A Platform Approach for Designing Sustainable Indole Thiosemicarbazone Corrosion Inhibitors with Enhanced Adsorption Properties
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Koushik, A. K. S. [Department of Chemical and Biol↗
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Results for “ligand design”
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Highly soluble copper(ι) iodide-based hybrid luminescent semiconductors containing molecular and one-dimensional coordinated anionic inorganic motifs
Copper(I) iodide-based inorganic–organic hybrid semiconductors are considered promising materials for various optoelectronic applications. Here, using imidazolium bridged benzotriazoles as multidentate ligands, we designed and synthesized a series of all-in-one (AIO)-type CuI hybrid materials that hold both ionic and coordinate bonds at the interface of organic and inorganic modules. Their structures range from 0D clusters to 2D extended networks built on various molecular (0D) and chain-like (1D) anionic inorganic motifs that are interconnected through cationic ligands via multiple Cu–N bonds. Benefiting from their unique bonding nature, these compounds exhibit high stability towards heat and moisture and can be well dissolved in polar aprotic solvents. They emit low-energy light spanning from yellow to red color (550–625 nm). Finally, the electronic structure, emission mechanism, and effect of different coordination modes on their photophysical properties were studied using both experimental and theoretical methods, which has provided insight into the structure–property relationship of these inorganic–organic semiconductors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Membrane potential sensing: Material design and method development for single particle optical electrophysiology
We review the development of “single” nanoparticle-based inorganic and organic voltage sensors, which can eventually become a viable tool for “non-genetic optogenetics.” The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark Effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (~2% Δλ spectral Stark shift up to ~30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home-built fluorescence microscope records spectrally resolved images to measure the QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfy anisotropic facet-selective coating, enabling effective compartmentalization beyond non-specific staining. Self-spiking- and patched-HEK293 cells and cortical neurons, when stained with hybrid nanobiomaterials, show clear photoluminescence intensity changes in response to membrane potential (MP) changes. Organic voltage nanosensors based on polystyrene beads and nanodisk technology utilize Fluorescence (Förster) Resonance Energy Transfer (FRET) to sense local electric fields. Voltage sensing FRET pairs achieve voltage sensitivity up to ~35% ΔF/F per 120 mV in cultures. Non-invasive MP recording from individual targeted sites (synapses and spines) with nanodisks has been realized. However, both of these QCSE- and FRET-based voltage nanosensors yet need to reach the milestone of recording individual action potentials from individual targeted sites.
59 BASIC BIOLOGICAL SCIENCES↗
Impact of Pendant Amine Basicity on Electrochemically-Promoted Cobalt Hydride Formation: Kinetic and Mechanistic Analysis
Here, we report the role of pendant amine basicity on the proton-coupled electron transfer (PCET) reactivity for the conversion of [Co III Cp(P Ph 2 N R 2 )(CH 3 CN)] 2+ complexes to [HCo III Cp(P Ph 2 N R 2 )] + , which is a key transformation involved in catalytic CO 2 conversion to formate and in H 2 evolution. Three complexes were studied, where the amine substituent (R) varies from benzyl, methoxyphenyl, or phenyl. In previous work on the benzyl system, we showed that the amine on the P Ph 2 N Bn 2 ligand serves as a kinetically accessible protonation site and enables three participating hydride formation mechanisms. In this work, a combination of electrochemical measurements and theoretical calculations were used to show that the electronic donation at the pendant amine influences the accessible PCET mechanism and proton transfer kinetics related to cobalt hydride formation under analogous reaction conditions. Notably, the amine with the most electron-donating substituent correlates to the lowest barrier for amine protonation, and specific cobalt hydride formation mechanisms can be shut off for the amine with the least electron-donating substituent. The mechanistic and kinetic changes upon modulation of the amine substituent have great implications for overall catalytic efficiency and selectivity, especially to generate the cobalt hydride intermediate involved in selective CO 2 reduction to formate. This work shows how to exploit kinetic basicity using ligand-cooperative design to facilitate PCET reactions involved in energy related transformations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dynamic, Adaptive, Systems and Materials: Complex, Simple and Emergent Behaviors
