Semiempirical molecular orbital methods parameterization

Efforts to deduce transition state structures theoretically have until recently been retarded by the failure of even the more sophisticated molecular orbital treatments to predict accurate activation energies, and the need to avoid geometric and mechanistic assumptions has made the calculation of reaction pathways prohibitively expensive. The introduction of efficient gradient methods for minimizing energy with respect to all geometric parameters, coupled with the advent of faster computers, has now virtually overcome the latter problem, and careful parameterization of semiempirical molecular orbital methods has led to more... 

MOPAC is a general-purpose semiempirical molecular orbital program for the study of chemical structures and reactions. It is available in desktop PC running Windows, Macintosh OS, and Unix-based workstation versions. It uses semiempirical quantum mechanical methods that are based on Hartree-Fock (HF) theory with some parameterized functions and empirically determined parameters replacing some sections of the complete HF treatment. The approximations in... 

Tel. 913-268-3271, fax 913-268-3445, e-mail aholder vaxl.umkc.edu Semiempirical molecular orbital calculations with M. J. S. Dewar s SAMI parameterization, including d orbitals for transition metals, and a graphical user interface. MINDO/3, MNDO, MNDOC, AMI, and PM3 methods. DEC, Cray, Silicon Graphics, Sun, and PCs (under X-Windows). 

Another approach to treating the boundary between covalently bonded QM and MM systems is the connection atom method,119 120 in which rather than a link atom, a monovalent pseudoatom is used. This connection atom is parameterized to give the correct behavior of the partitioned covalent bond. The connection atoms interact with the other QM atoms as a (specifically parameterized) QM atom, and with the other MM atoms as a standard carbon atom. This avoids the problem of a supplementary atom in the system, as the connection atom and the classical frontier atom are unified. However, the need to reparameterize for each type of covalent bond at a given level of quantum chemical theory is a laborious task.121 The connection atom method has been implemented for semiempirical molecular orbital (AMI and PM3)119 and density functional theory120 levels of theory. Tests carried out by Antes and Thiel to validate the connection atom method at the semiempirical level suggested that the connection atom approach is more accurate than the standard link atom approach.119... 

The agreement between theory and experiment for commonly computed properties can be judged from the data in Tables 6-8. These data were drawn from the literature. Ab initio calculations give results that are close to experiment on average. Since the semiempirical and ab initio tests were not done on identical sets of molecules, it is hard to evaluate exactly how much better ab initio is. Although an ab initio molecular orbital calculation is based on first principles, predictions from such a calculation are not necessarily better than those from some of the recent semiempirical molecular orbital or empirical force field methods. A carefully parameterized, general force field can, in fact, predict molecular geometries as well as or better than an ab initio MO calculation. Overall, however, molecular models built quantum mechanically will be quite realistic. 

As in all molecular orbital theories, the fundamental computation in SEMOT is to determine the electronic wavefunction for the molecule of interest. Semiempirical approximations were developed of necessity, when computers were too slow for ab initio calculations to be chemically useful [53]. Although many of the approximations are severe, the use of empirical parameters was successful in restoring accuracy. In many cases, the resulting accuracy even exceeds that of simple ab initio calculations, since higher order effects are incorporated into the parameterization. Thus, semiempirical methods remain popular today despite the widespread availability of inexpensive, powerful computers. 

Garcia-Viloca M, JL Gao (2004) Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method. Theor. Chem. Acc. Ill (2-6) 280-286... 

---