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AOMix-CDA, AOMix-L, and AOMix-S are additional programs to AOMix.exe.

	AOMix	AOMix-CDA	AOMix-L	AOMix-S
CURRENT VERSION:	6.36	2.19	1.70	2.40	recent & planned software updates

Upcoming Events: Eastern Canadian Magnetism Meeting (May 9-10, 2008) Dr. S. Gorelsky will give a presentation on AOMix and its research capabilities at the Department of Chemistry and Chemical Biology, the University of New Mexico (Albuquerque, NM) on September 5, 2008.

AOMix-CDA generates a wave function of a multi-fragment molecular system from the fragment wave functions (refer to APPENDIX II of the AOMix manual for details); performs the analysis of MO compositions in terms of fragment molecular orbitals (FOs). The number of fragments can be from 1 (in this case, the analysis is performed relative to a user-defined, reference electronic state, see for example [PDF]) up to 99. The program is able to treat all spin-coupling cases: ferromagnetic coupling (alpha-spin FOs of Fragment X couple with alpha-spin FOs of Fragment Y, beta-spin FOs of Fragment X couple with beta-spin FOs of Fragment Y) anti-ferromagnetic coupling (alpha-spin FOs of Fragment X couple with beta-spin FOs of Fragment Y, beta-spin FOs of Fragment X couple with alpha-spin FOs of Fragment Y) any possible combination of ferromagnetic and anti-ferromagnetic for a case of multiple fragments; calculates the amount of electron donation between fragments (the charge decomposition analysis, CDA), calculates fragment orbital populations in a molecule, calculates atomic orbital populations in a molecule, in non-interacting fragments (or a reference molecule if the number of fragments is 1) and the difference in AO populations, prints the LCFO-MO coefficient matrix and the FO overlap matrix, (AOMix-CDA version 2.2 and up) calculates Green function matrix elements for molecular systems with 3 fragments (donor-bridge-acceptor), Gij(E); can be used for energy decomposition analysis (Morokuma's EDA), for Gaussian 98/03 calculations; and generates the plot data for orbital interaction diagrams (see the examples below).

With AOMix-CDA, you can analyze the electronic structure and bonding in molecules in great detail, calculate charge transfer (CT) and electronic polarization (PL) contributions, evaluate the sigma- and pi- bonding interactions, etc. [PDF file]

Here is an example of the AOMix-CDA output:

1. AOMix-CDA.txt
2. AOMix-MO-FO-alpha.txt

It is the charge decomposition analysis of the BH₃CO molecule (fragment 1 is BH₃ and fragment 2 is CO, HyperChem AM1 calculations). According to the analysis, the charge donation from CO to BH₃ is 0.417 electrons and the back-donation from BH₃ to CO is 0.143 electrons).

AOMix-CDA also sets up data files for plotting the MO interaction diagrams, see Figures below.

Similar donation/back-donation charges (0.47 and 0.18 electrons respectively) are obtained from Gaussian 03 calculations at the HF/6-31G* level:

1. AOMix-CDA.txt
2. AOMix-MO-FO-alpha.txt

Advantanges of the AOMix-CDA program:

1. AOMix-CDA can handle more than two molecular fragments (up to 99 fragments). This allows the analysis of more complex molecular systems (such as bridged metal complexes L1-M1-bridge-M2-L2, for example) than just simple binary donor-acceptor complexes;
2. AOMix-CDA can be used for spin-restricted, spin-unrestricted and "mixed" (spin-restricted and spin-unrestricted) calculations.

Here is an example of the AOMix-CDA calculation with 3 fragments where the whole molecule and the 1st fragment are treated at the spin-unrestricted DFT level (open-shell species), and the 2nd and 3rd fragments are treated at the spin-restricted DFT level (closed-shell species):

1. AOMix-CDA.txt
2. AOMix-MO-FO-a.txt
3. AOMix-MO-FO-b.txt

The orbital interaction diagram (using Gaussian 03 and AOMix-CDA at the B3LYP/TZVP level) of the Cu(HB(3,5-iPr₂pz)₃) and thiolate SC₆F₅ fragments forming the [Cu(HB(3,5-iPr₂pz)₃)(SC₆F₅)] complex. p (a₂ symmetry) orbitals are shown in blue color and s orbitals (a₁ symmetry) are in red.

For more details, check the following publications:

Spectroscopic and DFT Investigation of [M(HB(3,5-iPr₂pz)₃)(SC₆F₅)], (M = Mn, Fe, Co, Ni, Cu and Zn) Model Complexes: Periodic Trends in Metal-Thiolate Bonding.
S. I. Gorelsky, L. Basumallick, J. Vura-Weis, R. Sarangi, B. Hedman, K. O. Hodgson, K. Fujisawa, E. I. Solomon
Inorg. Chem., 2005, 44, 4947-4960 [PDF].

Metal-thiolate bonds in bioinorganic chemistry
E. I. Solomon, S. I. Gorelsky, A. Dey
J. Comput. Chem., 2006, 27, 1415-1428 [PDF].

The orbital interaction diagram (computed using Gaussian 03 and AOMix-CDA at the B3LYP/LanL2DZ level) of the Ru(NH₃)₂Cl₂ and BQDI fragments forming the [Ru(NH₃)₂Cl₂(BQDI)] complex.

