Reorganization Of Molecules Research Articles

Multi-scale analysis of virgin/aged/recycled asphalt self-healing performance based on molecular simulation and micro-macro tests

Conventional macro-micro experiments have not fully elucidated the thermal self-healing mechanism of virgin, aged, and recycled asphalt at the molecular level at different temperatures. Molecular dynamics and macro-micro experiments were used to investigate the multi-scale mechanism of thermal self-healing of nano-cracks in three asphalt types. The molecular characteristics (concentration, energy changes, and molecular diffusion properties) of the three asphalt types were simulated during self-healing using molecular dynamics simulations Macro-micro experimental tests were conducted to validate the simulation results. The self-healing process was analyzed at multiple scales, and correlation analysis between the self-healing parameters and the macroscopic healing characteristics was performed at nano- and microscopic scales. The results showed that the relative concentration increased significantly from 0 mol/L to 0.6 mol/L in the 60–80 Å range during the long-distance self-healing phase (0–40 ps), promoting the rapid reorganization of molecules around cracks and the formation of self-healing networks. The van der Waals forces were the dominant forces affecting self-healing, and the transition from repulsive to attractive forces promoted the self-healing of cracks. This study clarifies the thermal self-healing mechanism of asphalt cracks at multiple scales, ensuring the sustainable use of asphalt materials.

Thin Film Resistance Gating by Redox Charge Exchange: Evidence for a Quantum Transition State.

Field effect transistors (FETs) and related devices have enabled tremendous advances in electronics, as well as studies of fundamental phenomena. FETs are classically actuated as fields charge/discharge materials, thereby modifying their resistance. Here, we develop charge exchange transistors (CETs) that comprise thin films whose resistance is modified by quantum charge exchange processes, e.g., redox and bonding. We first use CETs to probe the metallocene-thin film interaction during cyclic voltammetry. Remarkably, CETs reveal transient resistance peaks associated with charge transfer during both oxidation and reduction. Our data combined with kinetics and density functional theory modeling are consistent with a multistep redox pathway, including the formation/destruction of a quantum transition state that overlaps molecule + thin film band states. As a further proof-of-principle demonstration, we also use CETs to monitor n-alkanethiol self-assembly on thin Au films in real-time. CETs exhibit monotonic resistance increase consistent with previously reported fast-then-slow kinetics attributed to thiol-thin film bond formation (charge localization) and etching and/or molecule reorganization.

High-Pressure and Temperature Effects on the Clustering Ability of Monohydroxy Alcohols.

This study examined the clustering behavior of monohydroxy alcohols, where hydrogen-bonded clusters of up to a hundred molecules on the nanoscale can form. By performing X-ray diffraction experiments at different temperatures and under high pressure, we investigated how these conditions affect the ability of alcohols to form clusters. The pioneering high-pressure experiment performed on liquid alcohols contributes to the emerging knowledge in this field. Implementation of molecular dynamics simulations yielded excellent agreement with the experimental results, enabling the analysis of theoretical models. Here we show that at the same global density achieved either by alteration of pressure or temperature, the local aggregation of molecules at the nanoscale may significantly differ. Surprisingly, high pressure not only promotes the formation of hydrogen-bonded clusters but also induces the serious reorganization of molecules. This research represents a milestone in understanding association under extreme thermodynamic conditions in other hydrogen bonding systems such as water.

Influence of acidity and alkalinity of water environments on the water stability of asphalt mixture: Phase I - molecular dynamics simulation

The pH of water environments surrounding asphalt pavements is not constant at 7.0. Previous studies have demonstrated that the erosion of asphalt mixtures is more severe in acidic or alkaline water environments. However, the underlying mechanism remains unclear. To fulfill this research gap, the molecular dynamics (MD) simulation was employed in this study to explore the erosion influence of three different aqueous solutions on asphalt and asphalt-aggregate interface. Asphalt-solution systems and asphalt-aggregate systems under the different water environments were established. Through investigating the nanostructure change of the asphalt and asphalt-aggregate interface, the relative concentration (RC) and mean square displacement (MSD) of asphalt molecules, and the adhesion work between asphalt and aggregate were analyzed. The results show that the nanostructure of asphalt changes under acidic and alkaline water conditions, which further results in the decrease of the asphalt cohesion. In addition, the study revealed that the acidic and alkaline water solutions promote the molecular migration of SARA (saturates, aromatics, resins, and asphaltene) components, leading to the molecule reorganization at the asphalt-aggregate interface, finally affecting the bonding performance of asphalt-aggregate and the water stability of asphalt mixtures. These findings are anticipated to provide new insights into the influence of acidic and alkaline water environments on the water stability of asphalt mixture from the molecular scale perspective.

