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Archive for the ‘Computational’ Category

Diels-Alder approach to galbulimima alkaloids

Posted by naturalproductman on August 25, 2015

Here’s a paper related to the galbulimima alkaloids, which were made famous by Lewis Mander’s group. Regan Thomson and co-workers report in JACS on the synthesis of galbulimima alkaloids. A nice collaboration with DFT calculations from Dean Tantillo’s group shows the orbital interactions in the transition state structures of the Diels-Alder reactions.
galbulimima

JACS paper

Posted in Alkaloids, DFT, Diels-Alder, Methodology, Total Synthesis | Leave a Comment »

Welcome to the future

Posted by naturalproductman on August 7, 2015

I read the title of this paper and immediately thought of David Baker’s work. I guess we are getting closer to having a logical approach available to design our own protein catalysts.
design
JACS paper

Posted in Computational, Enzymes, Methodology | 2 Comments »

Newman-Kwart reaction mechanism

Posted by naturalproductman on July 13, 2015

Hafize Ozcan and co-workers from Trakya University in Turkey have reported in Tetrahedron on an interesting mechanistic investigation of the Newman-Kwart reaction.

Newman-Kwart

Tetrahedron paper

Posted in Cascade Reactions, Computational, DFT, Electrocyclization, Mechanistic, Methodology, Named Reactions, Newman-Kwart, Sigmatropic Rearrangements | Leave a Comment »

Sufur ylide chemistry – intramolecular cyclopropanation

Posted by naturalproductman on May 28, 2015

Nuno Maulide and co-workers from the University of Vienna have reported in JOC on an intramolecular cyclopropanation from a sulfur slide precursor and what follows is a nice mechanistic investigation.

sulfur

JOC paper

Posted in Computational, DFT, Gold, Mechanistic, Methodology, Transition Metal | Leave a Comment »

Domino acylation Diels-Alder

Posted by naturalproductman on May 2, 2015

Jeffrey Aube (University of Kansas) and Dean Tantillo (UC Davis) have teamed up to study the mechanism of a domino acylation-Diels Alder reaction.

domino

OL paper

Posted in DFT, Diels-Alder, Mechanistic, Methodology, Named Reactions | Leave a Comment »

C-H activation within the ruthenium complex

Posted by naturalproductman on May 6, 2014

Another Houk collaboration – this time with Grubbs’ lab. They studied the mechanism of the carboxylate assisted C-H activation of the metathesis catalyst. The SDD basis set was used to approximate the orbitals of ruthenium in this report.

C-H

JACS paper

Posted in C-H activation, Computational, DFT, Methodology | Leave a Comment »

Copper catalyzed [3+2] mechanism

Posted by naturalproductman on May 6, 2014

When I saw the graphical abstract of this paper, the first thing that came to mind was Michael Kerr at the University of Western Ontario, but this paper was from Yong Tang’s group in SIOC in collaboration with Kendall Houk’s computational group to study the mechanism of this [3+2] reaction. They used the LANL2DZ basis set in this paper. Great to hear.

copper

JACS paper

Posted in Cascade Reactions, Computational, Copper, DFT, Methodology, Transition Metal | Leave a Comment »

Polyene cyclization with titanocene

Posted by naturalproductman on May 6, 2014

Juan Cuerva and co-workers from the University of Granada in Spain have reported in JACS on a titanocene mediated polyolefin cyclization reaction that studied with Gaussian calculations. The basis set used to approximate the titanocene catalyst was 6-31G*. From my little knowledge of Gaussian, when using QM calculations to study a reaction mechanism, you need two things: 1) the basis set and 2) the method. The basis set is the linear combination of a set of functions used to approximate the molecular orbitals. There are many kinds of basis sets that can be used for Gaussian. In my experience with transition metals however, I was unable to use the 6-31G* basis set because the transition metals have more complicated molecular orbitals since they have d-orbitals. I had to use the Los Alamos basis set: LANL2Dz. I eventually gave up on my time with Gaussian because I just kept running into problems and eventually had to focus my efforts into experimental work. But hopefully one day I can go back to this stuff again. Afterall, it helps us understand the reaction mechanisms better.

titanocene

JACS paper

Posted in Cascade Reactions, Computational, DFT, Methodology, Titanium, Transition Metal | Leave a Comment »

[3,3]-Sigmatropic

Posted by naturalproductman on May 9, 2013

Laszlo Kurti and co-workers from UT Southwestern have reported in JACS on a [3,3]-sigmatropic rearrangement approach to access BINAM derivatives using a phosphoric acid catalyst.

organocatalyst

JACS paper

Posted in Asymmetric, Computational, DFT, Methodology, Organocatalytic | Leave a Comment »

Asymmetric epoxidation

Posted by naturalproductman on April 19, 2013

Benjamin List and co-workers have reported in JACS on their studies of cinchona alkaloid catalyzed asymmetric epoxidation of activated olefins.

cinchona

JACS paper

Posted in Asymmetric, Computational, DFT, ESI, Mass Spectrometry, Mechanistic, Methodology, Organocatalytic | Leave a Comment »

 
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