forbiddenStructures.py

#!/usr/bin/env python
# encoding: utf-8

name = ""
shortDesc = u""
longDesc = u"""

"""
entry(
    label = "Ods",
    group =
"""
1 O ux c0 {2,D} {3,S}
2 R ux {1,D}
3 R ux {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
This forbids O with both single and double bonds WHILE keeping a zero partial charge.
This does not forbid ozone, [O-][O+]=O
""",
)

entry(
    label = "Od_rad",
    group =
"""
1 O u1 {2,D}
2 R ux {1,D}
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

entry(
    label = "N_birad_triplet_2singleBonds",
    group =
"""
1 N u2 p0 {2,S} {3,S}
2 R ux {1,S}
3 R ux {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

entry(
    label = "C_quintet",
    molecule =
"""
1 C u4 p0
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

entry(
    label = "Carbene_D_triplet",
    group =
"""
1 C u2 p0 {2,D}
2 C u0 {1,D}
""",
    shortDesc = u"""""",
    longDesc =
u"""
restricts C2O, see RMG-Py issue #514
""",
)

entry(
    label = "Carbene_S_triplet",
    group =
"""
1 C   u2 p0 {2,S}
2 R!H u0 {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

entry(
    label = "O3",
    group =
"""
1 O u[0,1] {2,S}
2 O u0     {1,S} {3,S}
3 O u[0,1] {2,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

entry(
    label = "O4..",
    group =
"""
1 O u1 {2,S}
2 O u0 {1,S} {3,S}
3 O u0 {2,S} {4,S}
4 O u1 {3,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

entry(
    label = "cyclic-C3O",
    group =
"""
1 C u0 {2,D} {3,S} {4,S}
2 O u0 {1,D}
3 C u0 {1,S} {4,T}
4 C u0 {1,S} {3,T}
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

entry(
    label = "cyclobutyne",
    group =
"""
1 R!H ux {2,T} {4,S}
2 R!H ux {1,T} {3,S}
3 R!H ux {2,S} {4,[S,D,T,B]}
4 R!H ux {1,S} {3,[S,D,T,B]}
""",
    shortDesc = u"""""",
    longDesc =
u"""
""",
)


entry(
    label = "LiCONSFCl",
    group =
"""
1 Li u0 p0 c0 {2,S}
2 C ux px c0 {3,[S,D,T]} {1,S}
3 [O,N,S,F,Cl] ux px c0 {2,[S,D,T]}
""",
    shortDesc = u"""""",
    longDesc =
u"""
In these species the other atom tends to take most of the charge from the Li
so it isn't really bonded to C
""",
)

entry(
    label = "CO_birad",
    species =
"""
multiplicity 3
1 C u2 p0 c0 {2,D}
2 O u0 p2 c0 {1,D}
""",
    shortDesc = u"""""",
    longDesc =
u"""
Forbidden after discussion with whgreen.
This species should quickly transform into a closed shell [C-]#[O+].
We don't need it as a resonance structure of carbon monoxide for reactivity since carbon monoxide has its designated
reaction families (CO_Disprop, R_Add_COm).
""",
)

entry(
    label = "CS_birad",
    species =
"""
multiplicity 3
1 C u2 p0 c0 {2,D}
2 S u0 p2 c0 {1,D}
""",
    shortDesc = u"""""",
    longDesc =
u"""
Forbidden after discussion with whgreen.
This species should quickly transform into a closed shell [C-]#[S+] similar to the carbon monoxide case above.
We don't need it as a resonance structure of carbon monsulfide for reactivity since carbon monsulfide has its designated
reaction families (CO_Disprop [also deals with CS], R_Add_CSm).
""",
)

entry(
    label = "N-N(S)",
    species =
"""
1 N u0 p2 c0 {2,S}
2 N u0 p2 c0 {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
This structure is not a stationary point, and should quickly become N#N
""",
)

entry(
    label = "[N][N]",
    species =
"""
multiplicity 5
1 N u2 p1 c0 {2,S}
2 N u2 p1 c0 {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
N#N can be excited to [N]=[N], but we shouldn't allow it to reach [N][N]
""",
)

entry(
    label = "SOO2",
    species =
"""
multiplicity 3
1 S u0 p2 c0 {2,S} {3,S}
2 O u0 p2 c0 {1,S} {4,S}
3 O u1 p2 c0 {1,S}
4 O u1 p2 c0 {2,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
The SO--O2 complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable SO--OO bond length),
yet it is predicted by RMG, e.g, by R_Recombination of [S][O] and [O][O].

