A DFT study of the chain growth probability in Fischer-Tropsch synthesis

The chain growth probability (alpha value) is one of the most significant parameters in Fischer-Tropsch (FT) synthesis. To gain insight into the chain growth probability, we systematically studied the hydrogenation and C-C coupling reactions with different chain lengths on the stepped Co(0001) surface using density functional theory calculations. Our findings elucidate the relationship between the barriers of these elementary reactions and the chain length. Moreover, we derived a general expression of the chain growth probability and investigated the behavior of the alpha value observed experimentally. The high methane yield results from the lower chain growth rate for C-1 + C-1 coupling compared with the other coupling reactions. After C-1, the deviation of product distribution in FT synthesis from the Anderson-Schulz-Flory distribution is due to the chain length-dependent paraffin/olefin ratio. (C) 2008 Elsevier Inc. All rights reserved.

Chain growth mechanism in Fischer-Tropsch synthesis: A DFT study of C-C coupling over Ru, Fe, Rh, and Re surfaces

A quantitative approach is used to understand the chain growth mechanism in FT synthesis on the Ru, Fe, Rh, and Re surfaces. The C-C coupling reactions are extensively calculated on the stepped metal surfaces. Combining the coupling barriers and reactant stabilities, we investigate the reaction rates of all possible C, + C-1 coupling pathways on the metal surfaces. It is found that (i) all the transition-state structures are similar on these surfaces, while some coupling barriers are very different; (ii) the dominant chain growth pathways on these surfaces are different: C + CH and CH + CH on Rh and Ru surfaces, C + CH3 on Fe surface, and C + CH on Re surface. The common features of the major coupling reactions together with those on the Co surface are also discussed.

Density functional study of reactions of phenoxides with polycarbonate

Density functional calculations with simulated annealing have been used to study the reactions of chains of bisphenol A polycarbonate (BPA-PC) with sodium phenoxide (NaOPh), diphenyl carbonate (DPC), and tetraphenylphosphonium phenoxide (PPh4OPh). These calculations extend our work on the reactions of LiOPh, NaOPh, and phenol with the cyclic tetramer of BPA-PC. We study, in particular, chain growth catalyzed by NaOPh and PPh4OH. The energy barriers for reactions with PPh4OPh are somewhat larger than those involving LiOPh and NaOPh, but they are significantly lower than those involving phenol (HOPh), due in part to the collective rearrangement of phenyl groups in the reacting molecules. We discuss in the Appendix the bonds between alkali metal atoms (Na in the present calculations) and other atoms (here oxygen) that are analogous to the more familiar "hydrogen bonds".

A quantitative determination of reaction mechanisms from density functional theory calculations: Fischer-Tropsch synthesis on flat and stepped cobalt surfaces

We systematically investigated the mechanism of the C-1 + C-1 coupling reactions using density functional theory. The activation energies of C-1 + C-1 coupling and carbon hydrogenation reactions on both flat and stepped surfaces were calculated and analyzed. Moreover, the coverages of adsorbed C-1 species were estimated, and the reaction rates of all possible C-1 + C-1 coupling pathways were quantitatively evaluated. The results suggest that the reactions of CH2 + CH2 and CH3 + C at steps are most likely to be the key C-1 + C-1 coupling steps in FT synthesis on Co catalysts. The reactions of C-2 + C-1 and C-3 + C-1 coupling also were studied; the results demonstrate that in addition to the pathways of RCH + CH2 and RCH2 + C, the coupling of RC + C and RC + CH also may contribute to the chain growth after C-1. (C) 2008 Elsevier Inc. All rights reserved.

