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At least 721 records · Page 40

Ab Initio Modeling of Aqueous Methanol Mixtures at DFT-SCAN Level Using Machine Learning Interatomic Potentials

Abstract Methanol–water mixtures find use in many applications, particularly catalytic energy conversion processes. Their importance has motivated numerous computational studies, most of which employed molecular dynamics based on classical force fields. These enable simulations of large systems on long time scales but do not reliably describe reactive dynamics involving bond breaking and bond formation. In contrast, ab initio molecular dynamics (AIMD) based on density functional theory (DFT) is generally more reliable for such applications but has a high computational cost, which discourages systematic studies of alcohol-water mixtures. To remedy this, we trained a machine learning interatomic potential capable of probing the properties of aqueous methanol mixtures at the DFT level using the SCAN functional. Our results show that SCAN qualitatively reproduces multiple key experimental features arising from the amphiphilic nature of methanol, including density, diffusion coefficients, X-ray structure factors, and Kirkwood–Buff integrals. We also find that structural correlations between water molecules are somewhat overestimated, leading to a stronger preferential association than that predicted by experiments. However, increasing the temperature by 30 K mitigates this effect and also recovers the correct mobilities of both methanol and water. These results indicate that SCAN provides an accurate description of methanol–water mixtures, making it a reliable choice for investigating the reactive dynamics in such systems.

Park, Sanghyun J. [Princeton University , , , ,]↗

Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions

The self-consistent iterative multistate empirical valence bond (SCI-MS-EVB) method is used to analyze the structure, thermodynamics, and dynamics of hydrochloric acid solutions. The reorientation timescales of irreversible proton transport are elucidated by simulating 0.43 M, 0.85 M, 1.68 M, and 3.26 M HCl solutions at 270 K, 285 K, 300 K, 315 K, and 330 K. The results indicate increased counter-ion pairing with increasing concentration, which manifests itself via a reduced hydronium oxygen–chloride (O*-Cl) structuring in the radial distribution functions. Increasing ionic concentration also reduces the diffusion of the hydrated excess protons, principally by reducing the contribution of the Grotthuss proton hopping (shuttling) mechanism to the overall diffusion process. In agreement with prior experimental findings, a decrease in the activation energy of reorientation timescales was also observed, which is explicitly explained using activated rate theory and an energy-entropy decomposition of the state-averaged radial distribution functions. Furthermore, these results provide atomistic verification of suggestions from recent two-dimensional infrared spectroscopy experiments that chloride anions (as opposed to hydrated excess protons) create entropic barriers to proton transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental and theoretical study of the soot-forming tendencies of furans as potential biofuels

Sustainably-produced biofuels, including furans derived from lignocellulosic biomass, are being studied as potential next-generation fuels. Biofuels have unique structures that are absent in conventional fuels and they potentially emit fewer particulates than conventional fuels because of the presence of oxygen atoms. In this work, we focus on quantification and measurement of sooting tendency. A set of furans was selected and their sooting tendencies were characterized by Yield Sooting Index (YSI), which was obtained by measuring the line-of-sight spectral radiance (LSSR) of a coflow laminar diffusion flame doped with 1000 ppm of each test fuel. The measured YSIs are lower than traditional gasoline fuels and benzenoid aromatics (e.g., YSIbenzene = 100). We also performed numerical simulations with a detailed chemical kinetic mechanism to analyze the flame chemistry of 2-methylfuran (2MF). 4→5 H-atom migration in the furan ring causes 31.0% of the total decomposition and is the dominant fuel consumption pathway leading to soot. DFT calculations via the G4 composite method were carried out to obtain activation energies (Ea) and bond dissociation energies (BDE). The results showed that the 4→5 H-atom migration in the furan ring has the second lowest Ea and subsequently forms a 1,2-diene-substituted ketone derivative as a stable species. The ring-opening products of the 4→5 H-atom migration are propyne + a linear ketene for 2-n-alkylfurans, and 1-butyne + a methyl-substituted ketene for 2-t-butylfuran. These results can explain the trends of the measured YSIs of 2-alkylfurans.

09 BIOMASS FUELS↗

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low–molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration—presumably a coiled coil—held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP—i.e., the long dimension of the pore—and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.

