RobertNachbar/ ConsistentForceField

Ermer-Lifson CFF for alkanes, alkenes, and alkylbenzenes

Contributed by: Robert Nachbar

The ConsistentForceField paclet provides functions for computing the Ermer-Lifson consistent force field (CFF) energy, gradient vector, and Hessian matrix of alkane, unconjugated alkene, and alkyl-substituted benzene molecules using analytic derivatives. Additionally, the geometry of molecules can be optimized to find conformational minima, transition states, and higher order partial maxima. Conformational reaction coordinates can be computed and animated. Normal modes of vibration and vibrational thermodynamic functions can also be computed for stationary structures.

Installation Instructions

To install this paclet in your Wolfram Language environment, evaluate this code:
PacletInstall["RobertNachbar/ConsistentForceField"]


To load the code after installation, evaluate this code:
Needs["RobertNachbar`ConsistentForceField`"]

Paclet Guide

Examples

Basic Examples (2) 

Build trans-cyclooctene:

In[1]:=
mol = Fold[MoleculeModify, Molecule[
   "C1CCCCCCC1"], {"ComputeAtomCoordinates", {"SetBondType", {3, 4} ->
      "Double"}}]
Out[1]=
In[2]:=
MoleculePlot3D[mol, ImageSize -> Small]
Out[2]=

Compute the CFF energy of the molecule:

In[3]:=
InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 307.0436840057373`], List[153.98200225830078`, 235.99870109558105`], List[195.`, 212.31669425964355`], List[195.`, 22.863691329956055`], List[30.928985595703125`, 117.59068870544434`], List[30.928985595703125`, 307.0436840057373`]], List[List[200.`, 410.42970085144043`], List[364.0710144042969`, 315.7036876678467`], List[241.01799774169922`, 244.65868949890137`], List[200.`, 220.97669792175293`], List[158.98200225830078`, 244.65868949890137`], List[35.928985595703125`, 315.7036876678467`], List[200.`, 410.42970085144043`]], List[List[376.5710144042969`, 320.03370475769043`], List[202.5`, 420.53370475769043`], List[200.95300006866455`, 421.42667961120605`], List[199.04699993133545`, 421.42667961120605`], List[197.5`, 420.53370475769043`], List[23.428985595703125`, 320.03370475769043`], List[21.882003784179688`, 319.1406993865967`], List[20.928985595703125`, 317.4896984100342`], List[20.928985595703125`, 315.7036876678467`], List[20.928985595703125`, 114.70369529724121`], List[20.928985595703125`, 112.91769218444824`], List[21.882003784179688`, 111.26669120788574`], List[23.428985595703125`, 110.37369346618652`], List[197.5`, 9.87369155883789`], List[198.27300024032593`, 9.426692008972168`], List[199.13700008392334`, 9.203690528869629`], List[200.`, 9.203690528869629`], List[200.86299991607666`, 9.203690528869629`], List[201.72699999809265`, 9.426692008972168`], List[202.5`, 9.87369155883789`], List[376.5710144042969`, 110.37369346618652`], List[378.1179962158203`, 111.26669120788574`], List[379.0710144042969`, 112.91769218444824`], List[379.0710144042969`, 114.70369529724121`], List[379.0710144042969`, 315.7036876678467`], List[379.0710144042969`, 317.4896984100342`], List[378.1179962158203`, 319.1406993865967`], List[376.5710144042969`, 320.03370475769043`]]]]], List[FaceForm[List[RGBColor[0.5529411764705883`, 0.6745098039215687`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["CFFEnergy", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"RobertNachbar/ConsistentForceField\"", ",", "\"RobertNachbar`ConsistentForceField`CFFEnergy\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["RobertNachbar/ConsistentForceField", "RobertNachbar`ConsistentForceField`CFFEnergy"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["RobertNachbar/ConsistentForceField", "RobertNachbar`ConsistentForceField`CFFEnergy"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][mol]
Out[3]=

Scope (5) 

Optimize the geometry of the molecule to minimize the energy:

