File:Lidocaine woctanol.webm

From Wikipedia, the free encyclopedia
Jump to navigation Jump to search

Lidocaine_woctanol.webm (file size: 1.6 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

Description
English: 3D space-filling model of Lidocaine under physiological conditions (pH 7.4) and under ALPB wetoctanol model.
Tiếng Việt: Mô hình không gian 3D của Lidocaine 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/C14H22N2O/c1-5-16(6-2)10-13(17)15-14-11(3)8-7-9-12(14)4/h7-9H,5-6,10H2,1-4H3,(H,15,17)/p+1
InChIKey: NNJVILVZKWQKPM-UHFFFAOYSA-O

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 woctanol
  • Protonation State: Net charge = +1 at physiological pH 7.4
  • Convergence: gnorm = 0.000020673206

Visualization Details

Color Scheme (CPK):

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

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 Lidocaine.webm)
  • InChI Generation: IUPAC InChI Web Demo

SDF and imaginary frequency check

Command : xtb Lidocaine.sdf --chrg 1 --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        12.70    29.72    48.37    59.85    74.25    86.58
eigval        97.73   132.44   154.72   169.61   183.13   188.44
eigval       210.20   221.81   252.11   278.47   293.70   308.74
eigval       317.57   338.09   416.64   452.53   466.11   481.35
eigval       486.00   495.47   502.26   539.79   547.55   575.37
eigval       659.01   697.35   738.10   796.60   814.54   828.93
eigval       837.12   880.77   895.49   909.07   927.03   930.76
eigval       956.84   969.25  1007.85  1025.50  1028.36  1032.40
eigval      1050.79  1051.49  1063.45  1081.69  1097.88  1123.56
eigval      1145.10  1162.29  1174.77  1186.59  1188.34  1198.89
eigval      1220.97  1236.04  1246.17  1260.10  1288.61  1298.12
eigval      1307.48  1319.90  1326.09  1337.66  1395.89  1396.00
eigval      1399.70  1410.19  1419.81  1426.48  1443.40  1450.32
eigval      1454.05  1458.56  1474.26  1474.72  1478.18  1478.85
eigval      1480.66  1484.32  1486.63  1487.99  1588.73  1591.03
eigval      1715.29  2718.28  2994.93  2997.25  2999.61  3002.52
eigval      3006.12  3007.55  3009.36  3017.45  3018.28  3028.40
eigval      3045.93  3047.40  3052.37  3053.45  3056.46  3058.41
eigval      3068.21  3068.63  3079.09  3084.55  3096.12  3394.56

