Behaviour of fused silica capillaries subjected to gamma radiation. Part 2: Physical aspects

Five commercial varieties of uncoated fused silica capillary tubing used in high resolution gas chromatography were subjected to cobalt-60 gamma radiation. The advantages and superior performance of fused silica open tubular columns coated with OV-1 and subsequently immobilized or crosslinked in situ by radiation is reported in a previous paper in this Journal; however, in this investigation a loss in flexibility of irradiated capillaries was also noted. Quantitative measurements on flexibility were performed on specimens of irradiated fused silica capillaries, indicating that changes do indeed occur upon irradiation. Scanning electron micrographs also illustrate slight deterioration of the outer protective polyimide coating. Most surprisingly, it was also established that a variation does exist in the flexibility of the commercially available raw material studied.     

Surflex-Dock 2.1: Robust performance from ligand energetic modeling,ring flexibility,and knowledge-based search

The Surflex flexible molecular docking method has been generalized and extended in two primary areas related to the search component of docking. First, incorporation of a small-molecule force-field extends the search into Cartesian coordinates constrained by internal ligand energetics. Whereas previous versions searched only the alignment and acyclic torsional space of the ligand, the new approach supports dynamic ring flexibility and all-atom optimization of docked ligand poses. Second, knowledge of well established molecular interactions between ligand fragments and a target protein can be directly exploited to guide the search process. This offers advantages in some cases over the search strategy where ligand alignment is guided solely by a “protomol” (a pre-computed molecular representation of an idealized ligand). Results are presented on both docking accuracy and screening utility using multiple publicly available benchmark data sets that place Surflex’s performance in the context of other molecular docking methods. In terms of docking accuracy, Surflex-Dock 2.1 performs as well as the best available methods. In the area of screening utility, Surflex’s performance is extremely robust, and it is clearly superior to other methods within the set of cases for which comparative data are available, with roughly double the screening enrichment performance.     

Inside Back Cover: Rigid-Flexible Hybrid Porous Molecular Crystals with Guest-Induced Reversible Crystallinity (Angew. Chem. Int. Ed. 13/2023)

A weak CH/O hydrogen-bonded organic framework (HOF) with both rigidity and flexibility that could easily and reversibly switch from a non-crystalline to a crystalline phase was constructed. The specific solvent molecule acts as a “key” to control the crystallinity, while the highly rigid triangle macrocycle as the building block is the “lock”. The introduction and removal of the “key” could influence the local flexibility of the whole framework and lead to switchable crystallinity. Furthermore, the obtained HOF exhibits excellent separation efficiency for benzene and cyclohexane (94.4 %).     

Crossover Sorption of C2H2/CO2 and C2H6/C2H4 in Soft Porous Coordination Networks

Porous sorbents are materials that are used for various applications, including storage and separation. Typically, the uptake of a single gas by a sorbent decreases with temperature, but the relative affinity for two similar gases does not change. However, in this study, we report a rare example of “crossover sorption,” in which the uptake capacity and apparent affinity for two similar gases reverse at different temperatures. We synthesized two soft porous coordination polymers (PCPs), [Zn₂(L1)(L2)₂]_n (PCP-1) and [Zn₂(L1)(L3)₂]_n (PCP-2) (L1= 1,4-bis(4-pyridyl)benzene, L2=5-methyl-1,3-di(4-carboxyphenyl)benzene, and L3=5-methoxy-1,3-di(4-carboxyphenyl)benzene). These PCPs exhibits structural changes upon gas sorption and show the crossover sorption for both C₂H₂/CO₂ and C₂H₆/C₂H₄, in which the apparent affinity reverse with temperature. We used in situ gas-loading single-crystal X-ray diffraction (SCXRD) analysis to reveal the guest inclusion structures of PCP-1 for C₂H₂, CO₂, C₂H₆, and C₂H₄ gases at various temperatures. Interestingly, we observed three-step single-crystal to single-crystal (sc-sc) transformations with the different loading phases under these gases, providing insight into guest binding positions, nature of host–guest or guest-guest interactions, and their phase transformations upon exposure to these gases. Combining with theoretical investigation, we have fully elucidated the crossover sorption in the flexible coordination networks, which involves a reversal of apparent affinity and uptake of similar gases at different temperatures. We discovered that this behaviour can be explained by the delicate balance between guest binding and host–guest and guest-guest interactions.     

Robust Proton Conduction against Mechanical Stress in Flexible Free-Standing Membrane Composed of Two-Dimensional Coordination Polymer

Introduction of mechanical flexibility into proton-conducting coordination polymers (CPs) is in high demand for future protonic applications such as fuel cells and hydrogen sensors. Although such mechanical properties have been primarily investigated in one-dimensional (1D) CPs, in this study, we successfully fabricated highly flexible free-standing CP membranes with a high surface-to-volume ratio, which is beneficial for enhanced performance in the aforementioned applications. We fabricated a layered CP, Cu₂(NiTCPP) (H₄(H₂TCPP); 5,10,15,20-tetrakis(4-carboxyphenyl) porphyrin), in which a two-dimensional (2D) square grid sheet composed of tetradentate nickel porphyrins and paddlewheel-type copper dimers was connected to each other by weak van der Waals forces. The mechanical flexibility was evaluated by bending and tensile tests. The flexural and Young's moduli of the membrane were significantly higher than those of conventional Nafion membranes. Electrochemical impedance spectroscopy analysis revealed that the in-plane proton conductivity of the membrane was maintained even under applied bending stress. Because the X-ray diffraction analysis indicates that the proton-conducting pathway through the hydrogen bonding network remains intact during the bending operation, our present study provides a promising strategy for the fabrication of new and advanced 2D CPs without using substrates or additional polymers for protonic devices.     

