Residence Time Of Molecules Research Articles

Boosting peroxymonosulfate activation via Fe–Cu bimetallic hollow nanoreactor derived from copper smelting slag for efficient degradation of organics: The dual role of Cu

Valorization of iron-rich metallurgical slags in the construction of Fenton-like catalysts has an appealing potential from the perspective of sustainable development. For the first time, copper smelting slag (CSS) was utilized as the precursor to synthesize hollow sea urchin-like Fe–Cu nanoreactors (Cu1.5Fe1Si) to activate peroxymonosulfate (PMS) for chlortetracycline hydrochloride (CTC) degradation. The hyper-channels and nano-sized cavities were formed in the catalysts owing to the induction and modification of Cu, not only promoting the in-situ growth of silicates and the formation of cavities due to the etching of SiO2 microspheres, but also resulting the generation of nanotubes through the distortion and rotation of the nanosheets. It was found that 100 % CTC degradation rate can be achieved within 10 min for Cu1.5Fe1Si, 75 times higher than that of Cu0Fe1Si (0.0024 up to 0.18 M−1‧min−1). The unique nanoconfined microenvironment structure could enrich reactants in the catalyst cavities, prolong the residence time of molecules, and increase the utilization efficiency of active species. Density functional theory (DFT) calculations show that Cu1.5Fe1Si has strong adsorption energy and excellent electron transport capacity for PMS, and Fe-Fe sites are mainly responsible for the activation of PMS, while Cu assists in accelerating the Fe(II)/Fe(Ⅲ) cycle and promotes the catalytic efficiency. The excellent mineralization rate (83.32 % within 10 min) and efficient treatment of CTC in consecutive trials corroborated the high activity and stability of the Cu1.5Fe1Si. This work provides a new idea for the rational design of solid waste-based eco-friendly functional materials, aiming at consolidating their practical application in advanced wastewater treatment.

Ab Initio Characterization of the CO2-Water Interface Using Unsupervised Machine Learning for Dimensionality Reduction.

Precise characterization of the supercritical CO2-water interface under high pressure and temperature conditions is crucial for the geological storage of carbon dioxide (CO2) in deep saline aquifers. Molecular dynamics (MD) simulations offer a valuable approach to gaining insight into the CO2-water interface at a microscopic level. However, no attempt has been made to characterize the CO2-water interface with the accuracy afforded by ab initio calculations. In this study, we performed ab initio MD (AIMD) simulations to investigate the structural and dynamical properties of the CO2-water interface, comparing the results with those obtained from classical force-field MD (FF-MD) simulations. Molecular orientation at the interface was well reproduced in both AIMD and FF-MD simulations. Characteristic structural fluctuations of water at the interface were unveiled by applying multidimensional scaling and time-dependent principal component analysis to the AIMD trajectories; however, they were not prominent in the FF-MD simulations. Furthermore, our study demonstrated a marked difference in the residence time of molecules in the interface region between AIMD and FF-MD simulations, indicating that time-dependent properties of the CO2-water interface strongly depend on the description of the intermolecular forces.

Constructing Hollow Multishelled Microreactors with a Nanoconfined Microenvironment for Ofloxacin Degradation through Peroxymonosulfate Activation: Evolution of High-Valence Cobalt-Oxo Species.

This study constructed hollow multishelled microreactors with a nanoconfined microenvironment for degrading ofloxacin (OFX) through peroxymonosulfate (PMS) activation in Fenton-like advanced oxidation processes (AOPs), resulting in adequate contaminant mineralization. Among the microreactors, a triple-shelled Co-based hollow microsphere (TS-Co/HM) exhibited optimal performance; its OFX degradation rate was 0.598 min-1, which was higher than that of Co3O4 nanoparticles by 8.97-fold. The structural tuning of Co/HM promoted the formation of oxygen vacancies (VO), which then facilitated the evolution of high-valence cobalt-oxo (Co(IV)═O) and shifted the entire t2g orbital of the Co atom upward, promoting catalytic reactions. Co(IV)═O was identified using a phenylmethyl sulfoxide (PMSO) probe and in situ Raman spectroscopy, and theoretical calculations were conducted to identify the lower energy barrier for Co(IV)═O formation on the defect-rich catalyst. Furthermore, the TS-Co/HM catalyst exhibited remarkable stability in inorganic (Cl-, H2PO4-, and NO3-), organic (humic acid), real water samples (tap water, river water, and hospital water), and in a continuous flow system in a microreactor. The nanoconfined microenvironment could enrich reactants in the catalyst cavities, prolong the residence time of molecules, and increase the utilization efficiency of Co(IV)═O. This work describes an activation process involving Co(IV)═O for organic contaminants elimination. Our results may encourage the use of multishelled structures and inform the design of nanoconfined catalysts in AOPs.

