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At least 145 records · Page 8

LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Pipeline Monitoring Using Highly Sensitive Vibration Sensor Based on Fiber Ring Cavity Laser

A vibration fiber sensor based on a fiber ring cavity laser and an interferometer based single-mode-multimode-single-mode (SMS) fiber structure is proposed and experimentally demonstrated. The SMS fiber sensor is positioned within the laser cavity, where the ring laser lasing wavelength can be swept to an optimized wavelength using a simple fiber loop design. To obtain a better signal-to-noise ratio, the ring laser lasing wavelength is tuned to the maximum gain region biasing point of the SMS transmission spectrum. A wide range of vibration frequencies from 10 Hz to 400 kHz are experimentally demonstrated. In addition, the proposed highly sensitive vibration sensor system was deployed in a field-test scenario for pipeline acoustic emission monitoring. An SMS fiber sensor is mounted on an 18” diameter pipeline, and vibrations were induced at different locations using a piezoelectric transducer. The proposed method was shown to be capable of real-time pipeline vibration monitoring.

47 OTHER INSTRUMENTATION↗

ECAR-6581 Rev 0 Hydraulic Assessment of Conceptual Design of Ring-type Spacer for MARVEL Reactor

The fuel rods in the nuclear reactor core can be deformed due to various reasons, such as thermal expansion, the effect of irradiation, hydrodynamic effects, etc. The deformation of the fuel rods can lead to contact between them, which can deteriorate the coolability of the nuclear fuel and increase the potential risk of failure. To prevent the fuel rods from coming into contact with each other, a ring-type spacer may be introduced in the MARVEL reactor. However, the ring spacers can result in an additional pressure drop, which could restrict the natural circulation operation of the MARVEL reactor. Therefore, this ECAR will examine the additional pressure drop caused by the introduction of the ring-type spacer by comparing with the bare rod condition.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

Ce IV 70 Oxosulfate Rings, Frameworks, Supramolecular Assembly, and Redox Activity**

Abstract M IV molecular oxo‐clusters (M=Zr, Hf, Ce, Th, U, Np, Pu) are prolific in bottoms‐up material design, catalysis, and elucidating reaction pathways in nature and in synthesis. Here we introduce Ce 70 , a wheel‐shaped oxo‐cluster, [Ce IV 70 (OH) 36 (O) 64 (SO 4 ) 60 (H 2 O) 10 ] 4− . Ce 70 crystallizes into intricate high pore volume frameworks with divalent transition metals and Ce‐monomer linkers. Eight crystal‐structures feature four framework types in which the Ce 70 ‐rings are linked as propellers, in offset‐stacks, in a tartan pattern, and as isolated rings. Small‐angle X‐ray scattering of Ce 70 dissolved in butylamine, with and without added cations (Ce IV , alkaline earths, Mn II ), shows the metals‘ differentiating roles in ring linking, leading to supramolecular assemblies. The large acidic pores and abundant terminal sulfates provide ion‐exchange behavior, demonstrated with U IV and Nd III . Frameworks featuring Ce III/IV ‐monomer linkers demonstrate both oxidation and reduction. This study opens the door to mixed‐metal, highly porous framework catalysts, and new clusters for metal‐organic framework design

Colliard, Ian↗

Ce IV 70 oxosulfate rings, frameworks, supramolecular assembly and redox activity

M IV molecular oxo-clusters (M=Zr, Hf, Ce, Th, U, Np, Pu) are prolific in bottoms-up material design, catalysis, and elucidating reaction pathways in nature and in synthesis. Here we introduce Ce 70 , a wheel-shaped oxo-cluster, [Ce IV 70 -(OH) 36 (O) 64 (SO 4 ) 60 (H 2 O) 10 ] 4- . Ce 70 crystallizes into intricate high pore volume frameworks with divalent transition metals and Ce-monomer linkers. Eight crystal-structures feature four framework types in which the Ce 70 -rings are linked as propellers, in offset-stacks, in a tartan pattern, and as isolated rings. In this work, small-angle X-ray scattering of Ce 70 dissolved in butylamine, with and without added cations (Ce IV , alkaline earths, Mn II ), shows the metals‘ differentiating roles in ring linking, leading to supramolecular assemblies. The large acidic pores and abundant terminal sulfates provide ion-exchange behavior, demonstrated with U IV and Nd III . Frameworks featuring Ce III/IV -monomer linkers demonstrate both oxidation and reduction. Furthermore, this study opens the door to mixed-metal, highly porous framework catalysts, and new clusters for metal-organic framework design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing Effects of Electron Addition to Polycyclic Conjugated Hydrocarbons Containing Four‐Membered Rings

