Molecular Motion Research Articles

Molecular-level insight into the effects of low moisture and trehalose on the thermostability of β-glucosidase

The high temperature induces conformational changes in β-glucosidase, making it inactive and limiting its application field. In this paper, the effect of trehalose on the thermostability of β-glucosidase from low-moisture Hevea brasiliensis seeds was investigated. The results showed that the residual enzyme activities of β-glucosidase supplemented with trehalose after high-temperature treatment were significantly higher than that of the control group. The improvement of thermostability could be explained by low-field nuclear magnetic resonance (LF-NMR) and molecular dynamics (MD) simulations at the molecular level. Moreover, adding trehalose increased the water activity and water content of β-glucosidase, leading to a more stable conformation. Trehalose replaced some water and formed a stable network of hydrogen bonds with protein and surrounding water. The glass formed by trehalose also reduced molecular movement, thus providing good protection for enzymes.

Collective dynamics of liquid sulphur across the polymerisation transition temperature probed by inelastic x-ray scattering

Inelastic x-ray scattering (IXS) experiments on liquid sulphur were carried out below (140 ∘C) and above (180 ∘C) the polymerisation temperature T λ of about 159 ∘C to investigate changes in the collective dynamics of this unique liquid, that exhibits a liquid–liquid transition. As reported earlier, broad longitudinal acoustic excitation signals were observed at both temperatures, and only the width of the quasielastic peaks slightly decreased when the temperature crossed the transition temperature. A model analysis was performed using a generalised Langevin formalism with a memory function having one thermal and two viscoelastic decay channels with the help of simple sparse modelling, and large positive deviations from the hydrodynamic sound velocity by 51%–54% were observed. The fast viscoelastic relaxation time τ µ is close to the correlation times of intermolecular stretching and bending motions of local sulphur connections in both ring and chain structures, and is similar to those of other molecular liquids. The small contrasts in the IXS spectra across the λ transition result in large changes in only the slow viscoelastic decay time τ α of the memory function. The τ α value at 140 ∘C matches the mixed internal/external torsional modes of S8 molecules well, whereas that at 180 ∘C has no corresponding molecular motion mode. The kinematic viscosity values at the Q→0 limit are much smaller than the minimum values of macroscopic shear viscosity, indicating that large changes in relaxation dynamics are expected with Q in the GHz and MHz excitation regimes.

Effect of microwave on coupled rheological and mechanical properties of cemented tailings backfill

Cement tailings backfill (CTB) is a mixture of tailings, binders and water that is widely utilized to fill underground mining areas. Once placed, the CTB needs to provide adequate ground support as soon as possible to improve mining efficiency. Microwave heating can accelerate the curing process of CTB, thereby improving the mechanical performance of CTB. However, if the CTB slurry is under the heating condition, the early hydration reaction process of the mixture can be accelerated, consuming more water in the CTB materials and thus resulting in reduced fluidity. Therefore, this study proposes an experimental scheme to incorporate microwave heating into the preparing and curing of CTB, so as to realize the improvement of the mechanical strength of CTB body under the condition of also ensuring the fluidity of fresh CTB. The results indicate that with the appropriate microwave heating time (2–4 min) and power (600 W) applied, both the flowing ability and strength in the plastic and hardened CTB can be improved. The improvement in fluidity of CTB is ascribed to the intensification of molecular thermal movement, while the enhancement in strength of CTB is due to the acceleration of binder hydration progress. The current study can also contribute to further practical application of microwave heating in the preparation process of CTB before it is placed into underground mined-out areas.

Green and sustainable extraction of phycocyanin from Spirulina platensis by temperature-sensitive polymer-based aqueous two-phase system and mechanism study

In this study, a sustainable and environmentally friendly method was developed for the enrichment and purification of phycocyanin from Spirulina platensis. This was achieved by utilizing a temperature-sensitive polymer, Pluronic F68, in an aqueous two-phase solvent system. The phase behavior of the temperature-sensitive polymer-based biphasic system was evaluated. The extraction conditions were optimized by both single-factor experiments and response surface methodology. Under the optimal conditions, the upper polymer-rich phase was recycled for sustainable phycocyanin extraction, resulting in a grade of 3.23 during the third extraction cycle. Pluronic F68 could be efficiently recovered and reused during the extraction process. The interaction mechanism between Pluronic F68 and phycocyanin was systematically studied using FT-IR and fluorescence analysis. This was further complemented by static and dynamic calculation of molecular motion through molecular docking and molecular dynamics simulation, indicating that hydrophobic segment of Pluronic F68 played a key role in the binding process with phycocyanin.

