Reactive Bond Research Articles

Advanced molecular structural mechanics model for carbon nanotubes incorporating the 2nd generation REBO potential

Molecular mechanics models like the molecular structural mechanics (MSM) model have been proven to be a valuable tool for the investigation of carbon nanotubes. This class of models is based on a chemical force field representing the bonds present in the structure. Up to now, the underlying chemical force field applied in the MSM model is usually based on harmonic potentials. This simple approach comes with major drawbacks limiting the abilities of the MSM approach. In order to overcome these limitations, the present work integrates the 2nd generation reactive bond order potential (REBO), which is a sophisticated chemical force field, into the MSM approach. The development of this advanced MSM model is given in detail. As a demonstration of its capabilities, the elastic properties of different armchair and zig-zag CNTs are investigated numerically. It was found, that the results for the elastic properties differ significantly with the choice of the underlying chemical force field. The arising differences are discussed and reasons for the occurring behavior are given. The developed advanced MSM approach on the basis of the REBO potential strongly enhances the capabilities of the MSM approach while maintaining its excellent accessibility and applicability together with a low computational effort.

Hierarchy in the Halogen Activation During Surface-Promoted Ullmann Coupling.

Within the collection of surface-supported reactions currently accessible for the production of extended molecular nanostructures under ultra-high vacuum, Ullmann coupling has been the most successful in the controlled formation of covalent single C-C bonds. Particularly advanced control of this synthetic tool has been obtained by means of hierarchical reactivity, commonly achieved by the use of different halogen atoms that consequently display distinct activation temperatures. Here we report on the site-selective reactivity of certain carbon-halogen bonds. We use precursor molecules halogenated with bromine atoms at two non-equivalent carbon atoms and found that the Ullmann coupling occurs on Au(111) with a remarkable predilection for one of the positions. Experimental evidence is provided by means of scanning tunneling microscopy and core level photoemission spectroscopy, and a rationalized understanding of the observed preference is obtained from density functional theory calculations.

Interfacial zone surrounding the diamond in reaction bonded diamond/SiC composites: Interphase structure and formation mechanism

Diamond/SiC composites have attracted considerable research interests due to their outstanding properties sought for a wide range of applications. Among a few techniques used for the fabrication of diamond/SiC composites, molten Si infiltration is an approach highly favored due to its cost-effectiveness and process flexibility. This study critically evaluated the interfacial zone surrounding the diamond in a reaction bonded (RB) diamond/SiC composite. XRD suggests that the composite consists of diamond, α-SiC, β-SiC, Si, and graphite. TEM reveals that a thin layer of graphite surrounds the diamond grain and it appears to form through a process of diamond graphitization and amorphous carbon transformation during the fabrication. In addition, a carbon dissolution and saturation process is proposed as a predominant mechanism for the formation of nano-crystalline SiC near the interface as well as the defects inside the SiC grits. A minor Al4C3 phase is occasionally detected near the interface region.

Catalytic Conversion of Lignin in Woody Biomass into Phenolic Monomers in Methanol/Water Mixtures without External Hydrogen

The valorization of lignin in renewable lignocellulosic biomass is an important target in the transition to a more sustainable production of fuels and chemicals. We present here a modification of the “lignin-first” approach that does not hinge on the use of external hydrogen. Instead, we use methanol/water mixtures as a suitable solvent that can be partly reformed into hydrogen. We propose a one-step process in which in planta lignin (wood sawdust) is converted to phenolic monomers over a Pt-based catalyst in an inert atmosphere. The role of the methanol/water mixture is not only to supply hydrogen but also to extract lignin fragments from the biomass matrix. Pt catalyzes methanol reforming to obtain hydrogen and the stabilization of reactive lignin intermediates by hydrogenation of reactive bonds. The latter aspect is crucial to avoid unfavorable condensation of fragments. Under optimized conditions, a yield of phenolic monomers of nearly 50% can be obtained from birch wood at a temperature of 230 °C in 3 h.

