Radial Distribution Function Research Articles

Molecular dynamics study on the physical compatibility of SEBS/plasticizer blend systems.

Thermoplastic elastomer styrene-ethylene-butylene-styrene block copolymer (SEBS) has excellent mechanical properties and aging resistance, so it has good application prospects in thermoplastic solid propellants. The selection of plasticizer is one of the keys to the formulation design of thermoplastic solid propellant. The compatibility of the plasticizer with the polymer determines the plasticizer's ability to plasticize the polymer's molecular chain segments. Herein, the compatibility of four plasticizers with SEBS was investigated, and the results declared that the order of compatibility between SEBS and the four plasticizers is SEBS/WO > SEBS/DOS > SEBS/DEP > SEBS/TA. Physical compatibility of SEBS binder with plasticizer triacetin (TA), diethyl phthalate (DEP), dioctyl sebacate (DOS), and 26# industrial white oil (WO) was simulated using molecular dynamics (MD) method via Materials Studio 8.0, and the simulation results were verified experimentally. The results showed that the compatibility of SEBS with these plasticizers can be comprehensively evaluated by analyzing solubility parameters, radial distribution functions, and blend miscibility simulations.

On the"Staple" Effect in the d-Glucose Acetylation by Choline-Chloride Ethylene Glycol and Choline-Chloride Urea Deep Eutectic Solvents.

This work employs hybrid quantum mechanics molecular mechanics simulations coupled with an umbrella sampling technique to investigate the acetylation of d-glucose with acetic anhydride in two deep eutectic solvents (DESs): choline-chloride ethylene glycol (ChCl/Etg) and choline-chloride urea (ChCl/U). The reaction proceeds spontaneously, with activation free energy barriers of 18.19 ± 0.15 and 19.83 ± 0.15 kcal/mol for ChCl/Etg and ChCl/U, respectively. These values align with literature data for similar reactions in ionic liquids, highlighting the potential of DESs as green reaction media for wood modifications, while minimizing lignocellulosic matrix degradation. Energy pair distribution analysis, radial distribution functions, and noncovalent interactions reveal a more solvated transition state compared to the initial reactant state within ChCl/Etg, facilitating the acetylation reaction. Interestingly, combined distribution function analysis unveils a "staple" effect in both solvents, potentially hindering efficient product separation. The work further explores hydrogen bond networks and Kamlet-Taft solvatochromic parameters to elucidate the role of solvents in the reaction mechanism. It was observed that a notable decrease in activation energy is accompanied by increasing net basicity, along with a reduction in the "staple" effect. This suggests that solvent parameters could serve as an effective screening tool for identifying novel and efficient DESs for wood modifications.

Mechanical Effect Produced by Photo‐Switchable Reactions: Insights from Molecular Simulations

AbstractLight‐responsive shape‐changing polymers are photonastic materials: they can convert light into mechanical energy through macroscopic transformations. Indeed, photochromic molecules embedded in these polymer films present light‐induced structural modifications that can trigger a significant macroscopic deformation. In this theoretical study based on molecular dynamics simulations, analysis tools ranging from atomic to supramolecular scales are developed to investigate this photonastic phenomenon. To this purpose, a model system built upon an azobenzene photochrome embedded in different environments (tetrahydrofuran, cis‐1,4‐polybutadiene and hydroxyl‐terminated polybutadiene) is considered. First, the impact of the environment on the photochrome properties is discussed through the analysis of the structural properties, ultra‐violet visible (UV–vis) absorption spectra and dynamical properties of the photoswitch. Then, the impact of the presence of the photochrome on the polymer is studied. At the atomic scale, the radial distribution functions show some differences between the cis and trans isomers due to geometrical effects. At the molecular scale, the analysis of the size and shape of the polymer chains reveals that the photochrome has no impact on the chain properties. Finally, at the macroscopic scale, the cohesive energy density shows that the polymer is stabilized by the presence of photochrome molecules.

Molecular understanding of the self-assembly of an N-isopropylacrylamide delivery system for the loading and temperature-dependent release of curcumin

Global changes and drug abuse are forcing humanity to face various disease problems, and alternative therapies with safe natural substances have important research value. This paper combines various techniques in quantum chemical calculations and molecular simulations to provide molecular-level insight into the dynamics of the self-assembly of N-isopropylacrylamide (NIPAM) for loading curcumin (CUR). The results indicate that increasing the chain length of NIPAM molecules reduces their efficiency in encapsulating and locking CUR, and electrostatic interactions and van der Waals interactions are the main driving forces behind the evolution of system configurations in these processes. The isopropyl groups of NIPAM and the two phenolic ring planes of CUR are the main contact areas for the interaction between the two types of molecules. The thermosensitive effect of NIPAM can alter the distribution of isopropyl groups in NIPAM molecules around CUR. As a result, when the temperature rises from ambient temperature (300 K) to human characteristic temperature (310 K), the NIPAM-CUR interactions and radial distribution functions suggest that body temperature is more suitable for drug release. Our findings offer a vital theoretical foundation and practical guidance for researchers to develop temperature-sensitive drug delivery systems tailored for CUR, addressing its clinical application bottleneck.

