File:Propofol woctanol.webm
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Propofol_woctanol.webm (file size: 1.16 MB, MIME type: video/webm)
This file is from Wikimedia Commons and may be used by other projects. The description on its file description page there is shown below.
Summary
| DescriptionPropofol woctanol.webm |
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:
| 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.
http://creativecommons.org/publicdomain/zero/1.0/deed.enCC0Creative Commons Zero, Public Domain Dedicationfalsefalse |
Captions
3D space-filling model of Propofol under physiological conditions (pH 7.4) and under ALPB wetoctanol model.
Mô hình không gian 3D của Propofol trong điều kiện sinh lý (pH 7.4) và mô hình dung môi ALPB wetoctanol.
15 November 2025
video/webm
File history
Click on a date/time to view the file as it appeared at that time.
| Date/Time | Dimensions | User | Comment | |
|---|---|---|---|---|
| current | 14:09, 15 November 2025 | (1.16 MB) | wikimediacommons>Geoopt1234 | Uploaded own work with UploadWizard |
File usage
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