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At least 199 records · Page 11

Understanding Gas Absorption in Multivalent Ionic Liquids via Solute-Solvent Interaction Analyses

Solute-solvent interactions are often evaluated to understand and explain gas solubilities. This information is regularly used to interpret gas solubility and separation within ionic liquids (ILs). Here, we use several different quantum chemical and previous molecular dynamics simulation results to show that strong solute-solvent interactions neither lead to high solubility nor to high selectivity, with respect to other solutes. Instead, the solute-solvent interaction strength with different isolated IL ions is affected by the electrostatic extremes. Also, the solute-solvent interaction with different IL molecules is strongly correlated to the molecular volumes or polarizabilities (within a series of same-anion based ILs).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identification of a Na + -Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II

The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions, and one redox-inactive Ca 2+ ion, with two nearby bound Cl – ions. Sodium is a common counter-ion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Furthermore, we find that the oxygen-evolution activity of spinach PSII increases with [Na + ], particularly at high pH. A Na + -specific binding site next to the OEC, upon deprotonation of the D1-H337 amino-acid residue, is suggested by the analysis of two recently published PSII cryo-EM maps in combination with quantum mechanical calculations and molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational Insights into Malononitrile-Based Carbanions for CO 2 Capture

Although anionic N and O sites have been widely used in chemisorption of CO 2 , carbanions are much less explored for CO 2 capture. Here, in this study, we employ ab initio calculations and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations to examine the interaction between CO 2 and the malononitrile carbanion, [CH(CN) 2 ] – . We have explored the potential energy surface of CO 2 binding by scanning the C–C distance between CO 2 and the central C site of the carbanion. We find that CO 2 prefers to bind to the nitrile group physically rather than to form a C–C bond via the carboxylation reaction at the sp 2 C site. Moreover, the two –CN groups can attract two CO 2 molecules at equal strength. The presence of an alkali metal ion enhances both physical and chemical interactions of CO 2 with the malononitrile carbanion. QM/MM MD simulations further confirm the preference of physical interaction in the condensed ionic liquid phase with a phosphonium cation. Our findings suggest that ionic liquids based on the malononitrile carbanion may have a high CO 2 solubility for carbon capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains

N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (S)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (R)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ~k B T). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. Furthermore, the more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extreme Metastability of Diamond and its Transformation to the BC8 Post-Diamond Phase of Carbon

Diamond possesses exceptional physical properties due to its remarkably strong carbon–carbon bonding, leading to significant resilience to structural transformations at very high pressures and temperatures. Despite several experimental attempts, synthesis and recovery of the theoretically predicted post-diamond BC8 phase remains elusive. Through quantum-accurate multimillion atom molecular dynamics (MD) simulations, we have uncovered the extreme metastability of diamond at very high pressures, significantly exceeding its range of thermodynamic stability. We predict the post-diamond BC8 phase to be experimentally accessible only within a narrow high pressure–temperature region of the carbon phase diagram. The diamond to BC8 transformation proceeds through premelting followed by BC8 nucleation and growth in the metastable carbon liquid. Here we propose a double-shock compression pathway for BC8 synthesis, which is currently being explored in experiments at the National Ignition Facility.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Mechanistic Insights on the Low-Temperature Oxidation of CO Catalyzed by Isolated Co Ions in N-Doped Carbon

Isolated cobalt ions on nitrogen-doped carbon (Co-N-C) catalyze CO oxidation at temperatures as low as 196 K, but the active site and mechanism for this reaction remain elusive. In this work, steady-state CO oxidation around 273 K over Co-N-C revealed nearly first order behavior in both CO and O 2 as well as a negative apparent activation energy. Isotopic transient analysis of the reaction confirmed a rapid turnover frequency and low surface coverage of adsorbed intermediates leading to CO 2 (< 10% of the Co). Results from kinetics experiments combined with quantum chemical calculations and molecular dynamics simulations are consistent with a reaction path involving weak adsorption of CO onto Co ions followed by a low barrier for the CO-assisted activation of weakly adsorbed O 2 . Furthermore, this proposed mechanism for dioxygen activation does not involve a redox cycle with the transition metal ion and may be important in other low temperature catalytic reactions involving O 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Time-Evolving Chirality Loss in Molecular Photodissociation Monitored by X-ray Circular Dichroism Spectroscopy

