Analyze a Molecule's Internal Coordinates

Explore the bond lengths and torsion angles present in disaccharide maltose

Query for the molecule representation of disaccharide maltose:

In[1]:=

maltose=Molecule["4-O-(alpha-D-Glucopyranosyl)-alpha-D-glucopyranose"]

Out[1]=

Molecule

Formula:

Atoms: 45 Bonds: 46



Use

MoleculeValue

to find all bond lengths. The list of bond lengths is returned using the efficient

QuantityArray

structure:

In[2]:=

MoleculeValue[maltose,{"BondLength",All}]

Out[2]=



1.41732

1.54001

1.44537

1.42702

1.43147

1.43953

1.53204

1.43801

1.53303

1.4424

1.54259

1.4237

1.41534

1.44093

1.53715

1.42798

1.54488

1.44257

1.52992

1.43825

1.52973

1.43162

1.54797

1.54807

0.972122

1.09496

1.09599

1.09725

1.09436

1.09762

1.09768

0.978415

1.096

0.982452

1.09404

0.97322

1.09757

1.09477

1.09468

0.974673

1.09587

0.979581

1.09789

0.977627

1.09687

0.978



Use

MeanAround

to find the average bond length:

In[3]:=

MeanAround[%]

Out[3]=

(1.274

0.033

)

Use

BondList

to extract the the atoms and lengths of each bond, then group the bond lengths by member atoms:

In[4]:=

groups=GroupBy[BondList[maltose,_,{"AtomicSymbol","BondLength"}],Sort[First[#]]&Last];

Find the average bond length for each bond type:

In[5]:=

Map[MeanAround,groups]

Out[5]=

{C,O}

(1.4330

0.0026

)

,{C,C}

(1.5385

0.0023

)

,{H,O}

(0.9770

0.0012

)

,{C,H}

(1.0961

0.0004

)



Finding bond angles is more complex if each angle involves two bonds. First, define a pattern representing any three sequentially bonded atoms:

In[6]:=

anglePattern=MoleculePattern["*~*~*"];

Use

FindMoleculeSubstructure

to find the indices of the atoms matching this pattern:

In[7]:=

Short[anglePositions=Values[FindMoleculeSubstructure[maltose,anglePattern,All]]]

Out[7]//Short=

{{1,2,3},{1,2,25},{1,2,26},{2,1,24},75,{22,3,27},{23,22,44},{25,2,26},{37,16,38}}

To group the bond angles by atom type, define a sorting function to make sure that CCH and HCC angles are grouped together:

In[8]:=

orderedSort[atoms_]:=If[OrderedQ[atoms],atoms,Reverse[atoms]];angleLabel[atomIndices_]:=orderedSort[maltose[{"AtomicSymbol",atomIndices}]];

Group the angle positions using the function

angleLabel

In[9]:=

bondAngles=GroupBy[anglePositions,angleLabel(maltose[{"BondAngle",#}]&)];Short[bondAngles]

Out[9]//Short=

{C,C,O}{

112.276

109.083

111.312

112.682

109.931

112.049

107.937

110.895

107.618

111.433

114.233

107.381

108.767

108.169

110.882

111.647

110.474

111.137

110.097

107.42

108.503

109.482

},6,{H,C,H}{

106.894

109.208

}

Visualize the variance for different types of bond angles in this molecule:

In[10]:=

BoxWhiskerChartValues[bondAngles],



Out[10]=

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Analyze a Molecule's Internal Coordinates

See Also

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Analyze a Molecule's Internal Coordinates

See Also

Related Symbols

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