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Merged
KEHANG merged 3 commits into from
Sep 8, 2017
Merged

Account for enantiomers in entropy #1179

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3c35afa
Make symmetry attribute a float
goldmanm Aug 24, 2017
aee7d1d
Account for chiral centers in getAtomSymmetryNumber
goldmanm Aug 24, 2017
88679b1
Updated documentation for chirality
goldmanm Aug 24, 2017
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10 changes: 9 additions & 1 deletion documentation/source/users/rmg/thermo.rst
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Expand Up @@ -266,6 +266,14 @@ Chiral molecules belong to point groups that lack a superposable mirror image
(i.e. point groups lacking :math:`\sigma_h`, :math:`\sigma_d`, :math:`\sigma_v`, and :math:`S_n`
symmetry elements).

In RMG, chirality is incorportated into the symmetry attribute by dividing the symmetry by
two which will increase entropy by :math:`+R * ln(2)`. RMG currently checks for each chiral
center, defined by 4 different groups attached to a carbon, and halves the symmetry
for each chiral center.

The effect of cis-trans isomers is currently not accounted for in RMG.


References
==========

Expand All @@ -283,4 +291,4 @@ References

.. [RDKit] Landrum, G. (2012). RDKit, http://rdkit.org.

.. [Benson] Benson, S.W. (1965), https://en.wikipedia.org/wiki/Benson_group_increment_theory
.. [Benson] Benson, S.W. (1965), https://en.wikipedia.org/wiki/Benson_group_increment_theory
4 changes: 2 additions & 2 deletions rmgpy/molecule/molecule.pxd
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Expand Up @@ -115,7 +115,7 @@ cdef class Bond(Edge):
cdef class Molecule(Graph):

cdef public bint implicitHydrogens
cdef public int symmetryNumber
cdef public float symmetryNumber
cdef public int multiplicity
cdef public object rdMol
cdef public int rdMolConfId
Expand Down Expand Up @@ -211,7 +211,7 @@ cdef class Molecule(Graph):

cpdef bint isArylRadical(self, list aromaticRings=?) except -2

cpdef int calculateSymmetryNumber(self) except -1
cpdef float calculateSymmetryNumber(self) except -1

cpdef list generateResonanceIsomers(self, bint keepIsomorphic=?)

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2 changes: 1 addition & 1 deletion rmgpy/molecule/molecule.py
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Expand Up @@ -658,7 +658,7 @@ class Molecule(Graph):
======================= =========== ========================================
Attribute Type Description
======================= =========== ========================================
`symmetryNumber` ``int`` The (estimated) external + internal symmetry number of the molecule
`symmetryNumber` ``float`` The (estimated) external + internal symmetry number of the molecule, modified for chirality
`multiplicity` ``int`` The multiplicity of this species, multiplicity = 2*total_spin+1
`props` ``dict`` A list of properties describing the state of the molecule.
`InChI` ``str`` A string representation of the molecule in InChI
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10 changes: 5 additions & 5 deletions rmgpy/molecule/symmetry.pxd
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Expand Up @@ -28,12 +28,12 @@ from .molecule cimport Atom, Bond, Molecule

################################################################################

cpdef int calculateAtomSymmetryNumber(Molecule molecule, Atom atom) except -1
cpdef float calculateAtomSymmetryNumber(Molecule molecule, Atom atom) except -1

cpdef int calculateBondSymmetryNumber(Molecule molecule, Atom atom1, Atom atom2) except -1
cpdef float calculateBondSymmetryNumber(Molecule molecule, Atom atom1, Atom atom2) except -1

cpdef int calculateAxisSymmetryNumber(Molecule molecule) except -1
cpdef float calculateAxisSymmetryNumber(Molecule molecule) except -1

cpdef int calculateCyclicSymmetryNumber(Molecule molecule) except -1
cpdef float calculateCyclicSymmetryNumber(Molecule molecule) except -1

