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MoleculeModify
✖
MoleculeModify

[Experimental]

✖
MoleculeModify[mol,"mod"]

gives a molecule or list of molecules derived from the molecule mol by applying the modification "mod".

✖
MoleculeModify[mol,{"mod",specs}]

gives a molecule or list of molecules derived from the molecule mol by applying the modification "mod" with additional specifications specs.

✖

represents an operator form of MoleculeModify that can be applied to a molecule.

Details and Options

    Atom Modifications
  • Operations that modify the molecule's atom list:
  • {"AddAtom",atom}add a disconnected atom
    {"AddAtom",{atom1,atom2,…}}add a list of atoms
    {"DeleteAtom",a}delete the atom with index a
    {"DeleteAtom",{a1,a2,…}}delete the indicated atoms
    {"ReplaceAtom",aatom}replace the atom with index a with atom
    {"ReplaceAtom",{a1atom1,…}}replace atoms ai with atomi
  • atom should have one of the following forms:
  • "sym"atom with atomic symbol "sym" (e.g. "C", "Cl")
    Entity["Element",element]atom of a given element
    Entity["Isotope",isotope]atom of the specified isotope
    Atom["sym","prop"val,…]atom with specified properties
  • "AddAtom" will add a disconnected atom, with no bonds to the rest of the molecule. To add a new atom and bond together use "AddBond".
  • "DeleteAtom" will remove any bonds to the atom in question.
  • When removing or replacing an atom, the number of explicit hydrogen atoms may be adjusted to maintain proper valence. Disconnected hydrogen atoms will be removed. To disable this behavior, use the option ValenceErrorHandlingFalse.
  • Implicit hydrogen atoms are added to the added atoms as normal. To disable implicit hydrogens, use "HydrogenCount"None in the new atom specification.
  • Operations that modify atom properties:
  • {"SetFormalCharge",aval}set the formal charge of the atom with index a to val
    {"SetMassNumber",aval}set the mass number of the atom with index a to val
    {"SetUnpairedElectronCount",aval}set the number of radical electrons for the given atom
  • To change a property for multiple atoms, use a list of rules {a1val1,a2val2,…}.
    • Bond Modifications
  • Operations that modify the molecule's bond list:
  • {"AddBond",{a1,a2}}add a single bond between atoms with indices a1 and a2
    {"AddBond",Bond[{a1,a2},"type"]}add a bond of the given type between the given atoms
    {"AddBond",Bond[{a1,atom},type]}a bond between an atom with index a1 and a new atom represented by atom
    {"DeleteBond",{a1,a2}}remove the bond between the atoms with the given indices
    {"SetBondType",{a1,a2}"type"}set the bond type for the bond between atoms with indices a1 and a2
    • General Modifications
  • "SetAromaticity"convert localized single and double bonds to aromatic
    "Kekulize"convert aromatic bonds to localized single and double bonds
    {"RenumberAtoms",{a1,a2,…}}reorder the atoms list so that the atom with index ai appears at position i in the atoms list
    {"SetMetaInformation",meta}set the molecule's MetaInformation to meta, which should be an association or key-value pair
    "MakeHydrogensExplicit"convert any implicit hydrogens to explicit
    "MakeHydrogensImplicit"remove explicit hydrogen atoms when their presence can be inferred by normal valence rules
    • Stereochemistry Modifications
  • Information about a molecule's 3D arrangement, independent of the 3D geometry, is stored in the StereochemistryElements option value. The following operations modify the stereo elements:
  • "AssignStereochemistryFromCoordinates"assign tetrahedral and double bond stereochemistry elements from 3D coordinates
    "RemoveStereochemistry"remove any defined stereochemistry
  • To change the defined stereochemistry for an atom or bond, use one of the following operations:
  • {"SetAtomChirality",aval}set the chiral value for an atom to "R" or "S"
    {"SetBondStereo",{a1,a2}val}set the bond stereo value to either "E" or "Z"
  • Changing the stereo for an atom or bond will affect the 3D coordinates that are generated on demand. If the molecule contains 3D coordinates already, these are discarded when changing the stereochemistry.
    • Substructure Replacement
  • {"ReplaceSubstructure",pattrepl}replace all occurrences of patt with repl
    {"ReplaceSubstructure",pattrepl,attchmts}replace patt with repl, using the specified attachment points between pattern and replacement
