Quantitative electronic Lewis structure derived from nuclear coordinates of a molecule:
Flunitrazepam (Rohypnol)


All computations are transparent. The run lasts about 1 sec on a i7-4790 CPU. (ES 16 June 2013/04 February 2015).

Input and Definitions


The coordinates are read in pm. We use atomic units, the universally applied system of theoretical chemistry and (micro) physics, see NIST. Length data are in Bohr : 1 a0 = 0.52917721 Å = 52.917721 pm; electric charges in ± electron charges, and energies in Hartrees : 1 Eh = 2 Rydberg = 627.5095 kcal/mol = 2625.50 kJ/mol.

Normal Input for a structure given as : Symbol, x, y, z

Flunitrazepam_M3_1.png

Normal Input for a structure downloaded from Wolfram ChemData repository

Flunitrazepam_M3_2.gif

Flunitrazepam_M3_3.gif

Flunitrazepam_M3_4.gif

Flunitrazepam_M3_5.png

Flunitrazepam_M3_6.png

Analyze the atomic constituents

Flunitrazepam_M3_7.png

Flunitrazepam_M3_8.png

Flunitrazepam_M3_9.png

Flunitrazepam_M3_10.png

Flunitrazepam_M3_11.png

Flunitrazepam_M3_12.png

Analyze Lewis structure

Compute Kimball radii from distance matrix, show core radii derived from CH4, NH3, H2O gauge molecules (cnofhydb.pas), (cnofhydb.ex_ to be renamed into runnable cnofhydb.exe after download), H excentricities, and number of σ bonds.

Distance Matrix :

Flunitrazepam_M3_13.gif

Flunitrazepam_M3_14.png

Nuclear repulsion

Flunitrazepam_M3_15.gif

Flunitrazepam_M3_16.png

Flunitrazepam_M3_17.gif

Flunitrazepam_M3_18.png

Select bonded pairs and their distances

Flunitrazepam_M3_19.png

Flunitrazepam_M3_20.png

Subtract proton excentricities

Flunitrazepam_M3_21.png

Flunitrazepam_M3_22.png

Flunitrazepam_M3_23.gif

Flunitrazepam_M3_24.png

Subtract core radius

Flunitrazepam_M3_25.gif

Flunitrazepam_M3_26.png

Show radii determined

Flunitrazepam_M3_27.gif

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Summary of Lewis properties

Flunitrazepam_M3_29.gif

Flunitrazepam_M3_30.png

Flunitrazepam_M3_31.png

Flunitrazepam_M3_32.png

Compute kinetic energy terms, bonding clouds, core clouds:

Flunitrazepam_M3_33.gif

Flunitrazepam_M3_34.png

Flunitrazepam_M3_35.gif

Partial kinetic energy for cores and σ clouds, π - clouds and lone pairs are added later

Flunitrazepam_M3_36.png

Flunitrazepam_M3_37.png

Flunitrazepam_M3_38.gif

Flunitrazepam_M3_39.png

Flunitrazepam_M3_40.png

Determine connectivity matrix:

Flunitrazepam_M3_41.gif

Flunitrazepam_M3_42.png

Localize double bonds and positions of π-clouds (PItrans.m

Transform the triangle of every target atom with two of its neighbors into the xy-plane and attach π-clouds above and below the plane to the target. Then back transform the π-clouds into the molecular coordinate array.

Flunitrazepam_M3_43.png

Flunitrazepam_M3_44.png

Flunitrazepam_M3_45.png

Flunitrazepam_M3_46.png

Flunitrazepam_M3_47.gif

Flunitrazepam_M3_48.png

Flunitrazepam_M3_49.png

Flunitrazepam_M3_50.png

Flunitrazepam_M3_51.png

Flunitrazepam_M3_52.png

Flunitrazepam_M3_53.png

Flunitrazepam_M3_54.png

Localize lone pairs, compute size and orientation:

Subroutines: XOtrans.m  XOYtrans.m  CNCtrans.m  LpyrNtrans.m
Transform the triangle of every target atom with two of its neighbors into the xy-plane and attach lone pair(s). Then back transform the lone pair(s) into the molecular coordinate array. See one of the subroutines. LpyrNtrans puts the base atoms of a pyramid into the xy plane and attaches LP's as needed, the moves these back into the molecule frame.

Flunitrazepam_M3_55.png

Flunitrazepam_M3_56.png

Flunitrazepam_M3_57.png

Flunitrazepam_M3_58.png

Flunitrazepam_M3_59.png

Flunitrazepam_M3_60.png

Flunitrazepam_M3_61.png

Flunitrazepam_M3_62.png

σ Bonding clouds: Connected atom pair, radius of cloud

Flunitrazepam_M3_63.gif

Flunitrazepam_M3_64.png

Flunitrazepam_M3_65.png

Flunitrazepam_M3_66.png

Flunitrazepam_M3_67.png

Flunitrazepam_M3_68.png

Flunitrazepam_M3_69.png

Graphics:Cloud radii (bohr)

Plot molecule and its partial constituents

Flunitrazepam_M3_71.gif

Graphics:Flunitrazepam

Graphics:Core skeleton

Graphics:σ skeleton

Graphics:π-clouds on skeleton

Graphics:Lone Pairs

Graphics:H atoms

Add coordinates of π-clouds and lone pairs. Prepare interaction matrices:

Flunitrazepam_M3_78.png

Flunitrazepam_M3_79.png

Flunitrazepam_M3_80.png

Compute energy components

Interactions for i not j

Flunitrazepam_M3_81.gif

Interactions for i equals j

Flunitrazepam_M3_82.png

Kinetic energy of π clouds and lone pairs

Flunitrazepam_M3_83.png

Flunitrazepam_M3_84.png

Flunitrazepam_M3_85.png

Add components of Ne[10] cores; Politzerratio

Flunitrazepam_M3_86.png

Flunitrazepam_M3_87.png

Results (energies in [Eh] Hartree)

Flunitrazepam_M3_88.png

Flunitrazepam_M3_89.png

Flunitrazepam_M3_90.png

Flunitrazepam_M3_91.png

Flunitrazepam_M3_92.png

Flunitrazepam_M3_93.png

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Flunitrazepam_M3_95.png

Flunitrazepam_M3_96.gif

Flunitrazepam_M3_97.png

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Flunitrazepam_M3_99.png

Flunitrazepam_M3_100.png

Flunitrazepam_M3_101.png

Flunitrazepam_M3_102.png

Created with the Wolfram Language