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All sourcesNASA NTRSDOE OSTI
NASA NTRS1986

The importance of atomic and molecular correlation on the bonding in transition metal compounds

The determination of accurate spectroscopic parameters for molecular systems containing transition metal atoms is shown to require extensive data sets and a high level correlation treatment, and techniques and their limitations are considered. Extensive results reported on the transition metal atoms, hydrides, oxides, and dimers makes possible the design of a calculation to correctly describe the mixing of different atomic asymptotes, and to give a correct balance between molecular bonding and exchange interactions. Examples considered include the dipole moment of the 2Delta state of NiH, which can help determine the mixture of 3d(8)4s(2) and 3d(9)4s(1) in the NiH wavefunction, and the bonding in CrO, where an equivalent description of the relative energies associated with the Cr 3d-3d atomic exchange and the Cr-O bond is important.

Bauschlicher, Charles W., Jr.↗
NASA NTRS2000

Constitutive and Stability Behavior of Soils in Microgravity Environment

All aspects of soil stability, bearing capacity, slope stability, the supporting capacity of deep foundations, and penetration resistance depend on soil strength. The stress-deformation and stress-deformation-time behavior of soils are of importance in any problem where ground movements are of interest. In most engineering materials, the strength is derived from internal chemical and physico-chemical forces of interaction, which bond the atoms, molecules, and particles together. In soils, the constitutive relations are mainly derived from interparticle friction between particles and particle groups and dilatancy, and to a lesser extent from particle bonding by weak electrostatic, physico-chemical, and coulomb forces. For engineering purposes, soils are classified as cohesive (clays and silts; typical particle sizes range from 10 nm to 10 micrometers) and cohesionless (sand and gravel; typical particle sizes range from 10 micrometers to 75 mm). The mechanical or constitutive properties of cohesionless soils or granular materials are highly fabric-dependent, highly non-linear, and non-conservative with engineering properties primarily depending on the effects of gravity through self-weight and on the tractions or forces applied to the soil mass. Under moderate-to-high stress levels, the influence of gravity on the behavior of laboratory test specimens may not be pronounced and, therefore, the test results in terrestrial (1-g) environment may be sufficiently conclusive. However at low interparticle stresses, which can result either from low applied (confining) stresses or from excess pore fluid pressures developed within the soil mass without corresponding changes in the applied stresses, the presence of gravitational body forces acting on solid particles and interstitial fluids exerts a pronounced influence on movement of individual particles or particle groups. Such motions, in turn, cause changes in soil fabric which results in significant changes in the interparticle friction forces contributing to the soil's strength and deformation characteristics.

Alshibli, Khalid A.↗
NASA NTRS1975

Correlation of materials properties with the atomic density concept

Based on the hypothesis that the number of atoms per unit volume, accurately calculable for any substance of known real density and chemical composition, various characterizing parameters (energy levels of electrons interacting among atoms of the same or different kinds, atomic mass, bond intensity) were chosen for study. A multiple exponential equation was derived to express the relationship. Various properties were examined, and correlated with the various parameters. Some of the properties considered were: (1) heat of atomization, (2) boiling point, (3) melting point, (4) shear elastic modulus of cubic crystals, (5) thermal conductivity, and (6) refractive index for transparent substances. The solid elements and alkali halides were the materials studied. It is concluded that the number of different properties can quantitively be described by a common group of parameters for the solid elements, and a wide variety of compounds.

