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.

A first principles study of methanol decomposition on Pd(111): Mechanisms for O-H bond scission and C-O bond scission

There is some dispute as to whether methanol decomposition occurs by O-H bond scission or C-O bond scission. By carrying out density functional theory calculations, we investigate both scenario of the reaction pathways of methanol decomposition on a Pd(111) surface. It is shown that the O-H bond scission pathway is much more energetically favorable than the C-O bond scission pathway. The high reaction barrier in the latter case is found to be due to the poor bonding abilities of CH3 and OH with the surface at the reaction sites. (C) 2001 American Institute of Physics.

Insight into electron-mediated reaction mechanisms: Catalytic CO oxidation on a ruthenium surface

Ruthenium is one of the poorest catalysts for CO oxidation under normal conditions (low or medium O coverage and normal temperature). However, a recent study [Science 285, 1042 (1999)] reveals that, under femtosecond laser irradiation, CO2 can be formed on the Ru surface, and the reaction follows an electron-mediated mechanism. We carried out density functional theory calculations to investigate CO oxidation via an electron-mediated mechanism on Ru(0001). By comparison to the reaction under normal conditions, following features emerge in the electron-mediated mechanism: (i) more reaction channels are open; (ii) the reaction barrier is significantly lowered. The physical origins for these novel features have been analyzed. (C) 2001 American Institute of Physics.

On the need to use steady-state or operando techniques to investigate reaction mechanisms: An in situ DRIFTS and SSITKA-based study example

The nature of the surface species formed at the surface of 2 wt.% Pt/CeO2 catalyst during the forward water-gas-shift (WGS, CO + H2O -> CO2 + H-2) and the reverse reaction (RWGS) were essentially identical. More, the surface concentration of formate, carbonate and carbonyl species was similar in each case. The presence of well-resolved IR bands allowed an unequivocal relative quantitative analysis of each species, avoiding the use of the carboxylate stretching region (1600-1200 cm(-1)). However, the quantitative analysis in the case of an isotopic study was complicated due to the overlapping of the various isotope bands, yet this problem could be overcome by integrating the high-wavenumber part of the bands. The reactivity of the surface species formed under RWGS conditions was followed under two different gaseous streams. Firstly, the reactivity of these intermediates were followed under an inert gas (i.e., At), in which case carbonates were essentially stable and less reactive than formates. Secondly, the reactivity of the same surface species was followed when switching to the corresponding C-13-labelled feed (i.e., (CO2)-C-13 + H-2), in which case carbonates were exchanged significantly faster than formates. While carbonates species have been reported as reaction intermediate under reaction conditions, the increased stability or surface poisoning by these carbonates in the absence of reaction mixture was highlighted. Ultimately, this work re-emphasises the need to use steady-state conditions if the true operando reactivity of the adsorbates and structure of the solid are to be determined. (c) 2005 Elsevier B.V. All rights reserved.

The investigation of mechanisms in environmental catalysis using time-resolved methods

The formation of nitrogen oxides (NOx) during a combustion process is difficult to avoid because of the large exotherm and the consequent problem of avoiding local high-temperature spikes. Consequently, for many applications, such as for automotive power generation, there will be a continuing need to use catalytic after-treatment to reduce harmful emissions. The investigation of the mechanisms of the key catalytic reactions in environmental catalysis can provide an insight into the action of the catalyst, and time-resolved methods offer a powerful means to study these processes under realistic conditions. The use of Temporal Analysis of Products (TAP) and Steady State Isotopic Transient Kinetic Analysis (SSITKA) methods to investigate the reduction of NOx under various experimental conditions is described. From a detailed analysis of the SSITKA profiles, it is shown that at low temperatures the mechanism for the formation of N-2 and N2O from NO may differ from the conventional high-temperature mechanism. This is supported by density functional theory calculations, which show that the barrier to the formation of N2O from the reaction of N(ads) and NO(ads) may be too high to allow this process to occur at low temperatures. The alternative reaction of NO(ads) + NO(ads) = N2O(g) + O(ads) is shown to be much more favorable and is consistent with the SSITKA analysis. The remarkable effect of hydrogen as a reductant at low temperatures is described, and alternative interpretations of the role of hydrogen are discussed.