The rectangular cyclobutadiene (CBD, C 4 H 4 ) is a unique moiety for building nonbenzenoid polycyclic conjugated hydrocarbons with interesting electron‐accepting properties. Herein, the investigation on chemical reduction of several CBD‐containing polycyclic hydrocarbons with increasing conjugation length is reported: biphenylene (C 12 H 8 ), dimethyl[2]naphthalene (C 22 H 16 ), and tetramethyl‐dibenzo‐[3]phenylene (C 30 H 22 ). The two‐step sequential reduction is first demonstrated by in situ spectroscopic investigation and then confirmed by the isolation of single crystals of the reduced products. The X‐ray crystallographic analysis reveals the formation of several mono‐ and doubly reduced products in solvent‐separated and complexed forms. The crystal structures for both neutral parents and corresponding reduced products unravel the changes in bond alternation in each ring of the fused systems. Density functional theory (DFT) and nucleus‐independent chemical shift (NICS) scan calculations reveal that the two‐electron addition reduces the aromatic character in the benzenoid rings but has minor influence on the antiaromatic CBD rings.

Zhu, Yikun [Department of Chemistry University at ↗

Electron‐Deficient and Quinoid Central Unit Engineering for Unfused Ring‐Based A 1 –D–A 2 –D–A 1 ‐Type Acceptor Enables High Performance Nonfullerene Polymer Solar Cells with High V oc and PCE Simultaneously

Abstract Here, a pair of A 1 –D–A 2 –D–A 1 unfused ring core‐based nonfullerene small molecule acceptors (NF‐SMAs), BO2FIDT‐4Cl and BT2FIDT‐4Cl is synthesized, which possess the same terminals (A 1 ) and indacenodithiophene unit (D), coupling with different fluorinated electron‐deficient central unit (difluorobenzoxadiazole or difluorobenzothiadiazole) (A 2 ). BT2FIDT‐4Cl exhibits a slightly smaller optical bandgap of 1.56 eV, upshifted highest occupied molecular orbital energy levels, much higher electron mobility, and slightly enhanced molecular packing order in neat thin films than that of BO2FIDT‐4Cl . The polymer solar cells (PSCs) based on BT2FIDT‐4Cl:PM7 yield the best power conversion efficiency (PCE) of 12.5% with a V oc of 0.97 V, which is higher than that of BO2FIDT‐4Cl ‐based devices (PCE of 10.4%). The results demonstrate that the subtle modification of A 2 unit would result in lower trap‐assisted recombination, more favorable morphology features, and more balanced electron and hole mobility in the PM7:BT2FIDT‐4Cl blend films. It is worth mentioning that the PCE of 12.5% is the highest value in nonfused ring NF‐SMA‐based binary PSCs with high V oc over 0.90 V. These results suggest that appropriate modulation of the quinoid electron‐deficient central unit is an effective approach to construct highly efficient unfused ring NF‐SMAs to boost PCE and V oc simultaneously.

Zhang, Chao↗

Thermal loading analysis of the ring injection dump for the Spallation Neutron Source facility

The ring injection dump (RID) is the largest beam dump in the Spallation Neutron Source facility at Oak Ridge National Laboratory and accepts a fraction of the beam from the ring that is not captured in the ring during injection. Thermo-fluid modeling of the RID components was performed during the initial design by using the software ANSYS CFX to characterize the power rating for the RID. From the calculations, the power rating was lowered from 200 kW to 150 kW, at 1.3 GeV beam energy due to concerns regarding the heating of the concrete structure. The Proton Power Upgrade project scope included reevaluating the power limit to the RID in anticipation that increasing it would provide more operational flexibility. The focus was on the shielding because it was the limiting factor, and data collected from thermocouples installed on the structure were used to benchmark the analysis. A three-stage process was adopted in the latest study. First, the already existing steady-state calculations were validated and extended with the latest Monte Carlo N-Particle source term calculations. Second, transient calculations were conducted to capture the dynamic state of the system in response to the energy dumped to the RID during the following operational period of the beam from 2005–2019 (14 years), and sensitivity analyses of crucial parameters were performed to benchmark the model with reasonable accuracy. Finally, an idealized transient cycle analysis was conducted with realistic duty factors to predict the temperature distribution at higher beam powers. Overall, the results confirmed the accuracy of the original steady state model but allowed the development of a new validated transient model with higher accuracy for future analyses.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Formation of five-membered ring structures via reactions of o -benzyne