Predicting Biomolecular Binding Kinetics: A Review.

Biomolecular binding kinetics including the association (kon) and dissociation (koff) rates are critical parameters for therapeutic design of small-molecule drugs, peptides, and antibodies. Notably, the drug molecule residence time or dissociation rate has been shown to correlate with their efficacies better than binding affinities. A wide range of modeling approaches including quantitative structure-kinetic relationship models, Molecular Dynamics simulations, enhanced sampling, and Machine Learning has been developed to explore biomolecular binding and dissociation mechanisms and predict binding kinetic rates. Here, we review recent advances in computational modeling of biomolecular binding kinetics, with an outlook for future improvements.

Surface Passivation with a Perfluoroalkane Brush Improves the Precision of Single-Molecule Measurements.

Single-molecule imaging is invaluable for investigating the heterogeneous behavior and interactions of biological molecules. However, an impediment to precise sampling of single molecules is the irreversible adsorption of components onto the surfaces of cover glasses. This causes continuous changes in the concentrations of different molecules dissolved or suspended in the aqueous phase from the moment a sample is dispensed, which will shift, over time, the position of chemical equilibria between monomeric and multimeric components. Interferometric scattering microscopy (iSCAT) is a technique in the single-molecule toolkit that has the capability to detect unlabeled proteins and protein complexes both as they adsorb onto and desorb from a glass surface. Here, we examine the reversible and irreversible interactions between a number of different proteins and glass via analysis of the adsorption and desorption of protein at the single-molecule level. Furthermore, we present a method for surface passivation that virtually eliminates irreversible adsorption while still ensuring the residence time of molecules on surfaces is sufficient for detection of adsorption by iSCAT. By grafting high-density perfluoroalkane brushes on cover-glass surfaces, we observe approximately equal numbers of adsorption and desorption events for proteins at the measurement surface (±1%). The fluorous-aqueous interface also prevents the kinetic trapping of protein complexes and assists in establishing a thermodynamic equilibrium between monomeric and multimeric components. This surface passivation approach is valuable for in vitro single-molecule experiments using iSCAT microscopy because it allows for continuous monitoring of adsorption and desorption of protein without either a decline in detection events or a change in sample composition due to the irreversible binding of protein to surfaces.

Ti3C2Tx MXene-Loaded 3D Substrate toward On-Chip Multi-Gas Sensing with Surface-Enhanced Raman Spectroscopy (SERS) Barcode Readout.

Gas sensors lie at the heart of various fields ranging from medical to environmental sciences, and the demand of gas sensors is instantly expanding. However, in the face of complex gas samples, how to maintain high sensitivity while performing multiplex detection still puzzles the researchers. Here, by introducing Ti3C2Tx MXene into a microfluidic gas sensor with a three-dimensional (3D) transferable SERS substrate, a powerful gas sensor having both multiplex detecting ability and high sensitivity is demonstrated. The employ of MXene endows the sensor with a universal high adsorption efficiency for various gases while the generation of in situ gas vortices in the sophisticated nanomicro structure extends the molecule residence time in SERS-active area, both leading to the increased sensitivity. In the proof-of-concept experiment, a limit of detection (LOD) of 10-50 ppb was achieved for three typical volatile organic compounds (VOCs) according to the intrinsic SERS signals of gas molecules. Besides, the well-designed periodic 3D structure solves the general repeatability problem of SERS substrates. In addition, the detailed composition of gas mixture was revealed using classic least-square analysis (CLS) with an average accuracy of 90.6%. Further, a chromatic barcode was developed based on the results of CLS to read out the complex composition of samples visually.

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.

Small-Molecule Permeation across Membrane Channels: Chemical Modification to Quantify Transport across OmpF.

Biological channels facilitate the exchange of molecules across membranes, but general tools to quantify transport are missing. Electrophysiology is the method of choice to study the functional properties of channels. However, analyzing the current fluctuation of channels typically does not identify successful transport, that is, distinguishing translocation from binding. To distinguish both processes, we added an additional barrier at the channel exit acting as a molecular counter. To identify permeation, we compare the molecule residence time in the native channel with one that is chemically modified at the exit. We use the well-studied outer membrane channel from E. coli, OmpF. Position 181, which is below the constriction region, was subsequently mutated into cysteine (E181C) in an otherwise cysteine-free system, then functionalized by covalent binding with one of the two blockers MTSES or GLT. We measured the passage of model peptides, mono-, tri-, hepta-arginine and of norfloxacin, as an example for antibiotic permeation.

