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NASA NTRS1995

Ab Initio Characterization of Triatomic Bromine Molecules of Potential Interest in Stratospheric Chemistry

The equilibrium structures, harmonic vibrational frequencies, quadratic force fields, dipole moments, and IR intensities of several triatomic bromine compounds of known or potential importance in stratospheric ozone depletion chemistry have been determined using the CCSD(T) electron correlation method in conjunction with a basis set of triple zeta double polarized (TZ2P) quality. Specifically, the molecules included in the present study are HOBr, HBrO, FOBr, FBrO, BrNO, BrON, Br2O, BrBrO, BrCN, BrNC, ClOBr, ClBrO, and BrClO. Very accurate isomeric energy differences have also been determined at the CCSD(T) level with atomic natural orbital basis sets that include through g-type functions. In most cases, the isomer with a normal neutral Lewis dot structure is the lowest energy form, with the single exception that FBrO is predicted to be 11.1 kcal/mol (0 K) lower in energy than FOBr. In all cases, however, the hypervalent isomer is more stable relative to the isomer with a normal Lewis dot structure as compared to the chlorine analogs. Consistent with this observation, the energy of the last three molecules given above increases in the order ClOBr less than ClBrO less than BrClO. The CCSD(T)/TZ2P geometries and vibrational frequencies are in good agreement with the available experimental data. Heats of formation are determined for all species using a combination of theoretical isomeric, homodesmic, and isodesmic reaction energies. The accuracy of these quantities is ultimately dependent on the reliability of the experimental heat of formation of HOBr.

Lee, Timothy J.↗

NASA NTRS2004

Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism

The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates.

Biogenesis↗

NASA NTRS1995

A molecular line study of NGC 1333/IRAS 4

Molecular line surveys and fully sampled spectral line maps at 1.3 and 0.87 mm are used to examine the physical and chemical characteristics of the extreme Class I sources IRAS 4A and 4B in the L1450/NGC 1333 molecular cloud complex. A very well collimated, jetlike molecular flow emanates from IRAS 4A, with a dynamical age of a few thousand years. Symmetric, clumpy structure along the outflow lobes suggests that there is considerable variability in the mass-loss rate or wind velocity even at this young age. Molecular emission lines toward IRAS 4A and 4B are observed to be weak in the velocity range corresponding to quiescent material surrounding the young stellar objects (YSOs). Depletion factors of 10-20 are observed for all molecules, including CO, even for very conservative mass estimates from the measured millimeter and submillimeter dust continuum. However, abundance scaled with respect to CO are similar to other dark molecular cloud cores. Such depletions could be mimicked by high dust and optical depths or increased grain emissivities at the observing frequencies of 230 and 435 GHz, but the millimeter and submillimeter spectral energy distributions suggest that this is unlikely over the single-dish size scales of 5000-10,000 AU. Dense, outflowing gas is found to be kinematically, but not spatially, distinct from the quiescent material on these size scales. If CO is used as a chemical standard for the high-velocity gas, we find substantial enhancements in abundances of several molecules in outflowing material, most notably CS, SIO, and CH3OH. The SiO emission is kinematically well displaced from the bulk cloud velocity and likely arises from directly shocked material. As is the case for CO, however, the outflow features from more volatile species are centered near the cloud velocity and are often characterized by quite low rotational temperatures. We suggest that grain-grain collisions induced by velocity shear zones surrounding the outflow axes transiently desorb the grain mantles, resulting in large abundance enhancements of selected species. Similar results have recently been obtained in several other low-mass YSOs, where outflowing gas is often both kinematically and spatailly distinct, and are illustrative of the ability of accretion and outflow processes to simultaneously modify the composition of the gas and dust surrounding young stars.

Blake, Geoffrey A.↗

NASA NTRS1994

Numerical Wave Propagation 211 Based on Wave Primitives

Compact higher order finite difference equations are applied to a sequence of problems in wave propagation and aeroacoustics. Systems of PDE's are reduced to a sequence of simple wave primitives using a local eigenvector decomposition. The wave primitives are first order PDE's in two independent variable and allow natural boundary conditions to be imposed for both single- and multidimensional problems. The method uses a "discrete dispersion relation" approach to obtain high order approximations to the wave primitives on a 3 spatial point / 2 time level computational molecule. The scheme is fourth order accurate for the class of system with constant coefficients, e.g., those that support exponential solutions. Weakly non-linear PDE's are solved in a similar manner using a variant of the "method of frozen coefficients." Experience with the new algorithm for linear, non-linear, and multi-dimensional test problems will be described.