This program has been funded by DoE/BES for twenty years. It has moved into and out of various subjects as it has developed, but it has retained its focus on complexity and complex systems. The project has evolved in the following way: Self-Assembly and Biomimetic Self-Assembly: All self-assembling systems depend upon a minimum of two types of interaction: a repulsion and an attraction. For the familiar molecular systems, attractive interactions are typically hydrogen bonds and electrostatic interactions. Repulsive interactions include steric effects, hydrophobic effects (in biological systems), and charge-charge repulsion. We have expanded this repertoire to include surface interactions, magnetic interactions, and others. I list these systems in the order in which we have explored them: i) A key emphasis in current work is in understanding how the movement of ions in a magnetic field (the Lorentz effect) interacts with catalytic systems. We have demonstrated that an acceleration in rate of reduction of CO 2 to CO can be accomplished by applying an external magnetic field. This acceleration is largely due to the application of the Lorentz effect on mass transport at the catalyst’s surface. ii) We have also extensively explored the influence of electrostatics, as exhibited in self-assembling systems, by tribocharging. iii) Another key system involves surface tension effects; examples include interactions between heavy particles floating at a liquid-air interface, and interacting by changes in surface area; interactions of bubbles and bubble rafts, behaviors of bubble trains in microfluidic networks, and behaviors of microorganisms in constraining environments. iv) This work has intentionally de-emphasized biological systems; but it does include some work on protein-ligand interactions and interactions among microorganisms. v) We have also explored applications of some of these effects, these explorations include bubble rafts as diffraction gratings, exploration of the structures that can be obtained by tribocharging and uses of these structures in exploring nucleation and melting of crystals. vi) Although not a major focus of this work, several other topics have emerged and offer opportunities for future work. These include the behavior of bubble trains and bubble rafts in microfluidic systems. A particularly interesting example is the formation of bubble trains that repeat in the alteration of large and small bubbles according to rules we do not presently understand, but are uniquely large-period oscillating systems. These systems offer a new route into understanding the instabilities of the type represented by oscillations. vii) We have also begun exploratory projects on magnetic levitation (especially to determine molecular density), and information storage (in molecules). Magnetic Levitation: Self-assembling and biomimetic systems require both attraction and repulsion. We have used electrostatics (tribocharging), interfacial free-energies (surface tension and related forces) and others. Potential uses include reconfigurable diffraction gratings and liquid lenses; exploration of mechanisms in tribocharging; tunneling in EGaIn junctions; and bubble trains (especially in micro-fluidic systems). Examples of systems representing these topics is included in the following papers: Complexity: Disks rotating at a water-air interface; Benard-Marangoni effects; Vortex-Crystals from spinning magnetic disks (Marangoni effects); EGaIn Electrode to study quantum tunneling; Self-Assembly of electrostatically-charged metallic spheres (electrets); Dynamically reconfigurable lens; Using computational designs of ligands for enzymes; Electrostatic self-assembly by tribocharging; Monodisperse bubble trains in microchannel systems; Inverted dripping faucet; Flames; Printing of micro-organisms to regenerate the “ink” of printing device; Using micro-organisms to move loads (“microoxen”); Motion of bacterial swarms near surfaces; Making monodisperse particles in microfluidic systems; Coding/decoding of information stored in droplet trains in microfluidic networks; Magnetic levitation; and Information storage. i) Tribocharging. The change in focus of this work on electrets from the fundamentals of charging to applications of these materials in studying self-assembly using electrostatic interactions. ii) Bubbles in Microchannels. The realization that systems of bubbles in microchannels represented a major opportunity to study complexity in a very tractable system, and the development of a semi-quantitative theory of this subject. iii) Flames. The growth of “flames” remains an exploratory subject for the research, although their currently relatively little active work involving it ongoing. iv) Systems with Microorganisms. The removal of work in biological systems from this project. Based on work supported in this program, we now have a significant project on the development of microfluidic tools for studying C. elegans (a nematode), but this work was not appropriate for a program focused on complexity, and we developed separate support for it. (It is, however, an example of successful seeding of a new area by BES.) The work on electrets has gone through a period in which a part of the program was the subject of a MURI; the focus of this work was to develop materials that did not charge electrostatically on friction or contact. The MURI is now over, and the work on dynamic self-assembly (supported by BES) is the major focus. “Flames” has also enjoyed synergistic support, in terms of a project supported by DARPA on flame suppression (in the absence of extinguishing agents, using acoustic and electrostatic interactions). This work was helpful in understanding some of the basics of flames, but is entirely distinct from the BES focus in complexity. A growing interest is in the Lorentz effect. The Lorentz effect is the force exerted on charged particles (electrons, ions, charged molecules) when they move through a perpendicular magnetic field. The Lorentz effect is almost ubiquitous in modern technology: examples of applications include electric motors, dynamos, cathode ray tubes, many batteries, and most systems that control electrical currents with magnetic forces. We have begun to explore the Lorentz effect in electrochemical systems and heterogeneous catalytic systems involving charged organic species and inorganic ions. This work is still at an early stage, but initial studies that Lorentz effects can be large when ions move through magnetic fields, or magnetic fields move in the presence of ions.