    {"ReplaceSubstructureList",pattrepl}replace each occurrence of patt with repl and return a list
  • Here repl should be a Molecule object or SMILES string, and patt can have one of the following forms:
  • MoleculePattern[…]a valid molecule pattern object
    {a1,a2,…}a list of atom indices constituting a connected substructure
    {{a1,a2,…},{b1,b2,…},…}a list of lists of atom indices, each of which will be replaced with repl
  • attchmts should be a list of rules {p1r1,…} from pattern atom index to replacement atom index. If no attachment points are provided, the first and last atoms from the pattern and replacement are matched.
    • Generating Coordinates
  • When a molecule is plotted in 3D or 2D, coordinates are taken from the AtomCoordinates and AtomDiagramCoordinates option values, respectively. If no coordinates are present in the molecule expression, they are generated automatically.
  • The following operations will precompute the automatic coordinates and return a Molecule object containing them:
  • "ComputeAtomCoordinates"compute automatic 3D coordinates for the molecule
    {"ComputeAtomCoordinates",opts}compute atom coordinates using the options opts
    {"GenerateConformers",n}compute 3D coordinates n times with a different seed value and return a list of molecules
    "ComputeAtomDiagramCoordinates"compute 2D coordinates
  • "ComputeAtomCoordinates" will make all implicit hydrogens explicit in order to embed the molecule.
  • "ComputeAtomCoordinates" takes the following options:
  • "Canonicalize"Truewhether to canonicalize the coordinates
    "EnergyMinimize"Truewhether to run a force-field minimization on the coordinates
    RandomSeeding1234how to seed randomness
  • "GenerateConformers" will return unminimized conformers by default.
  • "ComputeAtomDiagramCoordinates" will make implicit those hydrogens attached to carbon, and make explicit those attached to a heteroatom, to match the default output of MoleculePlot. Use {"ComputeAtomDiagramCoordinates",IncludeHydrogensTrue} to include all atoms.
    • Geometry Modifications
  • To change the coordinates for a single atom, use:
  • {"SetAtomPosition",a{x,y,z}}set the position of the specified atom
  • To canonicalize atom coordinates without changing internal geometry, use:
  • "CanonicalizeAtomCoordinates"translate the molecule's center of mass to the origin and align the principal axes with the Cartesian axes
  • For general geometry transformations use the following:
  • {"TransformAtomCoordinates",tfun}apply the transformation function tfun to the coordinates
  • Here tfun should be a TransformationFunction object, e.g. TranslationTransform, ReflectionTransform, etc., or any arbitrary function that operates on and returns a QuantityArray object.
  • The following operations modify the internal coordinates:
  • {"SetBondLength", {a1,a2}val}set the bond length between the specified atoms
    {"SetBondAngle", {a1,a2,a3}val}set the angle between the specified atoms
    {"SetTorsionAngle",{a1,a2,a3,a4}val}set the torsion angle for a group of four consecutively bonded atoms
  • These operations also support a list of length or angle changes, e.g. {{a1,a2}val1,…}.
  • Here val should be a Quantity object or numeric. If numeric, the units are taken to be "Angstroms" or "AngularDegrees".
  • For "SetBondLength", atoms a1 and a2 must be bonded and the bond between them should not be in a ring. All atoms connected to atom a2 are moved.
  • For "SetBondAngle", atoms {a1,a2} and {a2,a3} should be bonded and both bonds should not be in rings. All atoms connected to atom a3 are moved.
  • For "SetTorsionAngle", atoms {a1,a2}, {a2,a3} and {a3,a4} should be bonded, and bond {a2,a3} should not be in a ring. All atoms connected to atom a4 are moved.
  • To minimize the coordinates with respect to the MMFF force field, use the following:
  • "EnergyMinimizeAtomCoordinates"minimize the total force-field energy
    {"EnergyMinimizeAtomCoordinates",ff}minimize the energy using the force field ff, one of "UFF", "MMFF94" or "MMFF94s"
    {"EnergyMinimizeAtomCoordinates",constraints}minimize the energy with the given constraints added to the force field
  • constraints should be a list of bond, angle or torsion constraints of the following forms:
  • {a1,a2}dspecify a distance between two atoms
    {a1,a2,a3}θspecify an angle among three atoms
    {a1,a2,a3,a4}θspecify a torsion angle among four atoms
    <|…|>an association with keys "Atoms", "Value" and "ForceConstant"

