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At least 433 records · Page 24

Molecular Origin of Wettability Alteration of Subsurface Porous Media upon Gas Pressure Variations

Upon extraction/injection of a large quantity of gas from/into a subsurface system in shale gas production or carbon sequestration, the gas pressure varies remarkably, which may significantly change the wettability of porous media involved. Mechanistic understanding of such changes is critical for designing and optimizing a related subsurface engineering process. Using molecular dynamics simulations, in this work we have calculated the contact angle of a water droplet on various solid surfaces (kerogen, pyrophyllite, calcite, gibbsite, and montmorillonite) as a function of CO 2 or CH 4 gas pressure up to 200 atm at a temperature of 300 K. The calculation reveals a complex behavior of surface wettability alteration by gas pressure variation depending on surface chemistry and structure, and molecular interactions of fluid molecules with surfaces. As the CO 2 gas pressure increases, a partially hydrophilic kerogen surface becomes highly hydrophobic, while a calcite surface becomes more hydrophilic. Considering kerogen and calcite being the major components of a shale formation, we postulate that the wettability alteration of a solid surface induced by a gas pressure change may play an important role in fluid flows in shale gas production and geological carbon sequestration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Role of Molecular Simulations in the Design of Metal–Organic Frameworks for Gas-Phase Thermocatalysis: A Perspective

Here, metal organic frameworks (MOFs) are highly tunable porous crystalline solids with spatially and electronically isolated catalytically active sites that have been demonstrated for a variety of thermo-, redox-, and photocatalytic reactions. Their tunable natures and relatively well-defined active sites make them advantageous for catalyst design, and molecular simulations have proven highly valuable in this endeavor. However, complexities in the MOF structure require advanced simulation strategies that accurately capture quantum chemistry at the strongly correlated transition metal cation active sites, compositional and structural changes caused by finite temperature and pressure reaction conditions, and transport effects in variously sized pore environments. Luckily, several groups have started using such simulation strategies, paving the way for rich opportunities to design MOF catalysts. Herein, we highlight such examples and provide a perspective on the needs for molecular simulations in the design of MOF catalysts moving forward.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electric field sensitivity of molecular color centers

Molecular color centers with S=1 ground states are promising candidates for quantum sensing of electric fields. These molecules have an electronic structure similar to solid state color centers, but they allow for processing modalities that permit direct interfacing with an analyte. Currently, it is unknown how sensitive these molecules are to electric fields and what molecular properties affect their sensitivity. We perform density functional theory calculations to understand the impact of electric fields on the electronic structure of five nominally tetrahedral molecular color centers exhibiting variable transition metal chemistry and ligand densities. We then extract the Stark parameters from each of these molecules and compare them to molecular properties such as the dipole moment and inner shell stiffness and find that the dipole moment of the molecule largely governs sensitivity. We predict that polar heteroleptic molecules may have electric field sensitivities comparable to solid state color centers such as nitrogen-vacancy centers in diamond.

Physics↗

East River Surface and Pore Water FTICR-MS Data Associated with “Implications of sample treatment on characterization of the riverine environmental metabolome”

Surface and pore water samples were collected from distributed locations around Meander A in East River (Crested Butte, CO, USA) during the summer of 2018. This dataset consists of the characterization of dissolved organic matter using 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS; in .xml format) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory) using two different sample pre-treatment methods (solid phase extraction, no solid phase extraction) and two electrospray ionization methods (ESI-positive, ESI-negative) to identify the impacts of these choices on the final dataset. This study aimed to understand how the different sample processing methods influence the resulting FTICR-MS dataset. Any published work that utilizes data presented in this dataset should cite the dataset using the DOI number. If using the dataset, please acknowledge the U.S. Department of Energy (DOE) Office of Science (BER) Subsurface Biogeochemical Research (SBR) program, the Environmental Molecular Sciences Laboratory (EMSL), and Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (WHONDRS). The publication DOI will be added to this abstract when available.

