Study of methanol adsorption on mica, graphite and ITO glass by using tapping mode atomic force microscopy

Tapping mode atomic force microscopy (AFM) was applied to study the adsorption behavior of methanol on mica, highly oriented pyrolytic graphite (HOPG) and indium-tin oxide (ITO) coated glass substrates. On mica and HOPG substrates surfaces, the thin films of methanol with bilayer and multilayer were observed, respectively. The formation of irregular islands of methanol was also found on HOPG surface. On ITO surface only aggregates and clusters of methanol molecules were formed. The influence of sample preparation on the adsorption was discussed.

Developing molecular identification numbers by an all-paths method

A new topological index is devised from an all-paths method. This molecular topological index has highly discriminating power for various kinds of organic compounds such as alkane trees, complex cyclic or polycyclic graphs, and structures containing heteroatoms and thus can be used as a Molecular IDentification number (MID) for chemical documentation. Some published MIDs derived from an all-paths method and their structural selectivity for alkane trees are also reviewed.

On highly discriminating molecular topological index

A highly discriminating molecular topological index, EAID, is proposed based on the extended adjacency matrix. A systematic search for degeneracy was performed for 3 807 434 alkane trees, 202 558 complex cyclic or polycyclic graphs, and 430 472 structures containing heteroatoms. No counterexamples (two or more nonisomorphic structures with the same EAID number) were found. This is a hitherto unheard of power of discrimination. Thus EAID might be possibly used as supplementary reference for CAS Registry Numbers for structure documentation.

Sources and preservation of organic matter in Plum Island salt marsh sediments (MA, USA): long-chain n-alkanes and stable carbon isotope compositions

Elemental (TOC, TN, C/N) and stable carbon isotopic (delta(13)C) compositions and n-alkane (nC(16-38)) concentrations were measured for Spartina alterniflora, a C-4 marsh grass, Typha latifolia, a C-3 marsh grass, and three sediment cores collected from middle and upper estuarine sites from the Plum Island salt marshes. Our results indicated that the organic matter preserved in the sediments was highly affected by the marsh plants that dominated the sampling sites. delta(13)C values of organic matter preserved in the upper fresh water site sediment were more negative (-23.0+/-0.3) as affected by the C-3 plants than the values of organic matter preserved in the sediments of middle (-18.9+/-0.8) and mud flat sites (-19.4+/-0.1) as influenced mainly by the C4 marsh plants. The distribution of n-alkanes measured in all sediments showed similar patterns as those determined in the marsh grasses S. alterniflora and T. latifolia, and nC(21) to nC(33) long-chain n-alkanes were the major compounds determined in all sediment samples. The strong odd-to-even carbon numbered n-alkane predominance was found in all three sediments and nC(29) was the most abundant homologue in all samples measured. Both delta(13)C compositions of organic matter and n-alkane distributions in these sediments indicate that the marsh plants could contribute significant amount of organic matter preserved in Plum Island salt marsh sediments. This suggests that salt marshes play an important role in the cycling of nutrients and organic carbon in the estuary and adjacent coastal waters. (C) 2003 Elsevier Ltd. All rights reserved.

