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Results for “ligands”

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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Oxy-functionalization of Group 9 and 10 transition metal methyl ligands: use of pyridine-based hemi-labile ligands

Hemi-labile ligands (HLLs) are interesting candidates for catalysts since they may facilitate bond activation and bond formation through facile ligand dissociation/association. DFT studies are reported of hemi-labile ligands in conjunction with Group 9 and 10 metals for oxygen atom insertion into metal–methyl bonds. Analysis of the reaction of pyridine- N -oxide with d 8 -[L n M (Me)(THF)] q + (M = Co, Rh, Ir, Ni, Pd, Pt; L n = 2-(CH 3 OCH 2 )Py; q = 0 and +1 for Group 9 and 10 metals, respectively; Py = pyridine; THF = tetrahydrofuran) indicates that oxy-insertion for Group 9 complexes occurs with lower free energy barriers than their Group 10 congeners. Analysis of structural changes along the reaction coordinate indicates that the initial oxygen atom transfer and subsequent methyl migration steps are favored by a reduction and increase, respectively, in coordination number. This emphasizes that HLLs could be uniquely positioned to assist both transformations within a single complex. Additionally, such ligands are worthy of experimental study due to their ability to meet the disparate coordination demands for two-step, redox-based oxy-insertion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Ligand placement based on prior structures: the guided ligand-replacement method

A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Designing Janus Ligand Shells on PbS Quantum Dots using Ligand–Ligand Cooperativity

We present a combined experimental and theoretical study of ligand ligand cooperativity during X-type carboxylate-to-carboxylate ligand exchange reactions on PbS quantum dot surfaces. We find that the ligand dipole moment (varied through changing the substituents on the benzene ring of cinnamic acid derivatives) impacts the ligand-exchange isotherms; in particular, ligands with large electron withdrawing character result in a sharper transition from an oleate-dominated ligand shell to a cinnamate-dominated ligand shell. We developed a two-dimensional lattice model to simulate the ligand-exchange isotherms that accounts for the difference in ligand binding energy as well as ligand ligand cooperativity. Our model shows that ligands with larger ligand ligand coupling energy exhibit sharper isotherms indicating an order disorder phase transition. Lastly, we developed an anisotropic Janus ligand shell by taking advantage of the ligand ligand cooperative ligand exchanges. We monitored the Janus ligand shell using 19 F nuclear magnetic resonance, showing that when the ligand ligand coupling energy falls within the order region of the phase diagram, Janus ligand shells can be constructed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cation–Ligand Interactions Dictate Salt Partitioning and Diffusivity in Ligand-Functionalized Polymer Membranes

Membranes are an attractive alternative to current thermal separations due to their scalability and energy efficiency in desalinating water. Unfortunately, many of the conventional membrane materials available today are unable to differentiate between ionic solutes, especially alkali cations, compromising their use in ion–ion separations. Inspired by the ion-specific interactions exhibited by biological ion channels, recent research efforts have focused on synthesizing and characterizing new polymeric materials that incorporate ligands into polymer networks to bias solubility and/or diffusivity of one cationic species over another. Despite these efforts, little is known about the influence of incorporating ligands into polymer membranes on solubility and diffusivity of the complexing species. In this study, we first build a qualitative model of salt partitioning, diffusivity, and permeability in generic cation-complexing ligand-functionalized polymer membranes. Next, to validate our model and hypotheses, we perform atomistic molecular dynamics simulations of a 12-crown-4-functionalized membrane in the presence of alkali halide salts at low concentration. Generally, cation complexation enhances cation solubility but decreases diffusivity. Interestingly, the reduction in diffusivity is predicted to be larger than the enhancement in solubility for materials which operate by the mechanisms proposed in our physical picture, ultimately resulting in a reduction in the permeability of the selectively complexing ion.

36 MATERIALS SCIENCE↗
DOE OSTI2020

The Role of Ligand–Ligand Interactions in Multimodal Ligand Conformational Equilibria and Surface Pattern Formation

Multimodal chromatography uses multiple modes of interaction such as charge, hydrophobic, or hydrogen bonding to separate proteins. Recently, we used molecular dynamics (MD) simulations to show that ligands immobilized on surfaces can interact and associate with neighboring ligands to form hydrophobic and charge patches, which may have important implications for the nature of protein–surface interactions. Here, we study interfacial systems of increasing complexity—from a single immobilized multimodal ligand to high density surfaces—to better understand how ligand behavior is affected by the presence of a surface and the presence of other ligands in the vicinity, and how this behavior scales to larger systems. Furthermore, we find that tethering a ligand to a surface restricts its conformations to a subset of those observed in free solution, yet the ligand maintains flexibility in the plane of the surface and can form contacts with neighboring ligands. We find that although the formation of a contact between two neighboring ligands is slightly unfavorable, three neighboring ligands exhibit a preference for the formation of a fully connected cluster. To explore how these trends in ligand association extend to a larger surface with high density of ligands, we performed coarse-grained Monte Carlo (MC) simulations of a 132-ligand surface using ligand interactions parametrized based on free energies obtained from the three-ligand MD simulations. Despite their simplicity, the coarse-grained simulations qualitatively capture the cluster size distribution of ligands observed in detailed MD simulations. Quantitative differences between the two suggest opportunities for improvements in the coarse-grained energy function for efficient predictions of cluster and pattern formations. Our approach presents a promising route to the engineering of multimodal patterns for future chromatographic resin design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Preparation of Core-Shell Coordination Molecular Assemblies via the Enrichment of Structure-Directing "Codes" of Bridging Ligands and Metathesis of Metal Units

