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Low molecular weight liquid polybutadiene polymer flow behavior as function of shear rate, temperature, molecular structure and hydrogen bonding
Results of molecular dynamics calculations on phenol at the water liquid-vapor interface are presented. The density profile of the center of mass of phenol exhibits a maximum 1 A from the Gibbs surface toward the vapor phase, indicating that the molecule is surface-active. Changes in the profile caused by the interface extend 6 A from the Gibbs surface into the liquid, significantly more than change in the density profile of water. The most probable orientation of the solute at the surface is such that its symmetry axis is perpendicular to the interface with the OH substituent pointing toward the liquid. An additional simulation with benzene shows that this molecule at the surface most often adopts orientations parallel to the interface. Deeper in the liquid all the solutes are preferentially ordered perpendicular to the surface. In the interfacial region the orientational preferences of the solute are primarily determined by cavity formation needed to accommodate the hydrophobic portion of the dissolved molecule.
Liquid-phase resonant soft X-ray scattering (LP-RSoXS) is an emerging label-free technique to probe chemically resolved nanostructures of molecular or hybrid materials in liquid environments. Still, quantitative analysis is hindered by the pressure-induced deformation of thin silicon nitride (SiN) membranes used as windows in microfluidic flow cells, which attenuates the signal in nonlinear ways, making experimental optimization difficult. Here, in this work, we directly characterize this deformation under experimental conditions for a variety of cell configurations. We use this to develop a predictive model that combines transmission effects of SiN bowing, incident X-ray beam profiles, and material-dependent resonant scattering cross sections to simulate the effective scattering intensity at the detector across the carbon K-edge. Maps of the total signal across the flow cell window reveal that increasing the window width and polymer concentration shifts the anisotropic intensity distributions from the center toward the edges of the window. It was determined that an optimal SiN thickness of 50 nm, with a window aperture of 104 μm, maximizes the total signal for typical solute concentrations and energies across the carbon K-edge. Our results overturn the assumption that corner regions dominate the scattering signal, offering explicit design guidelines for maximizing LP-RSoXS signals and significantly advancing the quantitative application of this technique to the characterization of molecular and hybrid nanostructured materials in liquids.
Solid–liquid phase transitions are basic physical processes, but atomically resolved microscopy has yet to capture their full dynamics. A new technique is developed for controlling the melting and freezing of self–assembled molecular structures on a graphene field–effect transistor (FET) that allows phase–transition behavior to be imaged using atomically resolved scanning tunneling microscopy. This is achieved by applying electric fields to 2,3,5,6–tetrafluoro–7,7,8,8–tetracyanoquinodimethane–decorated FETs to induce reversible transitions between molecular solid and liquid phases at the FET surface. Nonequilibrium melting dynamics are visualized by rapidly heating the graphene substrate with an electrical current and imaging the resulting evolution toward new 2D equilibrium states. An analytical model is developed that explains observed mixed–state phases based on spectroscopic measurement of solid and liquid molecular energy levels. The observed nonequilibrium melting dynamics are consistent with Monte Carlo simulations.
Here, we performed ab initio molecular dynamics (AIMD) simulations to benchmark bulk liquid structures and to evaluate results from all-atom force field molecular dynamics (FFMD) simulations with the generalized Amber force field (GAFF) for organophosphorus (OP) and organochlorine (OC) compounds. Our work also addresses the current and important topic of force field validation, applied here to a set of nonaqueous organic liquids. Our approach differs from standard treatments, which validate force fields based on thermodynamic data. Utilizing radial distribution functions (RDFs), our results show that GAFF reproduces the AIMD-predicted asymmetric liquid structures moderately well for OP compounds that contain bulky alkyl groups. Among the OCs, RDFs obtained from FFMD overlap well with AIMD results, with some offsets in position and peak structuring. However, re-parameterization of GAFF for some OCs is needed to reproduce fully the liquid structures predicted by AIMD. The offsets between AIMD and FFMD peak positions suggest inconsistencies in the developed force fields, but, in general, GAFF is able to capture short-ranged and long-ranged interactions of OPs and OCs observed in AIMD. Along with the local coordination structure, we also compared enthalpies of vaporization. Overall, calculated bulk properties from FFMD compared reasonably well with experimental values, suggesting that small improvements within the FF should focus on parameters that adjust the bulk liquid structures of these compounds.
