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At least 1,243 records · Page 69

Photoinitiated Reactions of Molecules and Radicals in Molecular Beams

The UV photochemistry of organic molecules is a fundamental process that governs reactions in the atmosphere, synthetic chemistry, processing of organic aerosols, and biological damage in living tissues. In many organic molecules, the ensuing evolution involves pathways that are in competition, giving rise to different products, isomerization, coupling to other electronic states, and secondary reactive collisions. Because photodissociation is usually fast (picoseconds to microseconds), these processes are far from equilibrium and are controlled by kinetic competition and dynamical forces. The work accomplished was focused primarily on the photochemistry of alpha-keto carboxylic acids, a group of acids produced from natural sources, which are implicated in aerosol formation and biological processes. In the atmosphere, they are destroyed mainly by solar radiation. Studying their photochemistry has been surprisingly difficult because of the complexity of their excited electronic states, and the effect of collisions and secondary reactions. The second project investigated the lifetime of excited electronic states of pyrazine and picoline and had both experimental and theoretical aspects. The work focused on a model molecule, pyruvic acid (PA), because it was hypothesized that it should be a good source of the unstable carbene, methylhydroxycarbene (MHC). PA has an internal hydrogen bond that controls the evolution of its decomposition. The decomposition was studied following excitation to two of its lowest excited states reached by laser irradiation at 351 and 193 nm. The photodissociation dynamics in the absence and presence of collisions was monitored and compared. Understanding the UV photochemistry requires the use of complementary experimental approaches. Two methods were enlisted, which together generated a comprehensive and detailed set of results: (i) The time-sliced velocity map imaging (SVMI) instrument at USC was exploited to determine kinetic energy release of fragments, fast dissociation timescales, and internal state distributions of fragments for which Resonance Enhanced Multiphoton Ionization (REMPI) schemes exist; and (ii) The multiplexed photoionization mass spectrometer (MPIMS) setup developed at the Sandia Combustion Research Facility was used for product discovery, achieved by exploiting tunable narrowband VUV radiation at the Advanced Light Source (ALS), and to follow in real time their subsequent unimolecular and bimolecular reactions. The experimental conditions ranged from collisionless molecular beams to study nascent products to flow reactors of variable pressures to study subsequent bimolecular reactions of the products. The goals stated above were successfully accomplished. By exciting PA to its lowest excited state, MHC was identified as the only primary product and its isomerization to vinylalcohol and acetaldehyde was directly observed in real time. Moreover, we reported the first bimolecular reaction of MHC, which was with acetaldehyde, and identified its reaction product. This paves the way for the study of other reactions of this important carbene intermediate. When excitation was carried out at 193 nm, which imparted much higher energy to PA, many more products were directly observed in real time, some deriving from three-body dissociation. Quantitative branching ratios and secondary reactions of radical products were also determined and analyzed. The studies of pyrazine and picoline focused on the second excited state of these molecules and showed (via ionization studies) that their excited states were very short lived (<100 fs) because of efficient couplings to lower electronic states via vibronic coupling. Theoretical work on modeling the absorption spectrum and decay mechanisms of the excited states are in progress in collaboration with theoreticians.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Programmable Catalyst Structures via Adsorbate-Induced Adatom Assembly

The electronic structure and geometric configuration of oxide-supported metal ions are important coordination properties that can be related to catalytic activity and stability. Herein, we interrogate the coordination environment of mononuclear Pd ions supported on ceria using CO adsorption, infrared vibrational spectroscopy, and DFT modeling. We observed the 15 h continuous co-evolution of a palladium- (2167 cm -1 ) and cerium-carbonyl (2177 cm -1 ) complex by monitoring the $\nu$(CO) infrared region. The slow CO adsorption kinetics were caused by the reactive ligand exchange between an oxygen atom of the support and the CO adsorbate to yield an oxygen vacancy and adsorbed CO 2 . We hypothesize that the co-evolved cerium-carbonyl complex was formed upon CO adsorption at or adjacent to this oxygen vacancy. Our hypothesis was experimentally supported by a dramatic attenuation of the cerium carbonyl signal upon pre-adsorption of water through an apparent competitive adsorption mechanism. The attenuation was also accompanied by a 6 cm -1 redshift of the palladium carbonyl band (2161 cm -1 ) attributed to hydrogen bonding between the carbonyl and a nearby hydroxyl. Characteristic n(CO) stretch frequencies catalogued through CO adsorption onto single crystal ceria by Wöll et al.1 led us to index the cerium carbonyl to the {100} nanofacet of the polycrystalline ceria support. It follows from the observed co-evolution of the two carbonyl complexes that Pd was also adsorbed at the {100} nanofacet. Redeployment of a previously developed DFT model by Ivanova-Shor et al.2 featuring square-planar coordination of Pd2+ at the {100} nanofacet (O 4 Pd) of a Ce 21 O 42 nanoparticle model qualitatively reproduced several experimental observations.