Source record↗
NASA NTRS2019

X-Ray Photoelectron Spectroscopy

The interaction of photon and the electron goes back to the early part of 19th century emanating from the photo-electric effect depicted by none other than Albert Einstein (Ref 1) described in 1905, and the redistribution of kinetic energy resulting from the interaction of x-ray and solids reported during early part of the century (Ref.2). The spectrum resolutions obtained at that time was not sufficient to observe distinct peaks in spectra for materials. Thus, these phenomena hardly attracted any attention for many years following these discoveries. The modern X-ray Photoelectron Spectroscopy (XPS) has been possible by the extensive and significant contribution from Kai Siegbahn and others (Ref.3, 4) of Uppsala University. Siegbahn developed and employed a high-resolution electron spectrometer that revealed electron peaks in a spectrum emerging from the interaction of x-rays and solids. Eventually, Kai Siegbahn received Nobel Prize in 1981 for his contributions to XPS. Around 1958, shifts in elemental peaks were realized in compounds when the same elements are bound to other but different elements. This discovery resulted in the chemical state identification in various chemicals as well as the oxidation states of atoms in compounds. Because of these useful physical effects, the Uppsala group named XPS with a synonymous name of ESCA (Electron Spectroscopy for Chemical Analysis) used widely today and will be used here alternatively. Therefore, XPS or ESCA not only identifies the element, but also the compound these elements form, from their chemical shifts. Compared to other micro-analytical techniques such as Energy Dispersive (EDS) or Wavelength Dispersive (WDS) techniques, XPS analyzes only few atomic layers present on the surface. This was discovered early in 1966 (Ref. 5). While this has awarded a merit to the analytical technique to analyze very thin layers such as films and coatings, it often analyzes the adsorbed superficial gases and contaminations on a sample introduced to its analytical chamber. This necessitates the surface is cleaned and the underlying material, material of interest, is exposed in a clean environment such that the material of interest is analyzed. The cleaning is accomplished by a scanning ion gun within the analytical chamber of the instrument. Ion gun uses an argon gas and is commonly attached in most modern machines. Reliable and efficient vacuum systems employed in modern machines does not allow adsorbed layers to rebuild after the surface is cleaned. Development of efficient and reliable vacuum pumps over these developmental years is yet another important step in the commercialization of XPS machines. Vacuum levels of better than 10-7 torr are essential to increase the mean free path of electrons released from the sample surface. Thus, modern machines are equipped with high capacity ion, turbo or cryogenic pumps in their analytical chambers. Today, XPS has advanced from an applied physics laboratory to industry for use in quality control as well as analysis of contaminants and has taken a dominant role in microanalysis. Its uniqueness arises from the fact that it is considered non-destructive compared to other common micro-analytical techniques using the electron and ion excitation sources. Polymers and plastics could be analyzed since the binding energies of saturated and unsaturated bonds in atoms could be separated. Extremely thin layers could be analyzed including materials with layered structures. The technique, though did not advance for many years, has now opened a new window for research as well as applications in industry due to its ability to separate and measure the chemical shifts in bound elements. Principles

Panda, Binayak↗
NASA NTRS1991

Applying NASA's explosive seam welding

The status of an explosive seam welding process, which was developed and evaluated for a wide range of metal joining opportunities, is summarized. The process employs very small quantities of explosive in a ribbon configuration to accelerate a long-length, narrow area of sheet stock into a high-velocity, angular impact against a second sheet. At impact, the oxide films of both surface are broken up and ejected by the closing angle to allow atoms to bond through the sharing of valence electrons. This cold-working process produces joints having parent metal properties, allowing a variety of joints to be fabricated that achieve full strength of the metals employed. Successful joining was accomplished in all aluminum alloys, a wide variety of iron and steel alloys, copper, brass, titanium, tantalum, zirconium, niobium, telerium, and columbium. Safety issues were addressed and are as manageable as many currently accepted joining processes.

