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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.

Biochemistry & Molecular Biology↗
DOE OSTI2020

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↗
DOE OSTI2026

Cyclodextrin-Derived Porous Liquids Enabled by In Situ Solvation Shell Formation

Porous liquids (PLs) represent a unique platform for molecular separations by combining permanent porosity with liquid-phase mobility. However, it remains a formidable challenge to construct and stabilize PLs with sub-5 Å pores using readily available porous host and liquid media. Here, we report the construction of cyclodextrin (CD)-derived PLs enabled by in situ solvation shell formation. The acid–base neutralization reaction between CD and an organic base was leveraged to generate a thin ionic solvation shell around the CD host, effectively liquefying CD and preventing its segregation in the liquid base medium while preserving accessible molecular-scale cavities. Spectroscopic analysis, neutron scattering, density functional theory calculations, and molecular dynamics simulations collectively confirm the structural evolution and existence of abundant internal porosity in PLs. The unique architectures of CD-derived PLs enable highly selective encapsulation of fluorinated alkanes and significantly enhanced uptake of inert gases. This facile and generalizable strategy enables construction of high-quality PLs with engineered ultramicroporosity to facilitate molecular separations.

Cavities↗
DOE OSTI2021

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this “on-the-fly” approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. Furthermore, this approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH 2 O → H 2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Ab-Initio Simulation Studies of Cr Solvation in Fluoride Molten Salts

Understanding molten salt chemistry is essential in ongoing research of the molten salt nuclear reactor (MSR). In this context, detailed understanding of the mechanisms underlying selective oxidation of metal species, such as Cr, is required to guide the design of effective corrosion mitigation strategies in molten salts. An important starting point for such mechanistic understanding is knowledge of the solvation structure and its role in controlling metal speciation. In this work, we use ab initio molecular dynamics simulations to study the short-range (on the scale of the nearest-neighbor bond lengths) and medium-range (over length scales of several neighbor spacings) structure in three different fluoride melts with and without Cr addition; namely, 2KF-NaF, 2LiF-BeF 2 , and 3LiF-AlF3. We find that Cr 0 ,Cr 2+ ,Cr 3+ can each be coordinated by different numbers of F-, with the variance in coordination number decreasing as oxidation state increases, and that these coordination geometries are largely independent of solvent. The manner by which Cr changes the medium-range structure, however, is found to be solvent-dependent. While 2KF-NaF melts show short and medium range order that is highly dynamic, 2LiF-BeF 2 and 3LiF-AlF 3 are characterized by molecular associates that are relatively long-lived that organize into oligomer structures on larger length scales. Rather than being solvated by F- ions alone, we find that Cr can incorporate into and be solvated within this oligomer structure. Fluoroacidity, alone, may therefore prove too simple a metric for assessing the corrosivity of molten fluorides. As our work suggests, the ability of Cr to solvate must be understood in the context of the short- and medium-range structure of the solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The role of pre-existing heterogeneities in materials under shock and spall

There has been a challenge for many decades to understand how heterogeneities influence the behavior of materials under shock loading, eventually leading to spall formation and failure. Experimental, analytical, and computational techniques have matured to the point where systematic studies of materials with complex microstructures under shock loading and the associated failure mechanisms are feasible. This is enabled by more accurate diagnostics as well as characterization methods. As interest in complex materials grows, understanding and predicting the role of heterogeneities in determining the dynamic behavior becomes crucial. Early computational studies, hydrocodes, in particular, historically preclude any irregularities in the form of defects and impurities in the material microstructure for the sake of simplification and to retain the hydrodynamic conservation equations. Contemporary computational methods, notably molecular dynamics simulations, can overcome this limitation by incorporating inhomogeneities albeit at a much lower length and time scale. This review discusses literature that has focused on investigating the role of various imperfections in the shock and spall behavior, emphasizing mainly heterogeneities such as second-phase particles, inclusions, and voids under both shock compression and release. Pre-existing defects are found in most engineering materials, ranging from thermodynamically necessary vacancies, to interstitial and dislocation, to microstructural features such as inclusions, second phase particles, voids, grain boundaries, and triple junctions. This literature review explores the interaction of these heterogeneities under shock loading during compression and release. Systematic characterization of material heterogeneities before and after shock loading, along with direct measurements of Hugoniot elastic limit and spall strength, allows for more generalized theories to be formulated. Further, continuous improvement toward time-resolved, in situ experimental data strengthens the ability to elucidate upon results gathered from simulations and analytical models, thus improving the overall ability to understand and predict how materials behave under dynamic loading.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Probing Hydrogen-Bond Anharmonicity in Cocrystals with Colossal Thermal Expansion

