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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.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Recent Insights Into Interfacial Transport and Chemical Reactions of Plasma–Generated Species in Liquid

The chemistry of plasma–liquid interactions involves a complex interplay of physical and chemical processes at the plasma–liquid interface. These interactions give rise to the generation, transport, and transformation of various reactive species. Since the publication of the Lorenz Roadmap in 2016, significant progress has been made in understanding the interfacial transport and coupled reactions of plasma-generated species with inorganic and organic compounds. However, critical aspects of plasma–liquid chemistry and mass transfer still require further investigation. Here, this review summarizes recent work on processes at the plasma–liquid interface and the coupled reactions in the liquid phase. We highlight key findings related to the involvement of O atoms, H radicals, solvated electrons, photons, and nitrogen-derived species at the interface and within the bulk liquid.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Different dynamics and pathway of disulfide bonds reduction of two human defensins, a molecular dynamics simulation study

Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5 (HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds in oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order have been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released in reducing condition. The structure of hBD-3 was found to be more dynamic and flexible than HD5, based on RMSD, RMSF, and radius of gyration calculations. The disulfide bridge breaking order of HD5 and hBD-3 in reducing condition was predicted by two kinds of methods, which gave consistent results. It was found that the disulfide bonds breaking pathways for HD5 and hBD-3 are very different. The breaking of disulfide bonds can influence the dimer interface by making the dimer structure less stable for both kinds of defensin. In order to understand the difference in dynamics and disulfide bond breaking pathway, hydrophilic and hydrophobic accessible surface areas (ASA), buried surface area between cysteine pairs, entropy of cysteine pairs, and internal energy were calculated. Comparing to the wildtype, hBD-3 analog is more hydrophobic, while HD5 is more hydrophilic. For hBD-3, the disulfide breaking is mainly entropy driven, while other factors such as the solvation effects may take the major role in controlling HD5 disulfide breaking pathway. Proteins 2017; 85:665–681. © 2016 Wiley Periodicals, Inc.

Biochemistry & Molecular Biology↗
DOE OSTI2016

Charge distribution and hydrogen bonding of a collagen α 2 ‐chain in vacuum, hydrated, neutral, and charged structural models

A challenging task in computational biophysics is to ascertain the solvent effect on the electronic structure and interatomic bonding at the atomistic level. Simulations must be carried out on reasonably large biomolecules for accurate calculations to yield valid results. We report the results of a calculation on collagen model in the form of a peptide under three different environments: vacuum, solvated and with neutral and charged sites. Quantitative results and analysis of the partial charge (PC) distribution on each amino acid are discussed. A significant charge transfer of more than 1 electron from protein to water molecules is found with similar results when the model contains charged sites. The main contributions to the interatomic bonding are from hydrogen bonds (HBs) between water‐water and water‐protein pairs. A connection between PC and HBs can be established since the nonpolar amino acids form no HBs and have the smallest PC and vice versa. The ab initio PC obtained are used in the NAMD simulation showing significant improvement over the default values as reflected in the root mean square deviation of atomic positions in the MD steps and the total free energy in energy minimization. These results could facilitate the interpretation of data on interaction of various ligands in charged proteins in relation to isoelectric points. © 2016 Wiley Periodicals, Inc.

Eifler, Jay↗
DOE OSTI2018

Theoretical and experimental evidence of conformational transformation in stereoisomers of nucleoside analogues

A theoretical and experimental characterization of N(1)-(2',3'-dihydroxypropil)thymine (DHPT), a potential prebiotic nucleoside analogue of 5-methyluridine, is performed. A proposed methodology based on a solvation method was used to study conformational transformations of the different low-energy conformers of DHPT according to time-dependent IR spectroscopy. NMR and CD spectroscopy provides additional evidence of these transformations. The conformational transformations appear to be due to solvent and DHPT interactions. This highlights the importance of experimental conditions on conformer ratio equilibrium, in particular, the interpretation of experimental conditions used for determining the stereoisomers' absolute configuration.

