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At least 55 records · Page 3

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides

Proton-Responsive Ligands Promote CO 2 Capture and Accelerate Catalytic CO 2 /HCO 2 – Interconversion

The synthesis and investigation of [Rh(DHMPE) 2 ][BF 4 ] (1) are reported. 1 features proton-responsive 1,2-bis[(dihydroxymethyl)phosphino]ethane (DHMPE) ligands, which readily capture CO 2 from atmospheric sources upon deprotonation. The protonation state of the DHMPE ligand was observed to have a significant impact on the catalytic reactivity of 1 with CO 2 . Deprotonation and CO 2 binding to 1 result in a ∼10-fold rate enhancement in catalytic degenerate CO 2 reduction with formate, monitored by 12 C/ 13 C isotope exchange between H 12 CO 2 – and 13 CO 2 . Studies performed using a similar complex lacking the hydroxyl ligand functionality ([Rh(DEPE) 2 ][BF 4 ] where DEPE = 1,2-bis(diethylphosphino)ethane) do not show the same rate enhancements when base is added. Based upon the cation-dependent activity of the catalyst, Eyring analysis, and cation sequestration experiments, CO 2 binding to 1 is proposed to facilitate preorganization of formate/CO 2 in the transition state via ligand-based encapsulation of Na + or K + cations to lower the activation energy and increase the observed catalytic rate. Incorporation of proton-responsive DHMPE ligands provides a unique approach to accelerate the kinetics of catalytic CO 2 reduction to formate.

Anions

Uranyl Naphthylsalophen and Pyrasal Complexes: Oxo Ligands Acting as Hydrogen Bond Acceptors in the Solid State

Uranium is most stable when it is exposed to oxygen or water in its +6 oxidation state as the uranyl (UO 2 2+ ) ion. This ion is subsequently particularly stable and very resistant to functionalization due to the inverse trans effect. Uranyl oxo ligands are typically not considered good hydrogen bond acceptors due to their weak Lewis basicity; however, the ligands bound in the equatorial plane greatly affect the strength of the oxo ligands’ hydrogen bonding. Here, in this work, new naphthylsalophen and pyrasal complexes of uranium were synthesized and crystallized for characterization in the solid state. The bond lengths and angles of the uranyl ion and the ligand conformation are compared. In the solid state, one of the pyrasal complexes showed a hydrogen bond directly from a water molecule to the uranyl oxo ligand, which resulted in an asymmetric lengthening of the U–O yl bonds from 1.789 to 1.862 Å and 1.784 to 1.844 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Ligand Control of Ultrafast Hot-Carrier Cooling in CdSe Quantum Dots by a Coherent Nonadiabatic Mechanism

Using the results from global modeling of the broadband two-dimensional electronic spectrum and an analysis of the concurrent damping of excited-state vibronic coherences, we show herein that a coherent nonadiabatic mechanism converts the electronic excitation energy of the X3 (1P 3/2 –1P e ) exciton state to ligand vibrations on the <50 fs time scale in oleate- and hexadecylamine-capped CdSe quantum dots. A comparison of the rates for the two ligands suggests that this process is promoted by mid-frequency vibrations of the ligands due to modulation of their electron-donating tendency. An intramolecular vibrational redistribution process then follows on the ∼200 fs time scale with both ligands, which accompanies thermalization in the band-edge X1 (1S 3/2 –1S e ) state and dephasing of the spectator ligand vibrations. These findings suggest that charge-separated intermediates associated with photoinduced charge transfer or triplet–triplet excitation energy transfer will be produced with retention of phase coherence in the vibrations that modulate the charge-transfer character of surface-bound organic acceptors.

14 SOLAR ENERGY

Modulating Hole Transfer from CdSe Quantum Dots by Manipulating the Surface Ligand Density

The structure and density of surface capping ligands in cadmium chalcogenide quantum dots (QDs) are important considerations for controlling the efficiency of charge separation via the transfer of electrons or holes to molecular acceptors. Here we show how the manipulation of the surface ligand density of oleic acid-capped cadmium selenide (CdSe) QDs impacts the efficiency of hole transfer (HT) to polyoxovanadate alkoxides. Meerwein’s salt is used as a ligand-stripping agent, providing opportunities to quantitatively manipulate the ligand density at the surface of the nanocrystal, as evidenced by 1 H NMR spectroscopy. Time-resolved photoluminescence and transient absorption spectroscopies reveal that the extent of HT is quantitatively related to increased surface accessibility. Collectively, these results show that the reduction of surface ligand density can be used to tune the extent of interactions of molecular acceptors with QDs, providing a route to control charge-transfer processes relevant to improving the efficiency of QDs as photosensitizers.

