Notes on the comparison of PM7 and Materials Studio
calculation of an amorphous solid

Introduction

The geometries resulting from a Materials Studio calculation of an amorphous solid were compared with the results of an unconstrained PM7 optimization of the same system.

Results of MOPAC calculation

A 1SCF calculation on the Materials Studio geometry was compared with the fully-optimized PM7 geometry in which the starting point was the Materials Studio geometry.  The amorphous repeat unit consisted of 58 formula units.

Geometry optimization resulted in the formula unit DH_f decreasing by 14.9 kcal∙mol^-1, and the unit cell dimension decreasing by an average of 2.8% = 100((1.100/1.013)^1/3 - 1.0).

The unit cell changed from 22.766 Å, 22.766 Å,  22.766 Å  90.00˚,  90.00˚,  90.00˚ to 22.504 Å, 21.061 Å, 23.037 Å,  88.99˚,  95.12˚,  89.36˚.

Comparison of Geometries

The data set for comparing geometries was named "Compare PM7 and Materials studio.mop" and consisted of two lines:

Line 1: geo_dat="resin 1SCF.arc" geo_ref="resin Unconstrained optimization.arc"0 0scf html output"
Line 2: Comparison of PM7 and Materials Design geometries of an amorphous solid

Line 1: Keyword GEO_DAT specifies the geometry of one of the two species being compared. Keyword GEO_REF specifies the other geometry.  The "0" after the GEO-REF keyword is needed by MOPAC, but doesn't do anything.  This needs to be deleted "some time."  Keyword 0SCF suppresses any SCF calculations, and keyword HTML requests that a JSmol HTML web-page be written - this shows the two systems one superimposed on the other.  Keyword OUTPUT suppresses most of the output.

Line 2: A one-line description of the system.  This is useful when working with HTML files.

Results of comparison of geometries

The Root Mean Square Difference between the two geometries was 1.63 Å, most of this was caused by the formation of hydrogen bonds.  In the Material Studio structure the water molecules did not form hydrogen bonds with other moieties.

The largest individual difference in a bond-length was 0.094 Å in a water molecule.  In general, Materials Studio under-estimated O-H bond-lengths by 0.04 Å.  A single spurious O-H bond length (0.338 Å) was reported for PM7.  This was an artifact caused by the translation vectors of one geometry (Materials Studio) being used by the other geometry.

In the PM7 geometry, there were 18 hydrogen bonds in the Materials Studio structure, and 57 hydrogen bonds in the PM7 structure.  These contributed 4.16 kcal∙mol^-1 of stabilization to the PM7 structure.

Summary

Both the PM7 and Materials Studio geometries were similar.  The main differences were the result of the formation of more hydrogen bonds in the PM7 structure. No anomalies in either geometry were found.