59 BASIC BIOLOGICAL SCIENCES↗

The 3.2-3.6 micron spectra of monoceros R2/IRS-3 and Elias 16

We have obtained 3.2-3.6 micron spectra, with a resolution lambda/delta-lambda approximately 750, of the protostar Mon R2/IRS-3 and of Elias 16, a background K giant behind the Taurus molecular cloud. A feature at 3,482 microns (2872/cm), with a full width at half-maximum of 0.09 microns (76/cm), is clearly seen in Mon R2/IRS-3. This feature is not detected in Elias 16. The 3.482 micron feature in Mon R2/IRS-3 is similar to a feature at 3.466-3.478 microns (2875-2885/cm) detected by Allamandola et al. in four protostars and attributed by these authors to a CH stretch in hydrocarbons dominated by sp3-bonded carbon. Neither Mon R2/IRS-3 nor Elias 16 shows absorption at 3.540 microns (2825/cm), which has been detected in two of the four protostars observed by Allamandola et al. and attributed by them to CH3OH ice. Our limit on CH3OH ice toward Elias 16 is compared to models of gas-grain chemistry in dark clouds. Our results confirm those of Allamandola et al. that at this resolution the 3.4 micron absorption due to dust in molecular clouds has very different spectral structure than that due to dust in the diffuse interstellar medium.

Sellgren, K.↗

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine learning-accelerated path integral molecular dynamics simulations of reactive organic electrolytes

Hydrogen bonded electrolytes that exhibit accelerated proton transport via sequential reactive hops have drawn interest for their promise in clean energy applications. Molecular dynamics simulations of these electrolytes offer the opportunity to uncover microscopic mechanistic details that could be used to design and tune the properties of candidate electrolyte technologies. However, accurately modeling the proton transfer reactions and transport properties that give rise to high charge conductivites in these electrolytes proves computationally challenging because of the need to perform lengthy condensed phase simulations, treating both the electronic and nuclear degrees of freedom quantum mechanically. In this paper, we demonstrate that such a modeling task can be efficiently achieved with the use of density functional theory (DFT)-trained machine learning potentials (MLP) to accelerate path integral molecular dynamics (PIMD) simulations. We highlight the practical utility of this approach by using it to benchmark how closely PIMD simulations employing different DFT exchange–correlation functionals reproduce the composition-dependent densities, diffusion coefficients, and electrical conductivities of mixtures consisting of imidazole and levulinic acid. Even with the speedup afforded by our MLPs, PIMD simulations remain quite expensive. Furthermore, in order to render PIMD more computationally tractable, we introduce and benchmark the accuracy of a ring polymer contraction approach that leverages a computationally efficient short-range MLP to accelerate our PIMD simulations by an additional factor of four.

Chemical bonding↗

Atomically Precise Single Metal Oxide Cluster Catalyst with Oxygen–Controlled Activity

Single cluster catalysts (SCCs) consisting of atomically precise metal nanoclusters dispersed on supports represent a new frontier of heterogeneous catalysis. However, the ability to synthesize SCCs with high loading and to precisely introduce non-metal atoms to further tune their catalytic activity and reaction scope of SCCs have been longstanding challenges. In this work, a new interface confinement strategy is developed for the synthesis of a high density of atomically precise Ru oxide nanoclusters (Ru 3 O 2 ) on reduced graphene oxide (rGO), attributed to the suppression of diffusion-induced metal cluster aggregation. Ru 3 O 2 /rGO exhibits a significantly enhanced activity for oxidative dehydrogenation of 1,2,3,4-tetrahydroquinoline (THQ) to quinoline with a high yield (≈86%) and selectivity (≈99%), superior to Ru and RuO 2 nanoparticles, and homogeneous single/multiple-site Ru catalysts. In addition, Ru 3 O 2 /rGO is also capable of efficiently catalyzing more complex oxidative reactions involving three reactants. The theoretical calculations reveal that the presence of two oxygen atoms in the Ru 3 O 2 motif not only leads to a weak hydrogen bonding interaction between the THQ reactant and the active site, but also dramatically depletes the density of states near the Fermi level, which is attributed to the increased positive valence state of Ru and the enhanced oxidative activity of the Ru 3 O 2 cluster for hydrogen abstraction.

36 MATERIALS SCIENCE↗

Potential Foldamers Based on an ortho- Terphenyl Amino Acid

We describe the synthesis and characterization of a new class of oligomers built from a terphenyl-based amino acid. Here, these oligomeric amides are of interest because the adoption of specific conformations could potentially be driven by the coordinated formation of inter-residue hydrogen bonds and aromatic interactions. Although high-resolution structural data have proven inaccessible, circular dichroism and nuclear magnetic resonance studies suggest that the new oligomers fold concomitantly with discrete self-association in chloroform. Molecular simulations find no sign of folding as a monomer, and in fact suggest that hydrogen bond patterning is anti-cooperative, inhibiting longer helices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The overlapping fragment approach for non-orthogonal configuration interaction with fragments

