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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Dehydration of UO 2 Cl 2 ·3H 2 O and Nd(NO 3 ) 3 ·6H 2 O with a Soft Donor Ligand and Comparison of Their Interactions through X-ray Diffraction and Theoretical Investigation [plus Supplemental Information]

Herein we investigated whether the relatively Lewis basic imidazole-2-thiones could be used to substitute water ligands bound to f-element cations and generate f-element soft donor complexes. Reactions of 1,3-diethylimidazole-2-thione (C 2 C 2 ImT) with Nd(NO 3 ) 3 ·6H 2 O and UO 2 Cl 2 ·3H 2 O led to the isolation of the anhydrous thione complexes Nd(NO 3 ) 3 (C 2 C 2 ImT) 3 and UO 2 Cl 2 (C 2 C 2 ImT) 2 , characterized by single crystal X-ray diffraction. Differences in the strength of metal–thione interactions have been examined by means of the crystal structure analysis and density functional theory (DFT) calculations. The C 2 C 2 ImT ligands were found to be affected by both coordination and noncovalent interactions, making it impossible to deconvolute the effects of one from the other. Calculated partial atomic charges indicated greater ligand-to-metal charge transfer in the [UO 2 ] 2+ complex, indicative of a stronger interaction. The reactivity of C 2 C 2 ImT demonstrates its usefulness in the preparation of f-element soft donor complexes from readily available hydrates that could be useful intermediates for promoting the coordination and studying the effects of soft donor anions.

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

Method for accurately predicting solvation structure

Accurately predicting the molecular structure of solutions is a fundamental scientific challenge. Using quantum mechanical density functional theory (DFT) to make these predictions is hindered by significant variation depending on which DFT functional is used. Here, we present a simple metric that can determine the reliability of a DFT functional for predicting solvation structure. We then show that including a simple interaction term to correct this metric leads to quantitative agreement with experimental measurements of liquid structure. We demonstrate the utility of this method by using it to accurately describe the hydration structure around the Na+ a

basis sets, molecular structure, cluster chemistry↗
DOE OSTI2021

Ion Solvation and Transport in Narrow Carbon Nanotubes: Effects of Polarizability, Cation-π Interaction, and Confinement

Understanding ion solvation and transport under confinement is critical for a wide range of emerging technologies, including water desalination and energy storage. While molecular dynamics (MD) simulations have been widely used to study the behavior of confined ions, considerable deviations between simulation results depending on the specific treatment of intermolecular interactions remain. In the following, we present a systematic investigation of the structure and dynamics of two representative solutions, that is, KCl and LiCl, confined in narrow carbon nanotubes (CNTs) with a diameter of 1.1 and 1.5 nm, using a combination of first-principles and classical MD simulations. Our simulations show that the inclusion of both polarization and cation-π interactions is essential for the description of ion solvation under confinement, particularly for large ions with weak hydration energies. Beyond the variation in ion solvation, we find that cation-π interactions can significantly influence the transport properties of ions in CNTs, particularly for KCl, where our simulations point to a strong correlation between ion dehydration and diffusion. Finally, our study highlights the complex interplay between nanoconfinement and specific intermolecular interactions that strongly control the solvation and transport properties of ions.

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

MD Simulation of Water Using a Rigid Body Description Requires a Small Time Step to Ensure Equipartition

In simulations of aqueous systems, it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time step δt for integrating the equations of motion. Thus, δt = 2 fs is often used in simulating rigid models of water. We simulate the SPC/E model of water using δt from 0.5 to 3.0 fs and up to 4 fs using hydrogen mass repartitioning. In these simulations, we find that for all but δt = 0.5 fs, equipartition is not obtained between translational and rotational modes, with the rotational modes exhibiting a lower temperature than the translation modes. To probe the reasons for the lack of equipartition, we study the autocorrelation of the translational velocity of the center of mass and the angular velocity of the rigid water molecule, respectively. Here, we find that the rotational relaxation occurs on a timescale comparable to vibrational periods, calling into question the original motivations for freezing the vibrations. Furthermore, a time step with δt ≥ 1 fs is not able to capture accurately the fast rotational relaxation, which reveals its impact as an effective slowing-down of rotational relaxation. The fluctuation–dissipation relation then leads to the conclusion that the rotational temperature should be cooler for δt greater than the reference value of 0.5 fs. Consideration of fluctuation–dissipation in equilibrium molecular dynamics simulations also emphasizes the need to capture the temporal evolution of fluctuations with fidelity and the role of δt in this regard. The time step also influences the solution thermodynamic properties: both the mean system potential energies and the excess entropy of hydration of a soft repulsive cavity are sensitive to δt.

