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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1996

Template-Directed Ligation of Peptides to Oligonucleotides

Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

Bruick, Richard K.↗
NASA NTRS2002

RNA-Catalyzed RNA Ligation on an External RNA Template

Variants of the hc ligase ribozyme, which catalyzes ligation of the 3' end of an RNA substrate to the 5' end of the ribozyme, were utilized to evolve a ribozyme that catalyzes ligation reactions on an external RNA template. The evolved ribozyme catalyzes the joining of an oligonucleotide 3'-hydroxyl to the 5'-triphosphate of an RNA hairpin molecule. The ribozyme can also utilize various substrate sequences, demonstrating a largely sequence-independent mechanism for substrate recognition. The ribozyme also carries out the ligation of two oligonucleotides that are bound at adjacent positions on a complementary template. Finally, it catalyzes addition of mononucleoside '5-triphosphates onto the '3 end of an oligonucleotide primer in a template-dependent manner. The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth.

McGinness, Kathleen E.↗
DOE OSTI2020

Light Exposure Promotes Degradation of Intermediates and Growth of Phosphine-Ligated Gold Clusters

Subnanometer clusters exhibit unique properties not observed at the bulk or nanometer scale. Many applications, however, require clusters to be monodisperse in size and composition.While substantial progress has been made empirically on producing specific-sized gold clusters using different ligands, the mechanisms of cluster formation remain insufficiently understood. Using high mass-resolution electrospray ionization mass spectrometry (ESI-MS), we characterized the formation of cationic triphenylphosphine-ligated gold clusters [Aux(PPh3)y z+] in solution. Our data provides evidence that small hydrogen-containing intermediate “building blocks” (i.e., Au2(PPh3)2H+, Au4(PPh3)4H+, and Au7(PPh3)7H5 2+) are responsible for the growth of larger gold clusters (i.e., Au6(PPh3)6 2+ and Au8(PPh3)7 2+) over several hours. In addition, intermediate degradation and cluster growth are shown to be dependent on irradiation of the reacting solution with light. Specifically, the rate of growth of large clusters is demonstrated to scale with the intensity of light exposure. Complementary theoretical calculations were also performed that provide molecular-level insight into the nature of the bonding between the hydrogens and gold atoms in the intermediate Au-phosphine clusters. Collectively, our joint experimental and theoretical findings advance the understanding of the factors at play in the size-selective synthesis of ligated gold clusters in solution.

Hewitt, Michael A.↗
DOE OSTI2022

Prediction of Multiple Hydrogen Ligation at a Vanadium(II) Site in a Metal–Organic Framework

Densifying hydrogen in a metal-organic framework (MOF) at moderate pressures can circumvent challenges associated with high-pressure compression. The highly tunable structural and chemical composition in MOFs affords vast possibilities to optimize binding interactions. At the heart of this search are the nanoscale characteristics of molecular adsorption at the binding site(s). Using density functional theory (DFT) to model binding interactions of hydrogen to the exposed metal site of cation-exchanged MFU-4 l , we predict multiple hydrogen ligation of H 2 at the first coordination sphere of V(II) in V(II)-exchanged MFU-4 l . We find that the strength of this binding between the metal site and H 2 molecules can be tuned by altering the halide counterion adjacent to the metal site and that the fluoride containing node affords the most favorable interactions for high-density H 2 storage. In conclusion, using energy decomposition analysis, we delineate electronic contributions that enable multiple hydrogen ligation and demonstrate its benefits for hydrogen adsorption and release at modest pressures.

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

A Thioether-Ligated Cupric Superoxide Model with Hydrogen Atom Abstraction Reactivity

The central role of cupric superoxide intermediates proposed in hormone and neurotransmitter biosynthesis by noncoupled binuclear copper monooxygenases like dopamine-β-monooxygenase has drawn significant attention to the unusual methionine ligation of the Cu M (“Cu B ”) active site characteristic of this class of enzymes. The copper–sulfur interaction has proven critical for turnover, raising still-unresolved questions concerning Nature’s selection of an oxidizable Met residue to facilitate C–H oxygenation. We describe herein a model for Cu M , [( TMG N 3 S)Cu I ] + ([1] + ), and its O 2 -bound analog [( TMG N 3 S)Cu II (O 2 •– )] + ([1·O 2 ] + ). The latter is the first reported cupric superoxide with an experimentally proven Cu–S bond which also possesses demonstrated hydrogen atom abstraction (HAA) reactivity. Introduction of O2 to a precooled solution of the cuprous precursor [1]B(C 6 F 5 ) 4 (-135 °C, 2-methyltetrahydrofuran (2-MeTHF)) reversibly forms [1·O 2 ]B(C 6 F 5 ) 4 (UV/vis spectroscopy: λ max 442, 642, 742 nm). Resonance Raman studies (413 nm) using 16 O 2 [ 18 O 2 ] corroborated the identity of [1·O 2 ] + by revealing Cu–O (446 [425] cm –1 ) and O–O (1105 [1042] cm –1 ) stretches, and extended X-ray absorption fine structure (EXAFS) spectroscopy showed a Cu–S interatomic distance of 2.55 Å. HAA reactivity between [1·O 2 ] + and TEMPO–H proceeds rapidly (1.28 × 10 –1 M –1 s –1 , -135 °C, 2-MeTHF) with a primary kinetic isotope effect of kH/kD = 5.4. Comparisons of the O 2 -binding behavior and redox activity of [1] + vs [2] + , the latter a close analog of [1]+ but with all N atom ligation (i.e., N 3 S vs N 4 ), are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1980