77 NANOSCIENCE AND NANOTECHNOLOGY

Chloride, Alkoxide, or Silicon: The Bridging Ligand Dictates the Spin State in Dicobalt Expanded Pincer Complexes

We report the synthesis and characterization of a series of high- and low-spin dicobalt complexes of the tBu PNNP expanded pincer ligand. Reacting this dinucleating ligand in its neutral form with two equiv of CoCl 2 (tetrahydrofuran) 1.5 yields a high-spin dicobalt complex featuring one Co inside and one Co outside of the dinucleating pocket. Performing the same reaction in the presence of two equivalents of KOtBu provides access to a high-spin dicobalt complex wherein both Co centers are bound within the PNNP pocket, and this complex also features a bridging OtBu ligand. Reacting either of the high-spin complexes with excess diethyl silane affords a low-spin dicobalt complex containing two unusual bridging Si-based ligands. These complexes were investigated using NMR spectroscopy, XAS, single crystal X-ray structure determination, and computational methods, showing that the Si-based ligands are best described as base-stabilized silylenes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Torsional Flexibility Tuning of Hexa-Carboxylate Ligands to Unlock Distinct Topological Access to Zirconium Metal–Organic Frameworks

Zirconium-based metal–organic frameworks (Zr-MOFs) exhibit remarkable structural diversity and functionality. However, uncovering new topological types within this family remains a considerable challenge today. Herein, we report two new hexa-topic ligands designed through the introduction of torsional flexibility, which enable the construction of two Zr-MOFs featuring rare network topologies. The (4,4′,4″,4‴,4‴′,4‴′′-((2-carboxybenzene-1,3,5-triyl)tris(9H-carbazole-9,3,6-triyl))hexabenzoic acid ligand (BTCH)) was obtained by replacing the rigid triptycene core in the H6PET-1 ligand (4,4′,4″,4‴,4‴′,4‴′′-(9,10-dihydro-9,10-[1,2]benzenoanthracene-2,3,6,7,14,15-hexayl)hexabenzoic acid) with a benzene-tricarbazole unit. Owing to its torsionally flexible core that allows rotational freedom to the arms, this ligand directs the construction of NU-2620 (NU represents Northwestern University), a Zr-MOF with 8-connected Zr6 clusters and the rare nuh topology. Further flexibilization of the carbazole units to benzene rings yielded the even more torsionally flexible 5′,5‴-bis(4-carboxyphenyl)-5″-(4,4″-dicarboxy-[1,1′:3′,1″-terphenyl]-5′-yl)-[1,1′:3′,1″:3″,1‴:3‴,1‴′-quinquephenyl]-4,4‴′-dicarboxylic acid ligand (CCTT), which forms NU-2630 featuring 6-connected clusters and the pcu topology. Both frameworks exhibit good chemical stability, prompting evaluation of their performance in CO2 photoreduction catalysis. Under low-concentration CO2 conditions, NU-2620 displays markedly higher catalytic activity than its benzene-based analogue, NU-2630, thanks to the abundance of photoactive carbazole units within its structure. These results demonstrate that introducing torsional flexibility in high-connected linkers can unlock access to new topologies and accelerates the reticular expansion of Zr-MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

NASA Discipline Neuroscience

Molecular-Scale Insights into the Heterogeneous Interactions between an m -Terphenyl Isocyanide Ligand and Noble Metal Nanoparticles

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand–metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Machine Learning‐Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands

Abstract The challenge of targeting RNA with small molecules necessitates a better understanding of RNA–ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand‐induced stabilization, and how conformational changes influence gene expression pose significant difficulties for experimental investigation. This work employs a combination of computational and experimental methods to address these challenges. By integrating structure‐informed design, crystallography, and machine learning‐augmented all‐atom molecular dynamics simulations (MD), we synthesized, biophysically and biochemically characterized, and studied the dissociation of a library of small molecule activators of the 5‐aminoimidazole–4–carboxamide ribonucleotide triphosphate (ZTP) riboswitch, a ligand‐binding RNA motif that regulates bacterial gene expression. We uncovered key interaction mechanisms, revealing valuable insights into the role of ligand binding kinetics on riboswitch activation. Further, we established that ligand on‐rates determine activation potency as opposed to binding affinity and elucidated RNA structural differences, which provide mechanistic insights into the interplay of RNA structure on riboswitch activation.

