Chemistry-ID: Information Dynamics for Chemical Reaction Simulations

Information dynamics provides a unified computational architecture for chemical reaction simulations—integrating non-adiabatic dissociation (NaI), adiabatic dissociation (Cl₂), and formation (H₂) into a single abstract framework.

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Overview

Information Dynamics reformulates chemical reactions as a three-element system:

Element	Description	Chemical Equivalent
Virtual Space	Absolute rules defining allowed states	Potential Energy Surfaces (PESs)
Real Space	Observational data with uncertainty	Initial wave packet distribution
Coupling Matrix	Projection mechanism driving evolution	Gradient flow / Landau-Zener transitions

The framework demonstrates that three distinct reaction types—non-adiabatic dissociation (NaI), adiabatic dissociation (Cl₂), and formation (H₂)—can be described with the same abstract architecture, enabling consistent parameter calibration and cross-reaction comparison.

Key features:

• Single code framework for three reaction types
• Velocity Verlet integrator with energy conservation
• Landau-Zener surface hopping for non-adiabatic transitions
• Multi-ensemble statistics for robust error estimation
• Parallel grid scanning for parameter calibration

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Quick Start

Run all three simulations

# NaI photodissociation (default parameters: De=3.30 eV, V12=0.034 eV)
cd NaI_photodissociation
python nai_photodissociation.py

# Cl₂ photodissociation
cd ../Cl2_photodissociation
python cl2_photodissociation.py

# H₂ formation (threshold behavior)
cd ../H2_formation
python h2_formation.py

Run the NaI parameter scan

cd NaI_photodissociation
python nai_photodissociation_sensitivityscan.py

This performs a 2D grid scan over:

• De_ionic: 2.8–3.4 eV (step 0.1 eV)
• V12 (coupling): 0.020–0.034 eV (step 0.002 eV)
• Each point: 3 ensembles × 300 trajectories (coarse) or 5 × 2000 (refined)

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Results

1. NaI Photodissociation

Model: Non-adiabatic, two crossing PESs

• Virtual space: Ionic state (Morse well, $D_e=3.30$ eV, $R_0=2.5$ Å) + covalent state (repulsive wall + linear descent)
• Real space: Gaussian wavepacket ($\sigma_R=0.15$ Å), initial outward velocity $\bar{v}=5.0$ Å/ps, initial state: covalent (repulsive branch)
• Coupling matrix: Landau-Zener probability ($V_{12}=0.034$ eV)

Result:

• Dissociation yield: 65.3% ± 1.5%
• Matches Zewail's experimental value: 65%

Parameter	Value
$D_e$ (well depth)	3.30 eV
$V_{12}$ (electronic coupling)	0.034 eV
Simulated yield	65.3% ± 1.5%
Experimental yield (Zewail)	~65%

Figures:

Figure	Description
nai_potentials.png	Potential energy surfaces (ionic in red, covalent in blue)
nai_trajectories.png	Example trajectories (red=ionic, blue=covalent)
2d_scan_heatmap_extended.png	2D parameter scan: yield vs. $D_e$ and $V_{12}$
2d_scan_contour_extended.png	Contour plot of the same scan

The system is initially prepared on the covalent (repulsive) state, corresponding to laser excitation. At the crossing ($R_c=6.9$ Å), a Landau-Zener transition may populate the ionic (bound) state. Trajectories that hop to ionic are trapped; those remaining on covalent dissociate.

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2. Cl₂ Photodissociation

Model: Adiabatic, single repulsive PES

• Virtual space: Exponential repulsive potential $V(R) = 4.0\exp[-2.0(R-1.98)]$ eV
• Real space: Gaussian wavepacket ($\sigma_R=0.05$ Å), zero initial velocity
• Coupling matrix: Gradient flow (Velocity Verlet)

Result:

• Dissociation yield: 100%
• Mean relative kinetic energy: 3.84 ± 0.39 eV (1.92 eV per fragment)

Quantity	Value
Dissociation yield	100%
Mean relative kinetic energy	3.84 ± 0.39 eV
Mean kinetic energy per fragment	1.92 ± 0.20 eV
Literature range	3.5–4.0 eV (total)

Figures:

Figure	Description
cl2_potential.png	Exponential repulsive potential
cl2_kinetic_energy.png	Fragment kinetic energy distribution

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3. H₂ Formation

Model: Attractive potential, bound state formation

• Virtual space: Morse potential ($D_e=4.746$ eV, $\beta=1.942$ Å⁻¹, $R_0=0.741$ Å)
• Real space: Fixed bond length at equilibrium, scanning initial outward velocity (0–600 Å/ps)
• Coupling matrix: Gradient flow (Velocity Verlet)

Result:

• $E_{\text{tot}} < 0$ eV: binding probability = 1.00 (trapped in Morse well)
• $E_{\text{tot}} > 0$ eV: binding probability drops to 0 (dissociation)
• Sharp transition at the dissociation threshold

Condition	Binding Probability
$E_{\text{tot}} < D_e$	1.00 (bound)
$E_{\text{tot}} > D_e$	0.00 (dissociated)

Figures:

Figure	Description
h2_formation_prob.png	Binding probability vs. initial velocity (threshold behavior)

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License

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