Basics to rez molecules in 3D

Most of the organic molecules could be rez in 2D.
But the carbon have 4 bonds, 4 rods. Methane, ammonium are tetrahedral.
And we must study the geometry of tetrahedron !

For chemistry, Wikipedia say :

“The tetrahedron shape is seen in nature in covalent bonds of molecules. For instance in a methane molecule (CH4) the four hydrogen atoms lie in each corner of a tetrahedron with the carbon atom in the centre. For this reason, one of the leading journals in organic chemistry is called Tetrahedron.”

1) First step : geometry of a triangle

Triangles

from the positions of triangles to the orientation of covalents bonds.

Carboxyl

 

 

 

x

y

z

1

C

a

b

c

2

C

a+d

b

c

3

O

a-d/3

b+2*sqr(2)/3*d

c

4

O

a-d/3

b-2*sqr(2)/3*d

c

2) Second step : geometry of a tetrahedron

Tetrahedron

Tetrahedron : differents views…

vertical projection of methane

 

 

 

d: covalent bond & a: side of the terahedron

[More with this source ]

a = 2*sqr(2/3) * d

EF=EG=FG=DE=DF=DG=a

CE=CD=CF=CG=d

AC=d/3

AE=a/sqr(3)

AM=a/[2*sqr(3)]

EM=a*sqr(3)/2

CM=a/[2*sqr(2)]

Methane positions

Side view of the methane

 

 

 

x

y

z

z’

1

C

a

b

c

 

2

H

a+d

b

c

 

3

H

a-d/3

b

c+2*sqr(2)/3*d

c-2*sqr(2)/3*d

4

H

a-d/3

b-sqr(2/3)*d

c-2*sqr(2)/3*d

c+sqr(2)/3*d

5

H

a-d/3

b+sqr(2/3)*d

c-2*sqr(2)/3*d

c+sqr(2)/3*d

 

3) Data : colors and dimensions

The common colors used for molecular models are those defined by Corey, Pauling and Kultun (the CPK system).

 

Element

Symbol

Color

Hexa code

SL vector

Covalent radius (Ǻ)

Carbon / carbone

C

Clear grey / gris clair

#c8c8c8

<0.784,0.784,0.784>

0,77

Oxygen / oxygène

O

Red / rouge

#ff0000

<1.0,0.0,0.0>

0,73

Hydrogen / hydrogène

H

White / blanc

#ffffff

<1.0,1.0,1.0>

0,37

Nitrogen / azote

N

Clear blue / bleu clair

#8f8fff

<0.5608,0.5608,1.0>

0,75

Sulfur / soufre

S

Yellow / jaune

#ffc832

<1.0,0.784,0.196>

1,02

Phosphorus / phosphore

P

Orange

#ffa500

<1.0,0.647,0.0>

1,06

Chlorine / chlore

Cl

Green / vert

#00ff00

<0.0,1.0,0.0 >

0,99

Bromine / brome, Zinc

Br, Zn

Brown / marron

#a52a2a

<0.647,0.1647,0.1647>

1,14 , 1,31

Natrium / sodium

Na

Blue / bleu

#0000ff

<0.0,0.0,1.0>

1,54

Iron / fer

Fe

Purple / violet

#a020f0

<0.6275,0.1255,0.9412>

1,25

Calcium, métaux

Ca

Dark grey / gris foncé

#808090

<0.5,0.5,0.5647>

1,74

Unknown

Deep pink / rose foncé

#ff1493

<1.0,0.0784,0.5765 >

d (C/H) = 1,02 Ǻ

d (O/H) = 0,96 Ǻ

d (N/H) = 1,01 Ǻ

d (C/C) = 1,54 Ǻ

d (C//C) = 1,33 Ǻ

d (C///C) = 1,20 Ǻ

d (C//C) benzen = 1,40 Ǻ

d (C/O) = 1,43 Ǻ

d (C//O) = 1,26 Ǻ

d (C/N) = 1,47 Ǻ

d (C///N) = 1,15 Ǻ

d (C/Cl) = 1,77 Ǻ

d (C/Br) = 1,94 Ǻ

d (C/S) = 1,82 Ǻ

More on chemical bond

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