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At least 109 records · Page 6

Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

Macelroy, R. D.

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Feasibility of Surfactant-Free Supported Emulsion Liquid Membrane Extraction

Supported emulsion liquid membrane (SELM) is an effective means to conduct liquid-liquid extraction. SELM extraction is particularly attractive for separation tasks in the microgravity environment where density difference between the solvent and the internal phase of the emulsion is inconsequential and a stable dispersion can be maintained without surfactant. In this research, dispersed two-phase flow in SELM extraction is modeled using the Lagrangian method. The results show that SELM extraction process in the microgravity environment can be simulated on earth by matching the density of the solvent and the stripping phase. Feasibility of surfactant-free SELM (SFSELM) extraction is assessed by studying the coalescence behavior of the internal phase in the absence of the surfactant. Although the contacting area between the solvent and the internal phase in SFSELM extraction is significantly less than the area provided by regular emulsion due to drop coalescence, it is comparable to the area provided by a typical hollow-fiber membrane. Thus, the stripping process is highly unlikely to become the rate-limiting step in SFSELM extraction. SFSELM remains an effective way to achieve simultaneous extraction and stripping and is able to eliminate the equilibrium limitation in the typical solvent extraction processes. The SFSELM design is similar to the supported liquid membrane design in some aspects.

Hu, Shih-Yao B.

Designing Cure Cycles for Matrix/Fiber Composite Parts

A methodology has been devised for designing cure cycles to be used in the fabrication of matrix/fiber composite parts (including laminated parts). As used here, cure cycles signifies schedules of elevated temperature and pressure as functions of time, chosen to obtain desired rates of chemical conversion of initially chemically reactive matrix materials and to consolidate the matrix and fiber materials into dense solids. Heretofore, cure cycles have been designed following an empirical, trial-and-error approach, which cannot be relied upon to yield optimum results. In contrast, the present methodology makes it possible to design an optimum or nearly optimum cure cycle for a specific application. Proper design of a cure cycle is critical for achieving consolidation of a reactive matrix/fiber layup into a void-free laminate. A cure cycle for a composite containing a reactive resin matrix usually consists of a two-stage ramp-and-hold temperature profile. The temperature and the duration of the hold for each stage are unique for a given composite material. The first, lower-temperature ramp-and hold stage is called the B stage in composite- fabrication terminology. At this stage, pressure is not applied, and volatiles (solvents and reaction by-products) are free to escape. The second, higher-temperature stage is for final forced consolidation.

Hou, Tan-Hung

Hydrogen Adsorption over Transition Metals in Water

The adsorption free energy of atomic hydrogen on Pt(111), Pd(111), Ni(111), Ru(0001), Cu(111), and Rh(111) in liquid water was computed using a quantum mechanical/molecular mechanical free-energy perturbation scheme. The Pt(111) computations indicate that the solvent effect on H adsorption on atop sites (+0.20 eV) is almost twice that on fcc (+0.12 eV), showing it is less likely to find adsorbed hydrogen in atop position in the presence of water than in the gas phase. The solvent effect for the fcc site, which is the most favorable site for adsorbed H on Pt(111), agrees qualitatively with experimental work by Lercher et al., who reported an effect of +0.2 eV. Overall, an endergonic solvent effect for hydrogen adsorption is observed for all metals, indicating a lower hydrogen coverage relative to free site coverage at metal-water interfaces compared to metal-gas interfaces, even when hydrogen transport effects through the fluid phase are negligible; a result with important implications for (de)hydrogenation catalysis.

Zare, Mehdi

Method of neutralizing the corrosive surface of amine-cured epoxy resins

The corrosive alkaline surface layer of an epoxy resin product formed by the curing of the epoxy with an aliphatic amine is eliminated by first applying a non-solvent to remove most or all of the free unreacted amine and then applying a layer of a chemical reagent to neutralize the unused amine or amine functional groups by forming a substituted urea. The surface then may be rinsed with acetone and then with alcohol. The non-solvent may be an alcohol. The neutralizing chemical reagent is a mono-isocyanate or a mono-isothiocyanate. Preferred is an aromatic mono-isocyanate such as phenyl isocyanate, nitrophenyl isocyanate and naplthyl isocyanate.