Investigation of the nanostructure and nanomechanical properties of the interphase in carbon fiber reinforced polyamide-6 composite

Carbon fiber reinforced polyamide-6 (CF/PA-6) composites have been widely applied in automobile, aerospace, and biomedical industries for their high mechanical properties, high thermal resistance and recyclability. On the purpose of finding ways to improve the interfacial properties, the investigation of the nanostructure and nanomechanical properties of the interphase in CF/PA-6 composites were essential. In this study, MD simulation was carried out to show the interfacial formation and nanostructure of the CF/PA-6 composite model directly at the atomic level and compute the radial distribution function, interfacial energy, total energy. Then the nanomechanical properties of the CF/PA-6 composite, such as interfacial thickness, interfacial modules, interfacial adhesion, were investigated by AFM PF-QNM model. The changes of the radical distribution function and energies over the MD simulation time indicated that the PA-6 chains adsorbed and then regularly folded on the CF surface, displaying the interfacial crystallization of the CF/PA-6 composite model. What stood out in the AFM PF-QNM tests were the abrupt decreasing of the interfacial modulus and the sharp increasing of the interfacial adhesion from those of the carbon fiber to those of the PA-6. The average interfacial thickness of the CF/PA-6 composite was 72 nm. Consistent with the simulation results, the interfacial properties were distinct from the properties of the carbon fiber and PA-6, owning to the adsorption and orderly folding of the PA-6 chains on the CF surface and the changes of the RDF and energies.

Mechanical and structural properties of monatomic zirconium metallic glass under pressure variations and annealing processes: A molecular dynamics study

The aim of this study is to investigate how different pressure levels and annealing times affect the local atomic structure and mechanical properties of pure zirconium metallic glasses. Using molecular dynamics simulations with the embedded atom method, we explored how these changes influence the material's inherent characteristics. Analysis of the radial distribution function, coordination number, and Voronoi tessellation revealed a spectrum of structural arrangements in metallic glass formed across a pressure range of 0–70 GPa. Additionally, the glass transition temperature increased with increasing pressure, accompanied by reduced free volume. The annealing process, ranging from 0 to 5 ns on metallic glass synthesized under 0 GPa pressure, showed the coordination number's significance in achieving a glassy state. Regarding mechanical behavior, both elastic constants and moduli showed a progressive increase with rising pressure, while Young's modulus and hardness displayed enhanced values with longer annealing times.

The structure of water from hot to supercooled temperatures based on analysis of experimental X-ray scattering data

An increasing number of studies support the existence of a liquid–liquid critical point (LLCP) in water, implying that under ambient conditions, water is a supercritical mixture of low-density (LDL) and high-density liquid (HDL) structures. Here, we analyse X-ray scattering data in terms of this model. Small-angle X-ray scattering data shows that anomalies are seen at temperatures as high as 360 K. By assuming the local structure in LDL-domains resembles that of the corresponding amorphous solid, we estimate the population of LDL-domains at different temperatures from pair-correlation functions (PCFs). By subtracting the LDL contribution, we isolate the PCF of the HDL component. The temperature-dependent HDL-PCFs show a feature around 4 Å in the supercooled regime, interpreted as interstitials resulting from collapse of the second coordination shell. We define the first coordination shell as neighbours up to 3.3 Å, based on an isosbestic point in the running coordination number. Our analysis shows that the HDL-domains have on average two strongly and two weakly H-bonded neighbours. The LDL population in TIP4P/2005-water is less temperature dependent than in real water, and the HDL component contains more structures with three strongly H-bonded neighbours, leading to a slight overestimation of the first peak of the PCF.