36 MATERIALS SCIENCE↗
Divergent Stabilities of Tetravalent Cerium, Uranium, and Neptunium Imidophosphorane Complexes
The study of the redox chemistry of mid-actinides (U–Pu) has historically relied on cerium as a model, due to the accessibility of trivalent and tetravalent oxidation states for these ions. Recently, dramatic shifts of lanthanide 4+/3+ non-aqueous redox couples have been established within a homoleptic imidophosphorane ligand framework. Herein we extend the chemistry of the imidophosphorane ligand (NPC=[N=P t Bu(pyrr) 2 ] – ; pyrr=pyrrolidinyl) to tetrahomoleptic NPC complexes of neptunium and cerium (1-M, 2-M, M=Np, Ce) and present comparative structural, electrochemical, and theoretical studies of these complexes. Large cathodic shifts in the M 4+/3+ (M=Ce, U, Np) couples underpin the stabilization of higher metal oxidation states owing to the strongly donating nature of the NPC ligands, providing access to the U 5+/4+ , U 6+/5+ , and to an unprecedented, well-behaved Np 5+/4+ redox couple. Furthermore, the differences in the chemical redox properties of the U vs. Ce and Np complexes are rationalized based on their redox potentials, degree of structural rearrangement upon reduction/oxidation, relative molecular orbital energies, and orbital composition analyses employing density functional theory.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Advancing Rare-Earth Separation by Machine Learning
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Hydrogenation of ethylene over molybdenum–sulfur complexes supported on UiO-66
Development of supported single-site catalysts using small metal sulfide complexes could significantly help in the development of cost-effective catalytic materials to drive selective hydrogenation and hydrogenolysis. The goal of this study is to contribute to the development of metal sulfide catalysts by calculating the thermodynamics of a catalytic cyclic involving a metal organic framework functionalized by insertion of metal sulfide. Anchored metal sulfide complexes can potentially be designed with ligands with distinctly different electronic and catalytic properties for specific catalytic applications. Here we examine the hydrogenation of ethylene as a model. We use density functional theory to investigate molybdenum–sulfur complexes as active catalysts anchored on the metal–organic framework UiO-66 as a stable support. Our calculations show that the anchored complexes with more than two sulfur ligands are unfavorable for ethylene adsorption, so we study complexes with one or two sulfur ligands. Hydrogenation of the unsaturated carbon double bond requires the transfer of two hydrogen atoms, which can occur via heterolytic activation of hydrogen to form a Mo-hydride and a protonated sulfur – either by hydride transfer followed by proton transfer or via proton transfer followed by hydride transfer, and we find that both mechanisms proceed via two-state reactivity involving two spin states along the reaction path. Of the two catalysts studied in gas the phase, the MoS single-sulfur–ligand complex with lower oxidation states produces thermodynamically more favorable intermediates along the pathway for the first hydrogen transfer for both the hydride-first mechanism and the proton-first mechanism. As a result, the quantum mechanical calculations provide experimentally inaccessible partial atomic charges and geometries of the various intermediates encountered along the steps of the reaction mechanisms.
Kermani, Maryam Mansoori [University of Minnesota,↗
Design of stimulus-responsive two-state hinge proteins
In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here, in this work, we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.
59 BASIC BIOLOGICAL SCIENCES↗
ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design
Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are likely to be synthesized. Here we provide a solution to this impediment with our ReaLigands library that contains >30,000 monodentate, bidentate (didentate), tridentate, and larger ligands cultivated by dismantling experimentally reported crystal structures. Individual ligands from mononuclear crystal structures were identified using a modified depth-first search algorithm and charge was assigned using a machine learning model based on quantum-chemical calculated features. In the library ligands are sorted based on direct ligand-to-metal atomic connections and on denticity. Representative principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analyses were used to analyze several tridentate ligand categories, which revealed both the diversity of ligands and connections between ligand categories. Furthermore, we also demonstrated the utility of this library by implementing it with our building and optimization tools, which resulted in the very rapid generation of barriers for 750 bidentate ligands for Rh-hydride ethylene migratory insertion.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Adsorption of hydroxamic acid ligands for improved extraction of rare earth elements from monazite ores
Efficient separation of rare earth element (REE) ores via froth flotation requires the development of novel ligands with enhanced adsorption capacity and selectivity. To realize these advances, understanding the mechanisms underlying interactions between the ligand and mineral surfaces is essential. This study systematically evaluates the adsorption behavior of alkyl- and aromatic alkyl-substituted hydroxamic acid ligands on monazite surfaces using complementary spectroscopic techniques, including UV–visible (UV–vis) spectroscopy, Raman spectroscopy, infrared spectroscopy, and vibrational sum frequency generation (SFG) spectroscopy, together with the ab initio molecular dynamics (AIMD) simulations. Among the studied ligands, octanohydroxamic acid (OHA) and 4-ethoxy-N,2-dihydroxybenzamide (EDHBA) exhibit high adsorption capacity under basic pH (8–10) by forming multilayers on the surface. OHA has a higher equilibrium adsorption capacity compared to EDHBA, but it forms a less stable multilayer susceptible to disruption in the presence of interfering ions. AIMD results show that OHA adopts a single stable chelating geometry, while EDHBA exhibits multiple binding modes involving distinct interactions with La surface atoms and phosphate-bound oxygens, resulting in more complex adsorption kinetics. The variations in surface binding and intermolecular interactions observed between alkyl and aromatic molecules influence the differences in adsorption kinetics, equilibrium adsorption capacities on the mineral surface, and their flotation performance. This work provides valuable insight into the adsorption mechanism of ligands at mineral interfaces, which is crucial for guiding the design of new ligands with enhanced separation performance.