Organic cocrystals with sizable anisotropic thermal expansion (TE) are attractive building blocks for thermally responsive soft actuators. Such materials often display intermolecular H-bonding, whose thermal strength fluctuations are frequently overlooked if displacements and/or conformational changes are visible during TE. In this work, we employed variable-temperature single-crystal synchrotron diffraction to investigate the linear expansion coefficients of two organic cocrystals, 1 and 2, which exhibit colossal thermal expansivity exceeding 140 MK –1 . Despite such pronounced TE, solid-state 2 H and 13 C NMR experiments show no evidence of fast internal reorientations or large-amplitude molecular displacement during expansion. Although nondirectional π–π stacking dominates the colossal TE, our results indicate that hydrogen bonds play a non-negligible role in the anisotropic response. Molecular dynamics simulations reveal a temperature-dependent broadening of H-bond length distributions, which arises from the increased thermal sampling of an anharmonic potential energy surface. Our data support an expansion mechanism based on cooperativity in π-π interactions, accompanied by thermal softening and fluctuation-driven stretching of directional hydrogen bonds in these molecular solids. This mechanism underscores the significance of directional interactions in organic cocrystals, which is a key factor in the design of organic thermoresponsive crystalline materials.

Hernández-Morales, Ernesto A. [Univ. Nacional Auto↗
DOE OSTI2026

Atomic-Scale Imaging Reveals Polar-π Interactions in Two-Dimensional Molecular Superlattices

Controlling coassembly of synthetic oligomers into binary superlattices at the atomic level is challenging. Here, we report a strategy for programming polar-π interactions in oligomeric peptoids, a class of sequence-defined peptidomimetics, facilitating the formation of homogeneous two-dimensional (2D) superlattices. N-2-phenylethyl and N-(2-perfluorophenyl)ethyl side chains, similar in size, but with contrasting electrostatic characteristics, were introduced at defined sequence positions to generate favorable dipolar aromatic interactions. The resulting nanosheets exhibit different crystal motifs depending on the side chain interactions: systems containing only one type of aromatic side chain form a parallel V-shaped motif driven by π-π interactions, whereas a combination of both types of aromatic side chains, either within one backbone or through the coassembly of two distinct peptoids, adopt an antiparallel V-shaped superlattice with higher thermal stability, driven by polar-π interactions. Cryogenic transmission electron microscopy directly resolved the packing arrangement of perfluorophenyl and phenyl rings in individual nanosheet superlattices, confirming that intermolecular polar-π interaction dominates the superlattice motifs and increases lattice stability. Molecular dynamics simulations and density functional theory calculations further substantiate the energetic favorability of polar-π interactions over π-π interactions, rationalizing the formation of homogeneous superlattices with enhanced thermal stability. Our discoveries establish a design principle for binary coassembly using sequence-defined oligomers, which enables control over unit cell geometry, lattice stability, and molecular registration through aromatic side chain polarization and sequence control. This ability to program atomic-scale binary superlattices opens new avenues for designing functional 2D soft materials.

Lee, Yen Jea [Lawrence Berkeley National Laborator↗
DOE OSTI2026

Conformational Isomerization of Imide Anions Governs Solvation and Transport in Water-in-Salt Electrolytes

The behavior of highly concentrated electrolytes departs radically from the dilute-solution theory, yet the molecular origin of this transformation remains unresolved. Here, we identify the conformational isomerization of molecular ions as a decisive, previously unrecognized control parameter governing structure and transport in crowded aqueous electrolytes. Across a series of fluorosulfonimide anions, we show that increasing concentration drives a collective shift from extended transoid to compact cisoid conformers, revealed by small-angle X-ray scattering, vibrational spectroscopy, pulsed-field gradient NMR, and molecular dynamics simulations. This conformational transition triggers a collapse of the hydrogen-bonded water network and the emergence of densely packed ionic domains with confined water, producing a qualitative change in Li+ transport from solvent-mediated diffusion to network-confined hopping. Anion size and asymmetry systematically tune the onset of this transition, demonstrating that molecular geometry dictates mesoscale organization and dynamics in the ion-rich regime. Our results establish ion conformation, not merely composition or coordination, as a fundamental thermodynamic variable in concentrated solutions, providing a chemical framework that unifies solvation structure and transport in water-in-salt electrolytes and suggesting new principles for designing dense ionic media.

