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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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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Elucidating molecular interactions of L-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance

Emtricitabine (FTC) and lamivudine (3TC), containing an oxathiolane ring with unnatural (-)-stereochemistry, are widely used nucleoside reverse transcriptase inhibitors (NRTIs) in anti-HIV therapy. Treatment with FTC or 3TC primarily selects for the HIV-1 RT M184V/I resistance mutations. Here we provide a comprehensive kinetic and structural basis for inhibiting HIV-1 RT by (-)-FTC-TP and (-)-3TC-TP and drug resistance by M184V. (-)-FTC-TP and (-)-3TC-TP have higher binding affinities (1/K d 200-fold) K d for the L-nucleotides and moderately higher (>9-fold) K d for the D-isomers compared to dCTP. The M184V RT structure illustrates how the mutation repositions the oxathiolane of (-)-FTC-TP and shifts its triphosphate into a non-productive conformation.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2017

In Situ Characterization of the Initial Effect of Water on Molecular Interactions at the Interface of Organic/Inorganic Hybrid Systems

Probing initial interactions at the interface of hybrid systems under humid conditions has the potential to reveal the local chemical environment at solid/solid interfaces under real-world, technologically relevant conditions. Here in this paper, we show that ambient pressure X-ray photoelectron spectroscopy (APXPS) with a conventional X-ray source can be used to study the effects of water exposure on the interaction of a nanometer-thin polyacrylic acid (PAA) layer with a native aluminum oxide surface. The formation of a carboxylate ionic bond at the interface is characterized both with APXPS and in situ attenuated total reflectance Fourier transform infrared spectroscopy in the Kretschmann geometry (ATR-FTIR Kretschmann). When water is dosed in the APXPS chamber up to 5 Torr (~28% relative humidity), an increase in the amount of ionic bonds at the interface is observed. To confirm our APXPS interpretation, complementary ATR-FTIR Kretschmann experiments on a similar model system, which is exposed to an aqueous electrolyte, are conducted. These spectra demonstrate that water leads to an increased wet adhesion through increased ionic bond formation.

36 MATERIALS SCIENCE↗
DOE OSTI2016

SANS study on the solvated structure and molecular interactions of a thermo-responsive polymer in a room temperature ionic liquid

Here, we utilized small-angle neutron scattering (SANS) to quantitatively characterize the LCST-type phase behavior of the poly(benzyl methacrylate) (PBnMA) derivative poly(2-phenylethyl methacrylate) (PPhEtMA) in the deuterated ionic liquid (IL) d 8 -1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide (d 8 -[C 2 mIm + ][TFSA - ]). The SANS curves showed a discontinuous change from those characteristics of dispersed polymer chains to those of large aggregates of PPhEtMA chains suspended in the IL solution, indicating that phase separation occurs discontinuously at T c . We also evaluated the enthalpic and entropic contributions to the effective interaction parameter χ eff of PPhEtMA in [C 2 mIm + ][TFSA - ] and compared them with those of PBnMA. The absolute value of the enthalpic contribution observed for PPhEtMA was smaller than that for PBnMA. This difference in the enthalpic term can be attributed to the unfavorable interaction between the IL and the alkyl group in the side chain of PPhEtMA. In addition, the temperature dependence of χ eff was smaller than the previously reported value for a thermo-responsive polymer in an aqueous system. Finally, it was found out that the strong dependence of T c on the chemical structure in IL systems originated from the relatively smaller temperature dependence of χ eff .

36 MATERIALS SCIENCE↗
DOE OSTI2014

A combined experimental and computational study of the molecular interactions between anionic ibuprofen and water

In this work, we report a detailed study of the microsolvation of anionic ibuprofen, Ibu{sup −}. Stochastic explorations of the configurational spaces for the interactions of Ibu{sup −} with up to three water molecules at the DFT level lead to very rich and complex potential energy surfaces. Our results suggest that instead of only one preponderant structure, a collection of isomers with very similar energies would have significant contributions to the properties of the solvated drug. One of these properties is the shift on the vibrational frequencies of the asymmetric stretching band of the carboxylate group in hydrated Ibu{sup −} with respect to the anhydrous drug, whose experimental values are nicely reproduced using the weighted contribution of the structures. We found at least three types of stabilizing interactions, including conventional CO {sub 2}{sup −}⋯H{sub 2}O, H{sub 2}O⋯H{sub 2}O charge assisted hydrogen bonds (HBs), and less common H{sub 2}O⋯H–C and H{sub 2}O⋯π interactions. Biological water molecules, those in direct contact with Ibu{sup −}, prefer to cluster around the carboxylate oxygen atoms via cyclic or bridged charge assisted hydrogen bonds. Many of those interactions are strongly affected by the formal carboxylate charge, resulting in “enhanced” HBs with increased strengths and degree of covalency. We found striking similarities between this case and the microsolvation of dymethylphosphate, which lead us to hypothesize that since microsolvation of phosphatidylcholine depends mainly on the formal charge of its ionic PO {sub 2}{sup −} group in the polar head, then microsolvation of anionic ibuprofen and interactions of water molecules with eukaryotic cell membranes are governed by the same types of physical interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models

Earlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids, TIPnP-type models of water, protein force fields, and others, where interactions and dynamics of inherently polarizable species can be accurately described by nonpolarizable models. To describe electrostatic interactions, the effective charges of simple ionic liquids are obtained by scaling the actual charges of ions by a factor of 1/√(ε{sub el}), which is due to electronic polarization screening effect; the scaling factor of neutral species is more complicated. Here, using several theoretical models, we examine how exactly the scaling factors appear in theory, and how, and under what conditions, polarizable Hamiltonians are reduced to nonpolarizable ones. These models allow one to trace the origin of the scaling factors, determine their values, and obtain important insights on the nature of polarizable interactions in condensed matter systems.

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

Selectivity in gas–liquid interactions: Molecular beam scattering of CD 4 and ND 3 from an aqueous flat liquid jet

The dynamics of polar and nonpolar molecules colliding with an aqueous surface are characterized by scattering molecular beams of deuterated methane and ammonia, CD 4 and ND 3 (E i = 28.9 and 30.3 kJ mol −1 , respectively), from a flat liquid jet of cold salty water (8 m LiBr, 230 K). Translational energy distributions of scattered species collected as a function of collision geometry probe both impulsive scattering (IS) and thermal desorption (TD) mechanisms. Here, we find that CD 4 scattering is dominated by IS and exhibits a super-specular angular distribution. The fraction of TD scattering events is notably smaller for cold salty water than for dodecane, consistent with a higher free energy of solvation for CD 4 in the water jet. In contrast, no scattering signal is seen for ND 3 from the water jet, a result attributed to the high solubility and efficient protonation of ND 3 in liquid water. The IS channel for CD 4 was analyzed using a soft-sphere model, yielding a higher internal energy (E int ) and lower effective surface mass (m eff ) than was seen for Ne/water; the higher value of E int is attributed to rotational excitation of the scattered CD 4 . These findings demonstrate that the outcomes of a gas–liquid collision—scattering trajectory, surface adherence, and energy transfer—are directed at the molecular level by both the gaseous scatterer and liquid surface.

Foreman, Madison M. [University of California, Ber↗
DOE OSTI2014

Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Molecular interactions from the density functional theory for chemical reactivity: Interaction chemical potential, hardness, and reactivity principles

In the first paper of this series, the authors derived an expression for the interaction energy between two reagents in terms of the chemical reactivity indicators that can be derived from density functional perturbation theory. While negative interaction energies can explain reactivity, reactivity is often more simply explained using the “|dμ| big is good” rule or the maximum hardness principle. Expressions for the change in chemical potential (μ) and hardness when two reagents interact are derived. A partial justification for the maximum hardness principle is that the terms that appear in the interaction energy expression often reappear in the expression for the interaction hardness, but with opposite sign.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Tunable ultraviolet laser studies of photon-molecular interactions of cometary interest

Most of the cometary radicals are thought to be formed in the coma by photodissociation processes. Successful modeling of the coma requires a detailed knowledge of the products that are formed from the various parent molecules and the energy partitioning among these products. This information has to be obtained as a function of wavelength, because the sun is not a monochromatic source. In this review, the status of the experimental knowledge of some key molecules is discussed, along with the prospects of some new laboratory techniques that can fill in the gaps in the present knowledge.

Jackson, William M.↗
NASA NTRS1989

Semiclassical approach to atomic and molecular interactions

A general approach, combining quantum and classical mechanics, is used to determine the electron position and velocity distributions in atoms and atomic ions (positive and negative). The Hartree-Fock electronic wave functions and the classical central field approximation are used for evaluation of the dynamic properties of the localized electrons. The distributions, which are of fundamental importance in applications of the binary encounter approximation to description of atomic and ionic collissions, are obtained in the form of simple analytical expressions. The quantum-classical distributions of this work are compared with several other distributions in Ne, Ar, and Al atoms in the ground state.

Kunc, Joseph A.↗