Lidocaineopt.sdf 

energy: -51.327977043049 gnorm: 0.000020673206 xtb: 6.7.1pre (5071a88)
         11182520423D
40 40  0     0  0            999 V2000
   0.8242   -0.3337   -0.8775 O   0  0  0  0  0  0  0  0  0  0  0  0
   3.1003   -0.2156    0.2554 N   0  0  0  0  0  0  0  0  0  0  0  0
  -0.4296    0.3391    0.9073 N   0  0  0  0  0  0  0  0  0  0  0  0
   1.9973    0.3048    1.0859 C   0  0  0  0  0  0  0  0  0  0  0  0
   4.2117    0.7508    0.0683 C   0  0  0  0  0  0  0  0  0  0  0  0
   3.5725   -1.5533    0.7080 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.7057    0.0712    0.2710 C   0  0  0  0  0  0  0  0  0  0  0  0
   3.8176    1.8992   -0.8473 C   0  0  0  0  0  0  0  0  0  0  0  0
   4.2276   -2.3403   -0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.7319    0.2205    0.3384 C   0  0  0  0  0  0  0  0  0  0  0  0
  -2.5301    1.3669    0.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
  -2.1914   -1.0125   -0.1241 C   0  0  0  0  0  0  0  0  0  0  0  0
  -3.8037    1.2646   -0.2458 C   0  0  0  0  0  0  0  0  0  0  0  0
  -3.4702   -1.0712   -0.6656 C   0  0  0  0  0  0  0  0  0  0  0  0
  -2.0150    2.6776    0.8094 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.3515   -2.2489   -0.0340 C   0  0  0  0  0  0  0  0  0  0  0  0
  -4.2695    0.0542   -0.7289 C   0  0  0  0  0  0  0  0  0  0  0  0
   2.6127   -0.3638   -0.6716 H   0  0  0  0  0  0  0  0  0  0  0  0
   1.9562   -0.2055    2.0483 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.1237    1.3744    1.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
   4.5167    1.1174    1.0503 H   0  0  0  0  0  0  0  0  0  0  0  0
   5.0502    0.2176   -0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
   4.2653   -1.4107    1.5392 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.7041   -2.1140    1.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
   4.6801    2.5414   -1.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
   3.4966    1.5282   -1.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
   3.0218    2.5117   -0.4324 H   0  0  0  0  0  0  0  0  0  0  0  0
   4.4800   -3.3320   -0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
   3.5441   -2.4576   -1.2544 H   0  0  0  0  0  0  0  0  0  0  0  0
   5.1449   -1.8801   -0.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
  -0.3920    0.7697    1.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
  -4.4328    2.1407   -0.2923 H   0  0  0  0  0  0  0  0  0  0  0  0
  -3.8427   -2.0151   -1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
  -2.7161    3.4736    0.5751 H   0  0  0  0  0  0  0  0  0  0  0  0
  -1.8938    2.6470    1.8925 H   0  0  0  0  0  0  0  0  0  0  0  0
  -1.0551    2.9221    0.3576 H   0  0  0  0  0  0  0  0  0  0  0  0
  -1.9615   -3.1314   -0.2042 H   0  0  0  0  0  0  0  0  0  0  0  0
  -0.5681   -2.2224   -0.7911 H   0  0  0  0  0  0  0  0  0  0  0  0
  -0.8834   -2.3302    0.9456 H   0  0  0  0  0  0  0  0  0  0  0  0
  -5.2609   -0.0115   -1.1510 H   0  0  0  0  0  0  0  0  0  0  0  0
 1  7  2  0  0  0  0
 2  4  1  0  0  0  0
 2  5  1  0  0  0  0
 2  6  1  0  0  0  0
 2 18  1  0  0  0  0
 3  7  1  0  0  0  0
 3 10  1  0  0  0  0
 3 31  1  0  0  0  0
 4  7  1  0  0  0  0
 4 19  1  0  0  0  0
 4 20  1  0  0  0  0
 5  8  1  0  0  0  0
 5 21  1  0  0  0  0
 5 22  1  0  0  0  0
 6  9  1  0  0  0  0
 6 23  1  0  0  0  0
 6 24  1  0  0  0  0
 8 25  1  0  0  0  0
 8 26  1  0  0  0  0
 8 27  1  0  0  0  0
 9 28  1  0  0  0  0
 9 29  1  0  0  0  0
 9 30  1  0  0  0  0
10 11  2  0  0  0  0
10 12  1  0  0  0  0
11 13  1  0  0  0  0
11 15  1  0  0  0  0
12 14  2  0  0  0  0
12 16  1  0  0  0  0
13 17  2  0  0  0  0
13 32  1  0  0  0  0
14 17  1  0  0  0  0
14 33  1  0  0  0  0
15 34  1  0  0  0  0
15 35  1  0  0  0  0
15 36  1  0  0  0  0
16 37  1  0  0  0  0
16 38  1  0  0  0  0
16 39  1  0  0  0  0
17 40  1  0  0  0  0
M  CHG  1   2   1
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 Lidocaine under physiological conditions (pH 7.4) and under ALPB wetoctanol model.

Items portrayed in this file

depicts

lidocaine

inception

18 November 2025

media type

video/webm

File history

Click on a date/time to view the file as it appeared at that time.

Date/TimeDimensionsUserComment
current15:17, 18 November 2025 (1.6 MB)wikimediacommons>Geoopt1234Uploaded own work with UploadWizard

The following page uses this file:

Retrieved from "https://wiki.sarg.dev/index.php/File:Lidocaine_woctanol.webm"