Protein–ligand docking with multiple flexible side chains

In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For these cases, we identify the side chains to be made flexible during docking calculation by superimposing receptors and analyzing steric overlap between various ligands and receptor side chains. We demonstrate that allowing these side chains to assume rotameric conformations enables the successful cross docking of 19 complexes (ligand all atom RMSD < 2.0 A) using our docking software FLIPDock. The number of side receptor side chains interacting with a ligand can vary according to the ligand's size and shape. Hence, when starting from a complex with a particular ligand one might have to extend the region of potential interacting side chains beyond the ones interacting with the known ligand. We discuss distance-based methods for selecting additional side chains in the neighborhood of the known active site. We show that while using the molecular surface to grow the neighborhood is more efficient than Euclidian-distance selection, the number of side chains selected by these methods often remains too large and additional methods for reducing their count are needed. Despite these difficulties, using geometric constraints obtained from the network of bonded and non-bonded interactions to rank residues and allowing the top ranked side chains to be flexible during docking makes 22 out of 25 complexes successful.     

Molecular modeling study of DNA abasic sites

We use molecular modeling calculations to study the structure and the flexibility of abasic (AP sites) and for the design of anticancer drugs targeted against AP sites. For either adenine or cytosine on the opposing strand within the same sequence context, the results are in line with experimental data which show that the two unpaired bases lead to intrahelical forms, but with differences in induced curvature. Results on flexibility, indicate that the two duplexes have the same bending rigidity for cytosine. In previous work a series of polyfunctional molecules, such as ATAc, were designed to selectively recognize and cleave abasic sites in DNA. The nitrobenzamide group which was added to the ATAc molecule to obtain a new molecule, termed ATAc4, can induce a second lesion under irradiation in close proximity to the abasic site. The different conformations of ATAc4 interacting with a DNA oligomer containing a stable analog of the abasic site were compared to the photoinduced cleavage pattern observed experimentally. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 12 May 2000     

Formability and properties of self-standing clay film by montmorillonite with different interlayer cations

Influences of exchangeable interlayer cations were investigated on self-standing film formability, film morphology, and properties of the clay films such as flexibility and gas barrier property. Ion-exchanged montmorillonite samples were prepared by a cation exchange from naturally bearing cation, mostly Na⁺, to Li⁺, Mg²⁺, Ca²⁺, Al³⁺, and Fe^{2+, 3+}. Self-standing films were prepared from aqueous colloidal dispersions of these montmorillonite samples with no additives. The montmorillonite samples with monovalent or divalent cation formed flat self-standing films while the Al-montmorillonite sample produced a distorted film. The Fe-montmorillonite sample formed many separated reddish-brown rod-shaped pieces. Clay film microstructures were different with interlayer cations. The films with monovalent interlayer cations were constructed by the stacking of units with delicately waved thin clay sheets in the whole film, but other films show different morphologies between the upper side and lower side; the upper side is laminated with thin sheets; the lower side is laminated with large thick sheets.The self-standing films’ flexibility and gas barrier property differed according to the interlayer cations. These properties were good in cases of samples with monovalent cations. The innumerable short wave and sheet thinness are considered to foster good flexibility and gas barrier properties. The differences in film formability and properties of the films are attributable to different swellability among samples with different interlayer cations. The montmorillonite samples with monovalent cations swell sufficiently by water, but those with polyvalent cations swell poorly. In the latter case, clay crystals aggregate in water, then the aggregate grows into large particles, creating a film with large particles.     

Graphs with flexible labelings allowing injective realizations

We consider realizations of a graph in the plane such that the distances between adjacent vertices satisfy the constraints given by an edge labeling. If there are infinitely many such realizations, counted modulo rigid motions, the labeling is called flexible. The existence of a flexible labeling, possibly non-generic, has been characterized combinatorially by the existence of a so called NAC-coloring. Nevertheless, the corresponding realizations are often non-injective. In this paper, we focus on flexible labelings with infinitely many injective realizations. We provide a necessary combinatorial condition on existence of such a labeling based also on NAC-colorings of the graph. By introducing new tools for the construction of such labelings, we show that the necessary condition is also sufficient up to 8 vertices, but this is not true in general for more vertices.     

Static analysis of Euler–Bernoulli beams with multiple unilateral cracks under combined axial and transverse loads

The paper deals with the static analysis of pre-damaged Euler–Bernoulli beams with any number of unilateral cracks and subjected to tensile or compression forces combined with arbitrary transverse loads. The mathematical representation of cracks with a bilateral behaviour (i.e. always open) via Dirac delta functions is extended by introducing a convenient switching variable, which allows each crack to be open or closed depending on the sign of the axial strain at the crack centre. The proposed model leads to analytical solutions, which depend on four integration constants (to be computed by enforcing the boundary conditions) along with the Boolean switching variables associated with the cracks (whose role is to turn on and off the additional flexibility due to the presence of the cracks). An efficient computational procedure is also presented and numerically validated. For this purpose, the proposed approach is applied to two pre-damaged beams, with different damage and loading conditions, and the results so obtained are compared against those given by a standard finite element code (in which the correct opening of the cracks is pre-assigned), always showing a perfect agreement.