Chain Molecules Research Articles

Molecular Dynamics Simulations of the Mutated Proton-Transferring a-Subunit of E. coli FoF1-ATP Synthase

The membrane Fo factor of ATP synthase is highly sensitive to mutations in the proton half-channel leading to the functional blocking of the entire protein. To identify functionally important amino acids for the proton transport, we performed molecular dynamic simulations on the selected mutants of the membrane part of the bacterial FoF1-ATP synthase embedded in a native lipid bilayer: there were nine different mutations of a-subunit residues (aE219, aH245, aN214, aQ252) in the inlet half-channel. The structure proved to be stable to these mutations, although some of them (aH245Y and aQ252L) resulted in minor conformational changes. aH245 and aN214 were crucial for proton transport as they directly facilitated H+ transfer. The substitutions with nonpolar amino acids disrupted the transfer chain and water molecules or neighboring polar side chains could not replace them effectively. aE219 and aQ252 appeared not to be determinative for proton translocation, since an alternative pathway involving a chain of water molecules could compensate the ability of H+ transmembrane movement when they were substituted. Thus, mutations of conserved polar residues significantly affected hydration levels, leading to drastic changes in the occupancy and capacity of the structural water molecule clusters (W1–W3), up to their complete disappearance and consequently to the proton transfer chain disruption.

A Hadal Streptomyces-Derived Echinocandin Acylase Discovered through the Prioritization of Protein Families

Naturally occurring echinocandin B and FR901379 are potent antifungal lipopeptides featuring a cyclic hexapeptide nucleus and a fatty acid side chain. They are the parent compounds of echinocandin drugs for the treatment of severe fungal infections caused by the Candida and Aspergilla species. To minimize hemolytic toxicity, the native fatty acid side chains in these drug molecules are replaced with designer acyl side chains. The deacylation of the N-acyl side chain is, therefore, a crucial step for the development and manufacturing of echinocandin-type antibiotics. Echinocandin E (ECE) is a novel echinocandin congener with enhanced stability generated via the engineering of the biosynthetic machinery of echinocandin B (ECB). In the present study, we report the discovery of the first echinocandin E acylase (ECEA) using the enzyme similarity tool (EST) for enzymatic function mining across protein families. ECEA is derived from Streptomyces sp. SY1965 isolated from a sediment collected from the Mariana Trench. It was cloned and heterologously expressed in S. lividans TK24. The resultant TKecea66 strain showed efficient cleavage activity of the acyl side chain of ECE, showing promising applications in the development of novel echinocandin-type therapeutics. Our results also provide a showcase for harnessing the essentially untapped biodiversity from the hadal ecosystems for the discovery of functional molecules.

Generic low-density corrections to the equation of state of chain molecules with repulsive intermolecular forces

Molecular-based equations of state for describing the thermodynamics of chain molecules are often based on mean-field like arguments that reduce the problem of describing the interactions between chains to a simpler one involving only nonbonded monomers. While for dense liquids such arguments are known to work well, at low density they are typically less appropriate due to an incomplete description of the effect of chain connectivity on the local environment of the chains’ monomer segments. To address this issue, we develop three semi-empirical approaches that significantly improve the thermodynamic description of chain molecules at low density. The approaches are developed for chain molecules with repulsive intermolecular forces; therefore, they could be used as reference models for developing equations of the state of real fluids based on perturbation theory. All three approaches are extensions of Wertheim’s first-order thermodynamic perturbation theory (TPT1) for polymerization. The first model, referred to as TPT1-v, incorporates a second-virial correction that is scaled to zero at liquid-like densities. The second model, referred to as TPT1-y, introduces a Helmholtz-energy contribution to account for correlations between next-nearest-neighbor segments within chain molecules. The third approach, called TPT-E, directly modifies TPT1 without utilizing an additional Helmholtz energy contribution. By employing TPT1 at the core of these approaches, we ensure an accurate description of mixtures and enable a seamless extension from chains of tangentially bonded hard-sphere segments of equal size to hetero-segmented chains, fused chains, and chains of soft repulsive segments (which are influenced by temperature). The low-density corrections implemented in TPT1 are designed to preserve these good characteristics, as confirmed through comparisons with novel molecular simulation results for the pressure of various chain fluids. TPT1-v exhibits excellent transferability across different chain types, but it relies on knowing the second virial coefficient of the chain molecules, which is non-trivial to obtain and determined here using Monte Carlo simulation. The TPT1-y model, on the other hand, achieves comparable accuracy to TPT1-v while being fully predictive, requiring no input besides the geometry of the chain molecules.