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

Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

The fragment molecular orbital method in GAMESS is parallelized in a multithreaded OpenMP implementation combined with the MPI version of the two-level generalized distributed data interface. The energy and analytic gradient in gas phase and the polarizable continuum model of solvation are parallelized in this hybrid three-level scheme, achieving a large memory footprint reduction and a high parallel efficiency on Intel Xeon Phi processors. The parallel efficiency is demonstrated on the Stampede2 and Theta supercomputers using up to 2048 nodes (262 144 threads).

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

Superatomic nature of metal encapsulated dodecahedrane: The case of M@ C 20 H 20 (M = Li, Na, Mg + )

The idea of designing unprecedented materials made of superatomic building blocks, motivated the present study on endohedral M@C 20 H 20 (M = Li, Na, Mg + ) species. Here, ground and excited electronic structures of M@C 20 H 20 (M = Li, Na, Mg + ) were analyzed by means of high-level quantum calculations. In their ground states, one electron occupies a defuse superatomic s-orbital that lies around the C 20 H 20 cage. These entities populate higher angular momentum p-, d-, f-, g-superatomic orbitals in their low-lying electronic states. The proposed superatomic Aufbau shell model for Li@C 20 H 20 and Na@C 20 H 20 is 1s, 1p, 1d, 2s, 1f, 2p, 2d, 1g, 2f slightly different from that of Mg@C 20 H 20 + which is 1s, 1p, 1d, 2s, 1f, 2p, 2d, 1g, 3s, 2f, 2g, 3p. These introduced superatomic orbital series resemble the Aufbau principle of solvated electron precursors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Phase Equilibria and Condensed Phase Properties of Fluorinated Alkanes via First Principles Simulations

Vapor liquid equilibria (VLE) of organic compounds is governed by weak non-covalent interactions. This presents a significant challenge in predicting VLE using a first principles approach where density functional theory is used to model system potential. However, a dispersion corrected approach has significantly improved the performance of traditional density functionals. Here, we predict the VLE for a nonpolar carbon tetrafluoride (R14) and polar 1,1,1,2-tetrafluoroethane (R134a)via first principles Gibbs ensemble Monte Carlo simulations using PBED3 density functional. We find that the saturated liquid density for R14 is slightly under predicted for subcritical temperatures, while for R134a it is under predicted at lower reduced temperatures and over predicted at higher reduced temperatures. In the liquid phase, angle-resolved pair correlation functions indicate slight preference for R143a to align in parallel and antiparallel orientation in the first solvation shell.The vibrational spectra reveal peak broadening in the condensed phase due to solvothermal effects. Altogether, we find thePBED3 functional performance is better for the nonpolar molecule as compared to the polar one.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here?: Adaptive QM/MM

Adaptive quantum-mechanics/molecular-mechanics (QM/MM) methods feature on-the-fly reclassification of atoms as QM or MM during a molecular dynamics(MD) simulation, allowing the location and contents of the QM subsystem to be dynamically updated as needed. Such flexibility is a distinct advantage over conventional QM/MM, where a ‘static’ boundary is retained between the QM and MM subsystems. The ‘dynamic’ boundary in adaptive QM/MM allows a finite-size QM to sustain simulations with an arbitrary length of time. Here, to ensure smooth transitions between QM and MM, the energy or forces are interpolated.Special treatments are applied so that artifacts are eliminated or minimized.Recent developments have shed light on the relationship between the adaptive algorithms that describe Hamiltonian and non-Hamiltonian systems. Originally developed to model an ion solvated in bulk solvent, adaptive QM/MM has been enhanced in many aspects, including the treatment of molecular fragments in macromolecules, monitoring molecules entering/leaving binding sites, and tracking proton transfer via the Grotthuss mechanism. Because the size of the QM region can be set as small as possible in adaptive QM/MM, the computational costs can be kept low. Small QM subsystems also facilitate the utilization of high-level QM theory and long simulation time, which can potentially lead to new insights.