Preparation of Graphene Oxide/Polymer Hybrid Microcapsules via Photopolymerization for Double Self-Healing Anticorrosion Coatings.

In this work, graphene oxide (GO)/polymer hybrid microcapsule-loaded self-healing agents were prepared via the combination of the emulsion template method and photopolymerization technology. The incorporation of GO in the microcapsule shell not only improved the impermeability, mechanical property, and solvent resistance property of the microcapsules significantly but also endowed the microcapsules with photothermal conversion property. By incorporating GO/polymer hybrid microcapsules in water-borne epoxy resin, a novel kind of anticorrosion coating with a double self-healing property was successfully fabricated. When the coating was scratched, the linseed oil (LO) encapsulated in the microcapsules could fill the crack, and the photothermal conversion property of GO could promote the molecular chain movement of the damaged area under near-infrared (NIR) irradiation to realize the close of the crack. Based on the filling of LO and photothermal conversion-induced scratch narrowing, the "filling" and "close" double self-healing effect can be realized under temporal NIR irradiation, which could lead to the complete recovery of the scratched coating. The |Z|f=0.1Hz value of the damaged coating with GO/polymer microcapsules after double healing was comparable to that of the intact coating, which was about 4 orders of magnitude higher than that of the scratched blank coating and single self-healing coating. As to the neutral salt spray test, the scratched blank coating failed in protection after 100 h, while the healed composite coating did not show any corrosion after 300 h.

Photoluminescence Enhancement of 0D Organic-Inorganic Metal Halides via Aggregation-Induced Emission and Halide Substitution.

0D organic-inorganic metal halides (OIMHs) provide unprecedented versatility in structures and photoluminescence properties. Here, a series of bluish-white emissive 0D OIMHs, (TPE-TPP)2Sb2BrxCl8-x (x = 1.16 to 8), are prepared by assembling the 1-triphenylphosphonium-4-(1,2,2-triphenylethenyl)benzene cation (TPE-TPP)+ with antimony halides anions. Based on experimental characterizations and theoretical calculations, the emission of the 0D OIMHs are attributed to the fluorescence of the organic cations with aggregation-induced emission (AIE) properties. The 0D structure minimized the molecular motion and intermolecular interactions between (TPE-TPP)+ cations, effectively suppressing the non-radiative recombination processes. Consequently, the photoluminescence quantum efficiency (PLQE) of (TPE-TPP)2Sb2Br1.16Cl6.84 is significantly enhanced to 55.4% as compared to the organic salt (TPE-TPP)Br (20.5%). The PLQE of (TPE-TPP)2Sb2BrxCl8-x can also be readily manipulated by halide substitution, due to the competitive processes between non-radiative recombination on the inorganic moiety and the energy transfer from inorganic to organic. In addition, electrically driven light-emitting diodes (LEDs) are fabricated based on (TPE-TPP)2Sb2Br1.16Cl6.84 emitter, which exhibited bluish-white emission with a maximum external quantum efficiency (EQE) of 1.1% and luminance of 335cdm-2. This is the first report of electrically driven LED based on 0D OIMH with bluish-white emission.

Compressing generalized trajectories of molecular motion for efficient detection of chemical interactions

Molecular Dynamics (MD) simulation is often used to study properties of various chemical interactions in domains such as drug discovery and development, particularly when executing real experimental studies is costly and/or unsafe. Studying the motion of trajectories of molecules/atoms generated from MD simulations provides a detailed atomic level spatial location of every atom for every time frame in the experiment. The analysis of this data leads to an atomic and molecular level understanding of interactions among the constituents of the system of interest. However, the data is extremely large and poses storage and processing challenges in the querying and analysis of associated atom level motion trajectories. We take a first step towards applying domain-specific generalization techniques for the data representation, subsequently used for applying trajectory compression algorithms towards reducing the storage requirements and speeding up the processing of within-distance queries over MD simulation data. We demonstrate that this generalization-aware compression, when applied to the dataset used in this case study, yields significant improvements in terms of data reduction and processing time without sacrificing the effectiveness of within-distance queries for threshold-based detection of molecular events of interest, such as the formation of Hydrogen Bonds (H-Bonds).

