The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site

Biological formation and consumption of molecular hydrogen (H2) are catalyzed by hydrogenases, of which three phylogenetically unrelated types are known: [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenase. We present a crystal structure of [Fe]-hydrogenase at 1.75 angstrom resolution, showing a mononuclear iron coordinated by the sulfur of cysteine 176, two carbon monoxide (CO) molecules, and the sp2-hybridized nitrogen of a 2-pyridinol compound with back-bonding properties similar to those of cyanide. The three-dimensional arrangement of the ligands is similar to that of thiolate, CO, and cyanide ligated to the low-spin iron in binuclear [NiFe]- and [FeFe]-hydrogenases, although the enzymes have evolved independently and the CO and cyanide ligands are not found in any other metalloenzyme. The related iron ligation pattern of hydrogenases exemplifies convergent evolution and presumably plays an essential role in H2 activation. This finding may stimulate the ongoing synthesis of catalysts that could substitute for platinum in applications such as fuel cells.     

Biogenic methane, hydrogen escape, and the irreversible oxidation of early Earth

The low O2 content of the Archean atmosphere implies that methane should have been present at levels approximately 10(2) to 10(3) parts per million volume (ppmv) (compared with 1.7 ppmv today) given a plausible biogenic source. CH4 is favored as the greenhouse gas that countered the lower luminosity of the early Sun. But abundant CH4 implies that hydrogen escapes to space (upward arrow space) orders of magnitude faster than today. Such reductant loss oxidizes the Earth. Photosynthesis splits water into O2 and H, and methanogenesis transfers the H into CH4. Hydrogen escape after CH4 photolysis, therefore, causes a net gain of oxygen [CO2 + 2H2O --> CH4 + 2O2 --> CO2 + O2 + 4H(upward arrow space)]. Expected irreversible oxidation (approximately 10(12) to 10(13) moles oxygen per year) may help explain how Earth's surface environment became irreversibly oxidized.     

影响甲烷排放量的两种细菌——产甲烷细菌和甲烷氧化菌的研究进展

产甲烷细菌能够利用环境中的甲酸、乙酸、氢和二氧化碳等小分子化合物生成甲烷,对提高沼气池的甲烷产量具有很高的经济价值。甲烷氧化菌以甲烷为其惟一的碳源和能源,在全球大气甲烷平衡中起着重要的作用。环境中的甲烷在厌氧生境中由产甲烷细菌形成后,经土壤和水层,逸散入大气,在途经土壤和水层时可被栖息于其间的甲烷氧化菌所氧化,土壤中甲烷氧化细菌的氧化作用,大约占大气甲烷消耗量的10%,而且甲烷氧化菌能降解卤化碳氢化合物,具有潜在的商业价值。分别对两种细菌的形态、分类、生理特征、代谢途径、研究方法及其潜在应用价值等进行了综述。     

影响甲烷排放量的两种细菌——产甲烷细菌和甲烷氧化菌的研究进展

产甲烷细菌能够利用环境中的甲酸、乙酸、氢和二氧化碳等小分子化合物生成甲烷,对提高沼气池的甲烷产量具有很高的经济价值.甲烷氧化菌以甲烷为其惟一的碳源和能源,在全球大气甲烷平衡中起着重要的作用.环境中的甲烷在厌氧生境中由产甲烷细菌形成后,经土壤和水层,逸散入大气,在途经土壤和水层时可被栖息于其间的甲烷氧化菌所氧化,土壤中甲烷氧化细菌的氧化作用,大约占大气甲烷消耗量的10%,而且甲烷氧化菌能降解卤化碳氢化合物,具有潜在的商业价值.分别对两种细菌的形态、分类、生理特征、代谢途径、研究方法及其潜在应用价值等进行了综述.     

Efficient oxidative dechlorination and aromatic ring cleavage of chlorinated phenols catalyzed by iron sulfophthalocyanine

An efficient method has been developed for the catalytic oxidation of pollutants that are not easily degraded. The products of the hydrogen peroxide (H(2)O(2)) oxidation of 2,4,6,-trichlorophenol (TCP) catalyzed by the iron complex 2,9,16,23-tetrasulfophthalocyanine (FePcS) were observed to be chloromaleic, chlorofumaric, maleic, and fumaric acids from dechlorination and aromatic cycle cleavage, as well as additional products that resulted from oxidative coupling. Quantitative analysis of the TCP oxidation reaction revealed that up to two chloride ions were released per TCP molecule. This chemical system, consisting of an environmentally safe oxidant (H(2)O(2)) and an easily accessible catalyst (FePcS), can perform several key steps in the oxidative mineralization of TCP, a paradigm of recalcitrant pollutants.     

