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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber↗
DOE OSTI2024

Rh → Sb Interactions Supported by Tris(8-quinolyl)antimony Ligands

The study of ambiphilic systems combining L-type and Z-type ligands within the same construct has emerged as a field of active investigation, especially in the cases of ligands containing a group 13 element as a σ-acceptor for transition metals. (1) Parallel to these developments, several groups have investigated more atypical systems in which the Z-type ligand is a group 15 element. (2) Our contributions to this area have focused on the use of phosphinostibine ligands for the generation of transition metal complexes in which the antimony moiety acts as a Z-type ligand. (1d,3) We have shown that the magnitude of the resulting M → Sb interaction can be readily modulated by the oxidation state of the antimony atom (4) as well as its charge which can be manipulated by abstraction of anionic ligands. (5) Our work has also shown that these effects can be leveraged to enhance the catalytic properties of the transition metal center. (4,5) Some of the simplest systems that we have investigated are those resulting from the reaction of platinum dichloride with the bis- or tris-phosphinostibines ClSb(o-dppp) 2 and Sb(o-dppp) 3 , respectively (o-dppp = o-(Ph 2 P)C 6 H 4 ). These reactions proceed by oxidative insertion of the stibine into a Pt- Cl bond to produce complexes A and B, (6) respectively (Chart 1). Reasoning that the properties of these complexes may also be influenced by the nature of the L-type buttresses, we have now questioned whether stibines featuring nitrogen donor ligands could also display the redox noninnocence of their phosphine counterparts and support the formation of such complexes. Following up on some of our work with ambiphilic tellurium-quinoline ligands, (7) we now report on the reaction of tris-(8-quinolyl)stibines (8) toward (MeCN) 3 RhCl 3 .

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

Tunable magnetic order in low-symmetry SeO 3 ligand linked TM 3 (SeO 3 ) 3 H 2 O ( TM =Mn , Co, and Ni) compounds

The ability to design crystal lattices with specific sublattice geometries has long been sought after especially in the context of harnessing magnetic frustration to elicit emergent physics. One approach which has seen some success recently is to design magnetic sublattices chemically through the use of nonmagnetic linker ligands as scaffolding for the magnetic ions. In this work we report the magnetic properties of one such family of materials, the transition metal (TM) selenite hydrates with chemical formula TM 3 (SeO 3 ) 3 H 2 O. These materials link highly distorted TMO 6 octahedra via nonmagnetic [SeO 3 ] 2+ linkers. Studying members with TM = Mn, Co, and Ni we use magnetic susceptibility and neutron powder diffraction to identify antiferromagnetic order in all three compounds with moderate frustration indexes. A comparison of the magnetic structures suggests that while the overall structure of the SeO 3 scaffolding remains unchanged the TM effects changes in the magnetic properties through tuning the internal bonding parameters and the single-ion physics. Changing from Mn to Co is found to be particularly consequential manifesting changes in both the ordered-moment direction and in the direction of the ordering vector. Field-dependent measurements of the susceptibility and heat capacity reveal metamagnetic transitions in both Mn 3 (SeO 3 ) 3 H 2 O and Co 3 (SeO 3 ) 3 H 2 O indicating nearby magnetic ground states accessible under relatively small applied fields. Density functional theory calculations broadly confirm these results, showing both a sensitivity of the magnetic structure to the TM and its local environment. Although no spin liquid behavior is achieved, these results suggest the fruitfulness of such synthesis philosophies and encourage future work to engender higher frustration in these materials via doping, field, pressure, or larger linker ligands.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Covalently Linked, Two-Dimensional Quantum Dot Assemblies

Using nanoscale building blocks to construct hierarchical materials is a radical new branch point in materials discovery that promises new structures and emergent functionality. Understanding the design principles that govern nanoparticle assembly is critical to moving this field forward. By exploiting mixed ligand environments to target patchy nanoparticle surfaces, we have demonstrated a novel method of colloidal quantum dot (QD) assembly that gives rise to 2D structures. The equilibration of solutions of spherical and quasispherical QDs, including CdS, CdSe, and InP, with 2,2'-bipyridine-5,5'-diacrylic acid resulted in the preferential formation of 2D assemblies over the course of days as determined by transmission electron microscopy analysis. Small-angle X-ray scattering confirms the existence of the QD assemblies in solution. The dependence of the assembly on linker properties (length and rigidity), linker concentration, and total concentration was investigated, together with the data point to a mechanism involving ligand redistribution to create a patchy surface that maximizes the steric repulsion of neighboring QDs. By operating in an underexchanged regime, the arising patchiness results in enthalpically preferred directions of cross-linking that can be accessed by thermal equilibration.

