Radial Distribution Function Research Articles

Molecular dynamics-based targeted adsorption of hazardous substances from rubberized asphalt VOCs by UiO-67

The interplay among UiO-67 and rubberized-asphalt components has been examined according to its molecular scale. The adhesion kinetics of UiO-67 to VOCs molecules in asphalt was modeled. The binding energy, radial distribution function (RDF), solubility parameters (SP), mean square displacement (MSD) and other parameters among UiO-67 to rubberized-asphalt components were evaluated in depth. The Sorption module was simulated the adsorption behavior of UiO-67 on 12 malodorous gases and 5 primary carcinogens. In combination with GC-MS results, the conjugative bonds and target attachment mechanisms for UiO-67 with VOCs were clarified. It was indicated that the binding energy among UiO-67 to the components were all negative. The radial distribution of asphalt was characterized as proximally ordered and remotely disordered. The ΔSP was less than 1.6, which was indicated that UiO-67 could be compatible with asphalt. The overall inhibition effect of UiO-67 on a group of carcinogens was exceeded 70 %. The presence of conjugation effect was allowed the adsorption sites of vinyl chloride and 1,3 butadiene to occur at high densities within the benzenoid. The concentration reduction of UiO-67 for hydrogen sulfide, carbon disulfide, and dimethyl sulfide was more than 80 %. The higher polarity was predisposed substances such as hydrogen sulfide and isobutanol to interact with the non-benzene ring region of UiO-67.

Exploring the structural feature of water, alcohols, and their binary mixtures with concrete atomic charge assignments in Dreiding forcefield

The water, alcohols, and their binary mixtures are widely used in molecular simulations. However, the Dreiding force field lacks a generally accepted method for assigning atomic charges to these solvents during simulations. In this study, we propose a universal charge assignment for water and eight water-miscible alcohols in Dreiding. Through extensive molecular simulations, we demonstrate the good accuracy of our charge assignments in displaying characteristic of these solvents and their mixtures, including liquid density and structure. Moreover, we investigate equilibrium snapshot, radial distribution function, coordination number and hydrogen bonding, all of which confirm the miscibility of alcohols with water or ethanol. Notably, we reveal that the structure diversity among different mixtures can be attributed to distinctive characteristic of alcohols, including molecular volume, as well as the number and position of hydroxyls.

Kinetic Study of the Effect of Cu Content on the Structure of CuZr Alloys

Copper-zirconium alloys are industrial materials with significant application value. Their mechanical and thermal stability properties are determined by their microstructure and dynamic characteristics. To gain a deeper comprehension of the characteristics of copper-zirconium alloys, they have been subjected to investigation through the utilization of molecular dynamics simulations. The simulations were conducted using the Materials Studio software, with the EAM potential function employed to describe the interatomic interactions. The microcanonical system synthesis (N, V, E) was selected as the method of system generation. The atomic structure, radial distribution function, and kinetic properties of three distinct ratios of copper-zirconium alloys, namely Cu300Zr700, Cu400Zr600, and Cu500Zr500, at varying temperatures were examined through the utilization of molecular dynamics simulations. The findings indicate that the mutual free energy of CuZr alloys rises in conjunction with elevated Cu atomic content, yet exerts minimal influence on their atomic diffusion state. An escalation in temperature results in a surge in the mutual free energy of the alloys and a pronounced impact on the extent of atom diffusion within the alloy system. The results are of significant value in optimizing the properties and material design of CuZr alloys.

Structural mechanism of glass transition uncovered by unsupervised machine learning

Uncovering the structural origins of the ubiquitous dynamic arrest phenomenon at the glass transition has long been a challenge due to the difficulty in identifying a rational structural representation from a disordered medium. To address this challenge, we propose a novel approach based on unsupervised learning to define a set of structural fingerprints. In this approach, complex local atomic environments, ranging from short to medium range, are captured by the discretized radial distribution function and projected onto a simple two-dimensional space using a neural network-based autoencoder. This two-dimensional space is characterized by two static structural indicators, P1 and P2, providing a comprehensive and user-friendly representation of the mysterious “glassy structure”. By employing Gaussian mixture modeling, the structural space is autonomously divided into three sections, each representing a unique cluster with similar environments. These indicators not only elucidate the glass transition but also allow for the quantitative prediction of activation barriers for local structural excitations. Furthermore, the unsupervised clustering technique can distinguish between the structural features of “hard zones” and “soft zones”, as well as recently proposed superfast “liquid-like” atoms in glass. This unsupervised machine learning approach demonstrates the utility of seemingly agnostic local structure in amorphous materials, offering insights into the long-sought structural origins of the glass transition.