36 MATERIALS SCIENCE↗

The Role of Cooperative Interactions Among Surfaces, Solvents, and Reactive Intermediates on Catalysis at Liquid–Solid Interfaces (Final Report DE-SC0020224)

This project established quantitative links between inner‑sphere chemistry (active metal identity, coordination, and zeolite topology) and outer‑sphere organization (solvent identity, hydrogen‑bond networks, and pore condensation) that govern rates, activation barriers, and selectivities for alkene epoxidation and epoxide ring‑opening at solid–liquid and quasi‑liquid–solid interfaces. We deconvoluted contributions from covalent interactions at active sites and noncovalent, solvent‑mediated interactions within pores by pairing well‑defined metal substituted zeolites with controlled solvent environments. We then mapped those contributions onto measurable kinetics (ΔH‡, ΔS‡), adsorption thermodynamics (ITC), and in situ spectroscopy. The transferrable outcomes include a set of design rules that include the following understandings. First, tune silanol ((SiOH)x) density and pore topology to organize solvent networks that selectively stabilize transition states. Second, exploit activity‑coefficient‑normalized rates and adsorption– barrier correlations to diagnose when solvent reorganization rather than surface chemistry limits performance. Third, use partial pore condensation (e.g., acetonitrile, water but also generalizable to other solvents) to elicit liquid‑like stabilization effects even in nominally vapor‑phase reactors. Collectively, these results provide strategies to increase epoxidation rates, improve oxidant utilization (i.e., selectivities), and steer regioselectivity in zeolite‑based catalytic processes relevant to sustainable oxidation chemistry. These outcomes should be transferable to other classes of reactions that proceed in microporous materials and under confinement provided by organized solvents (e.g., electrochemical double layers).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular To Mesoscale Targeting of Oxoanions with Multi-Tasking Hosts

Achieving a better understanding of anion interactions both in solution and crystalline state was the overarching goal of this project. Anions are everywhere throughout Nature and play important roles in biological and environmental processes. They can be beneficial or deleterious or both in different situations and concentrations. For either reason it is important to have molecules that can bind anions for key needs that benefit society. However, recognition of specific anions is challenging due to the diffuse nature of their negative charge(s) as well as their various shapes and sizes. Understanding the basic properties of anions and how they interact with other molecules and ions in surrounding environments is key to selective recognition. In this project multi-tasking molecules for selective binding of targeted anions were designed to achieve cooperativity and synergism in one rather than multiple host molecules, including (1) cation:anion pair hosts for anions with charges of -2 or greater; (2) pH and redox activated hosts for on-off binding and release; and (3) multiple anion capture in extended host networks. Our design strategy was to combine the use of simple inexpensive building blocks and high yield synthetic pathways to provide economically feasible scale-up for applications. Oxoanions representing multiple shapes and charges were chosen based on having the potential for significant impact on DOE separations needs. Amide/amine-based macrocycles and urea/amine-based chelates and macrocycles with multiple hydrogen bonding sites provided the basic anion-binding frameworks. Successful multi-tasking outcomes were forthcoming in all three tasks. In Task 1, successful ion pair binding for anions with multiple charges was achieved. Furthermore, the ion pair molecules were capable of extended interactions through supramolecular intertwining, like fishing nets for capturing pools of fish (also fitting with Task 3). In Task 2, molecules were synthesized possessing on-off switches. These included a pH sensitive sensor for on-off binding of anions in general, as well as an electrochemical sensor selective for sulfate capture. Three new classes of extended anion host networks capable of binding multiple ions was a major outcome of Task 3. These systems included: anion sensitive, fluorescent organogels; channel-forming macrocycles for studying anion-water including larger macrocyclic cluster sandwiches; and, the offshoot of Task 1, fishing net ion-pair networks for higher valent anions. These strategies can be expanded in the future to other ions and molecules for a better understanding of intermolecular and interionic interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State

The COVID-19 pandemic underwent a rapid transition with the emergence of a dominant viral variant (from the “D-form” to the “G-form”) that carried an amino acid substitution D614G in its “Spike” protein. The G-form is more infectious in vitro and associated with increased viral loads. To gain insight into the molecular-level underpinnings of these characteristics, we employed microsecond all-atom simulations. Here we show that changes in the protein energetics favor a higher population of infection-capable (open) states through release of hydrogen bonds of an asymmetry present in the D-form but not the G-form. Thus, the increased infectivity of the G-form is likely due to a higher rate of profitable binding encounters with the host receptor. It is also predicted to be more neutralization sensitive due to enhanced exposure of the receptor binding domain, a key target region for neutralizing antibodies. These results are significant for vaccine design. The Molecular Dynamics Simulations datasets generated in this study, namely that of the soluble form SARS-CoV-2 Spike protein are made available here. Details of the trajectory and supporting files are given in the README.txt file.