Epoxidation Kinetics of High-Linolenic Triglyceride Catalyzed by Solid Acidic-Ion Exchange Resin

Epoxidation of high-linolenic perilla oil was carried out in the presence of solid acidic ion-exchange resin at varying reaction temperatures for 8 h. A pseudo two-phase kinetic model that captures the differences in reactivity of double bonds at various positions in the fatty acid of a triglyceride molecule during both epoxy formation and cleavage was developed. The proposed model is based on the Langmuir-Hinshelwood-Hougen-Watson (L-H-H-W) postulates and considers the adsorption of formic acid on the catalyst as the rate-determining step. To estimate the kinetic rate constants of various reactions, genetic algorithm was used to fit experimentally obtained iodine and epoxy values of epoxidized perilla oil. A re-parametrized form of Arrhenius equation was used in the proposed model to facilitate the precise estimation of parameters with least computational effort. The obtainment of the least error between experimentally determined and theoretically predicted iodine and epoxy values indicates the robustness of the proposed model.

Reactivity of Zinc Thiolate Bonds: Oxidative Organopolysulfide Formation and S3 Insertion.

Zinc thiolate bonds are intriguing targets of study because of their redox noninnocence and prevalence in bioinorganic sites. A five-coordinate zinc dithiolate complex [Et4N]2[LZn] (H4L = N,N'-di(2-sulfhydrylphenyl)-pyridine-2,6-dicarboxamide) was synthesized to study the oxidative reactivity of zinc thiolate bonds. Multiple chemically reversible reactions of the zinc thiolate bonds were identified. Oxidation of [Et4N]2[LZn] with iodine resulted in structural rearrangement to a bimetallic disulfide-bridged complex. In contrast, the addition of elemental sulfur to [Et4N]2[LZn] resulted in the insertion of a neutral S3 fragment into the Zn-thiolate bond to selectively form an unusual monometallic tetrasulfanido complex. When oxidized, this tetrasulfanido compound rearranged to form a bimetallic trisulfide-bridged complex. The observed diversity of zinc thiolate reactivity, particularly with sulfur, is likely important in biological contexts.

Silane reactivity and resin bond strength to lithium disilicate ceramic surfaces

ObjectiveTo evaluate the silane status in commercially available products and their bonding capacity with polished glass-ceramic surfaces before and after hydrofluoric (HF) acid-etching. MethodsThe products tested were Calibra Silane Coupling Agent/CS, G-Multi Primer/GM, Kerr Silane Primer/KS, Monobond Plus/MB and Scotchbond Universal Adhesive/SB. The silane status was studied by 13C nuclear magnetic resonance spectroscopy (13C-NMR). The roughness parameters of polished (group A) and HF acid-etched (group B) lithium disilicate glass-ceramic surfaces were measured by optical profilometry (n = 5/group). The interaction of the products with group A and B ceramic surfaces was examined by attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). The shear strength (SBS) of a flowable composite bonded to the ceramic surfaces (groups A, B) was assessed before (NS) and after silane treatment (n = 20/group, product). ResultsThe NMR analysis showed the presence of silanol monomers only in CS. Methoxylated-siloxane adducts were found in GM, silanol–siloxane adducts in MB, SB, and siloxane polymers in KS. Acid-etching greatly increased Sa, Sz, Sdr, Sc and Sv parameters (p < 0.001) and ATR-FTIR analysis demonstrated evidence of bonding with the substrate in CS. Weibull analysis of SBS revealed the following rankings in characteristic life (p < 0.05): CS > SB,KS,MB > GM > NS (group A) and CS > GM > SB,KS,MB,NS (group B). The most reliable treatment in both groups was CS. For the same silane treatment, the SBS of group B were significantly higher from group A. Failures were mainly of adhesive type, except of several partial resin cohesive failures found in group B. SignificanceThe chemical bonding capacity of the silanes was highest in products with silanol monomers. Acid-etching increased bond strength to a level that neutralized the silane contribution in products with silanol–siloxane adducts and siloxane polymers, providing thus bond strength values similar to silane-free treatments.

