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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling

Here, we investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system studied here, with particles interacting through a repulsive screened Coulomb Yukawa potential, proceeds from vapor to dense liquid droplet to crystalline phases across multiple high barriers. Employing a one-dimensional reaction coordinate derived from the State Predictive Information Bottleneck framework, our simulations capture back-and-forth phase transitions across multiple barriers effectively in biased metadynamics simulations. We obtain relative free energy differences between different phases and also quantify the roles of different molecular level features in driving the phase changes.

Chemistry↗
DOE OSTI2025

Photoactivation Transition State and Dynamical Response of the Orange Carotenoid Protein

The orange carotenoid protein (OCP) regulates light harvesting in cyanobacteria by acting as a photoreceptor in its resting form, OCP O , and by effecting the quenching of bilin excitons upon binding to the core of the phycobilisome in its photoactivated red form, OCP R . We show herein using fluorescence anisotropy measurements and the action spectra for the rate constants of the two light-driven steps in the mechanism that the photoactivation of the OCP from Synechocystis sp. PCC 6803 is triggered by excited-state motions of the canthaxanthin chromophore that yield a twisted and bent conformation. Well-tempered metadynamics simulations reveal that a bicycle-pedal configuration, due to twisting of the two adjacent C=C bonds at the C13−C14 and C15−C15′ positions in the center of canthaxanthin’s π-conjugated isoprenoid backbone, can be accommodated by the binding site in the OCP, with the energy of a captured photon required to cross the local activation energy barriers from the dark equilibrium structure. The bicycle-pedal configuration breaks the conserved hydrogen-bonding interactions between the carbonyl substituent of the β-ionone end ring of canthaxanthin and the adjacent W288 and Y201 residues in the C-terminal domain. The action spectra are modulated by the vibronic excitation prepared by absorption transitions to the S 2 state, indicating that the photoactivation reactions are triggered by the canthaxanthin chromophore well prior to vibrational equilibration. These findings show that an ultrafast structural response of the OCP protein to the excited-state motions of the canthaxanthin chromophore controls the photoactivation yield and the sensing of blue light.

Fluorescence↗
DOE OSTI2022

Volatile Products of the Autoxidation of Poly(ethylenimine) in CO 2 Sorbents

Poly(ethyleneimine) (PEI)-based CO 2 sorbents are a promising material class for use in CO 2 capture applications, particularly direct air capture (DAC), due to their high amine content and CO 2 capacities. The sorbent lifetime is a key uncertainty in the deployment of these materials in such applications, as they oxidize under conditions relevant to candidate DAC process cycles. Here, in this study, we utilize thermogravimetric analysis/differential scanning calorimetry/FTIR spectroscopy to characterize the nature, rate, and quantity of volatile species formed from the oxidation of PEI when supported on mesoporous Al 2 O 3 . We show that NH 3 , CO 2 , and H 2 O are primary volatile species formed from PEI oxidation and that their production rate matches the overall oxidation rate as measured via heat flow from a differential scanning calorimeter. We show that the total quantity of NH 3 evolved is consistent with terminal primary amines being cleaved from the polymer chain and that approximately one hydrogen atom per PEI repeat unit reacts to form H 2 O during the reaction. Finally, metadynamics and quantum chemical simulations performed on a simplified system are used to highlight the likely importance of radicals in the elementary reactions that comprise the oxidation reaction set. The findings here represent the first characterization of the volatile products from the oxidation of PEI in CO 2 sorbents and lead to a greater understanding of the mechanisms behind the oxidative degradation of these materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Hydrophobic Nanoconfinement Enhances CO 2 Conversion to H 2 CO 3

Understanding the formation of H 2 CO 3 in water from CO 2 is important in environmental and industrial processes. Although numerous investigations have studied this reaction, the conversion of CO 2 to H 2 CO 3 in nanopores, and how it differs from that in bulk water, has not been understood. We use ReaxFF metadynamics molecular simulations to demonstrate striking differences in the free energy of CO 2 conversion to H 2 CO 3 in bulk and nanoconfined aqueous environments. We find that nanoconfinement not only reduces the energy barrier but also reverses the reaction from endothermic in bulk water to exothermic in nanoconfined water. Also, charged intermediates are observed more often under nanoconfinement than in bulk water. Stronger solvation and more favorable proton transfer with increasing nanoconfinement enhance the thermodynamics and kinetics of the reaction. Here our results provide a detailed mechanistic understanding of an important step in the carbonation process, which depends intricately on confinement, surface chemistry, and CO 2 concentration.

