Naturalproductman’s Blog

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Archive for the ‘DFT’ Category

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 »

Carbon-carbon coupling constants for stereochemical determination

Posted by naturalproductman on January 17, 2013

R. Thomas Williamson and co-workers at Merck have reported in Organic Letters on the use of DFT to calculate and assign stereochemistry from the C-C coupling constants in NMR.

NMR

OL paper

Posted in Alkaloids, Computational, DFT, Methodology, Stereochemistry | Leave a Comment »

Rhodium catalyzed reaction

Posted by naturalproductman on November 6, 2012

P. Andrew Evans (University of Liverpool) and Mu-Hyun Baik (Indiana University) and co-workers have published in JACS on a mechanistic investigation of a rhodium catalyzed [3+2+1] cyclization. The Los Alamos LACVP basis set was used to represent rhodium.

rhodium

JACS paper

Posted in Computational, DFT, Mechanistic, Methodology, Rhodium, Ring forming, Silver, Transition Metal | Leave a Comment »

Structural reassignment of aquatolide using DFT/NMR

Posted by naturalproductman on November 6, 2012

Dean Tantillo and co-workers have used Gaussian in conjunction with NMR and crystallography to reassign the structure of aquatolide.

structural reassignment

JACS paper

Posted in Computational, DFT, Lactones, Sesquiterpenes | Leave a Comment »

Phomopsichalasin is actually diaporthichalasin

Posted by naturalproductman on July 2, 2012

Thomas Hoye and co-workers from the University of Minnesota have reported in the Journal of Natural Products on the structural reassignment of a natural product using DFT to calculate the NMR chemical shifts.

DFT

JNP paper

Posted in Alkaloids, Computational, DFT, Structural Reassignment | Leave a Comment »

NMR spectra prediction

Posted by naturalproductman on April 10, 2012

It’s very surprising how accurate PERCH software can be for predicting chemical shifts in an NMR spectrum.

NMR

JNP paper

Posted in Computational, DFT | Leave a Comment »

 
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