Examples

open allclose all

Basic Examples  (4)Summary of the most common use cases

Add a carbon atom to propane:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-qf7fcx
Out[2]=2

Add a bond to the new atom:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-i370h8
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-rrgm0t
Out[4]=4

Add a bond to turn hexane into cyclohexane:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-lu2s5t
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-ji165q
Out[2]=2

Delete a bond to convert cyclohexane to hexane:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-cqpj92
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-1c8yer
Out[2]=2

Replace all nitro groups in TNT with methyl groups:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-svxd92
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-b568a2
Out[2]=2

Use "ReplaceSubstructureList" to replace one nitro group at a time:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-snusl2
Out[3]=3

Scope  (37)Survey of the scope of standard use cases

"AddAtom"  (1)

Add an atom to a molecule:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-t2qr4y
Out[1]=1

Add a list of atoms:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-rnw1b9
Out[2]=2

"AddBond"  (1)

Add a bond to a molecule:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-bpny3w
Out[1]=1

Add a list of bonds to a molecule:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-ra8nnl
Out[2]=2

"AssignStereochemistryFromCoordinates"  (1)

Use a molecule's 3D coordinates to infer stereochemistry. First create a molecule with atoms, bonds and coordinates, but no defined stereochemistry:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-1co4l8
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-4r01j8
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-76vtuy
Out[3]=3

"CanonicalizeAtomCoordinates"  (1)

Import a structure from an "XYZ" file and canonicalize the 3D coordinates:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-tjk2y3
Out[1]=1

After importing, compute the molecule's center of mass and principal axes:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-fhsqtp
Out[2]=2

"CanonicalizeAtomCoordinates" will translate the molecule, move the center of mass to the origin and rotate to align the principal axes with the Cartesian axes:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-wp79km
Out[3]=3

"ComputeAtomCoordinates"  (2)

When a molecule is created from an identifier like a SMILES string or name, coordinates are not computed immediately:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-bs10rd
Out[1]=1

Use "ComputeAtomCoordinates" to compute the coordinates and store them in the molecule expression:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-gyzkie
Out[2]=2

Generate different conformations using the RandomSeeding option:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-emvl2v
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-j69ine
Out[2]=2

The resulting molecules have different conformational energy:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-0tfpdh
Out[3]=3

"ComputeAtomDiagramCoordinates"  (2)

When a molecule is visualized in 2D using MoleculePlot, hydrogen atoms attached to carbon atoms are hidden by default. Only the hydroxyl hydrogen is shown by default in octanol:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-lkvzud
Out[1]=1

"ComputeAtomDiagramCoordinates" will remove those hydrogens that are not shown, and make explicit those that are shown:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-kya2l
Out[2]=2

The coordinates are now stored in the molecule expression:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-3gwqb7
Out[3]=3

As there is only one hydrogen shown by default, the returned molecule has one explicit hydrogen:

In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-ylb9kl
Out[4]=4

The coordinates match exactly those used in a molecule plot:

In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-tq3jv3
Out[5]=5

Compute the atom diagram coordinates showing the default hydrogens, all hydrogens or none:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-6xlod4
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-erkrgy
Out[2]=2

"DeleteAtom"  (2)

Convert hexanol to hexane using "DeleteAtom":

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-e4f748
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-c3rsot
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-56a9aw
Out[3]=3

Find an Entity to match:

In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-8hpwwf
Out[4]=4

When an atom is deleted, any hydrogens attached to it are also removed, and unfilled valences on heavy atoms are filled by implicit hydrogens. Use ValenceErrorHandling->False to disable this behavior and leave unpaired electrons instead:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-4od0hl
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-0mg0wr
Out[2]=2

"DeleteBond"  (2)

Delete an acyclic bond to create disconnected structures:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-n5vorx
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-9onj58
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-52x3ox
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-i1mjqz
Out[4]=4

Delete a ring bond:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-80a2xt
Out[1]=1

"EnergyMinimizeAtomCoordinates"  (1)

Import a structure from an "XYZ" file and use the MMFF force field to minimize the energy:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-r8euvw
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-c5nldc
Out[2]=2