Nguyen, Huong TD↗
DOE OSTI2021

Simulations of the IR and Raman spectra of water confined in amorphous silica slit pores

Water in nano-scale confining environments is a key element in many biological, material, and geological systems. The structure and dynamics of the liquid can be dramatically modified under these conditions. Probing these changes can be challenging, but vibrational spectroscopy has emerged as a powerful tool for investigating their behavior. A critical, evolving component of this approach is a detailed understanding of the connection between spectroscopic features and molecular-level details. In this paper, this issue is addressed by using molecular dynamics simulations to simulate the linear infrared (IR) and Raman spectra for isotopically dilute HOD in D 2 O confined in hydroxylated amorphous silica slit pores. The effect of slit-pore width and hydroxyl density on the silica surface on the vibrational spectra is also investigated. The primary effect of confinement is a blueshift in the frequency of OH groups donating a hydrogen bond to the silica surface. This appears as a slight shift in the total (measurable) spectra but is clearly seen in the distance-based IR and Raman spectra. Analysis indicates that these changes upon confinement are associated with the weaker hydrogen-bond accepting properties of silica oxygens compared to water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Water, Ion, and Proton Dynamics and Interactions in Nanoconfined Systems

The research was directed at understanding the role that nanoconfinement has on the dynamics and structure of liquids confined in nanometer size structures. Experiments were conducted using ultrafast infrared methods. The methods were two dimensional infrared (2D IR) spectroscopy and polarization pump-probe (PSPP) experiments. In addition FT-IR spectroscopy was used. To augment the experimental work, high level molecular dynamics simulations of the systems were conducted. The system used for confinement were nanoporous silica with essentially monodispersed pores. Pores of different diameters were studies, i.e., 2.5 nm to 8 nm. Water and organic liquids were investigated. The experiments were performed on a vibrational probe molecule, i.e., the CN stretch of the anion SeCN-. The 2D IR experiments measured spectral diffusion, which directly reported on the structural dynamics of the confined liquids. 2D IR was also used to perform chemical exchange measurements, which observed the formation and dissociation of molecular complexes with surface silanols. The PSPP experiments measured orientational relaxation of the probe molecule as well as it vibrational lifetime. All of the observables depended on the diameter of the pores and the type of liquid. The simulations of the observables provided detailed structural information on the structure of the confined liquids and there interactions with the surfaces. In addition to the study of the confinement in nanopores, water in hydrogels was also studied. The same experimental methods were used along with MD simulations. It was found the influence of hydrogels on water did not come from confinement of the water in the hydrogel polymer network, but rather from the interactions of the water with the individual monomers that compose the polymer. In addition, the temperature dependence of a polymer/water system was tracked from below to above the lower critical solution temperature to observe the nature of the phase separated polymer and how water responded to the phase separation.

36 MATERIALS SCIENCE↗
DOE OSTI2026

First-principles simulation of a shocked H-He mixture along the principal Hugoniot

Recent laser-shock experiments on an H–He mixture containing 11% helium (atomic fraction) have suggested the presence of an immiscibility region inside Jupiter. Reflectivity measurements were used as the primary diagnostic of H–He demixing, with discontinuities in the optical reflectivity proposed as a signature of phase separation under conditions relevant to Jupiter's interior. Here, we investigate shock-compressed H–He using ab initio molecular dynamics simulations with optical properties evaluated within the Kubo–Greenwood formalism. The equation of state and ionic configurations were obtained using the thermal Tr 2 SCANL meta-GGA exchange–correlation (XC) functional, while optical properties were computed using the recently developed RS-KDT0 range-separated thermal hybrid XC, which provides state-of-the-art accuracy for band-gap predictions in the warm dense matter regime. The calculated reflectivity shows overall good agreement with experimental measurements; however, no discontinuity is observed at elevated temperatures. Moreover, the reflectivity predictions for the mixed system are consistent with the experimental measurements in the temperature range where the mixture is inferred to be demixed. Furthermore, these results suggest that reflectivity alone may not provide a unique or sensitive diagnostic of H–He demixing at low helium concentrations under these conditions.