Effects of sodium ions on the tribological and antioxidation properties of borates

A borate ester (BMBS) and its sodium salts (BMBSNa) were synthesized and used as multifunctional lubricant additives in oleic acid. Results showed that BMBSNa possessed better anti-oxidation and tribological properties than BMBS. Worn surfaces analysis revealed that BMBSNa was more favorable to forming boundary film containing h-BN and FeS. Theoretical calculation suggested that BMBSNa had a higher chemical reactivity and better metal adsorption ability than BMBS. Fukui indices showed that sodium ions favor free radical reaction. Radial distribution functions (RDF) indicated that sodium ions help the adsorption of BMBSNa on the iron surface. It can be concluded that sodium ions benefit the oxidation resistance of base oil, and contribute to forming good boundary lubrication film to achieve good tribological properties.

VASE: A High-Entropy Alloy Short-Range Order Structural Descriptor for Machine Learning.

The short-range order (SRO) structure in high-entropy alloys (HEAs) is closely associated with many properties, which can be studied through density functional theory (DFT) calculations. Atomic-scale modeling and calculations require substantial computational resources, and machine learning can provide rapid estimations of DFT results. To describe SRO information in HEAs, a new descriptor based on Voronoi Analysis and Shannon Entropy (VASE) is proposed. Based on Voronoi analysis, the Shannon entropy is introduced to directly characterize atomic spatial arrangement information except for composition and atomic interactions, which is necessary for describing the disorder atomic occupancy in HEAs. The new descriptor is used for predicting the formation energy of FeCoNiAlTiCu system based on machine learning model, which is more accurate than other descriptors (Coulomb matrices, partial radial distribution functions, and Voronoi analysis). Moreover, the model trained based on VASE descriptors exhibits the best predictive performance for unrelaxed structures (24.06 meV/atom). The introduction of Shannon entropy provides an effective representation of atomic arrangement information in HEAs, which is a powerful tool for investigating the SRO phenomena.

Structure and interactions of CO2 with reline (a 1:2 choline chloride – Urea mixture) according to quantum chemical calculations and molecular dynamics simulation

Quantum chemical DFT calculations [B3LYP+GD3/6-311++g(2d,2p)] of the structure and interactions in various complexes of CO2 molecule with a choline cation, a chloride anion, urea molecules, a choline chloride ion pair and a 1:2 choline chloride – urea complex were carried out. The contributions of Coulomb and van der Waals interactions were calculated. The QTAIM method was used to evaluate the strength of various bonds. A molecular dynamics simulation of CO2 molecules in reline in the NPT ensemble (1 atm, 298 K) was also carried out. The radial distribution functions of the particle centers of mass, local mole fraction functions, spatial distribution functions, and density profiles were calculated. Stronger interactions, compared to the other DES components, were observed in case of the chloride anion and the CO2 molecule according to the DFT calculations. However, in the system, stronger interactions were observed between the chloride anion and the system components, namely NHCl and OHCl hydrogen bonds. This made the chloride anion inaccessible and unable to interact with the CO2 molecule, according to the MD simulation results. Additionally, the presence of a fairly extensive surface layer containing DES and CO2 molecules was shown.

Biomineral photonic materials with a gradient structure: The ligament of the pearl oyster Pinctada margaritifera

The bivalve fibrous ligaments (FLs) are unusual biomineralized materials evolved to open two shell valves as needed. For a long time, the inside beautiful structural colors of the FLs have received little attention. Here, using optical microscopy, SEM, and fiber optic spectrometry combined with the image processing method and pair correlation function (Pcf) analysis, we investigate the structure and optical property of the FL of the pearl oyster Pinctada margaritifera. In this FL, we find that: (1) the aragonite fibers are uniform in diameter with an average of 98 ± 10 nm; (2) they are spatially organized with short-range order; and (3) they vary gradiently in their nearest-neighbor distance (d) from 148 nm to 103 nm along the lateral-inner direction of the FL. Therefore, this FL possesses a 2D amorphous gradient photonic structure, which results in that the FL displays extremely variable structural colors spanning from blue to yellow. In short, this work provides a new model of biological photonic structure, which may inspire the design and synthesis of novel photonic materials.

The acquisition and calibration of coarse-grained force field parameters for graphene/nitrile rubber nanocomposites

Graphene (GNS) is an ideal reinforcing material for developing high-performance nitrile rubber (NBR) nanocomposites to withstand complex and harsh working conditions. The mesoscale molecular simulation is significant in exploring the microscopic mechanism of nanocomposites. Initially, a coarse-grained (CG) scheme for NBR was established, and the potential parameter files were obtained through the iterative Boltzmann inversion method. Then, the bond and angle parameters were fitted by harmonic potential, the non-bonded interactions were fitted by LJ 12–6 potential. The CG force field parameters were coefficients of the potential function. The parameters such as the stiffness values, potential well parameter, etc., were calibrated by stretching the NBR molecular chains, and comparing the density and stretching performances of the NBR all-atomic and CG models. A rapid method for obtaining the non-bonded parameters between NBR and GNS was proposed based on the radial distribution function curves. The non-bonded parameters were calibrated by comparing GNS pull-out simulations, and the density and tensile properties of the GNS/NBR models. Finally, the CG force field parameters applicable to the GNS/NBR nanocomposites were obtained. The study is expected to be significant for subsequent mesoscale studies on GNS/NBR nanocomposites.