Bement, Laurence J.↗
NASA NTRS2005

Structures Self-Assembled Through Directional Solidification

Nanotechnology has created a demand for new fabrication methods with an emphasis on simple, low-cost techniques. Directional solidification of eutectics (DSE) is an unconventional approach in comparison to low-temperature biomimetic approaches. A technical challenge for DSE is producing microstructural architectures on the nanometer scale. In both processes, the driving force is the minimization of Gibb's free energy. Selfassembly by biomimetic approaches depends on weak interaction forces between organic molecules to define the architectural structure. The architectural structure for solidification depends on strong chemical bonding between atoms. Constituents partition into atomic-level arrangements at the liquid-solid interface to form polyphase structures, and this atomic-level arrangement at the liquid-solid interface is controlled by atomic diffusion and total undercooling due to composition (diffusion), kinetics, and curvature of the boundary phases. Judicious selection of the materials system and control of the total undercooling are the keys to producing structures on the nanometer scale. The silicon-titanium silicide (Si-TiSi2) eutectic forms a rod structure under isothermal cooling conditions. At the NASA Glenn Research Center, directional solidification was employed along with a thermal gradient to promote uniform rods oriented with the thermal gradient. The preceding photomicrograph shows the typical transverse microstructure of a solidified Si-TiSi2 eutectic composition. The dark and light gray regions are Si and TiSi2, respectively. Preferred rod orientation along the thermal gradient was poor. The ordered TiSi2 rods have a narrow distribution in diameter of 2 to 3 m, as shown. The rod diameter showed a weak dependence on process conditions. Anisotropic etch behavior between different phases provides the opportunity to fabricate structures with high aspect ratios. The photomicrographs show the resulting microstructure after a wet chemical etch and a dry plasma etch. The wet chemical etches the silicon away, exposing the TiSi2 rods, whereas plasma etching preferentially etches the Si-TiSi2 interface to form a crater. The porous architectures are applicable to fabricating microdevices or creating templates for part fabrication. The porous rod structure can serve as a platform for fabricating microplasma devices for propulsion or microheat exchangers and for fabricating microfilters for miniatured chemical reactors. Although more work is required, self-assembly from DSE can have a role in microdevice fabrication.

Dynys, Frederick W.↗
NASA NTRS2019

Physically-Informed Artificial Neural Networks for Atomistic Modeling of Materials

A new approach is presented for the development of classical interatomic potentials using physically-informed neural networks (PINN) combined with an analytical bond-order atomic interaction model. Due to the strong physical underpinnings, the PINN potentials demonstrate much better transferability than the existing machine-learning potentials while drastically improving the accuracy in comparison with traditional potentials. PINN potentials can be constructed for both metallic and covalent materials in a unified manner. A number of applications of PINN potentials to large-scale molecular dynamics and Monte Carlo simulations and calculation of thermal and mechanical properties of diverse materials are demonstrated. Some of the specific materials systems include silicon and aluminum, as well as alloys and compounds. Computational aspects of PINN potentials are discussed and future developments in this field are outlined.

J Hickman↗
NASA NTRS2022

Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution

Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfde minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infnite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are fnite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a fnite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere

Kenneth N. McGuinness↗
NASA NTRS1999

Accurate In Bond Energies

InXn atomization energies are computed for n = 1-3 and X = H, Cl, and CH3. The geometries and frequencies are determined using density functional theory. The atomization energies are computed at the coupled cluster level of theory. The complete basis set limit is obtained by extrapolation. The scalar relativistic effect is computed using the Douglas-Kroll approach. While the heats of formation for InH, InCl and InCl3 are in good agreement with experiment, the current results show that the experimental value for In(CH3)3 must be wrong.