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

Computational analysis of the tryptophan cation radical energetics in peroxidase Compound $\mathrm{I}$

Three well-characterized heme peroxidases (cytochrome c peroxidase = CCP, ascorbate peroxidase = APX, and Leishmania major peroxidase = LMP) all have a Trp residue tucked under the heme stacked against the proximal His heme ligand. The reaction of peroxidases with H 2 O 2 to give Compound I results in the oxidation of this Trp to a cationic radical in CCP and LMP but not in APX. Considerable experimental data indicate that the local electrostatic environment controls whether this Trp or the porphyrin is oxidized in Compound I. Attempts have been made to place the differences between these peroxidases on a quantitative basis using computational methods. These efforts have been somewhat limited by the approximations required owing to the computational cost of using fully solvated atomistic models with well-developed forcefields. This now has changed with available GPU computing power and the associated development of software. Here we employ thermodynamic integration and multistate Bennett acceptance ratio methods to help fine-tune our understanding on the energetic differences in Trp radical stabilization in all three peroxidases. These results indicate that the local solvent structure near the redox active Trp plays a significant role in stabilization of the cationic Trp radical.

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

Geometry, spin coupling, and dielectric control of redox potentials in [4Fe–4S] Clusters

Iron–sulfur (Fe–S) clusters are common biological cofactors that facilitate vital redox reactions. Despite extensive research, the molecular basis of redox potential tuning in ferredoxin-like proteins remains an active area of debate. In this study, we combine statistical analysis of over one thousand [4Fe–4S]-containing protein structures from the Protein Data Bank (PDB) with broken-symmetry and extended broken-symmetry density functional theory to examine how cysteine ligand orientations and environmental screening affect redox properties of the clusters. We identified five main ligand configurations, three of which are predominant in natural structures. Among these, the adiabatic electron affinity differs by less than 0.1 V, indicating that, while geometry plays a secondary role, it allows localized fine-tuning of redox properties. In contrast, electrostatic and solvation effects primarily determine the overall potential range.

Computational Chemistry↗
DOE OSTI2017

Pentavalent neptunyl ([OΞNpΞO] + ) cation–cation interactions in aqueous/polar organic mixed-solvent media

Bonding interactions between polyvalent cations and oxo-anions are well known and characterized by predictably favorable Gibbs energies in solution-phase coordination chemistry. In contrast, interactions between ions of like charge are generally expected to be repulsive and strongly influenced by cation solvation. An exception to this instinctive rule is found in the existence of complexes resulting from interactions of pentavalent actinyl cations ([O≡An≡O] + ) with selected polyvalent cations. Such cation–cation complexes have been known to exist since the 1960s, when they were first reported by Sullivan and co-workers. The weak actinyl cation–cation complex, resulting from a bonding interaction between a pentavalent linear dioxo actinyl cation donor and hexavalent actinyl or trivalent/tetravalent metal cation acceptor, has been most commonly seen in media in which water activities are reduced, principally highly-salted aqueous media. Such interactions of pentavalent actinides are of relevance in ongoing research that focuses on advanced nuclear fuel processing systems based on the upper oxidation states of americium. This investigation focuses on exploring the thermodynamic stability of complexes between selected highly-charged metal cations (Al 3+ , Sc 3+ , Cr 3+ , Fe 3+ , In 3+ and UO 2+ 2 ) and the pentavalent neptunyl cation (NpO + 2 , whose coordination chemistry is similar to that of AmO + 2 while exhibiting significantly greater oxidation state stability) in aqueous–polar organic mixed-solvents. As a result, the Gibbs energies for the cation–cation complexation reactions are correlated with general features of electrostatic bonding models; the NpO + 2 • Cr 3+ complex exhibits unexpectedly strong interactions that may indicate significant covalency in the cation–cation bonding interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Synthesis and crystal structure of the coordination polymer [{Li(H_2O)_3}{sub 2}(C{sub 36}H{sub 36}N{sub 24}O{sub 12})]Cl{sub 2}•6H{sub 2}O

The coordination polymer of the composition [{Li(H_2O)_3}{sub 2}(C{sub 36}H{sub 36}N{sub 24}O{sub 12})]Cl{sub 2}•6H{sub 2}O (1) was synthesized by heating an aqueous solution of lithium chloride and cucurbit[6]uril (CB[6]). According to single-crystal X-ray diffraction data, solvated lithium cations in compound 1 form coordination bonds with oxygen atoms of CB[6] molecules. Compound 1 was characterized by X-ray diffraction, IR spectroscopy, thermogravimetric and elemental analysis. Luminescence spectra of the new compound were measured.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Chemical assembly of the heteronuclear pivalate complex with the Li{sup I} and Fe{sup III} ions

