Theoretical design of tetra(arenediyl)bis(allyl) derivatives as model compounds for Cope rearrangement transition states

Salvatella, Luis

doi:10.1039/c4ra16381h

Cited by 2 publications

(2 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The computational work reported involved Cope rearrangement transition states using the DFT method to compute electronic energies for various substituted allyl derivatives [35]. This example consisted of a PDF file wherein the coordinates data was submitted in a comma separated format in the supplementary file.…”

Section: Resultsmentioning

confidence: 99%

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Karthikeyan

Vyas

2016

J Cheminform

View full text Add to dashboard Cite

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher’s resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract. Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0175-x) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Karthikeyan

Vyas

2016

J Cheminform

View full text Add to dashboard Cite

show abstract

“…This is not an uncommon problem when dealing with structures with diradical character. The Cope reaction is a good example of this phenomenon, where the contribution of diradical components is large at the transition state. − Another recent example of the importance of taking into account the diradical character of relevant transition structures along a mechanism is provided by the study of the isomerization of vinyl allene oxides. , The need to check the stability of wave functions so that we make sure that it is a real minimum in the function space is as relevant as the more widely recognized need to calculate the Hessian with respect to the coordinates to characterize stationary points as minima or transition states . Thus, for all stationary points, the stability of the wave function has been computed to guarantee that the wave functions are minima in the configuration space of the basis used.…”

Section: Methodsmentioning

confidence: 99%

A Radical Mechanism for the Vanadium-Catalyzed Deoxydehydration of Glycols

et al. 2016

View full text Add to dashboard Cite

We propose a novel mechanism for the deoxydehydration (DODH) reaction of glycols catalyzed by a [Bu 4 N][VO 2 (dipic)] complex (dipic= pyridine-2,6-dicarboxylate) using triphenylphosphine as a reducing agent. Using density functional theory (DFT) we have confirmed that the preferred sequence of reaction steps involves reduction of the V(V) complex by phosphine, followed by condensation of the glycol into a [VO(dipic)(- (6), which then evolves to the alkene product and the recovery of the catalyst. In contrast to the usually invoked closed-shell mechanism for the latter steps, where 6 suffers a [3+2] retrocycloaddition, we have found that the homolytic cleavage of one of the C-O bonds in 6 is preferred by 12 kcal/mol. The resulting diradical intermediate then collapses to a metallacycle which evolves to the product through an aromatic [2+2] retrocycloaddition. We use this key change in the mechanism to propose ways to design better catalysts for this transformation. The analysis of the mechanisms in both singlet and triplet potential energy surfaces, together with the location of the MECPs between them, showcase this reaction as an interesting example of two-state reactivity.2

show abstract

Theoretical design of tetra(arenediyl)bis(allyl) derivatives as model compounds for Cope rearrangement transition states

Cited by 2 publications

References 37 publications

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

A Radical Mechanism for the Vanadium-Catalyzed Deoxydehydration of Glycols

Contact Info

Product

Resources

About