First-principles study of oxygenates on Co surfaces in Fischer-Tropsch synthesis

Extensive density function theory calculations are performed to study the mechanism of the formation of aldehyde and alcohol on Co surfaces in Fischer-Tropsch synthesis, a challenging issue in heterogeneous catalysis. Three possible pathways for the production of formaldehyde and methanol on flat and stepped Co(0001) surfaces are investigated: (i) CO + 4H -> CHO + 3H -> CH2O + 2H -> CH3O + H -> CH3OH; (ii) CO + 4H -> COH + 3H -> CHOH + 2H -> CH2OH + H -> CH3OH; and (iii) the coupling reactions of CH2 + O -> CH2O and CH3 + OH -> CH3OH. It is found that these pathways are generally favored at step sites, and the preferred mechanism is pathway (i) via CHO. Furthermore, the three traditional chain growth mechanisms in Fischer-Tropsch synthesis are semi quantitatively compared and discussed. Our results suggest that the two mechanisms involving oxygenate intermediates (the CO-insertion and hydroxycarbene mechanisms) are less important than the carbene mechanism in the production of long chain hydrocarbons. However, the CO-insertion mechanism may be responsible for the production of long-chain oxygenates.

Some Understanding of Fischer-Tropsch Synthesis from Density Functional Theory Calculations

The combination of density functional theory (DFT) calculations and kinetic analyses is a very useful approach to study surface reactions in heterogeneous catalysis. The present paper reviews some recent work applying this approach to Fischer-Tropsch (FT) synthesis. Emphasis is placed on the following fundamental issues in FT synthesis: (i) reactive sites for both hydrogenation and C-C coupling reactions; (ii) reaction mechanisms including carbene mechanism, CO-insertion mechanism and hydroxyl-carbene mechanism; (iii) selectivity with a focus on CH(4) selectivity, alpha-olefin selectivity and chain growth probability; and (iv) activity.

Density Functional Theory Study of Iron and Cobalt Carbides for Fischer-Tropsch Synthesis

Carbides are important phases in heterogeneous catalysis. However, the understanding of carbide phases is inadequate: Fe and Co are the two commercial catalysts for Fischer-Tropsch (FT) synthesis, and experimental work showed that Fe carbide is the active phase in FT synthesis, whereas the appearance of Co carbide is considered as a possible deactivation cause, TO understand very different catalytic roles of carbides, all the key elementary steps in FT synthesis, that is, CO dissociation, C(1) hydrogenation, and C(1)+C(1) coupling, are extensively investigated on both carbide surfaces using first principles calculations. In particular, the most important issues in FT synthesis, the activity and methane selectivity, on the carbide surfaces are quantitatively determined and analyzed. They are also discussed together with metallic Fe and Co surfaces. It is found that (i) Fe carbide is more active than metallic Fe and has similar methane selectivity to Fe, being consistent with the experiments; and (ii) Co carbide is less active than Co and has higher methane selectivity, providing evidence on the molecular level to support the suggestion that the formation of Co carbide is a cause of relatively high methane selectivity and deactivation on Co catalysts.

An Energy Descriptor To Quantify Methane Selectivity in Fischer-Tropsch Synthesis:A Density Functional Theory Study

Selectivity is a fundamental issue in heterogeneous catalysis. In this study, the CH(4) selectivity in Fischer-Tropsch synthesis is chosen to be investigated: CH4 selectivity on Rh, Co, Ru, Fe, and Re surfaces is computed by first-principles methods. In conjunction with kinetic analyses, we are able to derive the effective barrier difference between methane formation and chain growth (Delta E(eff)) to quantify the CH(4) selectivity. By using this energy descriptor, the ranking of methane selectivity predicted from density functional theory (DFT) calculations is consistent with experimental work. Moreover, a linear correlation between Delta E(eff) and the chemisorption energy of C + 4H (Delta H) is found. This fundamental finding possesses the following significance: (i) it shows that the selectivity, which appears to have kinetic characteristics, is largely determined by thermodynamic properties; and (ii) it suggests that an increase of the binding strength of C + 4H will suppress methane selectivity.