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

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

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

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

Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

In this work, we describe the development and implementation of a quasi-equilibrium hydration shell model of biomolecular solvation with adaptive boundaries. Applying the model to microsecond-long molecular dynamics simulations of several protein systems of varying complexity, we find that the model simulation results are of comparable quality to those obtained from simulations of fully solvated systems, but at a reduced computational cost. We discuss the dominant sources of error in the model and outline directions for future improvements.

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

Gas-Phase Complexes of Americium and Lanthanides with a Bis-triazinyl Pyridine: Reactivity and Bonding of Archetypes for F-Element Separations

Bis-triazinyl pyridines (BTPs) exhibit solution selectivity for trivalent americium over lanthanides (Ln), the origins of which remain uncertain. Here in this paper, electrospray ionization was used to generate gas-phase complexes [ML 3 ] 3+ , where M = La, Lu, or Am and L is EtBTP 2,6-bis(5,6-diethyl-1,2,4-triazin-3-yl)-pyridine. Collision-induced dissociation (CID) of [ML 3 ] 3+ in the presence of H 2 O yielded a protonated ligand [L(H)] + and hydroxide [ML 2 (OH)] 2+ or hydrate [ML(L–H)(H 2 O)] 2+ , where (L–H) - is a deprotonated ligand. Although solution affinities indicate stronger binding of BTPs toward Am 3+ versus Ln 3+ , the observed CID process is contrastingly more facile for M = Am versus Ln. To understand the disparity, density functional theory was employed to compute potential energy surfaces for two possible CID processes, for M = La and Am. In accordance with the CID results, both the rate determining transition state barrier and the net energy are lower for [AmL 3 ] 3+ versus [LaL 3 ] 3+ and for both product isomers, [ML 2 (OH)] 2+ and [ML(L–H)(H 2 O)] 2+ . More facile removal of a ligand from [AmL 3 ] 3+ by CID does not necessarily contradict stronger Am 3+ –L binding, as inferred from solution behavior. In particular, the formation of new bonds in the products can distort kinetics and thermodynamics expected for simple bond cleavage reactions. In addition to correctly predicting the seemingly anomalous CID behavior, the computational results indicate greater participation of Am 5f versus La 4f orbitals in metal–ligand bonding.

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 OSTI2022

Water Network Shape-Dependence of Local Interactions with the Microhydrated –NO 2 – and –CO 2 – Anionic Head Groups by Cold Ion Vibrational Spectroscopy

We report the structural evolutions of water networks and solvatochromic response of the CH 3 NO 2 – radical anion in the OH and CH stretching regions by analysis of the vibrational spectra displayed by cryogenically cooled CH 3 NO 2 – ·(H 2 O) n=1–6 clusters. The OH stretching bands evolve with a surprisingly large discontinuity at n = 6, which features the emergence of an intense, strongly red-shifted band along with a weaker feature that appears in the region assigned to a free OH fundamental. Very similar behavior is displayed by the perdeuterated carboxylate clusters, RCO 2 – ·(H 2 O) n=5–7 (R = CD 3 CD 2 ), indicating that this behavior is a general feature in the microhydration of the triatomic anionic domain and not associated with CH oscillators. Electronic structure calculations trace this behavior to the formation of a “book” isomer of the water hexamer that adopts a configuration in which one of the water molecules resides in an acceptor–acceptor–donor (AAD) (A = acceptor, D = donor) H-bonding site. Excitation of the bound OH in the AAD site explores the local network topology best suited to stabilize an incipient –XO 2 H–OH–(H 2 O) 2 intracluster proton-transfer reaction. These systems thus provide particularly clear examples where the network shape controls the potential energy landscape that governs water network-mediated, intracluster proton transfer. The CH stretching bands of the CH 3 NO 2 – ·(H 2 O) n=1–6 clusters also exhibit strong solvatochromic shifts, but in this case, they smoothly blue-shift with increasing hydration with no discontinuity at n = 6. Furthermore, this behavior is analyzed in the context of the solute-ion polarizability response and partial charge transfer to the water networks.