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

Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism

Enzymes catalyze biochemical reactions through precise positioning of substrates, cofactors, and amino acids to modulate the transition-state free energy. However, the role of conformational dynamics remains poorly understood due to poor experimental access. This shortcoming is evident with Escherichia coli dihydrofolate reductase (DHFR), a model system for the role of protein dynamics in catalysis, for which it is unknown how the enzyme regulates the different active site environments required to facilitate proton and hydride transfer. Here, we describe ligand-, temperature-, and electric-field-based perturbations during X-ray diffraction experiments to map the conformational dynamics of the Michaelis complex of DHFR. We resolve coupled global and local motions and find that these motions are engaged by the protonated substrate to promote efficient catalysis. This result suggests a fundamental design principle for multistep enzymes in which pre-existing dynamics enable intermediates to drive rapid electrostatic reorganization to facilitate subsequent chemical steps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Liquid bicontinuous stabilized assemblies by interfacial jamming of nanoparticles

A method for preparing a stabilized assembly includes combining a first liquid phase including nanoparticles and a second, immiscible liquid phase, dissolving in the second phase a first end-functionalized polymer having a first molecular weight, and a second end-functionalized polymer having a second molecular weight, wherein the second molecular weight is greater than the first molecular weight, applying a shearing external deformation field to increase the surface area of the first phase to create a new interface, wherein the nanoparticle surfactants form a disordered, jammed assembly at the new interface, and releasing the shearing external deformation field. The polymer and the nanoparticles can interact at an interface through ligand interactions to form nanoparticle surfactants and upon releasing the external deformation field the jammed assembly at the new interface traps the first phase in a deformed state having the first liquid phase and the second liquid phase as interpenetrating domains.

Huang, Caili↗
NASA NTRS1991

The binding energies of Cu(+)-(H2O)n and Cu(+)-(NH3)n (n = 1-4)

The successive binding energies of up to four H2O and NH3 ligands to Cu(+) are computed at the self-consistent-field and modified coupled-pair functional levels. The most stable structures are those where all ligands are equivalent. Replacing Cu(+) by a point charge gives binding energies that are in good agreement with ab initio and experimental results, and is consistent with bonding that is largely charge dipole in nature. About two-thirds of the large reduction in ligand binding energy between the second and third ligand is due to ligand-ligand repulsion, while one-third is due to increased metal-ligand repulsion resulting from a loss of sd-sigma hybridization. The first and second ligand binding energies increase substantially at the correlated level due to an improved description of sd-sigma hybridization.

Bauschlicher, Charles W., Jr.↗
DOE OSTI2023

Quantifying the Impact of Electric Fields on the Local Structure and Migration of Potassium Ions at the Orthoclase (001) Surface

Developing an understanding of the response of mineral/water interfaces to applied electric fields is central to detecting and interpreting signatures of interfacial processes in the subsurface. Here we focus density functional theory calculations on understanding K + cation binding and diffusion across the (001) surface of orthoclase feldspar under various applied electric fields with and without surface hydration. The calculations reveal how water ligands labilize surface K + cations for diffusion while also increasing their sensitivity to electric field effects on the binding energy at different surface sites. The calculations also show how the direction and strength of the electric field systematically affect surface cation mobility, sorption, and hydration behavior. Specifically, electric fields directed toward the surface increase the potassium binding energies, facilitate K + diffusion across multiple binding sites, and increase the propensity of surface K + ions to lose their hydration shells. Furthermore, the findings help fill a major knowledge gap into the impact of electric fields on mineral/water interface structure and dynamics more generally, featuring in this case a commonly found type of feldspar involved in a multitude of atmospheric and geochemical processes.

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

Nickel(ii)-methyl complexes adopting unusual seesaw geometries

Here, we report four-coordinate nickel(II)-methyl complexes of tris-carbene borate ligands which adopt rare seesaw geometries. Experimental and computational results suggest the structural distortion from threefold symmetry results from a combination of electronic stabilization of the singlet state, strong field donors, and constrained angles from the chelating ligand.

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

Superatomic molecules with internal electric fields for light harvesting

Traditional p–n junctions used for photovoltaics require an interface where a light induced electron–hole pair is separated by an electric field. Developing alternative strategies for forming strong internal electric fields for electron–hole pair separation offers the possibility for better performance. We demonstrate that fusing two superatomic clusters with donor/acceptor ligands on opposite sides of the cluster leads to such a strong internal electric field. In two fused metal–chalcogenide Re6S8Cl2(L)4 clusters with donor PMe3 ligands and acceptor CO ligands on the opposite sides of the fused clusters, the electronic levels undergo shifts analogous to band bending in traditional p–n junctions. The fused cluster has a large dipole moment, and an optical spectrum that strongly absorbs excitation above the HOMO–LUMO gap of the fused clusters, but is optically very weak for the lowest energy excitation that can lead to electron–hole pair recombination. This is because the electron is localized on the CO portion of the fused cluster, while the electron–hole pair is localized on the PMe3 side of the cluster. It is shown that the electronic states localized on each side of the cluster can be aligned/misaligned by applying a voltage in different directions, offering diode like characteristics.

