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Results for “molecular functionalization”

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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

A lignin-specific peroxidase in tobacco whose antisense suppression leads to vascular tissue modification

A tobacco peroxidase isoenzyme (TP60) was down-regulated in tobacco using an antisense strategy, this affording transformants with lignin reductions of up to 40-50% of wild type (control) plants. Significantly, both guaiacyl and syringyl levels decreased in essentially a linear manner with the reductions in lignin amounts, as determined by both thioacidolysis and nitrobenzene oxidative analyses. These data provisionally suggest that a feedback mechanism is operative in lignifying cells, which prevents build-up of monolignols should oxidative capacity for their subsequent metabolism be reduced. Prior to this study, the only known rate-limiting processes in the monolignol/lignin pathways involved that of Phe supply and the relative activities of cinnamate-4-hydroxylase/p-coumarate-3-hydroxylase, respectively. These transformants thus provide an additional experimental means in which to further dissect and delineate the factors involved in monolignol targeting to precise regions in the cell wall, and of subsequent lignin assembly. Interestingly, the lignin down-regulated tobacco phenotypes displayed no readily observable differences in overall growth and development profiles, although the vascular apparatus was modified.

NASA Program Fundamental Space Biology↗
DOE OSTI2024

Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters

Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence–function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ~400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Combined Machine Learning and Molecular Dynamics Reveal Two States of Hydration of a Single Functional Group of Cationic Polymeric Brushes

The state of hydration of a macromolecular system regulates a plethora of different properties of such a system. In this article, we develop a novel machine learning (ML) approach, based on the unsupervised clustering algorithm, for probing the hydration behavior of the {N(CH 3 ) 3 } + functional group of the PMETAC [Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] polyelectrolyte (PE) brush system. The PE brushes and the brush-supported water molecules and counterions (chloride ions) are first described using all-atom molecular dynamics (MD) simulations. The simulation data is subsequently used in our ML framework to identify that (1) the {N(CH 3 ) 3 } + functional groups of the PMETAC brushes have two distinct hydration states with one state (state 1) being characterized by less structured water molecules and the other state (state 2) being characterized by more structured water molecules and (2) an enhancement in the brush grafting density leads to the progressive dissapparenace of state 2. An increase in the grafting density increases the number of chloride counterions in a given volume around the {N(CH 3 ) 3 } + functional group and increases the number of shared water molecules between the {N(CH 3 ) 3 } + and Cl - . The chloride counterions are associated with a hydration layer with much less structured water molecules. Therefore, with an increase in the grafting density, an increase in the percentage of shared water molecules leads to the prevalence of the hydration state [of the {N(CH 3 ) 3 } + moiety] with less structured water molecules. Finally, we explain how the present findings are commensurate with two key previous related results, namely a significantly large chloride ion mobility inside the PMETAC brush layer and the {N(CH 3 ) 3 } + -Cl - average distance remaining independent of the PMETAC brush grafting density. Furthermore, we anticipate that the combined ML-MD-simulation approach proposed in this study can be adapted to probe other soft matter systems to reveal new insights of the underlying mechanisms of emergent phenomenon.

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

Trapping Ca + inside a molecular cavity: computational study of the potential energy surfaces for Ca + -[ n ]cycloparaphenylene, n = 5–12

Ion trap quantum computing utilizes electronic states of atomic ions such as Ca + to encode information on to a qubit. To explore the fundamental properties of Ca + inside molecular cavities, we describe here a computational study of Ca + bound inside neutral [n]-cycloparaphenylenes (n = 5–12), often referred to as “nanohoops”. This ab initio study characterizes optimized structures, harmonic vibrational frequencies, potential energy surfaces, and ion molecular orbital distortion as functions of increasing nanohoop size. Here the results of this work provide a first step in guiding experimental studies of the spectroscopy of these ion-molecular cavity complexes.