59 BASIC BIOLOGICAL SCIENCES↗

Mesoscale fractal whey protein particles derived from microscale linear-shaped protein assemblies (Part 1): Manufacturing method and particle characteristics

Whey protein isolates (WPI) are widely used in processed foods for their versatile functional properties. Modifying the structural properties of proteins by assembling them into mesoscale or microscale particles may improve their functionality and broaden their applications. This study aims to manufacture and characterize mesoscale whey protein particles (WPP) derived from WPI. Two types of WPP, WPP1 (0.05 mL/min) and WPP2 (0.25 mL/min), were prepared through a multistep approach involving liquid antisolvent (LAS) precipitation, heat treatment, and microfluidization. Liquid antisolvent precipitation was performed by injecting a 20% (wt/vol) WPI dispersion (pH 7) into an ethanol-glycerol mixture (75:25, vol/vol) under laminar flow, followed by heat treatment at 80°C for 20 min as a particle hardening step. This process produced stable fiber- and ribbon-shaped whey protein assemblies (WPA), which served as precursors to WPP. Subsequent microfluidization (150 MPa, 6 passages) reduced the size of WPA, yielding mesoscale WPP with irregular morphologies and a more uniform size distribution, as revealed by microscopy and dynamic light scattering. ζ-Potential and fluorescence labeling indicated higher surface charge and surface hydrophobicity of WPP compared with untreated WPI. The WPP showed internal mass fractal and surface fractal structures at larger length scales, analyzed using small-angle X-ray scattering. Fourier transform infrared spectroscopy demonstrated an increased fraction of intermolecular β-sheets in WPP, suggesting that hydrogen bonding contributed to their formation. Gel electrophoresis confirmed that disulfide bonds served as the primary cross-links stabilizing the WPP structure. Furthermore, turbidity measurements showed that WPP exhibited superior colloidal phase stability compared with untreated WPI and maintained high colloidal stability under both acidic and neutral pH conditions.

Antisolvent precipitation↗

Covalent integration of polymers and porous organic frameworks

Covalent integration of polymers and porous organic frameworks (POFs), including metal-organic frameworks (MOFs), covalent organic frameworks (COFs) and hydrogen-bonded organic frameworks (HOFs), represent a promising strategy for overcoming the existing limitations of traditional porous materials. This integration allows for the combination of the advantages of polymers, i.e., flexibility, processability and chemical versatility etc., and the superiority of POFs, like the structural integrity, tunable porosity and the high surface area, creating a type of hybrid materials. These resulting polymer-POF hybrid materials exhibit enhanced mechanical strength, chemical stability and functional diversity, thus opening up new opportunities for applications across a large variety of fields, such as gas separation, catalysis, biomedical applications, environmental remediation and energy storage. In this review, an overview of synthetic routes and strategies on how to covalently integrate different polymers with various POFs is discussed, especially with a particular focus on methods like polymerization within, on and among POF structures. To investigate the unique properties and functions of these resultant hybrid materials, the characterization techniques, including nuclear magnetic resonance spectroscopy (NMR), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), transmission electron microscopy (TEM) and scanning electron microscopy (SEM), gas adsorption analysis (BET) and computational modeling and machine learning, are also presented. The ability of polymer-POFs to manipulate the pore environments at the molecular level affords these materials a wide range of applications, providing a versatile platform for future advancements in material science. Looking forward, to fully realize the potential of these hybrid materials, the authors highlight the scalability, green synthesis methods, and potential for stimuli-responsive polymer-POF materials as critical areas for future research.