14 SOLAR ENERGY↗
DOE OSTI2023

Engineering ligand reactivity enables high-temperature operation of stable perovskite solar cells

Perovskite solar cells (PSCs) consisting of interfacial two- and three-dimensional heterostructures that incorporate ammonium ligand intercalation have enabled rapid progress toward the goal of uniting performance with stability. However, as the field continues to seek ever-higher durability, additional tools that avoid progressive ligand intercalation are needed to minimize degradation at high temperatures. We used ammonium ligands that are nonreactive with the bulk of perovskites and investigated a library that varies ligand molecular structure systematically. Here, we found that fluorinated aniliniums offer interfacial passivation and simultaneously minimize reactivity with perovskites. Using this approach, we report a certified quasi–steady-state power-conversion efficiency of 24.09% for inverted-structure PSCs. In an encapsulated device operating at 85°C and 50% relative humidity, we document a 1560-hour T85 at maximum power point under 1-sun illumination.

14 SOLAR ENERGY↗
DOE OSTI2024

Ligand exchange of nanocrystal films

A method includes at least partially submerging a substrate in a colloidal mixture of nanocrystals and a first solvent. The nanocrystals have first ligands coupled thereto. The method also includes applying an electric field to the colloidal mixture to form a solvated nanocrystal film and removing the solvated nanocrystal film from the first solvent. The method further includes applying a second solvent to the solvated nanocrystal film for ligand exchange. The second solvent comprises second ligands. A nanocrystal film product formed by one-step ligand exchange includes at least one dimension greater than 100 nm and ordered nanocrystals characterized as having a domain size of greater than 100 nm.

Xu, Xiaojie↗
DOE OSTI2025

Prolonging All-Optical Molecular Electron Spin Coherence in the Tissue Transparency Window

Coherent electron spin states within paramagnetic molecules hold significant potential for microscopic quantum sensing. However, all-optical coherence measurements amenable to high spatial and temporal resolution under ambient conditions remain a significant challenge. Here we conduct room-temperature, picosecond time-resolved Faraday ellipticity/rotation (TRFE/R) measurements of the electron spin decoherence time T 2 * in [IrBr 6 ] 2- . Decoherence is strongly sensitive to solution phase viscosity, pointing to molecular tumbling as an important decoherence mechanism. Accordingly, immobilization of [IrBr 6 ] 2- molecules in thin polymer films results in an order-of-magnitude increase in coherence lifetime and significantly greater magnetic field sensitivity. Here, by tuning energies of ligand-to-metal charge transfer (LMCT) states, TRFE/R enables spin initialization and readout in the tissue transparency window, paving the way toward all-optical, ultrafast molecular electron spin coherence imaging in biological systems.

Electron paramagnetic resonance spectroscopy↗
DOE OSTI2021

Built-in electric field control of magnetic coupling in van der Waals semiconductors

Electrical control of magnetism in a two-dimensional (2D) semiconductor is of great interest for emerging nanoscale low-dissipation spintronic devices. Here, we propose a general approach of tuning magnetic coupling and anisotropy of a van der Waals (vdW) 2D magnetic semiconductor via a built-in electric field generated by the adsorption of superatomic ions. Using first-principles calculations, we predict a significant enhancement of ferromagnetic coupling and a great change of magnetic anisotropy in 2D semiconductors when they are sandwiched between superatomic cations and anions. The magnetic coupling is directly affected by the built-in electric field, which lifts the energy levels of mediated ligands' orbitals and enhances the superexchange interactions. Finally, these findings will be of interest for ionic gating controlled ferromagnets and magnetoelectronics based on vdW 2D semiconductors.

2-dimensional systems↗
DOE OSTI2020

Functional Ion Pair Receptors Targeting Cesium, Lithium, Sulfate, and Uranyl (Final Technical Report)

The major goal of this project was the synthesis and study of receptors for key ions of interest to the DOE mission, namely cesium, lithium, sulfate, hydroxide, carbon dioxide/bicarbonate, and early actinides. The work, fundamental in nature, had as its objective achieving an increased understanding of how changes in receptor design could be used to optimize binding energies, ion specificity, complex structure, extraction efficiency, and substrate release. Within this broad paradigm, particular emphasis was placed on systems that could be used to sense the cesium cation in mixed aqueous media and act as extractants for the lithium cation and, separately, the carbon dioxide/bicarbonate and hydroxide anions in the form of ion pairs likely to be encountered under conditions of putative use in the field. The development of new nitrogen-rich ligands that act as receptors for early, high-valent actinide cations was also a major point of emphasis. The first in-plane actinide complexes were synthesized using a hexa-aza porphyrin analogue. The complexes exhibited an increase in the ligand–metal bonding covalency on passing from thorium(IV) to uranium(IV) to neptunium(IV) and illustrates how the use of appropriate porphyrinoid-like ligands could be used to modulate the covalency interactions between an f-element metal center and a ligand.

