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 simple precursors, can be downloaded using the ZIP hyperlinks. The methods used in locating the transition state are shown under "Methods" The different methods are LOCATE-TS, SADDLE, SYMMETRY, and PATH, see Locating Transition States. Vibrations are generated starting with a FORCE calculation.

Animation  Hyperlinks   

LOCATE-TS

Methods
SADDLE

SYMMETRY
 

PATH

 

FORCE

Remarks
SN2 reaction CH3Cl + F- = CH3F + Cl- IRC DRC ZIP
LOCATE-TS         The nucleophilic substitution of chlorine by fluorine, in aqueous solution.
Uncatalyzed ester hydrolysis IRC DRC ZIP LOCATE-TS         Activation barrier = 33.8 kcal.mol-1. A comparison of the acid-catalyzed and uncatalyzed hydrolysis shows that catalysis by acid reduces the activation barrier by 11.5 kcal.mol-1.
Fulminic acid + Ethylene IRC DRC ZIP

LOCATE-TS

        Simple bond-making.  Shows the formation of a C-C and a C-O bond.
Acid-catalyzed ester hydrolysis IRC with charges ZIP LOCATE-TS SADDLE       Activation barrier = 22.3 kcal.mol-1. That the products are higher in energy than the reactants can be rationalized by concentration and entropy considerations.
Cyclohexane chair ↔ boat IRC DRC ZIP LOCATE-TS

SADDLE

      Understanding this reaction requires rotating the cyclohexane ring. It is more complicated than it looks!
Cyclopentadiene + ethylene Diels Alder IRC ZIP LOCATE-TS SADDLE       A straightforward Diels-Alder reaction.
Pentadiene sigmatropic reaction IRC ZIP LOCATE-TS   SYMMETRY     A narcissistic reaction where a hydrogen atom migrates from one end of a pentadiene to the other.
Cyclopentadiene sigmatropic reaction IRC DRC ZIP LOCATE-TS   SYMMETRY     Another narcissistic reaction. In the DRC, watch for the hydrogen atom (proton?) migration.
Hexadiene ↔ hexadiene reaction IRC ZIP

LOCATE-TS

 

SYMMETRY

    A narcissistic reaction where a hexadiene carbon atoms 1 - 2 - 3 - 4 - 5 - 6 end up as 6 - 5 - 4 - 1 - 2 - 3.
Reaction of N2O + C2H2
IRC ZIP LOCATE-TS and SADDLE       Simple bond-making.  Shows the formation of a C-N and a C-O bond.
Cyclopentadiene dimerization
IRC ZIP LOCATE-TS and SADDLE       There is a small difference between the heats of formation at the ends of the IRC and the isolated reactants and product heats of formation. This is expected.
Isochorismic acid decomposing IRC DRC ZIP LOCATE-TS and SADDLE       Isochorismic acid decomposes into pyruvic acid plus salicylic acid.
Making Dihydrocyclobutabenzene
IRC ZIP LOCATE-TS and SADDLE       Another Hoffman - Woodward reaction.
Hydrazoic acid reaction with ethylene IRC ZIP  LOCATE-TS and SADDLE       Simple bond-making.  Shows the formation of two C-N bonds.
Hexatriene → Cyclohexadiene
IRC ZIP

 LOCATE-TS and SADDLE

      A sigma bond forms and a double bond is lost.
CH3-C(OH)=CH2 <=>
CH3-CO-CH3
IRC Charges ZIP LOCATE-TS and SADDLE       Acid-catalyzed conversion of acetone keto and ene-ol tautomers
Nitration of benzene IRC DRC DRC with charges ZIP LOCATE-TS and SADDLE       All three components - H2SO4, HNO3, and benzene, are needed for this reaction. Atomic partial charges are shown as sizes and numbers.
CH2-NH-CH2 + C2H4 IRC DRC ZIP LOCATE-TS and SADDLE       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.
Diels-Alder C2H4 + C4H6 => C6H10
IRC ZIP   SADDLE       Simple Diels-Alder reaction.
Butane + butyl =
butyl + butane
IRC DRC ZIP   SADDLE SYMMETRY     A very sharp transition state as shown by the very large imaginary vibration frequency in the SADDLE calculation.  When the job is run using SYMMETRY, the resulting geometry can be used to start the IRC calculation without further processing of the type needed in SADDLE calculations.
Ring-opening of cyclobutene
IRC DRC ZIP   SADDLE

 

    Demonstration of the Hoffman - Woodward rules.
HCN ↔ HNC IRC DRC ZIP  

SADDLE

      Isomerization of HCN.
Hydrogen atom abstraction by methyl radical IRC DRC ZIP    

SYMMETRY

    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!

