Semi Ab initio Method

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. 

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. 

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Numerous other semiempirical methods have been proposed. The MNDO method has been extended to d functions by Theil and coworkers and is referred to as MNDO/d.155>156 For second-row and heavier elements, this method does significantly better than other methods. The semi-ab initio method 1 (SAM1)157>158 is based on the NDDO approximation and calculates some one- and two-center two-electron integrals directly from atomic orbitals. 

AMI and PM3 perform similarly and usually give quite good geometries, but less satisfactory heats of formation and relative energies. A modification of AMI called SAMI (semi-ab initio method 1), relatively little-used, is said to be an improvement over AMI. AMI and SAMI represent work by the group of M. J. S. Dewar. PM3 is a version of AMI, by J. J. P. Stewart, differing mainly in a more automatic approach to parameterization. Recent extensions of AMI (RM1) and PM3 (PM6) seem to represent substantial improvements and are likely to be the standard general-purpose semiempirical methods in the near future. 

The philosophy in the Semi-ab initio Method 1 (SAMI and SAMID) modelis slightly different from the other modified methods. It is again based on the NDDO approximation, but instead of f lacmg all integrals by parameters, Uie one- and two-... 

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... 

The newest semiempirical method is Semi-Ab initio Model 1 (SAM 1) by Dewar et al. [83]. As the acronym suggests, it is based on AML The two-electron integrals (jiv (tt), however, are calculated analytically over Gaussian-type functions and scaled empirically. Up to the present, no comprehensive list of SAMI parameters and error... 

In 1993, Dewar and co-workers modified AMI to give the SAMI (semi-ab initio model 1) method [M. J. S. Dewar, C. lie, and G. Yu, Tetrahedron, 23,5003 (1993) A. J. Holder and E. M. Evleth in D. A. Smith (ed.). Modeling the Hydrogen Bond, American Chemical Society, 1994, p. 113]. A major difference between SAMI and AMI is that SAMI evaluates the two-center ERIs as (/ii Acr)sAMi = s( ab)(m Ko-)stc)-3g> where ( v Ao-)sto-3g is the accurate value of the ERI calculated using a STO-3G basis set, and the function (Rab) is a certain function of the intemuclear distance that reduces the magnitudes of the ERIs so as to allow for electron correlation and use of a minimal basis set. The function (Rab) contains parameters whose values have been adjusted to maximize the performance of the method. Because of the need to calculate two-center ERIs accurately, SAMI is slower than AMI, but is still far faster than ab initio methods, due to the NDDO approximation. 

The semi ab initio model 1 (SAMI) is another modified NDDO method, but it does not replace integrals by parameters. The one- and two-center electron repulsion integrals are explicitly calculated from the basis functions [employing a standard STO-3G (Slater-type orbital from three Gaussian functions) Gaussian basis set] and scaled by a function which has to be parametrized. SAM 1 calculations take about twice as long as AMI or PM3 calculations do. 

A common way to benefit from the ability to combine different molecular orbital methods in ONIOM is to combine a DFT or ab-initio description of the reactive region with a semi-empirical treatment of the immediate protein environment, including up to 1000 atoms. Due to the requirement for reliable semi-empirical parameters, as discussed in Section 2.2.1, this approach has primarily been used for non-metal or Zn-enzymes. Examples include human stromelysin-1 [83], carboxypeptidase [84], ribonucleotide reductase (substrate reaction) [85], farnesyl transferase [86] and cytosine deaminase [87], Combining two ab-initio methods of different accuracy is not common in biocatalysis applications, and one example from is an ONIOM (MP2 HF) study of catechol O-methyltransferase [88],... 

Chapter 1 gives a short description of ab initio methods, Hartree-Fock and post-Hartree-Fock, focusing on the Gaussian computer programs. Chapter 2 describes semi-empirical calculations and their applications to biological systems. Chapter 3 addresses itself to electrostatic properties of molecules, as determined by quantum-chemical methods. The density functional method is discussed in chapter 4. Chapter 5 compares theoretically obtained parameters to experimental data. 

AMI semi-empirical and B3LYP/6-31G(d)/AMl density functional theory (DFT) computational studies were performed with the purpose of determining which variously substituted 1,3,4-oxadiazoles would participate in Diels-Alder reactions as dienes and under what conditions. Also, bond orders for 1,3,4-oxadiazole and its 2,5-diacetyl, 2,5-dimethyl, 2,5-di(trifluoromethyl), and 2,5-di(methoxycarbonyl) derivatives were calculated <1998JMT153>. The AMI method was also used to evaluate the electronic properties of 2,5-bis[5-(4,5,6,7-tetrahydrobenzo[A thien-2-yl)thien-2-yl]-l,3,4-oxadiazole 8. The experimentally determined redox potentials were compared with the calculated highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO/LUMO) energies. The performance of the available parameters from AMI was verified with other semi-empirical calculations (PM3, MNDO) as well as by ab initio methods <1998CEJ2211>. 

Three coordination modes are considered possible in transition metal C02 complexes, as shown in Figure 3. They were theoretically investigated with semi-empirical [16, 17] and ab initio methods [18, 19]. A short summary of these results is collected in Table 1 [20], where the importance of the frontier orbitals of C02 for this interaction is apparent. 

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