Explaining Conformational Diversity in Protein Families through Molecular Motions

Proteins play a central role in biological processes, and understanding their conformational variability is crucial for unraveling their functional mechanisms. Recent advancements in high-throughput technologies have enhanced our knowledge of protein structures, yet predicting their multiple conformational states and motions remains challenging. This study introduces Dimensionality Analysis for protein Conformational Exploration (DANCE) for a systematic and comprehensive description of protein families conformational variability. DANCE accommodates both experimental and predicted structures. It is suitable for analysing anything from single proteins to superfamilies. Employing it, we clustered all experimentally resolved protein structures available in the Protein Data Bank into conformational collections and characterized them as sets of linear motions. The resource facilitates access and exploitation of the multiple states adopted by a protein and its homologs. Beyond descriptive analysis, we assessed classical dimensionality reduction techniques for sampling unseen states on a representative benchmark. This work improves our understanding of how proteins deform to perform their functions and opens ways to a standardised evaluation of methods designed to sample and generate protein conformations.

Recent Progress in Solid-State Room Temperature Afterglow Based on Pure Organic Small Molecules.

Organic room temperature afterglow (ORTA) can be categorized into two key mechanisms: continuous thermally activated delayed fluorescence (TADF) and room-temperature phosphorescence (RTP), both of which involve a triplet excited state. However, triplet excited states are easily quenched by non-radiative transitions due to oxygen and molecular vibrations. Solid-phase systems provide a conducive environment for triplet excitons due to constrained molecular motion and limited oxygen permeation within closely packed molecules. The stimulated triplet state tends to release energy through radiative transitions. Despite numerous reports on RTP in solid-phase systems in recent years, the complexity of these systems precludes the formulation of a universal theory to elucidate the underlying principles. Several strategies for achieving ORTA luminescence in the solid phase have been developed, encompassing crystallization, polymer host-guest doping, and small molecule host-guest doping. Many of these systems exhibit luminescent responses to various physical stimuli, including light stimulation, mechanical stimuli, and solvent vapor exposure. The appearance of these intriguing luminescent phenomena in solid-phase systems underscores their significant potential applications in areas such as light sensing, biological imaging, and information security.

Micropattern Fabricated by Acropetal Migration Controlled through Sequential Photo and Thermal Polymerization.

Bottom-up patterning technology plays a significant role in both nature and synthetic materials, owing to its inherent advantages such as ease of implementation, spontaneity, and noncontact attributes, etc. However, constrained by the uncontrollability of molecular movement, energy interaction, and stress, obtained micropatterns tend to exhibit an inevitable arched outline, resulting in the limitation of applicability. Herein, inspired by auxin's action mode in apical dominance, a versatile strategy is proposed for fabricating precision self-organizing micropatterns with impressive height based on polymerization-induced acropetal migration. The copolymer containing fluorocarbon chains (low surface energy) and tertiary amine (coinitiator) is designed to self-assemble on the surface of the photo-curing system. The selective exposure under a photomask establishes a photocuring boundary and the radicals would be generated on the surface, which is pivotal in generating a vertical concentration difference of monomer. Subsequent heating treatment activates the material continuously transfers from the unexposed area to the exposed area and is accompanied by the obviously vertical upward mass transfer, resulting in the manufacture of a rectilinear profile micropattern. This strategy significantly broadens the applicability of self-organizing patterns, offering the potential to mitigate the complexity and time-consuming limitations associated with top-down methods.

Switching of Circularly Polarized Luminescence via Dynamic Axial Chirality Control of Chiral Bis(Boron Difluoride) Complexes with Salen Ligands

AbstractThe intensity and handedness of circularly polarized luminescence (CPL) were successfully controlled by dynamic molecular motion in solutions. Bis(boron difluoride) complexes with chiral salen ligands were synthesized and their photophysical properties were investigated. Although these complexes showed rapid molecular rotation about the C−N bond axis in solution at room temperature, two conformers assigned as atropisomers were observed in the NMR spectra at low temperature. Furthermore, the equilibrium of these atropisomers was found to change depending on the external environment, such as the solvent and temperature, allowing precise control of the intensity and handedness of CPL without luminescence color shifts. Theoretical calculations based on density functional theory (DFT) revealed that intramolecular chiral exciton coupling is the key to changes in CPL properties.