Lee, S. Y.

Physicochemical and Performance Characterization of Six Commercial Organic Solvent Nanofiltration Membranes

This work introduces a novel, gradient-free metamaterial design method based on Gaussian process regression to represent the density field of a unit cell. The dimension of the design space is determined by the covariance matrix dimension in the Gaussian process regression. We propose compressing this matrix using an autoencoder, enabling the decoder to generate the density field and effectively reduce the originally large design space to a lower-dimensional subspace. In this compressed space, we employ an active learning method, Bayesian Adaptive Direct Search (BADS), for efficient exploration of the design space. We demonstrate that for simple 2D designs aimed at maximizing unit cell stiffness, our method yields results comparable to those of standard topology optimization. Furthermore, we extend our approach to various mechanical problems, from linear elasticity to hyperelastic large deformation and elasto-plasticity under finite deformation, to 3D metamaterial design. This illustrates the method’s versatility and effectiveness across a range of applications.

Wu, Haoran

NASA Lessons Learned from Space Lubricated Mechanisms

This document reviews the lessons learned from short-life and long life lubricated space mechanisms. A short-life lubricated mechanisms complete their life test qualification requirements after a few cycles. The mechanisms include the hinges, motors and bearings for deployment, release mechanisms, latches, release springs and support shops. Performance testing can be difficult and expensive but must be accomplished. A long-life lubricated mechanisms requires up to 5 years of life testing, or 10 to 100 years of successful flight. The long-life mechanisms include reaction wheels, momentum wheels, antenna gimbals, solar array drives, gyros and despin mechanisms. Several instances of how a mechanisms failed either in test, or in space use, and the lessons learned from these failures are reviewed. The effect of the movement away from CFC-113 cleaning solvent to ODC (Ozone-Depleting Chemical) -free is reviewed, and some of the alternatives are discussed.

Predmore, Roamer E.

DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.

Carra, Claudio

Electrolyte Organization Leads to Potential-Dependence in Thermochemical Catalysis of Nonpolar Reactions

Electrochemical polarization is now known to play a key role in thermochemical catalysis at solid–liquid interfaces. However, existing frameworks cannot account for why even nonpolar, nonfaradaic reactions are sensitive to interfacial polarization. In order to uncover the molecular basis of this phenomenon, we herein study the potential-dependent reaction kinetics of ethylene and trans-2-butene hydrogenation at Pt–liquid interfaces. Measurements were performed in aqueous and ortho-difluorobenzene (o-DFB) solutions, spontaneously polarizing the Pt–liquid interfaces by, respectively, varying the pH or dissolving distinct metallocene redox buffers into solution. Here, we find that at comparable mechanistic regimes, the rates of both ethylene and trans-2-butene hydrogenation are maximized near the same electrochemical potential, E. Moreover, the potential-dependence, defined as $\frac{∂ln 𝑟}{∂𝐸}$, of trans-2-butene hydrogenation is approximately 2.2× greater than that of ethylene hydrogenation across the full potential range studied. These observations are all consistent with a model in which polarization of the Pt surface away from the local potential of zero free charge (E PZFC ) induces electrostatic organization of the polar solvent and charged ions near the interface, which impedes olefin adsorption and surface reaction because these surface reactions induce electrolyte displacement. Accordingly, interfacial polarization alters the free energy landscape and thus the rate of nonpolar heterogeneous catalysis by controlling the degree of electrostatic organization of polar and charged spectators at the interface, which do not in general need to be specifically chemisorbed onto the surface but could simply be close enough to the surface to be perturbed by the olefin adsorption. These results point toward electrochemical design handles, namely, the electrolyte, catalyst potential, and local E PZFC of the catalyst, with which to tune interfacial catalysis of thermochemical organic transformations.

adsorption

A simulated RTM process for fabricating polyimide (AMB-21) carbon fiber composites

