PM3 calculation

Breindl et. al. published a model based on semi-empirical quantum mechanical descriptors and back-propagation neural networks [14]. The training data set consisted of 1085 compounds, and 36 descriptors were derived from AMI and PM3 calculations describing electronic and spatial effects. The best results with a standard deviation of 0.41 were obtained with the AMl-based descriptors and a net architecture 16-25-1, corresponding to 451 adjustable parameters and a ratio of 2.17 to the number of input data. For a test data set a standard deviation of 0.53 was reported, which is quite close to the training model. 

Calcu laLiii g th c extra in tegrals takes tim e. MNDO,. AM 1, an d PM3 calculation s typical ly take about on e and on e-h alf tim es as long as IXDO or MIXDO/3 calculations. 

File Fragment 9-2. Partial Energy Output File (Edited) for an Optimized PM3 Calculation on HE Using GAUSSIAN94-W. 

Calculating the extra integrals takes time. MNDO, AMI, and PM3 calculations typically take about one and one-half times as long as INDO orMINDO/3 calculations. 

Conqjutational methods can also be used to describe enolate stmcture. Most of the stmctural features of enolates are correctly modeled by B3LYP computations with dimethyl ether as the solvent molecule. Although semiempirical PM3 calculations give adequate representations of the geometries of the aggregates, the energy values are not accurate. 

Note that no basis set keyword is required for a PM3 calculation. 

Since the last review (76AHCS1, p. 243), progress has been made both in the synthesis as well as in tautomerization studies of 3-hydroxypyrroles (for a review see 92HC525).The parent compound can exist in at least two tautomeric forms (110 and 111). According to MINDO/3 and PM3 calculations (79JOC374 99UP1) 110 is more stable than 111 [AAHf =2.3 kcal/mol (PM3)]. 

Theoretical studies of the relative stabilities of tautomers 14a and 14b were carried out mostly at the semiempirical level. AMI and PM3 calculations [98JST(T)249] of the relative stabilities carried out for a series of 4(5)-substituted imidazoles 14 (R = H, R = H, CH3, OH, F, NO2, Ph) are mostly in accord with the conclusion based on the Charton s equation. From the comparison of the electronic spectra of 4(5)-phenylimidazole 14 (R2 = Ph, R = R3 = H) and 2,4(5)-diphenylimidazole 14 (R = R = Ph, R = H) in ethanol with those calculated by using ir-electron PPP method for each of the tautomeric forms, it follows that calculations for type 14a tautomers match the experimentally observed spectra better (86ZC378). The AMI calculations [92JCS(P1)2779] of enthalpies of formation of 4(5)-aminoimidazole 14 (R = NH2, R = R = H) and 4(5)-nitroimidazole 14 (R = NO2, R = R = H) point to tautomers 14a and 14b respectively as being energetically preferred in the gas phase. Both predictions are in disagreement with expectations based on Charton s equation and the data related to basicity measurements (Table III). These inconsistencies may be... 

According to semiempirical MNDO/PM3 calculations, the Te-methylated isomer 20 is energy-disfavored relative to 19. Moreover, the C—Te" bond in 20 is elongated (3.53 A) to such an extent that its stmcture should better be described as the carbenium ion 20a [94JCS(P2)2341]. 

Gas Phase (DGB) Basicities (333 K) [94JCS(P2)2341], Basicity Constants (pA bh+) Measured in Acetonitrile (25°C) (91KGS836), and MNDO PM3 Calculation [94JCS(P2)2341] PROTON AEEiNmES (PA) OF Compounds... 

Table 4 PM3 calculation of 5-X-cyclopentadenes at the transition states of Diels-Alder reactions with maleic anhydride...

Suga and Ibata [44] prepared binaphtyldiimine derivatives 36 (Scheme 19) affording 98% ee as best selectivity for the transformation of 1,1-diphenyl-ethylene with Z-menthyl diazoacetate. The authors performed PM3 calculations and proposed an optimized structure of the copper complex to explain the high enantioselectivity observed with 1,1-disubstituted olefins. 

It is believed that the reaction occurs through the monomer.166 Semiempirical MO (PM3) calculations suggest a boat TS.167 There do not seem to be any definitive experimental studies that define the mechanism precisely. 

The above complete regiospecificity of the cycloaddition across only the C=S+ bond was rationalized in terms of frontier molecular orbital coefficients in the salt 95. This cycloaddition was considered to be a LUMOsajt -HOMOdiene reaction. MOP AC 93 PM3 calculation of 95 showed the values of LLJMO coefficients for C(6), S, and N are 0.508, —0.502 and 0.364, respectively, as in Figure 1. These values strongly suggest the preference of the reaction site of the C=S+ bond. 

Uchiyama, S., Santa, T., Okiyama, N., Azuma, K. and Imai, K. (2000). Semi-empirical PM3 calculations predict the fluorescence quantum yields (Phi) of 4-monosubstituted benzofurazan compounds. J. Chem. Soc. Perkin Trans. II 6, 1199 1207. 

Studies using PM3 calculations of the alkaline hydrolysis of bicyclic P-lactam structures 82 (X = NNHCHO, 0, S) have shown that cleavage of the X-CO bond is the energetically favoured pathway both in the gas and solution phase <99MI287>. 