The heteronuclear complex [Fe{sub 4}Li{sub 2}(O){sub 2}(Piv)10(H{sub 2}O){sub 2}] (1, Piv is the pivalic acid anion) was obtained by refluxing Fe{sup III} pivalates with Li{sup I} pivalates in toluene and isolated as the 1•PhCH{sub 3} solvate with a toluene molecule. According to X-ray diffraction data, complex 1 contains the {Fe_4Li_2O_2} core. The Mössbauer spectroscopy data indicate that the core comprises para magnetic Fe{sup III} ions in the high-spin state located in the symmetric octahedral environment of oxygen atoms. Thermolysis of 1 studied by simultaneous thermal analysis demonstrated thermal stability of the complex up to 225 °С. The main end product of thermolysis at 600 °С is the mixed oxide LiFe{sub 5}O{sub 8}.

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

Oxide Solubility Minimum in Liquid Fe-M-O Alloy

The origin of the solubility minimum of oxide (M{sub x}O{sub y}) in liquid Fe-M-O alloy was investigated, and the minimum was predicted based on thermodynamic calculations. Due to the characteristic property of activities of M and O in the liquid, a maximum exists in the product between the two activities if the affinity of M to O is significantly high, as most deoxidizing elements are. A critical activity product is defined, which is an indicator of the solubility minimum of the M{sub x}O{sub y} in the liquid Fe-M-O alloy according to the following relationship: max(a{sub M}{sup x}×a{sub O{sub -}{sup y}})=K{sub M{sub xO{sub y}}}×a{sub M{sub xO{sub y}}}, where the a{sub M{sub xO{sub y}}} is unity if the alloy is in equilibrium with the pure M{sub x}O{sub y}. The origin of the solubility minimum was explained using the change of the activity product by composition. Available CALPHAD assessments for several binary Fe-M liquid alloys and Wagner’s solvation shell model were combined to calculate the activity product in the Fe-M-O alloy, which can be used to predict the solubility minimum of M{sub x}O{sub y}. A favorable agreement was obtained when M=Al, B, Cr, Mn, Nb, Si, Ta, Ti, V, and Zr. The Gibbs energy of dissolution of O in pure liquid M (Δg{sub O{sub -(M)}{sup ∘}}) and the Gibbs energy of the formation of M{sub x}O{sub y} per mole of atoms (Δg{sub M{sub xO{sub y}{sup ∘}}}/(x+y)) play important roles in determining the solubility minimum, as long as an interaction between Fe and M is less significant than the interaction between metal (Fe and M) and O. Predictions of the solubility minima of CaO and MgO were not satisfactory, requiring further improvement of the present analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Prediction of Mass Spectral Response Factors from Predicted Chemometric Data for Druglike Molecules

A method is developed for the prediction of mass spectral ion counts of drug-like molecules using in silico calculated chemometric data. Various chemometric data, including polar and molecular surface areas, aqueous solvation free energies, and gas-phase and aqueous proton affinities were computed, and a statistically significant relationship between measured mass spectral ion counts and the combination of aqueous proton affinity and total molecular surface area was identified. In particular, through multilinear regression of ion counts on predicted chemometric data, we find that log{sub 10}(MS ion counts) = –4.824 + c{sub 1}•PA + c{sub 2}•SA, where PA is the aqueous proton affinity of the molecule computed at the SMD(aq)/M06-L/MIDI!//M06-L/MIDI! level of electronic structure theory, SA is the total surface area of the molecule in its conjugate base form, and c{sub 1} and c{sub 2} have values of –3.912 × 10{sup –2} mol kcal{sup –1} and 3.682 × 10{sup –3} Å{sup –2}. On a 66-molecule training set, this regression exhibits a multiple R value of 0.791 with p values for the intercept, c{sub 1}, and c{sub 2} of 1.4 × 10{sup –3}, 4.3 × 10{sup –10}, and 2.5 × 10{sup –6}, respectively. Application of this regression to an 11-molecule test set provides a good correlation of prediction with experiment (R = 0.905) albeit with a systematic underestimation of about 0.2 log units. This method may prove useful for semiquantitative analysis of drug metabolites for which MS response factors or authentic standards are not readily available. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