Brookite TiO 2 , a rare natural polymorph of TiO 2 , has been reported to be an excellent photocatalyst for the production of hydrogen from water and aqueous alcohol solutions, especially when it is reduced and synthesized in the form of nanorods. Here, we investigate the reactivity of stoichiometric and reduced brookite nanorods in liquid water using ab initio molecular dynamics and hybrid density functional theory calculations. Our simulations show a much higher water dissociation fraction on reduced nanorods than on stoichiometric ones, with an accumulation of the resulting bridging hydroxyls (O br H) and terminal hydroxyls (Ti –OH) on different facets of the nanorod. ObrH groups accumulate preferentially on low-energy (210) facets, where they are stabilized by adjacent reduced Ti (Ti 3+ ) sites, while Ti –OH groups prefer to form at the four-fold coordinated Ti atoms on high-energy (010) facets. This hydroxylation pattern also favors the spatial localization of excited holes on the (010) facets. This coupling between water-induced surface chemistry and charge separation underpins the enhanced photocatalytic activity of brookite nanorods, providing useful information for the design of more efficient TiO2-based nanostructures for solar-driven hydrogen evolution.
Extractant aggregation in liquid–liquid extraction organic phases impacts extraction energetics and is related to the deleterious efficiency-limiting liquid–liquid phase transition known as third phase formation. Using small angle X-ray scattering, we find that structural heterogeneities across a wide range of compositions in binary mixtures of malonamide extractants and alkane diluents are well described by Ornstein–Zernike scattering. This suggests that structure in these simplified organic phases originates from the critical point associated with the liquid–liquid phase transition. To confirm this, we measure the temperature dependence of the organic phase structure, finding critical exponents consistent with the 3D Ising model. Molecular dynamics simulations were also consistent with this mechanism for extractant aggregation. Due to the absence of water or any other polar solutes required to form reverse-micellar-like nanostructures, these fluctuations are inherent to the binary extractant/diluent mixture. Further, we also show how the molecular structure of the extractant and diluent modulate these critical concentration fluctuations by shifting the critical temperature: critical fluctuations are suppressed by increasing extractant alkyl tail lengths or decreasing diluent alkyl chain lengths. This is consistent with how extractant and diluent molecular structure are known to impact metal and acid loading capacity in many-component LLE organic phases, suggesting phase behavior of practical systems may be effectively studied in simplified organic phases. Overall, the explicit connection between molecular structure, aggregation and phase behavior demonstrated here will enable the design of more efficient separations processes.
A dicationic ionic liquid ([DBU-PEG][Tf 2 N] 2 ) was studied using classical molecular dynamics simulations to examine its structural and gas separation properties. The dication was designed in an attempt to improve CO 2 solubility by means of tuning the cation-anion interactions of the ionic liquid (IL). The computational model was compared to experimentally obtained density, viscosity, and powder X-ray diffraction spectra. The structure of the IL was further investigated with radial distribution functions and free volume analysis through cavity distributions. It was found that the shape and charge distribution of the dication enhances CO 2 interaction: the CO 2 molecule is hugged by the dication along the PEG linker and close to one of the cationic ends. Here, the geminal design of the dication allows for strong interaction with CO 2 , showing promise as a means of carbon capture.
Understanding emergent phenomena of fluids under physical confinement requires the development of advanced tools for rapid and accurate simulation of their physiochemical properties. Simulating liquid molecules commensurate in size with the nanoscale enclosures that confine them is a key challenge. In this work, we demonstrate an accelerated molecular dynamics simulation technique that combines soft-core potentials (SCP) and simulated annealing (SA) to analyze confined liquids. This integrated SCP/SA method relies on a new spliced soft-core potential (SSCP), which enables tunable accuracy with respect to the target hard-core potential (HCP). SCP/SA enables the packing of enclosures with bulk material in a controlled, thermodynamically consistent manner. The enhanced SSCP accuracy is a critical feature of SCP/SA, enabling a smooth transition between the SCP and the HCP at a desired SCP hardness. We applied SCP/SA to the problem of filling a carbon nanotube (CNT) in periodic boundary conditions with a popular ionic liquid (IL), 1- butyl-3-methylimidazolium hexafluorophosphate $[\text{BMIM}^+][\text{PF}^–_6]$. We performed a series of triplicate simulations on systems with varying CNT diameter and charge to demonstrate SCP/SA’s versatility. Beyond this IL/CNT system, the SCP/SA simulation framework has a broad range of potential applications, not limited to nanoscale enclosures and interfaces, including both solid-state and biological systems.
Composition analysis in wine is gaining increasing attention because it can provide information about the wine quality, source, and nutrition. In this work, in situ liquid secondary ion mass spectrometry (SIMS) was applied to 14 representative wines, including six wines manufactured by a manufacturer in Washington State, United States, four Cabernet Sauvignon wines, and four Chardonnay wines from other different manufacturers and locations. In situ liquid SIMS has the unique advantage of simultaneously examining both organic and inorganic compositions from liquid samples. Principal component analysis (PCA) of SIMS spectra showed that red and white wines can be clearly differentiated according to their aromatic and oxygen-contained organic species. Furthermore, the identities of different wines, especially the same variety of wines, can be enforced with a combination of both organic and inorganic species. Meanwhile, in situ liquid SIMS is sample-friendly, so liquid samples can be directly analyzed without any prior sample dilution or separation. Taken together, we demonstrate the great potential of in situ liquid SIMS in applications related to the molecular investigation of various liquid samples in food science.