The removal of dyes from textile wastewater: a study of the physical characteristics and adsorption mechanisms of diatomaceous earth

The feasibility of using diatomite for the removal of the problematic reactive dyes as well as basic dyes from textile wastewater was investigated. Methylene blue, Cibacron reactive black and reactive yellow dyes were considered. Physical characteristics of diatomite such as pH(solution), pH(ZPC), surface area, Fourier transform infrared, and scanning electron microscopy were investigated. The surface area of diatomite was found to be 27.80 m(2) g(-1) and the pH(ZPC) occurred around pH of 5.4. The results indicated that the surface charge of diatomite decreased as the pH of the solution increased with the maximum methylene blue removal from aqueous solution occurring at basic pH of around (1011). Adsorption isotherms of diatomite with methylene blue, hydrolysed reactive black and yellow dyes were constructed at different pH values, initial dye concentrations and particle sizes. The experimental results were fitted to the Langmuir, Freundlich, and Henry models. The study indicated that electrostatic interactions play an important role in the adsorption of dyes onto diatomite. A model of the adsorption mechanism of methylene blue onto diatomite is proposed. (C) 2003 Elsevier Ltd. All rights reserved.

Resistance mechanisms to cancer chemotherapy

Resistance to chemotherapy ('drug resistance') is a fundamental problem that limits the effectiveness of many chemotherapies currently used to treat cancer. Drug resistance can occur due to a variety of mechanisms, such as increased drug inactivation, drug efflux from cancer cells, enhanced repair of chemotherapy-induced damage, activation of pro-survival pathways and inactivation of cell death pathways. In this article, we review some of the major mechanisms of drug resistance and discuss how new molecularly-targeted therapies are being increasingly used to overcome these resistance mechanisms.

HOX genes: seductive science, mysterious mechanisms

HOX genes are evolutionarily highly conserved. The HOX proteins which they encode are master regulators of embryonic development and continue to be expressed throughout postnatal life. The 39 human HOX genes are located in four clusters (A-D) on different chromosomes at 7p15, 17q21 [corrected] 12q13, and 2q31 respectively and are assumed to have arisen by duplication and divergence from a primordial homeobox gene. Disorders of limb formation, such as hand-foot-genital syndrome, have been traced to mutations in HOXA13 and HOXD13. Evolutionary conservation provides unlimited scope for experimental investigation of the functional control of the Hox gene network which is providing important insights into human disease. Chromosomal translocations involving the MLL gene, the human homologue of the Drosophila gene trithorax, create fusion genes which exhibit gain of function and are associated with aggressive leukaemias in both adults and children. To date 39 partner genes for MLL have been cloned from patients with leukaemia. Models based on specific translocations of MLL and individual HOX genes are now the subject of intense research aimed at understanding the molecular programs involved, and ultimately the design of chemotherapeutic agents for leukaemia. Investigation of the role of HOX genes in cancer has led to the concept that oncology may recapitulate ontology, a challenging postulate for experimentalists in view of the functional redundancy implicit in the HOX gene network.

Mechanisms and chemistry of dye adsorption on manganese oxides-modified diatomite

The investigations into structural changes which occur during adsorbent modification and the adsorption mechanisms are essential for an effective design of adsorption systems. Manganese oxides were impregnated onto diatomite to form the type known as delta-birnessite. Initial investigations established the effectiveness of manganese oxides-modified diatomite (MOMD) to remove basic and reactive dyes from aqueous solution. The adsorption capacity of MOMD for methylene blue (MB), hydrolysed reactive black (RB) and hydrolysed reactive yellow (RY) was 320, 419, and 204 mg/g, respectively. Various analytical techniques were used to characterise the structure and the mechanisms of the dye adsorption process onto MOMD such as Fourier transform infrared (FTIR), X-ray diffraction (XRD) and atomic absorption spectrometry (A.A.). A small shift to higher values of the cl-spacing of dye/MOMD was observed indicating that a small amount of the dye molecules were intercalated in the MOMD structure and other molecules were adsorbed on the external surface of MOMD. Two mechanisms of dye adsorption onto MOMD were proposed; intercalation of the dye in the octahedral layers and adsorption of the dye on the MOMD external surface. Moreover, the results demonstrated that the MOMD structure was changed upon insertion of MB and RY with an obvious decrease in the intensity of the second main peak of the MOMD X-ray pattern. (C) 2009 Elsevier Ltd. All rights reserved.

Monkey and humans exhibit similar motion-processing mechanisms

Single cell recording studies have resulted in a detailed understanding of motion-sensitive neurons in non-human primate visual cortex. However, it is not known to what extent response properties of motion-sensitive neurons in the non-human primate brain mirror response characteristics of motion-sensitive neurons in the human brain. Using a motion adaptation paradigm, the direction aftereffect, we show that changes in the activity of human motion-sensitive neurons to moving dot patterns that differ in dot density bear a strong resemblance to data from macaque monkey. We also show a division-like inhibition between neural populations tuned to opposite directions, which also mirrors neural-inhibitory behaviour in macaque. These findings strongly suggest that motion-sensitive neurons in human and non-human primates share common response and inhibitory characteristics.