Addressing a Common Misconception: Ammonium Acetate as Neutral pH “Buffer” for Native Electrospray Mass Spectrometry

Native ESI-MS involves the transfer of intact proteins and biomolecular complexes from solution into the gas phase. One potential pitfall is the occurrence of pH-induced changes that can affect the analyte while it is still surrounded by solvent. Most native ESI-MS studies employ neutral aqueous ammonium acetate solutions. It is a widely perpetuated misconception that ammonium acetate buffers the analyte solution at neutral pH. By definition, a buffer consists of a weak acid and its conjugate weak base. The buffering range covers the weak acid pK{sub a} ± 1 pH unit. NH{sub 4}{sup +} and CH{sub 3}-COO{sup −} are not a conjugate acid/base pair, which means that they do not constitute a buffer at pH 7. Dissolution of ammonium acetate salt in water results in pH 7, but this pH is highly labile. Ammonium acetate does provide buffering around pH 4.75 (the pK{sub a} of acetic acid) and around pH 9.25 (the pK{sub a} of ammonium). This implies that neutral ammonium acetate solutions electrosprayed in positive ion mode will likely undergo acidification down to pH 4.75 ± 1 in the ESI plume. Ammonium acetate nonetheless remains a useful additive for native ESI-MS. It is a volatile electrolyte that can mimic the solvation properties experienced by proteins under physiological conditions. Also, a drop from pH 7 to around pH 4.75 is less dramatic than the acidification that would take place in pure water. It is hoped that the habit of referring to pH 7 solutions as ammonium acetate “buffer” will disappear from the literature. Ammonium acetate “solution” should be used instead. .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Characterization of Electrospray Ionization (ESI) Parameters on In-ESI Hydrogen/Deuterium Exchange of Carbohydrate-Metal Ion Adducts

The conformations of glycans are crucial for their biological functions. In-electrospray ionization (ESI) hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is a promising technique for studying carbohydrate conformations since rapidly exchanging functional groups, e.g., hydroxyls, can be labeled on the timeframe of ESI. However, regular application of in-ESI HDX to characterize carbohydrates requires further analysis of the in-ESI HDX methodology. For instance, in this method, HDX occurs concurrently to the analyte transitioning from solution to gas-phase ions. Therefore, there is a possibility of sampling both gas-phase and solution-phase conformations of the analyte. Herein, we differentiate in-ESI HDX of metal-adducted carbohydrates from gas-phase HDX and illustrate that this method analyzes solvated species. We also systematically examine the effects of ESI parameters, including spray solvent composition, auxiliary gas flow rate, sheath gas flow rate, sample infusion rate, sample concentration, and spray voltage, and discuss their effects on in-ESI HDX. Further, we model the structural changes of a trisaccharide, melezitose, and its intramolecular and intermolecular hydrogen bonding in solvents with different compositions of methanol and water. These molecular dynamic simulations support our experimental results and illustrate how an individual ESI parameter can alter the conformations we sample by in-ESI HDX. Overall, this work illustrates how the fundamental processes of ESI alter the magnitude of HDX for carbohydrates and suggest parameters that should be considered and/or optimized prior to performing experiments with this in-ESI HDX technique.

Carbohydrate Conformation↗
DOE OSTI2019

Applying an Internal Standard to Improve the Repeatability of In-electrospray H/D Exchange of Carbohydrate-Metal Adducts

In-electrospray (ESI) hydrogen/deuterium exchange–mass spectrometry (HDX-MS) has been used to characterize solvated carbohydrate structures. However, the rapid exchange rate of hydroxyls, as well as variations in source conditions and ambient humidity, alter the extent of forward and back exchange, resulting in poor repeatability when quantifying D-uptake on different days. Herein, we compare two internal standards, a peptide and derivatized carbohydrate, to improve the repeatability of in-ESI HDX of carbohydrate-metal adducts. Our results show that maltoheptaose, derivatized with Girard’s T reagent, is a suitable internal standard for improving the repeatability of in-ESI HDX analyses of carbohydrates of varying size. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