Experimental Radial Distribution Functions Research Articles

Lessons Learned from Multiobjective Automatic Optimizations of Classical Three-Site Rigid Water Models Using Microscopic and Macroscopic Target Experimental Observables.

The development of accurate water models is of primary importance for molecular simulations. Despite their intrinsic approximations, three-site rigid water models are still ubiquitously used to simulate a variety of molecular systems. Automatic optimization approaches have been recently used to iteratively refine three-site water models to fit macroscopic (average) thermodynamic properties, providing state-of-the-art three-site models that still present some deviations from the liquid water properties. Here, we show the results obtained by automatically optimizing three-site rigid water models to fit a combination of microscopic and macroscopic experimental observables. We use Swarm-CG, a multiobjective particle-swarm-optimization algorithm, for training the models to reproduce the experimental radial distribution functions of liquid water at various temperatures (rich in microscopic-level information on, e.g., the local orientation and interactions of the water molecules). We systematically analyze the agreement of these models with experimental observables and the effect of adding macroscopic information to the training set. Our results demonstrate how adding microscopic-rich information in the training of water models allows one to achieve state-of-the-art accuracy in an efficient way. Limitations in the approach and in the approximated description of water in these three-site models are also discussed, providing a demonstrative case useful for the optimization of approximated molecular models, in general.

An Efficient Reactive Force Field without Explicit Coordination Dependence for Studying Caustic Aluminum Chemistry.

Reactive force fields (RFFs) are an expedient approach to sample chemical reaction paths in complex systems, relative to density functional theory. However, there is continued need to improve efficiencies, specifically in systems that have slow transverse degrees of freedom, as in highly viscous and superconcentrated solutions. Here, we present an RFF that is differentiated from current models (e.g., ReaxFF) by omitting explicit dependence on the atom coordination and employing a small parameter set based on Lennard-Jones, Gaussian, and Stillinger-Weber potentials. The model was parametrized from AIMD simulation data and is used to model aluminate reactivity in sodium hydroxide solutions with extensive validation against experimental radial distribution functions, computed free energy profiles for oligomerization, and formation energies. The model enables simulation of early stage Al(OH)3 nucleation which has significant relevance to industrial processing of aluminum and has a computational cost that is reduced by 1 order of magnitude relative to ReaxFF.

Kinetics and Mechanisms of Pressure-Induced Ice Amorphization and Polyamorphic Transitions in a Machine-Learned Coarse-Grained Water Model.

Water glasses have attracted considerable attention due to their potential connection to a liquid-liquid transition in supercooled water. Here we use molecular simulations to investigate the formation and phase behavior of water glasses using the machine-learned bond-order parameter (ML-BOP) water model. We produce glasses through hyperquenching of water, pressure-induced amorphization (PIA) of ice, and pressure-induced polyamorphic transformations. We find that PIA of polycrystalline ice occurs at a lower pressure than that of monocrystalline ice and through a different mechanism. The temperature dependence of the amorphization pressure of polycrystalline ice for ML-BOP agrees with that in experiments. We also find that ML-BOP accurately reproduces the density, coordination number, and structural features of low-density (LDA), high-density (HDA), and very high-density (VHDA) amorphous water glasses. ML-BOP accurately reproduces the experimental radial distribution function of LDA but overpredicts the minimum between the first two shells in high-density glasses. We examine the kinetics and mechanism of the transformation between low-density and high-density glasses and find that the sharp nature of these transitions in ML-BOP is similar to that in experiments and all-atom water models with a liquid-liquid transition. Transitions between ML-BOP glasses occur through a spinodal-like mechanism, similar to ice crystallization from LDA. Both glass-to-glass and glass-to-ice transformations have Avrami-Kolmogorov kinetics with exponent n = 1.5 ± 0.2 in experiments and simulations. Importantly, ML-BOP reproduces the competition between crystallization and HDA→LDA transition above the glass transition temperature Tg, and separation of their time scales below Tg, observed also in experiments. These findings demonstrate the ability of ML-BOP to accurately reproduce water properties across various regimes, making it a promising model for addressing the competition between polyamorphic transitions and crystallization in water and solutions.