Hossain, Md Amjad↗

Investigating intermolecular interactions among CO 2 , water and PEEK-ionene membrane using cryo ToF-SIMS and isotopic labeling

Cryogenic time-of-flight secondary ion mass spectrometry (cryo ToF-SIMS) has emerged as a powerful tool for investigating molecular interactions, speciation, and dynamics in materials for CO 2 capture. In this study, we apply cryo ToF-SIMS to probe interactions between CO 2 , water, and PEEK-ionene membranes—a promising material for direct CO 2 capture due to its selectivity, durability, and efficiency. Despite this potential, the mechanisms governing CO 2 diffusion and the influence of water vapor on CO 2 behavior remain unclear. To address this, we loaded PEEK-ionene membranes with 13 CO 2 and D 2 O and employed cryo ToF-SIMS to visualize the 3D distribution of CO 2 and water within the membrane. While prior studies suggest that 13 CO 2 is absorbed under ambient conditions, our cryo ToF-SIMS analysis revealed no enhancement of the 13 C/ 12 C ratio, suggesting weak CO 2 -membrane interactions. As a result, CO 2 vaporizes even at low temperatures (−140°C) under vacuum conditions. In contrast, D 2 O displayed a relatively homogeneous distribution in the membrane, suggesting stronger water-membrane interactions via hydrogen bonding (18–20 kJ/mol). Interestingly, CO 2 was not detected in D 2 O-loaded membranes, indicating minimal interference from water vapor on CO 2 diffusion. As a comparison, the cryo ToF-SIMS data show that 13 CO 2 can readily react with a basic Na 2 CO 3 aqueous solution to form NaH 13 CO 3 . These findings demonstrate cryo ToF-SIMS as a critical technique for understanding gas-water-membrane interactions, offering insights for membrane functionalization to improve CO 2 capture efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pathways and Mechanism of Caffeine Binding to Human Adenosine A 2A Receptor

Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the pathways and mechanism of CFF binding to the target receptors remain unclear. In this study, we have performed all-atom-enhanced sampling simulations using a robust Gaussian-accelerated molecular dynamics (GaMD) method to elucidate the binding mechanism of CFF to human adenosine A 2A receptor (A 2A AR). Multiple 500–1,000 ns GaMD simulations captured both binding and dissociation of CFF in the A 2A AR. The GaMD-predicted binding poses of CFF were highly consistent with the x-ray crystal conformations with a characteristic hydrogen bond formed between CFF and residue N6.55 in the receptor. In addition, a low-energy intermediate binding conformation was revealed for CFF at the receptor extracellular mouth between ECL2 and TM1. While the ligand-binding pathways of the A 2A AR were found similar to those of other class A GPCRs identified from previous studies, the ECL2 with high sequence divergence serves as an attractive target site for designing allosteric modulators as selective drugs of the A 2A AR.

59 BASIC BIOLOGICAL SCIENCES↗

Construction of nano slow-release systems for antibacterial active substances and its applications: A comprehensive review

At present, nano-carrier materials with antibacterial activity are of great significance. Due to the widespread resistance of many pathogenic microorganisms, it has seriously threatened human health. The natural antimicrobial substances extracted from fruits and vegetables can significantly improve their stability combined with nano-carrier materials. The resistance of pathogenic microorganisms will be substantially reduced, greatly enhancing the effect of active antimicrobial substances. Nanotechnology has excellent research prospects in the food industry, antibacterial preservation, food additives, food packaging, and other fields. This paper introduces nano-carrier materials and preparation techniques for loading and encapsulating active antibacterial substances in detail by constructing a nano-release system for active antibacterial substances. The antibacterial effect can be achieved by protecting them from adverse external conditions and destroying the membrane of pathogenic microorganisms. The mechanism of the slow release of the bacteriostatic active substance is also described. The mechanism of carrier loading and release is mainly through non-covalent forces between the bacteriostatic active substance and the carrier material, such as hydrogen bonding, π-π stacking, van der Waals forces, electrostatic interactions, etc., as well as the loading and adsorption of the bacteriostatic active substance by the chemical assembly. Finally, its wide application in food and medicine is introduced. It is hoped to provide a theoretical basis and technical support for the efficient utilization and product development of bacteriostatic active substances.

