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At least 163 records · Page 9

Molecular simulation using transfer-learned potentials for the disordered nanoscale structure of nitrogen-doped nanoporous carbons

Machine learning (ML)-based molecular dynamics (MD) simulations of the formation of a class of N-doped nanoporous carbons are performed to assess their disordered partially graphitized nanoscale structure. The study is motivated by the effectiveness of so-called nitrogen assembly carbons (NACs) for catalysis applications. Benchmark simulations for pure-C disordered graphitic systems reveal the importance of reliably capturing the vdW component of the potentials in order to accurately describe the tendency for layering of disordered graphene-like sheets. In our modeling, this is achieved by a transfer learning strategy incorporating features of the energetics from the optB88-vdW DFT functional into potentials initially trained with a less expensive functional, thereby providing a superior description of the pure-C systems. Generation from MD simulations of realistic partially graphitized structures is significantly more challenging for N-doped versus for pure C systems. However, such structures are achieved by a tailored MD simulation protocol mimicking the experimental synthesis process and in particular incorporating an annealing and subsequent quenching stages. Simulated PXRD patterns effectively reproduce the features of experimental observations for NACs, including the appearance of a prominent but broad (002) peak at around 25, and the development of another weaker feature associated with in-layer ordering of mixed C-N graphene-like sheets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular simulation of glycerol-derived triether podands for lithium ion solvation

Solvate ionic liquids (ILs) are promising candidates for several applications due to their stability, high coulombic efficiency, and low volatility. In this work, we investigate the solvation of lithium-bistriflimide by different glycerol-derived triether solvents, using molecular dynamics simulations. Very strong interactions between Li + and the solvent oxygen sites are found, leading to significant conformational changes in the solvent. Here, by comparing the conformation of the neat solvents with their IL mixtures at different concentrations and temperatures, we find that the presence of Li + induces a distinct crown-like structure in the solvent molecules. The Li + cations and the surrounding solvent form a podand complex, which is stable even at elevated temperatures. These glycerol-derived solvents exhibit distinct interactions with Li + cations which may be exploited in electrolytic applications or lithium recovery processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Simulation of MoS 2 Exfoliation

A wide variety of two-dimensional layered materials are synthesized by liquid-phase exfoliation. Here we examine exfoliation of MoS 2 into nanosheets in a mixture of water and isopropanol (IPA) containing cavitation bubbles. Using force fields optimized with experimental data on interfacial energies between MoS 2 and the solvent, multimillion-atom molecular dynamics simulations are performed in conjunction with experiments to examine shock-induced collapse of cavitation bubbles and the resulting exfoliation of MoS 2 . The collapse of cavitation bubbles generates high-speed nanojets and shock waves in the solvent. Large shear stresses due to the nanojet impact on MoS 2 surfaces initiate exfoliation, and shock waves reflected from MoS 2 surfaces enhance exfoliation. Structural correlations in the solvent indicate that shock induces an ice VII like motif in the first solvation shell of water.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Molecular simulations of heterogeneous ice nucleation. I. Controlling ice nucleation through surface hydrophilicity

Ice formation is one of the most common and important processes on earth and almost always occurs at the surface of a material. A basic understanding of how the physicochemical properties of a material’s surface affect its ability to form ice has remained elusive. Here, we use molecular dynamics simulations to directly probe heterogeneous ice nucleation at a hexagonal surface of a nanoparticle of varying hydrophilicity. Surprisingly, we find that structurally identical surfaces can both inhibit and promote ice formation and analogous to a chemical catalyst, it is found that an optimal interaction between the surface and the water exists for promoting ice nucleation.We use our microscopic understanding of the mechanism to design a modified surface in silico with enhanced ice nucleating ability. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Cox, Stephen J.↗

Molecular simulations and density functional theory calculations of bromine in clathrate hydrate phases

Bromine forms a tetragonal clathrate hydrate structure (TS-I) very rarely observed in clathrate hydrates of other guest substances. The detailed structure, energetics, and dynamics of Br{sub 2} and Cl{sub 2} in TS-I and cubic structure I (CS-I) clathrate hydrates are studied in this work using molecular dynamics and quantum chemical calculations. X-ray diffraction studies show that the halogen-water–oxygen distances in the cages of these structures are shorter than the sum of the van der Waals radii of halogen and oxygen atoms. This suggests that the stabilizing effects of halogen bonding or other non-covalent interactions (NCIs) may contribute to the formation of the unique tetragonal bromine hydrate structure. We performed molecular dynamics simulations of Br{sub 2} and Cl{sub 2} clathrate hydrates using our previously developed five-site charge models for the dihalogen molecules [Dureckova et al. Can. J. Chem. 93, 864 (2015)] which reproduce the computed electrostatic potentials of the dihalogens and account for the electropositive σ-hole of the halogen bond donor (the dihalogen). Analysis of the radial distribution functions, enthalpies of encapsulation, velocity and orientation autocorrelation functions, and polar angle distributions are carried out for Br{sub 2} and Cl{sub 2} guests in various cages to contrast the properties of these guests in the TS-I and CS-I phases. Quantum chemical partial geometry optimizations of Br{sub 2} and Cl{sub 2} guests in the hydrate cages using the M06-2X functional give short halogen-water distances compatible with values observed in X-ray diffraction experiments. NCI plots of guest-cage structures are generated to qualitatively show the relative strength of the non-bonding interactions between dihalogens and water molecules. The differences between behaviors of Br{sub 2} and Cl{sub 2} guests in the hydrate cages may explain why bromine forms the unique TS-I phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Perfluoropolyethers: Development of an All-Atom Force Field for Molecular Simulations and Validation with New Experimental Vapor Pressures and Liquid Densities

A force field for perfluoropolyethers (PFPEs) based on the general optimized potentials for liquid simulations all-atom (OPLS-AA) force field has been derived in conjunction with experiments and ab initio quantum mechanical calculations. Vapor pressures and densities of two liquid PFPEs, perfluorodiglyme (CF 3 –O–(CF 2 –CF 2 –O)2–CF 3 ) and perfluorotriglyme (CF 3 –O–(CF 2 –CF 2 –O) 3 –CF 3 ), have been measured experimentally to validate the force field and increase our understanding of the physical properties of PFPEs. Force field parameters build upon those for related molecules (e.g., ethers and perfluoroalkanes) in the OPLS-AA force field, with new parameters introduced for interactions specific to PFPEs. Molecular dynamics simulations using the new force field demonstrate excellent agreement with ab initio calculations at the RHF/6-31G* level for gas-phase torsional energies (<0.5 kcal mol –1 error) and molecular structures for several PFPEs, and also accurately reproduce experimentally determined densities (<0.02 g cm –3 error) and enthalpies of vaporization derived from experimental vapor pressures (<0.3 kcal mol–1). Additional comparisons between experiment and simulation show that polyethers demonstrate a significant decrease in enthalpy of vaporization upon fluorination unlike related molecules (e.g., alkanes and alcohols). Simulation suggests this phenomenon is a result of reduced cohesion in liquid PFPEs due to a reduction in localized associations between backbone oxygen atoms and neighboring molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Relationship between microporous structure and light gas transport through glassy polymeric membranes revealed by molecular simulations

Microporous glassy polymers are attractive materials for gas separation membranes, due to their high permeability and tailorable selectivity, provided physical aging can be delayed. The archetypal microporous glassy polymer, PTMSP, can be blended with a hyper-crosslinked isatin–triptycene porous polymer network (PPN) to delay physical aging. However, while PPN is effective at reducing physical aging, it also affects the permeability of light gases through PTMSP. Molecular dynamics simulations were used here to shed fundamental light on the mechanisms responsible for these effects. Atomistic models are developed that satisfactorily reproduce experimental observations such as matrix density and cavity size distributions for neat PTMSP as well as for PTMSP–PPN blends. Analysis of the simulation results suggests that physical aging is delayed because the PPN inclusions slow down PTMSP relaxation while reducing the connectivity between free volume pockets. To understand how PPN inclusions affect light gas permeability, the atomistic models developed are used to probe CO 2 and CH 4 diffusion and sorption. These simulations are conducted for PTMSP matrices exhibiting varying density, towards reproducing experimental permeability data. Interrogating the simulation trajectories, it is discovered that while CH 4 travels preferentially through the free volume cavities, CO 2 preferentially interacts with the available surfaces, especially in the presence of PPN. These differences help interpret experimental observations. The transport of C 2 H 6 and H 2 S through PTMSP matrices was also investigated. These gases, and in particular H 2 S, were found to absorb within PTMSP, yielding very low diffusion coefficients. The ability to predict differences in diffusion pathways for various natural gas components unveils the possibility of engineering membranes to control permeability and selectivity towards large-scale applications.

