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At least 685 records · Page 38

Saddle point sampling using scaled normal coordinates

The sampling of saddle points (SPs) on a potential energy surface (PES) is critical for describing the dynamics and transport properties of materials. In this paper we propose a saddle point search (SPS) method that enables efficient sampling of practically meaningful SPs around a local minimum by converting the PES to the scaled normal coordinates (SNCs), together with the dimer method. We find that the pathway leading to a SP using SNCs is highly efficient and is independent of the system size. This results in the significantly increased SPS efficiency and the enhanced possibility of a complete catalog of the SPs. In addition, we perform SPSs using the SNCs for the diffusion of a vacancy and a dumbbell in body-centered cubic Fe and demonstrate (1) the required number of system force evaluations for a SPS decreases by at least an order of magnitude, (2) the effects of the system size on the number of force evaluations are greatly decreased, and (3) the effects of the number of atoms involved in the SPS on the probability of finding practically meaningful SPs is mostly eliminated. We also discuss the computational cost of introducing the SNCs. It should be highlighted that the SNCs could also be applied to other minimum-mode following methods, demonstrating the general versatility of the proposed method.

36 MATERIALS SCIENCE↗

Revisiting point defect thermodynamics in group IVB and VB transition metal carbides

We present a comprehensive re-examination of point defect thermodynamics in group IVB and VB transition metal carbides (TMCs) with the rocksalt structure using a combination of density functional theory (DFT) calculations and a statistical mechanical Wagner-Schottky model within the canonical ensemble. The most stable configurations of point defects were discovered using basin-hopping global optimization, driven by either a machine learning interatomic potential (MLIP) or DFT. A key finding is the identification of previously unreported dicarbon antisites—a C–C dimer occupying a metal site—as the structural (constitutional) defects on the carbon-rich side of stoichiometry in all group IVB and VB TMCs except TaC. Furthermore, dicarbon antisite-containing thermal defect complexes, such as quadruple and interbranch defects, can dominate in TMCs under specific stoichiometric and temperature conditions. In conclusion, by incorporating dicarbon antisites into the defect landscape, this work provides a revised understanding of the thermodynamics of point defects in TMCs.

Carbides↗

Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies

Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NP RBD ) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NP RBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NP RBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.

59 BASIC BIOLOGICAL SCIENCES↗

Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus

Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3'-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII 170-755 , as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.

59 BASIC BIOLOGICAL SCIENCES↗

Rubredoxin 1 promotes the proper folding of D1 and is not required for heme b 559 assembly in Chlamydomonas photosystem II

Photosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme b 559 iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome b 559 , using the RBD1-lacking 2pac mutant from Chlamydomonas reinhardtii, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant 2pac ftsh1-1, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the 2pac ftsh1-1 background and found that α and β cytochrome b 559 subunits are still present and coordinate heme b 559 as in the WT. Interestingly, immunoblot analysis of dark- and low light–grown 2pac ftsh1-1 showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme b 559 assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly via delivery or reduction of the nonheme iron during PSII assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oxide-catalyzed self- and cross-condensation of cycloketones. Kinetically relevant steps that determine product distribution