Cao, Jiayong↗

Fluorogenic Biosensing with Tunable Polydiacetylene Vesicles

Polydiacetylenes (PDAs) are conjugated polymers that are well known for their colorimetric transition from blue to red with the application of energetic stimulus. Sensing platforms based on polymerized diacetylene surfactant vesicles and other structures have been widely demonstrated for various colorimetric biosensing applications. Although less studied and utilized, the transition also results in a change from a non-fluorescent to a highly fluorescent state, making polydiacetylenes useful for both colorimetric and fluorogenic sensing applications. Here, we focus on the characterization and optimization of polydiacetylene vesicles to tune their sensitivity for fluorogenic sensing applications. Particularly, we look at how the structure of the diacetylene (DA) hydrocarbon tail and headgroup affect the self-assembled vesicle size and stability, polymerization kinetics, and the fluorogenic, blue to red phase transition. Longer DA acyl tails generally resulted in smaller and more stable vesicles. The polymerization kinetics and the blue to red transition were a function of both the DA acyl tail length and structure of the headgroup. Decreasing the acyl tail length generally led to vesicles that were more sensitive to energetic stimuli. Headgroup modifications had different effects depending on the structure of the headgroup. Ethanolamine headgroups resulted in vesicles with potentially increased stimuli responsivity. The lower energy stimulus to induce the chromatic transition was attributed to an increase in headgroup hydrogen bonding and polymer backbone strain. Boronic-acid headgroup functionalization led to vesicles that were generally unstable, only weakly polymerized, and unable to fully transform to the red phase due to strong polar, aromatic headgroup interactions. This work presents the design of PDA vesicles in the context of biosensing platforms and includes a discussion of the past, present, and future of PDA biosensing.

Chemistry↗

Electronic Structure and Mechanical Properties of Solvated Montmorillonite Clay Using Large-Scale DFT Method

Montmorillonite clay (MMT) has been widely used in engineering and environmental applications as a landfill barrier and toxic waste repository due to its unique property as an expandable clay mineral that can absorb water easily. This absorption process rendered MMT to be highly exothermic due to electrostatic interactions among molecules and hydrogen bonds between surface atoms. A detailed study of a large supercell model of structural clay enables us to predict long-term nuclear waste storage. Herein, a large solvent MMT model with 4071 atoms is studied using ab initio density functional theory. The DFT calculation and analysis clarify the important issues, such as bond strength, solvation effect, elasticity, and seismic wave velocities. These results are compared to our previous study on crystalline MMT (dry). The solvated MMT has reduced shear modulus (G), bulk modulus (K), and Young’s modulus (E). We observe that the conduction band (CB) in the density of states (DOS) of solvated MMT model has a single, conspicuous peak at –8.5 eV. Moreover, the atom-resolved partial density of states (PDOS) summarizes the roles played by each atom in the DOS. These findings illuminate numerous potential sophisticated applications of MMT clay.

36 MATERIALS SCIENCE↗

A Molecular Description of Hydrogel Forming Polymers for Cement-Based Printing Paste Applications

This research endeavors to link the physical and chemical characteristics of select polymer hydrogels to differences in printability when used as printing aids in cement-based printing pastes. A variety of experimental probes including differential scanning calorimetry (DSC), NMR-diffusion ordered spectroscopy (DOSY), quasi-elastic neutron scattering (QENS) using neutron backscattering spectroscopy, and X-ray powder diffraction (XRD), along with molecular dynamic simulations, were used. Conjectures based on objective measures of printability and physical and chemical-molecular characteristics of the polymer gels are emerging that should help target printing aid selection and design, and mix formulation. Molecular simulations were shown to link higher hydrogen bond probability and larger radius of gyration to higher viscosity gels. Furthermore, the higher viscosity gels also produced higher elastic properties, as measured by neutron backscattering spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Proton Density of States in Confined Water (H2O)

The hydrogen density of states (DOS) in confined water has been probed by inelastic neutron scattering spectra in a wide range of its P–T phase diagram. The liquid–liquid transition and the dynamical crossover from the fragile (super-Arrhenius) to strong (Arrhenius) glass forming behavior have been studied, by taking into account the system polymorphism in both the liquid and amorphous solid phases. The interest is focused in the low energy region of the DOS ( E < 10 meV) and the data are discussed in terms of the energy landscape (local minima of the potential energy) approach. In this latest research, we consider a unit scale energy (EC) linked to the water local order governed by the hydrogen bonding (HB). All the measured spectra, scaled according to such energy, evidence a universal power law behavior with different exponents ( γ ) in the strong and fragile glass forming regions, respectively. In the first case, the DOS data obey the Debye squared-frequency law, whereas, in the second one, we obtain a value predicted in terms of the mode-coupling theory (MCT) ( γ ≃ 1.6 ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fullerene Negative Ions: Formation and Catalysis

We first explore negative-ion formation in fullerenes C 44 to C 136 through low-energy electron elastic scattering total cross sections calculations using our Regge-pole methodology. Then, the formed negative ions C 44 – to C 136 – are used to investigate the catalysis of water oxidation to peroxide and water synthesis from H 2 and O 2 . The exploited fundamental mechanism underlying negative-ion catalysis involves hydrogen bond strength-weakening/breaking in the transition state. Density Functional Theory transition state calculations found C 60 – optimal for both water and peroxide synthesis, C 100 – increases the energy barrier the most, and C 136 – the most effective catalyst in both water synthesis and oxidation to H 2 O 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors

A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗

The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS

The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