cpdef int calculateSymmetryNumber(Molecule molecule) except -1
cpdef float calculateSymmetryNumber(Molecule molecule) except -1
2 changes: 1 addition & 1 deletion rmgpy/molecule/symmetry.py
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Expand Up @@ -84,7 +84,7 @@ def calculateAtomSymmetryNumber(molecule, atom):
elif count == [3, 1]: symmetryNumber *= 3
elif count == [2, 2]: symmetryNumber *= 2
elif count == [2, 1, 1]: symmetryNumber *= 1
elif count == [1, 1, 1, 1]: symmetryNumber *= 1
elif count == [1, 1, 1, 1]: symmetryNumber *= 0.5 # found chirality
elif single == 3:
# Three single bonds
if count == [3]: symmetryNumber *= 3
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70 changes: 70 additions & 0 deletions rmgpy/molecule/symmetryTest.py
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Expand Up @@ -76,6 +76,76 @@ def testAtomSymmetryNumberEthane(self):
symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
self.assertEqual(symmetryNumber, 9)

def testAtomSymmetryNumberEthanewithDeuteriumTritium(self):
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more complicated molecules (based on RMG's imagination) might need to be tested. Can we justify the entropy changes for the molecules from eg1 in RMG-tests (https://travis-ci.org/ReactionMechanismGenerator/RMG-tests/builds/268177870?utm_source=github_status&utm_medium=notification)? They seem to differ by R*ln2. But I'm not fully clear about why the chiral center will half the symmetry number on top of previous symmetry calculation. Do you foresee any potential issues with kinetic estimation for a reaction with one side having chiral center?

"""
Test the Molecule.calculateAtomSymmetryNumber() on CC(D)(T)

This is meant to test whether chirality is accounted for, which
should half the symmetry term.

The total number is 1.5 because the methyl group contributes *3 and
the chiral center contributes *0.5
"""
molecule = Molecule().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 D u0 p0 c0 {1,S}
4 T u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}

""")
symmetryNumber = 1
for atom in molecule.atoms:
if not molecule.isAtomInCycle(atom):
symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
self.assertAlmostEqual(symmetryNumber, 1.5)

def testAtomSymmetryNumberWithTwoChiralCenters(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() on [CH2]CC([CH2])C(C)C=C

This is meant to test whether chirality is accounted for, which
should half the symmetry term.

The molecule has one methyl group (*3), two CH2dot groups (*2 each), and
two chiral centers (*0.5), leading to a total atom symmetry number of 3
"""
molecule = Molecule().fromAdjacencyList(
"""
multiplicity 3
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,S} {13,S} {14,S}
5 C u0 p0 c0 {4,S} {6,S} {9,S} {15,S}
6 C u1 p0 c0 {5,S} {7,S} {8,S}
7 H u0 p0 c0 {6,S}
8 H u0 p0 c0 {6,S}
9 C u0 p0 c0 {5,S} {10,S} {11,S} {16,S}
10 C u0 p0 c0 {9,S} {17,S} {18,S} {19,S}
11 C u0 p0 c0 {9,S} {12,D} {20,S}
12 C u0 p0 c0 {11,D} {21,S} {22,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
15 H u0 p0 c0 {5,S}
16 H u0 p0 c0 {9,S}
17 H u0 p0 c0 {10,S}
18 H u0 p0 c0 {10,S}
19 H u0 p0 c0 {10,S}
20 H u0 p0 c0 {11,S}
21 H u0 p0 c0 {12,S}
22 H u0 p0 c0 {12,S}
""")
symmetryNumber = 1
for atom in molecule.atoms:
if not molecule.isAtomInCycle(atom):
symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
self.assertAlmostEqual(symmetryNumber, 3)

def testAtomSymmetryNumberPropane(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() on CCC
Expand Down
2 changes: 1 addition & 1 deletion rmgpy/species.pxd
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Expand Up @@ -48,7 +48,7 @@ cdef class Species:
cdef public object energyTransferModel
cdef public dict props
cdef public str aug_inchi
cdef public short symmetryNumber
cdef public float symmetryNumber

cpdef generateResonanceIsomers(self,bint keepIsomorphic=?)

Expand Down