Effect of acylhydrazone self-healing agents with different structures on the properties of SBS modified asphalt waterproofing membrane

To prepare SBS modified asphalt (SMA) waterproofing membrane with excellent self-healing performance, in this paper, four self-healing agents (ASHA-A, ASHA-B, ASHA-C, ASHA-D) with acylhydrazone bonds and carbon-carbon double bonds (C=C) were synthesized, and were used to prepare self-healing SMA waterproofing membranes (SSMA-A, SSMA-B, SSMA-C, SSMA-D). The effects of ASHAs with different structures on the structure, high and low temperature properties, joint peel strength and self-healing performance of SSMAs were investigated. The Fourier transform infrared spectroscopy and fluorescence microscope results showed that acylhydrazone bonds of ASHAs were introduced into the chains of SBS molecules, and the SBS in SSMAs occurred crosslinking through the C=C of ASHAs and SBS, the crosslinked network structures of SBS in SSMA-C and SSMA-D were denser and more complete because ASHA-C and ASHA-D contained more C=C involved in the crosslinking reaction. The softening point and low temperature flexibility of SSMAs were enhanced by the formation of the SBS crosslinked network structure, and the optimum dosage of ASHAs was 0.6%. The joint peel strength of SSMA-A, SSMA-B, SSMA-C and SSMA-D increased by 26.68%, 31.25%, 49.52% and 56.97% compared to SMA. The introduction of acylhydrazone bonds with reversible fracture and rearrangement significantly improved the crack self-healing performance of SMA, the impermeability times of SMA, SSMA-A, SSMA-B, SSMA-C and SSMA-D were 13.28min, 37.29min, 42.53min, 53.34min and 59.67min after self-healing at 40℃ for 8h, which indicated that ASHA-D with benzene ring and multiple C=C had the best improvement in self-healing performance of SMA.

Carbene-Assisted Arene Ring-Opening.

Despite the significant achievements in dearomatization and C-H functionalization of arenes, the arene ring-opening remains a largely unmet challenge and is underdeveloped due to the high bond dissociation energy and strong resonance stabilization energy inherent in aromatic compounds. Herein, we demonstrate a novel carbene assisted strategy for arene ring-opening. The understanding of the mechanism by our DFT calculations will stimulate wide application of bulk arene chemicals for the synthesis of value-added polyconjugated chain molecules. Various aryl azide derivatives now can be directly converted into valuable polyconjugated enynes, avoiding traditional synthesis including multistep unsaturated precursors, poor selectivity control, and subsequent transition-metal catalyzed cross-coupling reactions. The simple conditions required were demonstrated in the late-stage modification of complex molecules and fused ring compounds. This chemistry expands the horizons of carbene chemistry and provides a novel pathway for arene ring-opening.

Material analysis of tool feed on scrap machines using the vibration method

Flexibility comes from the cutting force generated when the workpiece and tool react and are moved to different areas of the scrap machine. The chisel will get damaged as a result. The material and cutting speed that are used can cause damage. Given this, further studies employing the vibration method are required to determine the ways in which material affects the speed at which scrap is chopped. PVC, iron, and aluminum 5052 were the materials used in this investigation. The cutting rotational speeds varied from 32 to 80 m/min. To measure vibration, the accelerometer is positioned along the x, y, and z axes.  The measurement outputs of the accelerometer are connected to the FFT Analyzer, which performs analysis using Matlab. When comparing cutting speeds above or below 50 m/min, the research results indicate that the x-axis has the largest amplitude and the most form variants. The most widely used material is PVC, which is followed by iron and aluminum. This is because, unlike aluminum and iron, which have microstructures in the form of crystal grains, PVC is a thermoplastic polymer with a microstructure made of chain molecules. Because all of the cutting energy is used in the frictional action between the chip and the workpiece when the tool is being used, the high frequency is the result. As a result, the friction on the sliding plane is breaking up atomic or molecular bonds. Additionally, the cutting force exerts a significant amount of pressure on the tool's wearing active surface

