The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis
Abstract not provided
Fenwick, Michael K.↗
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A mononuclear nonheme {FeNO} 6 complex: synthesis and structural and spectroscopic characterization
While the synthesis and characterization of {FeNO} 7,8,9 complexes have been well documented in heme and nonheme iron models, {FeNO} 6 complexes have been less clearly understood. Herein, we report the synthesis and structural and spectroscopic characterization of mononuclear nonheme {FeNO} 6 and iron(III)–nitrito complexes bearing a tetraamido macrocyclic ligand (TAML), such as [(TAML)Fe III (NO)] - and [(TAML)Fe III (NO 2 )] 2- , respectively. First, direct addition of NO (g) to [Fe III (TAML)] - results in the formation of [(TAML)Fe III (NO)] - , which is sensitive to moisture and air. The spectroscopic data of [(TAML)Fe III (NO)] - , such as 1 H nuclear magnetic resonance and X-ray absorption spectroscopies, combined with computational study suggest the neutral nature of nitric oxide with a diamagnetic Fe center (S = 0). We also provide alternative pathways for the generation of [(TAML)Fe III (NO)] - , such as the iron–nitrite reduction triggered by protonation in the presence of ferrocene, which acts as an electron donor, and the photochemical iron–nitrite reduction. To the best of our knowledge, the present study reports the first photochemical nitrite reduction in nonheme iron models.
36 MATERIALS SCIENCE↗
Structural dynamics of a thermally silent triiron( II ) spin crossover defect grid complex
The structural evolution of spin crossover (SCO) complexes during their spin transition at equilibrium and out-of-equilibrium conditions needs to be understood to enable their successful utilisation in displays, actuators and memory components. In this study, diffraction techniques were employed to study the structural changes accompanying the temperature increase and the light irradiation of a defect [2 × 2] triiron(II) metallogrid of the form [Fe II 3 L H 2 (HL H ) 2 ](BF 4 ) 4 ·4MeCN (FE3), L H = 3,5-bis{6-(2,2'-bipyridyl)}pyrazole. Although a multi-temperature crystallographic investigation on single crystals evidenced that the compound does not exhibit a thermal spin transition, the structural analysis of the defect grid suggests that the flexibility of the grid, provided by a metal-devoid vertex, leads to interesting characteristics that can be used for intermolecular cooperativity in related thermally responsive systems. Time-resolved photocrystallography results reveal that upon excitation with a ps laser pulse, the defect grid shows the first two steps of the out-of-equilibrium process, namely the photoinduced and elastic steps, occurring at the ps and ns time scales, respectively. Similar to a previously reported [2 × 2] tetrairon(II) metallogrid, FE3 exhibits a local distortion of the entire grid during the photoinduced step and a long-range distortion of the lattice during the elastic step. Although the lifetime of the pure photoinduced high spin (HS) state is longer in the tetranuclear grid than in the defect grid, suggesting that the global nuclearity plays a crucial role for the lifetime of the photoinduced species, the influence of the co-crystalising solvent on the lifetime of the photoinduced HS state remains unknown. This study sheds light on the out-of-equilibrium dynamics of a thermally silent defect triiron SCO metallogrid.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site
Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.
59 BASIC BIOLOGICAL SCIENCES↗
Block-structured grids for complex aerodynamic configurations: Current status
The status of CFD methods based on the use of block-structured grids for analyzing viscous flows over complex configurations is examined. The objective of the present study is to make a realistic assessment of the usability of such grids for routine computations typically encountered in the aerospace industry. It is recognized at the very outset that the total turnaround time, from the moment the configuration is identified until the computational results have been obtained and postprocessed, is more important than just the computational time. Pertinent examples will be cited to demonstrate the feasibility of solving flow over practical configurations of current interest on block-structured grids.