Metal oxides with acid-base properties can be used to catalyze aldol condensation and potentially obtain valuable chemicals from biomass-derived oxygenates. Understanding the reaction mechanisms could enable the development of effective catalysts with controllable selectivity. In this work, we investigate the reaction parameters that affect the kinetics and product distribution of self- and cross-aldol condensation of cyclopentanone (CPO) and cyclohexanone (CHO) over CeO 2 and ZrO 2 catalysts by combining detailed analysis of experiments and DFT calculations. It is well-known that either the deprotonation of an α-C–H that generates an enolate or the C–C coupling that produces the dimers can be rate-limiting step. Indeed, the detailed kinetics analysis shows that the observed data can be fitted by unimolecular or bimolecular Langmuir-Hinshelwood models. Specifically, on the ZrO 2 catalyst, the unimolecular α-C–H activation is the rate limiting step for the CPO self-condensation, while the bimolecular C–C coupling limits the CHO self-condensation. By contrast, on CeO 2 , the bimolecular C–C coupling step seems to be rate-limiting for both CPO and CHO self-condensation reactions. The adsorption parameters derived from kinetics fitting indicate that when the two reactants are co-fed, the surface is preferentially covered by CHO. So, the condensation rate of [CPO]-activated products ([CPO]CPO + [CPO]CHO) decreases in the presence of CHO, due to the competitive adsorption. However, despite a higher surface coverage, CHO is not an effective electrophile because it imposes stronger steric constraints to the formation of the C–C bond than CPO. Therefore, for a given enolate, the product distribution shows that [CPO]CPO > [CPO]CHO and, similarly [CHO]CPO > [CHO]CHO. Likewise, the yields of [CPO]- and [CHO]-activated products in mixed CPO/CHO feeds are similar because the higher surface coverage and stability of the [CHO] enolate is counterbalanced by the inhibition of C–C coupling by steric constraints when CHO is involved. In summary, the overall rank of products observed experimentally can be explained in terms of a combination of the following effects: relative surface coverage of the reactants, steric constraints for the C–C coupling, stability of the enolate, and effectiveness of the electrophile to accept an electron.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure sensitivity of ammonia electro-oxidation on transition metal surfaces: A first-principles study

Ammonia electro-oxidation is a promising catalytic reaction for application in alkaline fuel cells. In this paper we study the trends in this reaction on the (1 0 0) facet of eight fcc transition metals: Au, Ag, Cu, Pt, Pd, Ni, Ir, and Rh. We calculate from first-principles (DFT-GGA-PW91) the energetics for two mechanisms: (i) the N + N mechanism and (ii) the Gerischer-Mauerer mechanism. The onset potentials for both mechanisms are provided for both (1 0 0) and (1 1 1) facets. We also calculate the activation energies for the N-N bond-making non-Faradaic events on Cu, Pt, Pd, Ni, Ir, and Rh. We discover that N* – which is considered a poison for Pt(1 1 1) – is a reactive intermediate on Pt(1 0 0), allowing for a facile dimerization to N2 on Pt(1 0 0) at high potentials. We draw similar analyses for the structure sensitivity on the other metals, and we conclude with some general principles to guide catalyst design for this reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Catalytic Site Requirements for N2O Decomposition on Cu-, Co-, and Fe-SSZ-13 Zeolites

N2O decomposition is investigated on Cu, Co and Fe-exchanged SSZ-13 zeolite catalysts at relatively low metal loadings. The catalysts are synthesized by solution ion exchange, and subjected to X-ray diffraction (XRD), temperature-programed-reduction by H2 (H2-TPR), temperature-programed-reaction of N2O (N2O-TPR) coupled with in-situ transmission FTIR, and finally steady-state flow reaction tests. At low N2O pressures (< 0.05 kPa), all catalysts display pseudo first-order kinetics. From Arrhenius analysis, Cu and Fe-SSZ-13 display very different apparent activation energies but similar pre-exponential factors, suggesting their similar reaction mechanisms. N2O decomposition follows a dual-site mechanism, occurring on dimeric M-O-M sites in these catalysts, and O2 is formed by the combination of two O ad-atoms from two vicinal metal sites. Under low N2O pressure (0.05 kPa) and first-order kinetic regime, the reaction is limited by N-O cleavage on bare metal active sites. In comparison to Cu-SSZ-13, the much higher N2O decomposition rate over Fe-SSZ-13 is attributed to the much lower activation barriers for the N-O cleavage step. N2O decomposition occurs on isolated Co2+ ions in Co-SSZ-13. The rate-limiting step is N-O cleavage on an O-occupied Co site in the low-pressure first order kinetic regime. This single-site mechanism leads to much higher pre-exponential factors as compared to the dual-site mechanism. This beneficial factor for reaction rate enhancement, however, is compromised by the much higher activation barriers over this catalyst.