Short range order of methanol

The structure of liquid methanol has previously been investigated using experimental and computational methods, such as density functional theory and molecular dynamics simulations. Some studies suggested that the liquid consists of cyclic structures and others of open chains of molecules, without agreement. We apply the quasi-crystalline model to analyze the short-range order represented in the radial distribution functions obtained from neutron diffraction experiments. This analysis is complemented by molecular dynamics simulations of methanol with the OPLS/2016 potential to obtain the radial distribution functions. The reference short-range orders examined in the model were selected from observed and proposed solid phases of methanol. The short-range order at T=-80°C and at ambient conditions matched that of the α-phase, corresponding to open chains, and the short-range order at T=253°C and P = 14.3 MPa matched the 4R structure corresponding to cyclic tetramer. We found no suitable structure to represent the order for the sub-critical and super-critical states, T = 253 °C and P = 117.7 MPa and T = 202 °C and P = 73.7 MPa. The OPLS/2016 radial distribution functions from the molecular dynamics simulations did not fit the experimental site-site radial distribution functions. However, the short-range orders found at ambient conditions and T=-80°C for the computed radial distribution functions with the quasi-crystalline model, agree with those found on the experimental radial distribution functions.

Ultimate sensitivity of radial distribution functions to architecture of PtCu bimetallic nanoparticles

Bimetallic nanoparticles containing platinum and another d-metal are highly perspective catalysts with stability and activity superior to a single-metal platinum materials. It is known that the improvement of catalytic properties depends both from the composition and from the structural arrangement of atoms in bimetallic nanoparticles. This leads to importance of the experimental determination of the nanoparticles architecture (random solid solution, Janus, core–shell or “gradient”) for the search of novel bimetallic systems. We considered the platinum–copper nanoparticles synthesized by simultaneous or multistage sequential depositions of metals. The insight of the architecture of bimetallic PtCu nanoparticles was obtained by the study of radial distribution functions (RDFs) of metal atoms. The RDFs were obtained both theoretically, using molecular dynamics simulations, and experimentally, from the analysis of the extended X-ray absorption fine structure (EXAFS) spectra at Pt L3- and Cu K- edges. Machine learning (ML) algorithms revealed the outstanding sensitivity of the theoretical RDFs to the architecture of the bimetallic nanoparticles: the correct architecture can be determined with 99 % confidence in terms of F1 score. The application of the variety of ML classification methods to the experimental RDFs showed the benefit K-Neighbors classification method.

Exploring the Formation Mechanism of Coamorphous Andrographolide-Oxymatrine Based on Molecular Dynamics and Spectroscopy

Coamorphous drug delivery systems have shown great potential in improving the solubility and bioavailability of poorly water-soluble drugs. However, the coamorphous formation mechanism remains unclear. In this study, coamorphous andrographolide (AP) - oxymatrine (OMT) was successfully prepared by solvent evaporation and characterized by PXRD and DSC. The potential groups of intermolecular interactions in coamorphous binary systems were predicted by the molecular electrostatic potential (ESP) in the density functional theory (DFT) and the HOMO and LUMO in the molecular frontier orbitals, which had been confirmed by FTIR, FT-NIR, and Raman spectroscopy. Molecular dynamics (MD) was used to explore the mechanism of coamorphous formation. The results of the solvent-state radial distribution function (RDF) showed that the hydrogen bonds between AP and OMT molecules were irregular and intermittent in the solvent system of AP-OMT-methanol (MeOH) until MeOH was completely volatilized to form a stable coamorphous AP-OMT system, which has been preliminarily verified by solvent-state FT-NIR and solvent-state Raman spectroscopy. In addition, the solubility of coamorphous AP-OMT was significantly higher than that of crystalline AP. The results of intrinsic dissolution experiments showed that the intrinsic dissolution rate (IDR) of coamorphous AP-OMT was 2.5 times that of crystalline AP, although recrystallization occurred during dissolution. In conclusion, the results of the experimental solvent-state RDF, solvent-state FT-NIR, and solvent-state Raman spectroscopy can be used to better understand the coamorphous formation process and to guide the preparation of coamorphous AP-OMT.