Free energy and temperature dependence of electron transfer at the metal-electrolyte interface

The rate constant of the electron-transfer reaction between a gold electrode and an electroactive ferrocene group has been measured at a structurally well-defined metal-electrolyte interface at temperatures from 1 degrees to 47 degrees C and reaction free energies from -1.0 to +0.8 electron volts (eV). The ferrocene group was positioned a fixed distance from the gold surface by the self-assembly of a mixed thiol monolayer of (eta(5)C(5)H(5))Fe(eta(5)C(5)H(4))CO(2)(CH(2))(16)SH and CH(3)(CH(2))(15)SH. Rate constants from 1 per second (s(-1)) to 2 x 10(4) s(-1) in 1 molar HClO(4) are reasonably fit with a reorganization energy of 0.85 eV and a prefactor for electron tunneling of 7 x 10(4) s(-1) eV(-1). Such self-assembled monolayers can be used to systematically probe the dependence of electron-transfer rates on distance, medium, and spacer structure, and to provide an empirical basis for the construction of interfacial devices such as sensors and transducers that utilize macroscopically directional electron-transfer reactions.     

干湿交替条件下铁氧化对水稻土CO_2排放的影响

以湖北省2种典型水稻土[咸宁市的中稻-冬闲水稻土(第四世纪红壤,XR)和潜江市的中稻-冬闲水稻土(钙质潮土,QR)]为材料,研究土壤干湿交替条件下[土壤落干(孔隙含水率55%)到完全淹水(土水比1∶1)]添加Fe2+对土壤Fe3+、可溶性有机碳(DOC)含量及CO2排放的影响,拟揭示水分转变过程中土壤活性铁氧化对土壤有机碳固持的影响。结果表明,整个培养期间,与CK(不添加Fe2+)相比,添加Fe2+促进了XR和QR土壤中活性铁的氧化,XR和QR土壤中Fe3+平均含量分别较CK提高了133.87%和95.66%。落干期间,与CK相比,添加Fe2+促进了CO2的排放,XR和QR土壤CO2累积排放量分别增加了59.77%和124.48%;促进了土壤DOC的积累,XR和QR土壤DOC平均含量分别提高了42.57%和23.71%。淹水期间,与CK相比,添加Fe2+抑制了CO2的排放,XR和QR土壤CO2累积排放量分别降低了54.03%和35.27%;培养前期促进了土壤DOC的积累,培养后期抑制了土壤DOC含量的积累,总体上XR土壤DOC平均含量降低了35.29%,QR土壤DOC含量提高了16.59%。整个培养期间,添加Fe2+后,XR和QR土壤CO2累积排放量分别降低了43.87%和22.14%。综上,我国南方富含铁氧化物的红壤具有更高的固碳减排潜力。     

预氧化强化混凝去除地下水中铁·锰的试验研究

[目的]筛选去除地下水中铁和锰的理想预氧化剂。[方法]针对长沙近郊某镇地下水中铁和锰含量较高的特点,通过烧杯试验考察了过氧化氢、高锰酸钾和高锰酸盐复合药剂（PPC）3种氧化剂的预氧化效果。[结果]3种预氧化剂对铁的氧化效率均很高,在试验所进行的投加质量浓度范围内均能使铁的去除率保持在90％以上,其中以PPc对铁的去除率最高。3种预氧化剂对锰的预氧化效果不尽相同,当过氧化氢投加质量浓度为0．13mg／L时,锰的去除率为25．6％;当高锰酸钾的投加质量浓度为9．25mg／L时,锰的去除率为87．5％;当PPC投加质量浓度为6．00mg／L时,锰的去除率为91．7％。[结论]PPC不仅具有预氧化的作用,其还原产物还具有助凝作用,是较为理想的预氧化剂。     

