(* Kimball model and energy derived from experimental molecule data source, ES end january 2013 *)
Clear[Plot9];
ChemicalData["Butane","MoleculePlot"]

t=0.01889726*ChemicalData["Butane","AtomPositions"];

bt=ChemicalData["Butane","BondTally"]

{{{{"C","C"},1},3},{{{"C","H"},1},10}}
bc=bt[[1,2]]
bh=bt[[2,2]]

u=ChemicalData["Butane","VertexTypes"]

n=Length[u]

DeleteFile[ "C:\\Kimb_Mathem\\tmp3"];
For[i=1,i<n+1,i++,
{u[[i]],Extract[t,{i}]}>>> "C:\\Kimb_Mathem\\tmp3"]
u1=Table[If[u[[i]]=="C",0.2556,If[u[[i]]=="H",0.1,If[u[[i]]=="N",0.213,If[u[[i]]=="O",0.178]]]],{i,1,n}]
u2=Table[If[u[[i]]=="C",0.2556,If[u[[i]]=="H",0.564,If[u[[i]]=="N",0.213,If[u[[i]]=="O",0.178]]]],{i,1,n}]

ChemicalData["Butane","MolecularFormulaString"]

v=0.01889726*ChemicalData["Butane","VertexCoordinates"];

Plot2=Table[Graphics3D[Text[i,{t[[i,1]]-0.5,t[[i,2]],t[[i,3]]} ,{1,0}]],{i,1,n}];
Plot1=Table[Graphics3D[{If[u[[i]]=="N",Lighter[Blue],If[u[[i]]=="O",Lighter[Red],Lighter[Brown]]],Sphere[{t[[i,1]],t[[i,2]],t[[i,3]]},u1[[i]]]}],{i,1,n}];

Show[Plot1,Plot2,{AspectRatio->Automatic}]

ChemicalData["Butane","CHStructureDiagram"]

x=Table[t[[i,1]],{i,1,n}];
y=Table[t[[i,2]],{i,1,n}];
z=Table[t[[i,3]],{i,1,n}];

(* Distance matrix Bohr *)
Dij=Table[If[i≥j,If[sq=Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]; sq<3.0,sq,0]," "],{i,1,n},{j,1,n}];
(*Dij=Table[If[sq=Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]; sq<3.0,sq," "],{i,1,n},{j,1,n}];*)
MatrixForm[Dij]

(*Eij=Table[If[i≥j,If[sq=Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]; sq<3.0,0.529177*sq,0]," "],{i,1,n},{j,1,n}];
MatrixForm[Eij];*)

Fij=Dij-u2;
(*MatrixForm[Fij];*)
Gij=Table[If[i≥j,If[Fij[[i,j]]>0,Fij[[i,j]],0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Gij]*)

Hij=Transpose[Gij];
(*MatrixForm[Hij];*)

Kij=Hij-u2;
(*MatrixForm[Kij];*)
Lij=Table[If[i≤j,If[Kij[[i,j]]>0,Kij[[i,j]],0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Lij]*)

Lij=Table[If[i≤j,If[Lij[[i,j]]>0,If[u[[j]]≠"H",0.5*Lij[[i,j]],Lij[[i,j]]],0]," "],{i,1,n},{j,1,n}]; 
(*MatrixForm[Lij];*)

Nij=Table[If[i≤j,If[Lij[[i,j]]>0,2.25/Lij[[i,j]]^2,0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Nij];*)

(* Total kinetic energy in Eh, = |Etot| *)
Tsigma=Sum[If[i≤j,Nij[[i,j]],0],{i,1,n},{j,1,n}]+Sum[If[u[[i]]≠"H",2.25/u2[[i]]^2,0],{i,1,n}]

Qij=Lij;
Mij=Prepend[Qij,u];
Oij=Transpose[Mij];
Pij=Prepend[Oij,Prepend[u," "]];

MatrixForm[Pij]

(* sigma bond cloud radii *)

For[i=2,i<n+2,i++,
For[j=2,j≤i,j++,
If[Pij[[i,j]]>0,Print[u[[i-1]],i-1," ",u[[j-1]],j-1,"  ",Extract[Pij,{i,j}]]]]]

DeleteFile[ "C:\\Kimb_Mathem\\tmp4"];
For[i=2,i<n+2,i++,
For[j=2,j≤i,j++,
If[Pij[[i,j]]>0,{i-1,j-1,Extract[Pij,{i,j}]}>>> "C:\\Kimb_Mathem\\tmp4"]]]

a=ReadList["C:\\Kimb_Mathem\\tmp4"]
nb=Length[a]

wx=Table[(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(x[[a[[i,2]]]]-x[[a[[i,1]]]])+x[[a[[i,1]]]],{i,1,bc}];     wy=Table[(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(y[[a[[i,2]]]]-y[[a[[i,1]]]])+y[[a[[i,1]]]],{i,1,bc}];      wz=Table[(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(z[[a[[i,2]]]]-z[[a[[i,1]]]])+z[[a[[i,1]]]],{i,1,bc}];
Plot7=Table[Graphics3D[{Darker[Gray],{Opacity[0.3],Sphere[{wx[[i]],wy[[i]],wz[[i]]},a[[i,3]]]}}],{i,1,bc}];

wx=Table[(a[[i,3]]+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(x[[a[[i,1]]]]-x[[a[[i,2]]]])+x[[a[[i,2]]]],{i,bc+1,nb}];
wy=Table[(a[[i,3]]+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(y[[a[[i,1]]]]-y[[a[[i,2]]]])+y[[a[[i,2]]]],{i,bc+1,nb}];
wz=Table[(a[[i,3]]+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(z[[a[[i,1]]]]-z[[a[[i,2]]]])+z[[a[[i,2]]]],{i,bc+1,nb}];
Plot8=Table[Graphics3D[{Opacity[0.4],Sphere[{wx[[i]],wy[[i]],wz[[i]]},a[[i,3]]]}],{i,1,bh}];

(*PLot9= Table[Graphics3D[{Cylinder[{{x[[a[[i,1]]]],y[[a[[i,1]]]],z[[a[[i,1]]]]},{x[[a[[i,2]]]],y[[a[[i,2]]]],z[[a[[i,2]]]]}},0.1]}],{i,1,nb}];*)
Plot9= Table[Graphics3D[{Darker[Red,0.8],Cylinder[{{x[[a[[i,1]]]],y[[a[[i,1]]]],z[[a[[i,1]]]]},{x[[a[[i,2]]]],y[[a[[i,2]]]],z[[a[[i,2]]]]}},0.05]}],{i,1,nb}];

Show[Plot1,Plot7,Plot8,Plot9,{AspectRatio->Automatic,Boxed->False}]