Similarly, other cycloadducts of nitrile oxides with C6o were synthesized. The cycloadducts were characterized by 13C NMR spectroscopy and high-resolution fast atom bombardment (FAB) mass spectrometry. It should be mentioned that X-ray structure determination of the 3-(9-anthryl)-4,5-dihydroisoxazole derivative of C6o, with CS2 included in the crystals, was achieved at 173 K (255). Cycloaddition of fullerene C60 with the stable 2-(phenylsulfonyl)benzonitrile oxide was also studied (256). Fullerene formed with 2-PhSC>2C6H4CNO 1 1 and 1 2 adducts. The IR, NMR, and mass spectra of the adducts were examined. Di(isopropoxy)phosphorylformonitrile oxide gives mono- and diadducts with C60 (257). Structures of the adducts were studied using a combination of high performance liquid chromatography (HPLC), semiempirical PM3 calculations, and the dipole moments. 

Katagi T (2005) Semi-empirical AMI and PM3 calculations of five- and six-coordinate oxo iron (IV) porphyrin complexes. J Mol Struct 728 49-56... 

Calculations were performed with few of these systems, either for their formation or properties. Thus, PM3 calculations of the cycloaddition of pyridinc-A -oxide with an isocyanate were performed, with R = H for simplification. Two consecutive transition states were postulated, pointing out a nonsynchronous process for this reaction, via a... 

Azolotriazines can be formed by cycloaddition reactions between diazoazoles and various substituted alkynes. In order to determine the mechanism of these reactions, semi-empirical AMI, MNDO, and PM3 calculations were run <1999JMT103>. Depending on the nature of the alkyne partner, these condensations may be viewed either as [7+2] cycloadditions, directly forming azolotriazines, or as [3+2] cycloadditions forming spirobicyclic intermediates, which quickly rearrange to azolotriazines. 

Kleinpeter et al. carried out ab initio and semi-empirical (PM3) calculation in order to rationalize the tautomeric equilibria of 7-hydroxy-5-methyl[l,2,4]triazolo[l,5- ]pyrimidine <1995JST(335)273, 1997JST(435)65>. This compound can exist in four tautomeric forms a-d (Figure 1). The authors concluded that the high computational level available can sufficiently reproduce the position of tautomeric equilibria in solution and, thus, can serve as a useful tool instead of time-consuming experimental studies. 

The scope of the rearrangement reaction whereby azido-l,2,3-triazolide ion (66) is converted to the (diazomethyl)tetrazolide ion (68) has been studied. Where R = H, substituted phenyl, Me, and C02Me the reaction proceeds at a rate which is largely independent of substituent extensive decomposition is observed where R = COMe, COAr, and CN. PM3 calculations used to explore the energy profile of the reaction pathway indicate that the order of anion stability is (67) < (66) < (68) and that the rearrangement is of the type (66) (67) (68) for which 2 and k i ki. 

PM3 calculations of the 2 + 3-cycloaddition of t-butylphosphaacetylene with 2,4,6-triazidopyridine are consistent with the dipole-LUMO-controlled reaction type. An FTIR spectroscopic study of the 1,3-dipolar cycloaddition of aryl azides with acetylenes shows that the rate of reaction increases logarithmically with pressure (below 1 GPa). The 3 -I- 2-cycloaddition between an azide (69) and a maleimide (70) has been greatly accelerated by utilizing molecular recognition between an amidopyridine and a carboxylic acid [see (71)] (Scheme 24). ... 

The rearrangement 12 13 is not straightforward and two alternatives routes have been suggested. One of them involves a 1,3 transfer from silicon to oxygen to give the silyl radical 15 followed by Sui reaction on the peroxide moiety [15]. The other indicated by PM3 calculations is a dioxirane-like three-membered intermediate 16 having a pentacoordinated central silicon followed by a 1,2 silyl migration to afford radical 13 [19]. 

The axial equatorial equilibrium of 5-OH-l, 3-dioxane was strongly solvent dependent alcohols favor the axial position, other solvents, more polar than CCI4, the equatorial orientation of the 5-hydroxy substituent, both effects being corroborated by PM3 calculations [92MI3 93JST(287)185],... 

As a semirigid model (77JCP2874), quantum-chemical AMI and PM3 calculations (90JST179), and many NMR studies (to be discussed later) claim the chair conformation to be also that preferred for 1,4-dioxane. From dipole moment measurements, the participation of the boat conformer was suggested (76BSF1649, 76CR11 77CR869). 

FIGURE 4. Optimized structures of CH2=CH0Li(Me20)2 (3a) as obtained from B3LYP/6-31+G calculations (3b) and CH2=CH0Li(Me20)3 as obtained from PM3 calculations. Reprinted with permission from Reference 12. Copyright 1997 American Chemical Society... 

Efficient kinetic resolntion was also observed dnring the deprotonation of the carbamates rac-91 and rac-100. Eqnation 21 shows the preferred prodncts [(2/()-98 and (25)-101] obtained from the racemates with recovery of the enantiomerically enriched starting materials (5 )-97 and (2/()-100 . Diastereomer (25 )-99 arises in low yield but high ee. Even simple PM3 calculations reflect the experimentally recorded (opposite) diastereoselectivities well . ... 

---