SAMI method

The details of the functional form and parameterization have not yet been published. The advantage is that basis sets involving d-orbitals are readily included (defining the SAMID method), making it possible to perform calculations on a larger fraction of the periodic table. The SAMI method explicitly uses the minimum STO-3G basis set, but it is in principle also possible to use extended basis sets with this model. The acmal calculation of the integrals makes the SAMI method somewhat slower than the MNDO/ AM1/PM3, but only by a factor of 2. The SAMI/SAMID methods have been parameterized for the elements H, Li, C, N, O, F, Si, P, S, Cl, Fe, Cu, Br and 1. 

MINDO/3 methods clearly have severe problems with some of the conjugated systems. The MNDO/AM1/PM3 family perform somewhat better, although none of them can predict the correct ordering. The SAMI method is not an improvement for this case. The mean absolute deviation (MAD) for the predicted stabilities is 10kcal/mol, which is a typical accuracy for semi-empirical methods. 

The SAMI parametrization [74] further extends the number of two-electron integrals included in the treatment. They are calculated first for the AOs taken as in the STO-3G Gaussian basis set, but then scaled using the distance dependent functions containing adjustable parameters. The SAMI method has been parametrized for the elements H, Li, C, N, O, F, Si, P, S, Cl, Fe, Cu, Br, and I. Unfortunately, this parametrization was never thoroughly published and studied. The same applies to the PM5 method [75] which is implemented only by a commercial software, without adequate explanation.2 Further refinement of the system of correcting Gaussian contributions to the interatomic interaction functions has been proposed in [71],... 

Simulated annealing calculations were performed to acquire the mechanisms of thermolysis of thiirane and thiiranium cation <2002JMT71>. The AMPAC 6.55 package along with AIMl and SAMI methods were used to estimate structures, which were then used as starting points for further ab initio calculations. Critical points were confirmed by calculation of the vibrational frequencies. The primary reactions thiirane 19 —> S-f ethene, thiirane—> vinyl thiol 20, and thiirane ethanethial (thioacetaldehyde) 21 were examined for thermolysis of thiirane Scheme 1. Many secondary reactions were also examined. The simulated annealing method was predicted to be very useful in the future for the study of competing chemical reactions. 

A comparison of AMI, PM3 and SAMI for describing 10 hydrogen-bonded species [J. Dannenberg, J. Mol. Struct. (Theochem), 401, 287 (1997)], foimd that for species with OHO hydrogen bonds, all three methods had serious problems, while for species with CHO hydrogen bonds, PM3 and SAMI performed rather poorly but AMI did fairly well. A study of SAMI results for H-bonded species concluded that Obviously improvements in die SAMI method are required before liberal application to hydrogen-bonded systems can be recommended fj. Mavri et al.,/. Mol. Struct., 416,261 (1997)]. 

The advantage is that basis sets involving d-orbitals are readily included (defining the SAMID method), making it possible to perform calculations on a larger fraction of the periodic table. The SAMI method explicitly uses the minimum STO-3G basis set. 

Table 8 is a collection of 22 calculated vertical IPs of different anions (EAs of the corresponding radicals) and of the corresponding experimental quantities. The corresponding anions are drawn in Scheme 4. Because the results of the OVGF calculations coupled with the MNDO, AMI, and PM3 approximations were published recently, we summarize in Table 8 only the results of the calculations of the new SAMI method together with the results of the AMI and OVGF(AMl) calculations. 

The SAMI method gives a little better agreement with experimental data (A = 0.41 eV for 22 anions) than the other KT-based semiempirical methods, but improvement over the AMI method is not so considerable (A = 0.50 eV). It should be especially noted that poor agreement between SAMI calculated values and experimental data was obtained for the pentachlorobenzenide (Table 8, entry 5) and trimethylsilanide (entry 10) anions, with a discrepancy of about 1.5 eV. The OVGF(AMI) values are in considerably better accord with experiment in comparison with the results of KT-based. semiempirical calculations. This becomes apparent from the mean deviation data in Table 8. The A value is reduced by about twofold in the OVGF(AMl) calculations and is only 0.25 eV. The importance of electron correlation and orbital relaxation... 

SAMI (semi-nh initio method one) a semiempirical method SASA (solvent-accessible surface area) algorithm for computing solvation elfects... 

Table 3.4 shows a comparison of some of the elements for which the MNDO, MNDO/ d, AMI, PM3, SAMI and SAMld methods have been parameterized. 

