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At least 361 records · Page 20

Hydrogen bonds and dispersion forces serving as molecular locks for tailored Group 11 bis(amidine) complexes

A flexible polydentate bis(amidine) ligand LH 2 , LH 2 = {CH 2 NH( t Bu)C=N-2-(6-MePy)} 2 , operates as a molecular lock for various coinage metal fragments and forms the dinuclear complexes [LH 2 (MCl) 2 ], M = Cu (1), Au (2), the coordination polymer [{(LH 2 ) 2 (py) 2 (AgCl) 3 }(py) 3 ] n (3), and the dimesityl-digold complex [LH 2 (AuMes) 2 ] (4) by formal insertion of MR fragments (M = Cu, Ag, Au; R = Cl, Mes) into the N–H∙∙∙N hydrogen bonds of LH 2 in yields of 43–95%. Complexes 1, 2, and 4 adopt C 2 -symmetrical structures in the solid state featuring two interconnected 11-membered rings that are locked by two intramolecular N–H∙∙∙R–M hydrogen bonds. QTAIM analyses of the computational geometry-optimized structures 1a, 2a, and 4a reveal 13, 11, and 22 additional bond critical points, respectively, all of which are related to weak intramolecular attractive interactions, predominantly representing dispersion forces, contributing to the conformational stabilization of the C2-symmetrical stereoisomers in the solid state. Variable-temperature 1 H NMR spectroscopy in combination with DFT calculations indicate a dynamic conformational interconversion between two C 2 -symmetrical ground state structures in solution (ΔG ‡ c = 11.1–13.8 kcal mol –1 ), which is accompanied by the formation of an intermediate possessing C i symmetry that retains the hydrogen bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The hTERT core promoter forms three parallel G-quadruplexes

The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.

59 BASIC BIOLOGICAL SCIENCES↗

Determining magnetic structures in GSAS-II using the Bilbao Crystallographic Server tool k-SUBGROUPSMAG

The embedded call to a special version of the web-based Bilbao Crystallographic Server tool k-SUBGROUPSMAG from within GSAS-II to form a list of all possible commensurate magnetic subgroups of a parent magnetic grey group is described. It facilitates the selection and refinement of the best commensurate magnetic structure model by having all the analysis tools including Rietveld refinement in one place as part of GSAS-II. It also provides the chosen magnetic space group as one of the 1421 possible standard Belov–Neronova–Smirnova forms or equivalent non-standard versions.

36 MATERIALS SCIENCE↗

Biophysical and Biochemical Characterization of TP0037, a D-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum

A longstanding conundrum in Treponema pallidum biology concerns how the spirochete generates sufficient energy to fulfill its complex pathogenesis processes during human syphilitic infection. For decades, it has been assumed that the bacterium relies solely on glucose catabolism (via glycolysis) for generation of its ATP. However, the organism’s robust motility, believed to be essential for human tissue invasion and dissemination, would require abundant ATP likely not provided by the parsimony of glycolysis. As such, additional ATP generation, either via a chemiosmotic gradient, substrate-level phosphorylation, or both, likely exists in T. pallidum. Along these lines, we have hypothesized that T. pallidum exploits an acetogenic energy conservation pathway that relies on the redox chemistry of flavins. Central to this hypothesis is the apparent existence in T. pallidum of an acetogenic pathway for the conversion of d-lactate to acetate. Herein we have characterized the structural, biophysical, and biochemical properties of the first enzyme (d-lactate dehydrogenase [d-LDH]; TP0037) predicted in this pathway. Binding and enzymatic studies showed that recombinant TP0037 consumed d-lactate and NAD+ to produce pyruvate and NADH. The crystal structure of TP0037 revealed a fold similar to that of other d-acid dehydrogenases; residues in the cofactor-binding and active sites were homologous to those of other known d-LDHs. The crystal structure and solution biophysical experiments revealed the protein’s propensity to dimerize, akin to other d-LDHs. This study is the first to elucidate the enzymatic properties of T. pallidum’s d-LDH, thereby providing new compelling evidence for a flavin-dependent acetogenic energy conservation (ATP-generating) pathway in T. pallidum.

59 BASIC BIOLOGICAL SCIENCES↗

Structural design and optimization of a series of 13.2 MW downwind rotors

The quest for reduced LCOE has driven significant growth in wind turbine size. A key question to enable larger rotor designs is how to configure and optimize structural designs to constrain blade mass and cost while satisfying a growing set of challenging structural design requirements. In this paper, we investigate the performance of a series of three two-bladed downwind rotors with different blade lengths (104.3-m, 122.9-m, and 143.4-m) all rated at 13.2 MW. The primary goals are to achieve 25% rotor mass and 25% LCOE reduction. A comparative analysis of the structural performance and economics of this family rotors is presented. To further explore optimization opportunities for large rotors, we present new results in a root and spar cap design optimization. In summary, we present structural design solutions that achieve 25% rotor mass reduction in a SUMR13i design (104.3-m) and 25% LCOE reduction in a SUMR13C design (143.4-m).