Davis, Sanford S.↗

NASA NTRS1996

Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation

The role of divalent cations in the mechanism of pyrophosphate-activated, template-directed oligoribonucleotide ligation has been investigated. The dependence of the reaction rate on Mg2+ concentration suggests a kinetic scheme in which a Mg2+ ion must bind before ligation can proceed. Mn2+, Ca2+, Sr2+, and Ba2+ can also catalyze the reaction. Although Pb2+ and Zn2+ do not catalyze the reaction in the absence of other divalent ions, they significantly modulate the reaction rate when added in the presence of Mg2+, with Pb2+ stimulating the reaction (up to 65-fold) and Zn2+ inhibiting the reaction. The logarithm of the ligation rate increases linearly, with slope of 0.95, as a function of pH, indicating that the reaction involves a single critical deprotonation step. The ligation rates observed with the different divalent metal ion catalysts (Mn2+ > Mg2+ > Ca2+ > Sr2+ = Ba2+) vary inversely with the pKa values of their bound water molecules. The pH profile and these relative ligation rates suggest a mechanism in which a metal-bound hydroxide ion located near the ligation junction promotes catalysis, most likely by deprotonation of the hydroxl nucleophile. The effects of changing either the leaving group or the attacking hydroxyl, together with the large delta S(++) value for oligonucleotide ligation (about -20 eu), are consistent with an associative transition state.

Non-NASA Center↗

NASA NTRS1988

Diode laser harmonic spectroscopy applied to in situ measurements of atmospheric trace molecules

With the emergence of lead-salt diode laser technology, a broad and important IR spectral region, roughly 3-30 microns, became accessible to tunable laser spectroscopy. More recent advances in fabrication techniques have provided experimenters with relatively high power quasi-single-mode high-temperature lasers that are readily adapted to compact automated instruments for field experiments. An especially attractive capability of diode lasers is the ease of using them for simultaneous multiconstituent sampling in the atmosphere. This paper presents a summary description of field instruments for atmospheric research which employ diode lasers and second-harmonic detection. Representative results obtained with some of these instruments are presented.

Loewenstein, Max↗

NASA NTRS1979

Measurement of diffusion coefficients from solution rates of bubbles

The rate of solution of a stationary bubble is limited by the diffusion of dissolved gas molecules away from the bubble surface. Diffusion coefficients computed from measured rates of solution give mean values higher than accepted literature values, with standard errors as high as 10% for a single observation. Better accuracy is achieved with sparingly soluble gases, small bubbles, and highly viscous liquids. Accuracy correlates with the Grashof number, indicating that free convection is the major source of error. Accuracy should, therefore, be greatly increased in a gravity-free environment. The fact that the bubble will need no support is an additional important advantage of Spacelab for this measurement.

Krieger, I. M.↗

NASA NTRS1998

Green Fluorescent Protein as a Model for Protein Crystal Growth Studies

Green fluorescent protein (GFP) from jellyfish Aequorea Victoria has become a popular marker for e.g. mutagenesis work. Its fluorescent property, which originates from a chromophore located in the center of the molecule, makes it widely applicable as a research too]. GFP clones have been produced with a variety of spectral properties, such as blue and yellow emitting species. The protein is a single chain of molecular weight 27 kDa and its structure has been determined at 1.9 Angstrom resolution. The combination of GFP's fluorescent property, the knowledge of its several crystallization conditions, and its increasing use in biophysical and biochemical studies, all led us to consider it as a model material for macromolecular crystal growth studies. Initial preparations of GFP were from E.coli with yields of approximately 5 mg/L of culture media. Current yields are now in the 50 - 120 mg/L range, and we hope to further increase this by expression of the GFP gene in the Pichia system. The results of these efforts and of preliminary crystal growth studies will be presented.