Study on a Strong Polymer Gel by the Addition of Micron Graphite Oxide Powder and Its Plugging of Fracture

It is difficult to plug the fracture water channeling of a fractured low-permeability reservoir during water flooding by using the conventional acrylamide polymer gel due to its weak mechanical properties. For this problem, micron graphite powder is added to enhance the comprehensive properties of the acrylamide polymer gel, which can improve the plugging effect of fracture water channeling. The chemical principle of this process is that the hydroxyl and carboxyl groups of the layered micron graphite powder can undergo physicochemical interactions with the amide groups of the polyacrylamide molecule chain. As a rigid structure, the graphite powder can support the flexible skeleton of the original polyacrylamide molecule chain. Through the synergy of the rigid and flexible structures, the viscoelasticity, thermal stability, tensile performance, and plugging ability of the new-type gel can be significantly enhanced. Compared with a single acrylamide gel, after adding 3000 mg/L of micrometer-sized graphite powder, the elastic modulus, the viscous modulus, the phase transition temperature, the breakthrough pressure gradient, the elongation at break, and the tensile stress of the acrylamide gel are all greatly improved. After adding the graphite powder to the polyacrylamide gel, the fracture water channeling can be effectively plugged. The characteristics of the networked water flow channel are obvious during the injected water break through the gel in the fracture. The breakthrough pressure of water flooding is high. The experimental results are an attempt to develop a new gel material for the water plugging of a fractured low-permeability reservoir.

DISCUSSION OF THE MECHANISM OF THE ELECTRICAL CONDUCTIVITY OF PURE WATER IN THE FRAMEWORK OF THE BJERRUM MODEL

An alternative mechanism of electrical conductivity and ionization of molecules in pure water is considered. Calculation of the temperature dependence for the activation energy of ionization of water molecules was carried out using data on the value of its ionic product. The calculated activation energies for the ionization and flow processes show the presence of a certain proportionality between them. This suggests that the ionization of water is caused by intermolecular forces rather than intramolecular forces. Accordingly, the electrical conductivity of water is associated with the appearance and movement in it of L and D defects of hydrogen bonds between water molecules, which have significant electrical pseudo charges and are considered in the Bjerrum model for ice. This work proposes a new interpretation of the mechanism of ionization (pseudoionization) of molecules and generation of L and D defects in water. Rotation is considered not for one, but for two of its molecules in opposite directions with partial compensation of their angular momentum, and the breaking of not three bonds for one molecule, but four bonds with neighbors for two molecules. Moreover, these four neighbors do not include molecules from water clusters that have stronger bonds, since neighboring molecules with weaker bonds can be found for the process of rotation activation. Accordingly, the exponential contribution made by molecules from water clusters is absent or small in the ionization activation energy. In this way, the activation energy for the flow, which occurs throughout the entire volume of the liquid and automatically includes molecules from clusters, differs from the activation energy of electrical conductivity, which occurs for individual molecules in chains of bonds. The presence of a maximum in the ionic product of water near 250 ⁰C can be explained by the rapid decrease in the lifetime of L and D defects with heating, which prevents the use of the standard equation for accurate calculation of the ionization activation energy above 100...200 ⁰C. However, the presence of this maximum contradicts the generally accepted model of proton hopping between neighboring hydronium and water molecules in the mechanism of its electrical conductivity.

4-(1H-2,3-Dihydronaphtho-[1,8-de][1,3,2]di-aza-borinin-2-yl)-1-ethylpyridin-1-ium iodide monohydrate.

The cation of the title hydrated salt, C17H17BN3 +·I-·H2O, is a di-aza-borinane featuring substitution at the 1, 2, and 3 positions in the nitro-gen-boron six-membered heterocycle. The cation is approximately planar with a dihedral angle between the pyridyl ring and the di-aza-borinane ring system of 5.40 (5)°. In the crystal, the cations stack along [100] in an alternating head-to-tail manner, while the iodide ion and water mol-ecule form one-dimensional hydrogen-bonded chains beside the cation stack. The cation stacks and I--water chains are crosslinked by N-H⋯I and N-H⋯O hydrogen bonds.