Growth-phase regulation of lipopolysaccharide O-antigen chain length influences serum resistance in serovars of Salmonella

The amount of lipopolysaccharide (LPS) O antigen (OAg) and its chain length distribution are important factors that protect bacteria from serum complement. Salmonella enterica serovar Typhi produces LPS with long chain length distribution (L-OAg) controlled by the wzz gene, whereas serovar Typhimurium produces LPS with two OAg chain lengths: an L-OAg controlled by Wzz(ST) and a very long (VL) OAg determined by Wzz(fepE). This study shows that serovar Enteritidis also has a bimodal OAg distribution with two preferred OAg chain lengths similar to serovar Typhimurium. It was reported previously that OAg production by S. Typhi increases at the late exponential and stationary phases of growth. The results of this study demonstrate that increased amounts of L-OAg produced by S. Typhi grown to stationary phase confer higher levels of bacterial resistance to human serum. Production of OAg by serovars Typhimurium and Enteritidis was also under growth-phase-dependent regulation; however, while the total amount of OAg increased during growth, the VL-OAg distribution remained constant. The VL-OAg distribution was primarily responsible for complement resistance, protecting the non-typhoidal serovars from the lytic action of serum irrespective of the growth phase. As a result, the non-typhoidal species were significantly more resistant than S. Typhi to human serum. When S. Typhi was transformed with a multicopy plasmid containing the S. Typhimurium wzz(fepE) gene, resistance to serum increased to levels comparable to the non-typhoidal serovars. In contrast to the relevant role for high-molecular-mass OAg molecules, the presence of Vi antigen did not contribute to serum resistance of clinical isolates of serovar Typhi.

O-antigen modal chain length in Shigella flexneri 2a is growth-regulated through RfaH-mediated transcriptional control of the wzy gene

Shigella flexneri 2a 2457T produces lipopolysaccharide (LPS) with two O-antigen (OAg) chain lengths: a short (S-OAg) controlled by WzzB and a very long (VL-OAg) determined by Wzz(pHS-2). This study demonstrates that the synthesis and length distribution of the S. flexneri OAg are under growth-phase-dependent regulation. Quantitative electrophoretic analysis showed that the VL-OAg increased during growth while the S-OAg distribution remained constant. Increased production of VL-OAg correlated with the growth-phase-regulated expression of the transcription elongation factor RfaH, and was severely impaired in a DeltarfaH mutant, which synthesized only low-molecular-mass OAg molecules and a small amount of S-OAg. Real-time RT-PCR revealed a drastic reduction of wzy polymerase gene expression in the DeltarfaH mutant. Complementation of this mutant with the wzy gene cloned into a high-copy-number plasmid restored the bimodal OAg distribution, suggesting that cellular levels of Wzy influence not only OAg polymerization but also chain-length distribution. Accordingly, overexpression of wzy in the wild-type strain resulted in production of a large amount of high-molecular-mass OAg molecules. An increased dosage of either wzzB or wzz(pHS-2) also altered OAg chain-length distribution. Transcription of wzzB and wzz(pHS-2) genes was regulated during bacterial growth but in an RfaH-independent manner. Overall, these findings indicate that expression of the wzy, wzzB and wzz(pHS-2) genes is finely regulated to determine an appropriate balance between the proteins responsible for polymerization and chain-length distribution of S. flexneri OAg.

C/EBP alpha Is Up-regulated in a Subset of Hepatocellular Carcinomas and Plays a Role in Cell Growth and Proliferation

BACKGROUND & AIMS: C/EBP alpha (cebpa) is a putative tumor suppressor. However, initial results indicated that cebpa was up-regulated in a subset of human hepatocellular carcinomas (HCCs). The regulation and function of C/EBP alpha was investigated in HCC cell lines to clarify its role in liver carcinogenesis. METHODS: The regulation of C/EBP alpha expression was studied by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), Western blotting, immunohistochemistry, methylation-specific PCR, and chromatin immunoprecipitation assays. C/EBP alpha expression was knocked-down by small interfering RNA or short hairpin RNA. Functional assays included colony formation, methylthiotetrazole, bromodeoxyuridine incorporation, and luciferase-reporter assays. RESULTS: Cebpa was up-regulated at least 2-fold in a subset (approximately 55%) of human HCCs compared with adjacent non tumor tissues. None of the up-regulated samples were positive for hepatitis C infection. The HCC cell lines Hep3B and Huh7 expressed high, PLC/PRF/5 intermediate, HepG2 and HCC-M low levels of C/EBP alpha, recapitulating the pattern of expression observed in HCCs. No mutations were detected in the CEBP alpha gene in HCCs and cell lines. C/EBP alpha was localized to the nucleus and functional in Hep3B and Huh7 cells; knocking-down its expression reduced target-gene expression, colony formation, and cell growth, associated with a decrease in cyclin A and CDK4 concentrations and E2F transcriptional activity. Epigenetic mechanisms including DNA methylation, and the binding of acetylated histone H3 to the CEBP alpha promoter-regulated cebpa expression in the HCC cells. CONCLUSIONS: C/EBP alpha is up-regulated in a subset of HCCs and has growth-promoting activities in HCC cells. Novel oncogenic mechanisms involving C/EBP alpha may be amenable to epigenetic regulation to improve treatment outcomes.