Study on the Repair Effect of Self-Healing Cementitious Material with Urea-Formaldehyde Resin/Epoxy Resin Microcapsule

Recent studies on microencapsulated self-healing cementitious materials have primarily focused on the particle size and preparation methods of the microcapsules. However, there has been limited attention paid to the microscopic aspects, such as the selection of curing agents and the curing duration of these materials. In this study, urea-formaldehyde resin/epoxy resin E-51 microcapsules were synthesized through in situ polymerization. This research investigates the feasibility of self-healing from a molecular mechanism perspective and evaluates the repair performance of microencapsulated self-healing cement mortar with varying microcapsule concentrations, curing agent types, and curing ages. The findings demonstrate that the microcapsule shells bond effectively with the cementitious matrix, with radial distribution function peaks all located within 3.5 Å. The incorporation of microcapsules enhanced the tensile strength of the modified cement mortar by 116.83% and increased the failure strain by 110%, indicating improved adhesion and mechanical properties. The restorative agent released from the microcapsule core provided greater strength after curing compared to the uncured state. Although the overall strength of the microencapsulated self-healing cement mortar decreased with higher microcapsule concentrations, the repair efficiency improved. The strength recovery rate of 28-day aged modified cement mortar had a significant improvement with the addition of X and Y curing agents, respectively.

Differential study on the thermal–physical properties of metal and its oxide nanoparticle-formed nanofluids: Molecular dynamics simulation investigation of argon-based nanofluids

Abstract The influence of nanoparticle shape, volume fraction, and temperature on the thermal properties of nanofluids plays a pivotal role in engineering applications. However, there remains a considerable lack of systematic research comprehensively considering these factors to study the similarities and differences in the thermal properties of nanofluids composed of metals and their oxides and to conduct in-depth analyses of their internal mechanisms and characteristics. In this study, molecular dynamics simulations were conducted, employing reversing perturbation non-equilibrium molecular dynamics and non-equilibrium molecular dynamics methods. The thermal conductivity and viscosity of Al–Ar and Al2O3–Ar nanofluids were thoroughly investigated under the various influencing factors. Results reveal that under identical conditions, the thermal conductivity of Al–Ar nanofluid surpasses that of Al2O3–Ar nanofluid, exemplified by values such as 0.1832 W/m K (Al–Ar, 1.5%, cylinder, 86 K) versus 0.17745 W/m K (Al2O3–Ar, 1.5%, cylinder, 86 K). Furthermore, the viscosity of Al–Ar nanofluid is lower than that of Al2O3–Ar nanofluid, demonstrated by values such as 0.0004882 Pa S (Al–Ar nanofluid, 86 K, 2.5%, platelets) compared to 0.008975 Pa S (Al2O3–Ar nanofluid, 86 K, 2.5%, platelets). Subsequently, this study analyzed the difference in thermal conductivity between the two nanofluids from the perspective of microscale interface heat conduction by comparing the phonon density of states curves of Al, Ar, and Al2O3 in the two nanofluids for overlap. Subsequently, through radial distribution function analysis, the viscosity difference between Al–Ar and Al2O3–Ar nanofluids is explained based on nanofluid–solid interface and microstructural considerations. This research addresses the comprehensive lack of comparative studies on the thermal properties of nanofluids formed by metals and their oxides. The internal mechanisms underlying the thermal property differences of nanofluids formed by metals and their oxides were revealed from a microscopic perspective, which holds significant implications for the engineering applications of nanofluids.

Binary phase behavior of select organosulfur compounds in supercritical carbon dioxide: A Monte Carlo molecular simulation study.

Pressure-composition binary phase diagrams were determined for methanethiol, dimethyl sulfide, thiophene, benzothiophene, or dibenzothiophene with carbon dioxide at temperatures from 363 to 453K and pressures from 2 to 20 MPa. Utilizing Gibbs ensemble Monte Carlo molecular simulation, phase coexistence compositions were determined, along with the impact of 4% water cosolvent on select results. Solution structure as a function of pressure and temperature is characterized via radial distribution functions. Comparison to available experimental composition data gives overall mean absolute percentage deviations of 2.2% for thiophene, 37% for methanethiol, and 99% for benzothiophene. Solubilities in a CO2-rich phase are calculated to be sufficient to allow extraction and detection of the compounds studied here via supercritical fluid chromatography and mass spectrometry as a possible analysis approach for future Mars rover missions.

PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics.

PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.

Instrumental broadening and the radial pair distribution function with 2D detectors.

The atomic pair distribution function (PDF) is a real-space representation of the structure of a material. Experimental PDFs are obtained using a Fourier transform from total scattering data which may or may not have Bragg diffraction peaks. The determination of Bragg peak resolution in scattering data from the fundamental physical parameters of the diffractometer used is well established, but after the Fourier transform from reciprocal to direct space, these contributions are harder to identify. Starting from an existing definition of the resolution function of large-area detectors for X-ray diffraction, this approach is expanded into direct space. The effect of instrumental parameters on PDF peak resolution is developed mathematically, then studied with modelling and comparison with experimental PDFs of LaB6 from measurements made in different-sized capillaries.

Mixing in two-dimensional shear flow with smooth fluctuations.

Chaotic variations in flow speed up mixing of scalar fields via intensified stirring. This paper addresses the statistical properties of a passive scalar field mixing in a regular shear flow with random fluctuations against its background. We consider two-dimensional flow with shear component dominating over smooth fluctuations. Such flow is supposed to model passive scalar mixing, e.g., inside a large-scale coherent vortex forming in two-dimensional turbulence or in elastic turbulence in a microchannel. We examine both the decaying case and the case of the continuous forcing of the scalar variances. In both cases dynamics possesses strong intermittency, which can be characterized via the single-point moments and correlation functions calculated in our work. We present general qualitative properties of pair correlation function as well as certain quantitative results obtained in the framework of the model with fluctuations that are short correlated in time.

Novel chitosan-oligosaccharide derivatives as fluorescent green corrosion inhibitors for P110 steel

In the exploitation of seawater resources, the transported pipelines are frequently corroded, resulting in economic losses and environmental pollution. The development of corrosion inhibitors is an effective measure to mitigate the corrosion of metals in seawater. In this work, novel chitosan oligosaccharide derivatives (CF) were synthesized as fluorescent eco-friendly corrosion inhibitor by modifying fluorescent monomers. The characterization of CF revealed excellent fluorescence intensity, promising the potential for on-line detection. The inhibition performance of CF on P110 in 3.5 wt% NaCl solution was investigated through experimental evaluation and theoretical analysis. The electrochemical measurements indicated that the corrosion inhibition efficiency was increased from 61.00 % to 91.19 % with the introduction of fluorane. Adsorption isotherm and XPS analysis demonstrated that CF is designed to protect metal by forming the composite film on P110 through physical and chemical adsorption. In addition, theoretical calculations revealed differences in the interaction energies, radial distribution functions and diffusion coefficients of inhibitors on the Fe (110) surface. These theoretical results aligned with the experiments and confirmed the excellent ability of CF in metal corrosion protection from the molecular perspective. This new chitosan derivative provides new possibilities for the development of the green composite inhibitor that allows on-line detection.

Investigating Shear Stress of Ice Accumulated on Surfaces with Various Roughnesses: Effects of a Quasi-Water Layer.

The investigation of the anti-icing/deicing is essential because the icing phenomenon deteriorates the natural environment and various projects. By conducting molecular dynamics simulation, this work analyzes the effect of the quasi-water layer on the ice shear stress over smooth and rough surfaces, along with the underlying physics of the quasi-water layer. The results indicate that the thickness of the quasi-water layer monotonically increases with temperature, resulting in a monotonic decrease in the ice shear stress on the smooth surface. Due to the joint effects of the smooth surface wettability and the quasi-water layer, the ice shear stress increases and then decreases to almost a constant value when the surface changes from a hydrophobic to a hydrophilic one. For rough surfaces with stripe nanostructures, when the width of the bump for one case equals the depression for the other case, the variations of shear stress with height for these two cases are almost the same. The rough surface is effective in reducing the ice shear stress compared to the smooth surface due to the thickening of the quasi-water layer. Each molecule in the quasi-water layer and its four nearest neighboring molecules gradually form a tetrahedral ice-like structure along the direction away from the surface. The radial distribution function also shows that the quasi-water layer resembles the liquid water rather than the ice structure. These findings shed light on developing anti-icing and deicing techniques.