AMI semi-empirical method

Example Researchers have used MNDO and AMI semi-empirical methods to calculate possible reaction pathways for the interaction of glycine and cocaine. In choosing possible interaction sites,... 

The energy calculated using both the AMI semi empirical method and B3PW91/6-31G calculations of the optimized complexes for each phenohc position indicated that position C, with Fe-O-C-C dihedral angle of +90° has the lowest total energy, followed by binding at position (ZFeOCC -90°). At Cj (ZFeOCC + 90°) position, the breaking of two bonds was observed, namely between and as well as... 

Diels-Alder cycloaddition reactions of iminium ions (Sect. 2.1.1) could take place with either the C=N bond or the C=C bond acting as the dienophile. This potential dual reactivity was investigated by Zora using the AMI semi-empirical method [231]. The results showed not only the preferred C=C reactivity (activation barrier is 4.20 kCal mol" lower than for reaction with the C=N bond) but also suggested that the reaction was stepwise. 

The potential tautomerism of l,2,3,4-tetrahydro-5,7-dimethyl-6//-pyrrolo[3,4-i/ pyridazine-l,4-diones has been examined by AMI semi-empirical methods <1998JMT(434)7, 1998JMT(427)65, 1998JMT(430)85>. 

Figure 8. Frontier electron population of naphthalene (eV) - HOMO for Ca and CB - using AMI semi-empirical method. () According to ref. [18].

By considering the respective molecular size of both entities which are present in the inclusion complexes, it is possible to propose a reasonable model for the structure of these inclusion complexes [18,21,22]. This model was obtained by means of simple calculations of the BPHT molecular structure, based on the AMI semi-empirical method. 

A new zeolite model, that features the a and c channels of clinoptilolite has been used to study the possible interactions of aspirin-water-zeolite, in order to know the behavior of the drug in a more complex system and the influence of water present in the zeolite channel. The calculations have been performed using the AMI semi-empirical method and acid and sodic clinoptilolite models. The results showed that the adsorption entalphy of aspirin in the acid structure is in the same order than that obtained for the sodic structure, although the nature of the interaction is different in each structure. The ester and aromatic groups were preferentially oriented to the model. In any case the chemical stability of aspirin is affected by the presence of water molecules in the system. 

A theoretical study of the A -methylpyrrole cycloaddition reaction with benzene has been performed using the hybrid Becke3LYP/6-31G DFT method in combination with the AMI semi-empirical method. The cycloadduct is theoretically transferred to A -methylindole, utilizing three different pathways elimination of acetylene, azomethine addition followed by pyrazole elimination, and the addition of 1,2,4,5-tetrazine, followed by nitrogen and 1,2-diazine elimination. For these three pathways, all the activation energies and the heats of reaction have been evaluated by the Becke3LYP/6-31G //AMl theoretical model <1996JMT(370)85>. 

The current practical limit for ab-initio codes is around 50 first row atoms. With new algorithms and direct methods this should be extended to 100-200, or possibly more, first row atoms within the next few years. At the present time, the study of larger molecules requires some simplifications to be made. These can take the form of approximations to the Fock Matrix using simple mathematical descriptions of the physics or, alternatively, experimental data can be used to calibrate a parameterised form of the Fock matrix. This is the basis of the widely used MNDO, MINDO/3 and AMI semi-empirical methods (Ref 15). 

A valuable review of the MOPAC program and the semi-empirical methods MNDO, MINDO/3, AMI, and PM3. Of particular use are theoretical discussions of these semi-empirical methods and many tables validating the accuracy of the MOPAC program and its associated Hamiltonians. 

In large systems there can be many orbitals in a small energy range, and the size of the Cl matrix can be very sensitive to the value of the maximum excitation if you use Biergy Criterion. Since calculation time depends heavily on the size of the Cl matrix, you can end up with very long calculations, especially if you use the ab initio methods or the MNDO, AMI, or PM3 semi-empirical methods. This could exhaust the memory of your system. Again, inspecting the results of an RHF (no Cl) calculation will help you avoid these pitfalls. 

The researchers established that the potential energy surface is dependent on the basis set (the description of individual atomic orbitals). Using an ab initio method (6-3IG ), they found eight Cg stationary points for the conformational potential energy surface, including four minima. They also found four minima of Cg symmetry. Both the AMI and PM3 semi-empirical methods found three minima. Only one of these minima corresponded to the 6-3IG conformational potential energy surface. 