The formation of five-membered ring structures is important for the generation of curved and bowl-shaped polycyclic aromatic hydrocarbons (PAHs) under combustion conditions. Here, we report the identification of the indenyl (C 9 H 7 ) radical – the simplest aromatic hydrocarbon radical carrying an adjacent five- and six-membered ring, as the major product of the o-benzyne (o-C 6 H 4 ) reaction with propargyl (C 3 H 3 ). Because real flames exhibit a complex chemistry, elucidation of a specific reaction is very challenging. Instead, we studied the o-C 6 H 4 + C 3 H 3 reaction in a resistively heated microtubular SiC reactor at controlled conditions of 1150 K and a pressure near 10–20 Torr. To this end, the reactants o-benzyne and propargyl were pyrolytically generated from benzoyl chloride and propargyl bromide. We identified the reactants and the indenyl radical isomer-selectively utilizing photoion mass-selected threshold photoelectron spectroscopy (ms-TPES). In conclusion, the experimentally observed predominant formation of indenyl radicals finally confirms the theoretical predictions of Matsugi and Miyoshi [Phys. Chem. Chem. Phys. 14 (2012), 9722–9728] and highlights a versatile route for the formation of five-membered rings and curved PAHs via reactions of o-benzyne that favor the formation of multiring species over aliphatically substituted aromatic species.

Molecular-weight growth↗

Vortex bursting and associated twist dynamics on helical vortex tubes and vortex rings

The interaction of opposite-signed twist waves on vortex tubes can lead to vortex bursting, a process where the core expands into a double ring-like structure with strong swirling flows. Previous works have studied vortex bursting on rectilinear vortices by axially perturbing the initial core size to generate the twist waves, and observed largely axisymmetric bursting dynamics. In this work, we numerically study bursting on vortical structures with curved centrelines, analysing the interaction between the centreline dynamics, twist wave generation and propagation, and vortex bursting. We focus on axially perturbed helical vortex tubes with small radius-to-pitch ratios up to$0.0625$, as well as vortex rings with a large radius-to-core size ratio$10$, both at a circulation-based Reynolds number$5000$. The results show that though the initial twist wave propagation speeds are relatively unaffected by the curvature and torsion of the centreline, the bursting process is altered significantly compared with rectilinear vortices. The self-induced rotation of the centreline of the helical tube induces a non-axisymmetric distortion of the bursting structure, which rapidly breaks up the vortex core into small-scale helical structures. A similar destabilization of the bursting structure also occurs on vortex rings. The enstrophy increase and accelerated energy decay associated with bursting are predominantly determined by the twist wave strength, rather than the curvature and torsion of the centreline. Combined, our findings imply that bursting could play an important role in transferring and dissipating energy of vortical structures in wakes, and turbulent flows in general.

Mechanics↗

Identifying Order and Disorder in Double Four-Membered Rings via Raman Spectroscopy during Crystallization of LTA Zeolite

Fluoride (F – ) has been essential for the synthesis of low-defect siliceous zeolites. It has been hypothesized that F – balances the positive charges from organic structure-directing agents (OSDAs) and stabilizes key building units during zeolite crystallization such as the double four-membered ring (D4R). However, due to the lack of characterization techniques for investigating medium-range structures, including rings and cages formed during zeolite crystallization, the roles of F – in stabilizing building units and maintaining local charge balance during zeolite assembly are not yet fully understood. Here, the crystallization of siliceous Linde type A (LTA) zeolite in the presence of F – was investigated using Raman spectroscopy and periodic density functional theory (DFT) calculations. We have discovered that the F – -filled double four-membered ring (F – /D4R) and the empty D4R exhibit rather distinct Raman features. Both the F – /D4R and empty D4R are formed in the LTA zeolite synthesized in the presence of F – using 1,2-dimethyl-3-(4-methylbenzyl) imidazolium as the OSDA. Observed Raman bands of the F – /D4R and empty D4R, along with predictive DFT calculations on LTA supercells, reveal an ordered distribution of these two D4R units in the final as-made LTA zeolite. The discovery of these distinct Raman signatures of F – /D4R and empty D4R units opens an interesting new window for studying defects in the D4R during zeolite formation. In particular, we have observed variation in Raman intensities of F – /D4R and empty D4R bands during LTA crystallization; periodic DFT calculations indicate that the observed Raman behavior is consistent with empty D4R units containing one or two Si vacancies surrounded by Q 3 Si—consistent also with solid-state nuclear magnetic resonance measurement. These defects appear to heal during further crystallization, leading to the formation of defect-free LTA zeolite crystals. Altogether, our results provide deeper understanding on the roles of F – in charge balancing and stabilizing intact D4R units during zeolite formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The UV Photoinduced Ring-Closing Reaction of Cyclopentadiene Probed with Ultrafast Electron Diffraction