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

Control of the Structural Charge Distribution and Hydration State upon Intercalation of CO 2 into Expansive Clay Interlayers

Numerous experimental investigations indicated that expansive clays such as montmorillonite can intercalate CO 2 preferentially into their interlayers and therefore potentially act as a material for CO 2 separation, capture, and storage. However, an understanding of the energy–structure relationship during the intercalation of CO 2 into clay interlayers remains elusive. Here, in this study, we use metadynamics molecular dynamics simulations to elucidate the energy landscape associated with CO 2 intercalation. Our free energy calculations indicate that CO 2 favorably partitions into nanoconfined water in clay interlayers from a gas phase, leading to an increase in the CO 2 /H 2 O ratio in clay interlayers as compared to that in bulk water. CO 2 molecules prefer to be located at the centers of charge-neutral hydrophobic siloxane rings, whereas interlayer spaces close to structural charges tend to avoid CO 2 intercalation. The structural charge distribution significantly affects the amount of CO 2 intercalated in the interlayers. These results provide a mechanistic understanding of CO 2 intercalation in clays for CO 2 separation, capture, and storage.

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

Molecular Mechanisms of Sorbed Ion Effects during Boehmite Particle Aggregation

Classical theories of particle aggregation, such as Derjaguin–Landau–Verwey–Overbeek (DLVO), do not explain recent observations of ion-specific effects or the complex concentration dependence for aggregation. Thus, here, we probe the molecular mechanisms by which selected alkali nitrate ions (Na + , K + , and NO 3 –) influence aggregation of the mineral boehmite (γ-AlOOH) nanoparticles. Nanoparticle aggregation was analyzed using classical molecular dynamics (CMD) simulations coupled with the metadynamics rare event approach for stoichiometric surface terminations of two boehmite crystal faces. Calculated free energy landscapes reveal how electrolyte ions alter aggregation on different crystal faces relative to pure water. Consistent with experimental observations, we find that adding an electrolyte significantly reduces the energy barrier for particle aggregation (~3–4×). However, in this work, we show this is due to the ions disrupting interstitial water networks, and that aggregation between stoichiometric (010) basal–basal surfaces is more favorable than between (001) edge–edge surfaces (~5–6×) due to the higher interfacial water densities on edge surfaces. The interfacial distances in the interlayer between aggregated particles with electrolytes (~5–10 Å) are larger than those in pure water (a few Ångströms). Together, aggregation/disaggregation in salt solutions is predicted to be more reversible due to these lower energy barriers, but there is uncertainty on the magnitudes of the energies that lead to aggregation at the molecular scale. By analyzing the peak water densities of the first monolayer of interstitial water as a proxy for solvent ordering, we find that the extent of solvent ordering likely determines the structures of aggregated states as well as the energy barriers to move between them. Further, the results suggest a path for developing a molecular-level basis to predict the synergies between ions and crystal faces that facilitate aggregation under given solution conditions. Such fundamental understanding could be applied extensively to the aggregation and precipitation utilization in the biological, pharmaceutical, materials design, environmental remediation, and geological regimes.

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

Exploring the Ion Solvation Environments in Solid-State Polymer Electrolytes through Free-Energy Sampling