54 ENVIRONMENTAL SCIENCES↗

Atomic-Layer-Deposited Aluminum Oxide Thin Films Probed with X-ray Scattering and Compared to Molecular Dynamics and Density Functional Theory Models

A better understanding of amorphous aluminum oxide’s structure and electronic properties is obtained through combined experimental and computational approaches. Grazing incidence X-ray scattering measurements were carried out on aluminum oxide thin films grown using thermal atomic layer deposition. The corresponding pair distribution functions (PDFs) showed structures similar to previously reported PDFs of solid-state amorphous alumina and molten alumina. Structural models based on crystalline alumina polymorphs (PDFgui) and amorphous alumina (molecular dynamics, MD) were examined for structural comparisons to the experimental PDF data. Smaller MD models were optimized and verified against larger models to allow for quantum chemical electronic structure calculations. The electronic structure of the amorphous alumina models yields additional insight into the band structure and electronic defects present in amorphous alumina that are not present in crystalline samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lithiation bridged molecular conducting magnets

Combining ferromagnetism and metallic conductivity has been extensively studied in contemporary materials science. However, building such multifunctionalities in molecular chemistry is particularly challenging, on which two collective properties are long considered as mutually exclusive. Here, we report molecular conducting magnet consisting of two-dimensional graphene and molecular planar magnetic networks bridged by electrochemical lithiation, exhibiting the co-existence of distinct magnetism and conductivity and magneto-electric coupling effects. Here, the room temperature magnetoresistance and magnetoelectric coupling coefficient of such complex solid reach 10.7% and 1.77 V/Oe cm, respectively, which can be further tailored by modulating the interaction between graphene and molecular magnetic network. In addition, the graphene passivation simultaneously introduces environmental stability of molecular mag-nets. The electrochemical lithiation offers a pathway towards coupling magnetism and conductivity in molecular complexes.

2D organic complexes↗

Vibrational Entropy of Crystalline Solids from Covariance of Atomic Displacements

The vibrational entropy of a solid at finite temperature is investigated from the perspective of information theory. Ab initio molecular dynamics (AIMD) simulations generate ensembles of atomic configurations at finite temperature from which we obtain the N-body distribution of atomic displacements, ρN. We calculate the information-theoretic entropy from the expectation value of lnρN. At a first level of approximation, treating individual atomic displacements independently, our method may be applied using Debye–Waller B-factors, allowing diffraction experiments to obtain an upper bound on the thermodynamic entropy. At the next level of approximation we correct the overestimation through inclusion of displacement covariances. We apply this approach to elemental body-centered cubic sodium and face-centered cubic aluminum, showing good agreement with experimental values above the Debye temperatures of the metals. Below the Debye temperatures, we extract an effective vibrational density of states from eigenvalues of the covariance matrix, and then evaluate the entropy quantum mechanically, again yielding good agreement with experiment down to low temperatures. Our method readily generalizes to complex solids, as we demonstrate for a high entropy alloy. Further, our method applies in cases where the quasiharmonic approximation fails, as we demonstrate by calculating the HCP/BCC transition in Ti.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Highly efficient interface stabilization for ambient-temperature quasi-solid-state sodium metal batteries

Solid-state sodium (Na) batteries (SSSBs) using sulfide-based solid electrolytes (SSEs) hold tremendous promise due to their high theoretical specific capacity, enhanced safety and abundant resources. However, detrimental interfacial issues between SSEs and Na metal present a major challenge to the advancement of sulfide-based SSSBs. To address interfacial issues, we demonstrate an efficient approach by incorporating an ionic liquid electrolyte ((PYR/Na)TFSI) as interlayer to stabilize the Na metal/SSE interface. The presence of the (PYR/Na)TFSI interlayer enables the formation of a stable solid electrolyte interphase (SEI) to prevent the harmful reactions and inhibit Na dendrites. Combination of ab initio molecular dynamics simulations and X-ray photoelectron spectroscopy revealed that this stable SEI is largely composed of reduced products of TFSI -, such as NaF and CF 3 . As a result, the symmetric cells exhibited stable Na plating/striping cycling for 300 h at 0.1 mA cm -2 . In addition, FeS2||Na quasi-solid-state batteries delivered an impressive specific capacity of over 300 mAh g -1 under the current density of 20 mA g -1 at room temperature. Under a higher current density (100 mA g -1 ), such batteries performed with long-term cycling stability and maintained a specific capacity of around 103 mAh g -1 after 330 cycles. This work demonstrates the novel perspective of using an ionic liquid interlayer to address interfacial issues, contributing to the advancement of high-performance SSSBs for the next-generation energy storage systems.