Nuclear Quantum Effects in Sodium Hydroxide Solutions from Neural Network Molecular Dynamics Simulations.

Nuclear quantum effects (NQEs) cause the nuclei of light elements like hydrogen to delocalize, affecting numerous properties of water and aqueous solutions, such as hydrogen-bonding and proton transfer barriers. Here, we address the prototypical case of aqueous NaOH solutions by investigating the effects of quantum nuclear fluctuations on radial distribution functions, hydrogen-bonding geometries, power spectra, proton transfer barriers, proton transfer rates, water self-exchange rates around the Na+ cations, and diffusion coefficients, for the full room-temperature solubility range. These properties were calculated from classical and ring-polymer molecular dynamics simulations employing a reactive high-dimensional neural network potential based on dispersion-corrected density functional theory reference calculations. We find that NQEs have a very small impact on the solvation structure around Na+, slightly strengthen the water-water and water-hydroxide hydrogen bonds, and lower the peak positions in the power spectra for the HOH bending and OH stretching modes by about 50 and 100 cm-1, respectively. Moreover, NQEs significantly lower the proton transfer barriers, thus increasing the proton transfer rates, resulting in an increase of the diffusion coefficient in particular of OH-, as well as a decrease of the mean residence time of molecules in the first hydration shell around Na+ at high NaOH concentrations.

Single-molecule electrochemistry in nanochannels: probing the time of first passage.

The diffusive mass transport of individual redox molecules was probed experimentally in microfabricated nanogap electrodes. The residence times for molecules inside a well-defined detection volume were extracted and the resulting distribution was compared with quantitative analytical predictions from random-walk theory for the time of first passage. The results suggest that a small number of strongly adsorbing sites strongly influence mass transport at trace analyte levels.

Impact of Zeolite Channel Structure on Structure of Hydrocarbon Compounds and Petrochemicals in Waste Tyre-Derived Oils

Waste tyre, a hydrocarbon-based material, exhibits potential to be used for a derivation of petrochemicals. Valuable chemicals such as benzene, toluene, and xylenes were observed in pyrolytic oils. Furthermore, sulphur compounds causing the low quality of oil products and environmental problem were also found. HBeta and HMOR acidic zeolites whose pore sizes are very close, which are 6.4x7.6 A and 6.5x7.0 A have different channel structures. The channel structure of HBETA is zigzag whereas that of HMOR is straight. Since the channel structure of zeolites may affect the residence time of molecules to stay in the pores; therefore, the objective of this work was to investigate the channel structure of zeolites that affect the structure and the size of pyrolysis products. The products were analyzed by using a SIMDIST-GC, GC and elemental analyser, whereas a GCxGC-TOF/MS was used to investigate species in oils. The catalysts were characterized by using XRD, TGA, and SAA. The results showed that the compositions of pyrolytic oils classified in terms of paraffins (P), olefins (O), naphthenes (N), and aromatics (A) were different with using different zeolites. Catalytic pyrolysis caused the decreases in olefins and naphthenes with the increases of aromatics. Furthermore, HBeta gave the higher amount of aromatics than HMOR, and gave the lower amounts of olefins and naphthenes than HMOR. It can be explained that the complex pore of HBeta converted more olefins and naphthenes to aromatics inside the pore than the straight pore of HMOR. In addition, HBeta gave a higher amount of light fractions in oils than HMOR that gave a higher amount of heavy fractions such as gas oil and long residue. However, these two zeolites can reduce sulphur in oils, and the species of sulphur were different. Moreover, both HBeta and HMOR catalysts caused the increment in the group of benzothiophenes and the reduction in the group of benzothiazoles.

Quantifying Short-Lived Events in Multistate Ionic Current Measurements

We developed a generalized technique to characterize polymer–nanopore interactions via single channel ionic current measurements. Physical interactions between analytes, such as DNA, proteins, or synthetic polymers, and a nanopore cause multiple discrete states in the current. We modeled the transitions of the current to individual states with an equivalent electrical circuit, which allowed us to describe the system response. This enabled the estimation of short-lived states that are presently not characterized by existing analysis techniques. Our approach considerably improves the range and resolution of single-molecule characterization with nanopores. For example, we characterized the residence times of synthetic polymers that are three times shorter than those estimated with existing algorithms. Because the molecule’s residence time follows an exponential distribution, we recover nearly 20-fold more events per unit time that can be used for analysis. Furthermore, the measurement range was extended from 11 monomers to as few as 8. Finally, we applied this technique to recover a known sequence of single-stranded DNA from previously published ion channel recordings, identifying discrete current states with subpicoampere resolution.