Chemistry

Trithiol ligand provides tumor-targeting 191 Pt-complexes with high molar activity and promising in vivo properties

The Auger electron-emitting radionuclide 191 Pt is a promising candidate for radiopharmaceutical therapy. Herein, we explored novel labeling methods for 191 Pt using thiol-containing ligands to improve the in vivo stability and targeting ability of 191 Pt-labeled complexes. We synthesized dithiol-containing N 2 S 2 and NS 2 ligands, and a trithiol ligand, and then compared their radiochemical reactivity with 191 Pt. [ 191 Pt]Pt-trithiol was synthesized and its biodistribution was evaluated in mice and compared with free 191 Pt. Finally, a 191 Pt-trithiol complex targeting prostate-specific membrane antigen (PSMA): [ 191 Pt]Pt-trithiol-PSMA was developed and evaluated in mice bearing tumor xenografts and compared with a 191 Pt-complex labeled via monothiol-containing Cys ([ 191 Pt]Pt-Cys-PSMA). A comparison of N 2 S 2 , NS 2 , and trithiol showed that the trithiol ligand is the best for producing 191 Pt-labeled compounds in high yield and as a single peak in preparative HPLC. Notably, the trithiol ligand made 191 Pt-labeled compounds and precursors separatable, achieving 191 Pt-labeled products with a high molar activity: 200–400 mCi/μmol (7.4–14.8 GBq/μmol) at EOS. Additionally, [ 191 Pt]Pt-trithiol and [ 191 Pt]Pt-trithiol-PSMA were stable in vivo with rapid clearance compared with free 191 Pt and [ 191 Pt]Pt-Cys-PSMA. [ 191 Pt]Pt-trithiol-PSMA resulted in a low uptake in most normal organs and a high uptake in the kidneys and prostate cancer with PSMA expression. Furthermore, this study demonstrated that a labeling method with trithiol for Pt radionuclides achieves 191 Pt-labeled products with high molar activity. 191 Pt-trithiol-PSMA showed promising in vivo stability and tumor-targeting specificity, which should facilitate the pharmaceutical development of Pt radionuclides for radiopharmaceutical therapy, especially Auger electron cancer therapy.

Auger emitters

CAML: Commutative Algebra Machine Learning─A Case Study on Protein–Ligand Binding Affinity Prediction

Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein−ligand binding affinities. Specifically, we apply persistent Stanley−Reisner theory, a key concept in combinatorial commutative algebra, to the affinity predictions of protein−ligand binding and metalloprotein−ligand binding. We present three new algorithms, i.e., element-specific commutative algebra, category-specific commutative algebra, and commutative algebra on bipartite complexes, to tackle the complexity of data involved in (metallo) protein−ligand complexes. We show that the proposed CAML outperforms other state-of-theart methods in (metallo) protein−ligand binding affinity predictions, indicating the great potential of commutative algebra learning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou

Modeling separation of lanthanides via heterogeneous ligand binding

Individual lanthanide elements have physical/electronic/magnetic properties that make each useful for specific applications. Several of the lanthanides cations (Ln 3+ ) naturally occur together in the same ores. They are notoriously difficult to separate from each other due to their chemical similarity. Predicting the Ln 3+ differential binding energies (ΔΔE) or free energies (ΔΔG) at different binding sites, which are key figures of merit for separation applications, will help design of materials with lanthanide selectivity. We apply ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) to calculate ΔΔG for Ln 3+ coordinated to ligands in water and embedded in metal–organic frameworks (MOFs), and ΔΔE for Ln 3+ bonded to functionalized silica surfaces, thus circumventing the need for the computational costly absolute binding (free) energies ΔG and ΔE. Perturbative AIMD simulations of water-inundated simulation cells are applied to examine the selectivity of ligands towards adjacent Ln 3+ in the periodic table. Static DFT calculations with a full Ln 3+ first coordination shell, while less rigorous, show that all ligands examined with net negative charges are more selective towards the heavier lanthanides than a charge-neutral coordination shell made up of water molecules. Amine groups are predicted to be poor ligands for lanthanide-binding. Finally, we also address cooperative ion binding, i.e., using different ligands in concert to enhance lanthanide selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Insights into the copolymerization of metal–organic nanotubes from ligand mixtures using small angle neutron scattering

Metal–organic nanotubes (MONTs) are porous, tunable 1D nanomaterials akin to metal–organic frameworks (MOFs). MONTs are synthesized via metal salts and coordinating ligands akin to MOFs, but crucially they are anisotropic, unlike most MOFs. Recently, MONTs have been shown to form statistically random copolymers; however, their mechanism of growth remains largely unexplored. Full realization of the potential of MONTs necessitates a thorough understanding of the mechanism of MONT growth. Herein, small-angle neutron scattering (SANS) was employed to investigate the copolymerization mechanism of two 1,2,4-ditriazole ligands and to quantify the inclusion of a solvent within the MONT pores. The results show parallelepiped-shaped structures are initially formed, which then aggregate to form larger lamellar structures. Additional experimentation with a deuterated ligand showed that the reactivities of all ligands are approximately equal, causing random ligand distribution within the resulting MONT. Finally, the results quantify the amount of solvent incorporated within the nanostructure pores at different stages of the formation process. These results show that early in the reaction the MONTs contain ca. 45% solvent, and they contain ca. 55% solvent late in the reaction when the MONTs are nearly fully formed.