Fe(Ⅲ)异化还原对聚磷菌厌氧性能的影响

以污水处理厂活性污泥中主要除磷功能菌为研究对象,探讨了Fe(Ⅲ)的异化还原对菌株生长和除磷特性的影响,并比较了不同Fe(Ⅲ)的质量浓度和不同pH值条件下的情况。实验表明,Fe(Ⅲ)的异化还原有利于菌株的生长,促进了菌株释磷和厌氧吸磷。Fe(Ⅲ)质量浓度为0.078 g/L时,菌生长情况较好,厌氧释磷和吸磷效果较佳;pH=6.5时,菌株释磷和厌氧吸磷效果较好。     

Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster

The homodimeric nickel-containing CO dehydrogenase from the anaerobic bacterium Carboxydothermus hydrogenoformans catalyzes the oxidation of CO to CO2. A crystal structure of the reduced enzyme has been solved at 1.6 angstrom resolution. This structure represents the prototype for Ni-containing CO dehydrogenases from anaerobic bacteria and archaea. It contains five metal clusters of which clusters B, B', and a subunit-bridging, surface-exposed cluster D are cubane-type [4Fe-4S] clusters. The active-site clusters C and C' are novel, asymmetric [Ni-4Fe-5S] clusters. Their integral Ni ion, which is the likely site of CO oxidation, is coordinated by four sulfur ligands with square planar geometry.     

FACE环境下不同秸秆与氮肥管理对稻田土壤产甲烷菌的影响

产甲烷菌是土壤中与甲烷产生和碳素循环有关的微生物菌群,大气CO2浓度升高可能对它们的数量产生影响。利用江都市小记镇的稻-麦轮作FACE平台,采用最大可能(MPN)法,在2004年水稻生长季研究了不同施肥情况(施常规氮量和低氮量)、不同秸秆还田情况(秸秆全还田、秸秆半还田、秸秆不还田)下,土壤中的产甲烷菌数量在大气CO2浓度升高条件下随时间的变化情况。结果表明,大气CO2浓度升高在秸秆全还田情况下对产甲烷菌数有明显的促进作用,在其他2种秸秆还田情况下,FACE与对照差异不显著。常氮处理仅在水稻生长初期促进产甲烷菌数,而在其他生长季不同氮肥处理之间无明显差异。总之,常氮处理产甲烷菌数量FACE比对照平均高104%～116%,低氮处理平均高101%～126%,进一步证实大气CO2浓度升高会促进稻田CH4的排放。     

利用甜高粱秸秆厌氧发酵制氢的研究

 在厌氧情况下从牛胃里提取的厌氧菌种——肺炎克氏杆菌,在用蔗糖作为诱导物质的条件下,保持一定温度和pH值,在自行研发制造的厌氧流化床生物反应器中,利用甜高粱秸秆厌氧发酵产生氢气。结果表明,该细菌不仅有产氢能力,还能在反应器中吸附的活性炭上形成白色细菌颗粒。当细菌颗粒形成之后,在保持液压恒定的情况下,反应进行3d之后,细菌会在蔗糖的诱导作用下,利用甜高粱秸秆产生氢气。肺炎克氏杆菌的最佳生长代时为10h,产氢温度和pH值分别为37℃和6.0。反应过程中液压恒定时间由9.3h维持14d之后降低为4.6h,试验证明,细菌利用甜高粱秸秆阶段的氢气产量明显高于直接利用蔗糖阶段的氢气产量,整个实验过程中氢气含量最高达到28%。     

Silver-catalyzed C-C bond formation between methane and ethyl diazoacetate in supercritical CO₂

Even in the context of hydrocarbons' general resistance to selective functionalization, methane's volatility and strong bonds pose a particular challenge. We report here that silver complexes bearing perfluorinated indazolylborate ligands catalyze the reaction of methane (CH(4)) with ethyl diazoacetate (N(2)CHCO(2)Et) to yield ethyl propionate (CH(3)CH(2)CO(2)Et). The use of supercritical carbon dioxide (scCO(2)) as the solvent is key to the reaction's success. Although the catalyst is only sparingly soluble in CH(4)/CO(2) mixtures, optimized conditions presently result in a 19% yield of ethyl propionate (based on starting quantity of the diazoester) at 40°C over 14 hours.     

Parent volatiles in comet 9P/Tempel 1: before and after impact

We quantified eight parent volatiles (H2O, C2H6, HCN, CO, CH3OH, H2CO, C2H2, and CH4) in the Jupiter-family comet Tempel 1 using high-dispersion infrared spectroscopy in the wavelength range 2.8 to 5.0 micrometers. The abundance ratio for ethane was significantly higher after impact, whereas those for methanol and hydrogen cyanide were unchanged. The abundance ratios in the ejecta are similar to those for most Oort cloud comets, but methanol and acetylene are lower in Tempel 1 by a factor of about 2. These results suggest that the volatile ices in Tempel 1 and in most Oort cloud comets originated in a common region of the protoplanetary disk.     