Lin, Fan↗

Effects of Water Vapor on the Reactivity of Aluminosilicates in Vapor-Phase Propanal Aldol Condensation

Aluminosilicate materials have been extensively studied as efficient aldol catalysts for C-C coupling reactions due to their acidic nature, high surface area, thermal stability, and porous structure. This work investigated the impact of water vapor pressure on the catalytic reactivity of aluminosilicates for the aldol condensation of propanal to 2-methyl-2-pentenal (MP). The catalytic performance of amorphous SiO2-Al2O3 (A-Si-Al) and aluminated MCM-41 (Al-MCM-41) for the vapor-phase aldol condensation of propanal was evaluated at 200 degrees C as a function of vapor-phase water content at atmospheric pressure. Our findings demonstrate that co-feeding low water vapor pressures (1-18 kPa) with propanal enhances the rates of MP production at 200 degrees C on A-Si-Al. Conversely, water vapor pressures of 25 kPa result in a decrease in aldol dimer formation rates. The rate of MP production evaluated on Al-MCM-41 also increased in the presence of 5 kPa water compared to anhydrous conditions. Propylamine temperature-programmed desorption analyses revealed an increase in Bronsted acid site density when both catalysts were exposed to water, which likely accounts for the observed enhancement in aldol condensation reactivity under hydrous conditions. Reversibility testing of the water vapor effect under reaction conditions, combined with X-ray diffraction analysis of fresh, spent, and regenerated catalysts, revealed no structural changes in either aluminosilicate upon exposure to water or reaction conditions. The rates of aldol condensation and the impact of water vapor were highly consistent across both materials, suggesting that zeolite crystallinity has minimal influence on the catalytic performance.

acid catalysts↗

Synthesis and structural characterization of the new Zintl phases Ba 3 Cd 2 P 4 and Ba 2 Cd 2 P 3 . Rare example of small gap semiconducting behavior with negative thermopower within the range 300 K-700 K

The new Zintl phases Ba 3 Cd 2 P 4 and Ba 2 Cd 2 P 3 have been synthesized using Pb flux, which allowed for the growth of 4-5 mm large crystals. The structures were determined utilizing single-crystal X-ray diffraction methods. Both compounds crystalize in the monoclinic crystal system (space group C2/m (No. 12)) and their structures are closely related. The structure of Ba 3 Cd 2 P 4 can be seen as being comprised of divalent Ba atoms and conjoined CdP 4 tetrahedra in the form of [Cd 2 P 4 ] 6- layers. Within the layers, homoatomic P–P bonds are present, which if cleaved, leave two infinite [CdP 3 ] 7- chains running along the crystallographic b-axis. The other structure, that of Ba 2 Cd 2 P 3 , can be rationalized as also having divalent Ba atoms and conjoined CdP4 tetrahedra in the form of [Cd 2 P 3 ] 6- layers. These layers, again, can be visualized as chains that run down the crystallographic b-axis, which are further connected by P-P dimers. Electronic band structure calculations show that each structure has an optimal number of valence electrons, and therefore conform to the Zintl-Klemm concept. Accordingly, the two compounds can be considered small band gap semiconductors, with band gaps of ca. 0.1 eV and 0.6 eV for Ba3Cd2P4 and Ba 2 Cd 2 P 3 , respectively. Electrical resistivity measurements show that Ba3Cd2P4 displays a large resistivity value at room temperature and an experimental band gap of ca. 0.05 eV, which fits reasonably well with the theoretical predictions. Thermopower measurements show that throughout the temperature range 300 K-700 K, Ba 3 Cd 2 P 4 displays a negative Seebeck coefficient. Here, the extremum value of -84 μV is reached at 630 K, suggestive of an n-type semiconductor, a rarity among Zintl phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen

Background: Fibrinogen is a soluble, multisubunit, and multidomain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin, initiating polymerization that substantially contributes to clot growth. Fibrinogen contains numerous, transiently accessible “cryptic” epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there have been limited integrative approaches characterizing the solution structure and internal flexibility of fibrinogen. Methods: Here, utilizing a multipronged, biophysical approach involving 2 solution-based techniques, temperature-dependent hydrogen-deuterium exchange mass spectrometry and small angle X-ray scattering, corroborated by negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution. Results: Our data reveal 4 major and distinct conformations of fibrinogen accommodated by a high degree of internal protein flexibility along its central scaffold. We propose that the fibrinogen structure in the solution consists of a complex, conformational landscape with multiple local minima. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia and posttranslational modifications, residing near the identified fibrinogen flexions. Conclusion: Further, this work provides a molecular basis for the structural “dynamism” of fibrinogen that is expected to influence the broad swath of its functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

59 BASIC BIOLOGICAL SCIENCES↗

Alkene adsorption and cracking on acidic zeolites – A gradual process of understanding

Cracking of light alkenes on solid acids and, in particular on zeolites, is ubiquitous in refineries. Different zeolite framework topologies in the catalysts used provide spatial constraints for reactants and products, leading to discrete reaction routes and varying selectivities. The conversion of alkenes in cracking proceeds either via monomolecular or bimolecular reaction pathways. In both routes, the reacting alkene adsorbs first on Brønsted acid sites forming the initial state (e.g., π-complex, carbenium ion or alkoxide), followed by β-cleavage in the carbenium transition state, generating a smaller alkene and a carbenium ion (monomolecular route) or forming a dimer by alkene addition that cracks subsequently (bimolecular route). The current state of understanding alkene sorption and cracking is critically discussed in this paper and four questions are formulated that may be the central questions from our perspective in further developing new generations of catalysts and processes for alkene conversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Variable hydrazine coordination modes from reactions with dichlorotris(triphenylphosphine)ruthenium(II)

The reactivity of the prominent ruthenium(II) catalyst and precursor, RuCl 2 (PPh 3 ) 3 , was explored with hydrazine and its derivatives. The reactions produced 6-coordinate ruthenium(II) products that bond with the hydrazine moiety in bridging (NH 2 NH 2 or NH 2 NHMe), end-on (NH 2 NHMe, NH 2 NHPh, or NH 2 NMe 2 ), or side-on (NH 2 NMe 2 ) fashions. The products have been characterized by single crystal X-ray diffraction and 31 P NMR spectroscopy. With NH 2 NH 2 , the dimeric product, [RuCl 2 (PPh 3 ) 2 ] 2 ($μ$-N 2 H 4 ) 2 , was formed under all conditions used. For other hydrazines, the reaction stoichiometry governed product formation to yield either bimetallic or monomeric products. When the RuCl 2 (PPh 3 ) 3 to hydrazine derivative ratio was 1:1 or lower, bimetallic complexes were formed while a 1:2 ratio produced monomeric compounds. The exception to the latter occurs with the production of the monomeric compound, RuCl 2 (PPh 3 ) 2 ($η$ 2 -NH 2 NMe 2 ), that forms employing a 1:1 ratio. In addition to stoichiometry, steric factors and hydrogen bonding played a significant role in dictating the bonding mode of hydrazines. The bimetallic complexes were further reacted to yield the corresponding monomeric products, adopting the form RuCl 2 (PPh 3 ) 2 (L) 2 (L = NH 2 NHMe, NH 2 NHPh, or NH 2 NMe 2 ). Reactions utilizing less than a 1:2 ratio of RuCl 2 (PPh 3 ) 3 to NH 2 NMe 2 produced a mixture of products that appear to be in equilibrium. In conclusion, FT calculations were performed to gain insight into the reaction energetics and molecular stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unique interface and dynamics of the complex of HSP90 with a specialized cochaperone AIPL1

Photoreceptor phosphodiesterase PDE6 is central for visual signal transduction. Maturation of PDE6 depends on a specialized chaperone complex of HSP90 with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1). Disruption of PDE6 maturation underlies a severe form of retina degeneration. Here, we report a 3.9 Å cryoelectron microscopy (cryo-EM) structure of the complex of HSP90 with AIPL1. This structure reveals a unique interaction of the FK506-binding protein (FKBP)-like domain of AIPL1 with HSP90 at its dimer interface. Unusually, the N terminus AIPL1 inserts into the HSP90 lumen in a manner that was observed previously for HSP90 clients. Deletion of the 7 N-terminal residues of AIPL1 decreased its ability to cochaperone PDE6. Multi-body refinement of the cryo-EM data indicated large swing-like movements of AIPL1-FKBP. Modeling the complex of HSP90 with AIPL1 using crosslinking constraints indicated proximity of the mobile tetratricopeptide repeat (TPR) domain with the C-terminal domain of HSP90. Our study establishes a framework for future structural studies of PDE6 maturation.