Agena, Sabine↗

NASA NTRS2019

Decomposition of Electron Ionization Mass Spectra for Space Application Using a Monte-Carlo approach

Rationale: Quadrupole mass spectrometers equipped with an electron ionization (EI) sources have been widely used in space exploration to investigate the composition of planetary surfaces and atmospheres. However, the complexity of the samples and the minimal calibration for the fragmentation of molecules in the ionization chambers have prevented the deconvolution of the majority of the mass spectra obtained at different targets, thus limiting the determination of the exact composition of the samples analyzed. We propose a Monte‐Carlo approach to solve this issue mathematically. Methods: We decomposed simulated mass spectra of mixtures acquired with unit resolving power mass spectrometers and EI sources into the sum of the single components fragmentation patterns weighted by their relative concentration using interior‐point least‐square fitting. To fit compounds with poorly known fragmentation patterns, we used a Monte‐Carlo method to vary the intensity of individual fragment ions. We then decomposed the spectrum thousands of times to obtain a statistical distribution. Results: By performing the deconvolution on a mixture of seven different molecules with interfering fragmentation patterns (H2O, O2, CH4, Ar, N2, C2H4, and C2H6) we show that this approach retrieves the mixing ratio of the individual components more accurately than regular mass spectra decomposition methods that rely on fragmentation patterns from general databases. It also provides the probability density function for each species's mixing ratio. Conclusions: By removing the solution degeneracy in the decomposition of mass spectra, the method described herein could significantly increase the scientific retrieval from archived space flight mass spectrometry data, where calibration of the ionization source is no longer an option.

Thomas Gautier↗

NASA NTRS2000

Fluorescence Studies of Protein Crystal Nucleation

We have postulated that, in the case of tetragonal chicken egg white lysozyme, crystal growth occurs by the addition of pre-critical nuclei sized n-mers that form in the bulk solution, and that the n-mer growth units were multiples of the tetrameric 4(sub 3) helical structure. These have the strongest intermolecular bonds in the crystal and are therefore likely to be the first species formed. High resolution AFM studies provide strong supporting evidence for this model, but the data also suggest that the actual species in solution may not be identical in structure to that found in the crystal. We are using fluorescence resonance energy transfer (FRET) to study the initial solution phase self-assembly process, using covalent fluorescent derivatives which crystallize in the characteristic P4(sub 3)2(sub 1)2(sub 1) space group. FRET studies are being carried out between the cascade blue (CB-lys, donor, Ex(sub max) 366 nm, Em 420 nm) and lucifer yellow (LY-lys, acceptor, Ex(sub max) 430 nm, Em 528 nm) asp101 derivatives. The estimated R(sub 0) for this probe pair, the distance where 50% of the donor energy is transferred to the acceptor, is approx. 1.2 nm, compared to 2.2 nm between the side chain carboxyls of adjacent asp101's in the crystalline 4(sub 3) helix. The short donor lifetime of 2.80 ns (chi(sup 2) = 0.644), coupled with the large average distances between the molecules (greater than or equal to 50 nm) in solution, ensure that any energy transfer observed is not due to random diffusive interactions. Lifetime data show that CB-lys has a single lifetime when it is the only species in solution. Similarly, LY-lys also exhibits a single lifetime of 4.63 ns (chi(sup 2) = 0.42) when alone in solution. Addition of LY-lys to CB-lys results in the appearance of a third lifetime component of 0.348ns for the CB-lys. The fractional intensities of the different species present can be used to estimate the distribution of monomer and n-mers in solution. The self-association process is a function of the protein concentration relative to the saturation concentration, and observing it in dilute solution (conc. less than or equal to 10(exp -5)M) requires that the experiments be performed under low solubility conditions, i.e., low temperatures and high salt concentrations. Data from preliminary steady state FRET studies with N-terminal bound pyrene acetic acid (PAA-lys, donor, Ex 340 nm, Em 376 nm) and asp101 LY-lys as an acceptor showed a consistent trend of decreasing donor fluorescence intensity with increasing total protein concentration. The FRET data have been obtained at pH 4.6, 0.1M NaAc buffer, at 5 and 7% NaCl, 4 C. The corresponding C(sub sat) values are 0.471 and 0.362 mg/ml (approx. 3.3 and approx. 2.5 x 10(exp -5)M respectively). The donor fluorescence decrease is more pronounced at7% NaCl, consistent with the expected increased intermolecular interactions at higher salt concentrations as reflected in the lower solubility. Results from these and other ongoing studies will be discussed in conjunction with an emerging model for how tetragonal lysozyme crystals nucleate and the relevance of that model to other proteins.