Native iron in the continental lower crust: petrological and geophysical implications

Lower crustal granulite xenoliths recovered from a kimberlite pipe in western Africa contain native iron (Fe(0)) as a decomposition product of garnet and ilmenite. Magnetic measurements show that less than 0.1 percent (by volume) of iron metal is present. Data from geothermometry and oxygen geobarometry indicate that the oxide and metal phases equilibrated between iron-wüstite and magnetite-wüstite buffers, which may represent the oxidation state of the continental lower crust, and the depleted lithospheric upper mantle. Ferromagnetic native iron could be stable to a depth of approximately 95 kilometers and should be considered in the interpretation of long-wavelength static magnetic anomalies.     

The Exclusion of D2O from the Hydration Sphere of FeSO4{middle dot} 7H2O Oxidized by Thiobacillus ferrooxidans

Infrared spectra demonstrate that neither FeSO(4) . 7H(2)O nor its bacterial or abiotic hydrated oxidation products incorporate deuterium in acid D(2)O solutions. Deuterium exchange occurred as bridging OD when bacterially oxidized iron was precipitated from D(2)O solutions as ferric hydroxysulfates. The exclusion of deuterium depended upon the stabilization of aquated Fe(II) and Fe(III) complexes by sulfate ions in outer-sphere coordination and is consistent with the requirement and postulated role of sulfate in iron oxidation by Thiobacillus ferrooxidans.     

Crystallization and X-ray Analysis of Stemphyloxin I, a Phytotoxin from Stemphylium botryosum

Certain isolates of the plant-pathogenic fungus Stemphylium botryosum produce a phytotoxin, stemphyloxin I. This toxin (C(21)H(34)O(6)) was crystallized and its structure was determined by x-ray crystallography to be a beta-ketoaldehyde trans-Decalin. This compound is a highly unusual natural product. Iron (Fe(3+)) controls production of toxin by this fungus. Furthermore, iron reacts with the toxin to yield a colored product which aids in its detection on chromatograms and in its quantitative estimation by colorimetry.;     

Fe对厌氧发酵生物制氢的影响研究

以污水处理厂的厌氧污泥作为天然厌氧微生物来源,以蔗糖为底物,考察不同价态铁离子对厌氧发酵产氢的影响,试验结果表明:Fe2+最佳,在此基础上,考察了不同浓度Fe2+对产氢的影响。当Fe2+1000mg/L时,产氢率最大,达到364.8mL H2/g蔗糖、产氢浓度56.5%,产氢量为空白样的1.54倍。     

The roaming atom: straying from the reaction path in formaldehyde decomposition

We present a combined experimental and theoretical investigation of formaldehyde (H2CO) dissociation to H2 and CO at energies just above the threshold for competing H elimination. High-resolution state-resolved imaging measurements of the CO velocity distributions reveal two dissociation pathways. The first proceeds through a well-established transition state to produce rotationally excited CO and vibrationally cold H2. The second dissociation pathway yields rotationally cold CO in conjunction with highly vibrationally excited H2. Quasi-classical trajectory calculations performed on a global potential energy surface for H2CO suggest that this second channel represents an intramolecular hydrogen abstraction mechanism: One hydrogen atom explores large regions of the potential energy surface before bonding with the second H atom, bypassing the saddle point entirely.     

Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere

Rice fields are a global source of the greenhouse gas methane, which is produced by methanogenic archaea, and by methanogens of Rice Cluster I (RC-I) in particular. RC-I methanogens are not yet available in pure culture, and the mechanistic reasons for their prevalence in rice fields are unknown. We reconstructed a complete RC-I genome (3.18 megabases) using a metagenomic approach. Sequence analysis demonstrated an aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for carbohydrate metabolism and assimilatory sulfate reduction, hitherto unknown among methanogens. These capacities and a unique set of antioxidant enzymes and DNA repair mechanisms as well as oxygen-insensitive enzymes provide RC-I with a selective advantage over other methanogens in its habitats, thereby explaining the prevalence of RC-I methanogens in the rice rhizosphere.