Semi-empirical PM3 calculations

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. 

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 conformational equilibria of three 2-substituted-l,3-dithianes 112-114 were studied by C NMR spectroscopy at various temperatures and in different solvents (Scheme 6), and both enthalpy and entropy differences were evaluated (Table 8) <1999T359>. The predominance of the axial conformers proved to be of enthalpic origin, in opposition to the entropic contribution which favors the equatorial conformers. The more polar solvent, on the other hand, stabilizes the more polar equatorial conformation. Parallel DFT calculations in the gas phase and in solution emphasized that both 2-substituents point outside the 1,3-dithiane ring system in the two conformations, for example 113-ax and 113-eq, and reproduce the experimentally observed conformational equilibria. Thus, the results of semi-empirical PM3 calculations <1997JMT(418)41> were able to be amended. 

Semi-empirical PM3 calculations" reveal that ylide 23 is a minimum on the potential energy surface and that both steps are exothermic. The enthalpy of the reaction of ylide formation in CH3CN was estimated to be —43 kcal/ mol and the enthalpy of reaction of the second step, 1,2-hydrogen shift, was calculated to be —12.5kcal/mol. 

The total energy, E, of 1 was calculated to be —4948.64 kcal mol 1 from semi-empirical PM3 calculations <2007JHC133>. 

One can consider not only open, but semi open and closed bottles also. As it follows directly from the results of semi empirical PM3-calculations the main peculiarities of construction to be described above are typical for all kinds of the (n,n)+(n,0) bottles. 

The results of semi-empirical PM3 calculations confirm the possibility of existence of the different types of nanotubes of variable diameter. 

Owing to the size of supramolecules semi-empirical methods are still in use. For instance, semi-empirical PM3 calculations were carried out for metalacryp-tands and metalacryptates and with lead as metal the theoretically predicted favorable cryptand formation was subsequently verified experimentally [123]. In another example, the rate of shuttling motions in rotaxanes was examined with semiempirical AMI calculation by Ghosh et al. [124] who generated different structures with a Monte Carlo procedure and subsequently optimized low-energy conformers. 

Our research in this area had its origin in a reinvestigation of the compound octachlorocyclotetrasilane Si4Cl8 (1) originally prepared by Hengge and Kovar [1]. The infrared and Raman spectra of 1 were interpreted in terms of a folded, D2d structure [1,2] similar to that known for several other cyclotetrasilanes [3]. However, a semi-empirical PM3 calculation predicted a planar, D4h conformation as the energy minimmn for 1 [4]. 

The choice of SbCls appears unfortunate for technical and theoretical reasons. From the experimental point of view, SbCls catalyses the reaction of chlorinated solvents with amines, which prevents the easy and accurate study of this very important class of nitrogen bases. In the same way, the frequently used solvent hexamethylphosphoric triamide does not give reliable results with SbCls. From the perspective of the theoretical prediction of DN, the 136 electrons of SbCls and the position of Sb in the fourth row of the periodic table make quantum chemical calculations on a series of SbCls complexes difficult. Semi-empirical PM3 calculations of complexation enthalpies have been performed [38] on SbCls complexes with 12 bases. At this low calculation level, only 43% of the variance of gas-phase calculated enthalpies is explained by experimental enthalpies in CH2CICH2CI. At the ab initio or DFT level, we are aware of only two studies the first [39] on five nitriles and pyridine and the second [40] on H2S complexes with SbCls. For the pyridine-SbCls complex, the gas-phase enthalpy, calculated without BSSE, is -115.5 kJ moF while the experimental value in CICH2CH2CI amounts to —142.3 kJ mol . It must be noted that antimony is described with the use of an effective core potential that incorporates major relativistic effects. In the end, the nature of the Sb—B dative bond does not seem to have been studied in depth and no theoretical prediction of the SbCls affinity can easily be made for Lewis bases. 

Kupka, T. 1997. P-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations Part I IR studies of complexation in peniciUin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds. SpectrochirtL Acta. A 53 2649-2658. 

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. 

The influence of selenium on the geometry of a number of aryl-substituted selenopyrans 12 was determined using quantum semi-empirical PM3 and DFT calculations. These results were compared with experimentally determined X-ray structures <2002J(P2)1909> (see Section 7.11.3.1). 

The creation of new nanoelectronic devices is not possible without using of elements with anisotropic conductivity. One of the ways to solve the problem is considered here. All calculations are performed in framework of semi empirical PM3-method [1-2],... 

The exceptional large value of forbidden gap width seems to be any doubtful. Perhaps it means that not all of the calculations results obtained for small clusters can be used for prediction of crystal structures properties. Must be noted that calculated bonds lengths in squares and hexagons and period of crystal lattice (1.607 A, 1.452 A, 5.894 A) differ from the values (1.503 A, 1.380 A, 5.545 A), obtained in [8], However one can not expect the better accordance from the results of clusters calculations performed moreover in the frames of semi-empirical PM3-basis. 

Equilibrium configurations, total energies, heats of formation, the electronic structure, the self vibrations frequencies and IR spectra of the various possible types of T-junctions are computed by employing of PC Gamess version of semi-empirical PM3-method. The results of our calculations in whole are in a good agreement with published earlier the data of theoretical and experimental researches devoted to the studying of T-junctions. 

Quantum chemistry computations based on employing of PC Gamess version of semi-empirical PM3-method [1-2] allows to define equilibrium configuration and calculate electronic structure of some of the simplest Y-junctions of carbon nanotubes, which have slang name twig . On the place of nanotubes conjunction defective cycles appear. Their type, number and mutual displacement can be enough various even in comparatively simple cases. Only the part of obtained results is presented here. 

The structures were fully optimized by semi-empirical quantum calculation with VAMP program of Material Studio package (Accelrys Co.). PM3 Hamiltonian was used in the calculations. 

PM3 semi-empirical MO calculations were performed by MOPAC version 3.5 (Fujitsu Limited) on a DELL XPS DXG061 personal computer. 

In this chapter, we present new results based on semi-empirical quantum calculations (PM3) that include solvation and charging effects simultaneously on the same model SFA.71 These calculations were carried out in HyperChem 5.0 (Hypercube, Inc.). Solvation was carried out with two approaches. In the first approach, the neutral, gas-phase SFA model was simulated, then this molecule was deprotonated at each of four carboxylic acid sites. Finally, a solvation sphere of H20 molecules was used to surround the anionic SFA and the structure obtained via molecular dynamics simulations and energy minimizations as an isolated nanodroplet. This approach has the advantage of allowing maximum flexibility of the model SFA. Larger model systems may require long simulation runs to sample all available conformations, but isolation of the SFA and water allows each component to move more freely. 

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