregate covalent bonding strength arise from a combination of M–M' (Au / Ag), metal–π, π–π interactions and hydrogen bonding in this charge-transfer complex, according to density functional theory analyses, yielding a computed binding energy of 66 kcal mol -1 between the two trimer moieties – a large value for intermolecular interactions between adjacent d 10 centres (nearly doubling the value for a recently claimed Au(I) / Cu(I) polar-covalent bond: Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E5042) – which becomes 87 kcal mol -1 with benzene stacking. Surprisingly, DFT analysis suggests that: (a) some other literature precedents should have attained a stacked M 3 @M' 3 product akin to the one herein, with similar or even higher binding energy; and (b) a high overall intertrimer bonding energy by inferior electrostatic assistance, underscoring genuine orbital overlap between M and M' frontier molecular orbitals in such polar-covalent M–M' bonds in this family of molecules. The Au / Ag bonding is reminiscent of classical Werner-type coordinate-covalent bonds such as H 3 N: → Ag in [Ag(NH 3 ) 2 ] + , as demonstrated herein quantitatively. Solidstate and molecular modeling illustrate electron flow from the p-basic gold trimer to the p-acidic silver trimer with augmented contributions from ligand-to-ligand’ (LL'CT) and metal-to-ligand (MLCT) charge transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Hydrotrope-enabled high concentration aqueous electrolytes for reversible and sustainable iron metal anodes

Iron metal-based energy storage devices hold great potential in stationary grid-scale sustainable energy due to the high theoretical specific capacity, ultralow cost, and abundance of iron. However, their practical deployment is limited by the poor reversibility of iron plating and stripping, as well as competitive hydrogen evolution. Here we introduce the concept of hydrotropy into iron electrolytes by developing an environmentally friendly and cost-effective high-concentration ferrous sulfate electrolyte using urea as a hydrotropic agent. The designed electrolyte increases the Coulombic efficiency of iron metal electrodes to approximately 96.5%, compared with ~84.6% for the dilute electrolyte. Molecular dynamics simulations and Raman spectroscopy illustrate that urea regulates the competitive coordination of anions and urea in the iron solvation sheath, while reconstructing the hydrogen-bond network in free water molecules. This reduces the activity of both solvated and free water, thereby alleviating hydrogen evolution. Moreover, the coordinated anions and urea molecules facilitate the in-situ formation of an organic-inorganic hybrid protective layer on the metallic iron, establishing a physical barrier against water and promoting homogeneous interfacial reactions. This work demonstrates an appealing opportunity to design cost-effective and high-performance electrolytes and propels the practical application of iron metal-based energy storage devices.

Feng, Guangxia [Stanford Univ., CA (United States)↗

DOE OSTI2022

Structural changes across thermodynamic maxima in supercooled liquid tellurium: a water-like scenario

Liquid polymorphism is an intriguing phenomenon which has been found in a few single-component systems, the most famous being water. By supercooling liquid Te to more than 130 K below its melting point and performing simultaneous small-angle and wide-angle X-ray scattering measurements, we observe clear maxima in its thermodynamic response functions around 615 K, suggesting the possible existence of liquid polymorphism. A close look at the underlying structural evolution shows the development of intermediate-range order upon cooling, most strongly around the thermodynamic maxima, which we attribute to bond-orientational ordering. The striking similarities between our results and those of water, despite the lack of hydrogen-bonding and tetrahedrality in tellurium, indicate that water-like anomalies may be a general phenomenon among liquid systems with competing bond- and density-ordering.

36 MATERIALS SCIENCE↗

NASA NTRS1995

Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

Karpas, Z.↗

NASA NTRS2006

A Quasi-Laue Neutron Crystallographic Study of D-Xylose Isomerase

Hydrogen atom location and hydrogen bonding interaction determination are often critical to explain enzymatic mechanism. Whilst it is difficult to determine the position of hydrogen atoms using X-ray crystallography even with subatomic (less than 1.0 Angstrom) resolution data available, neutron crystallography provides an experimental tool to directly localise hydrogeddeuteriwn atoms in biological macromolecules at resolution of 1.5-2.0 Angstroms. Linearisation and isomerisation of xylose at the active site of D-xylose isomerase rely upon a complex hydrogen transfer. Neutron quasi-Laue data were collected on Streptomyces rubiginosus D-xylose isomerase crystal using the LADI instrument at ILL with the objective to provide insight into the enzymatic mechanism (Myles et al. 1998). The neutron structure unambiguously reveals the protonation state of His 53 in the active site, identifying the model for the enzymatic pathway.

Meilleur, Flora↗

DOE OSTI2022

Deuterium incorporation into cellulose: a mini-review of biological and chemical methods

Isotopic enrichment offers structural insights that are not easily accessible with natural abundance isotopic composition. Deuterated cellulose has attracted considerable attention in the field of neutron scattering studies, providing information about the dynamics, structure of cellulose and its interactions with other plant cell wall components. The deuteration of cellulose also allows the analysis of cellulose hydrogen bonds by FTIR or NMR techniques. The chemical structure of cellulose contains both exchangeable hydroxyl and non-exchangeable alkyl hydrogens. Deuterium incorporation can be divided into two classifications: biological route which incorporates both alkyl and hydroxyl bound deuterium, and chemical route which typically replaces hydroxyl-bound exchangeable hydrogen. Additionally, the biological route involves cultivating plants or microorganisms in a deuterium-enriched medium. The chemical route typically involves an exchange reaction between hydroxyl-bound hydrogen and D 2 O, often facilitating with an alkaline reagent. This review provides an overview of recent advances in deuteration methods and characterization as well as the application of deuterated cellulose.

59 BASIC BIOLOGICAL SCIENCES↗