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At least 847 records · Page 47Linked to original sources
PubMed2004

Large-scale homogeneous molecular templates for femtosecond time-resolved studies of the guest-host interaction.

Self-assembled monolayer films based on iodobenzoyloxy-functionalized resorc[4]arenes were prepared on gold substrates to serve as model systems for future time-resolved studies of molecular recognition, a mechanism of outstanding importance in bioorganic systems. The film properties were tested using X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM) and imaging ellipsometry. An apparatus for time-resolved electron spectroscopy utilizing femtosecond soft X-ray pulses is capable of detecting iodine core-level photolines and the photoinduced dissociation after ultraviolet illumination. The developed technique holds promise for tracking the temporal evolution of chemical shifts of atomic markers as local probes for the dynamics of the guest-host interaction.

Benzoates↗
PubMed2005

Homo-nuclear 13C J-decoupling in uniformly 13C-enriched solid proteins.

Recently, we reported an analysis of carbon lineshapes in high resolution solid-state NMR spectra of uniformly 13C-enriched amino acids. Application of a 13C J-decoupling protocol during the carbon chemical shift evolution period allowed us to separate the contribution of the second-order dipolar shift from that of the 13C-13C J-coupling interactions to carbon linewidths. In this work, we have extended this approach to microcrystalline proteins. We describe the performance of the J-decoupling sequence applied to remove homo-nuclear 13C J-couplings in the 13C spectra of ubiquitin. Analysis of the J-decoupling efficiency for C(alpha) and carbonyl protein sites showed that a significant gain in resolution can be achieved.

Algorithms↗
PubMed2006

On the application of magic echo cycles for quadrupolar echo spectroscopy of spin-1 nuclei.

Magic echo cycles are introduced for performing quadrupolar echo spectroscopy of spin-1 nuclei. An analysis is performed via average Hamiltonian theory showing that the evolution under chemical shift or static field inhomogeneity can be refocused simultaneously with the quadrupolar interaction using these cycles. Due to the higher convergence in the Magnus expansion, with sufficient RF power, magic echo based quadrupolar echo spectroscopy outperforms the conventional two pulse quadrupolar echo in signal to noise. Experiments highlighting a signal to noise enhancement over the entire bandwidth of the quadrupolar pattern of a powdered sample of deuterated polyethelene are shown.

Algorithms↗
PubMed2006

Intramolecular interactions in aminoacyl cyclic-3',5'-nucleotides.

Polymerization of amino-acid acyl cyclic-3',5'-nucleotides is postulated to be the origin of RNA and associated protein in prebiotic molecular evolution. The enthalpy change in the intramolecular interaction between the nucleotide base and the amino-acid side chain determines the stability of the particular complex, resulting in a preferred association (or coding) of a base for a particular amino acid. The compounds studied were glycine acyl cyclic-3',5'-guanylate where the strong hydrogen bond between protonated glycine and guanine N7 gives an enthalpy change of -0.05 h. Similarly, hydrogen bonds in l-lysine acyl cyclic-3',5'-adenylate give an enthalpy change of -0.06 h. Hydrophobic interactions in l-phenylalanine acyl cyclic-3',5'-uridylate give an enthalpy change of -0.02 h and the corresponding value for l-proline acyl cyclic-3',5'-cytidylate is -0.01 h. These interactions were expected to be modified as the genetic code became a duplet and finally a triplet code. The interactions have been shown to be feasible from the overall enthalpy changes in the ZKE approximation at the MP2/6-31G* level.

Amino Acids↗
PubMed2005

Hypothesis: the origin of life in a hydrogel environment.

A hypothesis is proposed that the first cell(s) on the Earth assembled in a hydrogel environment. Gel environments are capable of retaining water, oily hydrocarbons, solutes, and gas bubbles, and are capable of carrying out many functions, even in the absence of a membrane. Thus, the gel-like environment may have conferred distinct advantages for the assembly of the first cell(s).

Biomimetic Materials↗
PubMed2004

Search for EPR markers of the history and origin of the insoluble organic matter in extraterrestrial and terrestrial rocks.

The insoluble organic matter (IOM) of three carbonaceous meteorites (Orgueil, Murchison and Tagish Lake meteorites) and three samples of cherts (microcrystalline SiO2 rock) containing microfossils with age ranging between 45 million years and 3.5 billion years is studied by electron paramagnetic resonance (EPR). The age of the meteorites is that of the solar system (4.6 billion years). The purpose of this work was to determine the EPR parameters, which allow us to discriminate between biogenic and extra terrestrial origin for the organic matter. Such indicators should be relevant for the controversy regarding the biogenicity of the organic matter in the oldest cheroot (3.5 billion years) and in Martian meteorites containing microbe-like microstructures. The organic matter of meteorites contains a high concentration of diradicaloid moieties characterised by a diamagnetic ground state S = 0 and a thermally accessible triplet state S = 1. The three meteorites exhibit the same singlet-triplet gap (ST gap) DeltaE approximately 0.1 eV. To the best of our knowledge, such diradicaloids are unknown in insoluble organic matter of terrestrial origin. We have also shown that the EPR linewidth of insoluble organic matter in cherts and coals decrease logarithmically with the age of the organic matter. We conclude from this result that the organic matter in the oldest cherts (3.5 billion years) has the same age as their SiO2 matrix, and is not due to a latter contamination by bacteria, as was recently found in meteoritic samples.