Regulating the Distribution and Accumulation of Charged Molecules by Progressive Electroporation for Improved Intracellular Delivery.

The cell membrane separates the intracellular compartment from the extracellular environment, constraining exogenous molecules to enter the cell. Conventional electroporation typically employs high-voltage and short-duration pulses to facilitate the transmembrane transport of molecules impermeable to the membrane under natural conditions by creating temporary hydrophilic pores on the membrane. Electroporation not only enables the entry of exogenous molecules but also directs the intracellular distribution of the electric field. Recent advancements have markedly enhanced the efficiency of intracellular molecule delivery, achieved through the utilization of microstructures, microelectrodes, and surface modifications. However, little attention is paid to regulating the motion of molecules during and after passing through the membrane to improve delivery efficiency, resulting in an unsatisfactory delivery efficiency and high dose demand. Here, we proposed the strategy of regulating the motion of charged molecules during the delivery process by progressive electroporation (PEP), utilizing modulated electric fields. Efficient delivery of charged molecules with an expanded distribution and increased accumulation by PEP was demonstrated through numerical simulations and experimental results. The dose demand can be reduced by 10-40% depending on the size and charge of the molecules. We confirmed the safety of PEP for intracellular delivery in both short and long terms through cytotoxicity assays and transcriptome analysis. Overall, this work not only reveals the mechanism and effectiveness of PEP-enhanced intracellular delivery of charged molecules but also suggests the potential integration of field manipulation of molecular motion with surface modification techniques for biomedical applications such as cell engineering and sensitive cellular monitoring.

Supramolecular organic frameworks (SOFs) membrane with ultra-high hydrogen permeability for hydrogen purification: Microstructural design of JLU-SOF2

Simulating results showed that JLU-SOF2 has ultra-high hydrogen permeability (0.696 × 106 GPU) but low selectivity (7.46). Given the good structural designability of JLU-SOF2, it is valuable to develop the structure design of JLU-SOF2 for on-site hydrogen purification to improve selectivity and maintain high H2 permeability. In this study, the functional groups of JLU-SOF2 were modified to construct 13 membrane materials containing functional groups of different lengths. The effect of membrane materials modified with each functional group on hydrogen permeability and selectivity in mixed gases (CO2, CO, and H2) was investigated from a microscopic point of view utilizing molecular simulations. Results showed that all 13 functional groups could improve the gas selectivity, especially the -SO3H, -OCH3, and -CH2NH2 modified JLU-SOF2 membrane materials, which can 100 % intercept CO2 and CO and maintain an excellent H2 permeability (0.54 × 106GPU), which exceeded the industry standard by nearly 105 times. Molecular motion behavior analysis showed that stretching direction and length of functional groups are the key factors leading to different membrane pore sizes and play a crucial role in affecting gas transport.

Octopus‐Inspired Adaptive Molecular Motion for Synergistic Photothermal and Nitric Oxide Antibacterial Therapy in Diabetic Wound Repair

AbstractBacterial infections, especially those from drug‐resistant strains, pose a significant threat to healing diabetic skin injuries, with current treatments being intricated and often unsatisfactory. Inspired by octopuses, a biomimetic material using α‐cyclodextrin (α‐CD) and polyethylene glycol (PEG) assembled with graphene oxide end‐capped polyrotaxanes (GO‐PR) is developed, where α‐CD mimics the flexible tentacles of an octopus. Further, α‐CD is cationically modified with polyethyleneimine (PEI) to resemble octopus suction cups, creating GO‐PRP, which effectively captures and adheres to bacteria. Importantly, to emulate an octopus's ink defense, GO‐PRP is used as a carrier for nitric oxide (NO), resulting in GO‐PRP/NONOate. Utilizing the photothermal conversion of GO, near‐infrared light exposure triggers rapid heating and NO release, providing efficient antibacterial activity and biofilm dispersion, significantly reducing inflammation in diabetic skin injuries in type I rats. During wound healing, sustained NO release promotes vascular endothelial growth factor production and blood vessel regeneration, enhancing collagen formation and shortening the healing time for diabetic skin infections. Thus, octopus‐inspired GO‐PRP/NONOate emerges as a novel biomaterial for treating drug‐resistant bacterial infections in diabetic wounds in the biomedical field.