The non-orthogonal configuration interaction with fragments (NOCI-F) approach is extended opening the possibility to study intramolecular processes and materials with covalent or ionic lattices. So far, NOCI-F has been applied to study intermolecular energy and electron transfer employing ensembles of fragments that do not have atoms or bonds in common. The here presented approach divides the target system into two overlapping fragments that share one or more atoms and/or one or more bonds. After the construction of a collection of (multiconfigurational) fragment wave functions in a state specific optimization procedure, the fragment wave functions are combined to form many-electron basis functions for the non-orthogonal configuration interaction of the whole system. The orbitals in the overlapping fragment are defined by a corresponding orbital transformation of the fragment orbitals through a singular value decomposition. The overlapping fragments approach is first illustrated for a model system and then used to highlight some possible applications of NOCI with overlapping fragments. In conclusion, the results of excited state diffusion in transition metal oxide, intramolecular singlet fission and magnetic interactions in organic biradicals and ionic compounds are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modification of Surface Density of a Porous Medium

A method for increasing density of a region of a porous, phenolic bonded ("PPB") body adjacent to a selected surface to increase failure tensile strength of the adjacent region and/or to decrease surface recession at elevated temperatures. When the surface-densified PPB body is brought together with a substrate, having a higher failure tensile strength, to form a composite body with a PPB body/substrate interface, the location of tensile failure is moved to a location spaced apart from the interface, the failure tensile strength of the PPB body is increased, and surface recession of the material at elevated temperature is reduced. The method deposits and allows diffusion of a phenolic substance on the selected surface. The PPB body and the substrate may be heated and brought together to form the composite body. The phenolic substance is allowed to diffuse into the PPB body, to volatilize and to cure, to provide a processed body with an increased surface density.

Stackpoole, Margaret M.↗

Demystifying the Diffuse Vibrational Spectrum of Aqueous Protons Through Cold Cluster Spectroscopy

The ease with which the pH is routinely determined for aqueous solutions masks the fact that the cationic product of Arrhenius acid dissolution, the hydrated proton, or H + (aq), is a remarkably complex species. Here, we review how results obtained over the past 30 years in the study of H + &middot;(H 2 O) n cluster ions isolated in the gas phase shed light on the chemical nature of H + (aq). This effort has also revealed molecular-level aspects of the Grotthuss relay mechanism for positive-charge translocation in water. Recently developed methods involving cryogenic cooling in radiofrequency ion traps and the application of two-color, infrared–infrared (IR–IR) double-resonance spectroscopy have established a clear picture of how local hydrogen-bond topology drives the diverse spectral signatures of the excess proton. This information now enables a new generation of cluster studies designed to unravel the microscopic mechanics underlying the ultrafast relaxation dynamics displayed by H + (aq).

Chemistry↗

Molecular insights into CO 2 -to-bicarbonate transformation in functionalized anion exchange ionomers for electrochemical separations

Bipolar membrane (BPM) electrochemical processes are a promising platform for carbon dioxide (CO 2 ) separations, but the molecular level thermodynamic and kinetic understanding of CO 2 -to-bicarbonate (HCO 3 − ) transformation remain poorly understood. This study employs a multiscale computational approach to systematically explore the adsorption and reactive transformation of CO 2 in five anion exchange ionomer systems. Classical molecular dynamics (MD) simulation results demonstrate that polymers with imidazolium groups significantly reduce CO 2 diffusion and enhance (OH − )–CO 2 interactions due to stronger electrostatic and π-interactions. Compared to the commonly used quaternary ammonium ionomers, imidazolium-functionalized ionomers show improved CO 2 proximity and interaction strength. Ab initio MD and density functional theory (DFT) calculations reveal that the benzyl-substituted imidazolium (IM-Ben) substantially reduces the energy barrier for HCO 3 − formation (∼72 meV lower) compared to the alkyl-substituted IM-nBu, while also mitigating imidazolium deprotonation under moderate hydration conditions. Transition state analysis shows IM-Ben forms more extensive hydrogen-bonding networks, which stabilize the transition state structure and contribute to a lower energy barrier for bicarbonate formation. These findings highlight the advantage of the adjacent benzyl moiety in enabling efficient CO 2 -to-bicarbonate transformation via hydrated hydroxide ion counterions, offering mechanistic insights and clear molecular design principles for optimizing anion exchange ionomers at bipolar membrane interfaces for electrochemical CO 2 separation applications.