Influence of lipophilicity of anthracyclines on the interactions with cholesterol in the model cell membranes – Langmuir monolayer and SEIRAS studies

The interactions of anthracyclines with biological membranes strongly depend on the drug lipophilicity, which might also determine the specific affinity to cholesterol molecules. Therefore, in this work we show the studies concerning the effect of two selected anthracyclines, daunorubicin (DNR) and idarubicin (IDA) on simple models of healthy (DMPC:Chol 7:3) and cancer cells membranes with increased level of cholesterol (DMPC:Chol 3:7) as well as pure cholesterol monolayers prepared at the air-water interface and supported on gold surface. It has been shown that more lipophilic IDA is able to penetrate cholesterol monolayers more effectively than DNR due to the formation of IDA-cholesterol arrangements at the interface, as proved by the thermodynamic analysis of compression-expansion cycles. The increased interactions of IDA were also confirmed by the time measurements of pre-compressed monolayers exposed to drug solutions as well as grazing incidence X-ray diffraction studies demonstrating differences in the 2D organization of cholesterol monolayers. Langmuir studies of mixed DMPC:Chol membranes revealed the reorganization of molecules in the cancer cell models at the air-water interface at higher surface pressures due to the removal of DNR, while increased affinity of IDA towards cholesterol allowed this drug to penetrate the layer more efficiently without its removal. The SEIRAS spectra obtained for supported DMPC:Chol bilayers proved that IDA locates both in the ester group and in the acyl chain region of the bilayer, while DNR does not penetrate the membranes as deeply as IDA. The increased penetration of the mixed phospholipid layers by idarubicin might be attributed to the higher lipophilicity caused by the lack of methoxy group and resulting in a specific affinity towards cholesterol.

Non‐Platinum Group Metal Electrocatalysts toward Efficient Hydrogen Oxidation Reaction

AbstractDeveloping non‐platinum group metal (non‐PGM) electrocatalysts for the hydrogen oxidation reaction (HOR) represents the efforts towards the more economical use of hydrogen fuel cells and hydrogen energy, which has attracted tremendous attention recently. However, non‐PGM electrocatalysts for the HOR are still in their early development stages as compared with the significant advances in those for the oxygen reduction reaction and hydrogen evolution reaction. Herein, this paper summarizes the recent progresses and highlights the key challenges for the rational design of non‐PGM electrocatalysts, aiming to promote the development of non‐PGM HOR electrocatalysts. Fundamental understandings of the HOR mechanism are firstly reviewed, where theoretical interpretations on the low HOR kinetics in alkaline media, including the hydrogen binding energy theory, the bifunctional mechanism, and the water molecule reorganization, are particularly discussed. Subsequently, progresses of typical non‐PGM HOR electrocatalysts in acid and alkaline media are summarized separately. For the HOR under alkaline conditions, the superiorities and challenges of Ni‐based catalysts are discussed with a particular focus as they are the most promising non‐PGM electrocatalysts. Finally, this paper highlights the challenges and provide perspectives on the future development directions of non‐PGM HOR electrocatalysts.

Metal-Catalyzed Carbon-Carbon Bond Cleavage of Unstrained Alcohols.

The functionalization of molecules by cleaving inert carbon-carbon single bonds is regarded as a great synthetic challenge due to their inherent stability. In recent years, significant progress has been made in the activation of small rings relying on the release of strain energy. By contrast, the number of catalytic methodologies for the activation of unstrained carbon-carbon single bonds is still limited. This review focuses on the recent developments in transition-metal-catalyzed cleavage of C-C bonds in unstrained alcohols via β-carbon elimination. Emphasis is placed on the mechanistic aspects of the discussed transformations and their applications to the deconstruction and reorganization of molecules.