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

High-Temperature Reaction Kinetics of the e aq – and HO 2 • Radicals with Iron(II) Ions in Aqueous Solutions

Pulsed electron radiolysis was used to determine the chemical reaction kinetics and Arrhenius parameters for iron(II) reactions in aqueous solutions under irradiation. The second-order Fe 2+ reactions with the hydrated electron (e aq – ) and the perhydroxyl radical (HO 2 • ), arising from water radiolysis, were measured to high temperatures using custom-built flow-through cells with a multichannel optical detection system. The reaction with the HO 2 • radical was found to proceed via the formation of a metal-ion adduct species, Fe 2+ –HO 2 • . Additionally, the adduct’s molar extinction coefficient and its first-order decay rate coefficients are reported.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Photoelectron Spectroscopy and Computational Study on Microsolvated [B 10 H 10 ] 2– Clusters and Comparisons to Their [B 12 H 12 ] 2– Analogues

Microhydrated closo-Boranes have attracted great interests due to their superchaotropic activity related to well-known Hofmeister effect and important applications in biomedical and battery fields. In this work, we report a combined negative ion photoelectron spectroscopy and quantum chemical investigation on hydrated closo-decaborate clusters [B 10 H 10 ] 2- ·nH 2 O (n = 1 – 7) with a direct comparison to their analogues [B 12 H 12 ] 2- ·nH 2 O and free water clusters. A single H 2 O molecule is found sufficient to stabilize the intrinsically unstable [B 10 H 10 ] 2- dianion. The first two water molecules strongly interact with the solute forming B-H···H-O dihydrogen bonds while additional water molecules show substantially reduced binding energies. Unlike [B 12 H 12 ] 2- ·nH 2 O possessing highly structured water network with the attached H 2 O molecules arranged in a unified pattern by maximizing B-H···H-O dihydrogen bonding, distinct structural arrangements of the water clusters within [B 10 H 10 ] 2– ·nH 2 O are achieved with the water cluster networks from trimer to heptamer resembling free water clusters. Such a distinct difference arises from the variations in size, symmetry, and charge distributions between these two dianions. Finally, the present finding again confirms the structural diversity of hydrogen-bonding networks in microhydrated closo-boranes and enrich our understanding of aqueous borate chemistry.

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

Formation of Water Networks on Anionic Perylene

We present infrared photodissociation spectra of hydrated perylene anion clusters with up to four water molecules, as well as electronic structure calculations based on density functional theory. Water molecules form weak hydrogen bonds to the π system of the perylene anion. For clusters with more than one water molecule, water−water hydrogen bonds are formed, which generally appear to be stronger than water−π hydrogen bonds, especially for the trihydrate and tetrahydrate. The resulting water networks exist as water subclusters on the surface of the carbon frame of perylene. Here, we observe temperature-dependent dynamic effects, which highlight large amplitude motions of the water network and the shallowness of the potential energy surfaces governing the structures of these clusters.

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

Hydrolysis Reaction Pathways of Thorium Oxide Nanoclusters

Density functional theory benchmarked by correlated molecular orbital theory is used to develop a fundamental and predictive understanding of the interaction of thorium oxide nanoclusters with gas phase water to provide insight into nuclear-waste storage, production of thorium nuclear reactor fuels, and reprocessing of spent fuel. The structures of Th n O 2n (n = 3 – 6) clusters and their interactions with water have been studied at the B3LYP, MP2, and CCSD(T) levels. Hydrolysis is initiated by the formation of Lewis acid-base adducts, with relative H 2 O binding energies (physisorption) ranging from −15 kcal/mol to −22 kcal/mol. The initial H 2 O physisorption energy is ca. −21 kcal/mol regardless of the cluster size and is consistent with the experimentally obtained initial adsorption energy on a thorium dioxide surface. The physisorption enthalpies for additional water molecules can be affected by the presence of terminal groups OH groups generated by proton transfer to a Th-O near the site of adsorption. The hydrolysis products (chemisorption) form either bridging or terminal hydroxides. More exothermic hydrolysis steps were predicted for the formation of terminal hydroxides as compared to the formation of bridging hydroxides. Here, the calculated transition state barriers for transfer of protons from bound water complexes to form the chemisorption products are very low. Overall, water readily reacts with thorium oxide clusters preferring hydroxide products over hydrated complexes. First and second order fits were predicted for the combined physisorption and chemisorption energies for the hydrolysis of thorium oxide clusters. Finally, ionization energies and electron affinities were calculated as were HOMO-LUMO gaps to provide additional insights into the properties of the thorium oxide and hydroxide clusters.