Vatsa, Veer N.↗
Variable-complexity aerodynamic-structural design of a high-speed civil transport wing
A variable-complexity strategy of combining simple and detailed analysis methods is presented for the design optimization of a high-speed civil transport (HSCT) wing. Two sets of results are shown: the aerodynamic design of the wing using algebraic weight equations for structural considerations, and optimization results of the internal wing structure for a fixed wing configuration. We show example results indicating that using simple analysis methods alone for the calculation of a critical constraint can allow an optimizer to exploit weaknesses in the analysis. The structural optimization results provide a valuable check for the weight equations used in the aerodynamic design. In addition, these results confirm the need for using simple, algebraic models in conjunction with more detailed analysis methods. A strategy of interlaced aerodynanic-structural design is proposed.
Hutchison, M. G.↗
Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction
Abstract mAbs to MHC class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti–MHC-I mAb, we determined X-ray crystal structures of four complexes of anti–MHC-I Fabs bound to peptide/MHC-I/β2-microglobulin (pMHC-I). An anti–H2-Dd mAb, two anti–MHC-I α3 domain mAbs, and an anti–β2-microglobulin mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.
Immunology↗
Dynamic modeling of structures from measured complex modes
A technique is presented to use a set of identified complex modes together with an analytical mathematical model of a structure under test to compute improved mass, stiffness and damping matrices. A set of identified normal modes, computed from the measured complex modes, is used in the mass orthogonality equation to compute an improved mass matrix. This eliminates possible errors that may result from using approximated complex modes as normal modes. The improved mass matrix, the measured complex modes and the higher analytical modes are then used to compute the improved stiffness and damping matrices. The number of degrees-of-freedom of the improved model is limited to equal the number of elements in the measured modal vectors. A simulated experiment shows considerable improvements, in the system's analytical dynamic model, over the frequency range of the given measured modal information.
Ibrahim, s. R.↗
Dynamic Modeling of Structures from Measured Complex Modes
A technique is presented to use a set of identified complex modes together with an analytical mathematical model of a structure under test to compute improved mass, stiffness and damping matrices. A set of identified normal modes, computed from the measured complex modes, is used in the mass orthogonality equation to compute an improved mass matrix. This eliminates possible errors that may result from using approximated complex modes as normal modes. The improved mass matrix, the measured complex modes and the higher analytical modes are then used to compute the improved stiffness and damping matrices. The number of degrees-of-freedom of the improved model is limited to equal the number of elements in the measured modal vectors. A simulated experiment shows considerable improvements, in the system's analytical dynamic model, over the frequency range of the given measured modal information.
Ibrahim, S. R.↗
Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II
Photosystem II (PSII) is a homodimeric protein complex that catalyzes water oxidation at the oxygen-evolving complex (OEC), a heterocubanoid calcium-tetra-manganese cluster. Here, we analyze the omit electron-density peaks of the OEC’s metal ions in five X-ray free-electron laser PSII structures at a resolution between 2.15 Å and 1.95 Å. The omit peaks can be described by the total number of electrons and approximated by the variance of electron density distribution when the distributions are spherically symmetric. We show that the number of electrons of metal centers are different in the two OECs of PSII dimers, implying that either the oxidation states and/or occupancies of individual metal ions are different in the two monomers. In either case, we find that the two OECs of dark-adapted PSII dimers in crystals are not fully synchronized in the same expected S 1 state. Differences in redox states of the OEC in PSII only partially account for the observation that the electron densities integrate to a smaller number of electrons than expected. Differences between the determined and expected relative electron numbers are much larger than the estimated errors, indicating heterogeneity in the OEC composition. Here, the reported findings suggest that two OECs of dark-adapted PSII crystals are typically not fully synchronized in the S 1 state and likely generate heterogeneity in the crystallographical data of PSII intermediate structures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computing virtual dark-field X-ray microscopy images of complex discrete dislocation structures from large-scale molecular dynamics simulations
Dark-field X-ray microscopy (DFXM) is a novel diffraction-based imaging technique that non-destructively maps the local deformation from crystalline defects in bulk materials. While studies have demonstrated that DFXM can spatially map 3D defect geometries, it is still challenging to interpret DFXM images of the high-dislocation-density systems relevant to macroscopic crystal plasticity. This work develops a scalable forward model to calculate virtual DFXM images for complex discrete dislocation structure(s) (DDS) obtained from atomistic simulations. Our new DDS-DFXM model integrates a non-singular formulation for calculating the local strain from the DDS and an efficient geometrical optics algorithm for computing the DFXM image from the strain field. We apply the model to complex DDS obtained from a large-scale molecular dynamics simulation of compressive loading on single-crystal silicon. Simulated DFXM images exhibit prominent contrast for dislocation features between the multiple slip systems, demonstrating the potential of DFXM to resolve features from dislocation multiplication. In conclusion, the integrated DDS-DFXM model provides a toolbox for DFXM experimental design and image interpretation in the context of bulk crystal plasticity for a range of measurements across shock plasticity and the broader materials science community.
