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
S_N2 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
S_N2 reaction CH₃Br + F^- ↔ CH₃F + Br^-	IRC DRC ZIP			SYMMETRY			An almost narcissistic S_N2 reaction.
[NH₄](+) + NH₃ = NH₃ +[NH₄](+)	IRC Charges DRC ZIP			SYMMETRY			A simple narcissistic reaction involving a cation.
S_N2 reactionCH₃Cl + Cl^- ↔ Cl^- + CH₃Cl	IRC DRC ZIP			SYMMETRY			A simple narcissistic reaction. Compare the IRC and DRC.
S_N2 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 D_2d 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 D_3h 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.