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Ion cyclotron resonance application to propanol ion structure formed in double McLafferty rearrangement, demonstrating direct enol ion formation instead of by isomerization or ketonization
Dialkyl ketone ion in double McLafferty rearrangement, applying ion cyclotron resonance to structural study
Isolation and characterization of voacristine hydroxyindolenine
The ErbB family of protein kinases plays an important role in major cellular functions and consequently mutations in the functional regions of these proteins are implicated in several types of cancer growths. To envision rational design of small molecule drugs that target the diseased proteins it is important to quantify the structural effects of the mutations, as some of these mutants render the protein resistant to tyrosine kinase inhibitors (TKIs). Herein we use advanced sampling techniques and long-timescale molecular dynamics simulations to predict the effect of major exon 20 mutations on the ErbB family, specifically EGFR and HER2 proteins. Exon 20 mutations have been clinically known to induce TKI resistance, though the mechanisms of such an effect is poorly understood. By mapping out the free energy landscape of the mutants and comparing them against the wild-type, we elucidate the structural differences in the binding pocket region that alter the nature of drug-protein interactions. We believe that these insights will play a pivotal role in developing small molecule drugs that overcome the TKI resistance.
The composition and structure of an ablative polymer has a multifaceted influence on its thermal, mechanical and ablative properties. Understanding the molecular level information is critical to the optimization of material performance because it helps to establish correlations with the macroscopic properties of the material, the so-called structure-property relationship. Moreover, accurate information of molecular structures is also essential to predict the thermal decomposition pathways as well as to identify decomposition species that are fundamentally important to modeling work. In this presentation, I will describe the use of infrared transmission spectroscopy (FT-IR) as a convenient tool to aid the discovery and development of thermal protection system materials.
Mass spectrometry fragmentation of lignans containing tetrahydrofuran ring, noting application to molecular structure elucidation
The measurements obtained here indicate ways in which micro-Raman spectroscopy can be used to elucidate structural characteristics and distribution of carbon in meteorites and interplanetary dust particles (IDPs). Existing information about structurally significant aspects of Raman measurements of graphite is combined with structurally relevant findings from the present micro-Raman studies of carbons prepared by carbonization of polyvinylidine chloride (PVDC) at various temperatures and natural material, as well as several acid residues from the Allende and Murchison meteorites in order to establish new spectra-structure relationships. Structural features of many of the materials in this study have been measured by x ray analysis and electron microscopy: thus, their structural differences can be directly correlated with differences in the Raman spectra. The spectral parameters consequently affirmed as indicators of structure are used as a measure of structure in materials that have unknown carbon structure, especially IDPs. The unique applicability of micro-Raman spectroscopy is realized not only in the ability to conveniently measure spectra of micron-size IDPs, but also micro-sized parts of an inhomogeneous material. Microcrystalline graphite is known to give Raman spectra that differ dependent on crystallite size (see e.g., Lespade, et. al., 1984, or Nemanich and Solin, 1979). The spectral changes that accompany decreasing particle size include increase in the ratio (R) of the intensity of the band near 1350 cm(-1) (D band) to that of the band near 1600 cm(-1) (G band) increase in the half width of the D band (wD) increase in the frequency maximum of the G band and increase in the half-width (wG) of the 2nd order band near 2700 cm(-1) (G) band.
Configurational study of S1-Myosin is an important step towards understanding force generation in muscle contraction. Previously reported NMR studies were corroborated. A new compound was synthesized, 3-(Bromoacetamido)-propylamine hydrochloride. Its potential as a sulfhydryl reagent provides an indirect but elegant approach towards future structural elucidation of S1-Myosin. The preliminary investigation has shown that this compound, BAAP, reacted with S1 in the absence of MgADP. The modified enzyme had a 2-fold increase in CaATPase activity and no detectable K-EDTA ATPase activity. Reaction of BAAP with S1 in the presence of MgADP resulted in a modified enzyme which retained a Ca-ATPase activity that was about 60 percent of the unmodified S1 and had essentially zero K-EDTA ATPase activity. Sulfhydryl titration indicated that about 1.5 and 3.5 SH groups per S1 molecule were blocked by BAAP in the absence and presence of MgADP, respectively. When coupled to a carboxyl group of EDTA, the resulting reagent could become a useful SH reagent in which chelated paramagnetic or luminescent lanthanide ions can be exploited to probe S1 conformation.
