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When posting a chemical structure, which colors can/should be used to identify various atoms?

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  • 1
    $\begingroup$ Related on main: chemistry.stackexchange.com/q/6287/4945 $\endgroup$ Commented Sep 25, 2017 at 6:02
  • 1
    $\begingroup$ Why not ask on main? It could be duped there... :D $\endgroup$
    – Mithoron
    Commented Sep 25, 2017 at 14:46
  • $\begingroup$ @Mithoron Actually, I just wanted to share the MathJax color palette I use for myself in case anybody else needs it -- just post the structure and copy-paste the necessary lines. Also, it was me who edited that "dupe" post month and a half ago, so yep, there was some influence :P $\endgroup$
    – andselisk Mod
    Commented Sep 25, 2017 at 14:50

3 Answers 3

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For 2D structures, except when emphasis is desired, use of colour should be avoided.

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Many 2D and 3D molecular editors utilize distinctive Jmol color scheme , which can be defined in a legend as such (all colors except for hydrogen are preserved; hydrogen was intentionally made light-gray instead of white):

$\color{#EEEEEE}{\Large\bullet}~\ce{H}$; $\color{#D9FFFF}{\Large\bullet}~\ce{He}$; $\color{#CC80FF}{\Large\bullet}~\ce{Li}$; $\color{#C2FF00}{\Large\bullet}~\ce{Be}$; $\color{#FFB5B5}{\Large\bullet}~\ce{B}$; $\color{#909090}{\Large\bullet}~\ce{C}$; $\color{#3050F8}{\Large\bullet}~\ce{N}$; $\color{#FF0D0D}{\Large\bullet}~\ce{O}$; $\color{#90E050}{\Large\bullet}~\ce{F}$; $\color{#B3E3F5}{\Large\bullet}~\ce{Ne}$; $\color{#AB5CF2}{\Large\bullet}~\ce{Na}$; $\color{#8AFF00}{\Large\bullet}~\ce{Mg}$; $\color{#BFA6A6}{\Large\bullet}~\ce{Al}$; $\color{#F0C8A0}{\Large\bullet}~\ce{Si}$; $\color{#FF8000}{\Large\bullet}~\ce{P}$; $\color{#FFFF30}{\Large\bullet}~\ce{S}$; $\color{#1FF01F}{\Large\bullet}~\ce{Cl}$; $\color{#80D1E3}{\Large\bullet}~\ce{Ar}$; $\color{#8F40D4}{\Large\bullet}~\ce{K}$; $\color{#3DFF00}{\Large\bullet}~\ce{Ca}$; $\color{#E6E6E6}{\Large\bullet}~\ce{Sc}$; $\color{#BFC2C7}{\Large\bullet}~\ce{Ti}$; $\color{#A6A6AB}{\Large\bullet}~\ce{V}$; $\color{#8A99C7}{\Large\bullet}~\ce{Cr}$; $\color{#9C7AC7}{\Large\bullet}~\ce{Mn}$; $\color{#E06633}{\Large\bullet}~\ce{Fe}$; $\color{#F090A0}{\Large\bullet}~\ce{Co}$; $\color{#50D050}{\Large\bullet}~\ce{Ni}$; $\color{#C88033}{\Large\bullet}~\ce{Cu}$; $\color{#7D80B0}{\Large\bullet}~\ce{Zn}$; $\color{#C28F8F}{\Large\bullet}~\ce{Ga}$; $\color{#668F8F}{\Large\bullet}~\ce{Ge}$; $\color{#BD80E3}{\Large\bullet}~\ce{As}$; $\color{#FFA100}{\Large\bullet}~\ce{Se}$; $\color{#A62929}{\Large\bullet}~\ce{Br}$; $\color{#5CB8D1}{\Large\bullet}~\ce{Kr}$; $\color{#702EB0}{\Large\bullet}~\ce{Rb}$; $\color{#00FF00}{\Large\bullet}~\ce{Sr}$; $\color{#94FFFF}{\Large\bullet}~\ce{Y}$; $\color{#94E0E0}{\Large\bullet}~\ce{Zr}$; $\color{#73C2C9}{\Large\bullet}~\ce{Nb}$; $\color{#54B5B5}{\Large\bullet}~\ce{Mo}$; $\color{#3B9E9E}{\Large\bullet}~\ce{Tc}$; $\color{#248F8F}{\Large\bullet}~\ce{Ru}$; $\color{#0A7D8C}{\Large\bullet}~\ce{Rh}$; $\color{#006985}{\Large\bullet}~\ce{Pd}$; $\color{#C0C0C0}{\Large\bullet}~\ce{Ag}$; $\color{#FFD98F}{\Large\bullet}~\ce{Cd}$; $\color{#A67573}{\Large\bullet}~\ce{In}$; $\color{#668080}{\Large\bullet}~\ce{Sn}$; $\color{#9E63B5}{\Large\bullet}~\ce{Sb}$; $\color{#D47A00}{\Large\bullet}~\ce{Te}$; $\color{#940094}{\Large\bullet}~\ce{I}$; $\color{#429EB0}{\Large\bullet}~\ce{Xe}$; $\color{#57178F}{\Large\bullet}~\ce{Cs}$; $\color{#00C900}{\Large\bullet}~\ce{Ba}$; $\color{#70D4FF}{\Large\bullet}~\ce{La}$; $\color{#FFFFC7}{\Large\bullet}~\ce{Ce}$; $\color{#D9FFC7}{\Large\bullet}~\ce{Pr}$; $\color{#C7FFC7}{\Large\bullet}~\ce{Nd}$; $\color{#A3FFC7}{\Large\bullet}~\ce{Pm}$; $\color{#8FFFC7}{\Large\bullet}~\ce{Sm}$; $\color{#61FFC7}{\Large\bullet}~\ce{Eu}$; $\color{#45FFC7}{\Large\bullet}~\ce{Gd}$; $\color{#30FFC7}{\Large\bullet}~\ce{Tb}$; $\color{#1FFFC7}{\Large\bullet}~\ce{Dy}$; $\color{#00FF9C}{\Large\bullet}~\ce{Ho}$; $\color{#00E675}{\Large\bullet}~\ce{Er}$; $\color{#00D452}{\Large\bullet}~\ce{Tm}$; $\color{#00BF38}{\Large\bullet}~\ce{Yb}$; $\color{#00AB24}{\Large\bullet}~\ce{Lu}$; $\color{#4DC2FF}{\Large\bullet}~\ce{Hf}$; $\color{#4DA6FF}{\Large\bullet}~\ce{Ta}$; $\color{#2194D6}{\Large\bullet}~\ce{W}$; $\color{#267DAB}{\Large\bullet}~\ce{Re}$; $\color{#266696}{\Large\bullet}~\ce{Os}$; $\color{#175487}{\Large\bullet}~\ce{Ir}$; $\color{#D0D0E0}{\Large\bullet}~\ce{Pt}$; $\color{#FFD123}{\Large\bullet}~\ce{Au}$; $\color{#B8B8D0}{\Large\bullet}~\ce{Hg}$; $\color{#A6544D}{\Large\bullet}~\ce{Tl}$; $\color{#575961}{\Large\bullet}~\ce{Pb}$; $\color{#9E4FB5}{\Large\bullet}~\ce{Bi}$; $\color{#AB5C00}{\Large\bullet}~\ce{Po}$; $\color{#754F45}{\Large\bullet}~\ce{At}$; $\color{#428296}{\Large\bullet}~\ce{Rn}$; $\color{#420066}{\Large\bullet}~\ce{Fr}$; $\color{#007D00}{\Large\bullet}~\ce{Ra}$; $\color{#70ABFA}{\Large\bullet}~\ce{Ac}$; $\color{#00BAFF}{\Large\bullet}~\ce{Th}$; $\color{#00A1FF}{\Large\bullet}~\ce{Pa}$; $\color{#008FFF}{\Large\bullet}~\ce{U}$; $\color{#0080FF}{\Large\bullet}~\ce{Np}$; $\color{#006BFF}{\Large\bullet}~\ce{Pu}$; $\color{#545CF2}{\Large\bullet}~\ce{Am}$; $\color{#785CE3}{\Large\bullet}~\ce{Cm}$; $\color{#8A4FE3}{\Large\bullet}~\ce{Bk}$; $\color{#A136D4}{\Large\bullet}~\ce{Cf}$; $\color{#B31FD4}{\Large\bullet}~\ce{Es}$; $\color{#B31FBA}{\Large\bullet}~\ce{Fm}$; $\color{#B30DA6}{\Large\bullet}~\ce{Md}$; $\color{#BD0D87}{\Large\bullet}~\ce{No}$; $\color{#C70066}{\Large\bullet}~\ce{Lr}$; $\color{#CC0059}{\Large\bullet}~\ce{Rf}$; $\color{#D1004F}{\Large\bullet}~\ce{Db}$; $\color{#D90045}{\Large\bullet}~\ce{Sg}$; $\color{#E00038}{\Large\bullet}~\ce{Bh}$; $\color{#E6002E}{\Large\bullet}~\ce{Hs}$; $\color{#EB0026}{\Large\bullet}~\ce{Mt}$.

