Function Repository Resource:

RotateBonds3D

Interactively manipulate the conformation of a flexible molecule and paste results along the way

Contributed by: Robert B. Nachbar

ResourceFunction["RotateBonds3D"][mol]

generates an interactive GUI that allows the user to dynamically rotate bonds in the molecule mol.

Details and Options

The GUI allows one to select rotatable bonds in the molecule and then use sliders to rotate portions of the molecule about those bonds.

Up to six rotatable bonds can be manipulated at one time, and all rotatable bonds are available for selection via the menus.

The Paste button can be used any number of times to paste a Molecule with the current conformation into the notebook.

The following options can be given:

"AnchorAtom"

Automatic

index of atom at which the spanning tree of rotatable bonds is anchored (rooted), or {anchor,azimuth} where azimuth is the index of an atom adjacent to anchor}.

"DiagramSize"

Automatic

the effective ImageSize for the schematic diagram showing the rotatable bonds and atom indices

IncludeHydrogens

False

controls the display of hydrogen atoms and the inclusion of rotatable bonds terminating in, for example, a methyl group

The IncludeHydrogens option controls the display of hydrogen atoms and the inclusion of bonds to hydroxyl, amino, methyl, and similar groups in the list of rotatable bonds. Explicit hydrogen atoms are always included in the pasted output.

Examples

Basic Examples (2)

Rotate butane about its central C-C bond and paste its gauche and anti conformations:

In[1]:=

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Copy each pasted Molecule and visualize the results:

In[2]:=

Molecule[{"C", "C", "C", "C", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"}, {
Bond[{1, 2}, "Single"],
Bond[{2, 3}, "Single"],
Bond[{3, 4}, "Single"],
Bond[{1, 5}, "Single"],
Bond[{1, 6}, "Single"],
Bond[{1, 7}, "Single"],
Bond[{2, 8}, "Single"],
Bond[{2, 9}, "Single"],
Bond[{3, 10}, "Single"],
Bond[{3, 11}, "Single"],
Bond[{4, 12}, "Single"],
Bond[{4, 13}, "Single"],
Bond[{4, 14}, "Single"]}, {AtomCoordinates -> QuantityArray[
StructuredArray`StructuredData[{14, 3}, {CompressedData["
1:eJwBYQGe/iFib1JlAgAAAA4AAAADAAAAO7tDAWLr+L8edherbDDiPw5mZrmh
5sC/AAMXR8Bb5r8pOajSXmfjv2zF0lzD2tM/tvfBG8Bb5j9sqerVXmfjv1N/
bk3D2tO/lm389MUx+D9r+r4YkkDkP0RHTIfasp4/j0xZ4ZoX+r8q1qoispzj
P/DgKiFikvO/rCtNXGePBMCee3QCO9bdPwH7PQbPX9E/5v8KFBxw8r/05FB/
o034P1hrgfrGE80/sXRlqEhL8799Hxok7JL4v+AcDzsW5Zk/DiJhX4rj479m
cz4vHITjv1qBce6ydfY/xWENkj/z4z+VlBXnf4/mv2VLuTMCZPa/nPgYk5rW
8z/urmRMXdL3v+BIIAVoRqo/NFKGGeJP+T+C8CttA7ToP2pfVTaQ0PE/cvOL
NCMo8T/kJL2/yIr4P3KnFdiLFNq/b6VBeEo6BEAomdlurR7hP15QghVbXde/
gqmuyQ==
"], "Angstroms", {{1}, {2}}}]]}] // MoleculePlot3D[#, ImageSize -> Small, PlotLabel -> Style["gauche", Italic]] &

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Scope (1)

Bonds in rings are excluded from consideration:

In[4]:=

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Options (6)

AnchorAtom (3)

By default, the spanning tree of rotatable bonds is anchored at the atom with the highest ClosenessCentrality, which tends to be in the middle of the molecule:

In[5]:=

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Anchor the spanning tree at one end:

In[6]:=

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When the anchor atom was chosen automatically, the initial direction of the spanning was toward atom 4. Use the two-atom form to change the direction:

In[7]:=

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DiagramSize (1)

Specify the size for the schematic diagram:

In[8]:=

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IncludeHydrogens (2)

By default, hydrogen atoms are not shown:

In[9]:=

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Displaying the hydrogen atoms also permits more bonds to be rotatable:

In[10]:=

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Possible Issues (1)

Cyclic molecules like cyclohexane have no rotatable bonds, and thus no sliders are presented in RotateBonds3D:

In[11]:=

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Neat Examples (2)

RotateBonds3D is a good way to make peptide turns. Start with a tetrapeptide:

In[12]:=

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Give the structure a type II β-turn. Set the torsion angles according to the values in the table (starting from the bottom of the menus):

In[13]:=

$Grid[{{"peptide angle", "torsion angle", "value"}, {"\!$\*SubscriptBox[\(\[Psi]$, $i$]\)", "5-2-3-12", -60}, {"\!$\*SubscriptBox[\(\[Phi]$, $i + 1$]\)", "2-3-12-13", -60}, {"\!$\*SubscriptBox[\(\[Psi]$, $i + 1$]\)", "12-13-14-17", 120}, {"\!$\*SubscriptBox[\(\[Phi]$, $i + 2$]\)", "14-17-18-19", 80}, {"\!$\*SubscriptBox[\(\[Psi]$, $i + 2$]\)", "17-18-19-22", 0}, {"\!$\*SubscriptBox[\(\[Phi]$, $i + 3$]\)", "19-22-23-24", 60} }, Dividers -> {None, {False, True, False}}, Spacings -> {2, Automatic}]$