Theoretical analysis of the structure, thermodynamics, and shear elasticity of deeply metastable hard sphere fluids.

The structure, thermodynamics, and slow activated dynamics of the equilibrated metastable regime of glass-forming fluids remain a poorly understood problem of high theoretical and experimental interest. We apply a highly accurate microscopic equilibrium liquid state integral equation theory, in conjunction with naïve mode coupling theory of particle localization, to study in a unified manner the structural correlations, thermodynamic properties, and dynamic elastic shear modulus in deeply metastable hard sphere fluids. Distinctive behaviors are predicted including divergent inverse critical power laws for the contact value of the pair correlation function, pressure, and inverse dimensionless compressibility, and a splitting of the second peak and large suppression of interstitial configurations of the pair correlation function. The dynamic elastic modulus is predicted to exhibit two distinct exponential growth regimes with packing fraction that have strongly different slopes. These thermodynamic, structural, and elastic modulus results are consistent with simulations and experiments. Perhaps most unexpectedly, connections between the amplitude of long wavelength density fluctuations, dimensionless compressibility, local structure, and the dynamic elastic shear modulus have been theoretically elucidated. These connections are more broadly relevant to understanding the slow activated relaxation and mechanical response of colloidal suspensions in the ultradense metastable region and deeply supercooled thermal liquids in equilibrium.

Study of molecular interaction between benzaldehyde and methanol using microwave dielectric relaxation spectroscopy and radial distribution function

A microwave dielectric relaxation study was conducted for mixtures of benzaldehyde (BZ) and methanol (MeOH) over a frequency range of 200 MHz to 20 GHz at seven different temperatures, ranging from 293.15 K to 323.15 K. The dielectric relaxation parameters, obtained through a fitting process, were used to examine their dependence on concentration and temperature. Thermodynamic parameters, such as Gibbs free energy (ΔG), molar enthalpy of activation (ΔH), and molar entropy of activation (ΔS), were evaluated using the temperature dependence of the dipolar relaxation time. The study provided valuable insights into the molecular interactions and dynamic behavior of the components in the binary mixture system. Additionally, a molecular dynamics (MD) simulation study was conducted on the binary mixture of BZ and MeOH to determine the Radial Distribution Function (RDF) and coordination number for different pairs of molecules and atoms, which revealed information about the binding and arrangement of the local structure.

Unraveling the Stability and Magnetic Properties of Bis-Hydrated Mn(II) Complexes via Tailored Ligand Design.

Exploring the electronic structure and dynamic behavior of Mn(II) complexes reveals fascinating magnetic properties and prospective biomedical applications. In this study, we investigate the solvent phase dynamics of heptacoordinated Mn(II) complexes through ab initio molecular dynamics simulations and density functional theory (DFT) calculations with effectively varying temperatures. We observed that the complex with high stability ([Mn(pmpa)(H2O)2]) remains relatively rigid as the temperature increases to 90 °C, with only a minor change in its radial distribution functions (RDFs), compared to the RDF peaks at 25 °C. To elucidate the impact of halogens on the magnetic anisotropy of seven-coordinated Mn(II) complexes, we performed both DFT and multireference calculations. This shows that the zero-field splitting (ZFS) parameter D follows the order D(I)> D(Br)> D(Cl). We observed a significant increase in the D-value following the substitution of soft Se-donors in the equatorial position and heavier halogens in the axial position. The D-value of halogen derivatives of Se-analogues varies in the order of D(Cl) < D(I) < D(Br), deviating from the regular spectrochemical series with the discrepancy between the covalency of the Mn(II)-Se bond and the ligand field strength. We anticipate that this study will enhance our understanding of the solvent phase dynamics and structural aspects of ZFS in various Mn(II) complexes with different electronic environments.