Here is MathJax code which has been used:

$\color{#EEEEEE}{\Large\bullet}~\ce{H}$;
$\color{#D9FFFF}{\Large\bullet}~\ce{He}$;
$\color{#CC80FF}{\Large\bullet}~\ce{Li}$;
$\color{#C2FF00}{\Large\bullet}~\ce{Be}$;
$\color{#FFB5B5}{\Large\bullet}~\ce{B}$;
$\color{#909090}{\Large\bullet}~\ce{C}$;
$\color{#3050F8}{\Large\bullet}~\ce{N}$;
$\color{#FF0D0D}{\Large\bullet}~\ce{O}$;
$\color{#90E050}{\Large\bullet}~\ce{F}$;
$\color{#B3E3F5}{\Large\bullet}~\ce{Ne}$;
$\color{#AB5CF2}{\Large\bullet}~\ce{Na}$;
$\color{#8AFF00}{\Large\bullet}~\ce{Mg}$;
$\color{#BFA6A6}{\Large\bullet}~\ce{Al}$;
$\color{#F0C8A0}{\Large\bullet}~\ce{Si}$;
$\color{#FF8000}{\Large\bullet}~\ce{P}$;
$\color{#FFFF30}{\Large\bullet}~\ce{S}$;
$\color{#1FF01F}{\Large\bullet}~\ce{Cl}$;
$\color{#80D1E3}{\Large\bullet}~\ce{Ar}$;
$\color{#8F40D4}{\Large\bullet}~\ce{K}$;
$\color{#3DFF00}{\Large\bullet}~\ce{Ca}$;
$\color{#E6E6E6}{\Large\bullet}~\ce{Sc}$;
$\color{#BFC2C7}{\Large\bullet}~\ce{Ti}$;
$\color{#A6A6AB}{\Large\bullet}~\ce{V}$;
$\color{#8A99C7}{\Large\bullet}~\ce{Cr}$;
$\color{#9C7AC7}{\Large\bullet}~\ce{Mn}$;
$\color{#E06633}{\Large\bullet}~\ce{Fe}$;
$\color{#F090A0}{\Large\bullet}~\ce{Co}$;
$\color{#50D050}{\Large\bullet}~\ce{Ni}$;
$\color{#C88033}{\Large\bullet}~\ce{Cu}$;
$\color{#7D80B0}{\Large\bullet}~\ce{Zn}$;
$\color{#C28F8F}{\Large\bullet}~\ce{Ga}$;
$\color{#668F8F}{\Large\bullet}~\ce{Ge}$;
$\color{#BD80E3}{\Large\bullet}~\ce{As}$;
$\color{#FFA100}{\Large\bullet}~\ce{Se}$;
$\color{#A62929}{\Large\bullet}~\ce{Br}$;
$\color{#5CB8D1}{\Large\bullet}~\ce{Kr}$;
$\color{#702EB0}{\Large\bullet}~\ce{Rb}$;
$\color{#00FF00}{\Large\bullet}~\ce{Sr}$;
$\color{#94FFFF}{\Large\bullet}~\ce{Y}$;
$\color{#94E0E0}{\Large\bullet}~\ce{Zr}$;
$\color{#73C2C9}{\Large\bullet}~\ce{Nb}$;
$\color{#54B5B5}{\Large\bullet}~\ce{Mo}$;
$\color{#3B9E9E}{\Large\bullet}~\ce{Tc}$;
$\color{#248F8F}{\Large\bullet}~\ce{Ru}$;
$\color{#0A7D8C}{\Large\bullet}~\ce{Rh}$;
$\color{#006985}{\Large\bullet}~\ce{Pd}$;
$\color{#C0C0C0}{\Large\bullet}~\ce{Ag}$;
$\color{#FFD98F}{\Large\bullet}~\ce{Cd}$;
$\color{#A67573}{\Large\bullet}~\ce{In}$;
$\color{#668080}{\Large\bullet}~\ce{Sn}$;
$\color{#9E63B5}{\Large\bullet}~\ce{Sb}$;
$\color{#D47A00}{\Large\bullet}~\ce{Te}$;
$\color{#940094}{\Large\bullet}~\ce{I}$;
$\color{#429EB0}{\Large\bullet}~\ce{Xe}$;