A major long-term goal of the Materials Division at the NASA Langley Research Center is the characterization of new high-performance materials that have potential applications in the aircraft industry, and in space. The materials used for space applications are often subjected to a harsh and potentially damaging radiation environment. The present study constitutes the application of a novel technique to obtain reliable data for ascertaining the molecular basis for the resilience and durability of materials that have been exposed to simulated space radiations. The radiations of greatest concern are energetic electrons and protons, as well as galactic cosmic rays. Presently, the effects of such radiation on matter are not understood in their entirety. It is clear however, that electron radiation causes ionization and homolytic bond rupture, resulting in the formation of paramagnetic spin centers in the polymer matrices of the structural materials. Since the detection and structure elucidation of paramagnetic species are most readily accomplished using Electron Paramagnetic Resonance (EPR) Spectroscopy, the NASA LaRC EPR system was brought back on-line during the 1991 ASEE term. The subsequent 1992 ASEE term was devoted to the adaptation of the EPR core system to meet the requirements for EPR Imaging (EPRI), which provides detailed information on the spatial distribution of paramagnetic species in bulk media. The present (1994) ASEE term was devoted to the calibration of this EPR Imaging system, as well as to the application of this technology to study the effects of electron irradiation on Ultem(exp R), a high performance polymer which is a candidate for applications in aerospace. The Ultem was exposed to a dose of 2.4 x 10(exp 9) Rads (1-MeV energy/electron) at the LaRC electron accelerator facility. Subsequently, the exposed specimens were stored in liquid nitrogen, until immediately prior to analyses by EPRI. The intensity and dimensions of the EPR Images that were generated for the irradiated specimens showed that the electrons penetrated the material to a depth of approximately 0.125 inch. These data show a very high degree of correlation to the energy deposition profile as predicted by the Tiger Code, a Monte Carlo code that provides guidelines for the transport of electrons in matter. Subsequent efforts will focus on delineating the transport properties of energetic protons in Ultem(R).
The utility of MS/MS for both target compound analysis and the structure elucidation of unknowns has been described in a number of references. A broader acceptance of this technique has not yet been realized as it requires large, complex, and costly instrumentation which has not been competitive with more conventional techniques. Recent advancements in ion trap mass spectrometry promise to change this situation. Although the ion trap's small size, sensitivity, and ability to perform multiple stages of mass spectrometry have made it eminently suitable for on-line, real-time monitoring applications, advance automation techniques are required to make these capabilities more accessible to non-experts. Towards this end we have developed custom software for the design and implementation of MS/MS experiments. This software allows the user to take full advantage of the ion trap's versatility with respect to ionization techniques, scan proxies, and ion accumulation/ejection methods. Additionally, expert system software has been developed for autonomous target compound analysis. This software has been linked to ion trap control software and a commercial data system to bring all of the steps in the analysis cycle under control of the expert system. These software development efforts and their utilization for a number of trace analysis applications will be described.
Groups at the Johnson Space Center and the University of Tokyo have been using electron back-scattered diffraction (EBSD) to reveal the crystal structures of extraterrestrial minerals for many years. Even though we also routinely use transmission electron microscopy, synchrotron X-ray diffraction (SXRD), and conventional electron diffraction, we find that EBSD is the most powerful technique for crystal structure elucidation in many instances. In this talk I describe a few of the cases where we have found EBSD to provide crucial, unique information. See attachment.
Many papers have been published that further elucidate the structure of coronas in cool stars as determined from EUVE, HST, FUSE, Chandra, and XMM-Newton observations. Highlights of these are summarized in several pages folk wing that were presented at, the AAS Meeting in Albuquerque in June 2002 during the Topical Session.
Many papers have been published that further elucidate the structure of coronas in cool stars as determined from EUVE, HST, FUSE, Chandra, and XMM-Newton observations. Highlights of these are summarized including publications during this reporting period and presentations.
Many papers have been published that further elucidate the structure of coronas in cool stars as determined from EUVE, HST, FUSE, Chandra, and XMM-Newton observations. In addition we are exploring the effects of coronas on the He I 1083081 transition that is observed in the infrared. Highlights of these are summarized below including publications during this reporting period and presentations. Ground-based magnetic Doppler imaging of cool stars suggests that active stars have active regions located at high latitudes on their surface. We have performed similar imaging in X-ray to locate the sites of enhanced activity using Chandra spectra. Chandra HETG observations of the bright eclipsing contact binary 44i Boo and Chandra LETG observations for the eclipsing binary VW Cep show X-ray line profiles that are Doppler-shifted by orbital motion. After careful analysis of the spectrum of each binary, a composite line-profile is constructed by adding the individual spectral lines. This high signal-to-noise ratio composite line-profile yields orbital velocities for these binaries that are accurate to 30 km/sec and allows their orbital motion to be studied at higher time resolutions. In conjunction with X-ray lightcurves, the phase-binned composite line-profiles constrain coronal structures to be small and located at high latitudes. These observations and techniques show the power of the Doppler Imaging Technique applied to X-ray line emission.