Electrochemistry of cyclic triimidazoles and their halo derivatives: A casebook for multiple equivalent centers and electrocatalysis

A family of cyclic triazines, based on the triimidazo[1,2-a:1′,2′-c:1″,2″-e][1,3,5]triazine scaffold, has recently caught attention due to its variegated solid state photoluminescent properties (e.g., crystallization induced emission, fluomechanochromism, dual fluorescence, room temperature ultralong phosphorescence), tuned by proper functionalization of the cyclic core. From an electrochemical point of view, this family of heteroaromatic cyclic triazines is unexplored. A cyclic voltammetry study is here performed aiming to clarify structure/electroactivity relationship. The peculiar molecular structure of this class of molecules offers a multi-approach case study, spanning from multiple equivalent redox site interactions in small hoops (due to ideally C3h symmetry) to carbon-halogen bond reactivity in the presence of catalytic metal electrode surfaces (for –Br and –I derivatives). Results point to a poor heteroannular aromaticity along the rigid, planar cyclotrimer, with each equivalent redox site acting quite independently. An unusually higher electrocatalytic performance of gold with respect to silver electrode for the electrocleavage of carbon-halogen bonds (that decreases by increasing number of halo substituents) is tentatively explained in term of a specific interaction between gold and the nitrogen-rich planar cyclotrimer platform.

Influence of monomer reactivity on radiation grafting of phosphorus flame retardants on flax fabrics

Flax fabrics were modified by radiation grafting method to improve their flame retardancy. Several phosphonated monomers with different carbon-carbon double bond reactivity were grafted. According to 1H NMR carried out on irradiated monomers solubilized in water, the reactivity is the highest for (acryloyloxy)methyl phosphonic acid (hPAAPC1), and the lowest for allyl phosphonic acid (APA). Nevertheless, grafting yield on flax, assessed by X-ray fluorescence and scanning electron microscopy showed a different tendency. Especially (methacryloyloxy)methyl phosphonic acid (hPMAPC1) and vinyl phosphonic acid (VPA) appear to be highly grafted. In all cases, diffusion of the molecules into the flax elementary fibers bulk was observed. The choice of the solvent in washing step after the irradiation step showed to be effective to control the final phosphorus content in flax fabrics. The effect of phosphorus grafting on thermal properties and fire behavior was studied using thermogravimetric analysis, pyrolysis combustion flow calorimetry and a preliminary fire test. According to the latter, self-extinguishing and non-flammable fabrics were obtained for phosphorus content of 0.5 wt% and 1.2 wt% respectively. Correlations with flammability at microscale were pointed out. Additional cone calorimeter tests highlight the influence of flame retardant treatment on flammability under forced flaming conditions.

Toward deposition of organic solid with controlled morphology on selected surfaces

Multilayer organic and inorganic systems of thin solid films are widely used in novel optoelectronic devices. The required properties of the system depend on the morphology of the films and transition zone at interfaces. We studied the formation of deposits of fluorinated azo-dyes, polymethine, merocyanine and sulfur-terminated organic compounds (STOC) by evaporation and condensation in vacuum. The films were deposited on glass, silicon (Si), gold (Au) and polytetrafluoroethylene (PTFE) substrates. The influence of dye chemical structure and substrate on deposit morphology was studied using atomic force microscopy (AFM). Depending on the ratio between thermodynamic and kinetic processes, islands, crystalline aggregates or nano-structures were obtained. A difference in the morphology of the same dye solid, but deposited on various substrates was detected. Changes in the dye end or side groups caused variation in the morphology of the dye solid film. STOC formed a smooth film on the Au surface, while on the glass and PTFE it formed various islands. Thin films of the dyes in PTFE matrix exhibited unique stability to action of external factors. A new type of evaporable dyes with unsaturated reactive bond at the end was synthesized. Using new evaporation–activation–polymerization methods, the films with enhanced hardness and thermal stability were prepared from new dyes. Several dyes formed nano-micro-wires during the self-assembly process, in some cases between two neighboring Au strips. Adjusting the structure of the molecule by changing the end groups allows purposeful control of the deposit morphology on the selected surface.

Morphology on Reaction Mechanism Dependency for Twin Polymerization.

