Bond Scan

Use a bond scan when you want a simple structural probe along one distance coordinate between two fragments. This is not a full reaction-path search, but it is useful for quickly checking whether a chosen bond-forming or bond-breaking coordinate behaves sensibly before running a more expensive reaction search.

Typical chemistry questions

Bond scans are useful when you want to ask questions such as:

• What happens as two selected atoms are brought closer together?

• Does a close-contact structure look chemically reasonable before a full AFIR run?

• Which distance range should be explored more carefully?

• Is a simple coordinate scan enough, or is a full reaction search needed?

Basic command

Run a scan between atom 1 in the first structure and atom 2 in the second structure:

pyar-cli scan-bond 1 2 A.xyz B.xyz -N 8
pyar-cli --scan-bond 1 2 A.xyz B.xyz -N 8

The two numbers identify the atoms involved in the distance scan. The two XYZ files provide the starting fragments.

How to use the results

A bond scan should be treated as a preliminary probe. If the scan suggests a chemically interesting close-contact region, use the resulting structures as starting points for a reaction search, higher-level optimisation, or manual mechanistic analysis.

A scan is not a substitute for transition-state confirmation. It does not, by itself, prove a minimum-energy path or a transition state.