Search NASA⌕ Search

SEARCH · Search NASA

Results for “solvation dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Protein–Ligand Binding Free-Energy Calculations with ARROW–A Purely First-Principles Parameterized Polarizable Force Field

Protein–ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)–a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein–ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ~0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Hydrated Metal and Metal-Nitrate Complexes in Water: Full Lanthanide(III) Series plus Miscellaneous Metal Ions

This is a dataset of hydrated metal complexes and metal–nitrate hydrated complexes intended for public use, reproducibility, and downstream structural analysis. A key feature is coverage across the full lanthanide(III) series (La–Lu), enabling systematic comparisons of coordination motifs and bonding trends across the entire lanthanide sequence. In addition to the lanthanides, the dataset also includes other metal ions such as UO2(VI), Fe(II), and Fe(III). The dataset provides optimized geometries for hydrated and nitrate-containing hydrated complexes, together with representative ab initio molecular dynamics (AIMD) trajectories saved in standard XYZ formats. The accompanying NWChem input decks enable reproduction of the reported calculations and provide a starting point for extending the simulations to related coordination environments. Computationally, DFT calculations employ the B3LYP functional with DFT-D3BJ dispersion corrections and a COSMO continuum solvent model (dielectric constant 78.4) to represent solvation beyond the explicitly treated first hydration shell. AIMD simulations are performed with the NWChem qmd module at 298 K, integrating nuclear motion with the velocity-Verlet algorithm and controlling temperature using a Nosé–Hoover thermostat. Trajectories are approximately 4.8 ps in length and are used primarily to assess short-time stability of candidate coordination motifs, including (for lanthanides) differences between 8- versus 9-water coordination and comparisons between nitrate-bound and nitrate-free hydrated complexes.

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗
DOE OSTI2023

Theoretical Examination of the Hydroxide Transport in Cobaltocenium-Containing Polyelectrolytes

Polymers incorporating cobaltocenium groups have received attention as promising components of anion-exchange membranes (AEMs), exhibiting a good balance of chemical stability and high ionic conductivity. In this work, we analyze the hydroxide diffusion in the presence of cobaltocenium cations in an aqueous environment based on the molecular dynamics of model systems confined in one dimension to mimic the AEM channels. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the density-functional tight-binding level. We find that the hydroxide diffusion depends on the channel size, modulation of the electrostatic interactions by the solvation shell, and its rearrangement ability. Hydroxide diffusion proceeds via both the vehicular and structural diffusion mechanisms with the latter playing a larger role at low diffusion coefficients. The highest diffusion coefficient is observed under moderate water densities (around half the density of liquid water) when there are enough water molecules to form the solvation shell, reducing the electrostatic interaction between ions, yet there is enough space for the water rearrangements during the proton hopping. Furthermore, the effects of cobaltocenium separation, orientation, chemical modifications, and the role of nuclear quantum effects are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Investigating the Effect of Water on the Mechanical Properties of Cellulose from Multiscale Molecular Dynamics Simulations

Classical molecular dynamics (MD) simulations provide insight into the structure and physicochemical properties of materials with atomic resolution. However, the length and time scales accessible to atomistic MD are orders of magnitude smaller than many relevant processes such as the response of a bulk material to experimentally accessible strain rates, which presents challenges when comparing models to experimental measurements. Bottom-up coarse-graining provides a means for systematically mapping atomistic information to lower resolution models to increase the length and time scales achievable by simulation. Cellulose is an abundant carbohydrate biopolymer with applications to many fields of research, such as materials science and renewable energy, due to its desirable mechanical properties and viability for conversion into biofuel. The effect of moisture content on the Young's modulus of cellulose is of special interest due to its native environment often being in the hydrated secondary plant cell wall and the grinding energy requirements for biomass feedstock preprocessing. The current work investigates the effects of water solvent on the Young's modulus of cellulose calculated from coarse-grained MD mechanical stress simulations. The coarse-grained model was parametrized from atomistic MD calculations of cellulose-cellulose potentials of mean force using umbrella sampling techniques under vacuum and solvated conditions. The Young's moduli of the coarse-grained cellulose assemblies parametrized from cellulose in vacuum or solvated in water were computed via mechanical stress simulations to highlight the importance of capturing solvent interactions for modeling the mechanical behavior of cellulose.