Bauschlicher, Charles W., Jr.↗
NASA NTRS2003

Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase

Thiamin pyrophosphate (TPP), the biologically active form of vitamin BI, is a cofactor of enzymes catalyzing reactions involving the cleavage of a carbon-carbon bond adjacent to an oxo group. TPP-dependent enzymes show a common mechanism of TPP activation by: (1) forming the ionic N-H...O(sup -) hydrogen bonding between the N1' atom of the aminopirymidine ring of the coenzyme and intrinsic gamma-carboxylate group of glutamate and (2) imposing an "active" V-conformation that brings the N4' atom of the aminopirymidine to the distance required for the intramolecular C-H.. .N hydrogen bonding with the thiazolium C2 atom. Within these two hydrogen bonds that rapidly exchange protons, protonation of the N1' atom is strictly coordinated with the deprotonation of the 4' -amino group and eventually abstraction of the proton from C2. The human pyruvate dehydrogenase Elp, component of human pyruvate dehydrogenase complex, catalyzes the irreversible decarboxylation of the pyruvate followed by the reductive acetylation of the lipoyl group of dihydrolipoyl acyltransferase. Elp is alpha(sub 2)beta(sub2)-heterotetrameric with a molecular mass of I54 kDa, which has two catalytic sites, each providing TPP and magnesium ion as cofactors and each formed on the interface between the PP and PYR domains. The dynamic nonequivalence of two otherwise chemically equivalent catalytic sites has been observed and the flip-flop mechanism was suggested, according to which two active sites affect each other and in which different steps of the catalytic reaction are performed in each of the sites at any given moment. Based on specific futures of human pyruvate dehydrogenase including rigid and flexible connections between domains that bind the cofactor we propose a mechanistic model for the flip-flop action of this enzyme. We postulate that the dynamic protein environment drives the exchange of tautomers in the 4' -aminopyrimidine ring of the cofactor through a concerted shuttl-like motion of tightly connected domains. The dynamic exchange of those tautomers, in turns, is required during the reactions of pyruvate decarboxylation and reductive acetylation of lipoamide. Thus the shuttle-like motion of the domains is coordinated with the reactions of decarboxylation and acetylation, which are carried out in each of the cofactor sites resulting in a flip-flop action of the enzyme. The structure-derived mechanism of action of human pyruvate dehydrogenase may be likely common for other TPP-dependent enzymes.

Dominiak, Paulina↗
NASA NTRS2016

Synthesis, Structure, Characterization, and Decomposition of Nickel Dithiocarbamates: Effect of Precursor Structure and Processing Conditions on Solid-State Products

Single-crystal X-ray structures of four nickel dithiocarbamate complexes, the homoleptic mixed-organic bis-dithiocarbamates Ni[S2CN(isopropyl)(benzyl)]2, Ni[S2CN(ethyl)(n-butyl)]2, and Ni[S2CN(phenyl)(benzyl)]2, as well as the heteroleptic mixed-ligand complex NiCl[P(phenyl)3][(S2CN(phenyl)(benzyl)], were determined. Synthetic, spectroscopic, structural, thermal, and sulfide materials studies are discussed in light of prior literature. The spectroscopic results are routine. A slightly distorted square-planar nickel coordination environment was observed for all four complexes. The organic residues adopt conformations to minimize steric interactions. Steric effects also may determine puckering, if any, about the nickel and nitrogen atoms, both of which are planar or nearly so. A trans-influence affects the Ni-S bond distances. Nitrogen atoms interact with the CS2 carbons with a bond order of about 1.5, and the other substituents on nitrogen display transoid conformations. There are no strong intermolecular interactions, consistent with prior observations of the volatility of nickel dithiocarbamate complexes. Thermogravimetric analysis of the homoleptic species under inert atmosphere is consistent with production of 1:1 nickel sulfide phases. Thermolysis of nickel dithiocarbamates under flowing nitrogen produced hexagonal or -NiS as the major phase; thermolysis under flowing forming gas produced millerite (-NiS) at 300 C, godlevskite (Ni9S8) at 325 and 350 C, and heazlewoodite (Ni3S2) at 400 and 450 C. Failure to exclude oxygen results in production of nickel oxide. Nickel sulfide phases produced seem to be primarily influenced by processing conditions, in agreement with prior literature. Nickel dithiocarbamate complexes demonstrate significant promise to serve as single-source precursors to nickel sulfides, a quite interesting family of materials with numerous potential applications.

microscopy↗
NASA NTRS1998

Substrate Effects on Electronic Properties of Atomic Chains

When the device size is reduced down to 0.07 micrometers, the number of dopant atoms in the channel will no longer be macroscopic, typically less than a hundred. A spatial distribution of these dopant atoms will fluctuate statistically from device to device even in identically designed devices, and this places a serious limitation for integration. It is, however, impractical to control dopant positions within atomic dimension. One fundamental solution to this problem is to create electronics with atomically precise, but preferably simple structures. Atomic chains, precise structures of adatoms created on an atomically regulated surface, are candidates for constituent components in future electronics. All the adatoms will be placed at designated positions on the substrate, and all the device structures will be precise, free from any deviations. It was predicted using the tight-binding calculation with universal parameters that silicon chains were metallic and magnesium chains were semiconducting regardless of the lattice spacing, and a possible doping method was also proposed. In these treatments, the substrate was assumed to serve as a non-interacting template holding the adatoms without a formation of chemical bonding with substrate atoms. However, this scheme may not be easy to implement experimentally. Adatoms will have to be fixed with a van der Waals force on the substrate, but the force is generally weak and an extremely low temperature environment has to be prepared to suppress their unwanted thermal displacement. It may be logical to seek a scheme to allow the adatoms to form chemical bonding with the substrate atoms and secure their positions. The substrate effects are studied in detail.