Molecular Dynamics Simulation Model of Alkali Metal Reduction of Gaseous Halides and Reaction Mechanism Analysis.

The reaction of gaseous hydrogen halides with alkali metals provides a new pathway for producing hydrogen. The structure and reactivity of alkali metals are crucial for the reduction of gaseous halides. However, traditional gas-phase reaction models fail to provide insights into the dynamic processes occurring during alkali metal reactions. In this paper, based on the reaction between Hydrogen fluoride (HF) and alkali metal sodium (Na), we have established a metallic Na slab. HF molecules were randomly inserted above the surface of the Na slab, creating a reaction model for the reduction of HF by metallic Na. The reaction of HF on the Na surface was calculated using first-principles molecular dynamics. The configuration and reaction of the Na surface and HF molecules at different times were judged by analyzing the radial distribution function and mean squared displacement. Na atoms reacted with HF to produce intermediate NaFH, and then the F-H bond broke to form NaF and H. The F-H bond breaking of intermediate NaFH was the key step, and the kinetic parameters of this key step were calculated.

Two Bond-Exchange modes in sodium silicate liquids

Because of their network structure, the diffusion mechanism of network-forming elements, namely silicon and oxygen, remains unclear. Several diffusion mechanisms have been proposed based on molecular dynamics simulations; however, the bond-exchange motion has not been quantitatively analyzed. This study introduces the concept of bond-breaking/forming particles. By treating the bond-breaking/forming events as instant particles, the bond-exchange event can be interpreted as a pair-correlation function of these particles. Here, examples of sodium silicate liquids at various pressures are presented using the results of force-field molecular dynamics simulations. Analyses of the pair correlation of bond-breaking/forming particles revealed two distinct bond-exchange modes. Only the short mode contributed to the diffusion of the network-forming elements based on comparative analysis of the pressure dependence of the integrated peaks of the pair-correlation functions and the self-diffusion coefficients of silicon.

Solvent diffusion mechanism of gun propellant revealed through molecular dynamics simulation

Drying is an important operational unit in the preparation of nitrocellulose-based gun propellant, which affects the drying quality and drying rate of the product. The diffusion properties of solvents during the drying process determine the rate of internal solvent removal from the gun propellant, so the diffusion behaviors of ethanol and acetone in the gun propellant were investigated based on molecular dynamics simulations. Three models of single-, double- and triple-base gun propellant components were established, and the interactions between the solvent and the components of gun propellant were investigated by radial distribution function, hydrogen bonding and interaction energy calculations, and the free volumes, diffusion coefficients and the activation energies of the solvents were used to describe the solvent diffusion performances. The results showed that the interaction between ethanol and the components of the gun propellant was mainly hydrogen bonding, and the interaction between acetone and the components was mainly van der Waals forces. When the mass ratio of ethanol and acetone is 1:1, the interaction energy between ethanol and the components is greater due to the presence of strong hydrogen bonding, which resulted in a higher diffusion activation energy of ethanol. However, since the molecular volume of ethanol is higher than that of acetone, it makes the diffusion coefficient of ethanol larger. Compared with single-base gun propellant, after adding nitroglycerin and nitroguanidine, the free volume fraction decreases, the sum of the interaction energies between the solvent and the components in gun propellant increases, and the diffusion activation energy increases. Hence, this present work regarding the study of solvent diffusion mechanism of gun propellant can provide theoretically guiding suggestion to the actual drying process and manufacture of gun propellant.

Comparisons between full molecular dynamics simulation and Zhang's multiscale scheme for nanochannel flows.