An in-depth knowledge of the structure formation process and the resulting dependency of the morphology on the reaction mechanism is a key requirement in order to design application-oriented materials. For twin polymerization, the basic idea of the reaction process is established, and important structural properties of the final nanoporous hybrid materials are known. However, the effects of changing the reaction mechanism parameters on the final morphology is still an open issue. In this work, the dependence of the morphology on the reaction mechanism is investigated based on a previously introduced lattice-based Monte Carlo method, the reactive bond fluctuation model. We analyze the effects of the model parameters, such as movability, attraction, or reaction probabilities on structural properties, like the specific surface area, the radial distribution function, the local porosity distribution, or the total fraction of percolating elements. From these examinations, we can identify key factors to adapt structural properties to fulfill desired requirements for possible applications. Hereby, we point out which implications theses parameter changes have on the underlying chemical structure.

The theoretical investigation on the properties of fluorine-substituted uracil

An investigation was conducted of Fluorine-substituted uracils (5-fluorouracil, 6-fluorouracil and 5, 6-difluoro-uracil) at the B3LYP [6-311G(d, p)/6-311+G(d, p)/6-311++G(d, p)] levels. A calculation was performed of their equilibrium structures and harmonic frequencies in gas and water. A combination of CF binding energies, Natural bond orbital (NBO), reactivity descriptors, Fukui functions, and aromaticity was applied to figure out the impact made by the numbers and location of fluorine atoms on the structural parameters, infrared spectrum, active site and aromaticity of the uracil. In this paper, a systematic research is carried out into the similarities and differences between fluorine-substituted at 5-position of uracil and 6-position. The outcomes are expected to provide a theoretical guidance with regard to the development of the fluoridated drugs.

Successive modification of polydentate complexes gives access to planar carbon- and nitrogen-based ligands

Polydentate complexes containing combinations of nitrogen and carbon (N and C) ligating atoms are among the most fundamental and ubiquitous molecules in coordination chemistry, yet the formation of such complexes with planar high-coordinate N/C sites remains challenging. Herein, we demonstrate an efficient route to access related complexes with tetradentate CCCN and pentadentate CCCCN and NCCCN cores by successive modification of the coordinating atoms in complexes with a CCCC core. Combined experimental and computational studies reveal that the rich reactivity of metal-carbon bonds and the inherent aromaticity of the metallacyclic skeletons play key roles in these transformations. This strategy addresses the paucity of synthetic approaches to mixed N/C planar pentadentate chelating species and provides valuable insights into the synthesis of carbon-based high-coordinate complexes. Furthermore, the resulting complexes are the examples of organometallic species with combined photoacoustic, photothermal, and sonodynamic properties, which makes them promising for application in related areas.

Influence of the weight ratio of an epoxy resin modified by castor oil and an epoxidiacrylate oligomer on photocrosslinking and properties of UV‐cured coatings

AbstractThe influence of the weight ratio of a castor oil modified epoxy resin (CE) and an epoxidiacrylate resin (EDA) on photocrosslinking and properties of the coatings containing these resins, hexandioldiacrylate monomer (HDDA) and photoinitiator Darocur 1173 (D.1173) upon UV‐exposure have been studied. The variation of acrylate groups during the photoinitiated polymerization was evaluated by FTIR analysis. The crosslinking of the UV‐cured coatings was proved by gel fraction and swelling degree determinations. In addition, some of the properties of the UV‐cured coatings such as relative hardness, flexibility, impact resistance, adhesion onto steel plates and gloss have also been examined. It was shown that the increase of the CE/EDA ratio from 10/40 to 40/10 in investigated coatings led to the decrease of the conversion rate of acrylate groups, and significantly changed some properties of the cured coatings after 14.4 s of UV irradiation: Decrease of gel fraction from 96 to 61 %, but improved the flexibility from 10 to 3 mm, impact resistance from 40 to 140 kG.cm, adhesion from 5 to 2 points. The gloss of the coatings remained to be 100 % in all cases. Long hydrocarbon chains of castor oil residue in CE, lower reactivity of double bonds and radicals formed in the chains compared with those of acrylate groups have been attributed to the obtained relationship between the CE/EDA ratio and photocrosslinking, properties of the cured coatings.