Yamada, Toshishige↗
NASA NTRS2007

Large Solar-Rejection Filter

NASA utilized Image Intensified Video Cameras for ATV data acquisition from a jet flying at 12.8 km. Afterwards the video was digitized and then analyzed with a modified commercial software package, Image Systems Trackeye. Astrometric results were limited by saturation, plate scale, and imposed linear plate solution based on field reference stars. Time-dependent fragment angular trajectories, velocities, accelerations, and luminosities were derived in each video segment. It was evident that individual fragments behave differently. Photometric accuracy was insufficient to confidently assess correlations between luminosity and fragment spatial behavior (velocity, deceleration). Use of high resolution digital video cameras in future should remedy this shortcoming. A scenically accurate description of matter interpreted as a substance made up of corpuscular constituents was established during the course of the 19th century. In this description, atoms--the building blocks of the matter--form molecules. The properties of the molecules were described by chemistry or thermodynamics depending on what characteristics of the matter were investigated. In both theories, the molecules can dissociate to atoms when the kinetic energies of the atoms exceed the strength of the chemical bonds. The number of atoms is always preserved in a closed system. This is not true, however, when the matter takes up much higher energies at relativistic scales. New particles can be produced at the expense of the kinetic energy. The number of particles is no longer preserved. There are other conserved quantities, however, these quantities, the charge, baryon number, lepton number, are associated with particles that are considered elementary today. The properties and behavior of these elementary particles is the subject of Particle Physics or High Energy Physics. Practice Page: A crewmember touching a positively charged surface was thought to be galvanically isolated from the vehicle ground analogous to a bird on a high voltage power wire. Recent analysis confirms that positive floating potentials, ionospheric currents to the EVA suit, can be hazardous. The analysis is wrong in that the ionospheric plasma itself can close the circuit. Parametric analysis of very low voltage exposures (2 to 15 volts) could cause pain and/or involuntary muscle tetani or spinal cord shock. NASA worked with the Naval Health Research Center Detachment Directed Energy Bioeffects Laboratory to examine the affects electrical hazards could have on extravehicular activity using two models. The results of the two computational models were combined to predict areas of the body in which neurons of different diameters would be excited. They predicted that physiologically active current could be conducted across the crew member causing catastrophic hazards. Future work to analyze additional current paths was proposed. The FUSE spectrum of BB Dor, observed in a high state, is modeled with an accretion disk with a very low inclination (possibly lower than 10 degrees). Assuming an average WD mass of 0.8 solar mass leads to a distance of the order of approximately 650pc, consistent with the extremely low galactic reddening in its direction, and a mass accretion rate of 10 (exp -9) solar mass a year. The spectrum presents some broad and deep silicon and sulfur absorption lines, indicating that these elements are over-abundant: silicon is 3 times solar, and sulfur is 20 times solar. The FUSE spectrum of BB Dor, observed in a high state, is modeled with an accretion disk with a very low inclination (possibly lower than 10 degrees). Assuming an average WD mass of 0.8 solar mass leads to a distance of the order of approximately 650pc, consistent with the extremely low galactic reddening in its direction, and a mass accretion rate of 10 (exp -9) solar mass a year. The spectrum presents some broad and deep silicon and sulfur absorption lines, indicating