Tunability of monodispersed intermetallic AuCu nanoparticles through understanding of reaction pathways

Synthesis of size selective monodispersed nanoparticles particularly intermetallic with well-defined compositions represents a challenge. This paper presents a way for the synthesis of intermetallic AuCu nanoparticles as a model system. We show that reduction of Au and Cu precursors is sensitive to the ratio of total molar concentrations of surfactant to metal precursors. A careful design of experiments to understand the kinetics of the reduction process reveals initial formation of seed nanoparticles of pure Au. Reduction of Cu occurs on the surface of the seed followed by diffusion to yield AuCu. This understanding allows us to develop a two step synthesis where the precise size controlled seed of Au nanoparticles produced in the first step is used in the second step reaction mixture as an Au precursor to allow deposition and interdiffusion of Cu that yields size selected AuCu intermetallics of sub 10 nm sizes.

Design and analysis of nucleic acid reaction pathways

Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.

CO oxidation on Pd(100) and Pd(111): A comparative study of reaction pathways and reactivity at low and medium coverages

We have performed density functional theory calculations with the generalized gradient approximation to investigate CO oxidation on a close-packed transition metal surface, Pd(lll), and a more open surface, Pd(100), aiming to shed light on surface structure effects on reaction pathways and reactivity, an important issue in catalysis. Reaction pathways on both surfaces at two different coverages have been studied. It is found that the reaction pathways on both surfaces possess crucial common features despite the fact that they have different surface symmetries. Having determined reaction barriers in these systems, we find that the reaction on Pd(lll) is strongly coverage dependent. Surface coverages, however, have little effect on the reaction on Pd(100). Calculations also reveal that the low coverage reactions are structure sensitive while the medium coverage reactions are not. Detailed discussions on these results are given.

Formation and decomposition of N-alkyinaphthalimides: experimental evidences and ab initio description of the reaction pathways

The kinetics of hydrolysis of 1,8-N-butyl-naphthalimide (1,8-NBN) to 1,8-N-butyl-naphthalamide (1,8-NBAmide) and of 2,3-N-butyl-naphthalimide (2,3-NBN) to 2,3-N-butyl-naphthalamide (2,3-NBAmide), as well as the formation of the respective anhydrides from the amides were investigated in a wide acidity range. 1,8-NBN equilibrates with 1,8-NBAmide in mild alkali. Under the same conditions 2,3-NBN quantitatively yields 2,3-NBAmide. Over a wide range of acidities the reactions of the 1,8- and 2,3-N-butyl-naphthalamides (or imides) yield similar products but with widely different rates and at distinct pH`s. Anhydride formation in acid was demonstrated for 1,8-NBAmide. The reactions mechanisms were rationalized in the manifold pathways of ab initio calculations. The differences in rates and pH ranges in the reactions of the 1,8- and 2,3-N-butyl-naphthalamides were attributed to differences in the stability of the tetrahedral intermediates in alkali as well as the relative stabilities of the five and six-membered ring intermediates. The rate of carboxylic acid assisted 1,8-N-Butyl-naphthalamide hydrolysis is one of the largest described for amide hydrolysis models. Copyright (C) 2010 John Wiley & Sons, Ltd.

Reaction pathways in the solid state synthesis of multiferroic BiFeO 3

The obtaining of multiferroicBiFeO3 as a pure single-phase product is particularly complex since the formation of secondary phases seems to be unavoidable. The process by which these secondary impurities are formed is studied by analyzing the diffusion and solidstate reactivity of the Bi2O3–Fe2O3 system. Experimental evidence is reported which indicates that the progressive diffusion of Bi3+ ions into the Fe2O3 particles governs the solidstatesynthesis of the perovskite BiFeO3 phase. However a competition is established between the diffusion process which tends to complete the formation of BiFeO3, and the crystallization of stable Bi2Fe4O9 mullite crystals, which tend to block that formation reaction.

