Periodic Table of Chemical Elements

• Periodic Table Tab
• Advanced Tab

Periodic Table Tab

Chemical elements are available as buttons on the Periodic Table panel of MarvinSketch. Atom buttons are arranged according to the standard periodic table layout.

When the mouse cursor is over a specific atom button, the information panel displays the name of the atom, the atomic number, mass, electronegativity, and the oxidation states. When one of the atom buttons is pressed, the corresponding atom can be placed on the canvas. The atom symbol appears under the mouse cursor, while the button is highlighted.

The Atom List and NOT List buttons can be used to create special atom lists that can be used in queries. When one of these buttons is pressed, atoms can be added to the list by pressing atom buttons one after the other. The lists are not cleared when the list buttons become unselected, use the Clear list button. The atoms of the list are also shown under the mouse cursor above the canvas. For more information regarding atom lists and not lists, see Query features.

The following color schemas are available on this dialog:

• CPK: Colors the atoms according to the Corey-Pauling-Kultun coloring scheme.
• Standard state: Colors according to the standard state of the element (gas, liquid, or solid).
• Blocks: Colors elements according to the highest-energy electron's orbital (s-, p-, d-, or f-block).
• Metals/Nonmetals: Colors according to the metallic character of the elements (alkali, alkaline earth, metalloid, transition metal, other metal, or nonmetal).

Advanced Tab

The figure below shows the Advanced tab of the Periodic Table. For a detailed explanation of the buttons, see Query features.

Generic Query Atoms

Name	Description
A	Any atom except hydrogen.
AH	Any atom including hydrogen.
Q	Heteroatom (any atom except hydrogen and carbon).
QH	Heteroatom or hydrogen (any atom except carbon).
M	Metal (contains alkali metals, alkaline earth metals, transition metals, actinides, lanthanides, poor(basic) metals, Ge, Sb, and Po).
MH	Metal or hydrogen.
X	Halogen (F, Cl, Br, or I).
XH	Halogen or hydrogen.

Atom Query Properties

Name	Description
.H+	Increases the number of hydrogen substituents.
.H-	Decreases the number of hydrogen substituents)
.v+	Increases the valence count (total bond order).
.v-	Decreases the valence count (total bond order).
.X+	Increases the number of connections (number of substituents including hydrogens).
.X-	Decreases the number of connections (number of substituents including hydrogens).
.R-	Increases the number of rings (number of rings the atom is a member of).
.R+	Decreases the number of rings (number of rings the atom is a member of).
.r+	Increases the smallest ring size (size of the smallest ring the atom is a member of).
.r-	Decreases the smallest ring size (size of the smallest ring the atom is a member of).
.rb+	Increases ring bond count (number of ring bonds next to the atom).
.rb-	Decreases ring bond count (number of ring bonds next to the atom).
.s+	Increases substitution count (number of non-hydrogen and isotopic hydrogen substituents).
.s-	Decreases substitution count (number of non-hydrogen and isotopic hydrogen substituents).
.h+	Increases the number of implicit hydrogen substituents.
.h-	Decreases the number of implicit hydrogen substituents.
.D+	Increases degree (equivalent to substitution count except for s*).
.D-	Decreases degree (equivalent to substitution count except for s*).
.u	Marks as an unsaturated atom (atom has double, triple or aromatic bond).
.a/A	Marks as aromatic/aliphatic atom (aromatic means at least one aromatic bond).

Periodic Table Groups

Name	Description
Group 1 (IA, IA)	The alkali metals or hydrogen family/lithium family.
Group 2 (IIA, IIA)	The alkaline earth metals or beryllium family.
Group 3 (IIIA, IIIB)	The scandium family.
Group 4 (IVA, IVB)	The titanium family.
Group 5 (VA, VB)	The vanadium family.
Group 6 (VIA, VIB)	The chromium family.
Group 7 (VIIA, VIIB)	The manganese family.
Group 8 (VIII)	The iron family.
Group 9 (VIII)	The cobalt family.
Group 10 (VIII)	The nickel family.
Group 11 (IB, IB)	The coinage metals or copper family.
Group 12 (IIB, IIB)	The zinc family.
Group 13 (IIIB, IIIA)	The boron family.
Group 14 (IVB, IVA)	The carbon family.
Group 15 (VB, VA)	The pnictogens or nitrogen family.
Group 16 (VIB, VIA)	The chalcogens or oxygen family.
Group 17 (VIIB, VIIA)	The halogens or fluorine family.
Group 18 (Group 0)	The noble gases or helium family/neon family.

Special Nodes and R-groups

Name	Description
Homology groups	The drop-down list contains the default homology groups.
Pol	Pseudo atom Pol. This button changes the selected atom to a pseudo atom labeled Pol (polymer).
*	This button creates a * atom, which indicates an unspecified end group in polymers.

R-groups can be used to describe unknown or unspecified molecule parts or to draw R-group queries or Markush structures.

Custom Properties

Name	Description
R-group	Converts the atom to an R-group with the given number (only numerical characters are allowed). The maximum index is 32767. This atom can be used to describe an unknown or unspecified molecule part or to draw an R-group query or Markush structure.
Alias	The given value is shown as an atom label but the atom itself does not change.
Pseudo	The given value is shown as an atom label and the type of the atom is changed to Any.
SMARTS	Converts the given value to a complex SMARTS query molecule or atom. If the cursor is kept over the canvas during typing, the conversion can be seen on-the-fly.
Value	Adds the given value to an atom as a custom property (Atom value).