Crystal structures of tri-chlorido-(4-methyl-piperidine)gold(III) and two polymorphs of tri-bromido(4-methyl-piperidine)-gold(III).

Tri-chlorido-(4-methyl-piperidine)-gold(III), [AuCl3(C6H13N)], 1, crystallizes in Pbca with Z = 8. Tri-bromido-(4-methyl-piperidine)-gold(III), [AuBr3(C6H13N)], 2, crystallizes as two polymorphs, 2a in Pnma with Z = 4 (imposed mirror symmetry) and 2b, which is isotypic to 1. The Au-N bonds trans to Cl are somewhat shorter than those trans to Br, and the Au-Cl bonds trans to N are longer than those cis to N, whereas the Au-Br bonds trans to N are slightly shorter than the cis bonds. The methyl and AuX 3 groups (X = halogen) occupy equatorial positions at the six-membered ring. The packing of all three structures involves chains of mol-ecules with offset stacking of the AuX 3 moieties associated with short Au⋯X contacts; for 1 and 2b these are reinforced by N-H⋯X hydrogen bonds, whereas for 2a there are no classical hydrogen bonds and the chains are inter-connected by Br⋯Br contacts.

Manganese Oxide / Silica catalysed Decarboxylative Ketonization of Aliphatic Carboxylic Acids in a Continuous Flow Reactor.

The sustainable synthesis of long carbon chain molecules from carbon dioxide, water and electricity relies on the development of waste-free, highly selective C-C bond forming reactions. An example for such a power-to-chemicals process is the industrial-scale fermentation for the production of hexanoic acid. Herein, we describe how this product is transformed into 6-undecanone via decarboxylative ketonization using a heterogeneous manganese oxide / silica catalyst. The reaction reaches full conversion with near-complete selectivity when carried out in a continuous flow reactor, requires no solvent or carrier gas, and releases carbon dioxide and water as the only by-products. The reactor was operated for several weeks with no loss of reactivity, producing 7 kg of 6-undecanone from 10 g of catalyst and achieving a productivity of 1.135 kg per litre of reactor volume per hour. 6-Undecanone and other long-chain ketones accessible this way can be hydrogenated to industrially meaningful alkanes, or converted into valuable fatty acids via a hydrogenation / elimination / isomerizing hydrocarboxylation sequence.

Crystallization‐Driven Optimization of Morphology and Performance in Near‐Infrared Organic Photodetectors via Alkyl Side Chain Tuning of Narrow Bandgap Non‐Fullerene Acceptors

AbstractNarrow bandgap non‐fullerene acceptors (NBG NFAs) are crucial in advancing near‐infrared organic photodetectors (NIR OPDs). However, the polymorphous behavior of NFAs introduces energetic disorder and charge‐trapping sites in the bulk heterojunction (BHJ) active layers, thereby hindering the NIR performance of OPDs. This study demonstrates the design and optimization of the molecular structures of alkyl side chains in NFAs to morphologically address these electrical limitations and shed light on how side chains affect the crystallization‐driven control of the morphogenesis process in BHJ layers. The structure, linearity, and length of the alkyl side chain molecules are strategically designed and controlled to synthesize a series of NBG NFAs, namely COT‐R (R = EH, BO, Oct, or Dod). The in‐depth quantitative investigations into the morphological and electrical factors reveal that side‐chain optimization effectively enhances various morphological properties, such as the molecular alignment and compatibility between components in the BHJ layer, resulting in the mitigation of energetic disorders and charge traps in the BHJ layers. Therefore, the optimized BHJ system, comprising COT‐Oct blended with PTB7‐Th, achieves a reduced dark current and increased responsivity, contributing to the development of high‐performance NIR OPDs with an impressive specific detectivity of 1.49 × 1012 Jones at 1000 nm under ‐0.5 V.

Flexible and Energy-Efficient Synaptic Transistor with Quasi-Linear Weight Update Protocol by Inkjet Printing of Orientated Polar-Electret/High-k Oxide Composite Dielectric.

