AOMix

CURRENT VERSION: 6.11, the recent and planned software modifications

AOMix is a user-friendly software for the molecular orbital (MO) analysis. It calculates the MO compositions in terms of the constituent chemical fragments (you can specify them as atoms, groups of atoms, atomic orbitals, fragment molecular orbitals, groups of atomic orbitals, etc.) in the molecule or atom. AOMix automatically processes output files of multiple quantum-chemical packages (see the list below). AOMix also allows you to analyze chemical structure (bonding/antibonding nature of molecular orbitals) using overlap populations (total and per molecular orbital), 2-center (Mayer, Lowdin, Wiberg) and 3-center bond orders, charge decomposition analysis, CDA (total and per molecular orbital), and condensed Fukui functions.

In addition, AOMix generates total, partial and overlap population density-of-states (DOS) plots (see Figures 1 and 2). Overlap population DOS plots are also refered in the literature as Crystal Orbital Overlap Population (COOP) diagrams.

A very important part of quantum chemical research is to interpret the results in terms of qualitative concepts. This software was developed to help in the analysis of the nature of the chemical bonding in molecular systems and to monitor changes in the electron density distribution upon the electron excitation. Let's say, there is a band in an absorption spectrum of a molecule or an ion at 400 nm which is assigned to a HOMO -> LUMO+2 electron excitation. What does it tell us about properties of this molecule/ion? What do we know about the nature of the corresponding excited state? What will happen with this molecule / ion after the photoexcitation? AOMix helps to answer these questions.

With AOMix and its AOMix-x modules, you can

calculate molecular orbital compositions in terms of fragment atomic or molecular orbitals;
analyze bonding / antibonding contributions of molecular orbitals to the electronic structure (using overlap populations);
calculate the amount of electron donation and back-donation between molecular fragments (using the charge decomposition analysis, CDA, implemented in the AOMix-CDA module);
create total, partial and overlap population density-of-states plots;
calculate condensed Fukui functions;
calculate charge transfer characters of electronic transitions; and
calculate the two-center (Mayer, Wiberg, Lowdin) and three-center bond orders between molecular fragments.

Examples of the data generated using AOMix are given in the following publications:

Structure & Bonding 2003, 107, 77-114 [PDF file].
J. Amer. Chem. Soc. 2003, 125, 15708-15709. [PDF file].
S.I.Gorelsky, in Comprehensive Coordination Chemistry II Volume 2. Elsevier, 2004. Chapter 2.51, pp 651-660.
Canadian J. of Analytical Sciences and Spectroscopy 2003, 48 (1), 93-105 (Tables 1-4) [PDF file].
J. Organomet. Chem. 2001, 635, 187-196 [PDF file]. (Table 2)
Coord. Chem. Rev. 1998, 174, 469-494 (Tables 4-6).


	The following procedures for the electron population analysis are available in the AOMix package:

Mulliken population analysis (MPA)

modified Mulliken population analysis (MMPA) (using AOMix-S)

C² population analysis (SCPA)

Lowdin population analysis (LPA) and other methods based on the S^a x P x S^1-a formula (using AOMix-L)

charge decomposition analysis (CDA) (using AOMix-CDA)

Supported operating systems	AOMix	AOMix-x
MS Windows 2000, Windows XP	+	+
Red Hat Linux 9.0 and Fedora	n/a	will be available in 2005


	DOWNLOAD: Software download, available for AOMix registered users (if you forgot the login username/password or your password does not allow to login, please contact the author); AOMix-manual.pdf – a manual for AOMix and its additional modules; Adobe Acrobat Reader 5.0 or higher is required to open this pdf file; EXAMPLES.zip – a zip file with a set of AOMix input and output examples.


	How to refer to the AOMix program in publications:

Compositions of molecular orbitals, overlap populations between molecular fragments, bond orders and density-of-states spectra were calculated using the AOMix program [1,2].

S. I. Gorelsky, AOMix program, http://www.sg-chem.net/
S. I. Gorelsky, A. B. P. Lever, J. Organomet. Chem. 2001, 635, 187-196.


	AOMix processes output files from the following programs (other quantum chemistry packages can be also included)

	ADF 200x (Scientific Computing & Modelling NV). AOMix has been tested with the following versions: ADF 2000.01, ADF 2002.03, ADF 2003.01 and ADF 2004.01; please note that ADF calculations with core functions cannot be processed by the current version of AOMix.
	CNDO/INDO (by J.R. Reimers, University of Sydney, Australia)
	The General Atomic and Molecular Electronic Structure System GAMESS from Iowa State University and PC GAMESS from Moscow State University. AOMix has been tested with the following versions: GAMESS-US 6, GAMESS VERSION = 12.
	Gaussian 98 and Gaussian 03 (Gaussian, Inc.)
	HyperChem 4.x-7.x (HyperCube, Inc.)
	Jaguar 3.x-5.x (Schrodinger, Inc.). AOMix has been tested with the following versions: Jaguar 3.5, Jaguar 4.1, Jaguar 4.2, Jaguar 5.0 and Jaguar 5.5
	MOPAC (J. J. P. Stewart, Fujitsu Limited) AOMix has been tested with the following versions: MOPAC 2002
	Spartan ‘0x (Wavefunction, Inc.). AOMix has been tested with the following versions: Spartan ’02 and Spartan ’03
	ZINDO (by M.C. Zerner, Quantum Theory Project, University of Florida; ZINDO is available in Cerius² (Accelrys Inc.) and CAChe (CAChe Group, Fujitsu))


	How to obtain a copy of AOMix:

If you would like to obtain the AOMix program for yourself, your research group or company, please follow these instructions.

Last updated: March 2005.