In[4]:=
molOpt = InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 307.0436840057373`], List[153.98200225830078`, 235.99870109558105`], List[195.`, 212.31669425964355`], List[195.`, 22.863691329956055`], List[30.928985595703125`, 117.59068870544434`], List[30.928985595703125`, 307.0436840057373`]], List[List[200.`, 410.42970085144043`], List[364.0710144042969`, 315.7036876678467`], List[241.01799774169922`, 244.65868949890137`], List[200.`, 220.97669792175293`], List[158.98200225830078`, 244.65868949890137`], List[35.928985595703125`, 315.7036876678467`], List[200.`, 410.42970085144043`]], List[List[376.5710144042969`, 320.03370475769043`], List[202.5`, 420.53370475769043`], List[200.95300006866455`, 421.42667961120605`], List[199.04699993133545`, 421.42667961120605`], List[197.5`, 420.53370475769043`], List[23.428985595703125`, 320.03370475769043`], List[21.882003784179688`, 319.1406993865967`], List[20.928985595703125`, 317.4896984100342`], List[20.928985595703125`, 315.7036876678467`], List[20.928985595703125`, 114.70369529724121`], List[20.928985595703125`, 112.91769218444824`], List[21.882003784179688`, 111.26669120788574`], List[23.428985595703125`, 110.37369346618652`], List[197.5`, 9.87369155883789`], List[198.27300024032593`, 9.426692008972168`], List[199.13700008392334`, 9.203690528869629`], List[200.`, 9.203690528869629`], List[200.86299991607666`, 9.203690528869629`], List[201.72699999809265`, 9.426692008972168`], List[202.5`, 9.87369155883789`], List[376.5710144042969`, 110.37369346618652`], List[378.1179962158203`, 111.26669120788574`], List[379.0710144042969`, 112.91769218444824`], List[379.0710144042969`, 114.70369529724121`], List[379.0710144042969`, 315.7036876678467`], List[379.0710144042969`, 317.4896984100342`], List[378.1179962158203`, 319.1406993865967`], List[376.5710144042969`, 320.03370475769043`]]]]], List[FaceForm[List[RGBColor[0.5529411764705883`, 0.6745098039215687`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["CFFOptimizeGeometry", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"RobertNachbar/ConsistentForceField\"", ",", "\"RobertNachbar`ConsistentForceField`CFFOptimizeGeometry\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["RobertNachbar/ConsistentForceField", "RobertNachbar`ConsistentForceField`CFFOptimizeGeometry"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["RobertNachbar/ConsistentForceField", "RobertNachbar`ConsistentForceField`CFFOptimizeGeometry"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][mol]
Out[4]=
In[5]:=
MoleculePlot3D[molOpt, ImageSize -> Small]
Out[5]=

Compute the energy of the optimized conformation:

In[6]:=
InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 307.0436840057373`], List[153.98200225830078`, 235.99870109558105`], List[195.`, 212.31669425964355`], List[195.`, 22.863691329956055`], List[30.928985595703125`, 117.59068870544434`], List[30.928985595703125`, 307.0436840057373`]], List[List[200.`, 410.42970085144043`], List[364.0710144042969`, 315.7036876678467`], List[241.01799774169922`, 244.65868949890137`], List[200.`, 220.97669792175293`], List[158.98200225830078`, 244.65868949890137`], List[35.928985595703125`, 315.7036876678467`], List[200.`, 410.42970085144043`]], List[List[376.5710144042969`, 320.03370475769043`], List[202.5`, 420.53370475769043`], List[200.95300006866455`, 421.42667961120605`], List[199.04699993133545`, 421.42667961120605`], List[197.5`, 420.53370475769043`], List[23.428985595703125`, 320.03370475769043`], List[21.882003784179688`, 319.1406993865967`], List[20.928985595703125`, 317.4896984100342`], List[20.928985595703125`, 315.7036876678467`], List[20.928985595703125`, 114.70369529724121`], List[20.928985595703125`, 112.91769218444824`], List[21.882003784179688`, 111.26669120788574`], List[23.428985595703125`, 110.37369346618652`], List[197.5`, 9.87369155883789`], List[198.27300024032593`, 9.426692008972168`], List[199.13700008392334`, 9.203690528869629`], List[200.`, 9.203690528869629`], List[200.86299991607666`, 9.203690528869629`], List[201.72699999809265`, 9.426692008972168`], List[202.5`, 9.87369155883789`], List[376.5710144042969`, 110.37369346618652`], List[378.1179962158203`, 111.26669120788574`], List[379.0710144042969`, 112.91769218444824`], List[379.0710144042969`, 114.70369529724121`], List[379.0710144042969`, 315.7036876678467`], List[379.0710144042969`, 317.4896984100342`], List[378.1179962158203`, 319.1406993865967`], List[376.5710144042969`, 320.03370475769043`]]]]], List[FaceForm[List[RGBColor[0.5529411764705883`, 0.6745098039215687`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["CFFEnergy", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"RobertNachbar/ConsistentForceField\"", ",", "\"RobertNachbar`ConsistentForceField`CFFEnergy\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["RobertNachbar/ConsistentForceField", "RobertNachbar`ConsistentForceField`CFFEnergy"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["RobertNachbar/ConsistentForceField", "RobertNachbar`ConsistentForceField`CFFEnergy"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][molOpt]
Out[6]=

Generate a report of the contributions to the energy:

In[7]:=
InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 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Out[7]=

Compute the twist and out-of-plane angles at the distorted double bond:

In[8]:=
MoleculePlot[molOpt, AtomLabels -> "AtomIndex", IncludeHydrogens -> All]
Out[8]=
In[9]:=
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Out[9]=
In[10]:=
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Out[10]=

Compute the vibrational frequencies of the molecule:

In[11]:=
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Out[11]=

Publisher

Robert Nachbar

Disclosures

Compatibility

Wolfram Language Version 14

Version History

  • 1.1.2 – 15 October 2024
  • 1.1.1 – 15 October 2024
  • 1.1.0 – 06 June 2024
  • 1.0.1 – 26 March 2024
  • 1.0.0 – 25 March 2024

License Information

MIT License

Paclet Source

Source Metadata