In a very small surface separation, the fluid flow is actually multiscale consisting of both the molecular scale non-continuum adsorbed layer flow and the intermediate macroscopic continuum fluid flow. Classical simulation of this flow often takes over large computational source and is not affordable owing to using molecular dynamics simulation (MDS) to model the adsorbed layer flow, if the flow field size is on the engineering size scale such as of 0.01-10mm or even bigger like occurring in micro or macro hydrodynamic bearings. The present paper uses full MDS to validate Zhang's multiscale flow model, which yields the closed-form explicit flow equations respectively for the adsorbed layer flow and the intermediate continuum fluid flow. Here, full MDS was carried out for the pressure-driven flow of methane in the nano slit pore made of silicon respectively with the channel heights 5.79nm, 11.57nm, and 17.36nm. According to the number density distribution, the flow areas were respectively discriminated as the adsorbed layer zone and the intermediate fluid zone. The values of the characteristic parameters for Zhang's multiscale scheme were extracted from full MDS and input to Zhang's multiscale flow equations respectively for calculating the flow velocity profile and the volume flow rates of the adsorbed layers and the intermediate fluid. It was found that for these three channel heights, the flow velocity profiles calculated from Zhang's model approximate those calculated from full MDS, while the total flow rates through the channel calculated from Zhang's model are close to those calculated from full MDS. The accuracy of Zhang's multiscale flow model is improved with the increase of the channel height. The recent modification of the optimized potential for liquid simulation (MOPLS) model was used to calculate the interaction force between two methane molecules. In order to calculate the interaction force between the wall atoms and the methane molecules accurately, our previous non-equilibrium multiscale MDS was used. The interaction forces between the methane molecule and the wall atom were obtained from the coupled potential function by the L-B mixing rule when the fluid molecules arrived at near wall. The methane molecule diameter was obtained from the radial distribution function by using equilibrium MDS under the same initial conditions. The local viscosities across the adsorbed layer were obtained from the local velocity profile by using the Poiseuille flow method. The motion equation of the methane molecule was solved by the leapfrog method. The temperature of the simulation system was checked by Bhadauria's method, i.e., the system temperature was rectified by the velocities in the y- and z-directions. The flow velocity distributions across the channel height and the volume flow rates through the channel were also calculated from Zhang's closed-form explicit flow equations respectively for the adsorbed layer flow and the intermediate fluid flow. The results respectively obtained from full MDS and Zhang's multiscale flow equations were then compared.

Edge-functionalized graphene quantum dot as a nano-biosensor for simultaneous detection of glucose, galactose and lactose

The swift and accurate diagnosis of diseases, particularly diabetes, remains a pressing and critical concern in healthcare. Monitoring blood glucose levels is imperative for diabetic patients to manage their condition effectively. Addressing this necessity, developing non-invasive, simultaneous detection devices for sugars shows immense promise. Herein, we introduce the design of a novel nano-biosensor employing edge‐functionalized graphene quantum dots, enabling the concurrent detection of three pivotal sugars: glucose, galactose, and lactose. Through comprehensive molecular dynamics simulations, we demonstrate the feasibility and stability of the proposed biosensor. Our results show that the edge-functionalization of graphene quantum dots significantly enhances their binding affinity, with calculated average number of contacts of 2174 for glucose, 1085 for galactose, and 6274 for lactose. Furthermore, the radial distribution function analysis echoed these findings, highlighting lactose’s pronounced interaction with the biosensor, followed by glucose and then galactose. The detailed analysis reveals distinct and non-overlapping sugar bindings on the nano-biosensor surface, with lactose showing the highest affinity and interaction strength, followed by glucose and galactose. This innovative approach marks a significant stride forward in biosensor technology, providing a potential avenue for precise and dependable monitoring of blood sugar levels in diabetic patients.

Molecular dynamics simulation and experimental verification of a biphasic solvent for CO2 capture

In the context of solvent-based carbon capture, researchers and industries are often interested in improvements in the efficiency of CO2 capture along with the reduction in the required energy. This study employs molecular dynamics (MD) simulation based on a reax force field and experimental investigation to study the effects and main mechanisms of a mutual amine absorbent including diethylenetriamine (DETA) and diethylethanolamine (DEEA), accompanied by NMP and water co-solvents, on the performance of CO2 capture in a phase change system. The implementation of time-dependent partial radial distribution functions (TD-PRDF, gαβrtm) and coordination number (CN) analyses revealed the significant formation of C-N bonds between carbon (C) derived from CO2 and nitrogen (N) within the solution. The direct relationship between changes in DETA molar ratios and CO2 loading, coupled with examining the catalytic role of DEEA in facilitating CO2 removal through protonation, has been thoroughly studied with MD. The experimental methodology was followed to validate the MD results. The optimum composition, DETA: DEEA: NMP with a molar ratio of 3:2.5:1, as determined through MD simulations exhibitsgαβr|tm = 9.848, CN=0.403 at tm= 1 ns. The stable C-N absorption bond length is calculated to be between 1.7 and 1.77 Å. Experimental results confirm a CO2 loading capacity of 0.93 mol/mol for this composition.