25 ENERGY STORAGE↗

A Molecular Compound for Highly Selective Purification of Ethylene

Purification of C 2 H 4 from an C 2 H 4 /C 2 H 6 mixture is one of the most challenging separation processes, which is achieved mainly through energy-intensive, cryogenic distillation in industry. Sustainable, non-distillation methods are highly desired as alternatives. We discovered that the fluorinated bis(pyrazolyl)borate ligand supported copper(I) complex {[(CF 3 ) 2 Bp]Cu} 3 has features very desirable in an olefin–paraffin separation material. It binds ethylene exclusively over ethane generating [(CF 3 ) 2 Bp]Cu(C 2 H 4 ). This molecular compound exhibits extremely high and record ideal adsorbed solution theory (IAST) C 2 H 4 /C 2 H 6 gas separation selectivity, affording high purity (>99.5 %) ethylene that can be readily desorbed from separation columns. In-situ PXRD provides a “live” picture of the reversible conversion between [(CF 3 ) 2 Bp]Cu(C 2 H 4 ) and the ethylene-free sorbent in the solid-state, driven by the presence or removal of C 2 H 4 . As a result, molecular structures of trinuclear {[(CF 3 ) 2 Bp]Cu} 3 and mononuclear [(CF 3 ) 2 Bp]Cu(C 2 H 4 ) are also presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temporal dynamics of the multi-omic response to endurance exercise training

Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository (https://motrpac-data.org/).

59 BASIC BIOLOGICAL SCIENCES↗

Elucidating the Atomic Structures of the Gel Layer Formed during Aluminoborosilicate Glass Dissolution: An Integrated Experimental and Simulation Study

The altered glasses produced during aqueous dissolution of silicate and borosilicate glasses are among the most complex structures to understand at the atomic level due to their amorphous nature, random porosity and various levels of hydration. In this study, we gained insights of the complex atomic structures of altered aluminoborosilicate glasses by combining a range of experimental and computational approaches. The altered glasses were prepared by dissolution of three glasses with varying level of alumina in acid for 7 days. A comprehensive set of experimental [elemental analysis, high-energy X-ray diffraction, 29 Si and 27 Al solid-state nuclear magnetic resonance (NMR), and O 1s X-ray photoelectron spectroscopy (XPS)] and modeling (molecular dynamics (MD) simulations using non-reactive and reactive force fields) were used to study the atomic structures of these altered glasses. Elemental analysis showed that most of the B in the pristine glasses was leached into the solution and was not contained in the altered glass. The 29 Si and 27 Al solid-state NMR spectra revealed that the altered glasses have more polymerized silicate network as compared to those in the pristine glasses due to the reformation of linkages among Si and Al oxygen polyhedral in the altered glasses. The bridging and non-bridging (or hydroxyl O) atoms in the altered glasses were also quantified from their O 1s XPS spectra. Atomic structure models of the altered glasses were constructed by using MD simulations using the reactive force field based on the compositional information obtained from experiments. Various pore structures were generated using the charge-scaling (CS) method by using different initial densities and CS temperatures; the best CS parameters of each alternated glass were then determined by comparing with the experimental structure factors obtained from high energy X-ray diffraction. Pore and the atomic structures and vibrational properties around these pore surfaces were analyzed. Furthermore, these results from this comprehensive study thus provides a realistic insight into the pore morphology, atomic structure, and vibrational properties of altered glasses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Patchy particle model of hydrated amorphous silica

Glasses corroded in static aqueous conditions typically reach a slow, residual rate of dissolution as a result of the complex interplay between multiple processes. While intrinsically suited to address this problem, Monte Carlo (MC) models developed to date have relied on lattices to describe the amorphous structure of glass and are thus unable to reproduce the residual rate of glass corrosion. A recently developed MC approach based on amorphous structures derived from molecular dynamics simulations offers a solution [Kerisit and Du J. Non-Cryst. Solids 522 (2019) 119601], but it requires a simple model that can rapidly relax the glass-water interface upon each dissolution/condensation event to retain the ability of MC simulations to reach large spatial and temporal scales. To this end, a patchy particle model of hydrated amorphous silica was developed and evaluated against atomistic simulations in this work. Models of water and amorphous silica were first developed separately, and cross terms were then defined to enable simulations of hydrated amorphous silica structures with varying water content. While the nature of its interaction potential prevents the patchy particle model from reproducing simultaneously the structure and dynamics of the systems of interest with a single set of parameters, it described well the connectivity of hydrated amorphous silica structures and the local coordination geometry of individual species. Therefore, this model opens the door to MC simulations of the residual rate of glass corrosion and offers an alternative to atomistic models to investigate the evolution of silica gels over large spatial and temporal scales.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Thermal Hydroquinone Oxidation on Co/N-doped Carbon Proceeds by a Band-Mediated Electrochemical Mechanism