Verify that the conformational energy has lowered:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-itcsfo
Out[3]=3

Show the new structure together with the old:

In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-tasoho
Out[4]=4

"GenerateConformers"  (1)

It is often desirable to have a set of conformations for a molecule, for example, to sample a larger portion of the energy landscape. Generate 100 conformers for cyclohexane:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-mi8hvg

The conformers will have a large energy spread:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-u3p6tg
Out[2]=2

After minimizing the conformations using a force field, they fall into two groups energetically:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-o5vsd5
Out[3]=3

These groupings correspond to the so-called "chair" and "twist-boat" conformations, which are global and local minima on the potential energy surface, respectively. Select one conformer from each group and plot in 3D:

In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-nwgbe7
In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-shpjgs
Out[5]=5

"Kekulize"  (1)

By default, aromatic molecules have delocalized "Aromatic" bond types:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-eup4ej
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-l6fyzl
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-ygatfe
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-dtvq7b
Out[4]=4

"MakeHydrogensImplicit"  (1)

Remove all the hydrogen atoms from a molecule:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-6pm4cu
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-es4pdg
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-sqb84x
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-25qj4v
Out[4]=4

"RemoveStereochemistry"  (1)

Remove explicit stereo information from a molecule, leaving the chirality undefined:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-jgd6pj
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-6iscmx
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-jbld07
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-ou5ctm
Out[4]=4

"RenumberAtoms"  (1)

Change the ordering of atoms in a molecule:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-wd5xy4
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-0a8cav
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-kia26r
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-z10ilp
Out[4]=4

"ReplaceAtom"  (1)

Replace specific atoms in a molecule with a different atom type; for example, convert acetic acid to thioacetic acid:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-v01glj
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-9rj9ws
Out[2]=2

"ReplaceSubstructure"  (1)

Replace the hydroxyl in the aliphatic D ring of estradiol with a carbonyl to make estrone:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-9qs99h
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-vk3y0v
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-xj51vm
Out[3]=3

"ReplaceSubstructureList"  (1)

Make each of the methyl ethers of glycerol:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-gug3sc
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-1e1wj3
Out[2]=2

"SetAromaticity"  (1)

Change localized single and double bonds to aromatic:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-qmebg1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-msqj6l
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-lf8xpl
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-db9euy
Out[4]=4

"SetAtomChirality"  (1)

Convert D-glucose to D-mannose:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-2bjkh5
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-20yo7j
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-400ang
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-jzo5sm
Out[4]=4
In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-m8h6cq
Out[5]=5

"SetAtomPosition"  (1)

Import a molecule and set the coordinate for a single atom:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-exzblx
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-c8in8d
Out[2]=2

"SetBondAngle"  (3)

Set the angle between three atoms:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-3h3fl9
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-ftwas0
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-o5k2xu
Out[3]=3

Set multiple bond angles:

In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-52tyaz
Out[4]=4
In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-esibm
Out[5]=5

Angles cannot be set for nonbonded atoms:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-5ovlw1
Out[1]=1

Bond angles in a ring cannot be set:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-xgek8
Out[1]=1

"SetBondLength"  (1)

Set the distance between two bonded atoms:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-3xxba
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-x8c7ki
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-xet71
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-2polne
Out[4]=4
In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-vlpnj5
Out[5]=5

"SetBondStereo"  (1)

Convert natural E-cinnamaldehyde to the Z-form:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-rdsgry
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-ugsbh2
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-ri0k78
Out[3]=3

"SetBondType"  (1)

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-0hzs3g
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-w6ez2q
Out[2]=2

"SetFormalCharge"  (1)

Make the zwitterion of phenylalanine:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-5zgfoe
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-pp2ee5
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-7xeii5
Out[3]=3

"SetMassNumber"  (1)

Label the C-2 of mevalonolactone with  13C by setting the mass number to 13:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-2p9tgy
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-brc9k5
Out[2]=2

Use AtomList to find the labeled carbon:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-yctm61
Out[3]=3

Label the 5-pro-S hydrogen of mevalonolactone with deuterium by setting the mass number to 2:

In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-qafgs1
Out[4]=4
In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-8kuwlw
Out[5]=5

"SetMetaInformation"  (1)

Often, laboratories use a compound numbering system for samples and notebooks, and these identification numbers are used by chemists when writing internal reports, research papers and patents. Use the molecule's meta-information to store this kind of data.