The effects of restraint on uptake of radioactive sulfate in the salivary and gastric secretions of rats with pyloric ligation

The effects of restraint on the amount of nondialysable radioactive sulfate in the gastric wall and the gastric juice and saliva were investigated. It was found that restraint provokes a significant decrease in salivary radioactive sulfate. This, in turn, is responsible for the decrease of sulfate in the gastric contents observed under these conditions in rats with pyloric ligation. Esophageal ligation associated with this prevents passage of saliva and lowers the amount of radioactive sulfate in the gastric juice. Restraint causes then an increase in the amount of sulfate in the gastric juice, the value observed being very much lower than that of rats with a free esophagus. At the level of the gastric wall, the change observed during restraint does not reach a significant threshold.

Chayvialle, J. A.↗
DOE OSTI2020

Methods and compositions to increase the rate of ligation reactions catalyzed by a sortase

In various embodiments methods and compositions to increase the rate and/or activity of ligation reactions catalyzed by a sortase. In certain embodiments reagents are provided that comprises, inter alia, a polypeptide comprising an amino terminal polyglycine sequence comprising at least three contiguous Gly residues (e.g., a triglycine sequence, a tetraglycine sequence, a pentaglycine sequence, etc.) followed by a peptide that is to be ligated to a moiety followed by a sequence comprising the catalytic domain of a Sortase A enzyme.

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

Boosting the activity of non-platinum group metal electrocatalyst for the reduction of oxygen via dual-ligated atomically dispersed precursors immobilized on carbon supports

This paper describes the use of both atomically dispersed precursors (ADPs) and conductive carbon dispersion towards the synthesis of iron-based single atom electrocatalysts for the oxygen reduction reaction (ORR). For non-platinum group metal (non-PGM) catalysts, single iron, cobalt or manganese atoms coordinated with nitrogen are the most active structures towards the ORR. Achieving a high density of active sites made of single atoms is still challenging, requiring careful controls of pyrolysis to reduce the sintering of metal active sites. Herewith, we present a new strategy to synthesize iron-based single atom ORR electrocatalysts using a two pronged approach. We first designed a dual-ligated metal organic framework (MOF) precursor. This MOF was then immobilized onto Ketjen black carbon that serves as a conductive dispersion medium for creating the highly dispersed single atom sites. In this work, we demonstrate a near complete dispersion of the iron sites without obvious formation of nanoparticles. The activity of the resulting electrocatalyst exhibited an onset potential of 0.96 V and a half-wave potential of 0.84 V vs. reversible hydrogen electrode (RHE).

42 ENGINEERING↗
DOE OSTI2025

Differential Ligation Alters Electronic State and Coupling Signals of Iron-Sulfur Clusters in Flavin-Based Electron Bifurcation

Flavin-based electron bifurcation (FBEB) is employed by microorganisms for controlling pools of redox equivalents by reversibly splitting electron pairs into high- and low-energy levels from an initial midpoint potential. Our ability to harness this phenomenon is crucial for biocatalytic design which is limited by our understanding of energy coupling in the bifurcation system. In Pyrococcus furiosus, FBEB is carried out by the NADH-dependent ferredoxin:NADP+-oxidoreductase (NfnSL), coupling the uphill reduction of ferredoxin in NfnL to the downhill reduction of NAD+ in NfnS from oxidation of NADPH. Flanking the bifurcating flavin are two site-differentiated iron-sulfur clusters; the nearest is a glutamate-ligated [4Fe-4S] cluster in NfnL. Recent biochemical experiments substituting the native glutamate with cysteine led to loss of coupling between the uphill and downhill pathways, in contrast to the tight thermodynamic coupling in the native system. To understand how this decoupling is biochemically manifested by the cysteine-substituted [4Fe-4S] in NfnL, we employed electron paramagnetic resonance (EPR) spectroscopy to identify changes in electronic architecture and square wave voltammetry (SWV) to probe thermodynamic shifts produced by the substitution. We observed notable g-value shifts in the EPR for the cysteine-substituted iron-sulfur cluster in addition to significant downward shifts in the redox potential, as well as the disappearance of several low-field signals observed in the native NfnSL complex. These results suggest the site-differentiated glutamate residue facilitates higher spin states in the [4Fesingle bond4S] cluster to bridge energetic gaps in electron transfer to the bifurcating flavin in the native complex, preventing unwanted short-circuiting seen in the cysteine-substituted complex.