Another resonance structure of it which is forbidden as well via this entry is:
multiplicity 3
1 S u1 p1 c0 {2,S} {3,D}
2 O u0 p2 c0 {1,S} {4,S}
3 O u0 p2 c0 {1,D}
4 O u1 p2 c0 {2,S}
""",
)

entry(
    label = "SO2O2",
    species =
"""
multiplicity 3
1 S u0 p1 c0 {2,S} {3,S} {4,D}
2 O u0 p2 c0 {1,S} {5,S}
3 O u1 p2 c0 {1,S}
4 O u0 p2 c0 {1,D}
5 O u1 p2 c0 {2,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
The SO2--O2 complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable O2S--OO bond length),
yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of O=S=O and [O][O].
Also, it is described as a TS in doi: 10.1021/jp067499p (Fig. 1 structure 5, Fig. 2)

Another resonance structure of it which is forbidden as well via this entry is:
multiplicity 3
1 S u1 p0 c0 {2,S} {3,D} {4,D}
2 O u0 p2 c0 {1,S} {5,S}
3 O u0 p2 c0 {1,D}
4 O u0 p2 c0 {1,D}
5 O u1 p2 c0 {2,S}
""",
)

entry(
    label = "S2O2",
    species =
"""
multiplicity 3
1 O u0 p2 c0 {2,S} {3,S}
2 S u0 p2 c0 {1,S} {4,S}
3 O u1 p2 c0 {1,S}
4 S u1 p2 c0 {2,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
The S2--O2 complex isn't a sable species (has an imaginary frequency),
yet it is predicted by RMG, e.g, by R_Recombination of [S][S] and [O][O].

Another resonance structure of it which is forbidden as well via this entry is:
multiplicity 3
1 O u0 p2 c0 {2,S} {3,S}
2 S u1 p1 c0 {1,S} {4,D}
3 O u1 p2 c0 {1,S}
4 S u0 p2 c0 {2,D}
""",
)

entry(
    label = "N2SH",
    species =
"""
multiplicity 2
1 N u0 p0 c+1 {2,D} {3,D}
2 S u1 p1 c0 {1,D} {4,S}
3 N u0 p2 c-1 {1,D}
4 H u0 p0 c0 {2,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
The N2--SH complex isn't a sable species (i.e., its geometry cannot be optimized with a reasonable NN--SH bond length),
yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of [SH] to N#N.

Other resonance structures of it which are forbidden as well via this entry are:
multiplicity 2
1 N u0 p1 c0 {2,S} {3,D}
2 S u0 p2 c0 {1,S} {4,S}
3 N u1 p1 c0 {1,D}
4 H u0 p0 c0 {2,S}

multiplicity 2
1 N u1 p0 c+1 {2,S} {3,D}
2 S u0 p2 c0 {1,S} {4,S}
3 N u0 p2 c-1 {1,D}
4 H u0 p0 c0 {2,S}
""",
)

entry(
    label = "N2SO",
    group =
"""
1 O u0 {2,[S,D]}
2 S u0 {1,[S,D]} {3,[S,D]}
3 N u0 {2,[S,D]} {4,[S,D]}
4 N u0 {3,[S,D]}
""",
    shortDesc = u"""""",
    longDesc =
u"""
The N2--SO complex isn't sable (i.e., NNSO's geometry cannot be optimized with a reasonable NN--SO bond length),
yet it is predicted by RMG, e.g, by R_Addition_Multiple_Bond of [S][O] to N#N.
N2SO2 is forbidden as well in this group for the same reason.
""",
)

entry(
    label = "SO3(T)",
    species =
"""
multiplicity 3
1 O u0 p2 c0 {2,D}
2 S u1 p0 c0 {1,D} {3,D} {4,S}
3 O u0 p2 c0 {2,D}
4 O u1 p2 c0 {2,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
The geometry of SO3(T) could not be stabilized at either B3LYP/6-311G(2d,d,p) nor M06-2x
without getting negative frequency/ies.
""",
)