An experimental polyimide matrix, AMB-21 - supplied by NASA/LeRC, was especially formulated to be non-carcinogenic. It was also expected to be amenable to a Resin Transfer Molding Process (RTM). AMB-21 is a solid at room temperature and must be heated to a very high temperature to obtain a fluid state. However, even after heating it to a realistic high temperature, it was found to be too viscous for use in a RTM process. As a result, a promising approach was experimented leading to the introduction of the resin into a solvent solution in order to obtain a viscosity suitable for RTM. A mixture of methanol and tetrahydroferone was found to be a suitable solvent mixture. The matrix solution was introduced into carbon-fiber preform using two techniques: (1) injection of matrix into a Resin Transfer Mold after positioning the preform into the 'mold cavity', and (2) infiltration of matrix into the preform using the 'autoclave through-the-thickness transfer process'. After completing the resin transfer (infiltration) process, the 'filled' preform was heated to 300 F for one hour to reduce the solvent content. The temperature was then increased to 400 F under a vacuum to complete the solvent evaporation and to remove volatile products of the polyimide imidization. The impregnated preform was removed from the mold and press-cured at 200 psi and 600 FF for two hours. The resulting panel was found to be of reasonably good quality. This observation was based on the results obtained from short beam shear strength (700-8000 psi) tests and microscopic examination of the cross-section indicating a very low level of porosity. Further, the flash around the molded panels from the compression molding was free of porosity indicating the removal of volatiles, solvents, and other imidization products. Based on these studies, a new RTM mold containing a diaphragm capable of applying 200 psi at 600 F has been designed and constructed with the expectation that it will allow the incorporation of all of the above processing steps, including the consolidation with the preform in the mold cavity. Moreover, the new diaphragm design will enable to process larger preform panels. Processing studies with the diaphragm mold are being initiated.

Avva, V. Sarma

Expanding Parameter Space to Enable Low-Temperature Synthesis of Crystalline Indium Phosphide Quantum Dots

Established methods to synthesize indium phosphide quantum dots (QDs) require high temperatures (>180 °C) to make high-quality material for optoelectronic applications. Nonpolar solvent environments are overwhelmingly used in InP QD synthesis to reach the necessary high temperatures and for compatibility with the reactive precursors. In this study, we explored InP QD synthesis in polar aprotic solvent environments to dramatically decrease the temperature required for InP crystallization by imparting ionicity to the precursors and stabilizing charged reaction intermediates. A custom air-free 96- well plate setup was employed to identify key factors impacting low-temperature QD formation, including an increased percentage of polar solvent, carboxylic acid choice, and inclusion of polar additives. Guided by these insights, we developed a synthesis of crystalline, green-emitting InP QDs at 60 °C in a toluene-dimethylformamide mixture. Here's, the QDs withstood established Zn 2+ and HF surface treatments, which increased the photoluminescence quantum yield to 25%. Additionally, we demonstrated the rapid synthesis of quasi-wurtzite InP QDs at room temperature in a polar solvent environment using an acid-free indium myristate precursor.

absorption

Tunable Nanoscale Structure via Divalent Ion Identity in Charged-Neutral Polymer Blends

Charged-neutral polymer blends, wherein an ioncontaining polymer is blended with a neutral polymer, are potential candidates for battery electrolytes due to their improved ion transport properties and electrochemical stability. Though electrostatic interactions in charged polymer blends can theoretically stabilize ordered nanostructures analogous to those observed in neutral block copolymers, direct experimental evidence remains limited. Here, we investigate the effects of divalent cation identity on the nanoscale morphology of charged-neutral polymer blends composed of poly(ethylene oxide) (PEO) and Mg 2+ or Ca 2+ ioncontaining polymers, poly[3-(methylacryloxy)propylsulfonyl-1-(trifluoromethanesulfonylimide)] (P(Mg(MTFSI) 2 ) or P(Ca- (MTFSI) 2 ). By tuning the size of the divalent counterion, we are able to precisely tune the ion solvation between the free cation and PEO, which acts as a solvent in this system. Differential scanning calorimetry (DSC) and small-angle X-ray scattering (SAXS) measurements reveal that Mg 2+ and Ca 2+ ions induce distinct structural behavior. In both systems, the blends become more miscible as the concentration of ion-containing polymer is increased indicated by increased suppression of PEO crystallinity. At the highest concentrations of P(Mg(MTFSI) 2 ), the blends undergo microphase separation and generate nanostructures with shortranged ordering. In contrast, calcium ions, which are more readily solvated by PEO, produce more homogeneous blends characterized by a single glass-transition temperature and featureless SAXS data. The results demonstrate the novel experimental confirmation that charged-neutral polymer blends can undergo microphase separation and show that counterion identity can be exploited as a design parameter to control nanoscale morphology.

