Reaction Search

Reaction search

What to run

parameter	default	description
reaction_search	1	1: search for reactions, 0: do not.
pes *	0	0: search only for the reactions of the starting well, 1: explore the full multiwell PES.
simultaneous_kinbot	5	Maximum number of simultaneous kinbot runs during a full pes search.
high_level	0	1: run high-level (L2) optimizations and frequency calculations, 0: the low-level (L1) results are used.
calc_aie	0	1: run calculations of ionic counterparts to compute adiabatic ionization energies (requires a conformer search), 0: do not.

Which reactions

parameter	default	description
families	["all"]	List of the reaction types to be used in the reaction search. If "all" is in the list, all of the families are used. Otherwise any number of families can be chosen. Additionally, "combinatorial" searches for reactions in a combinatorial fashion (see below), which leads to a very large number of reaction searches.
bimol_families	["all"]	Same as families, for when the initial species is a bimolecular reaction.
skip_families	["none"]	List of reaction families to skip during a kinbot run.
family_restrict	0	1: in intra_H_migration, H shifts to an atom without a radical center are only tried towards atoms with a double bond or a lone pair (O, S, N) and carbenes. 0: they are tried towards every heavy atom. Cations are always searched without the restriction.
ringrange	[3, 9]	For cyclic transition states search for cycle sizes within this range.
rigid_reaction_cutoff	3.0	In intra_H_migration, intra_R_migration, intra_OH_migration and h2_elim, a candidate whose backbone bonds (apart from the one to the migrating group) are all multiple bonds is dropped if its two end atoms are farther apart than this distance (Å) in the reactant.
homolytic_bonds	{}	Restrict the hom_sci family to given bonds: {"<chemid of sp>": [[a, b], [c, d]]} breaks only the a–b and c–d bonds (zero-indexed atoms) of species sp; several species may be listed. Without it, every single bond is considered. Note that the chemids and atom numbers are only known once the species has been characterized, e.g. on a restart.
skip_chemids	["none"]	List of chemids to skip KinBot runs of during PES calculations. If "none" is in the list then all of the chemids generated during a PES calculation are submitted. Skipped chemids are entered as strings, e.g., ["842282702691721350181", "842282832261801180571"].
keep_chemids	["none"]	List of chemids to keep and run KinBot for during PES calculations. If "none" is in the list then all of the chemids generated during a PES calculation are submitted. The selected chemids are entered as strings, e.g., ["842282702691721350181", "842282832261801180571"]. Useful when an L1 PES is completed, but further calculations are wanted on a subset of these wells only.
skip_reactions	["none"]	List of reaction names (as in summary_<chemid>.out, e.g. "…_intra_H_migration_4_5") to leave out of a run; useful once the search is done.

One specific reaction

parameter	default	description
specific_reaction	0	Search for a specific reaction in which user-defined bonds are broken or formed based on the break_bonds and form_bonds parameters below. Feature is in testing/development.
break_bonds	[]	Bond between atoms listed will be broken (e.g. [2,5] breaks the bond between atoms 2 and 5). Atom numbering begins at index 0.
form_bonds	[]	Bond between atoms listed will be formed (e.g. [3,4] forms the bond between atoms 3 and 4). Atom numbering begins at index 0.
one_reaction_comb	0	Search for a specific reaction using the combinatorial algorithm.
one_reaction_fam	0	Search for a specific reaction using the reaction family algorithm.

Thresholds

parameter	default	description
barrier_threshold	none	Maximum electronic energy (i.e., no ZPE is included) in kcal mol-1 at L1 above which barriers are neglected and the search for products is terminated. One of barrier_threshold or barrier_threshold_L2 needs to be set.
barrier_threshold_L2	none	Maximum electronic energy (i.e., no ZPE is included) in kcal mol-1 at L2 above which barriers are neglected and the search for products is terminated. One of barrier_threshold or barrier_threshold_L2 needs to be set.
barrier_threshold_add	10.	Additional threshold allowance for L1 relative to L2 when barrier_threshold_L2 is set, to avoid excluding channels due to L1 uncertainties.
hom_sci_threshold_add	5.0	Additional energy over barrier_threshold specific to barrierless reactions.
scan_step	30	Number of scan points for reaction families where no geometry template is given but rather the TS is searched for via scanning the energy as a function of the bond length of two atoms.

Product complexes (van der Waals wells)

When a saddle point leads to two products, KinBot also optimizes the complex at the end of the IRC (not for hom_sci). The complex is kept as a separate well, between the saddle point and the separated products, if it lies deep enough below them and has no imaginary frequency larger than imagfreq_threshold; otherwise the saddle point is connected to the separated products directly. Whether kept complexes enter the MESS input is set by me_skip_vdW on the Master equation page.

parameter	default	description
vdW_detection	0.5	Minimum depth (kcal/mol, ZPE-corrected) of a product complex below the separated products for it to be kept as a well.

Combinatorial search

Used when "combinatorial" is in families.

parameter	default	description
min_bond_break	2	Minimum number of bonds to be broken per reaction (one fewer for radicals).
max_bond_break	3	Maximum number of bonds to be broken per reaction (one fewer for radicals).
comb_molec	1	Allow molecular pathways.
comb_rad	1	Allow radical pathways.
comb_lone	1	Allow reactions involving lone electron pairs.
comb_pi	1	Allow reactions involving pi-electrons.
break_valence	1	Allow atom valences to be altered.

Parameters marked with an asterisk (*) must not change when a run is restarted, see Restarting.