Haque, Md Ashraful [Univ. of Tennessee, Knoxville,

Dicopper( i ) complexes of a binucleating, dianionic, naphthyridine bis(amide) ligand

The dinucleating ligand, 1,8-naphthyridine-2,7-bis(2,6-diisopropylphenyl)carboxamide (NBDA), was synthesized by palladium-catalyzed aminocarbonylation. This ligand was treated with two equivalents of mesitylcopper(I) in the presence of [nBu4N]X (X = Cl, N3) to give the anionic complexes [nBu4N][Cu2(NBDA)(μ-Cl)] and [nBu4N][Cu2(NBDA)(μ-N3)]. Treatment of H2NBDA with mesitylcopper(I) and two equivalents of xylyl isocyanide led to the formation of a charge-neutral dicopper(I) complex, [Cu2(NBDA)(CNXyl)2], displaying two isocyanide ligands, each terminally bound to one of the copper atoms. The complexes were characterized by NMR and IR spectroscopy, as well as by single-crystal X-ray diffraction analysis. Electrochemical characterization of the complexes using cyclic voltammetry revealed a reversible ligand-based reduction between -1.65 and -2.0 V vs. Fc/Fc+. DFT calculations suggest a more ionic bonding character and weaker Cu-Cu interactions in the NBDA complexes compared to those with other 1,8-naphthyridine-based ligands. This is congruent with intermetallic separations of over 3 Å induced by relatively strong coordination of the copper atoms to the amide nitrogen donor atoms observed in the solid state molecular structures.

Sévery, Laurent

Luminescent N-heterocyclic carbene Cu( I ) complexes with N^O chelating ligands exhibit microsecond lifetimes and photocatalytic activity

To replace precious noble metal-based photosensitizers in applications involving photoinduced charge separation, energy transfer, or photocatalysis, Cu(I) complexes are considered to be cost-effective, earth-abundant, and sustainable alternatives. An emerging and effective design principle in Cu(I) photosensitizers involves heteroleptic structures where the HOMO and LUMO are spatially separated over two different ligands. In the present work, we introduce a complementary class of heteroleptic, three-coordinate copper photosensitizers that pairs variable N^O chelating ligands (8-hydroxyquinoline and 10-hydroxybenzo[h]quinoline) with a bulky 2,6-diisopropylphenyl-substituted N-heterocyclic carbene (NHC). In this design, both frontier orbitals are localized on the same ligand, the N^O chelate, such that structural modulation of the electron-rich N^O-chelates can substantially tune the energy levels of the HOMO and LUMO, thereby controlling the photoluminescence properties. Detailed photophysical and electrochemical experiments as well as DFT calculations suggest charge-transfer transitions with intra-ligand charge transfer (ILCT) character, involving the N^O ligands. This strategy successfully produced long triplet excited-state lifetimes (up to 44 µs) in compounds that are strong photoreductants (E([Cu] + /*[Cu] as negative as −2.0 V vs. the ferrocenium/ferrocene couple). These properties allow these photosensitizers to be used as photocatalysts in various transformations of organic compounds, such as hydrogenation of substituted benzophenones, hydrodehalogenation of aryl/alkyl halides (including challenging C–Cl bond activation) and E/Z isomerization of (E)-stilbene (an example of triplet–triplet energy transfer).

Chakraborty, Soumi [University of Houston, TX (Uni

Inter-ligand cross-links determine secondary building unit formation in oligoMOFs

OligoMOFs are a class of metal–organic frameworks (MOFs) that feature ligands covalently cross-linked into oligomers as intrinsic structural components. A recent study has demonstrated that the size and flexibility of the tether moieties can result in the formation of oligoMOFs with different isomeric structures via geometrical distortions in the secondary building unit (SBU). In this work, it is demonstrated that tethered dimeric ligands with slightly different carbon chain lengths can direct the formation of oligoMOFs with SBUs of different structure and nuclearity. Specifically, inter-ligand cross links are used as a sensitive probe of the phase landscape of MOFs with the composition [Zn 2 (R-bdc) 2 (bpy)] (bdc = 1,4-benzenedicarboxylate, bpy = 4,4′-bipyridine), showing that a hexyl tether results in a framework structure identical to MOF-508, based on dinuclear {Zn 2 } “paddlewheel” SBUs, while heptyl and octyl tethers result in a “honeycomb-like” framework structure based on an infinite rod-like Zn 2+ SBU bridged by carboxylate ligands. Furthermore, these results are the first examples of tether length influencing SBU chemistry in MOFs and help understand the interplay between the MOF lattice and the geometric constraints imposed by inter-ligand cross-links in oligoMOFs.

MOFs