The success of poly(ethylene oxide) (PEO) in solid-state polymer electrolytes for lithium-ion batteries is well established. Recently, in order to understand this success and to explore possible alternatives, we studied polyacetal electrolytes to deepen the understanding of the effect of the local chemical structure on ion transport. Advanced molecular dynamics techniques using newly developed, tailored interaction potentials have helped elucidate the various coordination environments of ions in these systems. In particular, the competition between cation-Anion pairing and coordination by the polymer has been explored using free-energy sampling (metadynamics). At equivalent reduced temperatures, with respect to the polymer-specific glass-Transition temperature, two-dimensional free-energy plots reveal the existence of multiple coordination environments for the lithium (Li) ions in these systems and their relative stabilities. Furthermore, we observe that the Li-ion movement in PEO follows a serial, stepwise pathway when moving from one coordination state to another, whereas this happens in a more continuous and concerted fashion in a polyacetal such as poly(1,3-dioxalane) [P(EO-MO)]. The implication is that interconversion between coordination states of the Li ions may be easier in P(EO-MO). However, the overarching observation from our free-energy analysis is that Li-ion coordination is dominated by the polymer (in either case) and contact-ion pairs are rare. We rationalize the observed higher increase in glass-Transition temperature (Tg) with salt loading in polyacetals as due to intermolecular Li-ion coordination involving multiple polymer chains, rather than just one chain for PEO-based electrolytes. This interchain coupling in the polyacetals, resulting in the higher Tg, works against any gains due to variations in Li-ion coordination that might enhance transport processes over PEO. Further research is required to overcome the interdependence between local coordination and macroscopic properties to compete with PEO electrolytes at the same absolute working temperature.

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

Teaching an Old Reagent New Tricks: Synthesis, Unusual Reactivity, and Solution Dynamics of Borohydride Grignard Compounds

Grignard reagents of general formula RMgX (X = Cl - , Br - , I - ) have been utilized in various chemistries for over 100 years. Here, we report that replacing the halide in a Grignard reagent with a reactive borohydride anion adds a new synthetic dimension for these influential compounds. Here, we synthesized the series RMgBH 4 (R=Et, n-Bu, Ph, Bn) and characterized the reactivity toward both organic and inorganic molecules. Using butylmagnesium borohydride (BuMgBH 4 ) as an exemplar, we demonstrate that these compounds possess unique reactivity due to the presence of reducing borohydride groups, resulting in tandem reactivity with organic amides/esters to generate secondary and primary alcohols. Molecular dynamics simulations indicate the stability of BuMgBH 4 is comparable to that of Mg(BH 4 ) 2 + MgBu 2 , validating the Schlenk equilibrium in borohydride Grignard compounds. Metadynamics simulations confirm that the equilibrium is kinetically accessible through solvent-mediated processes. BuMgBH 4 also reacts with CO 2 and NH 3 , revealing potential uses for CO 2 utilization and as a mixed-anion metal borohydride/amide precursor.

36 MATERIALS SCIENCE↗
DOE OSTI2025

CO Adsorbates Induced Framework-Associated Low-Valence Co δ+ Sites in Co-ZSM-5 for Ethane Dehydrogenation

The dynamic structural evolution of heterogeneous catalysts is a ubiquitous phenomenon that has attracted a lot of interest. Catalyst reconstruction can occur after appropriate pretreatment, resulting in more efficient active catalysts, which is an attractive but challenging issue. Here, we reveal a CO activation strategy that controls the microenvironment of the Co sites in the high-silica Co-ZSM-5 catalyst (denoted as 0.50Co-Z5(340)), resulting in three times higher initial conversion and superior regeneration durability in the ethane dehydrogenation reaction compared to the same catalyst without CO pretreatment. In situ spectroscopy and metadynamics simulations reveal that the Co 2+ sites in 0.50Co-Z5(340) dislodge from the framework and move toward the nearby Brønsted acid sites, forming framework-associated low-valence Co δ+ species. Mechanistic studies indicate that the Co δ+ species catalyze ethane C–H bond cleavage via an oxidative addition mechanism, and ethylene is produced simultaneously with H* coupling (direct pathway). The promoted C–H bond activation and facile ethylene desorption explain the superior ethane dehydrogenation performance of the herein CO preactivated 0.50Co-Z5(340) catalyst.

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

Confinement effects and acid strength in zeolites

Chemical reactivity and sorption in zeolites are coupled to confinement and—to a lesser extent—to the acid strength of Brønsted acid sites (BAS). In presence of water the zeolite Brønsted acid sites eventually convert into hydronium ions. The gradual transition from zeolite Brønsted acid sites to hydronium ions in zeolites of varying pore size is examined by ab initio molecular dynamics combined with enhanced sampling based on Well-Tempered Metadynamics and a recently developed set of collective variables. While at low water content (1–2 water/BAS) the acidic protons prefer to be shared between zeolites and water, higher water contents (n > 2) invariably lead to solvation of the protons within a localized water cluster adjacent to the BAS. At low water loadings the standard free energy of the formed complexes is dominated by enthalpy and is associated with the acid strength of the BAS and the space around the site. Conversely, the entropy increases linearly with the concentration of waters in the pores, favors proton solvation and is independent of the pore size/shape.