Carbon↗
PubMed2004

ESR studies of Anatolian gypsum.

Electron spin resonance (ESR) was used to date the formation and most recent recrystallization of three types of gypsum samples (massive, bedded and fracture filling gypsum) from the Sakarya Formation at Eskişehir in the middle of Turkey. The ESR spectra had the signals of Fe3+ and Mn2+ in addition to those of the G1 and G2 sensitive centers (g = 2.002 and 2.008) to artificial gamma-irradiation. ESR intensities of G1 and G2 were enhanced by gamma-ray irradiation to give equivalent doses DE) for each sample. The ESR ages derived from the annual doses of 238U, 232Th and 40K contents of the samples determined by thermal neutron activation analysis (TNAA) were between 43 +/- 18 ka (massive gypsum) and 1100 +/- 466 ka (bedded gypsum) as minimal and maximal values. The ages fall into the upper Miocene-Pliocene Epoch of the geological time scale, which agreed with the stratigraphy.

Calcium Sulfate↗
PubMed2005

Use of mode of action in risk assessment: past, present, and future.

The evolution of chemical risk assessment has been marked by a steadily increasing expectation for the use of chemical-specific dosimetric and mechanistic information to tailor the risk assessment approach. The information to be used can range from the broad physical properties of the chemical to detailed information on the mechanism by which it causes a particular toxic outcome, and the risk assessment decisions effected can in turn range from how to define equivalent exposures across species to whether a particular animal outcome is relevant to a human health assessment. A concept that has proven useful in support of these considerations is the "mode of action," a term coined by the USEPA in their new guidelines for carcinogen risk assessment. This paper describes the increasing use of mode-of-action considerations in risk assessment, beginning with early examples involving quantitative dosimetry on the one hand, and qualitative relevance on the other, which foreshadowed the current interest in mode of action. It then describes more recent developments regarding the use of the mode-of-action concept for the selection of a low-dose extrapolation approach, for harmonization of cancer and noncancer risk assessment approaches, and for cross-chemical evaluations. Finally, examples of recent controversies associated with the use of mode-of-action information in risk assessment are provided to demonstrate the challenges that must be overcome to assure the continued viability of the mode-of-action approach.

Humans↗
PubMed2000

Non-racemic amino acids in the Murray and Murchison meteorites.

Small (1.0-9.2%) L-enantiomer excesses were found in six alpha-methyl-alpha-amino alkanoic acids from the Murchison (2.8-9.2%) and Murray (1.0-6.0%) carbonaceous chondrites by gas chromatography-mass spectroscopy of their N-trifluoroacetyl or N-pentafluoropropyl isopropyl esters. These amino acids [2-amino-2,3-dimethylpentanoic acid (both diastereomers), isovaline, alpha-methyl norvaline, alpha-methyl valine, and alpha-methyl norleucine] are either unknown or rare in the terrestrial biosphere. Enantiomeric excesses were either not observed in the four alpha-H-alpha-amino alkanoic acids analyzed (alpha-amino-n-butyric acid, norvaline, alanine, and valine) or were attributed to terrestrial contamination. The substantial excess of L-alanine reported by others was not found in the alanine in fractionated extracts of either meteorite. The enantiomeric excesses reported for the alpha-methyl amino acids may be the result of partial photoresolution of racemic mixtures caused by ultraviolet circularly polarized light in the presolar cloud. The alpha-methyl-alpha-amino alkanoic acids could have been significant in the origin of terrestrial homochirality given their resistance to racemization and the possibility for amplification of their enantiomeric excesses suggested by the strong tendency of their polymers to form chiral secondary structure.

Amino Acids↗
PubMed1996

Homochirality as the signature of life: the SETH Cigar.

A characteristic hallmark of life is its homochirality: all biomolecules are usually of one hand, e.g. on Earth life uses only L-amino acids for protein synthesis and not their D mirror images. It is therefore suggested that a search for extra-terrestrial life can be approached as a Search for Extra-Terrestrial Homochirality (SETH). A novel miniaturized space polarimeter, called the SETH Cigar, is described which could he used to detect optical rotation as the homochiral signature of life on other planets. Moving parts are avoided by replacing the normal rotating polarizer by multiple fixed polarizers at different angles as in the eye of the bee. It is believed that homochirality will be found in the subsurface layers on Mars as a relic of extinct life.