Yao, Shulong↗

Chemical Recommender System: Replacement Suggestions for Small Molecules

The Chemical Recommender System (CRS) is an open-source, high-performance toolkit that enables real-time similarity searches across the complete PubChem database (over 50 million molecules) using commodity hardware. The CRS addresses critical limitations in existing chemical informatics platforms through a novel vector database infrastructure, extensible model integration capabilities, and complete algorithmic transparency. The system implements a vector database deployment with partitioned indexing that achieves a ~60x speedup over traditional approaches. A containerized model integration framework allows researchers to seamlessly incorporate custom predictive models into the full-scale search and scoring pipeline, while complete configurability of search parameters, filtering logic, and scoring functions provides capabilities not available in existing black-box solutions. Beyond structural similarity, the CRS integrates OPERA QSAR models for thermophysical and toxicity predictions, RDKit synthetic accessibility scoring, and user-defined models to compute weighted final replacement scores. The complete system is accessible through an interactive web application supporting real-time progress monitoring, post-processing score re-weighting, automated PDF reporting, and batch processing capabilities.

Nair, Parthiv Anand [Sandia National Laboratories ↗

Sovereign Credit Rating Processes Adapted to Critical Infrastructure Cyber Risk Assessment

United States critical infrastructure entities are increasingly targeted by motivated and capable threat actors and must be prepared to assess and treat a diverse range of cyber risks. Consequently, this necessitates some form of analytical process to evaluate risks and inform cyber security investment decisions. A potential solution for structuring cyber risk evaluation exists within the field of sovereign credit ratings – where agencies employ mature approaches that integrate quantitative and qualitative data to produce a singular value of assessment. Adapting such approaches, we present a novel criterion and methodology for measuring and communicating the likelihood element of cyber risk. The methodology is composed of three sequential phases: a quantitative baseline organized by distinct capability frames, a bounded qualitative adjustment per frame, and a greater-bounded qualitative adjustment spanning the entire process. The process culminates in publication of a cyber capability rating that communicates a critical infrastructure entity’s ability and willingness to mitigate discontinuous function due to cyberattack.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Spinning mode sound propagation in ducts with acoustic treatment

Recent acoustic data show larger noise attenuations than predicted for acoustically treated aircraft engine inlets without splitter rings. A theoretical study of the acoustic propagation of spinning modes in acoustically treated open circular ducts is presented, and a suppressor with splitter rings was modeled by using the rectangular approximation to the annular duct. Theoretical models were used to determine optimum impedance and maximum attenuation for several spinning lobe numbers from 0 to 50. Results of the analysis indicate that for circular ducts the maximum possible attenuation and the optimum wall impedance are strong functions of the lobe number, and for annular ducts the attenuation and optimum wall impedance are insensitive to the spinning lobe number for well cut-on modes. These results explain why suppressors with splitter rings were quite effective in spite of the lack of detailed information on the noise source modal structure. Conversely, effective use of outer wall treatment alone will require expanded knowledge of the noise source structure. Approximate solutions are presented to help interpret the more exact theoretical results.

Rice, E. J.↗

Spinning mode sound propagation in ducts with acoustic treatment

Recent acoustic data have shown larger noise attenuations than predicted for acoustically treated aircraft engine inlets without splitter rings. These data have stimulated a more detailed theoretical study of the acoustic propagation of spinning modes in acoustically treated open circular ducts. In addition, the suppressor with splitter rings was modeled by using the rectangular approximation to the annular duct. The theoretical models were used to determine optimum impedance and maximum attenuation for several spinning lobe numbers from 0 to 50. It is found that for circular ducts the maximum possible attenuation and the optimum wall impedance are strong functions of the lobe number. For annular ducts the attenuation and optimum wall impedance are insensitive to the spinning lobe number for well cut-on modes. The results help explain why suppressors with splitter rings have been quite effective in spite of the lack of detailed information on the noise-source modal structure. Conversely, effective use of outer-wall treatment alone will require expanded knowledge of the noise-source structure. Approximate solutions are presented to help interpret the more exact theoretical results.

Rice, E. J.↗

Finite dynamic element formulation for a plane triangular element

Higher order correction terms for the stiffness and inertia matrices associated with a triangular plane stress-strain finite dynamic element are developed in detail. Numerical results are presented which indicate that the adoption of these matrices along with a suitable quadratic matrix eigenproblem solver effects a significant economy in the free vibration solution of structure when compared with the analysis based on the usual finite element procedure. Finally, a FORTRAN IV computer program listing of the various relevant matrices is given.

Gupta, K. K.↗