The term "semi-empirical" has been reserved commonly for electronic-based calculations which also starts with the Schrodinger equation.9-31 Due to the mathematical complexity, which involve the calculation of many integrals, certain families of integrals have been eliminated or approximated. Unlike ab initio methods, the semi-empirical approach adds terms and parameters to fit experimental data (e.g., heats of formation). The level of approximations define the different semi-empirical methods. The original semi-empirical methods can be traced back to the CNDO,12 13 NDDO, and INDO.15 The success of the MINDO,16 MINDO/3,17-21 and MNDO22-27 level of theory ultimately led to the development of AMI28 and a reparameterized variant known as PM3.29 30 In 1993, Dewar et al. introduced SAMI.31 Semi-empirical calculations have provided a wealth of information for practical applications. 

The semiempirical molecular orbital (MO) methods of quantum chemistry [1-12] are widely used in computational studies of large molecules. A number of such methods are available for calculating thermochemical properties of ground state molecules in the gas phase, including MNDO [13], MNDOC [14], MNDO/d [15-18], AMI [19], PM3 [20], SAMI [21,22], OM1 [23], OM2 [24,25] MINDO/3 [26], SINDOl [27,28], and MSINDO [29-31]. MNDO, AMI, and PM3 are widely distributed in a number of software packages, and they are probably the most popular semiempirical methods for thermochemical calculations. We shall therefore concentrate on these methods, but shall also address other NDDO-based approaches with orthogonalization corrections [23-25],... 

SemiChem products are available at http //www.semichem.com. AMPAC , available as a stand-alone product with Windows-based and workstation level interfaces, is a semiempirical quantum mechanical program featuring SAMI, AMI, MNDO, MNDO/d, PM3, MNDO/C, MINDO/3 semiempirical methods. AMPAC also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results. The SYBYL/Base program offered by Tripos, Inc. (products described below) provides an interface with interactive graphing and structural display tools that can be used to access AMPAC s calculation tools. 

The performance of several semi-empirical (modified neglect of diatomic overlap (MNDO), AMI, PM3, and SAMI) and ab initio (Hartree-Fock (FIF) and MP2/6-31G ) methods for determining structural and electronic factors of a series of isothiazolo[5,4-b]pyridines was compared by Martinez-Merino et al. <1996T8947>. They found that most of the semi-empirical methods calculated reasonable molecular structures when compared to the actual X-ray structures (compounds 3-5) (see, for example. Table 1 for selected bond lengths of compound 3). Flowever, the dipole moments were not reproducible using these methods. 

Wildfong, P.L.D. Samy, A.-S. Corfa, J. etal., Accelerated fluid bed drying using NIR monitoring and phenomenological modeling Method assessment and formulation suitability /. Pharm. Sci. 2002, 91, 631-639. 

NDDO [21] goes beyond INDO in that the ZDO approximation (Section 6.2.1, point (3)) is not applied to orbitals on the same atom, i.e. ZDO is used only for atomic orbitals on different atoms. NDDO is the basis of the currently popular semiempirical methods developed by M. J. S. Dewar and by coworkers who took up the torch MNDO, AMI and PM3 (as well as SAMI, PM5, and PM6). NDDO methods are the gold standard in general-purpose semiempirical methods, and the rest of this chapter concentrates on them. 

NDDO-Based Methods from the Dewar Group MNDO, AMI, PM3 and SAMI, and Related Methods - Preliminaries... 

The first (1967) of the Dewar-type methods was PNDDO [35], partial NDDO), but because further development of the NDDO approach turned out to be unexpectedly formidable [33], Dewar s group temporarily turned to INDO, creating MINDO/1 [36] (modified INDO, version 1). The third version of this method, MINDO/3, was said [33] [to have] so far survived every test without serious failure , and it became the first widely-used Dewar-type method. Keeping their promise to return to NDDO the group soon came up with MNDO (modified NDDO). MINDO/3 was made essentially obsolete by MNDO, except perhaps for the study of carbocations (Clark has summarized the strengths and weaknesses of MINDO/3, and the early work on MNDO [37]). MNDO (and MNDOC and MNDO/d) and its descendants, the very popular AMI and PM3, are discussed below. Briefly mentioned are a modification of AMI called SAMI and an... 

SAMI (semi ab initio method number 1) was the last semiempirical method to be reported (1993, [76]) by Dewar s group. SAMI is essentially a modification of AMI in which the two-electron integrals are calculated ab initio using contracted... 

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