中国大中型气田天然气成藏物理化学模拟研究

Natural gas pays more important role in the society as clean fuel. Natural gas exploration has been enhanced in recent years in many countries. It also has prospective future in our country through "85" and "95" national research. Many big size gas fields have been discovered in different formations in different basins such as lower and upper Paleozoic in Erdos basin, Tertiary system in Kuche depression in Tarim basin, Triassic system in east of Sichuan basin. Because gas bearing basins had been experienced multiple tectogenesis. The characteristics of natural gases usually in one gas field are that they have multiple source rocks and are multiple maturities and formed in different ages. There has most difficult to research on the gas-rock correlation and mechanism of gas formation. Develop advanced techniques and methods and apply them to solve above problems is necessary. The research is focused on the critical techniques of geochemistry and physical simulation of gas-rock correlation and gas formation. The lists in the following are conclusions through research and lots of experiments. I 8 advanced techniques have been developed or improved about gas-rock correlation and gas migration, accumulation and formation. A series of geochemistry techniques has been developed about analyzing inclusion enclave. They are analyzing gas and liquid composition and biomarker and on-line individual carbon isotope composition in inclusion enclave. These techniques combing the inclusion homogeneous temperature can be applied to study on gas-rock correlation directly and gas migration, filling and formation ages. Technique of on-line determination individual gas carbon isotope composition in kerogen and bitumen thermal pyrolysis is developed. It is applied to determine the source of natural is kerogen thermal degradation or oil pyrolysis. Method of on-line determination individual gas carbon isotope composition in rock thermal simulation has being improved. Based on the "95"former research, on-line determination individual gas carbon isotope composition in different type of maceral and rocks thermal pyrolys is has been determined. The conclusion is that carbon isotope composition of benzene and toluene in homogenous texture kerogen thermal degradation is almost same at different maturity. By comparison, that in mixture type kerogen thermal pyrolysis jumps from step to step with the changes of maturity. This conclusion is a good proof of gas-rock dynamic correlation. 3. Biomarker of rock can be determined directly through research. It solves the problems such as long period preparing sample, light composition losing and sample contamination etc. It can be applied to research the character of source rock and mechanism of source rock expulsion and the path of hydrocarbon migration etc. 4. The process of hydrocarbon dynamic generation in source rock can be seen at every stage applying locating observation and thermal simulation of ESEM. The mechanism of hydrocarbon generation and expulsion in source rock is discussed according to the experiments. This technique is advanced in the world. 5. A sample injection system whose character is higher vacuum, lower leaks and lower blank has been built up to analyze inert gas. He,Ar,Kr and Xe can be determined continuously on one instrument and one injection. This is advanced in domestic. 7. Quality and quantity analysis of benzene ring compounds and phenolic compounds and determination of organic acid and aqueous gas analysis are applied to research the relationship between compounds in formation water and gas formation. This is another new idea to study the gas-rock correlation and gas formation. 8. Inclusion analysis data can be used to calculate the Paleo-fluid density, Paleo-geothermal gradient and Paleo-geopressure gradient and then to calculate the Paleo-fluid potential. It's also a new method to research the direction of hydrocarbon migration and accumulation. 9. Equipment of natural gas formation simulation is produced during the research to probe how the physical properties of rock affect the gas migration and accumulation and what efficiency of gas migrate and factors of gas formation and the models of different type of migration are. II study is focused on that if the source rocks of lower Paleozoic generated hydrocarbon and what the source rocks of weathered formation gas pool and the mechanism of gas formation are though many advanced techniques application. There are four conclusions. 1.The maturity of Majiagou formation source rocks is higher in south than that in north. There also have parts of the higher maturity in middle and east. Anomalous thermal pays important role in big size field formation in middle of basin. 2. The amount of gas generation in high-over maturity source rocks in lower Paleozoic is lager than that of most absorption of source rocks. Lower Paleozoic source rocks are effective source rocks. Universal bitumen exists in Ordovician source rocks to prove that Ordovician source rocks had generated hydrocarbon. Bitumen has some attribution to the middle gas pool formation. 3. Comprehensive gas-rock correlation says that natural gases of north, west, south of middle gas field of basin mainly come from lower Paleozoic source rocks. The attribution ratio of lower Paleozoic source rocks is 60%-70%. Natural gases of other areas mainly come from upper Paleozoic. The attribution ratio of upper Paleozoic source rocks is 70%. 4. Paleozoic gases migration phase of Erdos basin are also interesting. The relative abundance of gasoline aromatic is quite low especially toluene that of which is divided by that of methyl-cyclohexane is less than 0.2 in upper Paleozoic gas pool. The migration phase of upper Paleozoic gas may be aqueous phase. By comparison, the relative abundance of gasoline aromatic is higher in lower Paleozoic gas. The distribution character of gasoline gas is similar with that in source rock thermal simulation. The migration phase of it may be free phase. IH Comprehensive gas-rock correlation is also processed in Kuche depression Tarim basin. The mechanism of gas formation is probed and the gas formation model has been built up. Four conclusions list below. 1. Gases in Kuche depression come from Triassic-Jurassic coal-measure source rocks. They are high-over maturity. Comparatively, the highest maturity area is Kelasu, next is Dabei area, Yinan area. 2. Kerogen thermal degradation is main reason of the dry gas in Kuche depression. Small part of dry gas comes from oil pyrolysis. VI 3.The K12 natural gas lays out some of hydro-gas character. Oil dissolved in the gas. Hydro-gas is also a factor making the gas drier and carbon isotope composition heavier. 4. The mechanism and genesis of KL2 gas pool list as below. Overpressure has being existed in Triassic-Jurassic source rocks since Keche period. Natural gases were expulsed by episode style from overpressure source rocks. Hetero-face was main migration style of gas, oil and water at that time. The fluids transferred the pressure of source rocks when they migrated and then separated when they got in reservoir. After that, natural gas migrated up and accumulated and formed with the techno-genesis. Tectonic extrusion made the natural gas overpressure continuously. When the pressure was up to the critical pressure, the C6-C7 composition in natural gas changed. The results were that relative abundance of alkane and aromatic decreased while cycloalkane and isoparaffin increased. There was lots of natural gas filling during every tectonic. The main factors of overpressure of natural gas were tectonic extrusion and fluid transferring pressure of source rocks. Well preservation was also important in the KL2 gas pool formation. The reserves of gas can satisfy the need of pipeline where is from west to east. IV A good idea of natural gas migration and accumulation modeling whose apparent character is real core and formation condition is suggested to model the physical process of gas formation. Following is the modeling results. 1. Modeling results prove that the gas accumulation rule under cap layer and gas fraction on migration path. 2. Natural gas migration as free phase is difficult in dense rock. 3. Natural gases accumulated easily in good physical properties reservoirs where are under the plugging layer. Under the condition of that permeability of rock is more than 1 * 10~(-3)μm~(-1), the more better the physical properties and the more bigger pore of rock, the more easier the gas accumulation in there. On the contrary, natural gas canonly migrate further to accumulate in good physical properties of rock. 4. Natural gas migrate up is different from that down. Under the same situation, the amount of gas migration up is lager than that of gas migration down and the distance of migration up is 3 times as that of migration down. 5. After gas leaks from dense confining layer, the ability of its dynamic plug-back decreased apparently. Gas lost from these arils easily. These confining layer can confine again only after geology condition changes. 6. Water-wetted and capillary-blocking rocks can't block water but gases generally. The result is that water can migrate continuously through blocking rocks but the gases stay under the blocking rocks then form in there. The experiments have proved the formation model of deep basin gas.

