I. Mayer And A. Hamza
Chemistry, Chemical Research Center,
Hungarian Academy of Sciences, H-1525 Budapest, P.O. Box 17, Hungary
e-mails: email@example.com, firstname.lastname@example.org
This "tar" file contains the the APOST-MS program performing ab initio
"quasi-Koopmans" calculations for predicting primary electron impact mass
spectrometric cleavages, as described in the paper I. Mayer and A. Gomory,
Chem. Phys. Letters, 334, 553, 2001. [For the semiempirical counterpart see I.
Mayer and A.Gomory, J.Mol.Struct. (THEOCHEM) 311, 331 (1994).] The program
represents a version of our program APOST, specially modified for the
purposes of mass-spectrometric applications.
The program computes the
1. bond order and valence indices as defined in I. Mayer, Chem.
Letters 97, 270 (1083) [addendum with improved definitions for open-shell
systems: ibid 117, 396 (1985)] and subsequent papers, and the
2. energy components entering the approximate decomposition of
total Born-Oppenheimer energy of the molecule (ion) into one- and
two-center contributions ("Chemical Energy Component Analysis", CECA), as
defined in I. Mayer, Chem. Phys. Letters 332, 381 (2000).
The calculations are performed for the neutral molecule and the
"quasi-Koopmans" ions with one electron deleted from the HOMO and from
some next-to-HOMO orbitals. (The orbitals of the neutral molecule are used
for the ions, too.) The comparison of the bond orders and energy
components obtained for the molecule and the ions can be used to predict
the places in which the primary cleavages may be expected. Some global
data - bond order and valence indices and energy component matrix of the
neutral molecule and the charge distribution and the free valences of the
ionic states - are also given. (The code needs only trivial modifications
- deleting some "comment" C-s at the beginning of some lines - to get all
matrices for every ion, too.)
The program utilizes the "formatted checkpoint" file obtained in a
Gaussian run (G92, G94, G98...?).
Installation and use:
A) After unpacking the file (command "tar -xvf apost-ms") one has to
issue the command "make", and the "Makefile" will govern the
compilation of the program. (On AIX machines some option should be added
to the "link" step.) It may be worth to modify the small script "frun"
to put it into correspondence with the local usage of the Gaussian
program; then all calculations can be performed by issuing the single
where "inputfile" is the name of a standard Gaussian input in which
option "FormCheck" should be added. (The program uses as input the
formatted checkpoint file generated in the Gaussian run.)
Predicting bond cleavages:
One should study the tables containing "appreciably changing" bond
orders and bond energies. The primary bond cleavages are expected at the
places where the bond weakenings are significant for the ionization from
HOMO (sometimes - e.g. for aromatic molecules - for ionization from one of
the next-to-HOMO orbitals). One can expect a bond weakening if there is a
negative changes of bond order (smaller bond multiplicity) and/or a
positive changes of bond energy (less negative diatomic bonding energy
However, weakenings of double and aromatic bonds and - in most cases
bonds formed by hydrogen atoms should not be considered. (Sometimes
weakenings of the bond between the parent ion and a methyl group does not
show up on the MS spectrum, either.) The "static" data calculated here may
be used for predicting the _places_ of the primary bond cleavages, but
usually not the relative ion intensities, governed by a great number of
different (mostly "dynamic") factors.
The "tar" contains simple example input and output files of 2-butanone
(ethyl methyl ketone): the files "etmet" and "etmet.log". Inspection of
both bond order and energy component changes for HOMO indicates that one
can expect the breaking of bonds 1-2 (ethyl loss) and 2-5 (methyl loss).
The bond weakening of the ethyl bond is only slightly larger than that of
the methyl bond, but the dynamic effects mentioned (preference of forming
a larger free radical product) result in the experimental spectrum
dominated by the line at m/z=43 (ethyl loss), the line m/z=57 (methyl
loss) being present but small.
Suggested basis sets: 6-31G** and STO-3G (especially for large systems).