Bipolar membranes, Reactive transformation of CO2,↗

Extended analysis of Skylab experiment M558 data

A careful review of the data from Skylab M558 was made in an effort to explain the apparent anomaly of the existence of radial concentration gradients whereas none should bave been observed. The very close modelling of the experimental axial concentration profiles by the unsteady-state one-dimensional solution of Fick's Law of self-diffusion in liquid zinc, and the condition of initial uniform concentration in the radioactive pellet portion of the experimental specimens would have precluded the appearance of such radial concentration gradients. Statistical analyses were used to test the significance of the observed deviation from radial-concentration homogeneity. A student t-distribution test of significance showed that, at 90% or even at 80% level of significance, there were no significant deviations from uniformity in radial concentrations. It was also concluded that the two likely causes of any deviation that existed were the zinc to zinc-65 bonding procedure and surface phenomena such as surface tension and capillary action.

Ukanwa, A. O.↗

A chemo-mechanical model for describing sorption hysteresis in a glassy polyurethane

Abstract Hysteretic sorption and desorption of water is observed from 0 to 95% relative humidity and 298–333 K on a glassy polyurethane foam. It is postulated that sorption-induced swelling of the glassy polyurethane increases the concentration of accessible hydrogen-bonding adsorption sites for water. The accessibility of sites is kinetically controlled due to the restricted thermal motions of chains in the glassy polymer, causing a difference in accessible site concentrations during sorption and desorption. This discrepancy leads to hysteresis in the sorbed concentrations of water. A coupled chemo-mechanical model relating volumetric strain, adsorption site concentration, and sorbed water concentration is employed to describe water sorption hysteresis in the glassy polyurethane. This model not only describes the final mass uptake for each relative humidity step, but also captures the dynamics of water uptake, which exhibit diffusion and relaxation rate-controlled regimes.

36 MATERIALS SCIENCE↗

Fiber optic system for direct detection of CO 2 leakage in carbon storage wells (Abbreviated Final Report)

The feasibility study focused on the development of new fiber for distributed chemical sensing that will allow direct detection of CO2 leakages in the environment. This is particularly important for monitoring well integrity for carbon capture and storage (CSS), which can provide early warning for an incoming well failure and potential CO2 leaking through it. We proposed Raman or IR interrogation within gas-filled Holey Fibers (HoFs) interleaved with Fiber Bragg Grating (FBG) sections, so that the location and concentration of the gases would be provided simultaneously. The methodology would overcome current roadblocks to using fiber optics for CO2 (and other gases) detection in wells with direct in-situ measurements of concentration along with other important parameters such as temperature and pressure. We were able to assess commercially available IR/Raman hollow core fiber and demonstrated detection of CO2 through them in our controlled environment setups at various pressure conditions. We have also established the ability of drilling precisely with fs-lases side holes to enable penetration of CO2 into the hollow core fiber and reduce diffusion rates. Open joint collars were also explored with double functionality: to obtain splice to solid core fiber critical for field deployment and create gas ingress locations. Both diffusion-only and pressurized fiber system have been constructed following COMSOL based semi-hybrid optical /fluidodynamics models. FBGs have been identified and procured and characterized. Along the work we leveraged internal modeling/design, photonics/laser characterization, optical fiber fabrication, and AM lab capabilities to design, develop and test in-house components or assemblies. Our results indicate the potential of HoF for CO2 downhole direct detection.

25 ENERGY STORAGE↗

Dynamics of Glyceline and Interactions of Constituents: A Multitechnique NMR Study

In this work, the dynamics of the organic components of the deep eutectic solvent (DES) glyceline are analyzed using an array of complementary nuclear magnetic resonance (NMR) methods. Fast-Field Cycling 1 H relaxometry, Pulsed Field Gradient diffusion, Nuclear Overhauser Effect Spectroscopy (NOESY), 13 C NMR relaxation and pressure dependent NMR experiments are deployed to sample a range of frequencies and modes of motion of the glycerol and choline components of the DES. Generally, translational and rotational diffusion of glycerol are more rapid than those of choline while short range rotational motions observed from 13 C relaxation indicate slow local motion of glycerol at low choline chloride (ChCl) content. The rates of glycerol and choline local motions become more similar at higher ChCl. This result taken together with pressure dependent NMR studies show that the addition of ChCl makes it easier to disrupt glycerol packing. Finally, a relatively slow hydroxyl H-exchange process between glycerol and choline protons is deduced from the data. Consistent with this, NOESY results indicate relatively little direct H-bonding between glycerol and choline. These results suggest that the glycerol H-bonding network is disrupted as choline is added, but primarily in regions where there is intimate mixing of the two components. Thus, the local dynamics of most of the glycerol, resembles that of pure glycerol until substantial choline chloride is present.

13C NMR relaxation↗