Molecules catalyze aerobic oxidation reactions via redox cycling at the metal center to effect sequential activation of O 2 and the substrate. Metal surfaces can catalyze the same transformations by coupling independent half-reactions for oxygen reduction and substrate oxidation mediated via the exchange of band-electrons. Metal/nitrogen-doped carbons (MNCs) are promising catalysts for aerobic oxidation that consist of molecule-like active sites embedded in a conductive carbon host. Owing to their combining molecular and metallic features, it remains unclear whether they proceed via the sequential redox cycling pathways of molecules or the band-mediated pathways of metals. Herein, we simultaneously track the potential of the catalyst and the rate of the turnover of aerobic hydroquinone oxidation on a cobalt-based MNC catalyst contacted to a catalytically inactive carbon electrode. By comparing operando measurements of rate and potential with the current-voltage behavior of each constituent half-reaction under identical conditions, we show that these molecular materials can display the band-mediated reaction mechanisms of extended metallic solids. Further, we show that the action of these band-mediated mechanisms explains fractional reaction orders in both oxygen and hydroquinone, the time evolution of catalyst potential and rate, and the dependence of rate on overall reaction free energy. Selective poisoning experiments suggest that oxygen reduction proceeds at cobalt sites, whereas quinone oxidation proceeds at native oxidic defects on the carbon. These findings highlight that molecule-like active sites can take advantage of band-mediated mechanisms when coupled to conductive hosts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electric Field’s Dueling Effects through Dehydration and Ion Separation in Driving NaCl Nucleation at Charged Nanoconfined Interfaces

Investigating nucleation in charged nanoconfined environments under electric fields is crucial for many scientific and engineering applications. Here we study the nucleation of NaCl from aqueous solution near charged surfaces using machine-learning-augmented enhanced sampling molecular dynamics simulations. Our simulations successfully drive phase transitions between the liquid and solid phases of NaCl. The solid phase is stabilized under electric fields, particularly at an intermediate surface charge density. We examine which physical characteristics drive the nucleation of NaCl from aqueous solutions and find that the removal of solvent water from Cl– at the solid precursor surface plays a more critical role than the accumulation of ions. Our simulations reveal the competing effects of electric fields on nucleation processes: they facilitate the removal of water, promoting nucleation, but also promote the separation of ion pairs, thereby hindering nucleation. Here, this work provides a framework for studying nucleation processes in nanoconfined environments under electric fields and provides physical insights for the design of electrochemistry materials.

Electric fields↗

The molecular architecture distinctions between compression, opposite and normal wood of Pinus radiata

In gymnosperms compression wood is a specialised type of structural cell wall formed in response to biomechanical stresses. The differences in terms of gross structure, ultrastructure and chemistry are well-known. However, the differences between compression wood, normal wood, and opposite wood regarding the arrangements and interactions of the various polymers and water within their cell walls still needs to be established. The analysis of 13 C-labelled Pinus radiata by solid-state NMR spectroscopy and other complementary techniques revealed several new aspects of compression and opposite wood molecular architecture. Compared to normal wood, compression wood has a lower water content, its overall nanoporosity is reduced, and the water and matrix polymers have a lower molecular mobility. Galactan, which is a specific marker of compression wood, is broadly distributed within the cell wall, disordered, and not aligned with cellulose, and is found to be in close proximity to xylan. Dehydroabietic acid (a resin acid) is immobilised and close to the H-lignin only in compression wood. Although the overall molecular mobility of normal wood and opposite wood are similar, opposite wood has different arabinose conformations, a large increase in the amount of chain ends, contains significantly more galactan and has additional unassigned mobile components highlighting the different molecular arrangement of cell wall polymers in opposite and normal wood.