Since the Viking missions in the mid-1970s, traditional culture-based methods have been used for microbial enumeration by various NASA programs. Viable microbes are of particular concern for spacecraft cleanliness, for forward contamination of extraterrestrial bodies (proliferation of microbes), and for crew health/safety (viable pathogenic microbes). However, a "true" estimation of viable microbial population and differentiation from their dead cells using the most sensitive molecular methods is a challenge, because of the stability of DNA from dead cells. The goal of this research is to evaluate a rapid and sensitive microbial detection concept that will selectively estimate viable microbes. Nucleic acid amplification approaches such as the polymerase chain reaction (PCR) have shown promise for reducing time to detection for a wide range of applications. The proposed method is based on the use of a fluorescent DNA intercalating agent, propidium monoazide (PMA), which can only penetrate the membrane of dead cells. The PMA-quenched reaction mixtures can be screened, where only the DNA from live cells will be available for subsequent PCR reaction and microarray detection, and be identified as part of the viable microbial community. An additional advantage of the proposed rapid method is that it will detect viable microbes and differentiate from dead cells in only a few hours, as opposed to less comprehensive culture-based assays, which take days to complete. This novel combination approach is called the PMA-Microarray method. DNA intercalating agents such as PMA have previously been used to selectively distinguish between viable and dead bacterial cells. Once in the cell, the dye intercalates with the DNA and, upon photolysis under visible light, produces stable DNA adducts. DNA cross-linked in this way is unavailable for PCR. Environmental samples suspected of containing a mixture of live and dead microbial cells/spores will be treated with PMA, and then incubated in the dark. Thereafter, the sample is exposed to visible light for five minutes, so that the DNA from dead cells will be cross-linked. Following this PMA treatment step, the sample is concentrated by centrifugation and washed (to remove excessive PMA) before DNA is extracted. The 16S rRNA gene fragments will be amplified by PCR to screen the total microbial community using PhyloChip DNA microarray analysis. This approach will detect only the viable microbial community since the PMA intercalated DNA from dead cells would be unavailable for PCR amplification. The total detection time including PCR reaction for low biomass samples will be a few hours. Numerous markets may use this technology. The food industry uses spore detection to validate new alternative food processing technologies, sterility, and quality. Pharmaceutical and medical equipment companies also detect spores as a marker for sterility. This system can be used for validating sterilization processes, water treatment systems, and in various public health and homeland security applications.
The dissipation of solar wind turbulence at kinetic scales is believed to be important for the heating of the corona and for accelerating the wind. The linear Vlasov kinetic theory is a useful tool for identifying various wave modes, including kinetic Alfven, fast magnetosonic/whistler, and ion-acoustic (or kinetic slow), and their possible roles in the dissipation. However, the kinetic mode structure in the vicinity of ion-cyclotron modes is not clearly understood. The present paper aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion-Bernstein modes versus quasi-modes. The spontaneous emission theory and simulation also confirm the findings of the Vlasov theory in that the kinetic Alfven waves can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high-beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave-particle interactions.
Methyladenine and adenine N-phosphoryl derivatives of adenosine 5'-monophosphate (5'-AMP) and uridine 5'-monophosphate (5'-UMP) are synthesized, and their structures are elucidated. The oligomerization reactions of the adenine derivatives of 5'-phosphoramidates of adenosine on montmorillonite are investigated. 1-Methyladenine and 3-methyladenine derivatives on montmorillonite yielded oligoadenylates as long as undecamer, and the 2-methyladenine and adenine derivatives on montmorillonite yielded oligomers up to hexamers and pentamers, respectively. The 1-methyladenine derivative yielded linear, cyclic, and A5'ppA-derived oligonucleotides with a regioselectivity for the 3',5'-phosphodiester linkages averaging 84%. The effect of pKa and amine structure of phosphate-activating groups on the montmorillonite-catalyzed oligomerization of the 5'-phosphoramidate of adenosine are discussed. The binding and reaction of methyladenine and adenine N-phosphoryl derivatives of adenosine are described.
The role of gravity in the determination of bone structure is elucidated by observations in adult humans and juvenile animals during spaceflight. The primary response of bone tissue to microgravity is at the interface of the mineral and matrix in the process of biomineralization. This response is manifested by demineralization or retarded growth in some regions of the skeleton and hypermineralization in others. The most pronounced effects are seen in the heelbone and skull, the most distally located bones relative to the heart. Ground based flight simulation models that focus on changes in bone structure at the molecular, organ, and whole body levels are described and compared to flight results. On Earth, the morphologic and compositional changes in the unloaded bones are very similar to changes during flight; however, the ground based changes appear to be more transient. In addition, a redistribution of bone mineral in gravity-dependent bones occurs both in space and during head down positioning on Earth. Longitudinal data provided considerable information on the influence of endocrine and muscular changes on bone structure after unloading.