Pusey, Marc↗

NASA NTRS2000

Fluid Physics and Macromolecular Crystal Growth in Microgravity

The molecular structure of biological macromolecules is important in understanding how these molecules work and has direct application to rational drug design for new medicines and for the improvement and development of industrial enzymes. In order to obtain the molecular structure, large, well formed, single macromolecule crystals are required. The growth of macromolecule crystals is a difficult task and is often hampered on the ground by fluid flows that result from the interaction of gravity with the crystal growth process. One such effect is the bulk movement of the crystal through the fluid due to sedimentation. A second is buoyancy driven convection close to the crystal surface. On the ground the crystallization process itself induces both of these flows.

Pusey, M.↗

NASA NTRS2003

Catalytic Activity of a Binary Informational Macromolecule

RNA molecules are thought to have played a prominent role in the early history of life on Earth based on their ability both to encode genetic information and to exhibit catalytic function. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, due to the chemical instability of cytosine, which readily deaminates to uracil, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unie'. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyze the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalyzed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.

Reader, John S.↗

NASA NTRS2000

Comparison of repair of DNA double-strand breaks in identical sequences in primary human fibroblast and immortal hamster-human hybrid cells harboring a single copy of human chromosome 11

We have optimized a pulsed-field gel electrophoresis assay that measures induction and repair of double-strand breaks (DSBs) in specific regions of the genome (Lobrich et al., Proc. Natl. Acad. Sci. USA 92, 12050-12054, 1995). The increased sensitivity resulting from these improvements makes it possible to analyze the size distribution of broken DNA molecules immediately after the introduction of DSBs and after repair incubation. This analysis shows that the distribution of broken DNA pieces after exposure to sparsely ionizing radiation is consistent with the distribution expected from randomly induced DSBs. It is apparent from the distribution of rejoined DNA pieces after repair incubation that DNA ends continue to rejoin between 3 and 24 h postirradiation and that some of these rejoining events are in fact misrejoining events, since novel restriction fragments both larger and smaller than the original fragment are generated after repair. This improved assay was also used to study the kinetics of DSB rejoining and the extent of misrejoining in identical DNA sequences in human GM38 cells and human-hamster hybrid A(L) cells containing a single human chromosome 11. Despite the numerous differences between these cells, which include species and tissue of origin, levels of TP53, expression of telomerase, and the presence or absence of a homologous chromosome for the restriction fragments examined, the kinetics of rejoining of radiation-induced DSBs and the extent of misrejoining were similar in the two cell lines when studied in the G(1) phase of the cell cycle. Furthermore, DSBs were removed from the single-copy human chromosome in the hamster A(L) cells with similar kinetics and misrejoining frequency as at a locus on this hybrid's CHO chromosomes.

NASA Program Biomedical Research and Countermeasur↗

NASA NTRS1972

Interstellar hydrogen sulfide.

Hydrogen sulfide has been detected in seven Galactic sources by observation of a single line corresponding to the rotational transition from the 1(sub 10) to the 1(sub 01) levels at 168.7 GHz. The observations show that hydrogen sulfide is only a moderately common interstellar molecule comparable in abundance to H2CO and CS, but somewhat less abundant than HCN and much less abundant than CO.

Thaddeus, P.↗

NASA NTRS1994

Recombination of H(3+) and D(3+) ions with electrons

Flowing-afterglow measurements in decaying H3(+) or D3(+) plasmas suggest that de-ionization does not occur by simple binary recombination of a single ion species. We find that vibrational excitation of the ions fails to provide an explanation for the effect, contrary to an earlier suggestion. Instead, we suggest that collisional stabilization of H3** Rydberg molecules by ambient electrons introduces an additional dependence on electron density. The proposed mechanism would permit plasma de-ionization to occur without the need for dissociative recombination by the mechanism of potential-surface crossings.