Exploring hydrophobicity or hydrophilicity of borophene surface via reactive molecular dynamics simulation

Borophene, a novel two-dimensional material unveiled in 1998, has garnered significant interest among researchers due to its distinct mechanical and electrical characteristics. Efforts to experimentally synthesize borophene continue to captivate researchers’ interest in recent years. Given the current lack of experimental studies on the interaction between water and the borophene surface, molecular dynamics simulation offers a valuable approach for predicting the substance’s reactivity with water. Additionally, such simulations can assess the hydrophilicity and hydrophobicity of borophene, providing valuable insights into its properties. In our current research, we utilized reactive molecular dynamics simulation to investigate the wetting behavior of borophene. Our findings reveal that the borophene surface exhibits hydrophobic characteristics, demonstrating anisotropic wettability. Specifically, the water contact angle was calculated to be 149.11° along the zigzag direction and 148.4° along the armchair direction. The contour map of the interaction energy between a water molecule and the borophene surface revealed a notable energy barrier in the zigzag direction. This barrier contributes to the asymmetric spreading of the water droplet on the surface. Density profiles and radial pair distribution function (RDF) diagrams of the water droplet on the borophene surface further corroborated the hydrophobic nature of borophene by indicating a significant distance between the water droplet and the surface. Moreover, analysis of the number of hydrogen bonds demonstrated that borophene efficiently utilizes nearly all its capacity to form hydrogen bonds. Additionally, we compared the wettability of borophene with that of other two-dimensional materials, such as various graphene allotropes and phosphorene, which have been subjects of recent investigation.

A method for deriving oligomers from sulfamide monomer and their application as electrolytes

This paper describes the development of a method of catalytic polymerization that was then applied to synthesize sulfate-based oligomers from sulfamide. Two molecules, copper triflate and copper acetate, catalyzed the formation of oligomers with diol monomers. Two oligomers were identified as products of the reactions. Oligomers with sulfate incorporated in the backbone proved to have an ability for ion diffusion. When the oligomers were doped with lithium salt, anion transportation was predominant, as shown by solid-state NMR. The lithium ion was found to be strongly bonded to the backbone, while the anion was highly mobile. To corroborate this finding, we conducted molecular dynamics (MD) simulations, which revealed the structural characteristics and static properties of two electrolytes containing LiTFSI and two different polyethylene oxide oligomers. Interactions between the anion and cation were analyzed through computation of the radial distribution function (RDF) and the spatial distribution function (SDF). Our findings indicate that while the anion presents weak interactions with the polymer chain, the cation interacts strongly with the oligomer backbone.

Atomic-scale deformation behavior of SiC polytypes using molecular dynamics simulation

The atomic-scale deformation behavior of the Silicon carbide (SiC) polytypes, including 3 C-SiC and 4 H-SiC, during the nanoindentation with different square-based pyramid indenter angles was investigated by molecular dynamics (MD) simulations. Detailed analyses were conducted on atomic displacement magnitude, atomic structure, radial distribution function and dislocation distribution were analyzed in-depth in both loading and unloading processes. The results show that the indentation deformation phenomenon of ‘‘pile-up’’ occurs with indenter angles below 120°. Maximum load shows a non-linear increase trend as the indenter angles increase. The residual depth of the 3 C polytype has insignificant fluctuations while that of the 4 H polytype generally increases as the angle decreases and fluctuates at the indenter angles of 100° ∼ 110°. The number of amorphous atoms in 4 H is greater than that of 3 C polytype. Most of the amorphous atoms recover to their original structure after the indenter is fully withdrawn. Dislocation analysis indicates that the total length of dislocation lines increases with larger indenter angles. The length of the 3 C dislocation line is greater than that of 4 H. At the same indenter angle, the dislocation slip depth of 3 C polytype is greater than that of 4 H polytype due to the different lattice stacking order of 3 C polytype is greater than that of 4 H polytype due to the different lattice stacking order.

