File:Propofol woctanol.webm

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Propofol_woctanol.webm (file size: 1.16 MB, MIME type: video/webm)

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Summary

Description
English: 3D space-filling model of Propofol under physiological conditions (pH 7.4) and under ALPB wetoctanol model.
Tiếng Việt: Mô hình không gian 3D của Propofol trong điều kiện sinh lý (pH 7.4) và mô hình dung môi ALPB wetoctanol.
Date
Source Own work
Author Geoopt1234

Molecular Identifier

InChI: InChI=1S/C12H18O/c1-8(2)10-6-5-7-11(9(3)4)12(10)13/h5-9,13H,1-4H3
InChIKey: OLBCVFGFOZPWHH-UHFFFAOYSA-N

Computational Methodology

  • Geometry Optimization: GFN2-xTB (xtb 6.7.1pre) with triple-extreme accuracy (--acc 0.0001 --ohess extreme --input gbsa_extreme.inp)
  • Solvent Model: ALPB implicit solvation of wetoctanol
  • Protonation State: Net charge = 0 at physiological pH 7.4
  • Convergence: gnorm = 0.000031680080 (rigorous optimization criteria)

Visualization Details

Color Scheme (CPK):

  • Gray: Carbon
  • White: Hydrogen
  • Red: Oxygen

Software & Sources

  • Structure Source: PubChem CID
  • Geometry Optimization: xtb 6.7.1pre (5071a88)
  • Molecular Editor: Avogadro 2 (1.102.1)
  • Visualization: Jmol-16.3.33
  • Animation: FFmpeg (ffmpeg -y -framerate 20 -i frame_%03d.png -c:v libvpx-vp9 -pix_fmt yuva420p -b:v 0 -crf 18 -loop 0 Propofol.webm)
  • InChI Generation: IUPAC InChI Web Demo

SDF and imaginary frequency check

Command : xtb Propofol.sdf --alpb woctanol --acc 0.0001 --ohess extreme --input gbsa_extreme.inp where gbsa_extreme.inp file is

$gbsa
   gbsagrid=extreme
$end

ImaginaryFrequencyCheckFILE

eigval :       -0.00    -0.00    -0.00     0.00     0.00     0.00
eigval :       14.89    27.51    66.03   120.13   162.49   178.80
eigval :      192.29   212.99   218.62   220.54   249.46   258.13
eigval :      292.59   297.39   306.10   401.81   421.65   445.54
eigval :      490.61   513.38   516.33   577.35   605.96   696.50
eigval :      703.77   805.49   814.98   842.57   900.86   917.52
eigval :      934.07   941.96   945.09   961.87   983.61   986.05
eigval :     1067.92  1080.36  1110.27  1125.23  1135.43  1136.78
eigval :     1171.26  1183.63  1193.47  1206.77  1253.18  1289.79
eigval :     1295.59  1302.67  1309.82  1335.16  1359.36  1398.75
eigval :     1402.50  1413.40  1417.54  1455.13  1467.30  1488.77
eigval :     1491.40  1491.82  1492.86  1498.59  1500.41  1502.17
eigval :     1503.64  1588.32  1597.06  2896.73  2964.99  3021.00
eigval :     3021.17  3024.84  3025.05  3025.42  3027.46  3028.94
eigval :     3029.63  3035.65  3037.94  3045.68  3049.35  3069.62
eigval :     3082.20  3091.19  3470.33

Propofolopt.sdf

energy: -38.965756765824 gnorm: 0.000031680080 xtb: 6.7.1pre (5071a88)
         11152510393D
31 31  0     0  0            999 V2000
  -2.2896   -2.6773   -0.3050 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.4436   -2.1755   -2.6254 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.2970    2.3822    2.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
   2.2707    2.8600   -0.1584 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.8758   -1.4405    0.1198 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.6980   -1.9249   -0.4182 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.9779   -0.1023    0.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.6723   -1.6158   -1.2191 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.1022    2.2360    0.6110 C   0  0  0  0  0  0  0  0  0  0  0  0
  -0.3823   -1.0862   -0.6346 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.9218    0.7779    0.2361 C   0  0  0  0  0  0  0  0  0  0  0  0
  -0.2671    0.2712   -0.3020 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.3668    1.0497   -0.5313 O   0  0  0  0  0  0  0  0  0  0  0  0
  -2.4484   -2.2719    0.6919 H   0  0  0  0  0  0  0  0  0  0  0  0
  -3.2484   -3.0017   -0.7037 H   0  0  0  0  0  0  0  0  0  0  0  0
  -1.6398   -3.5453   -0.2233 H   0  0  0  0  0  0  0  0  0  0  0  0
  -0.7718   -3.0301   -2.5989 H   0  0  0  0  0  0  0  0  0  0  0  0
  -1.0066   -1.4148   -3.2687 H   0  0  0  0  0  0  0  0  0  0  0  0
  -2.3890   -2.4943   -3.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
   1.3794    3.4332    2.3924 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.2004    1.8723    2.4470 H   0  0  0  0  0  0  0  0  0  0  0  0
   0.4527    1.9512    2.6580 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.3402    3.9226    0.0650 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.1256    2.7383   -1.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   3.2122    2.3913    0.1139 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.7111   -2.1042    0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   0.6182   -2.9711   -0.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.9002    0.2686    0.8615 H   0  0  0  0  0  0  0  0  0  0  0  0
  -2.3741   -0.7808   -1.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
   0.2083    2.8130    0.3447 H   0  0  0  0  0  0  0  0  0  0  0  0
  -1.2028    1.9616   -0.2571 H   0  0  0  0  0  0  0  0  0  0  0  0
 1  8  1  0  0  0  0
 2  8  1  0  0  0  0
 3  9  1  0  0  0  0
 4  9  1  0  0  0  0
 5  6  2  0  0  0  0
 5  7  1  0  0  0  0
 6 10  1  0  0  0  0
 7 11  2  0  0  0  0
 8 10  1  0  0  0  0
 9 11  1  0  0  0  0
10 12  2  0  0  0  0
11 12  1  0  0  0  0
12 13  1  0  0  0  0
 1 14  1  0  0  0  0
 1 15  1  0  0  0  0
 1 16  1  0  0  0  0
 2 17  1  0  0  0  0
 2 18  1  0  0  0  0
 2 19  1  0  0  0  0
 3 20  1  0  0  0  0
 3 21  1  0  0  0  0
 3 22  1  0  0  0  0
 4 23  1  0  0  0  0
 4 24  1  0  0  0  0
 4 25  1  0  0  0  0
 5 26  1  0  0  0  0
 6 27  1  0  0  0  0
 7 28  1  0  0  0  0
 8 29  1  0  0  0  0
 9 30  1  0  0  0  0
13 31  1  0  0  0  0
M  END
$$$$

Licensing

I, the copyright holder of this work, hereby publish it under the following license:
Creative Commons CC-Zero This file is made available under the Creative Commons CC0 1.0 Universal Public Domain Dedication.
The person who associated a work with this deed has dedicated the work to the public domain by waiving all of their rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.

Captions

3D space-filling model of Propofol under physiological conditions (pH 7.4) and under ALPB wetoctanol model.

Items portrayed in this file

depicts

15 November 2025

video/webm

File history

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Date/TimeDimensionsUserComment
current14:09, 15 November 2025 (1.16 MB)wikimediacommons>Geoopt1234Uploaded own work with UploadWizard

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