Reaction pathways in the solid state synthesis of multiferroic BiFeO3

The obtaining of multiferroic BiFeO3 as a pure single-phase product is particularly complex since the formation of secondary phases seems to be unavoidable. The process by which these secondary impurities are formed is studied by analyzing the diffusion and solid state reactivity of the Bi2O3?Fe2O3 system. Experimental evidence is reported which indicates that the progressive diffusion of Bi3+ ions into the Fe2O3 particles governs the solid state synthesis of the perovskite BiFeO3 phase. However a competition is established between the diffusion process which tends to complete the formation of BiFeO3, and the crystallization of stable Bi2Fe4O9 mullite crystals, which tend to block that formation reaction.

Continuous flow nanocatalysis: reaction pathways in the conversion of levulinic acid to valuable chemicals

The selective production of 2-methyltetrahydrofuran from levulinic acid has been effectively conducted using designed Cu based catalysts and compared with a commercial Pd/C system under microwave irradiation. Optimised conditions for the most active catalysts Cu-MINT (>90% conversion, 75% selectivity to MTHF) and Pd/C (78% conversion, 92% selectivity to MTHF) were further translated into a continuous flow process using the proposed catalysts to find out the deactivation of Cu-MINT under flow conditions (79 vs. 13% conversion with a switch in selectivity to products after 30 min in flow), the high stability of Pd/C (73 vs. 70% conversion at stable selectivity under analogous conditions to those of Cu-MINT) but, most importantly, different relevant pathways to valuable products from levulinic acid depending on the type of catalyst employed.

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

Reaction of La2CuO4 with binary metal oxides in the solid state: Metathesis, addition, and redox metathesis pathways

Investigation of the reaction of La2CuO4 with several binary metal oxides in the solid state at elevated temperatures has revealed three different reaction pathways. Reaction of La2CuO4 with strongly acidic oxides such as Re2O7, MoO3, and V2O5 follows a metathesis route, yielding a mixture of products: La3ReO8/La2MoO6/LaVO4 and CuO. Oxides such as TiO2, MnO2, and RuO2 which are not so acidic yield addition products: La2CuMO6 (M = Ti, Mn, Ru). SnO2 is a special case which appears to follow a metathesis route, giving La2Sn2O7 pyrochlore and CuO, which on prolonged reaction transform to the layered perovskite La2CuSnO6. The reaction of La2CuO4 with lower valence oxides VO2 and MoO2, on the other hand, follows a novel redox metathesis route, yielding a mixture of LaVO4/LaCuO2 and La2MoO6/Cu, respectively. This result indicates that it is the redox reactivity involving V-IV + Cu-II --> V-V + Cu-I and Mo-IV + Cu-II --> Mo-VI + Cu-0, and not the acidity of the binary oxide, that controls the nature of the products formed in these cases. The general significance of these results toward the synthesis of complex metal oxides containing several metal atoms is discussed.

The surface-structure sensitivity of dioxygen activation in the anatase-photocatalyzed oxidation reaction

The reaction pathways by which oxygen is incorporated into the substrate in the photocatalytic oxidation of terephthalic acid (TPTA) are vastly different on {001} and {101} facets of an anatase single crystal. This was established by controlling the percentage of {101} and {001} facets, isotopically tracing the origins of the hydroxy group, and studying dioxygen consumption and variance in the concentration of hydroxylation intermediate.

The repertoire of nitrogen assimilation in Rhodococcus: Catalysis, pathways and relevance in biotechnology and bioremediation

The Rhodococcus genus exhibits diverse enzymatic activity that can be exploited in the conversion of natural and anthropogenic nitrogenous compounds. This catalytic response provides a selective advantage in terms of available nutrients while also serving to remove otherwise harmful xenobiotics. This review provides a critical assessment of the literature on bioconversion of organo-nitrogen compounds with a consideration of applications in bioremediation and commercial biotechnology. By examining the major nitro-organic compounds (amino acids, amines, nitriles, amides and nitroaromatics) in turn, the considerable repertoire of Rhodococcus spp. is established. The available published enzyme reaction data is coupled with genomic characterisation to provide a molecular basis for Rhodococcus enzyme activity with an assessment of the cellular properties that aid substrate accessibility and ensure stability. The metabolic gene clusters associated with the observed reaction pathways are identified and future directions in enzyme optimisation and metabolic engineering are assessed. © 2014 Society of Chemical Industry.