59 BASIC BIOLOGICAL SCIENCES↗

Application of First-Principles-Based Artificial Neural Network Potentials to Multiscale-Shock Dynamics Simulations on Solid Materials

The use of artificial neural network (ANN) potentials trained with first-principles calculations has emerged as a promising approach for molecular dynamics (MD) simulations encompassing large space and time scales while retaining first-principles accuracy. To date, however, the application of ANN-MD has been limited to near-equilibrium processes. Here we combine first-principles-trained ANN-MD with multiscale shock theory (MSST) to successfully describe far-from-equilibrium shock phenomena. Overall, our ANN-MSST-MD approach describes shock-wave propagation in solids with first-principles accuracy but a 5000 times shorter computing time. Accordingly, ANN-MD-MSST was able to resolve fine, long-time elastic deformation at low shock speed, which was impossible with first-principles MD because of the high computational cost. This work thus lays a foundation of ANN-MD simulation to study a wide range of far-from-equilibrium processes.

36 MATERIALS SCIENCE↗

ORNL_AISD_NiNb

This dataset describes the nickel-niobium solid solution binary alloy, where the two constituent elements nickel (Ni) and niobium (Nb) are randomly placed on an underlying crystal lattice. This dataset for nickel-niobium (Ni-Nb) alloys available includes the formation energy and bulk modulus for each crystal structure. Each atomic sample has a disordered phase which is obtained starting from an initial regular crystal structure of type body-centered cubic (BCC), face-centered cubic (FCC), or hexagonal compact packed (HCP). The geometry optimization ensures that all the alloy samples reached the equilibrium with negative formation energy. We perform geometry optimizations using the LAMMPS simulation package [1], a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. We utilized the embedded atom model (EAM) potential for Ni and Nb developed in a previous study [2]. The potential could describe behaviors of the liquid and solid phases of Ni-Nb alloy. The structural factors and angular distributions of three atoms are well-matched with X-ray and ab initio-based molecular dynamics data. We prepared the three different crystals with different initial lattice parameters (3.52 Ã… for FCC, 3.32 Ã… for BCC, and 3.5 Ã… for HCP). We performed energy minimization in two steps. Firstly, we minimized the structures with an isotropic unit cell to minimize the side effects from our arbitrary lattice parameters for all other compositions. Then, we applied geometry optimization with a triclinic (non-orthogonal) unit cell to fully minimize the stress components to calculate the elastic constants. In this procedure, we chose 10,000 as the maximum number of allowable steps aimed at obtaining fully relaxed atomic geometries. The dataset consists of three sets of crystal structures. The first set contains 46,086 irregular crystal structures, each of them with 54 atoms, obtained through optimization starting from a regular BCC crystal structure. The second set contains 24,543 irregular crystal structures, each of them with 32 atoms, obtained through optimization starting from a regular FCC crystal structure. The third set contains 39,303 irregular crystal structures, each of them with 48 atoms, obtained through optimization starting from a regular HCP crystal structure. The atomic configurations within each set span the possible compositional range. The three sets have been unified in a global dataset, which is extremely heterogeneous in terms of crystal structures, lattice volumes, and atomic configurations. Organization of files inside the dataset: the dataset contains three subdirectories called • BCC_opt • FCC_opt • HCP_opt based on the type of initial regular structure used to start the geometry optimization. Inside each of these folders, every atomic structure is identified by a string “A_B_Câ€, where A denotes the number of Nb in the system, B denotes index of structure with a given Nb number, and C denotes the total number of structures generated with a given Nb number. For each optimized crystal structure identified by the unique string of characters “A_B_Câ€, three files are provided: • A_B_C_opt.xyz: The optimized geometries in xyz format • A_B_C_opt.cfg: The optimized geometries in cfg format. It includes cell information and atomic energy, and forces calculated from LAMMPS. • A_B_C.elastic: Raw data of 21 elastic constants from LAMMPS output. • A_B_C.bulk: Calculated upper and lower bounds of bulk modulus and averaged one based on Voigt-Reuss-Hill approach from *.elastic. References: [1] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, and S. J. Plimpton. LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comp. Phys. Comm., 271:108171, 2022. [2] Y Zhang, R Ashcraft, MI Mendelev, CZ Wang, and KF Kelton. Experimental and molecular dynamics simulation study of structure of liquid and amorphous ni62nb38 alloy. The Journal of chemical physics, 145(20):204505, 2016.

36 MATERIALS SCIENCE↗