Interactions in the active site of Deinococcus radiodurans RNA polymerase during RNA proofreading

Co-transcriptional RNA proofreading by RNA polymerase (RNAP) is essential for accurate mRNA synthesis and reactivation of stalled transcription complexes, which can otherwise compromise genome integrity. RNAP from the stress-resistant bacterium Deinococcus radiodurans exhibits high levels of RNA cleavage in comparison with RNAP from Escherichia coli, which allows it to remove misincorporated nucleotides with high efficiency. Here, we show that the rate of RNA cleavage by D. radiodurans RNAP depends on the structure of the (mis)matched RNA 3′-nucleotide and its contacts with the active site. These interactions likely position the reactive phosphodiester bond in the cleavage-competent conformation, thus facilitating its hydrolysis catalyzed by metal ions in the active center. The universal RNA cleavage factor GreA largely alleviates defects in RNA cleavage caused by modifications in the RNA 3′-nucleotide or in its binding pocket in RNAP, suggesting that GreA functionally substitutes for these contacts. The results demonstrate that various RNAPs rely on a conserved mechanism for RNA proofreading, which can be modulated by changes in accessory parts of the active center.

Challenges and solutions in phosphinate chemistry

Abstract Several major challenges still remain in organophosphorus chemistry. Organophosphorus compounds are currently synthesized from phosphorus trichloride (PCl3), even though the final consumer products (such as pesticides, flame-retardants, extractants) do not contain reactive phosphorus-chlorine bonds. In order to bypass phosphorus trichloride, significant interest has been devoted to functionalizing elemental phosphorus (P4, the precursor to PCl3), red phosphorus (Pred), or phosphine (PH3). Yet, phosphinates (ROP(O)H2) are already available on an industrial scale and are the most environmentally benign, but their use as phosphorus trichloride replacements has been completely overlooked until a few years ago. An overview of some of the methodologies developed in my laboratory for P–C and P–O bond-forming reactions through phosphinate chemistry, as well as some selected applications, are presented. Another significant challenge remains the synthesis of P-stereogenic compounds. My group’s recent progress in this area is also discussed. Based on menthol as an inexpensive chiral auxiliary, various menthyl phosphinates can be synthesized. These phosphinates are precursor to P-stereogenic phosphines through well-established literature transformations.

A Reactive Inelasticity Theoretical Framework for Modeling Viscoelasticity, Plastic Deformation, and Damage in Fibrous Soft Tissue.

Fibrous soft tissues are biopolymeric materials that are made of extracellular proteins, such as different types of collagen and proteoglycans, and have a high water content. These tissues have nonlinear, anisotropic, and inelastic mechanical behaviors that are often categorized into viscoelastic behavior, plastic deformation, and damage. While tissue's elastic and viscoelastic mechanical properties have been measured for decades, there is no comprehensive theoretical framework for modeling inelastic behaviors of these tissues that is based on their structure. To model the three major inelastic mechanical behaviors of tissue's fibrous matrix, we formulated a structurally inspired continuum mechanics framework based on the energy of molecular bonds that break and reform in response to external loading (reactive bonds). In this framework, we employed the theory of internal state variables (ISV) and kinetics of molecular bonds. The number fraction of bonds, their reference deformation gradient, and damage parameter were used as state variables that allowed for consistent modeling of all three of the inelastic behaviors of tissue by using the same sets of constitutive relations. Several numerical examples are provided that address practical problems in tissue mechanics, including the difference between plastic deformation and damage. This model can be used to identify relationships between tissue's mechanical response to external loading and its biopolymeric structure.

Media Dependent Switching of Selectivity and Continuous near Infrared Turn-on Fluorescence Response through Cascade Interactions from Noncovalent to Covalent Binding for Detection of Serum Albumin in Living Cells.