A series of molybdenum- and copper-based MOPs were synthesized through coordination-driven process of a bridging ligand (3,3'-PDBAD, L-1) and dimetal paddlewheel clusters. Three conformers of the ligand exist with an ideal bridging angle between the two carboxylate groups of 0 degrees (H-2 zeta-L(1)), 120 degrees (H-2 beta-L-1), and of 90 degrees (H-2 beta-L-1), respectively. At ambient or lower temperature, (HL1)-L-2 and Mo-2(OAc)(4) or Cu-2(OAc)(4) were crystallized into a molecular square with ?-L-1 and Mo-2/Cu-2 units. With proper temperature elevation, not only the molecular square with ?-L-1 but also a lantern-shaped cage with a-L-1 formed simultaneously. Similar to how Watson-Crick pairs stabilize the helical structure of duplex DNA, the core-shell molecular assembly possesses favorable H-bonding interaction sites. This is dictated by the ligand conformation in the shell, coding for the formation and providing stabilization of the central lantern shaped core, which was not observed without this complementary interaction. On the basis of the crystallographic implications, a heterobimetallic cage was obtained through a postsynthetic metal ion metathesis, showing different reactivity of coordination bonds in the core and shell. As an innovative synthetic strategy, the site-selective metathesis broadens the structural diversity and properties of coordination assemblies.

Park, J↗
DOE OSTI2014

Heterolytic Cleavage of H2 by Bifunctional Manganese(I) Complexes: Impact of Ligand Dynamics, Electrophilicity, and Base Positioning

We report the synthesis, characterization, and reactivity with H2 of a series of MnI complexes of the type [(P-P)Mn(L2)CO]+ (L2 = dppm, bppm, or (CO)2; P-P = PPhNMePPh or PPh2 NBn2 ) that bear pendant amine ligands designed to function as proton relays. The pendant amine was found to function as a hemilabile ligand; its binding strength is strongly affected by the ancillary ligand environment around Mn. Tuning the electrophilicity of the Mn center leads to systems capable of reversible heterolytic cleavage of the H-H bond. The strength of pendant amine binding can be balanced to protect the Mn center while still leading to facile reactivity with H2. Neutral amine-bearing MnIH species were found to react with one-electron oxidants and, after proton and electron transfer reactions, regenerate MnI cationic species. The reactivity presented herein indicate that the Mn complexes we have developed are a promising platform for Mn-based H2 oxidation electrocatalyst development. The research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for DOE.

electrochemistry↗
DOE OSTI2017

Synthesis and Electrocatalytic Activity of [FeFe]‐Hydrogenase Model Complexes with Non‐Innocent Chelating Nitrogen‐Donor Ligands

To probe the influence of redox non‐innocent ligands on a well‐known class of [FeFe]‐hydrogenase models, three new asymmetrically disubstituted diiron complexes of the general formula (µ‐SRS)[Fe(CO) 3 ][Fe(CO)(N‐N)] {SRS = propane‐1,3‐dithiolate (pdt) or benzene‐1,2‐dithiolate (bdt), and N‐N = 2,2′‐bipyridine (bipy) or 2,2′‐bipyrimidine (bpym)} have been synthesized from their parent hexacarbonyls and characterized. The new complexes, (µ‐pdt)Fe 2 (CO) 4 (κ 2 ‐bpym) ( 2 ), (µ‐bdt)Fe 2 (CO) 4 (κ 2 ‐bipy) ( 3 ), and (µ‐bdt)Fe 2 (CO) 4 (κ 2 ‐bpym) ( 4 ), were fully characterized by spectroscopic and electrochemical techniques, and the results are compared to those of a related complex, (µ‐pdt)Fe 2 (CO) 4 (κ 2 ‐bipy) ( 1 ). The crystal structures of 2 – 4 show that, in each complex, the two iron units are in an eclipsed orientation, and the N‐N ligand lies in the basal plane. IR spectra and electrochemical analyses indicate that electron density at the iron centers decreases in the order 1 > 2 > 3 > 4 . Furthermore, compound 2 undergoes a ligand‐centered reduction at the same potential that the hexacarbonyl precursor undergoes its first reduction. However, unlike the 2,2′‐bipy derivatives 1 and 3 , the 2,2′‐bpym complexes 2 and 4 are not effective catalysts for electrochemical proton reduction from acetic acid.

Roy, Souvik↗