Astronomy↗
PubMed1997

The determination of ice composition with instruments on cometary landers.

The determination of the composition of materials that make up comets is essential in trying to understand the origin of these primitive objects. The ices especially could be made in several different astrophysical settings including the solar nebula, protosatellite nebulae of the giant planets, and giant molecular clouds that predate the formation of the solar system. Each of these environments makes different ices with different composition. In order to understand the origin of comets, one needs to determine the composition of each of the ice phases. For example, it is of interest to know that comets contain carbon monoxide, CO, but it is much more important to know how much of it is a pure solid phase, is trapped in clathrate hydrates, or is adsorbed on amorphous water ice. In addition, knowledge of the isotopic composition of the constituents will help determine the process that formed the compounds. Finally, it is important to understand the bulk elemental composition of the nucleus. When these data are compared with solar abundances, they put strong constraints on the macro-scale processes that formed the comet. A differential scanning calorimeter (DSC) and an evolved gas analyzer (EGA) will make the necessary association between molecular constituents and their host phases. This combination of instruments takes a small (tens of mg) sample of the comet and slowly heats it in a sealed oven. As the temperature is raised, the DSC precisely measures the heat required, and delivers the gases to the EGA. Changes in the heat required to raise the temperature at a controlled rate are used to identify phase transitions, e.g., crystallization of amorphous ice or melting of hexagonal ice, and the EGA correlates the gases released with the phase transition. The EGA consists of two mass spectrometers run in tandem. The first mass spectrometer is a magnetic-sector ion-momentum analyzer (MAG), and the second is an electrostatic time-of-flight analyzer (TOF). The TOF acts as a detector for the MAG and serves to resolve ambiguities between fragments of similar mass such as CO and N2. Because most of the compounds of interest for the volatile ices are simple, a gas chromatograph is not needed and thus more integration time is available to determine isotopic ratios. A gamma-ray spectrometer (GRS) will determine the elemental abundances of the bulk cometary material by determining the flux of gamma rays produced from the interaction of the cometary material with cosmic ray produced neutrons. Because the gamma rays can penetrate a distance of several tens of centimeters a large volume of material is analyzed. The measured composition is, therefore, much more likely to be representative of the bulk comet than a very small sample that might have lost some of its volatiles. Making these measurements on a lander offers substantial advantages over trying to address similar objectives from an orbiter. For example, an orbiter instrument can determine the presence and isotopic composition of CO in the cometary coma, but only a lander can determine the phase(s) in which the CO is located and separately determine the isotopic composition of each reservoir of CO. The bulk composition of the nucleus might be constrained from separate orbiter analyses of dust and gas in the coma, but the result will be very model dependent, as the ratio of gas to dust in the comet will vary and will not necessarily be equal to the bulk value.

Ammonia↗
PubMed1996

Hepatitis C virus types 7, 8 and 9 should be classified as type 6 subtypes.

Tokita et al. reported the identification of hepatitis C virus type 7, 8 and 9 in Southeast Asia, based on the unweighed pair-group method with the arithmetic mean, a method that may not be appropriate when the nucleotide substitution rate is not constant over time. To determine more accurately the relationship of these proposed types 7, 8, and 9 with other types, a more appropriate approach, the neighbor-joining method, was applied to re-evaluate the phylogenetic relationship. A total of 660 HCV sequences, including the reported sequences, were collected from DNA databases. For every region, the nucleotide substitution rate was estimated by the 6-parameter method, and phylogenetic trees were constructed using the neighbor-joining method. The results of this analysis indicate that the newly proposed HCV types 7, 8 and 9 should be classified as type 6 subtypes. HCV type 6 appears to be diversified.

Evolution, Chemical↗
PubMed1999

Peptides and the origin of life.

Considering the state-of-the-art views of the geochemical conditions of the primitive earth, it seems most likely that peptides were produced ahead of all other oligomer precursors of biomolecules. Among all the reactions proposed so far for the formation of peptides under primordial earth conditions, the salt-induced peptide formation reaction in connection with adsorption processes on clay minerals would appear to be the simplest and most universal mechanism known to date. The properties of this reaction greatly favor the formation of biologically relevant peptides within a wide variation of environmental conditions such as temperature, pH, and the presence of inorganic compounds. The reaction-inherent preferences of certain peptide linkages make the argument of 'statistical impossibility' of the evolutionary formation of the 'right' peptides and proteins rather insignificant. Indeed, the fact that these sequences are reflected in the preferential sequences of membrane proteins of archaebacteria and prokaryonta distinctly indicates the relevance of this reaction for chemical peptide evolution. On the basis of these results and the recent findings of self-replicating peptides, some ideas have been developed as to the first steps leading to life on earth.

Catalysis↗