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

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The non-adiabatic nanoreactor: towards the automated discovery of photochemistry

The ab initio nanoreactor has previously been introduced to automate reaction discovery for ground state chemistry. In this work, we present the nonadiabatic nanoreactor, an analogous framework for excited state reaction discovery. We automate the study of nonadiabatic decay mechanisms of molecules by probing the intersection seam between adiabatic electronic states with hyper-real metadynamics, sampling the branching plane for relevant conical intersections, and performing seam-constrained path searches. We illustrate the effectiveness of the nonadiabatic nanoreactor by applying it to benzene, a molecule with rich photochemistry and a wide array of photochemical products. Our study confirms the existence of several types of S 0 /S 1 and S 1 /S 2 conical intersections which mediate access to a variety of ground state stationary points. We elucidate the connections between conical intersection energy/topography and the resulting photoproduct distribution, which changes smoothly along seam space segments. The exploration is performed with minimal user input, and the protocol requires no previous knowledge of the photochemical behavior of a target molecule. We demonstrate that the nonadiabatic nanoreactor is a valuable tool for the automated exploration of photochemical reactions and their mechanisms.

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

Energetics of high temperature degradation of fentanyl into primary and secondary products

Fentanyl is a synthetic opioid used for managing chronic pain. Due to its higher potency (50–100×) than morphine, fentanyl is also an abused drug. A sensor that could detect illicit fentanyl by identifying its thermally degraded fragments would be helpful to law enforcement. While experimental studies have probed the thermal degradation of fentanyl, little theoretical work has been done to understand the mechanism. Here, we studied the thermal degradation pathways of fentanyl using extensive ab initio molecular dynamics simulations combined with enhanced sampling via multiple-walker metadynamics. We calculated the free energy profile for each bond suggested earlier as a potential degradation point to map the thermodynamic driving forces. In conclusion, we also estimated the forward attempt rate of each bond degradation reaction to gain information about degradation kinetics.

Poudel, Bharat↗
DOE OSTI2023

Low hydrogen solubility in clay interlayers limits gas loss in hydrogen geological storage

Gas intercalation into clay interlayers may result in hydrogen loss in the geological storage of hydrogen; a phenomenon that has not been fully understood and quantified. Here we use metadynamics molecular simulations to calculate the free energy landscape of H 2 intercalation into montmorillonite interlayers and the H 2 solubility in the confined water; in comparison with results obtained for CO 2 . Furthermore, the results indicate that H 2 intercalation into hydrated interlayers is thermodynamically unfavorable while CO 2 intercalation can be favorable. H 2 solubility in hydrated clay interlayers is in the same order of magnitude as that in bulk water and therefore no over-solubility effect due to nanoconfinement is observed – in striking contrast with CO 2 . These results indicate that H 2 loss and leakage through hydrated interlayers due to intercalation in a subsurface storage system, if any, is limited.

58 GEOSCIENCES↗
DOE OSTI2024

Impact of magnetic and electric fields on the free energy to form a calcium carbonate ion-pair

Electromagnetic fields are used in water treatment and desalination to regulate scale formation and extend the lifetime of membranes. External electric and magnetic fields can promote or suppress mineral nucleation and growth. However, the molecular-scale mechanisms of such processes remain unknown. Computing the free energies needed to form ion pairs under external fields provides important insights into understanding the elemental steps during the initial formation of mineral scales. In this paper, we used molecular dynamics combined with metadynamics simulations to investigate the free energies of forming the [Ca–CO 3 ] 0 ion pair, a fundamental building block of carbonate scales, under a range of magnetic (up to 10 T) and electric (up to 10 V m −1 ) fields in water. The presence of constant magnetic or electric fields favored the ion pairing reaction and lowered the free energies by up to 3% to 6%. The internal energy and entropic components of the free energy showed significant changes and exhibited non-linear behavior with increasing field strength. The [Ca–CO 3 ] 0 ion pairing is an entropy-driven process in the absence of an external field, but the mechanism shifts to an internal energy-driven process under selected external fields, suggesting possible changes in the nucleation pathways.

