MOP AC program

A valuable review of th e MOP,AC program an d th e sem i-etn pirical methods MNDO. MINDO/3, AM I. and PM 3, Of particular use are th eoretical discussion s of these sem i-em pirical meth -ods and many tables validating the accuracy of the MOP.AC program and its associated Hamiltonians. 

The calculations of the frontier molecular orbital (FMO), energies, and coefficients of the reactants were performed at the RHF/AMl level using the MOP AC program (Version 5.0). 

Schaeffer H F III (Editor) 1977. Applications of Electronic Structure Theory. New York, Plenum Press. Schaeffer H F III (Editor) 1977. Methods of Electronic Structure Theory. New York, Plenum Press. Stei. art J J P 1990. MOP AC A Semi-Empirical Molecular Orbital Program. Journal of Computer-Aided Molecular Design 4 1-45. 

Note that lines 1. 2, 3. and 6 are blank.) Does it run What do the results mean What tw o generalizations can you make about MOP.AC intmt files from this program run ... 

Molden (we tested Version 3.6) is a molecular display program. It can display molecular geometries read from a number of molecular file formats. Various views of the wave function can be displayed from the output of the Gaussian and GAMESS programs. Some functionality is available from MOP AC and AMP AC files. Conversion programs are available to import wave functions from ADF, MOLPRO, ACES II, MOLCAS, DALTON, Jaguar, and HONDO. 

The current status of the semiempirical methods pioneered by Michael J. S. Dewar is given. These methods are made available to non—theoreticians through the programs MOP AC and AMPAC. Some capabilities of MOPAC and the form of the data input to the program are outlined. 

Construction of the coordinate matrix, or Z—matrix, is the most difficult step in carrying out a MOP AC calculation. To make this task easier, special routines and programs have been written. One of these is DRAW. 

DRAW. Like MOP AC, DRAW is public domain software. Copies can be obtained from the Quantum Chemistry Program Exchange (QCPE) at the University of Indiana. DRAW allows the data input and output to be represented graphically. Because of the difficulty in assembling a valid Z—matrix, DRAW has been provided with an editor which allows a user to see how the geometry of the system changes as the coordinates are changed. 

MOP AC The name means Molecular Orbital Package, but is said to have been inspired by this geographical oddity The original program was written in Austin, Texas. One of the roads in Austin is unusual in that the Missouri-Pacific railway runs down the middle of the road. Since this railway was called the MO-PAC, when names for the program were being considered, MOP AC was an obvious contender (see website). 

To study the possible reasons and elementary mechanisms of the catalytic activity of CPs, we have modeled the electronic structure of some molecular CPs clusters and its adsorption complexes with oxygen. A MOP AC computer complex and, in particular, the PM3 quantum-chemical program of this complex was used for calculations. The results of calculations have shown that both oxygen atoms form bonds with two more active carbon atoms of CP molecular cluster (so-called bridge model of adsorption). The total energy of system after chemical adsorption at such active atoms is minimal (Fig. 2). 

The simulations in this study were done using the semiempirical MO method PM3(Stewart, 1989 Stewart, 1989 Stewart, 1991) within the context of the QM/MM coupled potential recently implemented within our lab.(Hartsough and Merz, 1995) A modified version of MOP AC 5.0 (Besler, Merz et al., 1990 Merz and Besler, 1990), was used for the QM calculations and the driver MD program was a customized version of AMBER (Pearlman, Case etal., 1991). The PM3 Hamiltonian was selected because of its superior correlation with experimental heats of formation for the compounds studied herein (Stewart, 1989). From a methodological perspective, AMI (Dewar, Zoebisch et al., 1985), or MNDO (Dewar and Thiel, 1977), or any other LCAO based method could have been used. 

Many popular semiempirical methods are based on the original MNDO method. The most prominent of these are Austin Model 1 (AMI) by Dewar et al. [73] and Parametric Method 3 (PM3) by Stewart [74], These three methods represent the semiempirical standard for the calculation of organic molecules and are included in popular program packages such as Gaussian [78], CERIUS [79], SPARTAN [80], MOP AC [81], and AMPAC [82], Recently, AM 1 and PM3 have also been extended for the treatment of transition metal compounds [75-77], In principle, they only differ in the parameterization and in the empirical function fAB [Eq. (42)]. 

Stewart JJP. Special Issue—MOP AC—A semiempirical molecular-orbital program. J Comput Aid Mol Des 1990 4 1-45. 

The AMI (Austin Model 1) Hamiltonian available in Version 3.10 of the MOP AC (Molecular Orbital PACkage) program was used to carry out QM calculations, for the purpose of estimating the partial atomic charges to be used in the electrostatic portion of the potential energy for the calculations on the interactions between pairs of model molecules. [34] The AMI calculations also yielded quantum mechanical estimates of the heats of formation of the model molecules. These heats of formation generally followed similar trends to the MM2 steric energies. 

The popularity of the MNDO, AMI and PM3 methods is due in large part to their implementation in the MOP AC and AMP AC programs. The programs are able to perform many kinds of calculation and to calculate many different properties. 

Because of their widespread irse, not least becarrse most of them are implemented in the MOP AC [5] single program package, what follows is a brief enumeration of the strong points and drawbacks of MNDO, AMI and PM3. 

In order for this model to be useful, programs must exist which can provide reasonable geometries for substituted diacetylenes and must properly model intermolecular interactions between monomer pairs. Ab initio programs are unsuitable for this project due to the size of the molecules involved. Since we are also interested in electronic properties as well as geometric properties, it was decided that the most suitable candidates available were the semiempirical SCF-MO methods MNDO, AMl, and PM3 . These methods are all found in the program MOP AC. It has been determined that these methods do indeed provide reasonable geometries for substituted diacetylenes 2 only... 

Stewart, J. J. P. MOP AC, A Semiempirical Molecular Orbital Program, QCPE 455... 

Three popular semiempirical programs, AMPAC, AMSOL, and MOP AC, are actually derivations of the same original code. AMPAC 1.0 and MOPAC 3.0 were both created from Version 2.0 of MOPAC. AMSOL was derived from... 

A semiempirical crystal band structure program, called BZ, is bundled with MOP AC 2000. There is also a utility, referred to as MAKPOL, for generating the input for band structure calculations with BZ. With the use of MAKPOL, the input for band-structure computations is only slightly more complicated than that for molecular calculations. 

---