The molecular model of Marcellus shale kerogen: Experimental characterization and structure reconstruction

A realistic three-dimensional (3D) kerogen molecular model adds significant values in petrographical evaluation in shale, especially it is essential to conduct molecular simulation for gas storage and transport behaviors in shale. In this study, the 3D kerogen molecular structure of Marcellus shale was reconstructed based on molecular simulation, and eight experimental techniques, including 13C nuclear magnetic resonance (13C NMR) spectroscopy, Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), high-resolution transmission electron microscopy (HRTEM), elemental analysis, helium porosimetry, low-pressure CO2 adsorption, and radial distribution function (RDF) obtained from synchrotron X-ray. The XPS data provides elemental compositions and the contents of functional groups of carbon, oxygen, nitrogen and sulfur on the kerogen surface. FTIR and 13C NMR spectroscopy provide the contents of aliphatic chains and aromatic rings. The two-dimensional (2D) kerogen molecular structure was initially constructed, and the connection of kerogen fragments was verified by comparing the experimental and calculated 13C NMR spectra. Then, fourteen 2D kerogen molecules were used to reconstruct the 3D kerogen molecular structure. Experimental helium density and micropore volume were used to verify the density and micropore structure of the final 3D model. Experimental RDF data were also used to analyze the spatial distribution of the kerogen atoms. The reconstructed 3D kerogen molecular structure of Marcellus shale contains 5936 atoms (C2856H2492N56O532), and the unit cell dimension is 3.755 × 3.755 × 3.755 nm. This study provides a systematic approach to establish a realistic 3D kerogen molecular model by leveraging the advantages of various techniques. The established Marcellus kerogen model lays the foundation for future fluid transport and storage studies.

Application of fragmentary model to analysis of the atomic structure of amorphous materials

Experimental atomic radial distribution functions, obtained from diffraction amorphous materials, are proposed to be interpreted using the model curves built upon the complete structural data of crystal analogues or upon the separate fragments of their structure. This modelling technique is called a fragmentary model. A model atomic radial distribution function is a radial cross section of the spherically symmetric function of interatomic distances. It characterises a nanodispersed diffraction amorphous polycrystal as uniquely as the values of interplanar spacings and intensities characterise a regular polycrystal. Comparing the model and experimental atomic radial distribution functions by the maxima positions we can perform the “identification” and “phase analysis” of nanodispersed diffraction amorphous polycrystals and define the crystalline compounds whose fragments form the structure of glass.

Parametrizing hydrogen bond interactions in dissipative particle dynamics simulations: The case of water, methanol and their binary mixtures

Simulating water has always been a challenge. Due to the intrinsic hydrogen bond interactions, water exhibits structural properties, such as a tetrahedral coordination resulting in a specific Radial Distribution Function (RDF), which are not trivial to predict computationally. In this paper, we attempt to use coarse-grained Dissipative Particle Dynamics (DPD) simulations to parameterize the hydrogen bond interactions without violating the classical DPD framework. We model the hydrogen bond interactions by incorporating a Morse potential, where the parameters are computed by taking the experimental enthalpy of evaporation and hydrogen bond distances as reference. We show that with the proposed procedure the RDF, the coordination number, the isothermal compressibility, and the three-body angular distributions (to demonstrate the tetrahedral structure) of pure water are predicted in great extent compatible with the experiments. To test the applicability of the procedure to mixtures, we simulated pure methanol and methanol/water mixtures at different molar fractions. The predicted RDF profiles for methanol-methanol, methanol-water and water-water represent the characteristic experimental RDF behavior. Moreover, the calculated negative excess volumes as a function of mole fraction compare quite well with the experimentally observed excess volumes. Our findings motivate the further development and use of DPD simulations in modeling hydrogen bond interactions, which are crucial not only in water (or alcohols), but in more complex systems such as biomolecules, proteins or biopolymers.