entry(
    label = "cN3HNH2",
    species =
"""
multiplicity 2
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 N u0 p1 c0 {1,S} {4,S} {5,S}
3 N u0 p1 c0 {1,S} {6,S} {7,S}
4 N u1 p1 c0 {1,S} {2,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {3,S}
7 H u0 p0 c0 {3,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
Geometry could not converge at CBS-QB3
""",
)

entry(
    label = "cN3HN",
    group =
"""
1 N u0     p1 c0 {2,S} {3,S} {5,S}
2 N u[0,1] p1 c0 {1,S} {3,S}
3 N u0     p0 c+1 {1,S} {2,S} {4,D}
4 N u0     p2 c-1 {3,D}
5 R ux     px cx {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
Geometry of the following species in this group could not converge at CBS-QB3
[N-]=[N+]1[N]N1
[N-]=[N+]1NN1
""",
)

entry(
    label = "NH3NNH",
    species =
"""
multiplicity 2
1 N u0 p0 c+1 {2,S} {4,S} {5,S} {6,S}
2 N u0 p2 c-1 {1,S} {3,S}
3 N u1 p1 c0 {2,S} {7,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {3,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
Geometry could not converge at wB97x-D3/6-311++G(3df,3pd) (alongd ref - xq1488)
""",
)

entry(
    label = "NNHNH",
    species =
"""
multiplicity 2
1 N u0 p0 c+1 {2,S} {3,D} {5,S}
2 N u0 p1 c0 {1,S} {4,D}
3 N u0 p2 c-1 {1,D}
4 N u1 p1 c0 {2,D}
5 H u0 p0 c0 {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
Geometry could not converge at wB97x-D3/6-311++G(3df,3pd) (alongd ref - xq1492)
""",
)

entry(
    label = "C2_triplebond",
    species =
"""
1 C u0 p1 c-1 {2,T}
2 C u0 p0 c+1 {1,T}
""",
    shortDesc = u"""""",
    longDesc =
u"""
https://pubs.acs.org/doi/pdf/10.1021/ct400867h discusses complex wavefunction for C2
and that it cannot be assigned definitive bond order. We are forbidding the C2 triple bond
becuase we do not have good thermo for `Ctc` (C u0 p0 c+1 {1,T}) atomtype
""",
)

entry(
    label = "LiX",
    species =
"""
1 Li u0 p0 c0 {2,S}
2 X  u0 p0 c0 {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
Don't allow Li to plate
""",
)

entry(
    label = "CO2X2",
    species =
"""
1 O u0 p2 c0 {3,S} {5,S}
2 O u0 p2 c0 {3,D}
3 C u0 p0 c0 {1,S} {2,D} {4,S}
4 X u0 p0 c0 {3,S}
5 X u0 p0 c0 {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
We assume that CO2 binds only via physisorption to the surface
""",
)

entry(
    label = "CO2X3",
    species =
"""
1 O u0 p2 c0 {3,S} {6,S}
2 O u0 p2 c0 {3,S} {5,S}
3 C u0 p0 c0 {1,S} {2,S} {4,D}
4 X u0 p0 c0 {3,D}
5 X u0 p0 c0 {2,S}
6 X u0 p0 c0 {1,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
We assume that CO2 binds only via physisorption to the surface
""",
)


entry(
    label = "O2X2",
    species =
"""
1 O u0 p2 c0 {2,S} {3,S}
2 O u0 p2 c0 {1,S} {4,S}
3 X u0 p0 c0 {1,S}
4 X u0 p0 c0 {2,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""
O2 dissociates upon adsorption
""",
)

entry(
    label = "OCX2",
    species =
"""
1 O u0 p2 c0 {2,S} {3,S}
2 C u0 p0 c0 {1,S} {4,T}
3 X u0 p0 c0 {1,S}
4 X u0 p0 c0 {2,T}
""",
    shortDesc = u"""""",
    longDesc =
u"""
CO binds in a monodentate configuration
""",
)