Johnsen, R.↗

NASA NTRS2017

Abiotic Synthesis of Nucleic Acids: Hypochromicity and Future Research

The earliest forms of life would likely have a protocellular form, with a membrane encapsulating some form of linear charged polymer. These polymers could have enzymatic as well as genetic properties. We can simulate plausible prebiotic conditions in the laboratory to test hypotheses related to this concept. In earlier work we have shown that mononucleotides organized within a multilamellar lipid matrix can produce oligomers in the anhydrous phase of dehydration- rehydration cycles (Rajamani, 2008). If mononucleotides are in solution at millimolar concentrations, then oligomers resembling RNA are synthesized and exist in a steady state with their monomers DeGuzman, 2014). We have used conventional and novel techniques to demonstrate that secondary structures stabilized by hydrogen bonds may be present in the condensation products produced in dehydration- rehydration cycles that simulate hydrothermal fields that were present on the early Earth. Gel electrophoresis data corroborates the presence of up to 200-base pair length RNA fragments in products of Hydration-Dehydration experiments. Furthermore, hypochromicity measurements demonstrate a degree of hypochromicity found in single RNA strand of known sequence, as well as results that indicate this is true also for a sample of complementary strands of RNA. Analysis of ionic current signatures of known RNA hairpin molecule as measured using a nanopore detector indicate a significant variability in pattern, different from the signatures produced by DNA hairpin molecules. This informs how we may interpret nanopore data gathered from prebiotic simulations.

Glass, K.↗

NASA NTRS1978

Single and multiple scattering contributions to circumsolar radiation

The contributions to the angular distribution of the almucantar radiance in the forward direction due to multiple scattering are compared to those due to single scattering. The contributions have been calculated by a computer code employing the Gauss-Seidel iterative approach to the solution of the radiative transfer equation for a plane parallel atmosphere composed of air molecules, aerosol particles, and ozone. The code is similar to that of Dave (1972) except in the construction of the source matrix. In the near-forward direction the multiple scattering contributions are significant for optical depths of the order of 0.4. The shape of the angular distribution of almucantar radiance to 10 degrees is less sensitive to multiple scattering.

Box, M. A.↗

NASA NTRS1996

Spectral Irradiance Measurements of Simulated Lightning in Planetary Atmospheres

Optical emissions from lightning provide information to estimate the altitude, latitude and longitude of lightning storms, the energy of the discharges, and the production of important trace species such as HCN and C2H2. Knowledge of the spectra of planetary lightning is needed to deduce the total energy dissipated by lightning (and thereby, the production of trace gases) and to help design experiments to detect and track lightning storms. Measurements of the spectral irradiance from approximately 380 to 820 nm are reported for laboratory simulations of lightning in the atmospheres of Venus, Jupiter, and Titan. In our laboratory, laser-induced plasmas (LIP) are used to simulate lightning discharges. This technique avoids contamination of the spectra by elect-ode material and maintains a safe environment while allowing the use of flammable gases, such as hydrogen and methane, found in outer planet atmospheres. The observations were made at I and 5 bars pressure for Venus and Jupiter and at 1 bar for the Titan mixture. At a pressure of one bar, our results show prominent lines from H(sub alpha), H(sub beta), H(sub gamma), and H(sub delta) lines of the Balmer Series of atomic hydrogen, a single line from Helium at 588 nm and strong continuum radiation. At pressures of 5 bars, the H(sub alpha) and H(sub beta) lines are wider, the H(sub gamma), and H(sub delta) lines merge into the continuum because of pressure broadening, and the helium line at 588 nm is no longer visible. The observed spectra of simulated lightning in the venusian atmosphere at 1 and 5 bars shows that the OI multiplet at 777.7 nm dominates the spectra, but weak features due to atomic carbon and singly excited and singly ionized oxygen atoms are also visible. Although lightning has not yet been observed on Titan, it conceivable that some form of lightning discharge could be occurring. Therefore experiments on a Titan atmosphere mixture were conducted. The most prominent features seen in the simulated spectra are the H(sub alpha) at 656 nm. from the dissociation of the methane and two strong features at 740 and 820 nm from singly excited nitrogen atoms. Most of the features between 400 and 656 nm are due to ionized nitrogen atoms. A broad, highly structured feature centered near 389 nm is molecular band radiation from CN molecules formed in the cooling plasma of atomic nitrogen, carbon, and hydrogen. It is observed in the lightning simulations of both the venusian and Titan atmospheres, For Venus, Jupiter, and Titan, narrow spectral features that are ideal for detecting lightning in the presence of sunlight are present in the spectra. These features could allow lightning to be detected and tracked by Earth-based instruments.

Borucki, W. J.↗