In this work, the ultrafast photoinduced chirality loss of 2-iodobutane is studied theoretically by time- and frequency-resolved X-ray circular dichroism (TRXCD) spectroscopy. Following an optical excitation, the iodine atom dissociates from the chiral center, which we capture by quantum non-adiabatic molecular dynamics simulations. At variable time delays after the pump, the resonant X-ray pulse selectively probes the iodine and carbon atom involved in the chiral dissociation through a selected core-to-valence transition. The TRXCD signal at the iodine L 1 edge accurately captures the timing of C–I photodissociation and thereby chirality loss, c.a 70 fs. The strong electric dipole–electric quadrupole (ED–EQ) response makes this signal particularly sensitive to vibronic coherence at the high X-ray regime. At the carbon K-edges, the signals monitor the molecular chirality of the 2-butyl radical photoproduct and the spin state of the iodine atom. The ED–EQ response is masked under the strong electric dipole-magnetic dipole response, making this signal intuitive for the electronic population. The evolution of the core electronic states and its chiral sensitivity is discussed. Overall, the element-specific TRXCD signal provides a detailed picture of molecular dynamics and offers a unique sensitive window into the time-dependent chirality of molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recombination of Autodissociated Water Ions in a Nanoscale Pure Water Droplet

The recombination of water ions has diverse scientific and practical implications, ranging from acid-base chemistry and biological systems to planetary environments and applications in fuel cell and carbon conversion technologies. While spatial confinement affects the physicochemical properties of water dynamics, its impact on the recombination process has rarely been studied. In this work, we investigate the dynamics of water, the water ion distribution, and the ion recombination process in water droplets as a function of droplet size through molecular dynamics simulations and adaptive quantum mechanical/molecular mechanical calculations. We compare the dynamics of recombination in water droplet sizes ranging from 100 to 18 000 waters, both in their interiors and on their surfaces. We found that the self-diffusion of water dramatically decreases in droplets with a diameter below 2.2 nm. Using a classical RexPoN force-field, we found that the ions in 1000 H2O's spend almost 50% of the time on the surface and 0.5 nm beneath it with a slight preference for OH- ion to reside longer on the surface. We estimate that, on average, recombination in these drops occurs at 400 ps in 1000 H2O's and 1 ns in 3000 H2O's. We also found that recombination is not limited by the local structure of the surface or the size of the droplet but can be influenced by the geometry of the water wire connecting the ions as they approach each other, which can often prevent recombination. Our results provide insights to the reaction microenvironments presented by nanoscopic water droplets.

Kwon, Soonho↗

Decoherence dynamics in molecular qubits: Exponential, Gaussian and beyond

In this article, we examine how the structure of system–bath interactions can determine commonly encountered temporal decoherence patterns, such as Gaussian and exponential decay, in molecular and other qubits coupled to a thermal bosonic bath. The analysis, based on a pure dephasing picture that admits analytical treatment, shows that decoherence, in general, is neither purely Gaussian nor exponential but rather the exponential of oscillatory functions, with periods determined by the bath’s frequencies. For initially unentangled qubit-bath states, Gaussian decay is always present at early times. It becomes increasingly dominant with increasing temperature, qubit–bath interaction strength, and bath correlation time. Initial system–bath entanglement that arises due to displacement in the position of the bath states preserves the Gaussian decay. By contrast, strict exponential decay arises only in very specific models that we isolate. However, it becomes dominant for times longer than the bath correlation time or for early times when there is initial entanglement due to momentum displacement of the bath states. For molecular electronic decoherence, the long-time exponential regime plays a limited role as it emerges after most coherence is lost. Thus, the Gaussian decay provides a more suitable (albeit imperfect) model of such decoherence. Furthermore, we discuss the connection between electronic decoherence dynamics and electronic spectroscopic line shape theory, where Gaussian spectral peaks correspond to Gaussian coherence decay and Lorentzian peaks correspond to exponential coherence decay. We find that Gaussian spectral peaks, usually associated with inhomogeneous broadening, can emerge from the entangling unitary system–bath dynamics even when there is no inhomogeneity in the initial conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Defects vibrations engineering for enhancing interfacial thermal transport in polymer composites

To push upper boundaries of thermal conductivity in polymer composites, understanding of thermal transport mechanisms is crucial. Despite extensive simulations, systematic experimental investigation on thermal transport in polymer composites is limited. To better understand thermal transport processes, we design polymer composites with perfect fillers (graphite) and defective fillers (graphite oxide), using polyvinyl alcohol (PVA) as a matrix model. Measured thermal conductivities of ~1.38 ± 0.22 W m -1 K -1 in PVA/defective filler composites is higher than those of ~0.86 ± 0.21 W m -1 K -1 in PVA/perfect filler composites, while measured thermal conductivities in defective fillers are lower than those of perfect fillers. We identify how thermal transport occurs across heterogeneous interfaces. Thermal transport measurements, neutron scattering, quantum mechanical modeling, and molecular dynamics simulations reveal that vibrational coupling between PVA and defective fillers at PVA/filler interfaces enhances thermal conductivity, suggesting that defects in polymer composites improve thermal transport by promoting this vibrational coupling.