Adsorption is an important step in heterogeneous catalysis as it predetermines how many reactant molecules can participate in a surface reaction per unit time. While the rate of adsorption processes is well studied in gas–solid adsorption in both theory and experiment, such rates are still not well studied for liquid–solid adsorption. This is partly because the ever-changing configurations of liquid-phase solvent molecules impede the ability to study a molecule approaching a surface from a liquid phase by either experiment or theory. In this work, we develop a method using molecular dynamics (MD) simulations to study the rate of adsorption in liquid–solid adsorption processes. Specifically, we use MD to model the diffusion of a methanol molecule in aqueous solvent and its adsorption to a Pt(111) surface. We find that by approximating the solute motion as following the same displacement rates as a random walk model, the adsorbed and non-adsorbed states of the methanol molecule near the Pt(111) surface can be discerned and quantified. In particular, this methodology enables extracting a sticking coefficient and a macroscopically relatable adsorption rate. This method can be applied to arbitrary types of reactants and surfaces, as well as different liquid environments, thus providing a general tool for predicting quantitative adsorption rates of liquid–solid adsorption systems.
LiF–NaF–ZrF 4 multicomponent molten salts are identified as promising candidates for coolant salts in molten salt reactors and advanced high-temperature reactors. This study focused on low-melting point salt compositions of interest: 38LiF–51NaF–11ZrF 4 , 42LiF–29NaF–29ZrF 4 , and 26LiF–37NaF–37ZrF 4 . Ab-initio molecular dynamics (AIMD) calculations were performed and compared with available experimental data to assess the ability of rigid ion models (RIM) to reproduce short- to intermediate-range structure, transport, and thermophysical properties of the LiF–NaF–ZrF 4 salt mixtures. It is found that as ZrF 4 mol% increases, the average cation–anion coordination number (CN) of monovalent cations (Li + , Na + ) obtained from RIM calculations decreases, while multivalent Zr 4+ CN varied from 15% to 19% in comparison to corresponding AIMD values. In addition, RIM is found to predict the existence of 7, 8, and 9 coordinated fluorozirconate complexes, while AIMD and the available experimental data showed an occurrence of 6, 7, and 8 coordinated complexes in the melt. The intermediate-range structure analysis revealed that while the RIM parameters are able to reproduce a local structure for lower ZrF 4 mol% salts such as in 38LiF–51NaF–11ZrF 4 , an extensive fluorozirconate network formation is observed in RIM simulations for higher ZrF 4 mol% compositions. The network generated by RIM parameters is found to be mainly connected by “corner-sharing” fluorozirconate complexes as opposed to both “edge-sharing” and “corner-sharing” connectively portrayed by AIMD. It is found that a close agreement between AIMD and the RIM salt structure for the 11-mol% ZrF 4 salt resulted in good agreement in the calculated Zr diffusivities and the viscosity values. However, due to the inaccurate short- to intermediate-range structure prediction by RIM for higher ZrF 4 mol% compositions, thermophysical properties such as densities and heat capacity differ by up to 26% and 27%, respectively, upon comparison with AIMD and experimental values. Also, the network-dominated properties such as diffusion coefficients and viscosities differed by up to two and three orders of magnitude, respectively. This study signifies the importance of accurate salt structure generation for an accurate prediction of transport and thermophysical properties of multicomponent molten salts.
In this study, the degradation of CH 3 NH 3 PbI 3 (MAPbI 3 ) hybrid organic inorganic perovskite (HOIP) by water has been the major issue hampering its use in commercial perovskites solar cells (PSCs) as MAPbI 3 HOIP have been known to easily degrade in the presence of water molecules. However, even though there have been numerous studies investigating this phenomenon, there is still no consensus on the mechanisms of initial stages of dissolution. Here, we attempt to consolidate differing mechanistic interpretations previously reported in the literature through the use of the first-principles constrained ab-initio molecular dynamics (AIMD) to study the mechanisms, kinetics, and thermodynamics that accompany the degradation of MAPbI 3 HOIP in liquid water. We consider not only the dissolution of the species found on the pristine MAPbI 3 HOIP surfaces, but also the dissolution from defect sites to imitate the successive degradation steps, and propose a sequence of events in the initial phase of MAPbI 3 HOIP dissolution. By comparing the dissolution free energy barrier between surface species of different surficial types, we find that the dominant dissolution mechanisms of surface species varies widely based on the specific surface features adjacent to the dissolving ion. The high sensitivity of dissolution mechanism to surface features has contributed to the many dissolution mechanisms proposed in the literature. In contrast, the dissolution free energy barriers are mainly determined by the dissolving species rather than the type of surfaces, and the type of surfaces the ions are dissolving from are inconsequential toward the dissolution free energy barrier. However, the presence of surface defects such as vacancy sites are found to significantly lower the dissolution free energy barriers. Based on the estimated dissolution free energy barriers from different types of surfaces that we investigated in this study, we proposed that the dissolution of MAPbI 3 HOIP in liquid water originates from surface defect sites that propagate laterally along the surface layer of the MAPbI 3 HOIP crystal.