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

Acidities of MgO surface sites: implications for the formation mechanism of Mg(OH) 2

The hydroxylation of periclase (MgO) to brucite (Mg(OH) 2 ) is thought to be an important intermediate step when using MgO to capture CO 2 from the atmosphere. However, the mechanism of hydroxylation of MgO to form Mg(OH) 2 is poorly understood. In this work, we used atomic-scale density functional tight binding simulations coupled with the metadynamics rare event method to analyze the surface chemistry of MgO and the acid dissociation equilibrium constants (pK a ) of its surface sites. The method and parameters were validated by calculating the pK a for hydroxylation of the first shell water bound to aqueous Mg 2+ ion. The pK a value derived using a probabilistic method was 12.3, which is in fair agreement with the accepted value of 11.4, with the difference between them equal to a ∼5 kJ mol −1 error in the calculations. We then extended these pK a calculations to probe the hydroxylation reactions of the surface sites of the MgO(100)–water interface, arriving at pK a s of 5.4 to deprotonate terminal water molecules bound to the surface magnesium sites (η-OH 2 or 〉MgOH 2 ), and 13.9 to deprotonate hydroxylated bridging oxygen sites (μ 5 -oxo or 〉O). Hydroxide (OH − ) adsorption on the surface was also probed and found to be less thermodynamically favorable than deprotonation of the terminal water molecule. The plausibility of the computed pK a s was verified using an activity-based speciation model and compared to pH measurements of water equilibrated with MgO nanoparticles and single crystals. The model predicted a solution pH of 7.1 when surface sites buffered and the pH of 12.0 when MgO dissolution dominated. These are close to the experimental initial solution pHs of 7–7.5 and the long term pHs of ∼10.5. The similarity suggests that the calculated pK a values from the DFTB+/metadynamics simulations are plausible and that these methods can be a useful tool to probe reaction mechanisms involving covalent bonds.

Adapa, Sai Krishna Reddy [Oak Ridge National Labor↗
DOE OSTI2026

Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces

Understanding ion adsorption at electrified metal–electrolyte interfaces is essential for accurate modeling of electrochemical systems. Here, in this study, we systematically investigate the free energy profiles of Na + , Cl − , and F − ions at the Au(111)–water interface using enhanced sampling molecular dynamics with both classical force fields and machine-learned interatomic potentials (MLIPs). Our classical metadynamics results reveal a strong dependence of predicted ion adsorption on the Lennard-Jones parameters, highlighting that—without due care—standard mixing rules can lead to qualitatively incorrect descriptions of ion–metal interactions. We present a systematic methodology for tuning the cross term LJ parameters to control adsorption energetics in agreement with more accurate models. As a surrogate for an ab initio model, we employed the recently released Universal Models for Atoms MLIP, which validates classical trends and displays strong specific adsorption for chloride, weak adsorption for fluoride, and no specific adsorption for sodium, in agreement with experimental and theoretical expectations. By integrating molecular-level adsorption free energies into continuum models of the electric double layer, we show that specific ion adsorption substantially alters the interfacial ion population, the potential of zero charge, and the differential capacitance of the system. Our results underscore the critical importance of force field parameterization and advanced interatomic potentials for the predictive modeling of ion-specific effects at electrified interfaces and provide a robust framework for bridging molecular simulations and continuum electrochemical models.

Roncoroni, Fabrice [Lawrence Berkeley National Lab↗
DOE OSTI2023

Unveiling the catalytic mechanism of GTP hydrolysis in microtubules

Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice versa. Depolymerization is coupled with hydrolysis of guanosine triphosphate (GTP) within β-tubulin. Hydrolysis is favored in the MT lattice compared to a free heterodimer with an experimentally observed rate increase of 500- to 700-fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP state and whether a “compacted” GDP-state lattice is required for hydrolysis. In this work, extensive quantum mechanics/molecular mechanics simulations with transition-tempered metadynamics free-energy sampling of compacted and expanded interdimer complexes, as well as a free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice, disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to a free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