42 ENGINEERING↗

New Methods for Predicting Non-Born-Oppenheimer Chemistry

Current methods for modeling non-adiabatic molecular dynamics face fundamental limitations when treating geometric phase effects: quantum mechanical phenomena where nuclear wavepackets acquire phase shifts when encircling conical intersections. Existing approaches either neglect these effects entirely or rely on potential energy surfaces arising from the Born-Oppenheimer approximation, which introduce artificial singularities and can overestimate geometric phase contributions. This project developed a new theoretical framework based on exact factorization (XF) methods to overcome these limitations. We derived mathematical formulations for hybrid quantum-classical XF dynamics that selectively treat critical nuclear degrees of freedom quantum mechanically while propagating others classically. This approach addresses the computational intractability that has previously limited exact methods to toy systems. Key innovations include a new approach to systematically identifying nuclear coordinates requiring quantum treatment, as well as novel implementation strategies that interface with existing quantum chemistry codes. The project also developed a proof-of-concept code for treating Jahn-Teller systems and creation of educational materials on non-adiabatic dynamics geared at the graduate level. The theoretical framework developed will enable future systematically improvable calculations of nuclear quantum effects in realistic molecular systems, filling a critical gap in non-adiabatic dynamics methods. This foundation supports future development of predictive tools for designing energy-relevant photochemical processes where quantum coherence effects may be exploited to control reaction outcomes.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Quantum mechanics based non-bonded force field functions for use in molecular dynamics simulations of materials and systems: The nitrogen and oxygen columns

Accurate Force Fields (FFs) are essential for Molecular Dynamics (MD) simulations of the dynamics of realistic materials in terms of atomic-level interactions. The FF parameters of short-range valence interactions can be derived through Quantum Mechanical (QM) calculations on model systems practical for QM (<300 atoms). Similarly, the dynamic electrostatic interactions can be described with methods such as QEq or PQEq that allow charges and polarization to adjust dynamically. However, accurately extracting long-range van der Waals (vdW) interactions from QM calculations poses challenges due to the absence of a definitive method to distinguish between the different energetic components of electrostatics, polarization, vdW, hydrogen bonding, and valence interactions. To do this we use the Perdew–Burke–Ernzerhof flavor of Density Functional Theory, including empirical D3 vdW corrections, to predict the Equation of State for each element (keeping any covalent bonds fixed), from which we obtain the two-body vdW nonbond potential. Here, we extend these calculations to include non-bonded parameters for the N and O columns of the periodic table so that we now describe columns 15 (N), 16 (O), 17 (F), and 18 (Ne) of the periodic table. For these 20 elements, we find that the two-body vdW potentials can all be mapped to a single universal two-body curve, with just three scaling parameters: Re, De, and L. We refer to this as the Universal NonBond (UNB) potential. We expect this to be useful for new MD simulations and a helpful starting point to obtain UNB parameters for the remainder of the periodic table.

Chemistry↗

The Energetic Origins of Pi–Pi Contacts in Proteins

Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein’s stability and structure. Pi–pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi–pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi–pi contact motifs. We find that neutral pi–pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter–Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi–pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi–pi contacts in polar media and like typical ion–pi interactions in nonpolar environments. Like-charged pairs such as arginine–arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi–pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum fluctuations in dense plasma simulations

Molecular dynamics (MD) simulations are a powerful tool for modeling warm and hot dense matter. Density functional theory (DFT) MD simulations are often preferred in dense plasmas in order to accurately model quantum electronic structure. However, DFT-MD simulations neglect interaction effects due to fluctuations in excited states. In this work, we present an MD approach that uses excited state method pseudoatoms to run dense plasma simulations with many different core-electron configurations at classical MD speeds. We also allow for transitions between different configurations in our simulations and find that these fluctuations are especially important for highly excited states. Our results suggest that finite configuration lifetimes that are comparable to the inverse ion plasma frequency need to be accounted for in order to accurately model ion distributions in dense plasma simulations. We also demonstrate that excited state fluctuations have a direct impact on ion plasma microfields, generate different plasma microfields for different excitation levels, and thereby induce absorption–emission line shape asymmetries even in steady-state plasmas.

36 MATERIALS SCIENCE↗

Stable Solid Molecular Hydrogen above 900 K from a Machine-Learned Potential Trained with Diffusion Quantum Monte Carlo

Here, we survey the phase diagram of high-pressure molecular hydrogen with path integral molecular dynamics using a machine-learned interatomic potential trained with quantum Monte Carlo forces and energies. Besides the HCP and C2/c–24 phases, we find two new stable phases both with molecular centers in the Fmmm–4 structure, separated by a molecular orientation transition with temperature. The high temperature isotropic Fmmm–4 phase has a reentrant melting line with a maximum at higher temperature (1450 K at 150 GPa) than previously estimated and crosses the liquid-liquid transition line around 1200 K and 200 GPa.

08 HYDROGEN↗

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