Total Facial Discrimination of 1,3-Dipolar Cycloadditions in a d-Erythrose 1,3-Dioxane Template: Computational Studies of a Concerted Mechanism

Synthesis of novel sugar derived aziridines, as starting materials giving access to sugar amino acid derivatives

D-Erythrosyl aziridines were obtained from D-erythrosyl triazoles either by photolysis or through diazirine intermediates. These were found to undergo rich, high yielding chemistry by reaction with protic acids (HCl, BiI₃/H₂O and trifluoroacetic acid) leading to two types of furanoid sugar α-amino acids, and polyhydroxylprolines. Based on experimental evidence, reaction mechanisms have been proposed for the syntheses.

Looking at the big picture in activation strain model/energy decomposition analysis: the case of the ortho-para regioselectivity rule in Diels-Alder reactions

The regioselectivity of the Diels-Alder reaction is predicted by the ortho-para rule which has been explained from FMO theory. Using DFT calculations, the activation-strain model and energy decomposition analysis we studied the reaction of methyl acrylate with four unsymmetrical dienes. We found that if the analysis is carried out considering the TS structures, the selectivity would not be explained by the interaction energy as expected considering the FMO arguments. However, a thorough analysis along the reaction path revealed that the interaction energy is responsible for the regioselectivity. A deeper analysis with the EDA model showed that the decisive term that accounts for the HOMO-LUMO interactions favors the ortho and para paths, as predicted by FMO arguments.

Total Stereoselective Michael Addition of N- and S- Nucleophiles to a d-Erythrosyl 1,5-Lactone Derivative. Experimental and Theoretical Studies Devoted to the Synthesis of 2,6-Dideoxy-4-functionalized-d- ribono-hexono-1,4-lactone

The synthesis of a 1,5-lactone 2,4- O-alkylidene-d-erythrose derivative was found to be a highly stereoselective template in Michael addition trough the reaction of a d-erythrosyl 1,5-lactone derivative with nitrogen and sulfur nucleophiles. The sulfur adducts formed are 1 (d-erythrose derivative):1 (nucleophile), and the nitrogen adducts are 1:2. Both were then treated under HCl to give 2,6-dideoxy-4-functionalized-d- ribono-hexono-1,4-lactone by a reaction cascade in high overall yield. Reaction's scale up even improves the yield. The theoretical and computational results clearly explain the origin of the stereoselectivity, and the energetic course of reactions starting with nitrogen and sulfide nucleophiles. Considering that the 1,4-lactones obtained in this work offer a new molecular scaffold for organic synthesis, these new results provide a solid theoretical platform that can be used to speed up synthesis of other derivatives in a stereo- and regioselective way.

molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software

The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations. The starting structures for these calculations can be imported from different chemical formats. A set of tools is available to help the user to examine or modify any geometry parameter. This includes the definition of layers in ONIOM calculations, choosing fixed atoms during geometry optimizations, the recalculation or adjustment of the atomic charges, performing SCANs or IRC calculations, etc. molUP also extracts the geometries from the output files as well as the energies of each of them. All of these tasks are performed in an interactive GUI that is extremely helpful for the user. MolUP was developed to be easy to handle by inexperienced users, but simultaneously to be a fast and flexible graphical interface to allow the advanced users to take full advantage of this plugin. The program is available, free of charges, for macOS, Linux, and Windows at the PortoBioComp page https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup. © 2018 Wiley Periodicals, Inc.