X-ray imaging↗
Monitoring the Formation and Reactivity of Organometallic Alkane and Fluoroalkane Complexes with Silanes and Xe Using Time-Resolved X-ray Absorption Fine Structure Spectroscopy
Complexes with weakly coordinating ligands are often formed in chemical reactions and can play key roles in determining the reactivity, particularly in catalytic reactions. Using time-resolved X-ray absorption fine structure (XAFS) spectroscopy in combination with time-resolved IR (TRIR) spectroscopy and tungsten hexacarbonyl, W(CO) 6 , we are able to structurally characterize the formation of an organometallic alkane complex, determine the W–C distances, and monitor the reactivity with silane to form an organometallic silane complex. Experiments in perfluorosolvents doped with xenon afford initially the corresponding solvated complex, which is sufficiently reactive in the presence of Xe that we can then observe the coordination of Xe to the metal center, providing a unique insight into the metal–xenon bonding. These results offer a step toward elucidating the structure, bonding, and chemical reactivity of transient species by X-ray absorption spectroscopy, which has sensitivity to small structural changes. The XAFS results indicate that the bond lengths of metal–alkane (W–H–C) bond in W(CO) 5 (heptane) as 3.07 (±0.06) Å, which is longer than the calculated W–C (2.86 Å) for binding of the primary C–H, but shorter than the calculated W–C (3.12 Å) for the secondary C–H. Here, a statistical average of the calculated W–C alkane bond lengths is 3.02 Å, and comparison of this value indicates that the value derived from the XAFS measurements is averaged over coordination of all C–H bonds consistent with alkane chain walking. Photolysis of W(CO) 6 in the presence of HSiBu 3 allows the conversion of W(CO) 5 (heptane) to W(CO) 5 (HSiBu 3 ) with an estimated W–Si distance of 3.20 (±0.03) Å. Time-resolved TRIR and XAFS experiments following photolysis of W(CO) 6 in perfluoromethylcyclohexane (PFMCH) allows the characterization of W(CO) 5 (PFMCH) with a W–F distance of 2.65 (±0.06) Å, and doping PFMCH with Xe allows the characterization of W(CO) 5 Xe with a W–Xe bond length of 3.10 (±0.02) Å.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Advanced Methodology for Simulation of Complex Flows Using Structured Grid Systems
Detailed simulations of viscous flows in complicated geometries pose a significant challenge to current capabilities of Computational Fluid Dynamics (CFD). To enable routine application of CFD to this class of problems, advanced methodologies are required that employ (a) automated grid generation, (b) adaptivity, (c) accurate discretizations and efficient solvers, and (d) advanced software techniques. Each of these ingredients contributes to increased accuracy, efficiency (in terms of human effort and computer time), and/or reliability of CFD software. In the long run, methodologies employing structured grid systems will remain a viable choice for routine simulation of flows in complex geometries only if genuinely automatic grid generation techniques for structured grids can be developed and if adaptivity is employed more routinely. More research in both these areas is urgently needed.