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

Bisoxazoline-pincer ligated cobalt-catalyzed hydrogenation of alkenes

The efficient and atom economical hydrogenation of alkenes using a novel bisoxazoline ligated cobalt complex has been developed here. The hydrogenation of a variety of alkenes containing electron neutral and electron-donating groups proceeds in high yield, while electron-withdrawing and sterically hindered groups are not tolerated. Heterocycles and internal alkenes were further hydrogenated in moderate to high yields. While the catalyst is enantiopure, no enantioinduction was observed suggesting that other factors are involved in achieving enantiocontrol.

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

Computational Study of Triphosphine-Ligated Cu(I) Catalysts for Hydrogenation of CO 2 to Formate

The catalyzed hydrogenation of CO 2 to formate via a triphosphine-ligated Cu(I) was studied computationally. Two bases, DBU and TBD, were studied in the context of two proposed mechanisms in MeCN solvent. Of the four functionals benchmarked, M06 was generally in the best agreement with the experimentally estimated values. Activation of H 2 was explored by using LCu(DBU) + to form LCuH. Dissociation of a ligand arm results in higher barriers to form the key hydride complex, LCuH. There is no significant difference between the choice of base, DBU or TBD with respect to the proposed mechanisms. We propose that the experimentally observed differences between DBU and TBD reactivity for this mechanism are due to off-pathway changes.

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

Role of Axial Ligation in Gating the Reactivity of Dimethylplatinum(III) Diimine Radical Cations

Electrochemical methods are coupled with chemical oxidant-based analytical strategies to evaluate the oxidative reactivity of the platinum(II) diimine complex (bpy)Pt II (CH 3 ) 2 (bpy = 2,2'-bipyridine) in coordinating and non-coordinating media. Through this mechanistic analysis, we show that the one-electron oxidation of (bpy)Pt II (CH 3 ) 2 generates a highly reactive, 15-electron Pt III radical cation and identify three reaction pathways that can follow this oxidation: radical–substrate dimerization, radical-radical dimerization, and oxidative disproportionation. Axial ligation of the initially generated [(bpy)Pt III (CH 3 ) 2 ] •+ species is a critical driver of this reactivity, gating the available mechanistic pathways and tuning the competition between radical–radical dimerization and oxidative disproportionation.

14 SOLAR ENERGY↗
DOE OSTI2025

Ligated Cluster Building Blocks as Chemical Donors and Acceptors for Two-Dimensional Metal Chalcogenides and Phosphorene Nanoribbons

Final report for studies on ligated transition metal chalcogenide clusters building blocks for serving as dopants in two dimensional semiconductors. The primary result is extending the superatom concept to transition metal chalcogenide clusters including a similarity with the perioidic electronic structures that are found in the periodic table. These results have found both new magic numbers, and new magic clusters with large spin magnetic moments.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Template-directed oligonucleotide ligation on hydroxylapatite

It has been suggested that the prebiotic synthesis of the precursors of biopolymers could have occurred on a solid surface such as that provided by clay or some other mineral. One such scheme envisages that growing polymers were localized by adsorption to a mineral surface where an activating agent or activated monomers were supplied continuously or cyclically. Here, it is reported that a sequence of reactions in which initially formed oligo(G)s are reactivated by conversion to phosphorimidazolides in the presence of poly(C) and then allowed to ligate is ideal, in that repeated cycles can be carried out on the surface of hydroxylapatite, whereas in the liquid phase the cycle could be achieved only with considerable difficulty.

Acevedo, O. L.↗
NASA NTRS1993

Is ligation the only solution to the pyrophosphate problem?

Pyrophosphate linkages are easily formed during the nonenzymatic oligomerization of activated nucleotides. They often form `caps' which terminate an oligonucleotide with a 5'-5' pyrophosphate. Owing to their structural resemblance to the intermediates in enzymatic ligation reactions, it has been suggested that pyrophosphate caps might have been capable of acting as activating groups in chain elongation processes. We argue that an alternative possibility would have been the specific hydrolysis of pyrophosphates.

Visscher, J.↗
NASA NTRS2000

Polyphosphorylation and non-enzymatic template-directed ligation of oligonucleotides

Oligonucleotide 5'-polyphosphates are formed under potentially prebiotic conditions from oligonucleotide 5'-phosphates and sodium trimetaphosphate. Oligonucleotides activated as polyphosphates undergo template-directed ligation. We believe that these reactions could have produced longer oligonucleotide products from shorter substrates under prebiotic conditions.

NASA Discipline Exobiology↗