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

HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160

HVEM is a TNF (tumor necrosis factor) receptor contributing to a broad range of immune functions involving diverse cell types. It interacts with a TNF ligand, LIGHT, and immunoglobulin (Ig) superfamily members BTLA and CD160. Assessing the functional impact of HVEM binding to specific ligands in different settings has been complicated by the multiple interactions of HVEM and HVEM binding partners. To dissect the molecular basis for multiple functions, we determined crystal structures that reveal the distinct HVEM surfaces that engage LIGHT or BTLA/CD160, including the human HVEM–LIGHT–CD160 ternary complex, with HVEM interacting simultaneously with both binding partners. Based on these structures, we generated mouse HVEM mutants that selectively recognized either the TNF or Ig ligands in vitro. Knockin mice expressing these muteins maintain expression of all the proteins in the HVEM network, yet they demonstrate selective functions for LIGHT in the clearance of bacteria in the intestine and for the Ig ligands in the amelioration of liver inflammation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

DNA Strand Displacement Driven Molecular Additive Manufacturing (DSD-MAM)

The goal of this project was to validate two-dimensional molecular printers, initially selfassembled from DNA and then actuated by externally driven cycles of DNA strand displacement, as prototype integrated nanosystems for molecular additive manufacturing. Novel functionalities of these nanomachines were explored during this project, including the following: nanometer-precision positioning mechanisms based on DNA strand displacement with multivalent interactions for discrete stepping or else diffusive capture; integration of independently moving layers of DNA origami to achieve 2D controllable motion; integration of spatial positioning with deposition functionality. The principal importance of this project was to provide an essential step in the development of a new technology for atomically precise manufacturing. Our first generation molecular 2D printer offers several advantages over conventional DNA-origami patterning, such as faster prototyping, faster dynamic rearrangement of patterns, and the ability to respond with feedback. We anticipate that our first-generation molecular printers may inspire future generations of molecular printers with iterative improvements in robustness and throughput. Potential applications of atomically precise manufacturing include the following: photovoltaics; photosynthetic and fuel cells; thermoelectrics and anisotropic heat spreaders; solid-state lighting; molecular electronic and plasmonic circuits; selectively preamble membranes; self-repairing materials with high strength-to-weight and fracture resistance.

36 MATERIALS SCIENCE↗
DOE OSTI2021

How well do self-interaction corrections repair the overestimation of static polarizabilities in density functional calculations?

Herein, we examine the effect of removing self-interaction error (SIE) on the calculation of molecular polarizabilities in the local spin density (LSDA) and generalized gradient approximations (GGA). To this end, we utilize a database of 132 molecules taken from a recent benchmark study [Hait and Head-Gordon, Phys. Chem. Chem. Phys. , 2018, 20 , 19800] to assess the influence of SIE on polarizabilities by comparing results with accurate reference data. Our results confirm that the general overestimation of molecular polarizabilities by these density functional approximations can be attributed to SIE. However, removing SIE using the Perdew–Zunger self-interaction-correction (PZ-SIC) method, implemented using the Fermi–Löwdin Orbital SIC approach, leads to an underestimation of molecular polarizabilities, showing that PZ-SIC overcorrects when combined with LSDA or GGA. Application of a recently proposed locally scaled SIC [Zope, et al., J. Chem. Phys. , 2019, 151 , 214108] is found to provide more accurate polarizabilities. We attribute this to the ability of the local scaling scheme to selectively correct for SIE in the regions of space where the correction is needed most.

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

Coupling and Decoupling between Stickers and Backbones in Associating Polymers with Terminally Functionalized Side Chains

Associating polymers have recently attracted tremendous attention as self-healing polymers due to the dynamic reversibility of sticker association–dissociation processes. These sticker dynamics inevitably slow significantly as segmental dynamics decelerate below the glass transition temperature that limits the operational temperatures of associating polymers. Using broadband dielectric spectroscopy on a new set of associating polymers composed side chains of various lengths and terminal carboxylic-acid sticker functionality, we discovered an unexpected decoupling near the glass transition (T g ) between the slower backbone and fast sticker motions. These two motions have distinct activation energies for the motion of the sulfur linkage adjacent to the backbone (~22 to 26 kJ/mol) and the carboxylic acid groups (~5 to 8 kJ/mol). A second decoupling appears in the polymer with the longest side chain length at T g – 20 K, reflecting the dynamics of various carboxylic acid binding configurations. Furthermore, our findings open the door to design associating polymers with the capability of sticker association/dissociation at low temperatures.