BASIC BIOLOGICAL SCIENCES,RADIATION PROTECTION AND↗
DOE OSTI2025

Enhanced Ion Transport and Molecular Packing Stability in Asymmetric 2D Nanostructured π‐Conjugated Thieno[3,2‐b]Thiophene‐Based Liquid Crystal

Organic semiconductors based on liquid crystal (LC) molecules have attracted increasing interest. Here, in this work, two linear LCs based on 2,5‐bis(thien‐2‐yl)thieno[3,2‐b]thiophene (BTTT) mesogen are designed and synthesized, including BTTT/dEO3 with two symmetrically attached tri(ethylene oxide) groups and BTTT/mEO6 with one asymmetrically attached hexa(ethylene oxide) group. These two molecules have comparable functional‐group compositions but different molecular geometries, leading to their moderately different material performances. Both LCs show smectic mesophases with relatively low transition temperatures as confirmed by differential scanning calorimetry and polarized optical microscopy. A combination of experimental grazing incidence wide‐angle X‐ray scattering and molecular dynamics (MD) simulations reveals a herringbone packing motif of BTTT segments in both LCs while a smaller molecular tilt angle in BTTT/mEO6. Ionic conductivities are measured by doping LCs with different amounts of ionic dopants, lithium bis(trifluoromethanesulfonyl)imide (LiTFSI). BTTT/mEO6 shows better smectic phase stability to higher LiTFSI doping ratios. Both LCs exhibit similar ionic conductivities in the smectic phases, but BTTT/mEO6 outperforms BTTT/dEO3 by a factor of three in the amorphous phase at higher temperatures. MD simulations, performed to examine the ion solvation environment, reveal that BTTT/mEO6 is more efficient in coordinating Li‐ions and screening their interactions with TFSI‐ions which further promote ionic transport.

grazing incidence wide-angle X-ray scattering↗
DOE OSTI2024

Physicochemical control of solvation and molecular assembly of charged amphiphilic oligomers at air-aqueous interfaces

Hypothesis : Understanding the rules that control the assembly of nanostructured soft materials at interfaces is central to many applications. We hypothesize that electrolytes can be used to alter the hydration shell of amphiphilic oligomers at the air-aqueous interface of Langmuir films, thereby providing a means to control the formation of emergent nanostructures. Experiments : Three representative salts – (NaF, NaCl, NaSCN) were studied for mediating the self-assembly of oligodimethylsiloxane methylimidazolium (ODMS-MIM + ) amphiphiles in Langmuir films. The effects of the different salts on the nanostructure assembly of these films were probed using vibrational sum frequency generation (SFG) spectroscopy and Langmuir trough techniques. Experimental data were supported by atomistic molecular dynamic simulations. Findings : Langmuir trough surface pressure – area isotherms suggested a surprising effect on oligomer assembly, whereby the presence of anions affects the stability of the interfacial layer irrespective of their surface propensities. In contrast, SFG results implied a strong anion effect that parallels the surface activity of anions. These seemingly contradictory trends are explained by anion driven tail dehydration resulting in increasingly heterogeneous systems with entangled ODMS tails and appreciable anion penetration into the complex interfacial layer comprised of headgroups, tails, and interfacial water molecules. These findings provide physical and chemical insight for tuning a wide range of interfacial assemblies.