The effect of hydrogen bonding on the diffusion of water in n-alkanes and n-alcohols measured with a novel single microdroplet method.

While the Stokes-Einstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that for small solutes, the diffusion coefficient is inversely proportional to the viscosity to a fractional power, and that solutes actually diffuse faster than SE predicts. For other solvent systems, attractive solute-solvent interactions, such as hydrogen bonding, are known to retard the diffusion of a solute. Some researchers have interpreted the slower diffusion due to hydrogen bonding as resulting from the effective diffusion of a larger complex of a solute and solvent molecules. We have developed and used a novel micropipette technique, which can form and hold a single microdroplet of water while it dissolves in a diffusion controlled environment into the solvent. This method has been used to examine the diffusion of water in both n-alkanes and n-alcohols. It was found that the polar solute water, diffusing in a solvent with which it cannot hydrogen bond, closely resembles small nonpolar solutes such as xenon and krypton diffusing in n-alkanes, with diffusion coefficients ranging from 12.5x10(-5) cm(2)/s for water in n-pentane to 1.15x10(-5) cm(2)/s for water in hexadecane. Diffusion coefficients were found to be inversely proportional to viscosity to a fractional power, and diffusion coefficients were faster than SE predicts. For water diffusing in a solvent (n-alcohols) with which it can hydrogen bond, diffusion coefficient values ranged from 1.75x10(-5) cm(2)/s in n-methanol to 0.364x10(-5) cm(2)/s in n-octanol, and diffusion was slower than an alkane of corresponding viscosity. We find no evidence for solute-solvent complex diffusion. Rather, it is possible that the small solute water may be retarded by relatively longer residence times (compared to non-H-bonding solvents) as it moves through the liquid.

2,4-dinitrophenol as an activating reagent in a facile preparation of cyclic phosphate trimesters

Abstract 2,4-Dinitrophenol was employed with benzyloxy-bis-(diisopropylamino)phosphine to synthesise the cyclic phosphate derivatives of a series of alkane diols (HO–(CH2)n–OH, n=2–6) in good isolated yields. Tetrazole and DNP were compared by 31P NMR spectroscopy for their ability to catalyse the cyclisation at the P(III) stage. Investigation of the phosphate triester stability under various oxidation and chromatographic conditions resulted in the optimisation of the isolation procedures of the chemically unstable cyclic compounds. Conditions for debenzylation were developed to yield the corresponding cyclic phosphodiesters quantitatively. The methodology was further applied to the preparation and isolation of the cyclic phosphate derivative of a carbohydrate.