Adsorption↗
DOE OSTI2026

Uranium Hexafluoride Hydrolysis Reaction Dynamics from Cryogenic Layering, FTIR Spectroscopy, and Isotopic Substitution

The first direct evidence that the hydrolysis reaction of uranium hexafluoride (UF 6 ) follows multiple competing pathways which are driven by the ratio of water to UF 6 , temperature, and isotopic composition is presented. Using temperature dependent infrared spectroscopy, it is shown the hydrolysis can be prevented at temperatures below 150 K, and that water-rich environments promote the formation of uranium oxyfluoride intermediates. Spectral shifts reveal isomeric transitions and the growth of polymeric species, with reaction reversibility observed at high water concentrations. Additionally, controlled heating rates affect the emergence of intermediates. The final particulate product consistently forms as uranyl fluoride hydrate, though its morphology and spectral signature vary with reaction conditions and annealing. These findings help clarify long-standing uncertainties surrounding UF 6 hydrolysis.

Chemical reactions↗
DOE OSTI2021

Pushing and Pulling: A Dual pH Trigger Controlled by Varying the Alkyl Tail Length in Heme Coordinating Peptide Amphiphiles

Some organisms in nature that undergo anaerobic respiration utilize 1D nanoscale arrays of densely packed cytochromes containing the molecule heme. The assemblies can be mimicked with 1D nanoscale fibrils composed of peptide amphiphiles designed to coordinate heme in dense arrays. To create such materials and assemblies it is critical to understand the assembly process and what controls the various aspects of hierarchical assembly. MD simulations suggest that shorter alkyl chains on the peptide lead to more dynamic structures than the peptides with longer chains that yield kinetically trapped states. The hydration parameters manifest themselves experimentally through the observation of a dual pH trigger which controls the peptide assembly rate, the heme binding affinity, and heme organization kinetics. Great strides in understanding the relative complexity of the self-assembly process in relation to incorporating a functional moiety like heme opens up many possibilities in developing abiotic assemblies for bioelectronic devices and assemblies

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

Structure of Sulfuric Acid Solutions Using Pair Distribution Function Analysis

Solvation and mesoscale ordering of sulfuric acid and other strong acid solutions leads to suppressed freezing points and strong rheological changes with varying concentration. While the solid-state structures are well-understood, studies focused on the evolving solvation structure in the solution phase have probed a limited concentration range (~1–6 M). This study applies a total scattering approach in both the wide-angle X-ray scattering (WAXS) and pair distribution function (PDF) regimes to elucidate the evolving solvation structure over its full range of acid concentration (0–18 M). The emergence of a prepeak in the WAXS regime at intermediate concentrations indicates a transition from noninteracting sulfate molecules in the dilute limit to sterically limited sulfates at concentrations near its deep eutectic point. Fits to the PDF data quantify this trend, showing a transition from octahedrally hydrated sulfates up to 6–7 M concentrations, followed by gradual dehydration, and eventually reaching a solution structure similar to that of water-in-salt electrolyte systems at high acid concentrations.

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

Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands

Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. In this report we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La 3+ ) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La 3+ –ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La 3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion–water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion–protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.

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

Elucidating the Mechanism for the Reaction of $o$-Phthalaldehyde with Primary Amines in the Presence of Thiols

The use of o-phthalaldehyde (OPA) in combination with a thiol reagent is a common method for detecting primary amines in amino acids, peptides, and proteins. Despite its widespread use, the exact reaction mechanism has been debated since the 1980s. Here, we measure the kinetics of the reaction between OPA, alanine, and a dithiol (1,4-dithiolthreitol, DTT) as a function of pH and reagent concentration. Using these new measurements and accompanying kinetic models, we find evidence that the pH dependence of the kinetics arises from both the protonation states of alanine and DTT, the hydration state of OPA, and the unproductive equilibrium with DTT, all of which are pH-dependent. Importantly, these results support the mechanism originally proposed by Sternson [Rational design and evaluation of improved o-phthalaldehyde-like fluorogenic reagents. Anal. Biochem. 1985, 144, 233–246] and Wong [Reaction of o-phthalaldehyde with alanine and thiols: kinetics and mechanism. J. Am. Chem. Soc. 1985, 107, 6421–6422], in which the primary amine first reacts with OPA, followed by a reaction with the thiol to form the fluorescent isoindole product.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