Bao Le, Tran Thi [Univ. of Oklahoma, Norman, OK (U↗

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence–structure–function relations remain poorly characterized. Here, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 20 3 = 8000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Validation of Accurate Cryogenic Fluid Vapor-Liquid Boundary Conditions Via Molecular Simulations

Vapor-liquid interfaces drive many important phenomena in cryogenic fluid management, including heat transfer, evaporation, and capillary flow. Design of cryogenic fluid systems, such as propellant storage, requires accurate predictions of fluid behavior, including evaporation rates. Many models have been proposed for heat and mass transfer at vapor liquid interfaces, but the accuracy of these models in the context of cryogenic fluids has not been performed. We use molecular dynamics simulations, which allow for nanometer scale resolution of fluid phenomena, to evaluate the accuracy of a variety of vapor-liquid boundary conditions at evaporating and condensing interfaces. We find that an anisotropic temperature distribution is a critical ingredient for accurate prediction of intensive evaporation and condensation.

Daniel Vigil↗

MISPR : an open-source package for high-throughput multiscale molecular simulations

Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure–Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure–property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.

36 MATERIALS SCIENCE↗

Probing Electric Double-Layer Composition via in Situ Vibrational Spectroscopy and Molecular Simulations.

At an electrode, ions and solvent accumulate to screen charge, leading to a nanometer-scale electric double layer (EDL). The EDL guides electrode passivation in batteries, while in (super)capacitors, it determines charge storage capacity. Despite its importance, quantification of the nanometer-scale and potential-dependent EDL remains a challenging problem. Here, we directly probe changes in the EDL composition with potential using in situ vibrational spectroscopy and molecular dynamics simulations for a Li-ion battery electrolyte (LiClO 4 in dimethyl carbonate). The accumulation rate of Li + ions at the negative surface and ClO 4 - ions at the positive surface from vibrational spectroscopy compares well to that predicted by simulations using a polarizable APPLE&P force field. The ion solvation shell structure and ion-pairing within the EDL differs significantly from the bulk, especially at the negative electrode, suggesting that the common rationalization of interfacial electrochemical processes in terms of bulk ion solvation should be applied with caution.

25 ENERGY STORAGE↗

Enhanced Gas Absorption in the Ionic Liquid 1- n -Hexyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)amide ([hmim][Tf 2 N]) Confined in Silica Slit Pores: A Molecular Simulation Study

Two-dimensional NP{sub xy}T and isostress-osmotic (N{sub 2}P{sub xy}Tf{sub 1}) Monte Carlo simulations were used to compute the density and gas absorption properties of the ionic liquid (IL) 1-n-hexyl-3- methylimidazolium bis(Trifluoromethylsulfonyl)amide ([hmim][Tf{sub 2}N]) confined in silica slit pores (25-45 Å). Self-diffusivity values for both gas and IL were calculated from NVE molecular dynamics simulations using both smooth and atomistic potential models for the silica. Simulations show that the molar volume for [hmim][Tf{sub 2}N] confined in 25-45 Å silica slit pores are 12-31% larger than for the bulk IL at 313-573 K and 1 bar. The amounts of CO{sub 2}, H{sub 2}, and N{sub 2} absorbed in the confined IL are typically 1.1-3 times larger than in the bulk IL due to larger molar volumes for the confined IL compared to the bulk IL. The CO{sub 2}, N{sub 2}, and H{sub 2} molecules are generally absorbed close to the silica wall where the IL density is very low. This arrangement causes the self-diffusivities for these gases in the confined IL to be 2 to 8 times larger than in the bulk IL at 298-573 K. The solubility for water in the confined and bulk ILs are similar, which is likely due to strong water interactions with [hmim][Tf{sub 2}N] through hydrogen-bonding resulting in the confined IL molar volume playing a less important role in determining H{sub 2}O solubility. Water molecules were largely absorbed in the IL-rich region rather than close to the silica wall. The self-diffusivities for water correlate with the confined IL. The confined IL exhibits self-diffusivities larger than the bulk IL at lower temperatures, but smaller than the bulk IL at higher temperatures. The findings from simulations are consistent with available experimental data for similar confined IL systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Membrane Permeability of Terpenoids Explored with Molecular Simulation