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

The birth and evolution of solvated electrons in the water

The photo-induced radiolysis of water is an elementary reaction in biology and chemistry, forming solvated electrons, OH radicals, and hydronium cations on fast time scales. Here, we use an optical-pump terahertz-probe spectroscopy setup to trigger the photoionization of water molecules with optical laser pulses at ~400 nm and then time-resolve the transient solvent response with broadband terahertz (THz) fields with a ~90 fs time resolution. We observe three distinct spectral responses. The first is a positive broadband mode that can be attributed to an initial diffuse, delocalized electron with a radius of (22 ± 1) Å, which is short lived (<200 fs) because the absorption is blue-shifting outside of the THz range. The second emerging spectroscopic signature with a lifetime of about 150 ps is attributed to an intermolecular mode associated with a mass rearrangement of solvent molecules due to charge separation of radicals and hydronium cations. After 0.2 ps, we observe a long-lasting THz signature with depleted intensity at 110 cm -1 that is well reproduced by ab initio molecular dynamics. We interpret this negative band at 110 cm -1 as the solvent cage characterized by a weakening of the hydrogen bond network in the first and second hydration shells of the cavity occupied by the localized electron.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Deciphering the Solvation Structure of Aqueous ZnCl 2 Solutions from X-ray Absorption Spectra Using the Interpretable Graph Neural Network

Machine learning (ML) provides powerful pathways for predicting spectroscopic observables from atomic structures, but its broader impact depends on making model predictions interpretable in terms of physical and chemical principles. Here, we introduce a physics-guided graph neural network (GNN) model that predicts Zn K-edge X-ray spectroscopy (XAS) spectra of aqueous ZnCl 2 solutions. Training data are generated from ab initio XAS calculations on molecular dynamics snapshots obtained using a machine learning interatomic potential. The GNN reproduces experimental spectra across concentrations from dilute (<0.1 m) to highly concentrated (30 m, “water-in-salt”) regimes and scales efficiently to large, disordered liquid systems beyond the reach of conventional ab initio approaches. Gradient-based attribution analysis reveals that the model learns physically meaningful structure-spectrum relationships. Ligand-specific attributions reflect orbital hybridization patterns and the origin of the excitations derived from the density functional theory. Bond-length attributions recover spectral shifts consistent with multiple-scattering theory. Finally, this work bridges data-driven prediction with electronic-structure theory, establishing a general paradigm for interpretable ML that links atomic structure, electronic structure, and spectroscopic observables.

25 ENERGY STORAGE↗
DOE OSTI2021

Local molecular environment drives speciation and reactivity of ion complexes in concentrated salt solution

The speciation and reactivity of aqueous salt solutions are important for a wide variety of applications. However, application of this information is inhibited by broad disagreement about composition, mechanisms, and structure in concentrated solutions especially. Here, neutron diffraction with isotopic substitution measurements on aqueous zinc chloride solutions are used to calibrate molecular dynamics simulations that include effective electronic polarization. This allows us to probe the origin of speciation and reactivity of zinc chloride-water ion complexes, ZnCl x (H 2 O) y 2-x (x ≤ 4 and y ≤ 6), by comparing the reactivity of species in concentrated (4.5 m) and dilute (0.01 m) conditions. Within the concentrated solution, it is found that the extended solvation environment is dominated by solvent-separated ion complexes whose presence increases the free energy of activation for interconversion of species while simultaneously enhancing their thermodynamic stability. This concentration-dependent reactivity and stability suggests that other reactions, such as the nucleation of solid phases, will also be affected.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Consequences of the failure of equipartition for the p – V behavior of liquid water and the hydration free energy components of a small protein

Earlier we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step δ t ≤ 0.5 fs to ensure equipartition between translational and rotational modes. Here we extend that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examine integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small δ t is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, and the dielectric constant, a measure of dipole moment fluctuations, are also seen to be sensitive to δ t . Using the mean volume estimated from the NpT simulation, we examine the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to δ t . In going from δ t = 2 fs to δ t = 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Influence of Electronic Polarization on the Spectral Density