$\color{#57178F}{\Large\bullet}~\ce{Cs}$;
$\color{#00C900}{\Large\bullet}~\ce{Ba}$;
$\color{#70D4FF}{\Large\bullet}~\ce{La}$;
$\color{#FFFFC7}{\Large\bullet}~\ce{Ce}$;
$\color{#D9FFC7}{\Large\bullet}~\ce{Pr}$;
$\color{#C7FFC7}{\Large\bullet}~\ce{Nd}$;
$\color{#A3FFC7}{\Large\bullet}~\ce{Pm}$;
$\color{#8FFFC7}{\Large\bullet}~\ce{Sm}$;
$\color{#61FFC7}{\Large\bullet}~\ce{Eu}$;
$\color{#45FFC7}{\Large\bullet}~\ce{Gd}$;
$\color{#30FFC7}{\Large\bullet}~\ce{Tb}$;
$\color{#1FFFC7}{\Large\bullet}~\ce{Dy}$;
$\color{#00FF9C}{\Large\bullet}~\ce{Ho}$;
$\color{#00E675}{\Large\bullet}~\ce{Er}$;
$\color{#00D452}{\Large\bullet}~\ce{Tm}$;
$\color{#00BF38}{\Large\bullet}~\ce{Yb}$;
$\color{#00AB24}{\Large\bullet}~\ce{Lu}$;
$\color{#4DC2FF}{\Large\bullet}~\ce{Hf}$;
$\color{#4DA6FF}{\Large\bullet}~\ce{Ta}$;
$\color{#2194D6}{\Large\bullet}~\ce{W}$;
$\color{#267DAB}{\Large\bullet}~\ce{Re}$;
$\color{#266696}{\Large\bullet}~\ce{Os}$;
$\color{#175487}{\Large\bullet}~\ce{Ir}$;
$\color{#D0D0E0}{\Large\bullet}~\ce{Pt}$;
$\color{#FFD123}{\Large\bullet}~\ce{Au}$;
$\color{#B8B8D0}{\Large\bullet}~\ce{Hg}$;
$\color{#A6544D}{\Large\bullet}~\ce{Tl}$;
$\color{#575961}{\Large\bullet}~\ce{Pb}$;
$\color{#9E4FB5}{\Large\bullet}~\ce{Bi}$;
$\color{#AB5C00}{\Large\bullet}~\ce{Po}$;
$\color{#754F45}{\Large\bullet}~\ce{At}$;
$\color{#428296}{\Large\bullet}~\ce{Rn}$;
$\color{#420066}{\Large\bullet}~\ce{Fr}$;
$\color{#007D00}{\Large\bullet}~\ce{Ra}$;
$\color{#70ABFA}{\Large\bullet}~\ce{Ac}$;
$\color{#00BAFF}{\Large\bullet}~\ce{Th}$;
$\color{#00A1FF}{\Large\bullet}~\ce{Pa}$;
$\color{#008FFF}{\Large\bullet}~\ce{U}$;
$\color{#0080FF}{\Large\bullet}~\ce{Np}$;
$\color{#006BFF}{\Large\bullet}~\ce{Pu}$;
$\color{#545CF2}{\Large\bullet}~\ce{Am}$;
$\color{#785CE3}{\Large\bullet}~\ce{Cm}$;
$\color{#8A4FE3}{\Large\bullet}~\ce{Bk}$;
$\color{#A136D4}{\Large\bullet}~\ce{Cf}$;
$\color{#B31FD4}{\Large\bullet}~\ce{Es}$;
$\color{#B31FBA}{\Large\bullet}~\ce{Fm}$;
$\color{#B30DA6}{\Large\bullet}~\ce{Md}$;
$\color{#BD0D87}{\Large\bullet}~\ce{No}$;
$\color{#C70066}{\Large\bullet}~\ce{Lr}$;
$\color{#CC0059}{\Large\bullet}~\ce{Rf}$;
$\color{#D1004F}{\Large\bullet}~\ce{Db}$;
$\color{#D90045}{\Large\bullet}~\ce{Sg}$;
$\color{#E00038}{\Large\bullet}~\ce{Bh}$;
$\color{#E6002E}{\Large\bullet}~\ce{Hs}$;
$\color{#EB0026}{\Large\bullet}~\ce{Mt}$.

