Advances in structure elucidation of small molecules using mass spectrometry

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules

Factors Affecting Methane Emissions from Rice Fields

Methane emissions from rice fields are affected by a number of environmental and agricultural factors. We have analyzed our 7-year data set on methane emissions from rice fields in Tu Zu, China, to delineate the relationships between emissions and a number of variables that were measured at the same time. Our work was done in fields that were managed under prevailing agricultural practices of the region. Consequently, only the effect of factors that vary from year to year or during the growing season can be calculated. In our study we measured the effects of environmental variables (soil temperature, wind speed, sky cover) and agricultural factors (planting density, water level, rice cultivars, organic fertilizer amounts, yield). Of these variables, soil temperature had the most significant effect on methane emissions resulting in Q₁₀ values of about 2 (1.5–3). The effect of sky cover, and even water levels, was to change the soil temperature, which in turn affected the methane flux. Wind tended to increase emissions, possibly by agitation of the soil. Of the agricultural variables, planting density had the most significant but complex effect on methane emissions. We studied emissions from up to 4 times the normal planting density under otherwise similar agricultural conditions in the same fields. For a four fold increase in planting density the seasonal average emissions increased by about a factor of 2. Rice cultivars had a small but detectable effect. The amount of organic fertilizer and the yields did not affect methane emissions in our fields. The lack of an effect from the fertilizers is attributed to a saturation phenomenon whereby methane emissions do not respond to continual increases in organic material after some sufficiently high level

Measurements of Methane Emissions from Rice Fields in China

Rice fields have always been regarded as one of the largest anthropogenic sources of atmospheric methane. Here we report the results of a 7-year study of methane emissions from rice fields in the Sichuan Province of China. In this region, there is one crop of rice per year, the fields are continuously flooded from transplanting to harvest, and there is heavy use of organic fertilizers. Emissions over the entire growing season were measured from each of up to 24 plots. Environmental variables were measured and relevant supporting data on the agricultural practices were recorded. The fields were studied under prevailing agricultural practices of the local farmers. The results represent emissions under standard agricultural practices and the year to year variability of climate, fertilizers, available irrigation water, and cultivars. Based on some 5000 flux measurements, the average emission rates between 1988 and 1994 were 30 mg/m²/h for a growing season of between 100 and 120 days. This emission rate is comparable to other published data from similar rice fields but somewhat on the high side of the range. There were no systematic trends of emissions during the 7 years of our experiment, but there was substantial year to year variability. The data have been subjected to exhaustive analyses for validity, accuracy, and reliability. From this, a high-quality, spatially averaged data set has been constructed representing average emissions from the rice fields for each day when measurements were taken. We describe here the main observational results and document the spatial and temporal variability observed on timescales ranging from a day to several years and on spatial scales ranging from 0.5 m² to 16 m²

Role of a secondary coordination sphere residue in halogenation catalysis of non-heme iron enzymes

Chemo- and regio-selective catalysis of C(sp3)-H halogenation reaction is a formidable goal in chemical synthesis. 2-oxo-glutarate (2OG) dependent non-heme iron halogenases catalyze selective chlorination/bromination of C-H bonds and exhibit high sequence and structural similarities with non-heme iron hydroxylases. How the secondary coordination sphere (SCS) of these two enzyme systems differentiate and determine their reactivity is not understood. In this work, we show that tyrosine placement in the SCS of non-heme iron halogenases have a huge impact on their structure, function, and reactivity. We discover that a tyrosine mutant (F121Y) in SyrB2 halogenase undergoes post-translational oxidation to dihydroxyphenylalanine (DOPA) physiologically. A combination of spectroscopic, mass-spectrometric, and biochemical studies show that the DOPA modification in SyrB2 renders the enzyme non-functional. Further bioinformatics analysis suggests that halogenases, unlike hydroxylases, have a conserved placement of phenylalanine at position 121 to preclude such unproductive oxidation. Overall, this study demonstrates the importance of the SCS in controlling the structure and enzymatic activity of non-heme iron halogenases. Our results will have significant implications towards the design of small-molecule and protein-based halogenation catalysts