Theoretical studies on the reaction mechanism of oxidation of primary alcohols by Zn/Cu(II)-phenoxyl radical catalyst

The catalytic mechanism for the oxidation of primary alcohols catalyzed by the two functional models of galactose oxidase (GOase), M-II L (M = Cu, Zn; L = N,N'-bis(3,5-di-tert-butyl-2-hydroxyphenyl)1-2-diiminoquinone)), has been studied by use of the density functional method B3LYP The catalytic cycle of Cu- and Zn-catalysts consists of two parts, namely, substrate oxidation (primary alcohol oxidation) and O-2 reduction (catalyst regeneration). The catalytic mechanisms have been studied for the two reaction pathways (route 1 and route 2). The calculations indicate that the hydrogen atom transfer within the substrate oxidation part is the rate-determining step for both catalysts, in agreement with the experimental observation.

Theoretical study on the mechanism for the addition reaction of SiH3 with propylene and acetic acid

To explore the reactivities of alkene (-CH=CH2) and carboxy (-COOH) group with H-Si under UV irradiation, the addition mechanism for the reactions of SiH3 radical with propylene and acetic acid was studied by using the B3LYP/6-311++ G(d,p) method. Based on the surface energy profiles, the dominant reaction pathways can be established; i.e., SiH3 adds to the terminal carbon atom of the alkene (-CH=CH2) to form an anti-Markovnikov addition product, or adds to the oxygen atom of the carboxy group (-COOH) to form silyl acetate (CH3-COOSiH3). Because the barrier in the reaction of the carboxy group (39.9 kJ/ mol) is much larger than that of alkene (11.97 kJ/mol), we conclude that the reaction of bifunctional molecules (e.g., omega-alkenoic acid) with H-Si under irradiation condition is highly selective; i.e., the alkene group (-CH= CH2) reacts with SiH3 substantially faster than the carboxyl group (-COOH), which agrees well with the experimental results. This provides the possibility of preparing carboxy-terminated monolayers on silicon surface from omega-alkenoic acids via direct photochemical reaction.

General rules for predicting where a catalytic reaction should occur on metal surfaces: A density functional theory study of C-H and C-O bond breaking/making on flat, stepped, and kinked metal surfaces

To predict where a catalytic reaction should occur is a fundamental issue scientifically. Technologically, it is also important because it can facilitate the catalyst's design. However, to date, the understanding of this issue is rather limited. In this work, two types of reactions, CH4 CH3 + H and CO C + 0 on two transition metal surfaces, were chosen as model systems aiming to address in general where a catalytic reaction should occur. The dissociations of CH4 - CH3 + H and CO --> C + O and their reverse reactions on flat, stepped, and kinked Rh and Pd surfaces were studied in detail. We find the following: First, for the CH4 Ch(3) + H reaction, the dissociation barrier is reduced by similar to0.3 eV on steps and kinks as compared to that on flat surfaces. On the other hand, there is essentially no difference in barrier for the association reaction of CH3 + H on the flat surfaces and the defects. Second, for the CO C + 0 reaction, the dissociation barrier decreases dramatically (more than 0.8 eV on Rh and Pd) on steps and kinks as compared to that on flat surfaces. In contrast to the CH3 + H reaction, the C + 0 association reaction also preferentially occurs on steps and kinks. We also present a detailed analysis of the reaction barriers in which each barrier is decomposed quantitatively into a local electronic effect and a geometrical effect. Our DFT calculations show that surface defects such as steps and kinks can largely facilitate bond breaking, while whether the surface defects could promote bond formation depends on the individual reaction as well as the particular metal. The physical origin of these trends is identified and discussed. On the basis of our results, we arrive at some simple rules with respect to where a reaction should occur: (i) defects such as steps are always favored for dissociation reactions as compared to flat surfaces; and (ii) the reaction site of the association reactions is largely related to the magnitude of the bonding competition effect, which is determined by the reactant and metal valency. Reactions with high valency reactants are more likely to occur on defects (more structure-sensitive), as compared to reactions with low valency reactants. Moreover, the reactions on late transition metals are more likely to proceed on defects than those on the early transition metals.