A novel structural class of photoswitchable oligonucleotide

Directed Michaelis–Arbuzov reactions of support-bound internucleotide O-benzyl- or O-methyl-phosphite triesters with meta-phenylazobenzylamine or alkane-/glycol-linked a,x-diamines were effected in the presence of iodine. The corresponding tritylated phosphoramidate-linked 11-mers were fully deprotected and released from the support under standard conditions and the fast- and slow-diastereoisomers of both the E- and the Z-meta-phenylazobenzyl-appended oligomers were readily resolved by RP-HPLC. The primary amine-functionalised oligonucleotides were either purified, detritylated and then finally treated with Nhydroxysuccinimidyl carboxylic acid ester derivatives of photoswitchable moieties (Route A) or first derivatised and then subsequently purified and detritylated (Route B). This latter route enabled resolution of fast- and slow-isomers of the trityl-on oligomers bearing novel photoswitchable azopyridine or 9-alkoxyanthracene moieties using RP-HPLC, following which the pure diastereoisomers were detritylated and characterised by MALDI-MS.

Speeds of sound and isentropic compressibilities of binary mixtures containing trialkylamines with alkanes and mono-alkylamines at 303.15 and 313.15 K

Isentropic compressibilities ?S, and excess isentropic compressibilities ?SE have been determined from measurements of speeds of sound u and densities ? of 14 binary mixtures of triethylamine (TEA) and tri-n-butylamine (TBA) with n-hexane, n-octane, iso-octane, n-propylamine, n-butylamine, n-hexylamine and n-octylamine. The relative magnitude and sign of ?SE have been interpreted in terms of molecular interactions and interstitial accommodation. The values of ?SE for TEA + alkane are positive while for TBA + alkane are negative. The values of ?SE for TEA + primary amine become progressively less positive and eventually to negative with the increase in chain length of alkylamine. In case of TBA + primary amine, the values of ?SE increase from n-propylamine to n-butylamine, and then decrease with chain length of primary amine. The experimental speeds of sound u have been analyzed in terms of collision factor theory, free length theory and Prigogine–Flory–Patterson statistical theory of solutions.

Hydroisomerisation of n-alkanes over partially reduced MoO3: Promotion by CoAlPO-11 and relations to reaction mechanism and rate-determining step

The reaction mechanism and the rate-determining step (RDS) of the isomerisation of n-alkanes (C-4-C-6) over partially reduced MoO3 catalysts were studied through the effects of the addition of an alkene isomerisation catalyst (i.e. CoAlPO- 11). When an acidic CoAlPO- 11 sample was mechanically mixed with the MoO3, a decrease of the induction period and an increase of the steady-state conversion of n-butane to isobutane were observed. These data support previous assumptions that a bifunctional mechanism occurred over the partially reduced MoO3 (a complex nanoscale mixture of oxide-based phases) during n-butane isomerisation and that the RDS was the skeletal isomerisation of the linear butene intermediates. The only promotional effect of CoAlPO-11 on the activity of partially reduced MoO3 for C-5-C-6 alkane hydroisomerisation was a reduction of the induction period, as the RDS at steady-state conditions appeared to be dehydrogenation of the alkane in this case. However, lower yields of branched isomers were observed in this case, the reason of which is yet unclear. (c) 2005 Elsevier B.V. All rights reserved.

Chymotrypsin-like serine proteinases are involved in the maintenance of cell viability

An increasing number of studies have implicated serine proteinases in the development of apoptosis. In this study, we assessed the ability of a set of highly specific irreversible inhibitors (activity probes), incorporating an a-amino alkane diphenyl phosphonate moiety, to modulate cell death. In an initial assessment of the cellular toxicity of these activity probes, we discovered that one example, N-a-tetramethylrhodamine phenylalanine diphenylphosphonate {TMR-Phe^P(OPh)₂} caused a concentration-dependent decrease in the viability of HeLa and U251 mg cells. This reduced cell viability was associated with a time-dependent increase in caspase-3 activity, PARP cleavage and phosphatidylserine translocation, establishing apoptosis as the mechanism of cell death. SDS-PAGE analysis of cell lysates prepared from the HeLa cells treated with TMR-Phe^P(OPh)₂, revealed the presence of a fluorescent band of molecular weight 58 kDa. Given that we have previously reported on the use of this type of activity probe to reveal active proteolytic species, we believe that we have identified a chymotrypsin-like serine proteinase activity integral to the maintenance of cell viability.