Accurate spectral densities are necessary for computing realistic exciton dynamics and nonlinear optical spectra of chromophores in condensed-phase environments, including multichromophore pigment–protein systems. However, due to the significant computational cost of computing spectral densities from first principles, requiring many thousands of excited-state calculations, most simulations of realistic systems rely on treating the environment as fixed-point charges. In this work, using a number of representative systems ranging from solvated chromophores to the photoactive yellow protein (PYP), we demonstrate that the quantum mechanical (QM) electronic polarization of the environment is key to obtaining accurate spectral densities and line shapes within the cumulant framework. We show that the QM environment can enhance or depress the coupling of fast chromophore degrees of freedom to the energy gap, altering the electronic–vibrational coupling and the resulting vibronic progressions in the absorption spectrum. In analyzing the physical origin of peaks in the spectral density, we identify vibrational modes that couple the electron and the hole as being particularly sensitive to the QM screening of the environment. For PYP, we reveal the need for careful determination of the appropriate QM region to obtain reliable spectral densities. Our findings suggest that the QM polarization of the environment can be crucial not just for excitation energies but also for electronic–vibrational coupling in complex systems with implications for the correct modeling of linear and nonlinear optical spectroscopy in the condensed phase as well as energy transfer in pigment–protein complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations

We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.

chemical physics↗
DOE OSTI2021

Chain conformations and phase separation in polymer solutions with varying solvent quality

Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the polymer-solvent interaction strength is increased further to be more than about twice the strength of the polymer-polymer and solvent-solvent interactions, the chain exhibits an unexpected collapsing behavior. Correspondingly, for strong polymer-solvent attractions, phase separation is observed in the solutions of multiple chains. These results indicate that the solvent becomes effectively poor again at very attractive polymer-solvent interactions. Nonetheless, the mechanism of chain collapsing and phase separation in this limit differs from the case with a poor solvent rendered by unfavorable polymer-solvent interactions. In the latter, the solvent is excluded from the domain of the collapsed chains while in the former, the solvent is still present in the pervaded volume of a collapsed chain or in the polymer-rich domain that phase separates from the pure solvent. Finally, in the limit of strong polymer-solvent attractions, the solvent behaves as a glue to stick monomers together, causing a single chain to collapse and multiple chains to aggregate and phase separate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structure and Dynamics of Aqueous Electrolytes Confined in 2D-TiO 2 /Ti 3 C 2 T 2 MXene Heterostructures

The synthesis of heterostructures of different two-dimensional (2D) materials offers an approach to combine advantages of different materials constituting the heterostructure and ultimately enhance their performance for applications such as electrochemical energy storage, achieving high energy, and high-power densities. Understanding the behavior of ions and solvents in confinement between these dissimilar layers is critical to understand their performance and control. Considering aqueous electrolytes, we explore the heterostructure of 2D lepidocrocite-type TiO 2 (2D-TiO 2 ) and hydroxylated or O-terminated Ti 3 C 2 MXene using ReaxFF molecular dynamics simulations and elastic/quasielastic neutron scattering techniques. Simulating a bilayer water intercalation, we find that the extent of interlayer hydration is impacted most by the surface terminations on the MXene and is marginally affected by 2D-TiO 2 . However, the introduction of 2D-TiO 2 decreases the water self-diffusion due to the notch sites (i.e., surface oxygen ridges) entrapping water molecules. Intercalating alkali cations into the heterostructures, we find that Li + is predominantly adsorbed at the 2D-TiO 2 surface instead of the MXenes with the preferential occupation of the notch sites. In contrast, Na+ forms a planar solvation with water, while K + is adsorbed both at the O-terminated MXene and 2D-TiO 2 . This behavior is altered when OH-terminated MXene is involved—the repulsion from the protons on the MXene surface forces the K + ions to be adsorbed exclusively to 2D-TiO 2 , while Na + retains some of its solvation in the water layer due to its smaller size. In OH-terminated MXenes, we see a consistent transfer of protons from the MXene surface toward 2D-TiO 2 , implying a greater capacity to store protons in the heterostructures. Of the three cations simulated, Na + hinders the proton migration the least and Li + the most because of its position near the 2D-TiO 2 surface. Furthermore, 2D-TiO 2 /MXene heterostructures are likely to exhibit a higher energy density but lower power density, especially with Na + intercalation.

