CPK coloring

In chemistry, the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models.

A plastic ball-and-stick model of proline. These models usually comply with CPK coloring.

HistoryEdit

In 1952, Corey and Pauling published a description of space-filling models of proteins and other biomolecules that they had been building at Caltech.[1] Their models represented atoms by faceted hardwood balls, painted in different bright colors to indicate the respective chemical elements. Their color schema included

They also built smaller models using plastic balls with the same color schema.

In 1965 Koltun patented an improved version of the Corey and Pauling modeling technique.[2] In his patent he mentions the following colors:

Typical assignmentsEdit

 
A box of ball-and-stick model pieces colored to represent several of the common elements.

Typical CPK color assignments include:

  hydrogen (H) white
  carbon (C) black
  nitrogen (N) blue
  oxygen (O) red
  fluorine (F), chlorine (Cl) green
  bromine (Br) dark red
  iodine (I) dark violet
  noble gases (He, Ne, Ar, Kr, Xe) cyan
  phosphorus (P) orange
  sulfur (S) yellow
  boron (B), most transition metals beige
  alkali metals (Li, Na, K, Rb, Cs, Fr) violet
  alkaline earth metals (Be, Mg, Ca, Sr, Ba, Ra) dark green
  titanium (Ti) grey
  iron (Fe) dark orange
  other elements pink

Several of the CPK colors refer mnemonically to colors of the pure elements or notable compound. For example, hydrogen is a colorless gas, carbon as charcoal, graphite or coke is black, sulfur powder is yellow, chlorine is a greenish gas, bromine is a dark red liquid, iodine in ether is violet, amorphous phosphorus is red, rust is dark orange-red, etc. For some colors, such as those of oxygen and nitrogen, the inspiration is less clear. Perhaps red for oxygen is inspired by the fact that oxygen is normally required for combustion or that the oxygen-bearing chemical in blood, hemoglobin, is bright red, and the blue for nitrogen by the fact that nitrogen is the main component of Earth's atmosphere, which appears to human eyes as being colored sky blue.

It is likely that the CPK colours were inspired by models in the nineteenth century. In 1865, August Wilhelm Hofmann, in a talk at the Royal Institution in London, was using models made from croquet balls to illustrate valence, so he used the coloured balls available to him. (At the time, croquet was the most popular sport in England, so the balls were plentiful.) "On the Combining Power of Atoms", Chemical News, 12 (1865, 176-9, 189, states that "Hofmann, at a lecture given at the Royal Institution in April 1865 made use of croquet balls of different colours to represent various kinds of atoms (e.g. carbon black, hydrogen white, chlorine green, 'fiery' oxygen red, nitrogen blue)."[3][4]

Modern variantsEdit

 
Example of Jmol coloring

The following table shows colors assigned to each element by some popular software products. Column C is the original assignment by Corey and Pauling,[1] and K is that of Koltun's patent.[2] Column J is the color scheme used by the molecular visualizer Jmol.[5] Column R is the scheme used by Rasmol; when two colors are shown, the second one is valid for versions 2.7.3 and later.[5][6] Column P consists of the colors in the PubChem database managed by the United States National Institute of Health. All colors are approximate and may depend on the display hardware and viewing conditions.

Colors
Z Symbol Element C K J R P
Corey
Koltun
Jmol
Rasmul
PubChem
1 H hydrogen          
1 2H (D) deuterium    
1 3H (T) tritium    
2 He helium      
3 Li lithium       
4 Be beryllium      
5 B boron      
6 C carbon           
6 13C carbon-13    
6 14C carbon-14    
7 N nitrogen           
7 15N nitrogen-15    
8 O oxygen           
9 F fluorine        
10 Ne neon      
11 Na sodium      
12 Mg magnesium      
13 Al aluminium       
14 Si silicon      
15 P phosphorus         
16 S sulfur         
17 Cl chlorine        
18 Ar argon      
19 K potassium      
20 Ca calcium       
21 Sc scandium      
22 Ti titanium       
23 V vanadium      
24 Cr chromium       
25 Mn manganese       
26 Fe iron         
27 Co cobalt        
28 Ni nickel         
29 Cu copper         
30 Zn zinc       
31 Ga gallium      
32 Ge germanium      
33 As arsenic      
34 Se selenium      
35 Br bromine         
36 Kr krypton      
37 Rb rubidium      
38 Sr strontium      
39 Y yttrium      
40 Zr zirconium      
41 Nb niobium      
42 Mo molybdenum      
43 Tc technetium      
44 Ru ruthenium      
45 Rh rhodium      
46 Pd palladium      
47 Ag silver       
48 Cd cadmium      
49 In indium      
50 Sn tin      
51 Sb antimony      
52 Te tellurium      
53 I iodine        
54 Xe xenon      
55 Cs caesium      
56 Ba barium       
57 La lanthanum      
58 Ce cerium      
59 Pr praseodymium      
60 Nd neodymium      
61 Pm promethium      
62 Sm samarium      
63 Eu europium      
64 Gd gadolinium      
65 Tb terbium      
66 Dy dysprosium      
67 Ho holmium      
68 Er erbium      
69 Tm thulium      
70 Yb ytterbium      
71 Lu lutetium      
72 Hf hafnium      
73 Ta tantalum      
74 W tungsten      
75 Re rhenium      
76 Os osmium      
77 Ir iridium      
78 Pt platinum      
79 Au gold      
80 Hg mercury      
81 Tl thallium      
82 Pb lead      
83 Bi bismuth      
84 Po polonium      
85 At astatine      
86 Rn radon      
87 Fr francium      
88 Ra radium      
89 Ac actinium      
90 Th thorium      
91 Pa protactinium      
92 U uranium      
93 Np neptunium      
94 Pu plutonium      
95 Am americium      
96 Cm curium      
97 Bk berkelium      
98 Cf californium      
99 Es einsteinium      
100 Fm fermium      
101 Md mendelevium      
102 No nobelium      
103 Lr lawrencium      
104 Rf rutherfordium      
105 Db dubnium      
106 Sg seaborgium      
107 Bh bohrium      
108 Hs hassium      
109 Mt meitnerium      
110 Ds darmstadtium    
111 Rg roentgenium    
112 Cn copernicium    
113 Nh nihonium  
114 Fl flerovium  
115 Mc moscovium  
116 Lv livermorium  
117 Ts tennessine  
118 Og oganesson  

See alsoEdit

ReferencesEdit

  1. ^ a b Robert B. Corey and Linus Pauling (1953): Molecular Models of Amino Acids, Peptides, and Proteins. Review of Scientific Instruments, Volume 24, Issue 8, pp. 621-627. doi:10.1063/1.1770803
  2. ^ a b "CPK" stands for Corey-Pauling-Koltun. Walter L. Koltun (1965), Space filling atomic units and connectors for molecular models. U. S. Patent 3170246.
  3. ^ Chemical News and Journal of Industrial Science, Volume 12.
  4. ^ Maurice P. Crosland (1962). Historical Studies in the Language of Chemistry. p. 336, and footnote 220 on page 336.
  5. ^ a b Jmol color table at sourceforge.net. Accessed on 2010-01-28.
  6. ^ Rasmol color table Archived 2001-05-13 at archive.today at bio.cmu.edu. Accessed on 2010-01-28.

External linksEdit