PLUTON Manual

The connectivity of atoms

DETACH atom-name/atom-type (TO) atom-name/atom-type

This instruction allows the elimination of bonds from the bond list, such as those resulting from intermolecular contact searches or between non-bonded metals.

        Example:
        DETACH CA C

DEFINE Me# TO atom-name1 atom-name2 (...)

Replace set of bonds by one bond to the centre of gravity of the specified atoms. This is particularly useful to represent the eta-5 bond of a metal to a cyclopentadienyl ring:

        Example:
        DEFINE Ti TO C1 C2 C3 C4 C5

JOIN (RADII (UNIQUE (EXPAND)) (NOMOVE) (TOLE tole[0.7]) (TOL tol[0.2])/(atom-type1 r1 atom-type2 r2 ...))

A PLOT instruction that, since the start of the program or after a RESET, was not preceded by any JOIN instruction will automatically invoke the execution of a JOIN RADII UNIQUE EXPAND instruction. This automatically produces a list of connections, an ARU-list and an atom list for the possibly symmetrical molecule(s) in the structure, based on internal covalent atomic radii. All distances between two, possibly symmetry transformed, atoms less than the sum of the covalent radii for the two atoms plus a tolerance (by default tol = 0.2 Angstrom per atom) will be entered in the connection list and related changes or additions are made to the molecule and atom lists. Atoms are moved (unless NOMOVE disables it to do so) to symmetry-equivalent positions in order to form connected fragments. If the molecule has symmetry coincident with space group symmetry operators and only the asymmetric coordinate set supplied, the program will look for connections between the symmetry-related portions of the molecule. This involves the generation of dummy atoms and modification of the molecule list as well so that the PLOT instruction will show the complete molecule.

The radii used for the automatic JOIN instruction can be inspected with the LIST TYPES instruction. The user may override this automatic feature by explicitly specifying the required JOIN instruction(s) before the first PLOT instruction. When the EXPAND sub-keyword is left out the molecules will not be fully symmetry expanded as is needed for molecules exceeding threefold site symmetry. Symmetry is not taken into account when in addition to this the UNIQUE sub-keyword is left out so that the user is held responsible to provide the correct set of atomic coordinates assumed to be already in bonding distance. Also the atomic radii used may be changed by their explicit specification:

        JOIN RADII BI 1.8 I 1.8 UNIQUE EXPAND
        JOIN RADII C 0.85 BR 1.35 H 0.4

This will find all C-C bonds less than 1.7, C-H less than 1.25 and C-Br less than 2.2 Angstrom. Tolerance values are not added to explicitly specified radii. The ARU list is reset to the input set before entering the connection search routine when a JOIN RADII instruction is read and the connection list is also emptied. The TOL sub-keyword may be used to change the value of tol to be used along with the radii drawn from the internal tables (see Appendix V). The single keyword instruction JOIN is equivalent with the expanded form JOIN RADII UNIQUE EXPAND. When appropriate an additional 0.7 Angstrom is added to the tolerance value in the automatic radii mode to catch (earth-)alkali to non-metal contacts.

JOIN RADII INTER (HBONDS) (EXPAND) (TOL tol)/(atom-type1 r1 atom-type2 r2 ..)

To generate intermolecular connections (e.g. Hydrogen bonds), the keyword INTER must follow RADII. This also involves generating dummy atoms and modifying the molecule list so that a subsequent plot will show several molecules unless the list is changed by a MOLES or PACK instruction.

        Example:
        JOIN RADII INTER N 1.5

would form the unique molecule first and then find all potential hydrogen bonding interactions between nitrogen atoms less than 3 Angstrom. Alternatively, the sub-keyword HBONDS may be used for which only H to acceptor contacts are generated:

         e.g. JOIN RADII INTER HBONDS

For JOIN RADII INTER, the molecule list is reset to the list generated by a previous JOIN RADII UNIQUE; the connection list remains at the current setting and the intermolecular connections are added to the list as they are found. When no explicit radii are given on a JOIN RADII INTER card the program will use radii equal to the covalent radii + 0.8 + tol. When only part of the inter radii is specified it is implied that the radii for the remaining atom types is to be set to zero. The instruction JOIN HBONDS is equivalent to the expanded form JOIN RADII INTER HBONDS.

JOIN atom-name TO atom-names (aru)

The first atom on the JOIN card is joined to each of the others.

        Example:
        JOIN Mn1 TO C1 C2 C3 C4

JOIN atom-names/atom-types

This instruction sets up connections explicitly, adding them to those already existing. Each atom is to be joined to the one preceding it and the one following it in the list. Thus to draw a benzene ring with atoms C1, C2, C3, C4, C5 and C6:

        JOIN C1 C2 C3 C4 C5 C6 C1

JOIN NONE/INTRA

A JOIN INTRA instruction deletes intermolecular connections (those generated by JOIN RADII INTER), leaving only intramolecular bonds, including those between symmetry-related parts of a molecule (generated by JOIN RADII UNIQUE). JOIN NONE empties the connection list.