that these elements are over-abundant: silicon is times solar, and sulfur is 20 times solar. From its previously observed optical emission lines, P831-57 (WD 0334 6400 or Ret 1 in A Catalog and Atlas of Cataclysmic Variables: Living Edition) has been suspected to contain an accretion disk associated with a companion star in orbit around a subdwarf star with a temperature T is greater than 21,000K. P831-57 has therefore been classified as a nova-like. However, our present observations show it to be a DA + dMe binary. The analysis of its Far Ultraviolet Spectroscopic Explorer (FUSE) spectrum (continuum and lines) reveal an average mass white dwarf (Log(g) approximately equals 7.8 plus or minus 0.1)with a temperature T approximately equals 37,000 plus or minus 500K, an extremely low projected rotational velocity, and a distance of about 115 plus or minus 5pc. The photosphere contains C, N, Si, and S (at about 1% of solar abundances). The dMe star is seen as a flux excess in near-infrared photometry and appears to show occasional flaring of about one magnitude as seen in the Harvard plates. There is no evidence of periodic variability in the spectroscopic or photometric data. We find no evidence of a an accretion disk, instead we find evidence of wind accretion as the stellar carbon abundance (N(C)/N(H) = 2.5 x 10 (exp -6) is about ten times larger than predicted by radiative levitation for such a gravity and temperature. The power needs and solutions for the space exploration and lunar mobility program are discussed. Long term missions in space and on the lunar surface require high energy batteries. Rechargeable batteries for mobility systems and portable utility pallet are needed for successful exploration missions. Nanomaterial usage increases the energy density of the cells apart from increasing the power density. The symptoms and threats from acute mountain sickness (AMS) are discussed. The underlying assumptions concerning spacecraft atmosphere mean there is a potential risk to astronauts. The baseline worst case scenario is about 25% based on direct ascent to 8.0 psia with 32% O2. The practical mitigation approach is a staged depressurization scheme. Due to the uncertainty about potential AMS risk the flight surgeon should prepare, focused research should proceed, and current analytical efforts should continue. This slide presentation reviews the threat astronauts face from acute mountain sickness (AMS). The incidence of AMS is highly variable and the risk to astronauts is unclear. However, the potential risk is higher than current EAAs suggest and precautions should be implemented. Due to the uncertain nature of the risk flight surgeons should prepare, and focused research should proceed. Quasiparticle tunneling can be understood at low temperatures using a non-equilibrium kinetic theory. Low-temperature tunneling can be suppressed using existing techniques: island-lead gap engineering, lead cooling with SIN junctions, and quasiparticle traps. The slide presentation reviews the science goals and mission planning for the proposed Jupiter System Observer (JSO). The spacecraft would accommodate 9 instruments making the instrument payload more capable than any previously flown to Jupiter. The would-be mission includes study programs for Jupiter's satellites, interior, magnetosphere and atmosphere. The power needs and solutions for the space exploration and lunar mobility program are discussed. Long term missions in space and on the lunar surface require high energy batteries. Rechargeable batteries for mobility systems and portable utility pallet are needed for successful exploration missions. Nanomaterial usage increases the energy density of the cells apart from increasing the power density. This slide presentation reviews the power requirements for the space exploration and the lunar surface mobility programs. It includes information about the specifications for high energy batteries and the power requirements for lunar rovers,

