Animations

 Animations of chemical processes can provide a good visual description of the motion of atoms.  Several different types of animation can be modeled, with the most common being:

(A) Dynamic reaction coordinates (DRC): These show the motion over time.
(B) Intrinsic Reaction Coordinates (IRC): These show motion over the Potential Energy Surface.
(C) Reaction Path (RP): Motion resulting from a single geometric parameter being steadily changed.

In the following table, the various animations can be seen by clicking on the hyperlinks labeled IRC, DRC, or RP.  All the files needed for generating the animations, starting with the reactants and products, can be downloaded using the ZIP hyperlinks

Animation  Hyperlinks  Remarks
SN2 reaction CH3Cl + F- = CH3F + Cl-
IRC DRC ZIP The nucleophilic substitution of chlorine by fluorine, in aqueous solution
2H2SO4 + HNO3 =  2([HSO4]-) + [NO2]+ + [H3O]+ DRC ZIP Hydronium ion, [H3O]+, forms only transiently, then it decomposes into H2O and sulfuric acid.
Nitration of benzene IRC DRC DRC with charges ZIP All three components - H2SO4, HNO3, and benzene, are needed for this reaction.
n-Butane rotation
RP ZIP Torsion rotation about C-C-C-C dihedral angle.
Azobenzene, rotation of phenyl group RP ZIP The barrier to rotation is small, and the surface near the minimum is very flat.
Formaldehyde vibrations
All six modes ZIP Simple normal modes of vibration of formaldehyde, unscaled, showing anharmonicity, if present.
Diels-Alder C2H4 + C4H6 => C6H10
IRC ZIP  
Cyclopentadiene dimerization
IRC ZIP There is a small difference, about 0.2 kcal.mol-1, between the heats of formation at the ends of the IRC and the isolated reactants and product heats of formation.
Ring-opening of cyclobutene
IRC DRC ZIP Demonstration of the Hoffman - Woodward rules.
Acid-catalyzed ester hydrolysis IRC IRC with charges ZIP Activation barrier = 29.5 kcal.mol-1. The small step between frames 113 and 114 is due to  a computational artifact, i.e., a bug. That the products are higher in energy than the reactants can be rationalized by concentration and entropy considerations.
Uncatalyzed ester hydrolysis IRC DRC ZIP Activation barrier = 40.2 kcal.mol-1. A comparison of the acid-catalyzed and uncatalyzed hydrolysis shows that catalysis by acid reduces the activation barrier by 10.7 kcal.mol-1.
Pentadiene sigmatropic reaction IRC ZIP A narcissistic reaction where a hydrogen atom migrates from one end of a pentadiene to the other.
Reaction of N2O + C2H2
IRC ZIP Simple bond-making.  Shows the formation of a C-N and a C-O bond.
Azulene to Naphthalene IRC DRC ZIP A very complicated mechanism. Azulene first folds so that a sigma bond forms, then the five-membered ring opens to form a six-membered ring, finally a hydrogen atom (proton?) migrates to form naphthalene.  The DRC shows the hydrogen migration.
Making Dihydrocyclobutabenzene
IRC ZIP Another Hoffman - Woodward reaction.
Hydrazoic acid reaction with ethylene IRC ZIP Simple bond-making.  Shows the formation of two C-N bonds.
Hexatriene → Cyclohexadiene
IRC ZIP A sigma bond forms and a double bond is lost.
HCN ↔ HNC IRC DRC ZIP Isomerization of HCN.
Fulminic acid + Ethylene IRC ZIP Simple bond-making.  Shows the formation of a C-C and a C-O bond.
CH2-NH-CH2 + C2H4 IRC DRC ZIP Simple bond-making.  Shows the formation of two C-C bonds. Locating the transition state required two steps - a LOCATE-TS and a SADDLE.  The DRC shows the effect of the drop in potential energy.
Cyclohexane chair ↔ boat IRC ZIP Understanding this reaction requires rotating the cyclohexane ring. It is more complicated than it looks!
Cyclohexane boat ↔ boat DRC ZIP This is a very complicated reaction to visualize.  Because of the low barrier, the IRC calculation did not work, however the DRC worked correctly.
Cyclobutane + ethylene Diels Alder IRC ZIP A straightforward Diels-Alder reaction.
Cyclopentadiene sigmatropic reaction IRC DRC ZIP Another narcissistic reaction. In the DRC, watch for the hydrogen atom (proton?) migration.
CH3Cl + Cl- ↔ Cl- + CH3Cl IRC DRC ZIP Still another narcissistic reaction.  Compare the IRC and DRC.
Hexadiene ↔ hexadiene reaction IRC ZIP A narcissistic reaction where a hexadiene carbon atoms 1 - 2 - 3 - 4 - 5 - 6 end up as 6 - 5 - 4 - 1 - 2 - 3.
Chymotrypsin catalytic cycle IRC ZIP A very complicated process.  To animate, click on "Specific script" or "Oxyanion hole".  This animation takes a long time - two or three minutes - to get started.  Also, it is incomplete - no charges or energies.
Proton abstraction by methyl radical IRC ZIP Transition states for proton abstraction are most easily generated using symmetry.  In a geometry optimization, the proton is defined as being mid-way between the donor and acceptor atoms.  After deleting the symmetry function, gradient minimization results in the transition state in one step!