Online degradation of biaxial-orientated polypropylene film from HVDC filter capacitors

A comparative study of biaxial-orientated polypropylene (BOPP) films extracted from one failed HVDC filter capacitor (serving for 10 years) and one fresh capacitor (spare capacitor from the same batch) is reported in this paper. Experimental results show that the 10-year online operation does not bring about molecular changes; however, molecule reorganization and recrystallization was detected using differential scanning calorimetry and dynamic mechanical analysis tests. Electrical measurements including dielectric spectra, DC conductivity measurement, DC breakdown strength and were also performed. The experimental results show that the aging process causes an increase in dielectric constant, dissipation factor, DC conductivity, and the DC breakdown strength. Thermal stimulated current measurements indicate that traps were introduced by aging and are responsible for such abnormal changes. The nano-cavitivies generated by molecule reorganization could possibly act as charge traps. Therefore, homo-charges can accumulate in the vicinity of the electrodes, leading to the degradation of long-term withstand strength but an enhancement of short-term breakdown strength.

Acceptor number-dependent ultrafast photo-physical properties of push-pull chromophores using time-resolved methods

Three push-pull chromophores comprising a triphenylamine (TPA) as electron-donating moiety and functionalized β-diketones as electron acceptor units are studied by various spectroscopic techniques. The time-correlated single-photon counting data shows that increasing the number of electron acceptor units accelerates photoluminescence relaxation rate of compounds. Transient spectra data shows that intramolecular charge transfer (ICT) takes place from TPA units to β-diketones units after photo-excitation. Increasing the number of electron acceptor units would prolong the generation process of ICT state, and accelerate the excited molecule reorganization process and the relaxation process of ICT state.

Caveolin-1 Influences LFA-1 Redistribution upon TCR Stimulation in CD8 T Cells.

TCR stimulation by peptide–MHC complexes on APCs requires precise reorganization of molecules into the area of cellular contact to form an immunological synapse from where T cell signaling is initiated. Caveolin (Cav)1, a widely expressed transmembrane protein, is involved in the regulation of membrane composition, cellular polarity and trafficking, and the organization of signal transduction pathways. The presence of Cav1 protein in T cells was identified only recently, and its function in this context is not well understood. We show that Cav1-knockout CD8 T cells have a reduction in membrane cholesterol and sphingomyelin, and upon TCR triggering they exhibit altered morphology and polarity, with reduced effector function compared with Cav1 wild-type CD8 T cells. In particular, redistribution of the β2 integrin LFA-1 to the immunological synapse is compromised in Cav1-knockout T cells, as is the ability of LFA-1 to form high-avidity interactions with ICAM-1. Our results identify a role for Cav1 in membrane organization and β2 integrin function in primary CD8 T cells.

Cell adhesion and spreading at a charged interface: Insight into the mechanism using surface techniques and mathematical modelling

We study the kinetics of adhesion and spreading of an algal cell and its plasma membrane vesicle at the charged interface. A simple system of an isolated plasma membrane vesicle without internal content has been developed and characterized by atomic force microscopy (AFM). We extend the methodology based on the reaction kinetics model and empirical fitting for the analysis of amperometric signals, and demonstrate its validity and pertinence in a wide range of surface charge densities. Adhesion kinetics of the algal cell is slower than that of its plasma membrane vesicle. Isolated plasma membrane contributes about one quarter to the cell contact area. The model reconstructs and quantifies individual states of the three-step adhesion process of the algal cell and makes it possible to associate them with various features of amperometric signal. At the time of current amplitude, the ruptured state predominates and the cell spread contact area is larger than its initial area as well as the contact area of the plasma membrane vesicle. These results suggest that a major structural disruption of the cell membrane, collapse of cytoskeleton and leakage of intracellular material could appear close to the time of current amplitude. Further, slow kinetics of the organic film spreading at the interface to its maximal extent is considered as the rate determining step, which could be a consequence of the attenuated effect of potential at the modified interface, stronger intermolecular interactions and reorganization of molecules in the film. Our findings offer an insight into the mechanism of algal cell adhesion and spreading at charged interfaces, relevant for electroporation based studies.

Irreversibility in redox molecular conduction: single versus double metal-molecule interfaces

In this work we analyze the onset and manifestation of irreversibility phenomena in the charge transport at single and double metal-redox molecule interfaces, with special emphasis on the role of the nuclear system reorganization energy in causing the distortion of cyclic voltammograms in the first case and the occurrence of hysteresis phenomena in the second case. Under physical conditions for which two states of the molecular system come into play, effects of irreversibility increase with the reorganization energy at a single interface, while an opposite trend is seen in the conduction through a molecular junction. The apparent contradiction between these two behaviors, which was raised in a previous work (Migliore, A.; Nitzan, A., J. Am. Chem. Soc. 2013, 135, 9420–32) is here resolved through detailed investigation of the connections between molecule reorganization energy, bias-dependent population of the molecular redox site(s), and threshold voltage scan rate for the onset of irreversible behavior. Moreover, our investigation of the effects of the reorganization energy on the voltammogram peaks proposes a strategy for extracting the value of the reorganization energy of the molecular system from the experimental behavior.

Rayleigh instability at small length scales.

The Rayleigh instability (also called the Plateau-Rayleigh instability) of a nanosized liquid propane thread is investigated using molecular dynamics (MD). The validity of classical predictions at small length scales is verified by comparing the temporal evolution of liquid thread simulated by MD against classical predictions. Previous works have shown that thermal fluctuations become dominant at small length scales. The role and influence of the stochastic nature of thermal fluctuations in determining the instability at small length scale is also investigated. Thermal fluctuations are seen to dominate and accelerate the breakup process only during the last stages of breakup. The simulations also reveal that the breakup profile of nanoscale threads undergo modification due to reorganization of molecules by the evaporation-condensation process.

Temperature-dependent polymorphism of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide: experimental and theoretical studies on intermolecular interactions in the crystal state

X-ray analysis of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide reveals the temperature-dependent polymorphism associated with the crystallographic symmetry conversion. The observed crystal structure transformation corresponds to a symmetry reduction from I41 /a (I) to P43 (II) space groups. The phase transition mainly concerns the subtle but clearly noticeable reorganization of molecules in the crystal space, with the structure of individual molecules left almost unchanged. The Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, revealing graphically the differences in spatial arrangements of the molecules in both polymorphs. The N-oxide oxygen atom acts as a formally negatively charged hydrogen bonding acceptor in intramolecular hydrogen bond of N–H…O− type. The combined crystallographic and theoretical DFT methods demonstrate that the observed intramolecular N-oxide N–H…O hydrogen bond should be classified as a very strong charge-assisted and closed-shell non-covalent interaction.

Dehydration of mildronate dihydrate: a study of structural transformations and kinetics

The dehydration of mildronate dihydrate (3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propionate dihydrate) was investigated by powder X-ray diffraction, thermal analysis, hot-stage microscopy, water sorption–desorption studies and dehydration kinetic studies. It was determined that mildronate dihydrate dehydrated in a single step, directly transforming into the anhydrous form. In order to understand the reasons for a one step dehydration mechanism, crystal structures of dihydrate, monohydrate and anhydrous forms were compared, proving the similarity of the dihydrate and anhydrous forms. In order to understand the reasons for molecule reorganization during dehydration, the energy of the anhydrous form was compared with that of a theoretical dihydrate structure without water molecules. It was proven that the experimentally observed anhydrous phase AP was thermodynamically more stable. By analyzing the effect of the particle size and sample weight on the dehydration kinetic parameters it was determined that besides the main rate limiting step, phase boundary advancement, contribution from the water diffusion outside the crystal and the water diffusion outside the powdered sample also appeared to affect the dehydration kinetics and contribution from these processes could be changed by changing the aforementioned factors.

Kinetic equation for the processes of local reorganization of molecular systems with charged species

A molecular dynamic theory based on the lattice-gas model for the local reorganization of multi-component systems containing charged species is considered. Expressions for the mono- and bimolecular stages of the elementary processes that describe chemical reactions and displacements and rotations of molecules in dense gases and liquids are derived, with consideration given to direct and indirect effects of the initiation of electron and proton transfer. The proposed kinetic equations describe small-scale restructuring of solutions containing components of different sizes under the influence of changes in the external parameters of the molecular system at the kinetic stage of evolution of the system. The theory retains the effects of direct spatial correlations in the distribution of all the components of the mixture with the help of pair distribution functions in the quasi-chemical approximation. The dynamics of the local reorganization of molecules includes the kinetic equations for the local densities and pair distribution functions. The equations derived are intended to describe liquid-phase reactions, ion charge exchange, mutual diffusion of components of different sizes in multicomponent solutions, extraction processes at liquid phase boundaries, and photochemical processes in condensed phases.

