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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 $\endgroup$ – Martin - マーチン Sep 25 '17 at 6:02
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    $\begingroup$ Why not ask on main? It could be duped there... :D $\endgroup$ – Mithoron Sep 25 '17 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 Sep 25 '17 at 14:50
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For 2D structures, except when emphasis is desired, use of colour should be avoided.

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    $\begingroup$ +1, I can imagine why paper journals might want to avoid colored atoms, but is there a good reason for 2D structures be B&W only when displayed on screen? It seems the majority of services such as Chemspider, PubChem, WolframAlpha actually do use CPK colors even when drawing 2D structures, and IMO it helps to comprehend the motif faster. Why stick to black-and-white these days? $\endgroup$ – andselisk Sep 25 '17 at 11:25
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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 :'( $\endgroup$ – Martin - マーチン Sep 25 '17 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 Sep 25 '17 at 6:01
  • $\begingroup$ This is more colour-blind friendly than I expected, but still not very much. =/ $\endgroup$ – SCH Sep 25 '17 at 19:47
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    $\begingroup$ Kirchner gave a seminar talk here recently. Are you affiliated? ;D (I though I recognised that type of structure xD) $\endgroup$ – Jan Sep 26 '17 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 Sep 26 '17 at 8:34
  • $\begingroup$ Here means the real-world here xD $\endgroup$ – Jan Sep 26 '17 at 8:38
  • $\begingroup$ @Jan Oh. This is the last thing I would have thought about [:| $\endgroup$ – andselisk Sep 26 '17 at 8:39
  • $\begingroup$ The JMol color scheme is, infact, the CPK coloring scheme, which JMol has adopted. $\endgroup$ – Pritt says Reinstate Monica Sep 29 '17 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 Sep 29 '17 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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