Ions

Elucidating and contrasting the mechanisms for Mg and Ca sulfate ion-pair formation with multi-level embedded quantum mechanics/molecular dynamics simulations

Here, solutions and minerals containing sulfate (SO 4 2- ), and Ca 2+ and Mg 2+ cations, are ubiquitous throughout the lithosphere and are significant components of seawater, thus presenting a prototypical system for the study of strong electrolytes and crystal nucleation mechanisms. However, despite their relative abundance, key questions remain unanswered about the most fundamental atomic-level steps of their mineralization pathways and aqueous dynamics. Here, we carry out enhanced sampling multi-level molecular dynamics (MD) embedded correlated wavefunction theory simulations to elucidate ion-pairing mechanisms for Mg–SO 4 and Ca–SO 4 in concentrated aqueous solution, accurately capturing effects arising from both structural dynamics and electron exchange–correlation. We predict contact-ion-pair formation to be barrierless and highly exoergic for Ca–SO 4 , in agreement with its minimal solubility, whereas for Mg–SO 4 , solvent-shared and contact ion pairs have similar free energies, qualitatively consistent with its higher solubility. Finally, we demonstrate that brief high-temperature pre-equilibration may be utilized to accelerate convergence of free energies in blue-moon-ensemble enhanced-sampling MD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Configurations of base-pair complexes in solutions

A theoretical search for the most stable conformations (i.e., stacked or hydrogen bonded) of the base pairs A-U and G-C in water, CCl4, and CHCl3 solutions is presented. The calculations of free energies indicate a significant role of the solvent in determining the conformations of the base-pair complexes. The application of the continuum method yields preferred conformations in good agreement with experiment. Results of the calculations with this method emphasize the importance of both the electrostatic interactions between the two bases in a complex, and the dipolar interaction of the complex with the entire medium. In calculations with the solvation shell method, the last term, i.e., dipolar interaction of the complex with the entire medium, was added. With this modification the prediction of the solvation shell model agrees both with the continuum model and with experiment, i.e., in water the stacked conformation of the bases is preferred.

Egan, J. T.

Physical aging of linear and network epoxy resins

Network and linear epoxy resins principally based on the diglycidyl ether of bisphenol-A and its oligomers are prepared and studied using diamine and anhydride crosslinking agents. Rubber modified epoxies and a carbon fiber reinforced composite are also investigated. All materials display time-dependent changes when stored at temperatures below the glass transition temperature after quenching (sub-T/g/ annealing). Solvent sorption experiments initiated after different sub-T(g) annealing times demonstrate that the rate of solvent uptake can be indirectly related to the free volume of the epoxy resins. Residual thermal stresses and water are found to have little effect on the physical aging process, which affects the sub-T(g) properties of uniaxial carbon fiber reinforced epoxy material. Finally, the importance of the recovery phenomenon which affects the durability of epoxy glasses is considered.

Kong, E. S.-W.

Contamination removal using various solvents and methodologies

Critical and non-critical bonding surfaces must be kept free of contamination that may cause potential unbonds. For example, an aft-dome section of a redesigned solid rocket motor that had been contaminated with hydraulic oil did not appear to be sufficiently cleaned when inspected by the optically stimulated electron emission process (Con Scan) after it had been cleaned using a hand double wipe cleaning method. As a result, current and new cleaning methodologies as well as solvent capability in removing various contaminant materials were reviewed and testing was performed. Bonding studies were also done to verify that the cleaning methods used in removing contaminants provide an acceptable bonding surface. The removal of contaminants from a metal surface and the strength of subsequent bonds were tested using the Martin Marietta and double-wipe cleaning methods. Results are reported.

Jeppsen, J. C.