We report that terpenoids constitute a class of compounds with remarkable potential for pharmaceutical, fragrance, specialty chemical, and biofuel applications. However, their industrial production is limited by their rarity within their native plant hosts, creating considerable interest in microbial hosts capable of manufacturing terpenoids. To reduce production costs, nondestructive product recovery from these microbial hosts is preferred, and is achievable using a hydrophobic organic overlay. Our prior research has indicated that oxidized fatty acyl products may permeate faster through host membranes, increasing overall biorefinery productivity. To test this hypothesis for terpenoids, we computed membrane permeabilities of conventional terpenoid target products (e.g., limonene, bisabolene, farnesene) and related oxidized compounds through molecular dynamics simulations. These simulations indicate that terpenoid product permeabilities from cytosol to overlay are oxidation independent, as increases in membrane extraction efficiency due to product oxidation are proportionally offset by decreases in the membrane crossing rate if the membrane and organic phase are in close contact. However, if aqueous extraction is required, oxidation will accelerate the slow product extraction from the membrane. Experimental toxicity assays performed indicated that most terpenoids tested were tolerated by microbial hosts, although exposure to oxidized terpenes often retarded microbial growth compared with conventional terpenes. Finally, terpenoid oxidation is not expected to significantly increase or decrease the extraction productivity in an industrial setting where cells are in close contact, unlike the previously studied fatty acyl products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

Computational methods have demonstrated success in identifying virucidal agents, effectively contributing to the discovery of novel virucidal molecules. In this study, we developed a machine learning (ML) model, trained on a small dataset, to predict inhibitors of human enterovirus 71 (EV71), a pathological agent that causes severe disease in children and immunocompromised adults. Despite the dataset’s limitation, comprising of only 36 compounds tested, our ML framework demonstrated significant predictive capability. Notably, experimental validation revealed that five out of the eight compounds predicted by our model from the Chinese cosmetic material list exhibited virucidal activity. The inhibitor effects displayed by the main active compounds were further confirmed by molecular dynamics simulation. This underscores the potential of our AI-driven approach to bypass data constraints in identifying active molecules against viral pathogens.

60 APPLIED LIFE SCIENCES↗

Dissociation Mechanism of Processive Cellulases Explored Through Molecular Simulation

Cellulose is the most abundant biopolymer on the planet, with significant potential as a feedstock for bioderived products. In nature, fungi and bacteria secrete cellulases to hydrolyze cellulose into smaller carbohydrates for incorporation into their own metabolic processes. For effective biomass utilization at industrial scale, these cellulases are coupled together to produce a clean sugar stream. One such cellulase is Cel7A from Trichoderma reesei, which is used extensively in biotechnological applications. However, dissociation of Cel7A from a bound cellulose strand is rate-limiting, reducing catalytic efficiency and yields within industrial applications. To explore this unknown dissociation mechanism and devise potential enzyme engineering strategies to mitigate slow dissociation, we conduct Hamiltonian replica exchange molecular dynamics simulations. Two postulated dissociation mechanisms were tested ('dethreading' of the bound cellulose strand from the binding tunnel and 'clamshell'-like opening of the binding tunnel and recrystallization of the bound cellulose). For each mechanism, free energy profiles were determined together with estimated diffusion coefficients. The kinetics for both mechanisms were then estimated and compared against experimentally measured dissociation rates, which suggest that the dethreading mechanism ought to be preferred. These findings are further supported by dissociation rates measured on engineered mutants incapable of undergoing the clamshell mechanism.

09 BIOMASS FUELS↗

Effect of Collective Dynamics and Anharmonicity on Entropy in Heterogenous Catalysis: Building the Case for Advanced Molecular Simulations

In this paper, we present a perspective on the computational determination of entropy and its effects and consequences on heterogeneous catalysis. Special attention is paid to the role of anharmonicity and the deviations from the standard harmonic oscillator approximations which can fail to provide a reliable assessment of entropy. To address these challenges, advanced methodologies are needed that can explicitly account for these thermodynamic drivers through the appropriate statistical sampling of reactive free energy surfaces. We discuss where anharmonicity should be expected, where it has been observed from a theoretical perspective, and the methods currently employed to address it. We concentrate on three types of systems where we have observed major, nonnegligible anharmonic effects: (1) supported nanoparticles, where the migration of metal atoms, complexes, and entire clusters exhibit anharmonic behavior in their dynamic motion; (2) porous solids where confinement effects distort potential energy surfaces and hinder molecular motions resulting in large entropic terms; and (3) solid/liquid interfaces, where interactions between solvent molecules and adsorbed species can result in large solvent organization free energy and unique reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