Roberts, William↗
NASA NTRS1998

Determining the Molecular Packing Arrangements on Protein Crystal Faces by Atomic Force Microscopy

Periodic Bond Chain (PBC) analysis of the packing of tetragonal lysozyme crystals have revealed that there are two possible molecular packing arrangements for the crystal faces. The analysis also predicted that only one of these, involving the formation of helices about the 4(sub 3) axes, would prevail during crystal growth. In this study high resolution atomic force microscopy (AFM) was employed to verify these predictions for the (110) crystal face. A computer program was developed which constructs the expected AFM image for a given tip shape for each possible molecular packing arrangement. By comparing the actual AFM image with the predicted images the correct packing arrangement was determined. The prediction of an arrangement involving 4(sub 3) helices was confirmed in this manner,"while the alternate arrangement was not observed. The investigation also showed the protein molecules were packed slightly closer about the 4(sub 3) axes than in the crystallographic arrangement of the crystal interior. This study demonstrates a new approach for determining the molecular packing arrangements on protein crystal faces. It also shows the power of combining a theoretical PBC analysis with experimental high resolution AFM techniques in probing protein crystal growth processes at the molecular level.

Li, Huayu↗
NASA NTRS2003

Structure-Derived Proton-Transfer Mechanism of Action Human Pyruvate Dehydrogenase

The derivative of vitamin B1 thiamin pyrophosphate (TPP) is a cofactor of pyruvate dehydrogenase (E1p) that is involved in decarboxylation of pyruvate followed by reductive acetylation of lipoic acid covalently bound to a lysine residue of dihydrolipoamide acetyltransferase. The structure of E1p recently determined in our laboratory revealed patterns of association of foul subunits and specifics of two TPP binding sites. The mechanism of action in part includes a conserved hydrogen bond between the N1' atom of the aminopyrimidine ring of the cofactor and the carboxylate group of Glu59 from the beta subunits, and a V-conformation of the cofactor that brings the N4' atom of the aminopyrimidine ring to the distance of the intramolecular hydrogen bond formed with the C2-atom of the thiazolium moiety. The carboxylate group of Glu59 is the local proton acceptor that enables proton translocation within the aminopyrimidine ring and stabilization of the rare N4' - iminopyrimidine tautomer. Based on the analysis of E1p structure, we postulate that the protein environment drives N4' - amino/N4' - imino dynamics resulting in a concerted shuttle-like movement of the subunits. We also propose that this movement of the subunits is strictly coordinated with the two enzymatic reactions carried out in E1p by each of the two cofactor sites. It is proposed that these reactions are in alternating phases such that when one active site is involved in decarboxylation, the other is involved in acetylation of lipoyl noiety.

Ciszak, Ewa↗
NASA NTRS2008

Fabricating Large-Area Sheets of Single-Layer Graphene by CVD

This innovation consists of a set of methodologies for preparing large area (greater than 1 cm(exp 2)) domains of single-atomic-layer graphite, also called graphene, in single (two-dimensional) crystal form. To fabricate a single graphene layer using chemical vapor deposition (CVD), the process begins with an atomically flat surface of an appropriate substrate and an appropriate precursor molecule containing carbon atoms attached to substituent atoms or groups. These molecules will be brought into contact with the substrate surface by being flowed over, or sprayed onto, the substrate, under CVD conditions of low pressure and elevated temperature. Upon contact with the surface, the precursor molecules will decompose. The substituent groups detach from the carbon atoms and form gas-phase species, leaving the unfunctionalized carbon atoms attached to the substrate surface. These carbon atoms will diffuse upon this surface and encounter and bond to other carbon atoms. If conditions are chosen carefully, the surface carbon atoms will arrange to form the lowest energy single-layer structure available, which is the graphene lattice that is sought. Another method for creating the graphene lattice includes metal-catalyzed CVD, in which the decomposition of the precursor molecules is initiated by the catalytic action of a catalytic metal upon the substrate surface. Another type of metal-catalyzed CVD has the entire substrate composed of catalytic metal, or other material, either as a bulk crystal or as a think layer of catalyst deposited upon another surface. In this case, the precursor molecules decompose directly upon contact with the substrate, releasing their atoms and forming the graphene sheet. Atomic layer deposition (ALD) can also be used. In this method, a substrate surface at low temperature is covered with exactly one monolayer of precursor molecules (which may be of more than one type). This is heated up so that the precursor molecules decompose and form one monolayer of the target material.

Bronikowski, Michael↗
NASA NTRS1981

Calculation of activation energies for hydrogen-atom abstractions by radicals containing carbon triple bonds

Activation energies are calculated by the bond-energy-bond-order (BEBO) and the bond-strength-bond-length (BSBL) methods for the reactions of C2H radicals with H2, CH4, and C2H6 and for the reactions of CN radicals with H2 and CH4. The BSBL technique accurately predicts the activation energies for these reactions while the BEBO method yields energies averaging 9 kcal higher than those observed. A possible reason for the disagreement is considered.

Brown, R. L.↗
NASA NTRS1999

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Crawford, Lisa↗