25 ENERGY STORAGE↗
DOE OSTI2020

Reversible Interlayer Sliding and Conductivity Changes in Adaptive Tetrathiafulvalene-Based Covalent Organic Frameworks

Ordered interlayer stacking is intrinsic in two-dimensional covalent organic frameworks (2D COFs) and has strong implications on COF's optoelectronic properties. Reversible interlayer sliding, corresponding to shearing of 2D layers along their basal plane, is an appealing dynamic control of both structures and properties, yet it remains unexplored in the 2D COF field. In this paper, we demonstrate that the reversible interlayer sliding can be realized in an imine-linked tetrathiafulvalene (TTF)-based COF TTF-DMTA. The solvent treatment induces crystalline phase changes between the proposed staircase-like sql net structure and a slightly slipped eclipsed sql net structure. The solvation-induced crystallinity changes correlate well with reversible spectroscopic and electrical conductivity changes as demonstrated in oriented COF thin films. In contrast, no reversible switching is observed in a related TTF-TA COF, which differs from TTF-DMTA in terms of the absence of methoxy groups on the phenylene linkers. This work represents the first 2D COF example of which eclipsed and staircase-like aggregated states are interchangeably accessed via interlayer sliding, an uncharted structural feature that may enable applications such as chemiresistive sensors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Understanding the Interplay between the Nonvalence and Valence States of the Uracil Anion upon Monohydration

In this work we present an ab initio investigation into the effect of monohydration on the interaction of uracil with low energy electrons. Electron attachment and photodetachment experimental studies have previously shown dramatic changes in uracil upon solvation with even a single water molecule, due to an inversion of the character of the ground state of the anion. Here we explore the interplay between the nonvalence and valence states of the uracil anion, as a function of geometry and site of solvation. Our model provides unambiguous interpretation of previous photoelectron studies, reproducing the binding energies and photoelectron images for bare uracil and a single isomer of the U•(H 2 O) 1 cluster. Furthermore, the results of this study provide insight into how electrons may attach to hydrated nucleobases. These results lay the foundations for further investigations into the effect of microhydration on the electronic structure and electron capture dynamics of nucleobases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Ionic Associations and Hydration in the Electrical Double Layer of Water-in-Salt Electrolytes

Water-in-Salt-Electrolytes (WiSEs) are an exciting class of concentrated electrolytes finding applications in energy storage devices because of their expanded electrochemical stability window, good conductivity and cation transference number, and fire-extinguishing properties. These distinct properties are thought to originate from the presence of an anion-dominated ionic network and interpenetrating water channels for cation transport, which indicates that associations in WiSEs are crucial to understanding their properties. Currently, associations have mainly been investigated in the bulk, while little attention has been given to the electrolyte structure near electrified interfaces. Here, we develop a theory for the electrical double layer (EDL) of WiSEs, where we consistently account for the thermoreversible associations of species into Cayley tree aggregates. The theory predicts an asymmetric structure of the EDL. At negative voltages, hydrated Li + dominates, and cluster aggregation is initially slightly enhanced before disintegration at larger voltages. At positive voltages, when compared to the bulk, clusters are strictly diminished. Performing atomistic molecular dynamics (MD) simulations of the EDL of WiSE provides EDL data for validation and bulk data for parametrization of our theory. Validating the predictions of our theory against MD showed good qualitative agreement. Furthermore, we performed electrochemical impedance measurements to determine the differential capacitance of the studied LiTFSI WiSE and also found reasonable agreement with our theory. Overall, the developed approach can be used to investigate ionic aggregation and solvation effects in the EDL, which, among other properties, can be used to understand the precursors for solid-electrolyte interphase formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