PM3 parameterization method

PLS (partial least-squares) algorithm used for 3D QSAR calculations PM3 (parameterization method three) a semiempirical method PMF (potential of mean force) a solvation method for molecular dynamics calculations... 

There are three modihed intermediate neglect of differential overlap (MINDO) methods MINDO/1, MINDO/2, and MINDO/3. The MINDO/3 method is by far the most reliable of these. This method has yielded qualitative results for organic molecules. However its use today has been superseded by that of more accurate methods such as Austin model 1 (AMI) and parameterization method 3 (PM3). MINDO/3 is still sometimes used to obtain an initial guess for ah initio calculations. 

PM3/TM is an extension of the PM3 method to transition metals. Unlike the parameterization of PM3 for organics, PM3/TM has been parameterized only to reproduce geometries. This does, of course, require a reasonable description of energies, but the other criteria used for PM3 parameterization, such as dipole moments, are not included in the PM3/TM parameterization. PM3/TM tends to exhibit a dichotomy. It will compute reasonable geometries for some compounds and completely unreasonable geometries for other compounds. It seems to favor one coordination number or hybridization for some metals. 

Semiempirical (CNDO, MNDO, ZINDO, AMI, PM3, PM3(tm) and others) methods based on the Hartree-Fock self-consistent field (HF-SCF) model, which treats valence electrons only and contains approximations to simplify (and shorten the time of) calculations. Semiempirical methods are parameterized to fit experimental results, and the PM3(tm) method treats transition metals. Treats systems of up to 200 atoms. 

In the course of the MNDO/d development [15-18] we have generated new validation sets for second-row and heavier elements. Those for Na, Mg, Al, Si, P, S, Cl, Br, I, Zn, Cd, and Hg have been published [16-18], The corresponding statistical evaluations for heats of formation [18] are summarized in Table 8.3. It is obvious that MNDO/d shows by far the smallest errors followed by PM3 and AMI. All four semiempirical methods perform reasonably well for normalvalent compounds, especially when considering that more effort has traditionally been spent on the parameterization of the first-row elements. For hy-pervalent compounds, however, the errors are huge in MNDO and AMI, and still substantial in PM3, in spite of the determined attempt to reduce these errors in the PM3 parameterization [20], Therefore it seems likely that the improvements in MNDO/d are due to the use of an spd basis set [16-18]. 

Parameterized methods like ZINDO/S are probably the only way to calculate reasonably accurate UV spectra for large molecules. AMI and PM3 have become extremely useful not only because they allow quantum mechanical calculations to be done on molecules which are still too big for ab initio or DFT (chapter 7) methods, but also as adjuncts to these latter methods, since they often allow a relatively rapid survey of a problem, such as an exploration of a potential energy surface one can locate minima and transition states, then use the semiempirical structures (size permitting) as inputs for initial geometries, wavefunctions and hessians (section 2.4) in a higher-level geometry... 

As in any parameterized method, best performance is expected where there are ample experimental data available for developing robust parameter values. For exotic species not represented in the parameterization sets, predictions should be viewed with skepticism. In particular, results for transition states of chemical reactions are likely to be only qualitatively correct. In Fig. 1, the thermochemical errors of PM3 and AMI, as compared with experimental benchmarks, are plotted for 200 compounds composed of the common organic elements C, H, N, and O. For this data set, the root-mean-square (rms) errors are 24 and 36kJmol for PM3 and AMI, respectively. For comparison, the rms error is lOkJmor for Benson s GA method. The data for Fig. 1 were taken from the CCCBDB [55]. 

PM3 Parameterized Model number 3 (a semi-empirical method)... 

Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Electrostatic Potentials Chemical Applications MNDO PM3 Semiempirical Methods Transition Metals SINDOl Parameterization and Application. 

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