Conjugated cyclic organic molecules are common across many fields such as pharmaceuticals, are naturally occurring in biological systems, and are used in synthetic materials. One particular area of interest from a photochemical point of view is the formation of highly strained cyclic organics. We investigate the photoinduced reaction of cyclopentadiene, a five-membered organic ring molecule which can form strained three and four carbon rings after photoexcitation with UV light, with the gas-phase ultrafast electron diffraction instrument at the SLAC MeV-UED facility. Electron diffraction offers a direct probe sensitive to the nuclear geometry during the reaction, allowing for the determination of the distribution of products formed following photoexcitation. We observe the simultaneous formation of the highly strained ring- closed bicyclo[2.1.0]pentene and vibrationally hot cyclopentadiene within the temporal resolution of the experiment, and determine the relative yield of all reaction products. Furthermore, the experimental results are in good agreement with the predictions of trajectory simulations.

Computational Chemistry↗

Capturing Ring Opening in Photoexcited Enolic Acetylacetone upon Hydrogen Bond Dissociation by Ultrafast Electron Diffraction

Photoinduced biological and chemical reactions are often based on key structural transformations of a molecule driven across multiple electronic states. Acetylacetone (AcAc) is a prototypical system for complex chemical pathways involving several conical intersections (CI) and singlet–triplet intersystem crossings (ISC) characterized by distinct geometries. In the gas phase, AcAc is predominantly in a planar ring-like enolic form stabilized by a strong intramolecular O–H···O hydrogen bond. Following excitation into the S 2 (ππ*) state at 266 nm, acetylacetone undergoes rapid internal conversion followed by intersystem crossing. Such relaxation pathways are associated with structural changes including ring opening, deplanarization, and bond elongation. In this work, ultrafast electron diffraction (UED) at the SLAC MeV-UED setup is employed as a direct structural probe with a time resolution of 160 fs. Together with trajectory surface hopping simulations, analysis of the UED data provides a new perspective on the early time nuclear dynamics in acetylacetone. Specifically, AcAc is observed to undergo ring opening, deplanarization, and bond elongation all within the first 700 fs after photoexcitation. The monitored dynamics is associated mainly with the nuclear motion on the S 1 potential energy surface, formed after very rapid transfer from S 2 to S 1 , allowing AcAc to reach the conical intersection to intersystem crossing. Such time scales of nuclear motion are contrasted with the time scales of electronic transitions in AcAc that were previously characterized with spectroscopic methods, specifically internal conversion (<100 fs) and intersystem crossing (∼1.5 ps).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resolving Competing Ultraviolet Photoinduced Ring-Opening and Dissociation Pathways in Iodothiophenes by Ultrafast Electron Diffraction

The ultraviolet photochemistry of halothiophenes is thought to proceed via competing pathways, prompt C–X (X = halogen) bond fission, and parent ring opening followed by fragmentation, yet direct structural evidence distinguishing these mechanisms is limited. Here, time-resolved gas-phase ultrafast electron diffraction (UED) has been used to directly follow the structural dynamics of 2- and 3-iodothiophene following photoexcitation at 247 nm. For both isomers, the time-resolved pair distribution functions reveal the appearance of new interatomic distances that cannot be explained by simple C–I bond cleavage and formation of C 4 SH 3 radical cofragments. The signatures, particularly those for 2-iodothiophene, are consistent with a rival ring-opening channel of the intact parent, which evolve on time scales distinct from those associated with the direct C–I bond cleavage. In addition, the extracted kinetics indicate that the ring-opening channel occurs faster in 2-iodothiophene than in the 3-isomer at this excitation wavelength. Furthermore, these measurements provide direct geometric evidence for competing pathways leading to different structures following photodissociation in a model heteroaromatic and further establish UED as a sensitive probe of complex excited-state chemistry.

