Intermolecular interaction energies

ECAL

This calculates the empirical potential energy for a coordination shell of molecules around a reference molecule. The potential parameters are those published by A.Gavezzotti, Acc. Chem. Res. (1994), 27, 309-314 and Crystallography Reviews (1998), 7, 5-121. This includes some H-bonding potentials, but is not comprehensive: if there are H-bonds present, not recognised as one of the types in the table, no special potential is applied. Note also that if elements are present outside the set C,H,N,O,S,Cl,F no potential energy is added for these atoms, giving misleading energy sums.

The method scans for all neighbouring molecules having a molecular centre within a radius (maximum molecular radius + 6.0 Å) of the reference molecular centre. The energy sum for the interactions of this set of neighbouring molecules with the central molecule is calculated, with a listing of each contribution. The screen display selects just those interactions which are less than a certain limit, Elimit, with the default as 1 kcal/mole.

The general purpose of this feature is to display those interactions between molecules which are most significant in energetic terms. Considering the approximate nature of the empirical potentials, the ECAL command should be used in a qualitative rather than a quantitative sense, for the recognition of packing patterns, and relative importance of interactions. Note that this energy sum is for the limited set of neighbouring molecules, and is not the lattice energy.

Typed commands

ECAL ALL selects all molecules using the defaults, and displays them with E < 1.0 kcal/mole.

ECAL ALL [Elimit] [Resopt] [Radopt] displays only molecules with E < Elimit, e.g. -0.5 (kcal/mole).

Resopt = residue number. This is the molecule number in the input coordinates, for example if there are two independent molecules input, ECAL ALL -2.0 2 displays E < -2.0 for molecule 2 as the centre.

Radopt = specific radius of scan for centres, e.g 12.0 (Å).

ECAL n1 n2 displays the interaction between molecules n1 and n2 as clicked in a packing diagram.

ECAL TOP n displays the top n interactions only, counting the lowest energy as being the strongest interaction.

ECAL KCAL displays energies in kcal/mole.

ECAL KJ displays energies in kJ/mole.

ECAL DIST displays the distances between molecular centres.

ECAL NONUM displays no numbers, only the contact lines.

ECAL [COL n1] [RAD n2] [LINES n3] [BREAK n4] displays the interaction lines in emphatic style, with

Example: ECAL COL 2 RAD 0.1 LINES 5 BREAK 9

ECAL DEFAULT resets the default display style. Default setting is COL 5 RAD 1 LINES 1 BREAK 9

ECAL XINTER sets up link-atoms for expansion of a network of molecules using the currently displayed set of molecules (selected by TOP n). This treats the molecular centres as if they are link atoms, so that the configuration of a network of strong interactions can be explored, using the Exp button.

ECAL HBOND includes H-bond parameters in the energy calculation (this is the default).

ECAL NOHBOND excludes H-bond parameters from calculation. The energy is only for the van der Waals interactions. Note that if H-bonds are present this often results in artificial positive contributions to the energy sum.

ECAL HIST outputs a printed set of histograms of distance distribution for each atom type pair in the structure. A calculation is also made of a total distance frequency curve for each atom type, with smoothing, and averaging over the set of atoms of the same type in the molecule. Also outputs RVMIN, the minimum contact distance found for each atom type pair when it is less than the van der Waals radius sum. The curves and RVMIN are also written to a file on Fortran unit 51.

ECAL HISTHYD outputs histograms as above, but with extra analysis of those contacts involving hydrogen.

ECAL OUTD outputs a total list of all interatomic distances contributing to the energy sum to a file on Fortran unit 52, named dijinter which may be useful for research purposes.

Menu buttons

ECal provides a menu interface to features for calculating empirical interaction energies between pairs of molecules.

For all molecule interactions < 1Kcal just click ECal twice.

If a packing diagram is shown, click on any two molecules to give the energy.

The other options available include: