Computational Study of a Model System of Enzyme-Mediated [4+2] Cycloaddition Reaction

<div><p>A possible mechanistic pathway related to an enzyme-catalyzed [4+2] cycloaddition reac-tion was studied by theoretical calculations at density functional (B3LYP, O3LYP, M062X) and semiempirical levels (PM6-DH2, PM6) performed on a model system. The calculations were carried out for the key [4+2] cycloaddition step considering enzyme-catalyzed biosynthesis of Spinosyn A in a model reaction, where a reliable example of a biological Diels-Alder reaction was reported experimentally. In the present study it was demonstrated that the [4+2] cycloaddition reaction may benefit from moving along the energetically balanced reaction coordinate, which enabled the catalytic rate enhancement of the [4+2] cycloaddition pathway involving a single transition state. Modeling of such a system with coordination of three amino acids indicated a reliable decrease of activation energy by ~18.0 kcal/mol as compared to a non-catalytic transformation.</p></div

Comparison of regular and proposed cycloaddition reactions.

<p>Comparison of regular (black line) and proposed in the present study (blue line) cycloaddition reactions (calculated at the PM6 level). Coordination of amino acids and schematic substrate transformations are shown in the case of enzyme-catalyzed reaction (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.s009" target="_blank">S9 Fig</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.s010" target="_blank">S10 Fig</a> for structures and geometries).</p

Calculated activation and reaction energies for the cycloaddition reactions.

<p>Calculated activation and reaction energies (B3LYP/6-311+G(d) level, kcal/mol) for the cycloaddition reactions (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.g002" target="_blank">Fig. 2</a>).</p><p>Calculated activation and reaction energies for the cycloaddition reactions.</p

Calculated activation barriers of Spinosyn A formation.

<p>Calculated ΔE^≠_2-TS activation barriers (in kcal/mol) of the cycloaddition step involved in the biosynthesis of Spinosyn A showing effect of amino acids coordination. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.s005" target="_blank">S5 Fig</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.s006" target="_blank">S6 Fig</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.s007" target="_blank">S7 Fig</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.s008" target="_blank">S8 Fig</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119984#pone.0119984.s016" target="_blank">S5 Table</a> for structures and geometric parameters.</p><p>^[a] Coordinated amino acids: 1—none; 2—Gln; 3—Gln and Ser; 4—Gln and 2 molecules of Ser.</p><p>^[b] Full geometry optimization of all stationary points.</p><p>^[c] Single point calculations at the PM6 geometry.</p><p>Calculated activation barriers of Spinosyn A formation.</p

Optimized molecular structure of transition state VIII-TS.

<p>Optimized molecular structure of transition state VIII-TS.</p

SpnF-mediated cyclization.

<p>SpnF-mediated cyclization leading to cyclohexene ring in the biosynthesis of Spinosyn A.</p

Noninnocent Nature of Carbon Support in Metal/Carbon Catalysts: Etching/Pitting vs Nanotube Growth under Microwave Irradiation

Microwave irradiation of Ni, Co, Cu, Ag, and Pt metal salts supported on graphite and charcoal revealed a series of carbon surface modification processes that varied depending on the conditions used (inert atmosphere, vacuum, or air) and the nature of metal salt. Carbon materials, routinely used to prepare supported metal catalysts and traditionally considered to be innocent on this stage, were found to actively change under the studied conditions: etching and pitting of the carbon surface by metal particles as well as growth of carbon nanotubes were experimentally observed by FE-SEM analysis. Catalyst preparation under microwave irradiation led to the formation of complex metal/carbon structures with significant changes in carbon morphology. These findings are of great value in developing an understanding of how M/C catalysts form and evolve and will help to design a new generation of efficient and stable catalysts. The energy surfaces of carbon support modification processes were studied with theoretical calculations at the density functional level. The energy surface of the multistage process of carbon nanotube formation from an etched graphene sheet was calculated for various types of carbon centers. These calculations indicated that interconversion of graphene layers and single wall carbon nanotubes is possible when cycloparaphenylene rings act as building units

Structural decomposition analysis of the cycloaddition reaction.

<p>Structural decomposition analysis of the cycloaddition reaction involved in the biosynthesis of Spinosyn A into principal components (the atom numbering was the same as in compound <b>1</b> for comparative purpose).</p

Computational Design of Radical Recognition Assay with the Possible Application of Cyclopropyl Vinyl Sulfides as Tunable Sensors

The processes involving the capture of free radicals were explored by performing DFT molecular dynamics simulations and modeling of reaction energy profiles. We describe the idea of a radical recognition assay, where not only the presence of a radical but also the nature/reactivity of a radical may be assessed. The idea is to utilize a set of radical-sensitive molecules as tunable sensors, followed by insight into the studied radical species based on the observed reactivity/selectivity. We utilize this approach for selective recognition of common radicals—alkyl, phenyl, and iodine. By matching quantum chemical calculations with experimental data, we show that components of a system react differently with the studied radicals. Possible radical generation processes were studied involving model reactions under UV light and metal-catalyzed conditions

Improvement of quality of 3D printed objects by elimination of microscopic structural defects in fused deposition modeling

<div><p>Additive manufacturing with fused deposition modeling (FDM) is currently optimized for a wide range of research and commercial applications. The major disadvantage of FDM-created products is their low quality and structural defects (porosity), which impose an obstacle to utilizing them in functional prototyping and direct digital manufacturing of objects intended to contact with gases and liquids. This article describes a simple and efficient approach for assessing the quality of 3D printed objects. Using this approach it was shown that the wall permeability of a printed object depends on its geometric shape and is gradually reduced in a following series: cylinder > cube > pyramid > sphere > cone. Filament feed rate, wall geometry and G-code-defined wall structure were found as primary parameters that influence the quality of 3D-printed products. Optimization of these parameters led to an overall increase in quality and improvement of sealing properties. It was demonstrated that high quality of 3D printed objects can be achieved using routinely available printers and standard filaments.</p></div