Inkjet printing artificial synapse is cost-effective but challenging in emulating synaptic dynamics with a sufficient number of effective weight states under ultralow voltage spiking operation. A synaptic transistor gated by inkjet-printed composite dielectric of polar-electret polyvinylpyrrolidone (PVP) and high-k zirconia oxide (ZrOx) is proposed and thus synthesized to solve this issue. Quasi-linear weight update with a large variation margin is obtained through the coupling effect and the facilitation of dipole orientation, which can be attributed to the orderly arranged molecule chains induced by the carefully designed microfluidic flows. Crucial features of biological synapses including long-term plasticity, spike-timing-dependence-plasticity (STDP), "Learning-Experience" behavior, and ultralow energy consumption (<10 fJ/pulse) are successfully implemented on the device. Simulation results exhibit an excellent image recognition accuracy (97.1%) after 15 training epochs, which is the highest for printed synaptic transistors. Moreover, the device sustained excellent endurance against bending tests with radius down to 8 mm. This work presents a very viable solution for constructing the futuristic flexible and low-cost neural systems.

Effect of catalysts on the mechanical, thermal, and adhesive properties of polyrotaxane-modified epoxy resin

Polyrotaxane (PR) is a supramolecular polymer, in which an axial polymer extends through multiple cyclic molecules. PR specifically comprises polyethylene glycol, α-cyclodextrin, and adamantane as the axial polymer, cyclic molecule, and terminal blocking group, respectively. It is a useful stress-relaxing material because the cyclic polymers can freely slide and rotate in cyclic motions on the axial polymer. In this study, diglycidyl ether of bisphenol A (DGEBA) epoxy resin cured with phenolic resin (PN) was blended with PR, which has methacryl groups at the ends of side chains of the cyclic molecules, as a toughness modifier. The effect of the methacryl group polymerization catalyst (DCP) on the cured properties of epoxy resin was reported. PR was homogeneously dispersed in the DGEBA/PN resin matrix. Increasing the PR concentration significantly improved the toughness, impact resistance, and adhesive properties of the DGEBA/PN/PR alloy. Moreover, adding DCP resulted in an increase in the glass transition temperature due to the decreased molecular mobility of the network. This phenomenon was attributed to the synergistic effect of the formation of an interpenetrating polymer network, which is an entangled network of the curing reaction of the DGEBA/PN resin and polymerization of PR, and the intermolecular hydrogen bonds between carbonyl and hydroxyl groups of PR and hydroxyl groups of the DGEBA/PN resin. In contrast, the increased interfacial adhesion between PR and the DGEBA/PN did not result in significant improvement of flexural properties.

Energetics of water expulsion from intervening space between two particles during aggregation

Solvent expulsion away from an intervening region between two approaching particles plays important roles in particle aggregation yet remains poorly understood. In this work, we use metadynamics molecular simulations to study the free energy landscape of removing water molecules from gibbsite and pyrophyllite slit pores representing the confined spaces between two approaching particles. For gibbsite, removing water from the intervening region is both entropically and enthalpically unfavorable. The closer the particles approach each other, the harder it is to expel water molecules. For pyrophyllite, water expulsion is spontaneous, which is different from the gibbsite system. A smaller pore makes the water removal more favorable. When water is being drained from the intervening region, single chains of water molecules are observed in gibbsite pore, while in pyrophyllite pore water cluster is usually observed. Water-gibbsite hydrogen bonds help stabilize water chains, while water forms clusters in pyrophyllite pore to maximize the number of hydrogen bonds among themselves. This work provides the first assessment into the energetics and structure of water being drained from the intervening region between two approaching particles during oriented attachment and aggregation.

