Utilities

Screenshot

IsoPat

IsoPat is a small Windows program to calculate isotope patterns for ions of a given elemental composition. It resembles the online Sheffield ChemPuter but has some additional features:

A self-extracting archive containing IsoPat v1.0.1 with a brief documentation can be downloaded here:

IsoPat_SFX.ex_ (376 kB) – rename to EXE
No adware, no viruses; MD5: CF88419621B3A1D9B3683F68FCCBBA72

IsoPat was created with Turbo Delphi 2006



Screenshot

AlignXYZ

AlignXYZ is a small Windows program to align multiple XYZ structures. It has various features:

A self-extracting archive containing AlignXYZ v1.0 with a brief documentation can be downloaded here:

AlignXYZ_SFX.ex_ (416 kB) – rename to EXE
No adware, no viruses; MD5: F909EC61223A4BB093EAE04EFD1F6EE0


AlignXYZ was created with Turbo Delphi 2006



Pentacoordinate geometry description

Pentacoordinate Geometry Analysis

To unambiguously determine the mechanism of stereomutation for five-coordinate compounds, I have developed a complete description of their geometry. In short, the algorithm works as follows:

  1. Given the coordinates of 6 atoms, the atom nearest their centroid is taken to be pentacoordinate;
  2. Based on valence angles, the other five atoms are divided into an axial pair, an equatorial pair, and the pivot;
  3. For each pair, a best-fitting plane through the pivot bond is constructed, and the bond directions are decomposed into in-plane and out-of-plane bending angles (see right);
  4. These are transformed into 7 independent geometrical parameters.

An Excel spreadsheet for performing this analysis on single geometries can be downloaded here; it also contains brief explanations:

Topology.xls (36.0 kB)


Do not hesitate to contact me with questions or comments.