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

Synthesis and characterization of magnetic ionic liquids containing multiple paramagnetic lanthanide and transition metal centers and functionalized diglycolamide ligands

Magnetic ionic liquids (MILs) containing paramagnetic centers have gained widespread recognition as sustainable solvents due to their ability to respond to an external magnetic field. The physico-chemical properties of MILs are dependent on the choice of anion/cation ligands and metal centers; the search for highly tunable ligands and precursors that can confer favorable characteristics, such as low viscosity, is ongoing. Diglycolamides employed as cationic ligands have been previously shown to form hydrophobic MILs that can simultaneously incorporate multiple lanthanide metal centers in both the anion/cation. Despite their enhanced magnetic susceptibility, the effect of diglycolamide chemical structure modifications on the physico-chemical properties of MILs has not been thoroughly studied. Additionally, the possibility of forming diglycolamide-based MILs with popularly employed transition metals has not been investigated and combinations that can simultaneously embed two different types of metal centers in both the anion/cation have not been explored. In this study, thirty (30) MILs comprised of lanthanide and transition metals were synthesized by examining their chelation to both straight-chained and branched diglycolamides. Here, transition metal-based MILs were found to possess high thermal stabilities up to 235 °C compared to 192 °C for those comprised of lanthanides. While MILs comprised of rare-earth metal centers exhibited the lowest viscosities, substituting lanthanides with transition metals in just the anion or cation resulted in enhanced thermal stability and reduced viscosity. The effective magnetic moment for these MILs varied between 4.71 and 21.08 µ B and was much higher compared to all previous classes of MILs prepared using the same metals. Results from this study explore all possible modifications that can be made to these MILs in an effort to demonstrate their structural tunability, which is often highly desirable in various applications, including organic synthesis and chemical separations.

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

Analysis of the thermodynamic stability of ThO 2 and UO 2 surfaces in the presence of surfactant ligands

Nanocrystals (NCs) with size and shape dependent properties are a thriving research field. Remarkable progress has been made in the controlled synthesis of NCs of stable elements in the past two decades; however, the knowledge of the NCs of actinide compounds has been considerably limited due the difficulties in handling them both experimentally and theoretically. Actinide compounds, especially actinide oxides, play a critical role in many stages of the nuclear fuel cycle. Recently, a non-aqueous surfactant assisted approach has been developed for the synthesis of actinide oxide NCs with different morphologies, but an understanding of its control factors is still missing to date. Herein we present a comprehensive study on the low index surfaces of thorium dioxide (ThO 2 ) and their interactions with relevant surfactant ligands using density functional calculations. A systematic picture on the thermodynamic stability of ThO 2 NCs of different sizes and shapes is obtained employing empirical models based on the calculated surface energies. It is found that bare ThO 2 NCs prefer the octahedral shape terminated by (111) surfaces. Oleic acid displays selective adsorption on the (110) surface, leading to the shape transformation from octahedrons to nanorods. Other ligands such as acetylacetone, oleylamine, and trioctylphosphine oxide do not modify the equilibrium shape of ThO 2 NCs. This work provides atomic level insights into the anisotropic growth of ThO 2 NCs that was recently observed in experiments, and thus may contribute to the controlled synthesis of actinide oxide NCs with well-defined size and shape for future applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Architector for high-throughput cross-periodic table 3D complex building

Abstract Rare-earth and actinide complexes are critical for a wealth of clean-energy applications. Three-dimensional (3D) structural generation and prediction for these organometallic systems remains a challenge, limiting opportunities for computational chemical discovery. Here, we introduce Architector , a high-throughput in-silico synthesis code for s-, p-, d-, and f-block mononuclear organometallic complexes capable of capturing nearly the full diversity of the known experimental chemical space. Beyond known chemical space, Architector performs in-silico design of new complexes including any chemically accessible metal-ligand combinations. Architector leverages metal-center symmetry, interatomic force fields, and tight binding methods to build many possible 3D conformers from minimal 2D inputs including metal oxidation and spin state. Over a set of more than 6,000 x-ray diffraction (XRD)-determined complexes spanning the periodic table, we demonstrate quantitative agreement between Architector-predicted and experimentally observed structures. Further, we demonstrate out-of-the box conformer generation and energetic rankings of non-minimum energy conformers produced from Architector , which are critical for exploring potential energy surfaces and training force fields. Overall, Architector represents a transformative step towards cross-periodic table computational design of metal complex chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