60 APPLIED LIFE SCIENCES↗

Mapping structural and dynamic divergence across the MBOAT family

Membrane-bound O-acyltransferases (MBOATs) are membrane-embedded enzymes that catalyze acyl chain transfer to a diverse group of substrates, including lipids, small molecules, and proteins. MBOATs share a conserved structural core, despite wide-ranging functional specificity across both prokaryotes and eukaryotes. The structural basis of catalytic specificity, regulation and interactions with the surrounding environment remain uncertain. Here, we combine comparative molecular dynamics (MD) simulations with bioinformatics to assess molecular and interactional divergence across the family. In simulations, MBOATs differentially distort the bilayer depending on their substrate type. Additionally, we identify lipid binding sites surrounding reactant gates in the surrounding membrane. Complementary bioinformatic analyses reveal a conserved role for re-entrant loop-2 in MBOAT fold stabilization and a key hydrogen bond bridging DGAT1 dimerization. Finally, we predict differences in MBOAT solvation and water gating properties. These data are pertinent to the design of MBOAT-specific inhibitors that encompass dynamic information within cellular mimetic environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cryo-electron microscopy structure of a zinc uptake ABC transporter

Zn2+ is an essential micronutrient required for many biological processes. Microorganisms employ high-affinity Zn2+ ABC transporters to take up zinc from the environment when it is scarce, yet the mechanism of zinc uptake and its regulation remain poorly understood. Here, we report the cryo-electron microscopy structure of the Zn2+ ABC transporter complex ZnuB-ZnuC from Escherichia coli. It contains two ZnuB transport and two ZnuC regulatory subunits. The ZnuB homodimer is in an outward-facing, closed conformation with a large hydrophilic cavity at the dimer interface. Each ZnuC subunit contains an N-terminal nucleotide-binding domain and a C-terminal zinc-sensing domain (ZSD). Zn2+ binding to the ZSD locks the transporter in a closed state, whereas under low-Zn2+ conditions, the disorder of ZSD permits ATP-driven zinc uptake. Zn2+ ABC transporters are ubiquitously utilized by pathogenic bacteria to compete with hosts for Zn2+. These findings reveal potential therapeutic targets for disrupting Zn2+ homeostasis in antibiotic-resistant pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

Stability and mobility of tungsten clusters on tungsten (110) surface: Ab initio and atomistic simulations

Quantifying the surface transport properties of tungsten (W) is of prime importance to understand the formation of nano-fuzz in fusion plasma-facing conditions. The stability and mobility of W adatom clusters (W n , n = 2-9) on the W(110) surface has been investigated by computer simulations, including ab initio calculations using density functional theory (DFT) and molecular statics (MS) simulations with multiple W interatomic potentials. The DFT results demonstrate that the sequential binding energy generally increases with number of W adatoms, except for the 5 th and 7 th W adatoms. The most common elemental migration steps of W n (n>2) clusters are observed to consist of monomer and dimer hops, while larger W n clusters can also diffuse by dissociation and recombination of smaller clusters. The threshold migration energy of W 9 is the highest, then followed by W 8 , W 4 , and W 6 , while W 3 , W 5 , and W 7 have similar migration energies. Compared to DFT, each interatomic potential evaluated overestimates the binding energies of W n clusters. Additionally, the embedded-atom potential developed by Juslin and Wirth adequately predicts the threshold migration energy of W n (n>2) clusters, although it predicts different underlying migration mechanisms. The results show that interaction mechanism between W adatoms controls the stability and mobility of W n clusters on the W(110) surface.

36 MATERIALS SCIENCE↗