Endocytic pathway rapidly delivers internalized molecules to lysosomes: An analysis of vesicle trafficking, clustering and mass transfer

Lysosomes play a critical role in intracellular drug delivery. For enzyme-based therapies, they represent a potential target site whereas for nucleic acid or many protein drugs, they represent the potential degradation site. Either way, understanding the mechanisms and processes involved in routing of materials to lysosomes after cellular entry is of high interest to the field of drug delivery. Most therapeutic cargoes other than small hydrophobic molecules enter the cells through endocytosis. Endocytosed cargoes are routed to lysosomes via microtubule-based transport and are ultimately shared by various lysosomes via tethering and clustering of endocytic vesicles followed by exchange of their contents. Using a combined experimental and numerical approach, here we studied the rates of mass transfer into and among the endocytic vesicles in a model cell line, 3T3 fibroblasts. In order to understand the relationship of mass transfer with microtubular transport and vesicle clustering, we varied both properties through various pharmacological agents. At the same time, microtubular transport and vesicle clustering were modeled through diffusion–advection equations and the Smoluchowski equations, respectively. Our analysis revealed that the rate of mass transfer is optimally related to microtubular transport and clustering properties of vesicles. Further, the rate of mass transfer is highest in the innate state of the cell. Any perturbation to either microtubular transport or vesicle aggregation led to reduced mass transfer to lysosome. These results suggest that in the absence of an external intervention the endocytic pathway appears to maximize molecular delivery to lysosomes. Strategies are discussed to reduce mass transfer to lysosomes so as to extend the residence time of molecules in endosomes or late endosomes, thus potentially increasing the likelihood of their escape before disposition in the lysosomes.

Gradual Immobilization Processes of Molecules during Transitions from Solute to Solid States

The adsorption/desorption behavior of mobile solute molecules at a solution−crystal interface has been explored using crystals of model protein hen egg-white lysozyme (HEWL) and fluorescent-labeled HEWL (F-HEWL) molecules. We have tracked the transient processes occurring during adsorption/desorption of identical F-HEWL molecules on a tetragonal HEWL crystal surface by single-molecule visualization using a total internal reflection fluorescent microscope and pulsed discontinuous laser illumination. We found an induction period (∼70 min) after which the number density of F-HEWL molecules adsorbed mainly on steps increased linearly with the adsorption time. We show direct evidence that the residence time of molecules on the crystal surface gradually increases during the transition process from a solute species to the crystal after successive multistep processes.

Properties of Free Surface of Water−Methanol Mixtures. Analysis of the Truly Interfacial Molecular Layer in Computer Simulation

Molecular dynamics simulations of the vapor-liquid interface of water-methanol mixtures of five different compositions were performed on the canonical (N,V,T) ensemble at 298 K. In addition, the vapor-liquid interface of the two neat systems was simulated, as well. The obtained configurations were analyzed by means of the novel identification of truly interfacial molecules method, which provides a full list of the molecules that are right at the surface (i.e., at the boundary of the two phases). The molecular level roughness of the surface, the adsorption of the methanol molecules at the surface layer, the orientation of the surface molecules, the residence time of the molecules at the surface layer, as well as the surface aggregation of the molecules were analyzed in detail. Both the frequency and the amplitude of the surface roughness were found to become larger with an increasing methanol content. This effect was found to be stronger for the amplitude, which falls in the range of 2-4 A, depending on the composition of the system. Methanol was found to be adsorbed at the surface layer, being preferentially at the humps of the molecularly rough surface. Surface methanol prefers to orient in such a way that the O-CH(3) bond remains perpendicular to the macroscopic plane of the surface, pointing the methyl group to the vapor phase. The main orientational preference of the water molecules is to lie parallel to the surface. Methanol was found to remain considerably longer at the surface layer of the mixed systems than water. Thus, contrary to the fact that the residence times of the two molecules were found to be rather similar to each other at the surface of their neat liquids, the residence time of the methanol molecules was an order of magnitude larger than that of water molecules at the surface of their mixtures. A strong lateral microscopic segregation of the molecules was observed at the surface layer; the minor component of the system (irrespective of whether it was water or methanol) was found to form two-dimensional aggregates, leaving the rest of the surface empty for the major component. The effect of the vicinity of the vapor phase on the properties of the molecules was found to vanish very quickly: the composition of the second layer as well as the properties of the molecules of this layer (e.g., dynamics and orientation) did not differ considerably from those in the bulk liquid phase.