36 MATERIALS SCIENCE↗
NASA NTRS2001

CAP: A Computer Code for Generating Tabular Thermodynamic Functions from NASA Lewis Coefficients

For several decades the NASA Glenn Research Center has been providing a file of thermodynamic data for use in several computer programs. These data are in the form of least-squares coefficients that have been calculated from tabular thermodynamic data by means of the NASA Properties and Coefficients (PAC) program. The source thermodynamic data are obtained from the literature or from standard compilations. Most gas-phase thermodynamic functions are calculated by the authors from molecular constant data using ideal gas partition functions. The Coefficients and Properties (CAP) program described in this report permits the generation of tabulated thermodynamic functions from the NASA least-squares coefficients. CAP provides considerable flexibility in the output format, the number of temperatures to be tabulated, and the energy units of the calculated properties. This report provides a detailed description of input preparation, examples of input and output for several species, and a listing of all species in the current NASA Glenn thermodynamic data file.

Zehe, Michael J.↗
NASA NTRS2002

CAP: A Computer Code for Generating Tabular Thermodynamic Functions from NASA Lewis Coefficients

For several decades the NASA Glenn Research Center has been providing a file of thermodynamic data for use in several computer programs. These data are in the form of least-squares coefficients that have been calculated from tabular thermodynamic data by means of the NASA Properties and Coefficients (PAC) program. The source thermodynamic data are obtained from the literature or from standard compilations. Most gas-phase thermodynamic functions are calculated by the authors from molecular constant data using ideal gas partition functions. The Coefficients and Properties (CAP) program described in this report permits the generation of tabulated thermodynamic functions from the NASA least-squares coefficients. CAP provides considerable flexibility in the output format, the number of temperatures to be tabulated, and the energy units of the calculated properties. This report provides a detailed description of input preparation, examples of input and output for several species, and a listing of all species in the current NASA Glenn thermodynamic data file.

Zehe, Michael J.↗
NASA NTRS2010

Reinforced Thermoplastic Polyimide with Dispersed Functionalized Single Wall Carbon Nanotubes

Molecular pi-complexes were formed from pristine HiPCO single-wall carbon nanotubes (SWCNTs) and 1-pyrene- N-(4- N'-(5-norbornene-2,3-dicarboxyimido)phenyl butanamide, 1. Polyimide films were prepared with these complexes as well as uncomplexed SWCNTs and the effects of nanoadditive addition on mechanical, thermal, and electrical properties of these films were evaluated. Although these properties were enhanced by both nanoadditives, larger increases in tensile strength and thermal and electrical conductivities were obtained when the SWCNT/1 complexes were used. At a loading level of 5.5 wt %, the Tg of the polyimide increased from 169 to 197 C and the storage modulus increased 20-fold (from 142 to 3045 MPa). The addition of 3.5 wt % SWCNT/1 complexes increased the tensile strength of the polyimide from 61.4 to 129 MPa; higher loading levels led to embrittlement and lower tensile strengths. The electrical conductivities (DC surface) of the polyimides increased to 1 x 10(exp -4) Scm(exp -1) (SWCNT/1 complexes loading level of 9 wt %). Details of the preparation of these complexes and their effects on polyimide film properties are discussed.

Lebron-Colon, Marisabel↗
NASA NTRS2003

The Chemistry and Excitation of Water in Molecular Clouds

We model the chemistry and thermal balance of opaque molecular clouds exposed to an external flux of ultraviolet photons. We include the processes of gas phase and grain surface chemical reactions; in particular we examine closely the freezing of atoms and molecules onto grain surfaces and the desorption of molecules from grain surfaces as a function of depth into a molecular cloud. We find that on the surface of a molecular cloud the gas phase water abundances are low because of photodissociation, and the grain phase water (ice) abundance is low because of photodesorption of water from the grain surfaces. Deeper into the cloud, at A(sub v) less than or approximately 2-8 depending on the strength of the external ultraviolet flux, the gas phase water abundance increases with depth as the photodissociation rates decline due to dust attenuation of the ultraviolet field. However, beyond A(sub v) less than or approximately 2-8 the gas phase water abundance declines because the water freezes as water ice on the grains, and photodesorption is no longer effective in clearing the ice. A peak water abundance of about 10(exp -6) to 10(exp -7) occurs at about A(sub v) approximately 2-8, relatively independent of the gas density and the ultraviolet field. We show that such a model matches very closely the observations of the Submillimeter Wave Astronomical Satellite (SWAS), a NASA Small Explorer Mission. The model elucidates several mechanisms that have been recently invoked to understand gas phase chemistry in clouds, including-the freeze-out of molecules onto grain surface, the desorption of these molecules from the surfaces, and the abundance gradients of molecules as functions of depth into molecular clouds.