Steinthorsson, Erlendur↗
Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and 2-hydroxyisoindoline-1,3-dione complex
Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and 2-hydroxyisoindoline-1,3-dione complex
Cui, Jiawen↗
New benzo[f]quinolino[3,4-b][1,7]naphthyridine-6,8(5H,9H)-diones: synthesis, electronic, molecular, and crystal structures. Protonation and complexation with lanthanum and europium salts
A series of novel benzo[f]quinolino[3,4-b][1,7]naphthyridine-6,8(5H,9H)-diones, which are promising ligands for the extractive separation of actinides and lanthanides, and also their complexes with lanthanum and europium were synthesized. The molecular and crystal structures of one among the ligands were determined by single crystal X-ray diffraction. The protonation of compounds was investigated by IR and NMR spectroscopy. The electronic structure of starting substances and protonated forms was estimated by DFT calculations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystal structures of inhibitor complexes of M‐PMV protease with visible flap loops
Abstract Mason‐Pfizer monkey virus protease (PR) was crystallized in complex with two pepstatin‐based inhibitors in P 1 space group. In both crystal structures, the extended flap loops that lock the inhibitor/substrate over the active site, are visible in the electron density either completely or with only small gaps, providing the first observation of the conformation of the flap loops in dimeric complex form of this retropepsin. The H‐bond network in the active site (with D26N mutation) differs from that reported for the P 2 1 crystal structures and is similar to a rarely occurring system in HIV‐1 PR.
Wosicki, Stanislaw↗
Bimolecular Reductive Elimination of Ethane from Pyridine(diimine) Iron Methyl Complexes: Mechanism, Electronic Structure, and Entry into [2+2] Cycloaddition Catalysis
The application of bimolecular reductive elimination to the activation of iron catalysts for alkene–diene cycloaddition is described. Key to this approach was the synthesis, characterization, electronic structure determination, and ultimately solution stability of a family of pyridine(diimine) iron methyl complexes with diverse steric properties and electronic ground states. Both the aryl-substituted, ( Me PDI)FeCH 3 and ( Et PDI)FeCH 3 ( R PDI = 2,6-(2,6-R 2 -C 6 H 3 N=CMe) 2 C 5 H 3 N), and the alkyl-substituted examples, ( Cy APDI)FeCH 3 ( Cy APDI = 2,6-(C 6 H 11 N=CMe) 2 C 5 H 3 N), have molecular structures significantly distorted from planarity and S = 3/2 ground states. The related N-arylated derivative bearing 2,6-di-isopropyl aryl substituents, ( iPr PDI)FeCH 3 , has an idealized planar geometry and exhibits spin crossover behavior from S = 1/2 to S = 3/2 states. At 23 °C under an N 2 atmosphere, both ( Me PDI)FeCH 3 and ( Et PDI)FeCH 3 underwent reductive elimination of ethane to form the iron dinitrogen precatalysts, [( Me PDI)Fe(N 2 )] 2 (μ-N 2 ) and [( Et PDI)Fe(N 2 )] 2 (μ-N 2 ), respectively, while ( iPr PDI)FeCH 3 proved inert to C–C bond formation. By contrast, addition of butadiene to all three iron methyl complexes induced ethane formation and generated the corresponding iron butadiene complexes, ( R PDI)Fe(η 4 -C 4 H 6 ) (R = Me, Et, i Pr), known precatalysts for the [2+2] cycloaddition of olefins and dienes. Kinetic, crossover experiments, and structural studies were combined with magnetic measurements and Mössbauer spectroscopy to elucidate the electronic and steric features of the iron complexes that enable this unusual reductive elimination and precatalyst activation pathway. Furthermore, transmetalation of methyl groups between iron centers was fast at ambient temperature and independent of steric environment or spin state, while the intermediate dimer underwent the sterically controlled rate-determining reaction with either N 2 or butadiene to access a catalytically active iron compound.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Pnictogen Bonding at the Core of a Carbene-Stiborane-Gold Complex: Impact on Structure and Reactivity
Our interest in the design of ambiphilic ligands and their coordination to gold has led us to synthesize an indazol-3-ylidene gold chloride complex functionalized at the 4-position of the indazole backbone by a stibine functionality. The antimony center of this new complex cleanly reacts with o-chloranil to afford the corresponding stiborane derivative. Structural analysis indicates that the stiborane coordination environment is best described as a distorted square pyramid whose open face is oriented toward the gold center, allowing for the formation of a long donor–acceptor, or pnictogen, Au → Sb bonding interaction. The presence of this interaction, which has been probed computationally, is also manifested in the enhanced catalytic activity of this complex in the cyclization of N-propargyl-4-fluorobenzamide.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