In this complex, the BQDI-to-Ru donation is produced by the interactions involving fragment orbitals of a₁ and b₂ symmetries, namely, HOFO-1 and HOFO-2 of the bqdi ligand and the LUFO and LUFO+1 of the Ru fragment (see the above figure, black and red lines). The Ru-to-BQDI back-donation is produced by the orbital interaction between the HOFO of the Ru fragment and the LUFO of the BQDI ligand of b₁ symmetry. The ECDA analysis shows that the LUMO of the the complex is an anti-bonding combination of 62 % LUFO(bqdi) and 33 % HOFO(Ru). The corresponding bonding orbital (HOMO-1 of the complex) is formed by 61% HOFO(Ru) and 29% LUFO(bqdi). These orbital contributions indicate the strong back-bonding interaction and account for a transfer of ~0.7 e- from the Ru fragment to the BQDI ligand. [PDF].

Here is another example of the AOMix-CDA output: the orbital interaction diagram (computed using Gaussian 03 at the B3LYP/TZVP level) of two methylidyne (CH) radicals (in the quartet spin state, S=4) forming the a linear acetelene molecule HCCH (alpha-spin orbitals are shown in blue, beta-spin orbitals are shown in red color):

The examples of ADF 2005, Gaussian 03 (Gaussian 98 examples are identical to those from Gaussian 03), Jaguar 5.5 and HyperChem 5.0 input files for AOMix-CDA and the corresponding AOMix-CDA output files can be downloaded by users at this link.

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AOMix-L

1. calculates the Wiberg bond order indices between molecular fragments (calculated in the canonical orbital basis: (P*S) x (P*S) and in the orthonormal Lowdin orbital basis);

2. calculates the Mayer bond orders (including the bond order contributions from alpha- and beta-spin occupied orbitals for open-shell systems) between molecular fragments;

3. if molecular symmetry is present, calculates symmetry components (for each irreducible representation) of Mayer bond orders (including the bond order contributions from alpha- and beta-spin MOs for open-shell systems) between fragments. Symmetry decomposition of bond orders helps in picturing electronic structure and contributions to chemical bonding;

4. calculates total and free valence of atoms / fragments;

5. calculates the eigenvalues and eigenvectors of the AO overlap matrix;

6. performs Lowdin population analysis (LPA) and other PA methods which are based on the S^a x P x S^1-a formula (where P is the density matrix and S is the overlap matrix);

7. calculates the three-center and four-center bond order indices, (P*S) x (P*S) x (P*S) and (P*S) x (P*S) x (P*S) x (P*S), between molecular fragments to help in finding possible multi-center orbital interations.

   AOMix-L output files also contain:
   

   • Lowdin and Mulliken alpha-spin electron populations,
   • Lowdin and Mulliken beta-spin electron populations,
   • Lowdin and Mulliken gross electron populations,
   • Lowdin and Mulliken spin densities,
   • (for spin-unrestricted calculations) the overlap matrix between beta-spin molecular orbitals and alpha-spin molecular orbitals (the so-called mutual overlap matrix).

   Here is one of the AOMix-L output files. In this example, fragments are defined by automatically by the program (each atom is a fragment).

   In addition, if each atom is a fragment, AOMix-L writes two UCSF Chimera attribute files. The first file (with the atomic attributes) allows easy visualization of the calculated atom-based properties:

   • atomic charges,
   • MPA and LPA spin densities,
   • total and free valence indices of atoms.
   

   Atomic valence indices in the anthracene molecule (C₁₄H₁₀)

   The second file (with the PseudoBond attributes) allows easy visualization of the calculated two-center properties:

   • Lowdin and Wiberg bond orders,
   • Mayer bond orders and its components.

Mayer bond orders for the C-C and C-H bonds in the anthracene molecule (C₁₄H₁₀)

AOMix-L also prints the S^0.5 x P x S^0.5 matrix for alpha- and beta-spin orbitals.

AOMix-L can be also used to recover the initial guess from the computed wave function (see Appendix I of the AOMix manual).

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AOMix-S provides:

1. faster calculation of molecular orbital compositions than AOMix.exe;
2. the MO composition analysis in terms of
   • ALL atomic orbitals in one run (number of fragments = number of molecular orbitals)
   • ALL atoms in one run (number of fragments = number of atoms), these include the automatic s,p,d,f-orbital contribution breakdown (see the example
   • or any large number of molecular fragments (defined as a list of atoms or/and atomic orbitals);
3. total and partial density-of-states (TDOS and PDOS) plot data (both continuos and line plots are available);
4. overlap populations density-of-states (OPDOS) plot data;
5. MS Windows and UNIX scripts for Gaussian CUBE file generation;
6. in addition to the regular AOMix-S output file (for atoms as individual fragments and for atomic orbitals as individual fragments), the file (AOMix-S-MPA-orb.html) is printed. It contains information about MO compositions in terms of MOST IMPORTANT atomic orbitals (6 largest contributions with values greater than 0.5%)

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Since the AOMix-x programs use output files from the main program (AOMix.exe), these programs can be used for post-processing of quantum-chemical packages which are usable with AOMix: ADF, CNDO/INDO, GAMESS(US), Gaussian 98, Gaussian 03, HyperChem 4.x-7.x, Jaguar, MOPAC, Q-Chem, Spartan, ZINDO (other packages can be also included).

The AOMix-x programs are written in such a way that it should be easy to interface them with any quantum chemistry software package.

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Last updated: April 2008