Abnormal level of proteins is proved to be associated with diseases. Thus, protein sensing is helpful for clinical diagnosis and therapy. However, there is a great variety of protein species and relatively low concentration of each protein in complicated biological systems including other nonprotein biomolecules. Therefore, it remains challenging to develop an effective method for detecting protein with high selectivity and sensitivity. Herein, a new self-assembly method based on a robust dye SQSS of which two squaraine molecules were conjugated through disulfide bond was developed for highly selective and sensitive detection of serum albumin (SA) in aqueous solution and live cells. SQSS can self-assemble into "compact" aggregates, offering "inert" disulfide group and very low background fluorescence through the combination of aggregation quenching and homogeneous fluorescence resonance energy transfer (homoFRET) quenching. The response of SQSS to SA undergoes two cascade stages. At the first stage, SA drives the compact assemblies of SQSS to form loose ones with fast speed (30 s) through noncovalent interaction, resulting in the enhancement of fluorescence to some extent. In this loose assembly state, the disulfide bond in SQSS is reactive. At the second stage, the Cys34 in SA slowly induced further disassembly through covalent binding with reactive disulfide bond, resulting in fluorescence further increasing and SQSS labeling to SA that cannot be displaced by site binding ligands of SA. The self-assemblies of SQSS can selectively detect SA with continuous near-infrared (NIR) turn-on fluorescence response in 100% aqueous buffer solution. In addition, SQSS showed the potential application of imaging SA in living cells. On the other hand, the loose assembly state of SQSS was also achieved in aqueous solution with 20% CH3CN. In this media, thiol-containing glutathione (GSH) caused the disassembly of SQSS with turn-on fluorescence response through interaction with disulfide bond. SQSS can selectively recognize GSH over other amino acids even in the presence of other sulfhydryl amino acids. As a proof-of-concept method, the molecular self-assembly through multisteps interactions would provide an ideal strategy for detection and live-cell imaging of biorelated molecules with high selectivity and signal-to-noise ratio.

Chemo-mechanical modeling of artificially and naturally bonded soils

Chemo-mechanical effects are known to be significant in a number of applications in modern geomechanics, ranging from slope stability assessment to soil improvement and CO2 sequestration. This work focuses on coupled chemo-mechanical modeling of bonded geomaterials undergoing either mechanical strengthening, due to increased cementation, or weakening, due to cement dissolution. A constitutive model is developed that accounts for the multi-scale nature of the chemo-mechanical problem, introducing some cross-scale functions establishing a relationship between the evolution of microscopic variables and the macroscopic material behavior, realistically following the evolution of the reactive surface area, cross-sectional area and the number of bonds along with dissolution/deposition. The model presented here builds up on a previously introduced framework. However, at variance with existing works, it is specialized on materials with only reactive bonds, such as carbonate cemented sandstone or microbially cemented silica sand. Model validation is provided upon reproducing different types of chemo-mechanical experimental datasets, on different naturally and artificially cemented materials, to establish the reliability of the proposed framework.

Concurrently improved dispersion and interfacial interaction in rubber/nanosilica composites via efficient hydrosilane functionalization

Surface modification of fillers has a profound influence on the dispersion of filler and interfacial adhesion, and thus the final performance of polymer-based composites. In this contribution, the modification of silica by polymethylhydrosiloxane (PMHS) is conducted via an efficient and fast tris(pentafluorophenyl)borane-catalyzed functionalization, which can be completed within a few minutes at room temperature. A highly hydrophobic surface and an uncompromised reactivity are concurrently observed in the modified silica. By comparison between the composites filled with pristine and modified silica, it is revealed that such PMHS modification can not only improve the dispersibility of silica by lowering the surface energy, but also enhance the interfacial interaction in virtue of the reactivity of the residual SiH bonds. With a PMHS grafting content as low as 1.5 wt%, the modified composite exhibits tremendous improvements in mechanical properties (116% increase in modulus) and dynamic performances (116% increase in wet traction and 26% reduction in rolling resistance). Considering the superior overall performance of the modified composites, together with the simplicity and rapidity of the modification process, we envision that the hydrosilane-modified silica has great potential in the fabrication of high-performance polymer composites such as energy-saving tire treads.