Inverse Isotope Kinetic Effect of the Charge Transfer Reactions of Ar+ with H2O and D2O.

Hydrogen isotopic effect, as the key to revealing the origin of Earth's water, arises from the H/D mass difference and quantum dynamics at the transition state of reaction. The ion-molecule charge-exchange reaction between water (H2O/D2O) and argon ion (Ar+) proceeds spontaneously and promptly, where there is no transition-state or intermediate complex. In this energetically resonant process, we find an inverse kinetic isotope effect (KIE) leading to the higher charge transfer rate for D2O, by the velocity map imaging measurements of H2O+/D2O+ products. Using the average dipole orientation capture model, we estimate the orientation angles of C2v axis of H2O/D2O relative to the Ar+ approaching direction and attribute to the difference of stereodynamics. According to the long-distance Landau-Zener charge transfer model, this inverse KIE could be also attributed to the density-of-state difference of molecular bending motion between H2O+ and D2O+ around the resonant charge transfer.

Multi-Objective Optimization in Support of Life-Cycle Cost-Performance-Based Design of Reinforced Concrete Structures

Surveys on the optimum seismic design of structures reveal that many investigations focus on minimizing initial costs while satisfying performance constraints. Although reducing initial costs while complying with earthquake design codes significantly ensures occupant safety, it may still cause considerable economic losses and fatalities. Therefore, calculating potential earthquake damages over the structure’s lifetime is essential from an optimal Life-Cycle Cost (LCC) design perspective. LCC analysis evaluates economic feasibility, including construction, operation, occupancy, maintenance, and end-of-life costs. The population-based, meta-heuristic Ideal Gas Molecular Movement (IGMM) algorithm has proven effective in solving highly nonlinear mono- and multi-objective engineering problems. This paper investigates the LCC-based mono- and multi-objective optimum design of a 3D four-story concrete building structure using the Endurance Time (ET) method, which is employed for its efficiency in estimating structural responses under varying seismic hazard levels. The novelty of this work lies in integrating the ET method with the IGMM algorithm to comprehensively address both economic and performance criteria in seismic design. The results indicate that the proposed technique significantly reduces minor injury costs, rental costs, and income costs by 22%, 16%, and 16%, respectively, achieving a total reduction of 10% in all structural Life-Cycle Costs, which is considered significant.

Molecular dynamics study of cross‐linking degrees effect on the aging resistance of epoxy asphalt: Insights from oxygen diffusion

AbstractTo interpret the diffusion behavior of oxygen in epoxy asphalt with different cross‐linking degrees, epoxy asphalt‐oxygen diffusion layer models were constructed. The effect of temperature on oxygen diffusion and the number of oxygen molecules penetrating the epoxy asphalt was quantitatively analyzed. Fick's second law was used to determine the oxygen diffusion coefficient. The Mean square displacement (MSD) was extracted to analyze the effect of cross‐linking degree on the molecular motion of the base asphalt. The results show that as the cross‐linking degree increases, the number of oxygen in the epoxy asphalt decreases, accompanied by a reduction in the oxygen diffusion coefficient. Temperature significantly affects the rate of oxygen diffusion, with higher temperatures leading to greater diffusion depths over the same simulation time. The oxygen diffusion coefficient of epoxy asphalt ranges from 4.60 × 10−11 to 2.20 × 10−10 m2/s at temperatures of 298–373 K. The epoxy system markedly restricts the movement of base asphalt molecules, with saturate being most affected by cross‐linking degree and asphaltene the least. A high cross‐linking network impedes the asphalt‐oxygen contact oxidation, enhancing epoxy asphalt's anti‐aging capacity. These findings provide support for optimizing epoxy asphalt formulations and guiding the development of anti‐oxidant epoxy asphalt.

Exploring the Crystal Structure, Thermodynamics, and Molecular Dynamics of NH(CH3)3CuCl3·2H2O Organic-Inorganic Hybrid Perovskite.