Methylcyclopenta-2,4-diene
                  <=>              IRC DRC ZIP
Methylcyclopenta-1,3-diene

    SYMMETRY     Pentadiene sigmatropic almost narcissistic reaction: 1-Methyl cyclopenta-2,4-diene <=> 1-Methyl cyclopenta-1,3-diene
SN2 reaction CH3Br + F- ↔ CH3F + Br- IRC DRC ZIP     SYMMETRY     An almost narcissistic SN2 reaction.
[NH4](+) + NH3 =
NH3 +[NH4](+)
IRC Charges DRC  ZIP     SYMMETRY     A simple narcissistic reaction involving a cation.
SN2 reactionCH3Cl + Cl- ↔ Cl- + CH3Cl IRC DRC ZIP     SYMMETRY     A simple narcissistic reaction.  Compare the IRC and DRC.
SN2 reaction CH3I + F- ↔ CH3F + I- IRC Charges ZIP     SYMMETRY     The nucleophilic substitution of iodine by fluorine, in aqueous solution. Atomic partial charges are shown as sizes and numbers.
methylhexadiene =>
heptadiene
IRC ZIP     SYMMETRY     An almost narcissistic reaction.  This can be used as a template for the general almost narcissistic reaction.
2-Methyl hexa-3,5-diene = 2-Methyl hexa-2,4-diene IRC DRC ZIP     SYMMETRY     A simple and straightforward hydrogen-atom migration results in the two double-bonds moving in this reaction. Note how all motion almost ceases at the transition state geometry - at this point, the system is very cold!
PF5 Berry pseudorotation IRC DRC ZIP     SYMMETRY    

An example of the Berry pseudorotation that exchanges axial atoms in D3h molecules with two of the equatorial atoms.

Hydride transfer to N-Methyl pyridinium IRC DRC ZIP     SYMMETRY     In this reaction, the anion of prop-2-enal transfers a hydride ion to N-methyl pyridine to form N-methyl-4-hydro-pyridine
Ethylene rotation IRC-RHF
IRC-UHF
IRC-OPEN
IRC-Singlet
IRC-Triplet
ZIP
    SYMMETRY     Simple closed-shell rotation of CH2 group from 0 to 180 about the C=C axis.  The top of barrier is sharp; this is not correct.
With UHF the top of the barrier looks normal, but this is misleading.
When a small C.I. is run, there is a shallow bowl at the top of the energy barrier.  Does this look correct?
The SINGLET surface looks normal. The shallow bowl is no longer present.
The TRIPLET surface drops below the SINGLET surface at 51.51 kcal. mol-1. This surface is responsible for the shallow bowl.
This system is a good example of intersystem crossing - The Triplet state drops below the Singlet state near the D2d structure.
Pyridinium + NH2Cl ↔  Pyridine + [NH3Cl](+) IRC DRC Charges ZIP     SYMMETRY     An almost narcissistic reaction involving aqueous media and a charge migration
Hydrogen migration in propyl radical IRC DRC ZIP     SYMMETRY and PATH   A hydrogen atom is moved from being attached to C1 to being attached to C2. This reaction, although apparently simple, requires a complicated data-set to avoid a discontinuity that prevented the transition state from being reached when a simple data-set was used.
n-Butane rotation
RP ZIP       PATH   Torsion rotation about C-C-C-C dihedral angle.
Azobenzene, rotation of phenyl group RP ZIP       PATH   The barrier to rotation is small, and the surface near the minimum is very flat.
F2 stretch DRC ZIP      

PATH

  Morse curve for F-F stretch.
Ammonia inversion IRC DRC ZIP         FORCE Ammonia inverting through the D3h conformation. In the DRC, 3 kcal mol-1 are added to the vibrational mode to ensure motion through the TS.
Formaldehyde vibrations
All six modes ZIP         FORCE Simple normal modes of vibration of formaldehyde, unscaled, showing anharmonicity, if present.
HCl vibration DRC ZIP         FORCE Morse curve for H-Cl vibration.
N2 vibration DRC ZIP         FORCE Morse curve for N-N vibration.
Heating ethylene DRC ZIP           Using DRC=-10 a system near to equilibrium is heated at the rate of doubling each 10 femtoseconds.