Surveying the adsorption energy changes of heptane-water-surfactant mixture on the calcite surface using molecular simulation

This study utilized molecular dynamics simulations to examine the impact of surfactant and brine on the interaction between oil and calcite rock. Sodium dodecyl sulfate (SDS) functioned as the surfactant, while NaCl represented the brine, and heptane served as the organic oil phase. The introduction of NaCl led to a decrease in energy between the oil and rock molecules, from 4.18E+03 to 2.36E+03 kcal/mol. This energy reduction was changed to 2.64E+03 kcal/mol by adding surfactant. When both NaCl and SDS were present, the energy dropped to −46.636159 kcal/mol. Through the utilization of radial distribution function and concentration profiles, the study explored the location and buoyancy of heptane molecules on the calcite surface. The results highlighted the efficacy of SDS as an anionic surfactant, particularly in combination with NaCl at a temperature of 373 K, in augmenting the buoyancy of heptane molecules on calcite rock.

EXPLORING THE STRUCTURAL AND ELECTRONIC CHARACTERISTICS OF AMORPHOUS Ge – Te - In MATERIAL THROUGH AB INITIO METHODS

This study employs density functional theory (DFT) and molecular dynamics to meticulously investigate the structural and electronic properties of ternary chalcogenide compounds, specifically (GeTe4 ) 1-x Inx, and (GeTe5 )1-x Inx across a range of compositions ( x = 0, 5, 10, 15, 20 at %). Utilizing the local density approximation within the framework of first-principles calculations, we comprehensively analyze the pair correlation function, static structural factor, electronic density of states, and electronic band gap energy. Our results reveal a notable decrease in the energy band gap of Germanium-Tellurium with the incorporation of Indium atoms. The structural changes observed in the Ge-Te matrix with Indium doping, as evidenced by the changes in the pair correlation function and static structure factor, are consistent with and supportive of the observed decrease in the band gap energy. This phenomenon is primarilyattributed to the significant contribution of Indium atoms to the conduction band edge, offering new insights into the material’s electronic behaviour.

Dressing a Nonpolarizable Force Field for OH- in TIP4P/2005 Aqueous Solutions with Corrected Hirshfeld Charges.

We present a rigid model for the OH- ion parametrized for binary mixtures with TIP4P/2005-type water molecules. Li+, Na+ and K+ were selected as counterions, hence mimicking the important and widely used solutions of soluble alkaline hydroxides. The optimized atomic charge distributions were obtained by scaling in a factor of 0.85 those derived from the atomic dipole corrected Hirshfeld approach. The agreement between experimental and Molecular Dynamics simulation results is remarkable for a set of properties, namely, the dependence of the density of the solutions on the hydroxide concentration and on temperature, the structure (i.e., positions of the atom-to-atom radial distribution functions and coordination numbers), the viscosity coefficients, the surface tension, or the freezing point depression. The proposed optimized potential parameters for OH- thus enlarge the set of models comprised within the Madrid-2019 force field and widen the potential applicability of the TIP4P/2005 water model in basic environments.

Molecular Dynamics Simulations of the miR-155 Duplex: Impact of Ionic Strength on Structure and Na+ and Cl- Ion Distribution.

MiR-155 is a multifunctional microRNA involved in many biological processes. Since miR-155 is overexpressed in several pathologies, its detection deserves high interest in clinical diagnostics. Biosensing approaches often exploit the hybridization of miR-155 with its complementary strand. Molecular Dynamics (MD) simulations were applied to investigate the complex formed by miR-155 and its complementary strand in aqueous solution with Na+ and Cl- ions at ionic strengths in the 100-400 mM range, conditions commonly used in biosensing experiments. We found that the main structural properties of the duplex are preserved at all the investigated ionic strengths. The radial distribution functions of both Na+ and Cl- ions around the duplex show deviation from those of bulk with peaks whose relative intensity depends on the ionic strength. The number of ions monitored as a function of the distance from the duplex reveals a behavior reminiscent of the counterion condensation near the duplex surface. The occurrence of such a phenomenon could affect the Debye length with possible effects on the sensitivity in biosensing experiments.