Add metadata to a molecule:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-1z39tt
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-o712rc
Out[2]=2

Store experimental data in this property:

In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-ebcr40
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-gw4t4n
Out[4]=4

Use an empty association to remove the metadata:

In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-lj8kqa
Out[5]=5
In[6]:=6
✖
https://wolfram.com/xid/0elsynzjvng3a88-6tkywd
Out[6]=6

"SetTorsionAngle"  (1)

Set the geometry of a molecule to a desired conformation, for example, for an internal hydrogen bond:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-ufx4yz
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-7cs2bj
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-xqlsus
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-fh4sm0
Out[4]=4

"SetUnpairedElectronCount"  (1)

Create a hydroxy radical by modifying water:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-sdae8p
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-rlpsek
Out[2]=2

"TransformAtomCoordinates"  (2)

Create a copy of a molecule with the coordinates translated in space:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-6w5p18
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-8haoi4
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-lnz7zo
Out[3]=3

Create a molecule's enantiomer using ReflectionTransform:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-kwhznv
Out[1]=1
In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-fzre86
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-4mqftz
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-ka90dd
Out[4]=4
In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-qwelh0
Out[5]=5

Neat Examples  (1)Surprising or curious use cases

Add distance constraints to the MMFF force field to find a conformation with a given distance between two atoms. First, create the base molecule:

In[1]:=1
✖
https://wolfram.com/xid/0elsynzjvng3a88-waw4k6

Find the two atoms that are farthest away in the standard configuration:

In[2]:=2
✖
https://wolfram.com/xid/0elsynzjvng3a88-pe1juy
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0elsynzjvng3a88-m0zd4p
Out[3]=3

The default conformation has these two atoms 32 ångströms apart:

In[4]:=4
✖
https://wolfram.com/xid/0elsynzjvng3a88-6vbsas
Out[4]=4
In[5]:=5
✖
https://wolfram.com/xid/0elsynzjvng3a88-q1hfnf
Out[5]=5

Use "EnergyMinimizeAtomCoordinates" to find new conformations with specific separations for these atoms:

In[6]:=6
✖
https://wolfram.com/xid/0elsynzjvng3a88-dnxdsv
Out[6]=6

Verify that the returned geometries match the requirement and get the force field energies:

In[7]:=7
✖
https://wolfram.com/xid/0elsynzjvng3a88-3s7rzu
Out[7]=7
In[8]:=8
✖
https://wolfram.com/xid/0elsynzjvng3a88-zqsy95
Out[8]=8
Wolfram Research (2019), MoleculeModify, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeModify.html (updated 2020).
✖
Wolfram Research (2019), MoleculeModify, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeModify.html (updated 2020).

Text

Wolfram Research (2019), MoleculeModify, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeModify.html (updated 2020).

✖
Wolfram Research (2019), MoleculeModify, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeModify.html (updated 2020).

CMS

Wolfram Language. 2019. "MoleculeModify." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2020. https://reference.wolfram.com/language/ref/MoleculeModify.html.

✖
Wolfram Language. 2019. "MoleculeModify." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2020. https://reference.wolfram.com/language/ref/MoleculeModify.html.

APA

Wolfram Language. (2019). MoleculeModify. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculeModify.html

✖
Wolfram Language. (2019). MoleculeModify. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculeModify.html

BibTeX

@misc{reference.wolfram_2025_moleculemodify, author="Wolfram Research", title="{MoleculeModify}", year="2020", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculeModify.html}", note=[Accessed: 11-May-2025 ]}

✖
@misc{reference.wolfram_2025_moleculemodify, author="Wolfram Research", title="{MoleculeModify}", year="2020", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculeModify.html}", note=[Accessed: 11-May-2025 ]}

BibLaTeX

@online{reference.wolfram_2025_moleculemodify, organization={Wolfram Research}, title={MoleculeModify}, year={2020}, url={https://reference.wolfram.com/language/ref/MoleculeModify.html}, note=[Accessed: 11-May-2025 ]}

✖
@online{reference.wolfram_2025_moleculemodify, organization={Wolfram Research}, title={MoleculeModify}, year={2020}, url={https://reference.wolfram.com/language/ref/MoleculeModify.html}, note=[Accessed: 11-May-2025 ]}