Density functional calculations↗
DOE OSTI2020

Electro-reduction of organics on metal cathodes: A multiscale-modeling study of benzaldehyde on Au (111)

Here, we present a multiscale modeling study on the electro-reduction of benzaldehyde (BZY) on Au(111) under realistic electrochemical conditions. To model the electrochemical cell, we adopt a capacitor model in which complex solvents are confined between a Au cathode and a carbon anode. Classical molecular dynamics simulations reveal that electrode charge density and the presence of alcohol show strong effects on the density, adsorption geometry and dynamics of benzaldehyde on the Au electrode. Under charging conditions, the surface concentration of benzaldehyde on the Au electrode decreases, while the content of other species increases. Finally, we proposed a scheme that correlates the electric current running through the Au/solvent interface with the applied bias. This study provides a molecular level understanding of how solvent composition, in this case water/alcohol content, controls the activity of electrocatalytic hydrogenation

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

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↗
DOE OSTI2023

Relationship of the Molecular Structure and Transport Properties of Imide-Based Lithium Salts of “Acetonitrile/Water-in-Salt” Electrolytes

“Water-in-salt” (WIS) electrolytes exhibit excellent safety and electrochemical performance. However, they possess high concentrations, relatively low diffusion coefficient, and high viscosity. “Acetonitrile/water in salt” (AWIS) electrolytes can overcome the disadvantages of WIS electrolytes. Under relatively low concentrations, AWIS electrolytes show good electrochemical performance comparable to WIS electrolytes and low conductivity. Herein, we investigate the relationship between the solvation structures and the transport properties using small-angle X-ray scattering and molecular dynamics simulation. We observed two solvation behaviors of AWIS: anions dissolved in acetonitrile forming small acetonitrile/anion clusters and additional water further dissolving the small acetonitrile/anion clusters. The introduction of acetonitrile weakens the water–solute interaction and enhances the cation–anion interaction, which results in an enhanced dynamical slowdown as the concentration increases. In conclusion, this work provides molecular-level understanding of the connection between two-stage solvation structures and transport properties for imide-based lithium salt solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, in this work, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effect of Molecular Structure of Quinones and Carbon Electrode Surfaces on the Interfacial Electron Transfer Process

Quinones can undergo thermodynamically reversible proton-coupled electron transfer reactions and are being applied as electroactive compounds in aqueous organic batteries. However, the electrochemical reversibility of these compounds is affected not only by their molecular structure but also by the properties of a carbon-based electrode surface. This study combines experimental and theoretical approaches to understand this dependence. Specifically, we study the electron transfer kinetics of two synthesized quinone derivatives and two commercially available ones with a glassy carbon, a highly ordered pyrolytic graphite, and a high-edge-density graphite electrode (HEDGE). The electrochemical reversibility is notably improved on the HEDGE, which shows a higher density of defects and presents oxygenated functional groups at its surface. The electron transfer kinetics are controlled by adsorbed species onto the HEDGE. Molecular dynamics simulation and quantum mechanics calculations suggest defects with oxygen-containing functional groups, such as C-O and C$=$O, on HEDGE surfaces drive the interaction with the functional groups of the molecules, during physisorption from van der Waals forces. The presence of sulfonic acid side groups and a greater number of aromatic rings in the molecular structure may contribute to a higher stabilization of quinone derivatives on HEDGEs. We propose that high-performance carbon-based electrodes can be obtained without catalysts for organic batteries, by the engineering of carbon-based surfaces with edge-like defects and oxygenated functional groups.

25 ENERGY STORAGE↗
DOE OSTI2024

The dynamic adsorption affinity of ligands is a surrogate for the passivation of surface defects

Abstract Surface defects in semiconducting materials, though they have been widely studied, remain a prominent source of loss in optoelectronic devices; here we sought a new angle of approach, looking into the dynamic roles played by surface defects under atmospheric stressors and their chemical passivants in the lifetime of optoelectronic materials. We find that surface defects possess properties distinct from those of bulk defects. ab initio molecular dynamics simulations reveal a previously overlooked reversible degradation mechanism mediated by hydrogen vacancies. We find that dynamic surface adsorption affinity (DAA) relative to surface treatment ligands is a surrogate for passivation efficacy, a more strongly-correlated feature than is the static binding strength emphasized in prior reports. This guides us to design targeted passivator ligands with high molecular polarity: for example, 4-aminobutylphosphonic acid exhibits strong DAA and provides defect passivation applicable to a range of perovskite compositions, including suppressed hydrogen vacancy formation, enhanced photovoltaic performances and operational stability in perovskite solar cells.

Science & Technology - Other Topics↗