Crystal structure and thermal behavior of cold-crystallized poly(trimethylene terephthalate)

The structure and thermal behavior of cold-crystallized poly(trimethylene terephthalate) (PTT) are revealed in detail by DSC, AFM, TEM, and WAXD as well as in situ FTIR and SAXS techniques. There is no effect of crystallization temperature and initial state on the crystal modification, yet the morphology is strongly affected by these two factors. First, the small rod-like lamellae for PTT are obtained during the cold crystallization instead of the spherulites formed in the melt crystallization. Second, the edge-on lamellar orientation in thin films is identified during the cold crystallization. The thickness and the lateral width of rod-like lamellae get larger and larger with increasing crystallization temperature. Thin lamellar crystals assemble randomly when the cold-crystallization temperature is lower, while lamellar stacks composed of thicker lamellae are observed when the PTT was annealed at elevated temperature. Moreover, for the cold-crystallized PTT, the final melting temperature does not vary with the crystallization temperature. This phenomenon is explained by the structural improvement during the heating process. For the cold-crystallized PTT sample at lower temperature, three transitions occur when it is heated again: the relaxation of the rigid amorphous phase, the reorganization of molecules in the intermediate phase, and then the melt–recrystallization behavior. Those transitions finally lead to thicker lamellae besides a higher crystallinity before the final fusion. Therefore, the final melting peak of these lamellae is at the same temperature.

Dissipation in rapid dynamic wetting

In this article, we present a modelling approach for rapid dynamic wetting based on the phase field theory. We show that in order to model this accurately, it is important to allow for a non-equilibrium wetting boundary condition. Using a condition of this type, we obtain a direct match with experimental results reported in the literature for rapid spreading of liquid droplets on dry surfaces. By extracting the dissipation of energy and the rate of change of kinetic energy in the flow simulation, we identify a new wetting regime during the rapid phase of spreading. This is characterized by the main dissipation to be due to a re-organization of molecules at the contact line, in a diffusive or active process. This regime serves as an addition to the other wetting regimes that have previously been reported in the literature.

Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy

Although internal electron transfer and oxygen reduction chemistry in cytochrome c oxidase are fairly well understood, the associated groups and pathways that couple these processes to gated proton translocation across the membrane remain unclear. Several possible pathways have been identified from crystallographic structural models; these involve hydrophilic residues in combination with structured waters that might reorganize to form transient proton transfer pathways during the catalytic cycle. To date, however, comparisons of atomic structures of different oxidases in different redox or ligation states have not provided a consistent answer as to which pathways are operative or the details of their dynamic changes during catalysis. In order to provide an experimental means to address this issue, FTIR spectroscopy in the 3,560-3,800 cm(-1) range has been used to detect weakly H-bonded water molecules in bovine cytochrome c oxidase that might change during catalysis. Full redox spectra exhibited at least four signals at 3,674(+), 3,638(+), 3,620(-), and 3,607(+) cm(-1). A more complex set of signals was observed in spectra of photolysis of the ferrous-CO compound, a reaction that mimics the catalytic oxygen binding step, and their D(2)O and H(2)(18)O sensitivities confirmed that they arose from water molecule rearrangements. Fitting with Gaussian components indicated the involvement of up to eight waters in the photolysis transition. Similar signals were also observed in photolysis spectra of the ferrous-CO compound of bacterial CcO from Paracoccus denitrificans. Such water changes are discussed in relation to roles in hydrophilic channels and proton/electron coupling mechanism.

Early Events in B Cell Activation

B cell activation is initiated by the ligation of the B cell receptor (BCR) with antigen and ultimately results in the production of protective antibodies against potentially pathogenic invaders. Here we review recent literature concerned with the spatiotemporal dynamic characterization of the early molecular events of B cell activation, including the initiation of BCR triggering, the formation of BCR microclusters, and the dynamic regulation of BCR signaling. Because these events involve the considerable reorganization of molecules within the membrane, an important role for the cytoskeleton is emerging in the regulation of B cell activation. At each stage we highlight the role of the cytoskeleton, establishing its pivotal position during the initiation and regulation of B cell activation.