Finding branched pathways in metabolic network via atom group tracking

Finding non-standard or new metabolic pathways has important applications in metabolic engineering, synthetic biology and the analysis and reconstruction of metabolic networks. Branched metabolic pathways dominate in metabolic networks and depict a more comprehensive picture of metabolism compared to linear pathways. Although progress has been developed to find branched metabolic pathways, few efforts have been made in identifying branched metabolic pathways via atom group tracking. In this paper, we present a pathfinding method called BPFinder for finding branched metabolic pathways by atom group tracking, which aims to guide the synthetic design of metabolic pathways. BPFinder enumerates linear metabolic pathways by tracking the movements of atom groups in metabolic network and merges the linear atom group conserving pathways into branched pathways. Two merging rules based on the structure of conserved atom groups are proposed to accurately merge the branched compounds of linear pathways to identify branched pathways. Furthermore, the integrated information of compound similarity, thermodynamic feasibility and conserved atom groups is also used to rank the pathfinding results for feasible branched pathways. Experimental results show that BPFinder is more capable of recovering known branched metabolic pathways as compared to other existing methods, and is able to return biologically relevant branched pathways and discover alternative branched pathways of biochemical interest. The online server of BPFinder is available at http://114.215.129.245:8080/atomic/. The program, source code and data can be downloaded from https://github.com/hyr0771/BPFinder.

Crystal structure and molecular Hirshfeld surface analysis of acenaphthene derivatives obeying the chlorine–methyl exchange rule

Instances of crystal structures that remain isomorphous in spite of some minor changes in their respective molecules, such as change in a substituent atom/group, can provide insights into the factors that govern crystal packing. In this context, an accurate description of the crystal structures of an isomorphous pair that differ from each other only by a chlorine–methyl substituent, viz. 5′′-(2-chlorobenzylidene)-4′-(2-chlorophenyl)-1′-methyldispiro[acenaphthene-1,2′-pyrrolidine-3′,3′′-piperidine]-2,4′′-dione, C34H28Cl2N2O2, (I), and its analogue 1′-methyl-5′′-(2-methylbenzylidene)-4′-(2-methylphenyl)dispiro[acenaphthene-1,2′-pyrrolidine-3′,3′′-piperidine]-2,4′′-dione, C36H34N2O2, (II), is presented. While there are two C—H...O weak intermolecular interactions present in both (I) and (II), the change of substituent from chlorine to methyl has given rise to an additional weak C—H...O intermolecular interaction that is relatively stronger than the other two. However, the presence of the stronger C—H...O interaction in (II) has not disrupted the validity of the chloro-methyl exchange rule. Details of the crystal structures and Hirshfeld analyses of the two compounds are presented.

Practical iron-catalyzed atom/group transfer and insertion reactions

Iron-catalyzed reactions are receiving a surge of interest owing to the natural abundance and biocompatibility of Fe and the urge to develop practically useful sustainable catalysis for fine chemical industries. This article is a brief account of our studies on the C–O and C–N bond formation reactions catalyzed by Fe complexes supported by oligopyridine, macrocyclic tetraaza, and fluorinated porphyrin ligands. The working principle is the in situ generation of reactive Fe=O and Fe=NR intermediates supported by these oxidatively robust N-donor ligands for oxygen atom/nitrogen group transfer and insertion reactions. The catalytic reactions include C–H bond oxidation of saturated hydrocarbons (up to 87 % yield), epoxidation of alkenes (up to 96 % yield), cis-dihydroxylation of alkenes (up to 99 % yield), epoxidation–isomerization (E–I) reaction of aryl alkenes (up to 94 % yield), amination of C–H bonds (up to 95 % yield), aziridination of alkenes (up to 95 % yield), sulfimidation of sulfides (up to 96 % yield), and amide formation from aldehydes (up to 89 % yield). Many of these catalytic reactions feature high regio- and diastereoselectivity and/or high product yields and substrate conversions, and recyclability of the catalyst, demonstrating the applicability of Fe-catalyzed oxidative organic transformation reactions in practical organic synthesis.

Analysis of the Valence Electron Structures of the Strengthening Phases Al8Fe4Ce and Al4Ce in Al-Fe-Ce Alloy

Based on the empirical electron theory of solids and molecules (EET), the valence electron structures (VESs) of the strengthening phases Al8Fe4Ce and Al4Ce in Al-Fe-Ce alloy were calculated, then the relationships between the VESs and strengthening, stability of the alloy and grain refining were analyzed. The results show that the distribution of the bond network of Al8Fe4Ce is uniform, the third and the fourth bonds in the bond network of Al4Ce is the weakest segment of the whole bond network structure, and the strongest bond in the bond network of Al8Fe4Ce and Al4Ce is stronger than that of the matrix of the alloy. The VES of Al8Fe4Ce is favourable to stability of the alloy. During solidifying of the alloy, because the bonds formed by Ce atom and its adjacent atoms are all strong, that hinders Al atoms adjacent to Ce atom to involve in the growth of other grains and at the same time hinders the growth of the Ce atom group, so the structure of the alloy can be refined.