Chemical Ordering in Ni66.7 In33.3 Liquid Alloy

Short range order structure of liquid Ni66,7In33,3 alloy has been studied by means of X-ray diffraction method at temperatures 1235; 1260 and 1335 K. Experimental structure factors and radial atomic distribution function are analyzed. It is shown that structure of Ni66,7In33,3 in liquid state reveals chemical ordering, like to Ni2In type structure

Molecular Dynamics Investigation of Graphene Nanoplate Diffusion Behavior in Poly-α-Olefin Lubricating Oil

Graphene as a type of novel additive significantly enhanced the tribological performance of blended lubricating oil. However, the dispersibility of graphene with long-term stability in lubricating oil is still a challenge. Chemical modification for graphene, rather than using surfactants, provided a better method to improve the dispersibility of graphene in lubricants. In this study, the equilibrium molecular dynamics (EMD) simulations were carried out to investigate the diffusion behavior of graphene nanoplates in poly-α-olefin (PAO) lubricating oil. The effects of graphene-size, edge-functionalization, temperature, and pressure on the diffusion coefficient were studied. In order to understand the influence of edge-functionalization, three different functional groups were grafted to the edge of graphene nanoplates: COOH, COON(CH3)2, CONH(CH2)8CH3 (termed GO, MG, and AG, respectively). The EMD simulations results demonstrated that the relationships between diffusion coefficient and graphene-size and number of functional groups were linear while the temperature and pressure had a nonlinear influence on the diffusion coefficient. It was found that the larger dimension and more functional groups provided the lower diffusion coefficient. AG with eight CONH(CH2)8CH3 groups exhibited the lowest diffusion coefficient. Furthermore, the experimental results and radial distribution function for graphene-PAO illustrated that the diffusion coefficient reflected the dispersibility of nanoparticles in nanofluids to some degree. To our best knowledge, this study is the first time the diffusion behavior of graphene in PAO lubricating oil was investigated using EMD simulations.

Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties.

The structural properties of three- and four-site water models are improved by extending the ForceBalance parametrization code to include a new methodology allowing for the targeting of any radial distribution function (RDF) during the parametrization of a force field. The mean squared difference (MSD) between the experimental and simulated RDFs contributes to an objective function, allowing for the systematic optimization of force field parameters to reach closer overall agreement with experiment. RDF fitting is applied to develop modified versions of the TIP3P and TIP4P/2005 water models in which the Lennard-Jones potential is replaced by a Buckingham potential. The optimized TIP3P-Buckingham and TIP4P-Buckingham potentials feature 93 and 98% lower MSDs in the OO RDF compared to the TIP3P and TIP4P/2005 models respectively, with marked decreases in the height of the first peak. Additionally, these Buckingham models predict the entropy of water more accurately, reducing the error in the entropy of TIP3P from 11 to 3% and the error in the entropy of TIP4P/2005 from 11 to 2%. These new Buckingham models have improved predictive power for many nonfitted properties particularly in the case of TIP3P. Our work directly demonstrates how the Buckingham potential can improve the description of water's structural properties beyond the Lennard-Jones potential. Moreover, adding a Buckingham potential is a favorable alternative to adding interaction sites in terms of computational speed on modern GPU hardware.

Atomic Structure of the Amorphous Metallic Alloy Al83.5Ni9.5Si1.4La5.6

The atomic structure of the amorphous metallic alloy Al83.5Ni9.5Si1.4La5.6 is investigated based on the analysis of the experimental atomic radial distribution function (ARDF) in the fragmentary model. A comparative analysis of the most probable interatomic distances in the alloy and possible compounds based on it has demonstrated the presence of crystalline nuclei of the following phases: Al3La, Al3Ni, Al2.12La0.88, Al3Ni5, and Al. The largest ones (1–2 nm) are nuclei of the Al3Ni and Al compound, while the majority nuclei of all the other phases had sizes of about 7 A. Al and Al3Ni, as well as Al11La3 and Al5.56LaNi1.44 are observed in the crystallized alloy.

Domain size polydispersity effects on the structural and dynamical properties in lipid monolayers with phase coexistence.