In order to conserve the total energy in molecular dynamics calculations using semi-empirical methods, the gradient needs to be very accurate. Although the gradient is calculated analytically, it is a function of wavefunction, so its accuracy depends on that of the wavefunction. Tests for CH4 show that the convergence limit needs to be at most le-6 for CNDO and INDO and le-7 for MINDO/3, MNDO, AMI, and PM3 for accurate energy conservation. ZINDO/S is not suitable for molecular dynamics calculations. 

The following data (Table 1) for molecules, including hydrocarbons, strained ring systems, molecules with heteroatoms, radicals, and ions comes from a review by Stewart.For most organic molecules, AMI reports heats of formation accurate to within a few kilocalories per mol. For some molecules (particularly inorganic compounds with several halogens, such asperchloryl fluoride, even the best semi-empirical method fails completely. 

The quality of the vibrational frequencies varies widely with the semi-empirical method that is used. Generally, AMI, and PM3 are in closer agreement with experiment than methods based on CNDO orINDO. 

Many problems with MNDO involve cases where the NDO approximation electron-electron repulsion is most important. AMI is an improvement over MNDO, even though it uses the same basic approximation. It is generally the most accurate semi-empirical method in HyperChem and is the method of choice for most problems. Altering part of the theoretical framework (the function describing repulsion between atomic cores) and assigning new parameters improves the performance of AMI. It deals with hydrogen bonds properly, produces accurate predictions of activation barriers for many reactions, and predicts heats of formation of molecules with an error that is about 40 percent smaller than with MNDO. 

This difference is shown in the next illustration which presents the qualitative form of a potential curve for a diatomic molecule for both a molecular mechanics method (like AMBER) or a semi-empirical method (like AMI). At large internuclear distances, the differences between the two methods are obvious. With AMI, the molecule properly dissociates into atoms, while the AMBERpoten-tial continues to rise. However, in explorations of the potential curve only around the minimum, results from the two methods might be rather similar. Indeed, it is quite possible that AMBER will give more accurate structural results than AMI. This is due to the closer link between experimental data and computed results of molecular mechanics calculations. 

Semi-empirical methods, such as AMI, MINDO/3 and PM3, implemented in programs like MOPAC, AMPAC, HyperChem, and Gaussian, use parameters derived from experimental data to simplify the computation. They solve an approximate form of the Schrodinger equation that depends on having appropriate parameters available for the type of chemical system under investigation. Different semi-emipirical methods are largely characterized by their differing parameter sets. 

Semi-empirical methods are characterized by their use of parameters derived from experimental data in order to simplify the approximation to the Schrbdinger equation. As such, they are relatively inexpensive and can be practically applied to very, very large molecules. There are a variety of semi-empirical methods. Among the best known are AMI, PM3 and MNDO. Gaussian includes a variety of semi-empirical models, and they are also the central focus or present in many other programs including AMPAC, MOPAC, HyperChem and Spartan. 

Semi-empirical methods are sometimes suggested for studying isodesmic reactions. We performed this same study using the AMI method the results are given in the following table ... 

The choices of quantum mechanical method typically include the semi-empirical methods AMI, PM3, and MNDO/d [1-A. These three methods (and some of their variations) are those most commonly used in the current literature. Of these semi-empirical methods, only MNDO/d includes the effects of d-orbitals. Some of the problems associated with these semiempirical methods include ... 

Despite these inconsistencies, the semi-empirical methods produce bond angles, bond lengths and heats of formation that are in reasonable agreement with experimental results. A new version, PM5, will soon be available and is four times more accurate than AMI or PM3. The advantage of PM5 over the other semi-empirical methods is that d-orbitals are being introduced [5]. 

The basis set is 6-31G(d,p), and electron correlation at the MP2 level is included. A similar structure is obtained with the AMI and PM3 semi-empirical methods. Density functional theory at the B3LYP/6-31G(dp,p) level also produced the same structure for this ion-pair. The only observed differences between the semi-empiri-cal and the ab initio structures were slightly shorter hydrogen bonds (PM3 and AMI) between FI, F2, and F5 and the G2-F1 (H18) on the imidazolium ring. 

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