β1 integrin-mediated mast cell immune-surveillance of blood vessel content

BackgroundImmunoglobulin E, IgE)-mediated degranulation of mast cells, MCs) provides rapid protection against environmental hazards, including animal venoms. A fraction of tissue-resident MCs intimately associates with blood vessels. These perivascular MCs were reported to extend projections into the vessel lumen and to be the first MCs to acquire intravenously injected IgE, suggesting that IgE loading of MCs depends on their vascular association. ObjectiveWe sought to elucidate the molecular basis of the MC-blood vessel interaction and to determine its relevance for IgE-mediated immune responses. MethodsWe selectively inactivated the Itgb1 gene, encoding the β1 chain of integrin adhesion molecules, ITGB1; in MCs by conditional gene targeting in mice. We analyzed skin MCs for blood vessel association, surface IgE density, capability to bind circulating antibody specific for MC surface molecules, as well as in vivo responses to antigen administered via different routes. ResultsLack of ITGB1 expression severely compromised MC blood vessel association. ITGB1-deficient MCs showed normal densities of surface IgE but reduced binding of intravenously injected antibodies. While their capacity to degranulate in response to IgE ligation in vivo was unimpaired, anaphylactic responses to antigen circulating in the vasculature were largely abolished. ConclusionITGB1-mediated association of MCs with blood vessels is key for MC immune-surveillance of blood vessel content, but is dispensable for slow steady-state loading of endogenous IgE onto tissue-resident MCs.

Crystal structure and Hirshfeld surface analysis of ethyl 2-(7-chloro-3-methyl-2-oxo-1,2-di-hydro-quinoxalin-1-yl)acetate.

The quinoxaline moiety in the title mol-ecule, C13H13ClN2O3, is almost planar (r.m.s. deviation of the fitted atoms = 0.033 Å). In the crystal, C-H⋯O hydrogen bonds plus slipped π-stacking and C-H⋯π(ring) inter-actions generate chains of mol-ecules extending along the b-axis direction. The chains are connected by additional C-H⋯O hydrogen bonds. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (37.6%), H⋯O/O⋯H (22.7%) and H⋯Cl/Cl⋯H (13.1%) inter-actions.

Crystal structure, Hirshfeld surface analysis, calculations of crystal voids, inter-action energy and energy frameworks as well as density functional theory (DFT) calculations of 3-[2-(morpholin-4-yl)eth-yl]-5,5-di-phenyl-imidazolidine-2,4-dione.

In the title mol-ecule, C21H23N3O3, the imidazolidine ring slightly deviates from planarity and the morpholine ring exhibits the chair conformation. In the crystal, N-H⋯O and C-H⋯O hydrogen bonds form helical chains of mol-ecules extending parallel to the c axis that are connected by C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis reveals that the most important contributions for the crystal packing are from H⋯H (55.2%), H⋯C/C⋯H (22.6%) and H⋯O/O⋯H (20.5%) inter-actions. The volume of the crystal voids and the percentage of free space were calculated to be 236.78 Å3 and 12.71%, respectively. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the nearly equal electrostatic and dispersion energy contributions. The DFT-optimized mol-ecular structure at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state. Moreover, the HOMO-LUMO behaviour was elucidated to determine the energy gap.

Synthesis and crystal structure of N-phenyl-2-(phenyl-sulfan-yl)acetamide.

N-Phenyl-2-(phenyl-sulfan-yl)acetamide, C14H13NOS, was synthesized and structurally characterized. In the crystal, N-H⋯O hydrogen bonding leads to the formation of chains of mol-ecules along the [100] direction. The chains are linked by C-H⋯π inter-actions, forming a three-dimensional network. The crystal studied was twinned by a twofold rotation around [100].

Preliminary study of the superlubricity behavior of ZrO2/PI lubricating with liquid crystal

This article has investigated the friction behavior of a tribological system composed of a liquid crystal and polyimide. In this tribological system, ZrO2 and PMDA-ODA polyimide film used as a friction pair, and the liquid crystals used as lubricants including the single liquid crystal 5CB and the mixed liquid crystals LCs1 (5CB-5CEPO2), LCs2 (5CB-3CEPC3), LCs3 (5CB-2CEPPN), and conducted friction coefficient comparison experiments with n-hexadecane. It was found that the average friction coefficient of the LCs3 (90% 5CB + 10% 2CEPPN) is the smallest at the load of 5 N and the velocity of 200 rpm, which is 0.00113. Load and velocity selection experiments were investigated of LCs3, as well as polyimide film’s surface analysis including scanning electron microscope, white-light interference, polarization microscope, and surface-enhanced Raman scattering spectra. The results of the surface analysis indicated that some groups in the main chain and branch chain of the polyimide molecules are oriented parallel to the polyimide surface after rubbing.