Understanding the physical properties of the organic-inorganic hybrid NH(CH3)3CuCl3·2H2O is necessary for its potential applications. Initially, the monoclinic structure of this crystal was discussed via single-crystal X-ray diffraction. Moreover, the previously unknown phase transition temperature was 350 K, as revealed by differential scanning calorimetry and powder X-ray diffraction. Attributed to ferroelasticity, domain walls were observed between the temperatures T c (Low) (223 K) and T c (High) (350 K). Furthermore, changes in chemical shifts for 1H and 13C indicated alterations in the molecular environment, whereas a notable decrease in line width was attributed to increased molecular motion freedom. Subsequently, spin-lattice relaxation times (T 1ρ values) for 1H and 13C (indicative of energy transfer) were influenced by tumbling motions. The high activation energy barrier for molecular reorientation was associated with the tumbling motion of methyl groups around the triple symmetry axis. These foundational properties guide the development of efficient organic-inorganic hybrids suitable for practical applications.

Mapping the molecular motions of 5-HT3 serotonin-gated channel by voltage-clamp fluorometry.

The serotonin-gated ion channel (5-HT3R) mediates excitatory neuronal communication in the gut and the brain. It is the target for setrons, a class of competitive antagonists widely used as antiemetics, and is involved in several neurological diseases. Cryo-electron microscopy (cryo-EM) of the 5-HT3R in complex with serotonin or setrons revealed that the protein has access to a wide conformational landscape. However, assigning known high-resolution structures to actual states contributing to the physiological response remains a challenge. In the present study, we used voltage-clamp fluorometry (VCF) to measure simultaneously, for 5-HT3R expressed at a cell membrane, conformational changes by fluorescence and channel opening by electrophysiology. Four positions identified by mutational screening report motions around and outside the serotonin-binding site through incorporation of cysteine-tethered rhodamine dyes with or without a nearby quenching tryptophan. VCF recordings show that the 5-HT3R has access to four families of conformations endowed with distinct fluorescence signatures: 'resting-like' without ligand, 'inhibited-like' with setrons, 'pre-active-like' with partial agonists, and 'active-like' (open channel) with partial and strong agonists. Data are remarkably consistent with cryo-EM structures, the fluorescence partners matching respectively apo, setron-bound, 5-HT bound-closed, and 5-HT-bound-open conformations. Data show that strong agonists promote a concerted motion of all fluorescently labeled sensors during activation, while partial agonists, especially when loss-of-function mutations are engineered, stabilize both active and pre-active conformations. In conclusion, VCF, though the monitoring of electrophysiologically silent conformational changes, illuminates allosteric mechanisms contributing to signal transduction and their differential regulation by important classes of physiological and clinical effectors.

Mapping the molecular motions of 5-HT3 serotonin-gated channel by voltage-clamp fluorometry

The serotonin-gated ion channel (5-HT3R) mediates excitatory neuronal communication in the gut and the brain. It is the target for setrons, a class of competitive antagonists widely used as antiemetics, and is involved in several neurological diseases. Cryo-electron microscopy (cryo-EM) of the 5-HT3R in complex with serotonin or setrons revealed that the protein has access to a wide conformational landscape. However, assigning known high-resolution structures to actual states contributing to the physiological response remains a challenge. In the present study, we used voltage-clamp fluorometry (VCF) to measure simultaneously, for 5-HT3R expressed at a cell membrane, conformational changes by fluorescence and channel opening by electrophysiology. Four positions identified by mutational screening report motions around and outside the serotonin-binding site through incorporation of cysteine-tethered rhodamine dyes with or without a nearby quenching tryptophan. VCF recordings show that the 5-HT3R has access to four families of conformations endowed with distinct fluorescence signatures: ‘resting-like’ without ligand, ‘inhibited-like’ with setrons, ‘pre-active-like’ with partial agonists, and ‘active-like’ (open channel) with partial and strong agonists. Data are remarkably consistent with cryo-EM structures, the fluorescence partners matching respectively apo, setron-bound, 5-HT bound-closed, and 5-HT-bound-open conformations. Data show that strong agonists promote a concerted motion of all fluorescently labeled sensors during activation, while partial agonists, especially when loss-of-function mutations are engineered, stabilize both active and pre-active conformations. In conclusion, VCF, though the monitoring of electrophysiologically silent conformational changes, illuminates allosteric mechanisms contributing to signal transduction and their differential regulation by important classes of physiological and clinical effectors.