Use of perfluorohexyloctane as a long-term internal tamponade agent in complicated retinal detachment surgery

PURPOSE: To report the use of perfluorohexyloctane, a liquid semifluorinated alkane that is heavier than water, as an internal tamponade agent in surgery for complicated retinal detachments. DESIGN: A consecutive interventional case series from three study centers. METHODS: In 23 consecutive eyes (23 patients, 19 men and four women, mean ± standard deviation (SD) age of 58.5 years ± 16.1) perfluorohexyloctane was used for long-term internal tamponade. Included were eyes with complicated retinal detachment involving the lower two quadrants of the fundus. Excluded were patients with diseases in the fellow eye or severe systemic disease. A pars plana vitrectomy was performed, including membrane peeling and retinotomy where necessary. RESULTS: The mean duration for perfluorohexyloctane being left in situ was 76 days (SD 37.64) (range, 35-202 days). Four weeks following the removal of perfluorohexyloctane 19 of the 23 patients had total reattachment of the retina; three eyes had a recurrence of retinal detachment. One patient was lost to follow-up. The mean follow-up after perfluorohexyloctane removal was 97 days (range, 48 to 169 days). Cataract formation or progression was noted in nine of the 10 eyes. There were two cases with high intraocular pressures. Dispersion into small droplets was observed as early as 3 days postoperatively in three of the 23 patients. At least 12 of the 23 patients had an obvious dispersion by the time of perfluorohexyloctane removal. There was no sign of optic atrophy, retinal necrosis, or retinal vascular occlusion. CONCLUSION: Perfluorohexyloctane was tolerated as a long-term internal tamponade agent without obvious signs of damage to the retina or optic disk. Of all the complications noted, the most common was that of dispersion of the perfluorohexyloctane bubble into droplets. © 2002 by Elsevier Science Inc. All rights reserved.

A spectroscopic study of the chemistry and reactivity of SO2 on Pt{111}: Reactions with O-2, CO and C3H6

The chemisorption and reactivity of SO2 on Pt{111} have been studied by HREELS, XPS, NEXAFS and temperature-programmed desorption. At 160 K SO2 adsorbs intact at high coverages, with eta(2) S-O coordination to the surface. On annealing to 270 K, NEXAFS indicates the SO2 molecular plane essentially perpendicular to the surface. Preadsorbed O-a reacts with SO2 to yield adsorbed SO4, identified as the key surface species responsible for SO2-promoted catalytic alkane oxidation. Coadsorbed CO or propene efficiently reduce SO2 overlayers to deposit S-a, and the implications of this for catalytic systems are discussed.

Solid phase synthesis of Smac/DIABLO-derived peptides using a 'Safety-Catch' resin:Identification of potent XIAP BIR3 antagonists

The N-terminal sequence of the Smac/DIABLO protein is known to be involved in binding to the BIR3 domain of the anti-apoptotic proteins IAPs, antagonizing their action. Short peptides and peptide mimetics based on the first 4-residues of Smac/DIABLO have been demonstrated to re-sensitize resistant cancer cells, over-expressing IAPs, to apoptosis. Based on the well-defined structural basis for this interaction, a small focused library of C-terminal capped Smac/DIABLO-derived peptides was designed in silico using docking to the XIAP BIR3 domain. The top-ranked computational hits were conveniently synthesized employing Solid Phase Synthesis (SPS) on an alkane sulfonamide 'Safety-Catch' resin. This novel approach afforded the rapid synthesis of the target peptide library with high flexibility for the introduction of various C-terminal amide-capping groups. The library members were obtained in high yield (>65%) and purity (>85%), upon nucleophilic release from the activated resin by treatment with various amine nucleophiles. In vitro caspase-9 activity reconstitution assays of the peptides in the presence of the recombinant BIR3-domain of human XIAP (500nM) revealed N-methylalanyl-tertiarybutylglycinyl-4-(R)-phenoxyprolyl-N-biphenylmethyl carboxamide (11a) to be the most potent XIAP BIR3 antagonist of the series synthesized inducing 93% recovery of caspase-9 activity, when used at 1µM concentration. Compound (11a) also demonstrated moderate cytotoxicity against the breast cancer cell lines MDA-MB-231 and MCF-7, compared to the Smac/DIABLO-derived wild-type peptide sequences that were totally inactive in the same cell lines.

Arene cis-Diol Dehydrogenase-Catalysed Regio- and Stereoselective Oxidation of Arene-, Cycloalkane- and Cycloalkene-cis-diols to Yield Catechols and Chiral α-Ketols

Benzene cis-diol dehydrogenase and naphthalene cis-diol dehydrogenase enzymes, expressed in Pseudomonas putida wild-type and Escherichia coli recombinant strains, were used to investigate regioselectivity and stereoselectivity during dehydrogenations of arene, cyclic alkane and cyclic alkene vicinal cis-diols. The dehydrogenase-catalysed production of enantiopure cis-diols, α-ketols and catechols, using benzene cis-diol dehydrogenase and naphthalene cis-diol dehydrogenase, involved both kinetic resolution and asymmetric synthesis methods. The chemoenzymatic production and applications of catechol bioproducts in synthesis were investigated.