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Top of Page MOLecular ARCHitecture+ - MolArch+ Movies
This page gives an overview on different types of molecular animations that were generated using the MolArch+ program.

MolArch+ Movies
Pseudorotation of Cyclohexane
Top of Page Pseudorotation of Cyclopentane
The motions of the ring of cyclopentane can be viewed as an almost barrierless reaction in which the C-H-bonds interconvert between pseudo-axial- and pseudo-equatorial orientations on a sub-picosecond timescale. Envelope (E) and twist-boat (T) conformations occur alternating along this pathway. The entire process is called pseudorotation, as is results in a structures that appears to have been produced by rotation of the entire initial molecule and are superposable on the initial one, unless different positions are distinguished by substitution, including isotopic substitution. The animations show a full pseudorotational cycle and the interconversion between all 10 different envelope and 10 twist conformers of cyclopentane due to the out of plane motion of carbon atoms, and visualize the "wave"-like alternating up and down movement of adjacent atoms.
All structures were calculated using the PIMM force-field program; see also "Hindered Pseudorotation in Substituted Cyclopentanes".

Pseudorotation of Cyclopentane
Cyclopentane
Pseudorotation of Cyclopentane Pseudorotation of Cyclopentane Pseudorotation of Cyclopentane Pseudorotation of Cyclopentane Pseudorotation of Cyclopentane Pseudorotation of Cyclopentane Pseudorotation of Cyclopentane
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Top of Page Pseudorotation of Cyclohexane
The two degenerate ring conformations (chair ant anti-chair) of cyclohexane interconvert rapidly at room temperature (every 10 microseconds) by rotation about carbon-carbon bonds. This interconversion moves the axial hydrogens into the equatorial position and vice versa. The intermediate in this interconversion is the skew-boat (= twist-boat) conformation. The low energy form of cyclohexane is a rather rigid chair, while the more flexible skew-boat conformation lies about 23 kJ/mol higher in energy. The animations on the left show a complete pseudorotational cycle between the altogether 12 skew-boat and boat conformations of cyclohexane. The boat conformations being transition states for converting from one skew-boat geometry to another lying approx. 6 kJ/mol above the skew-boat. The boat forms are not local minima because they contain two completely eclipsed carbon-carbon bonds and an unfavorable 1,4-steric interaction; twisting into a skew-boat relieves this strain.
In the final animation, a full chair/anti-chair conformational change of cyclohexane is simulated. These low-barrier conformational changes look like the molecule has rotated by 180 about an axis through the center of the ring, the process is also called "pseudorotation". See also the above examples and animations for cyclopentane. All structures were calculated using the PIMM force-field program.

Pseudorotation of Cyclohexane
Cyclohexane
Pseudorotation of Cyclohexane Pseudorotation of Cyclohexane Pseudorotation of Cyclohexane Pseudorotation of Cyclohexane
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Top of Page Ring Inversion of 1,4-Dimethyl-cyclohexane and 1,4-Di-tert-butyl-cyclohexane
As in the above example on the pseudorotation of cyclohexane, these animations show the chair/anti-chair transitions of cis- and trans-1,4-di-substituted cyclohexane derivatives which occur via intermediate skew-boat conformations. The conformational changes shown were obtained from a full grid-type analysis of all conformations of cyclohexane and evaluation of the energy barriers using the PIMM force-field program.
Ringinversion of Cyclohexanes
Dimethyl-cyclohexane Di-tert-butyl-cyclohexane
Ringinversion of cis-Dimethyl-Cyclohexane Ringinversion of trans-Dimethyl-Cyclohexane Ringinversion of Dimethyl-Cyclohexane Ringinversion of cis-Di-t-butyl-Cyclohexane Ringinversion of trans-Di-t-butyl-Cyclohexane Ringinversion of Di-t-butyl-Cyclohexane
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