Long-chain haloalkanes are incorporated into fatty-acids by Rhodococcus rhodochrous NCIMB-13064

The fatty acid composition of the cellular lipids of Rhodococcus rhodochrous NCIMB 13064 grown on various long-chain haloalkanes has been investigated and the influence of halogen substituents, carbon chain length and the position of halogen substitution in the growth substrate explored. Of the total fatty acids present in cells grown on 1-chloro-, 1-bromo- and 1-iodohexadecane, 75, 90 and 81%, respectively, were substituted in the omega-position by the corresponding halogen but only 1% of the fatty acids present after growth on 1-fluorotetradecane were fluorinated in this position. The extent of the halofatty acid incorporation with different halogen substituents in the growth substrate appears to reflect the degree to which oxygenase attack is restricted to the non-halogenated end of the haloalkane. Studies of the fatty acid composition of cells after growth on a series of 1-chloroalkanes containing an even number of carbon atoms between C-10 and C-18 indicated chlorofatty acid incorporation from C-12 to C-18 substrates at levels ranging from 21% with C-12 to 75% with C-16. The chlorofatty acids formed by initial oxidation of the chloroalkane were chain-lengthened or chain-shortened by from two to eight carbon atoms, with accompanying desaturation in some instances. Substantial quantities of a methyl-branched C-19:0 chlorofatty acid were also present with several chloroalkane substrates, When the fatty acid composition of cells after growth on 1-bromoalkanes containing an odd number of carbon atoms between C-11 and C-17 was examined, the incorporation of bromofatty acids was observed with C-13, C-15 and C-17 substrates; a maximum of 76% was recorded for the C-15 bromoalkane. As with even chain-length chloroalkanes, both chain-lengthening and -shortening occurred predominantly via two-carbon units so that most bromoacids present possessed an odd number of carbon atoms, When 1-bromododecane or 2-bromododecane were substrates, overall incorporations of bromofatty acids into the lipid fraction were very similar, demonstrating that the position of halogen substitution in the haloalkane was not critical in determining the extent of incorporation of the haloacids into cellular lipids. The results of the study indicate a mechanism by which degradation products of chlorinated paraffins could enter the biological food chain.

Elevated NRD1 metalloprotease expression plays a role in breast cancer growth and proliferation

Understanding the molecular etiology of cancer and increasing the number of drugs and their targets are critical to cancer management. In our attempt to unravel novel breast-cancer associated proteins, we previously conducted protein expression profiling of the MCF10AT model, which comprises a series of isogenic cell lines that mimic different stages of breast cancer progression. NRD1 expression was found to increase during breast cancer progression. Here, we attempted to confirm the relevance of NRD1 in clinical breast cancer and understand the functional role and mechanism of NRD1 in breast cancer cells. Immunohistochemistry data show that NRD1 expression was elevated in ductal carcinoma in situ and invasive ductal carcinomas compared with normal tissues in 30% of the 26 matched cases studied. Examination of NRD1 expression in tissue microarray comprising >100 carcinomas and subsequent correlation with clinical data revealed that NRD1 expression was significantly associated with tumor size, grade, and nodal status (P <0.05). Silencing of NRD1 reduced MCF10CA1h and MDA-MD-231 breast-cancer-cell proliferation and growth. Probing the oncogenic EGF signaling pathways revealed that NRD1 knock down did not affect overall downstream tyrosine phosphorylation cascades including AKT and MAPK activation. Instead, silencing of NRD1 resulted in a reduction of overall cyclin D1 expression, a reduction of EGF-induced increase in cyclin D1 expression and an increase in apoptotic cell population compared with control cells.