Hollenbach, David↗
DOE OSTI2020

Bidentate Lewis bases are preferred for passivation of MAPbI 3 surfaces: A time-domain ab initio analysis

We report chemical passivation is a predominant approach to inhibit intrinsic defects responsible for electron–hole recombination in perovskite solar cells. Using time-domain density functional theory combined with nonadiabatic molecular dynamics, we demonstrate defect passivation by separation of electrons and holes in metal halide perovskites (MHPs), and show that bidentate ligands exhibit the best performance. Defects in traditional semiconductors create deep midgap states, and passivation eliminates these states. In contrast, common defects produce no deep midgap states in MHPs. Instead, defects localize electrons and holes around defect sites, enhancing electron–hole interaction. Defect passivation in MHPs acts to separate charges, decreasing electron–hole and charge–phonon interactions, and increasing charge lifetimes. Bidentate ligands work best, because they can passivate both unsaturated chemical bonds created due to vacancy defects. Bidentate ligands with spatially separated binding sites are preferred, since they provide better match to the sparse inorganic lattice of MHPs. Similar to the Lewis base ligands, water also acts as a ligand and extends charge lifetimes, with the oxygen atom donating its lone electron pair to the defect site. However, water accelerates chemical degradation of MHPs. The binding energy of most ligands is larger than that of water, and therefore, the ligands displace water, increase MHP stability and prolong carrier lifetimes. The established physical mechanism of defect passivation, and the specific principles guiding the choice of passivating molecules advance our understanding of the exceptional properties of MHPs and suggest routes for further improvement of MHP performance in solar energy and optoelectronic applications.

36 MATERIALS SCIENCE↗
NASA NTRS1991

Effect of the rotational-vibrational excitation on molecular diameters

The kinetic molecular diameters of rotationally and vibrationally excited diatomic molecules and molecular ions are derived as functions of the rotational and vibrational quantum numbers of the molecules. Typical molecular diameters are studied in two cases: in low-temperature gas, where the molecular diameter is independent of the degree of rotational-vibrational excitation of the molecules, and in high-temperature gas, where the molecular diameter depends on the degree of rotational-vibrational excitation of the molecules. The rotational-vibrational excitation of molecules is shown to have a meaningful effect on the collisional properties of gases. The effect is stronger in gases of weakly-bound molecules.

Kang, S. H.↗
NASA NTRS1986

Dissociative excitation of the N(+)(5S) state by electron impact on N2 - Excitation function and quenching

Metastable N(+)(5S) ions were produced in the laboratory by dissociative excitation of N2 with energetic electrons. The resulting radiative decay of the N(+)(5S) state was observed with sufficient resolution to completely resolve the doublet from the nearby N2 molecular radiation. The excitation function was measured from threshold to 500 eV. The cross section peaks at a high electron energy and also exhibits a high threshold energy both of which are typical of dissociative excitation-ionization processes. This finding complicates the explanation of electron impact on N2 as the mechanism for the source of the 2145 A 'auroral mystery feature' by further increasing the required peak cross section. It is suggested that the apparent N(+)(5S) quenching in auroras may be an artifact due to the softening of the electron energy spectrum in the auroral E region.

Erdman, P. W.↗
DOE OSTI2020

Atomistic simulations of the thermal conductivity of liquids

We present a method based on sinusoidal approach to equilibrium molecular dynamics (SAEMD) to compute the thermal conductivity of liquids Similar to nonequilibrium molecular dynamics, and unlike equilibrium simulations based on the Green-Kubo formalism, the method only requires the calculation of forces and total energies. The evaluation of heat fluxes and energy densities is not necessary, thus offering the promise of efficiently implementing first principles simulations based on density functional theory or deep molecular dynamics. Our approach is a generalization of SAEMD for solids, where the thermal conductivity is computed in the steady state, instead of a transient regime, thus properly taking into account diffusive terms in the heat equation. We present results for liquid water at ambient conditions and under pressure and discuss simulation requirements to obtain converged values of the thermal conductivity as a function of size and simulation time.

36 MATERIALS SCIENCE↗