In lipid monolayers with phase coexistence, domains of the liquid-condensed phase always present size polydispersity. However, very few theoretical works consider size distribution effects on the monolayer properties. Because of the difference in surface densities, domains have excess dipolar density with respect to the surrounding liquid expanded phase, originating a dipolar inter-domain interaction. This interaction depends on the domain area, and hence the presence of a domain size distribution is associated with interaction polydispersity. Inter-domain interactions are fundamental to understanding the structure and dynamics of the monolayer. For this reason, it is expected that polydispersity significantly alters monolayer properties. By means of Brownian dynamics simulations, we study the radial distribution function (RDF), the average mean square displacement and the average time-dependent self-diffusion coefficient, D(t), of lipid monolayers with normally distributed size domains. For this purpose, we vary the relevant system parameters, polydispersity and interaction strength, within a range of experimental interest. We also analyze the consequences of using a monodisperse model to determine the interaction strength from an experimental RDF. We find that polydispersity strongly affects the value of the interaction strength, which is greatly underestimated if polydispersity is not considered. However, within a certain range of parameters, the RDF obtained from a polydisperse model can be well approximated by that of a monodisperse model, by suitably fitting the interaction strength, even for 40% polydispersities. For small interaction strengths or small polydispersities, the polydisperse systems obtained from fitting the experimental RDF have an average mean square displacement and D(t) in good agreement with that of the monodisperse system.

Structural parameters of the nearest environment of ions in aqueous solutions of ytterbium chloride

The radial distribution functions (RDFs) of aqueous solutions of ytterbium chloride were calculated using previously collected X-ray diffraction data for a wide range of solution concentrations under ambient conditions. Different solution structure models were constructed. Theoretical RDFs were calculated for each model. The optimum models for all systems studied were chosen based on the best fit between the theoretical and experimental RDFs. Quantitative characteristics of the nearest environment of Yb3+ and Cl– ions in solutions, namely, the coordination number, interparticle distances, and types of ion pairs were determined. The average number of water molecules in the first coordination sphere of the cation decreases from 8.2 to 6.0 as the solution concentration increases. The structure of all systems investigated is governed by non-contact ion associates throughout the concentration range studied.

Local structural behavior of PbZr0.5Ti0.5O3 during electric field application via in situ pair distribution function study

The local structural behavior of PbZr0.5Ti0.5O3 (PZT 50/50) ceramics during application of an electric field was investigated using pair distribution function (PDF) analysis. In situ synchrotron total scattering was conducted, and the PDFs were calculated from the Fourier transform of the total scattering data. The PDF refinement of the zero-field data suggests a local-structure model with [001] Ti-displacement and negligible Zr-displacement. The directional PDFs at different field amplitudes indicate the bond-length distribution of the nearest Pb-B (B = Zr/Ti) pair changes significantly with the field. The radial distribution functions (RDFs) of a model for polarization rotation were calculated. The calculated and the experimental RDFs are consistent. This result suggests the changes in Pb-B bond-length distribution could be dominantly caused by polarization rotation. Peak fitting of the experimental RDFs was also conducted. The peak position trends with increasing field are mostly in agreement with the calculation result of the polarization rotation model. The area ratio of the peaks in the experimental RDFs also changed with field amplitude, indicating that Zr atoms have a detectable displacement driven by the electric field. Our study provides an experimental observation of the behaviors of PZT 50/50 under field at a local scale which supports the polarization rotation mechanism.

STRUCTURE OF NEAREST ENVIRONMENT OF IONS IN AQUEOUS CESIUM IODIDE SOLUTIONS FROM X-RAY DIFFRACTION DATA

Comparatively large amount of works has been devoted to the investigation of the nearest environment of cesium ions in aqueous solutions. But up to date there are no precise quantitative parameters of it. Information about influence of concentration on cesium salts solutions structure is also absent. In order to get the coordination number of Cs+ ion and its dependence on the amount of dissolved salt the set of aqueous solutions of cesium iodide have been studied by X-ray diffraction method in wide concentration range under ambient conditions. Radial distribution functions (RDFs) of the solutions investigated have been calculated from experimental intensity curves of X-ray scattering. Interpretation of experimental peaks on RDFs has been made. On the basis of experimental results and literature information some physically reasonable models of solution have been constructed. Theoretical RDFs have been calculated for every model. Then an optimization procedure has also been made. On the ground of the best fitness between experimental and theoretical RDFs the optimal models for every solution have been found. All quantitative parameters have been tabulated and analyzed. Hydration numbers of Cs+ and I- increase with dilution, reaching in the solution of molar ratio 1:80 values 6.3 and 4.1, respectively. Interparticle distances of Cs+–ОН2 and I- –ОН2 are equal approximately to 0.312 and 0.359 nm. The ions do not form the second coordination shells. It has been determined that contact ion pairs Cs+–I- exist in whole concentration range investigated.Forcitation:Smirnov P.R., Grechin O.V., Voevodina E.A. Structure of nearest environment of ions in aqueous cesium iodide solutions from X-ray diffraction data. Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol. 2017. V. 60. N 7. P. 21-26.