Zhou, Muchu [ORNL] (ORCID:0000000182650215)↗
X-ray absorption spectroscopy of lanmodulin-derived peptides bound to rare earth elements
A sustainable and robust supply chain of rare earth elements (REEs) is necessary to meet our consumer, national security and clean energy goals. However, current intra-REE separation technologies (e.g. solvent extraction) are costly and carry a heavy environmental burden. Therefore, the development of new aqueous based ligands that are selective for individual REEs will be integral in future REE production systems. To develop these ligands, an understanding of how ligand coordination structure relates to selectivity is imperative. We used X-ray absorption spectroscopy (XAS) to observe the local structure around four lanthanide (Ln) ions (La, Ce, Pr and Nd) complexed by water and several relevant chelating ligands [lanmodulin EF-hand 1 peptides (LanM1), ethylenediaminetetraacetic acid (EDTA), aminotris(methylenephosphonic acid) (ATMP) and citric acid]. To collect these liquid-phase XAS spectra, we developed a new flow cell that prevents bubble interference and beam damage to the samples. In the X-ray absorption near-edge structure (XANES), we observed energy shifts in the white line, white line broadening and differences in the white line intensity of different Ln–ligand complexes between ligands. In the extended X-ray absorption fine structure (EXAFS), we distinguished differences in peak intensity and distance between coordinating ligands. Differences in the local coordination structure between Ln–LanM1 peptide complexes were more subtle compared with the other ligands (La–water, La–EDTA, La–ATMP and La–citric acid complexes). Further XANES and EXAFS studies, in combination with modelling and other techniques, could greatly improve our structural knowledge of how these aqueous ligands bind Ln ions and how they can be used to design more selective ligands for more efficient and sustainable REE separations.
EDTA↗
Ligand cross-links as a design element in oligo- and polyMOFs
Oligo- and polyMOFs based on DMOF-1 adopt distinct isomeric structures governed by the flexibility, length, and number of repeat units of tethering groups between terephthalate units.
Sensharma, Debobroto [Department of Chemistry and ↗
Highly multiplexed design of an allosteric transcription factor to sense new ligands
Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.
59 BASIC BIOLOGICAL SCIENCES↗
Assessing the potential of deep learning for protein–ligand docking
The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets.
Morehead, Alex [Lawrence Berkeley National Laborat↗
Design of substituted tetrahydrofuran derivatives for HIV-1 protease inhibitors: synthesis, biological evaluation, and X-ray structural studies
A series of potent HIV-1 protease inhibitors with novel P2-ligands have been designed, synthesized and evaluated.
Chemistry↗
The dynamic adsorption affinity of ligands is a surrogate for the passivation of surface defects
Abstract Surface defects in semiconducting materials, though they have been widely studied, remain a prominent source of loss in optoelectronic devices; here we sought a new angle of approach, looking into the dynamic roles played by surface defects under atmospheric stressors and their chemical passivants in the lifetime of optoelectronic materials. We find that surface defects possess properties distinct from those of bulk defects. ab initio molecular dynamics simulations reveal a previously overlooked reversible degradation mechanism mediated by hydrogen vacancies. We find that dynamic surface adsorption affinity (DAA) relative to surface treatment ligands is a surrogate for passivation efficacy, a more strongly-correlated feature than is the static binding strength emphasized in prior reports. This guides us to design targeted passivator ligands with high molecular polarity: for example, 4-aminobutylphosphonic acid exhibits strong DAA and provides defect passivation applicable to a range of perovskite compositions, including suppressed hydrogen vacancy formation, enhanced photovoltaic performances and operational stability in perovskite solar cells.
Science & Technology - Other Topics↗