Bond cleavage↗

Random Knotting in Fractal Ring Polymers

Many ring polymer systems of physical and biological interest exhibit both pronounced topological effects and nontrivial self-similarity, but the relationship between these two phenomena has not yet been clearly established. Here, we use theory and simulation to formulate such a connection by studying a fundamental topological property—the random knotting probability—for ring polymers with varying fractal dimension, d f . Using straightforward scaling arguments, we generalize a classic mathematical result, showing that the probability of a trivial knot decays exponentially with chain size, N, for all fractal dimensions: P 0 (N) ∝ exp(–N/N 0 ). However, no such simple considerations can account for the dependence of the knotting length, N 0 , on d f , necessitating a more involved analytical calculation. This analysis reveals a complicated double-exponential dependence, which is well supported by numerical data. By contrast, functional forms typical of simple scaling theories fail to adequately describe the observations. These findings are equally valid for two-dimensional ring polymer systems, where “knotting” is defined as the intersection of any two segments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward Efficient Entropic Recycling by Mastering Ring–Chain Kinetics

Traditional chemical recycling approaches for condensation polymers suffer compounding energy losses and CO 2 emissions across multiple polymerization and depolymerization cycles. Entropic recycling can address these energy losses by entrapping free energy within the deconstruction products. Entropic recycling involves depolymerization to macrocyclic monomers, but such processes have not been feasible due to the high dilutions typically required to generate macrocyclic compounds. Here, we leverage selective catalysis to allow entropic recycling at concentrations 20–2000× higher than typical for macrocyclization reactions. We find that Ru-based olefin metathesis catalysts containing bulky iodine ligands significantly bias the ring–chain kinetic product distribution during ring-closing metathesis (RCM) toward the formation of oligomeric cycloalkenes. Further improvements in reaction concentration and macrocycle yield are obtained by using high catalyst loadings and by predisposing the alkene substrates to undergo favorable macrocyclization. These RCM optimizations translate effectively to cyclodepolymerization (CDP) of an olefin-containing polymer, with RCM and CDP affording similar macrocycle product distributions under identical reaction conditions. Macrocycle polymerization by entropy-driven ring-opening metathesis provides much higher molecular weight polymers than condensation polymerization of linear analogues, reducing the time to achieve high molecular weight from hours to minutes and enabling polymerization at room temperature. Finally, our findings re-emphasize the importance of energy consumption during a polymer’s lifecycle and provide a framework for the design of efficient entropic recycling systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

U–C Bond Insertion, Ring-Opening, and C–H Activation in a Uranium Bis(diisopropylamino)cyclopropenylidene (BAC) Adduct

Reaction of [U(NR 2 ) 3 ] (R = SiMe 3 ) with 1 equiv of bis(diisopropylamino)cyclopropenylidene (BAC) in Et 2 O results in the formation of [(NR 2 ) 3 U(BAC)] (1), which can be isolated in modest yields. Thermolysis of 1 in C 6 D 6 at 85 °C results in the formation of the ring-opened U(IV) product, [(NR 2 ) 2 U{N(R)(SiMe 2 CH=C(NiPr 2 )C(NiPr 2 )=CH)}] (2), which can be isolated in low yields. Mechanistic studies suggest that the formation of 2 proceeds via dissociation of BAC from 1 to regenerate [U(NR 2 ) 3 ], which converts into [U{N(R)(SiMe 2 CH 2 )}(NR 2 ) 2 ] at the elevated temperatures. BAC then inserts into the U–C bond of [U{N(R)(SiMe 2 CH 2 )}(NR 2 ) 2 ] to generate a cyclopropenyl intermediate, which undergoes ring opening and C–H activation to afford the final product, 2. We hypothesize that the ring-opening generates an unobserved carbene intermediate. Notably, thermolysis of a 1:1 mixture of independently prepared [U{N(R)(SiMe 2 CH 2 )}(NR 2 ) 2 ] and BAC results in clean formation of 2, providing strong support for the proposed mechanism. The formulations of both 1 and 2 were confirmed by X-ray crystallography. Finally, theoretical calculations indicate that the hypothesized uranium carbene intermediate features strong U–C bonding, potentially with some carbyne character in the electronic structure.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Ring-Opening Dynamics of the Cyclopropyl Radical and Cation: the Transition State Nature of the Cyclopropyl Cation

Here, we provide compelling experimental and theoretical evidence for the transition state nature of the cyclopropyl cation. Synchrotron photoionization spectroscopy employing coincidence techniques together with a novel simulation based on high-accuracy ab initio calculations reveal that the cation is unstable via its allowed disrotatory ring-opening path. The ring strains of the cation and the radical are similar, but both ring opening paths for the radical are forbidden when the full electronic symmetries are considered. These findings are discussed in light of the early predictions by Longuet-Higgins alongside Woodward and Hoffman; we also propose a simple phase space explanation for the appearance of the cyclopropyl photoionization spectrum. The results of this work allow the refinement of the cyclopropane C–H bond dissociation energy, in addition to the cyclopropyl radical and cation cyclization energies, via the Active Thermochemical Tables approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