Example

Here is a structure of dicarbonyl-chloro-(N,N'-(pyridine-2,6-diyl)bis(P,P-diethyl(phosphinous amide)))-iron trifluoromethanesulfonate from a recent paper "Synthesis and Characterization of Cationic Dicarbonyl Fe(II) PNP Pincer Complexes" [1]:

$\color{#EEEEEE}{\Large\bullet}~\ce{H}$; $\color{#909090}{\Large\bullet}~\ce{C}$; $\color{#3050F8}{\Large\bullet}~\ce{N}$; $\color{#FF0D0D}{\Large\bullet}~\ce{O}$; $\color{#90E050}{\Large\bullet}~\ce{F}$; $\color{#FF8000}{\Large\bullet}~\ce{P}$; $\color{#FFFF30}{\Large\bullet}~\ce{S}$; $\color{#1FF01F}{\Large\bullet}~\ce{Cl}$; $\color{#E06633}{\Large\bullet}~\ce{Fe}$.

enter image description here

References

  1. Glatz, M.; Schröder-Holzhacker, C.; Bichler, B.; Stöger, B.; Mereiter, K.; Veiros, L. F.; Kirchner, K. Monatsh Chem 2016, 147 (10), 1713–1719 DOI: 10.1007/s00706-016-1811-x.
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  • $\begingroup$ Ugh.... "hypervalent" sulfur :'( $\endgroup$ Commented Sep 25, 2017 at 6:00
  • $\begingroup$ @Martin-マーチン Boo, S=O bond strikes again. I expected your comment, but not so soon:) Fixed. $\endgroup$
    – andselisk Mod
    Commented Sep 25, 2017 at 6:01
  • $\begingroup$ This is more colour-blind friendly than I expected, but still not very much. =/ $\endgroup$
    – SCH
    Commented Sep 25, 2017 at 19:47
  • 1
    $\begingroup$ Kirchner gave a seminar talk here recently. Are you affiliated? ;D (I though I recognised that type of structure xD) $\endgroup$
    – Jan
    Commented Sep 26, 2017 at 8:31
  • $\begingroup$ @Jan Unfortunately, no, we are not affiliated. I pretty much cherry-picked the structure from CCDC which contains many various atom types from the past 2 years which is compact and not particularly boring. And by "here", do you mean CSE, or Japan?:) $\endgroup$
    – andselisk Mod
    Commented Sep 26, 2017 at 8:34
  • $\begingroup$ Here means the real-world here xD $\endgroup$
    – Jan
    Commented Sep 26, 2017 at 8:38
  • $\begingroup$ @Jan Oh. This is the last thing I would have thought about [:| $\endgroup$
    – andselisk Mod
    Commented Sep 26, 2017 at 8:39
  • $\begingroup$ The JMol color scheme is, infact, the CPK coloring scheme, which JMol has adopted. $\endgroup$ Commented Sep 29, 2017 at 5:00
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    $\begingroup$ @PrittBalagopal Yep, that's what the URL in this answer points to as well. Also, it's Jmol, not JMol. $\endgroup$
    – andselisk Mod
    Commented Sep 29, 2017 at 5:03
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Atoms in JMol and in molecular modelling kits follow the CPK Coloring Scheme.

As a basic identification, hydrogen is white, carbon is grey, oxygen is red, nitrogen is blue, sulfur is yellow, and phosphorus is orange.

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