Doped Amorphous Ti Oxides To Deoptimize Oxygen Reduction Reaction Catalysis

The oxygen reduction reaction (ORR) is a major factor that drives galvanic corrosion. To better understand how to tune materials to better inhibit catalytic ORR, we have identified an in silico procedure for predicting elemental dopants that would cause common, natively formed titanium oxides to better suppress this reaction. In this work, we created an amorphous TiO2 surface model that is in good agreement with experimental radial distribution function data and contains reaction sites capable of replicating experimental ORR overpotentials. Dopant performance trends predicted with our quantum chemistry model mirrored experimental results, and our top three predicted dopants (Mn, Al, and V, each present at doping concentrations of 1%) were experimentally verified to lower ORR currents under alkaline conditions by up to 77% vs the undoped material. These results show the robustness of calculated thermodynamic descriptors for identifying poor, TiO2-based ORR catalysts. This also opens the possibility of usin...

The effects of refractory elements on Ni-excesses and Ni-depletions at γ(f.c.c.)/γ′(L12) interfaces in model Ni-based superalloys: Atom-probe tomographic experiments and first-principles calculations

The effects of refractory (R) elements (R = Re, Ru, W, or Ta) on a base Ni-Al-Cr alloy are studied, for an aging temperature of 1073 K (800 °C) and an aging time of 256 h, employing atom-probe tomography (APT) and first-principles calculations. We find that there are strong attractive chemical binding energies between R-elements and solute (S) atoms (S = Al, Cr) in Ni-Al-Cr based alloys utilizing experimental partial radial distribution function (RDF) results, and first-principles calculations performed at 0 K. We demonstrate that correlated R-S binding energies play a key role in the observed Ni retention-excesses at γ(f.c.c.)/γ′(L12-structure) interfaces at aging times as long as 256 h. The total reduction of the γ(f.c.c.)/γ′(L12) interfacial energy, as a result of Ni interfacial-excesses in both γ(f.c.c.)-matrix and γ′(L12)-precipitates, lies between −0.16 ± 0.06 mJ m−2 and −0.05 ± 0.02 mJ m−2. The R-S binding energies cause changes in the compositional diffusion flux-vectors in and out of γ′(L12)-precipitates, which result in larger solvent Ni retention-excesses and wider interfacial compositional widths at 256 h, when compared with the base Ni-Al-Cr alloy. Refractory elements are slow diffusers in nickel and the attractive R-Cr binding energies decelerate the solute diffusional fluxes, which results in a decrease of the Ni diffusivity, which in turn hinders the flux of Ni atoms away from the γ(f.c.c.)/γ′(L12) interfaces.

Li+ Local Structure in Li–Tetraglyme Solvate Ionic Liquid Revealed by Neutron Total Scattering Experiments with the 6/7Li Isotopic Substitution Technique

Equimolar mixtures of lithium bis(trifluoromethanesulfonyl)amide (LiTFSA) and tetraglyme (G4: CH3O-(CH2CH2O)4-CH3) yield the solvate (or chelate) ionic liquid [Li(G4)][TFSA], which is a homogeneous transparent solution at room temperature. Solvate ionic liquids (SILs) are currently attracting increasing research interest, especially as new electrolytes for Li-sulfur batteries. Here, we performed neutron total scattering experiments with (6/7)Li isotopic substitution to reveal the Li(+) solvation/local structure in [Li(G4)][TFSA] SILs. The experimental interference function and radial distribution function around Li(+) agree well with predictions from ab initio calculations and MD simulations. The model solvation/local structure was optimized with nonlinear least-squares analysis to yield structural parameters. The refined Li(+) solvation/local structure in the [Li(G4)][TFSA] SIL shows that lithium cations are not coordinated to all five oxygen atoms of the G4 molecule (deficient five-coordination) but only to four of them (actual four-coordination). The solvate cation is thus considerably distorted, which can be ascribed to the limited phase space of the ethylene oxide chain and competition for coordination sites from the TFSA anion.