Elliptic equation for random walks. Application to transport in microporous media

We consider a process of random walks with arbitrary residence time distribution. We show that in many cases this process may not be described by the classical (Fick) parabolic diffusion equation, but an elliptic equation. An additional term proportional to the second time derivative takes into account the distribution of the residence times of molecules in pores. The new elliptic diffusion equation is strictly derived by the operator approach. A criterion showing where the new equation should be applied instead of the standard diffusion equation is obtained. Boundary conditions are studied and a principle for selection of a unique bounded solution is formulated. Fundamental solutions are obtained and compared with the results of direct simulation of the random walks.

Dynamical Study of a Micellar System

We investigated the dynamical behavior of equilibrium micellar aggregates. We found the characteristic times associated with the processes of exchange between the free surfactants and aggregates in dilute solutions. We employed Monte-Carlo simulations on a two-dimensional lattice, each amphiphile molecule occupying three sites, while all the remaining sites of the lattice are filled with a single water molecule per site. For a fixed concentration of the amphiphiles, we studied the dependence of mean residence time of molecules in aggregates as a function of temperature and of the size of the aggregates. We showed that the distribution curves for the residence time and that for the aggregation number are closely related. In particular, we could also characterize the transition to a micellar state by the behavior of the representative curves of the mean residence times as a function of temperature.

Fluorescence studies of polymer–surfactant association

Fluorescence spectroscopy has been successfully used for the study of central issues of solutions of surfactants and associating polymers. Different fluorescence techniques and methods are uniquely adapted to investigate problems in this field and can, by using extrinsic or intrinsic probes, provide information on molecular association, microstructure and molecular dynamics. This constitutes an important contribution to the understanding and control of macroscopic properties, as well as to their biological functions and technical applications. Important aspects of these mixed systems, related to their self-assembly, are: formation of micelles and hydrophobic microdomains in general; size and shape of surfactant molecular aggregates; formation and stability of vesicles; intra- vs. intermolecular association in polymers; conformational changes in polymers as affected by polymer–surfactant association; surfactant organization in adsorbed layers; kinetic aspects of the formation and disintegration of self-assembly structures; residence times of molecules in microdomains and migration of active molecules. Some of these issues will be addressed in this paper.

Association of surfactants and polymers studied by luminescence techniques

Light emission spectroscopy has unique possibilities for the study of central issues of surfactants and associating polymers. With the help of luminescent probes, information may be obtained on matters such as molecular association, microstructure, and molecular dynamics; this constitutes an important contribution to the understanding and control of macroscopic properties, as well as biological function and technical applications. Important aspects of these systems considered in this review are: formation of micelles and hydrophobic microdomains; aggregation numbers of surfactants; shape of molecular aggregates; size of droplets in water or in oil in microemulsions; formation and stability of vesicles; intra- vs. intermolecular association in polymers; conformational changes in polymers; polymer–surfactant association; surfactant organization in adsorbed layers; kinetic aspects regarding the formation and disintegration of self-assembly structures; residence times of molecules in microdomains and migration of active molecules.

Mean residence time of molecules diffusing in a cell bounded by a semi-permeable membrane: Monte Carlo simulations and an expression relating membrane transition probability to permeability.

The rapid exchange of water across erythrocyte membranes is readily measured using an NMR method that entails doping a suspension of cells with a moderately high concentration of Mn(2-) and measuring the rate of transverse relaxation of the nuclear magnetisation. Analysis of the data yields an estimate of the rate constant for membrane transport, from which the membrane permeability can be determined. It is assumed in the analysis that the efflux rate of the water is solely a function of the rate of membrane permeation and that the time it takes for intracellular water molecules to diffuse to the membrane is relatively insignificant. The limits of this assumption were explored by using random-walk simulations of diffusion in cells modelled as parallel planes, spheres, and biconcave discs. The rate of membrane transport was specified in terms of a transition probability but it was not initially clear what the relationship should be between this parameter and the diffusional membrane permeability P(d). This relationship was derived and used to show that the mean residence time for a water molecule is determined by P(d) when the diffusion coefficient is above a certain threshold value; it is determined by the distance to the membrane below that value.