CP-PAW is a combined electronic structure and ab initio molecular dynamics code to perform mixed quantum and classical simulations of atomistic condensed phase systems, such as solids, liquids, and molecular systems. As the name suggests, the CP-PAW code unifies the all-electron projector augmented-wave (PAW) method with the Car–Parrinello (CP) approach to determine not only the electronic and nuclear ground states of condensed matter but also to study their properties and dynamics. In addition to briefly outlining the underlying theory, the focus will be on the unique aspects of CP-PAW and how to correctly employ them as a user. How to install CP-PAW using the new build system will also be briefly mentioned.
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The project resulted in the development of stimuli-responsive elastomer coatings formed by photopolymerized liquid crystal molecules. The molecular orientation of the liquid crystal elastomers is coupled to rubber-like elasticity. The project developed an approach to produce complex patterns of molecular orientation in elastomers by employing photopatterning technique based on plasmonic metamasks that convert unpolarized incoming light into a transmitted light beam with spatially-varying linear polarization. The polarization-modulated light beam aligns the film of azodye molecules, which serves as the substrate for liquid crystal elastomer coating. The alignment of the azodye molecules follows the polarization pattern with a phase shift of the alignment direction by 90 degrees. The azodye substrate imposes orientation of molecules in the adjacent liquid crystal layer which is preserved after the monomers are polymerized into a liquid crystal elastomer. By using differently aligned substrates one could produce various patterns of molecular orientation in the elastomer, which dictate the mechanical properties of the elastomers and their response to external stimuli such as temperature, humidity, and ultraviolet irradiation. In particular, the predesigned molecular orientation produces deterministically defined topography response of the liquid crystal coatings, in which their free surface changes from flat to either locally elevated or locally compressed, depending on whether the pre-inscribed molecular orientation is predesigned with a splay or bend deformation. The research established that the mechanism of this deterministic relation between the dynamic topography and pre-inscribed molecular orientation is rooted in the change of the tensorial order parameter that characterizes the degree of orientational order, and in the contraction/expansion of polymer molecules in response to the order parameter changes. In particular, lowering the order causes contraction of polymer globules. The work demonstrated that the dynamic topography of elastomer coatings with three-dimensional pattern of orientational order includes up and down motion of the material (along the normal to the coating) and also shifts in lateral directions. We demonstrate that the deterministic relationship between the orientational patterns and variations of coatings’ profile is caused by forces that are mathematically equivalent to active forces in the system of “pullers” or “pushers” in active matter, demonstrating universality of the out-of-equilibrium behavior. The project resulted in theoretical models that predictively describe the dynamic response of coatings. The topography of liquid crystal elastomers is sensitive to stimuli such as temperature, ultraviolet irradiation, and humidity. The applicability of the patterned approach to produce dynamic coatings was expanded from nematic elastomers to their smectic counterparts. The project combined a battery of imaging techniques to unveil the dynamic properties of the coatings, ranging from the state-of-the-art dynamic holographic microscopy to fluorescent confocal polarizing microscopy and polscope microscopy. The research uncovered potential applications of dynamic elastomer coatings, such as control placement of colloidal particles, engineering of living tissues with alignment patterns of cells that follow the orientational order of elastomer coatings. The approach developed in the project can be used to design programmable dynamic coatings with functionalities that mimic biological tissues such as skin.
Despite the ubiquity of ice, a molecular-resolution image of nanoscopic defects or microstructures in ice crystallized from liquid water has never been obtained. This is mainly due to the difficulties in preparing and preserving crystalline ice samples that can survive under high-resolution imaging conditions. Here, we report the stabilization and Å-resolution electron imaging of ice Ih crystallized from liquid water by developing cryogenic liquid-cell transmission electron microscopy (CRYOLIC-TEM). We combine lattice mapping with molecular dynamics simulations to reveal that ice formation is highly tolerant to nanoscale defects such as misoriented subdomains and trapped gas bubbles, which are stabilized by molecular-scale structural motifs. Importantly, bubble surfaces adopt low-energy nanofacets and create negligible strain fields in the surrounding crystal. These bubbles can dynamically nucleate, grow, migrate, dissolve, and coalesce under electron irradiation and be monitored in situ near a steady state. This work improves our understanding of water crystallization behaviors at a molecular spatial resolution.
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