Heats of formation of 119 closed- and open-shell carbocations calculated by the semiempirical quantum chemical methods MINDO/3 and MNDO are reported and compared with experimental data. With proper consideration of failures in specific areas, both methods can be used for the thermodynamics of carbocations containing C, H, N, and O. MINDO/3 predicts unrealistic values for nitrogen containing cations with nitrogen multiple bonds and is not suited for closed-shell cations containing oxygen. Saturated acyclic hydrocarbon radical cations often are computed with abnormally long CC bonds by MNDO. Otherwise, the standard deviation of the two methods is not very different, being in the range of ±13 kcal/mol. MINDO/3 tends to overestimate the cation stabilities, whereas MNDO calculates cations usually too high in energy. Some of the errors which were found in the calculations of the ions are related to the computed values for the parent neutral structures, but others are not.
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http://dx.doi.org/10.1002/jcc.540070202 | DOI Listing |
Spectrochim Acta A Mol Biomol Spectrosc
September 2005
Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C.U., A. Postal 70-543, 04510 México D.F., Mexico.
Imidazo[1,2-a]pyrazine-3,6-diones and imidazo[1,2-a]imidazo[1,2-d]pyrazine-3,8-diones can be produced by pyrolysis of simple amino acids. While such bicyclic and tricyclic amidines were detected and characterized by IR spectroscopy for some alpha-substituted amino acids, the parent systems composed of glycine fragments are unknown up to now. IR spectra for five amidines derived from glycine were calculated by using different semi-empirical (PM3, AM1, MNDO and MINDO/3), HF, and hybrid DFT (B3LYP, B3P86 and B3PW91) methods in conjunction with 6-31G(d) basis set (for HF and DFT).
View Article and Find Full Text PDFCalculations of valerolactam and N-methylacetamide dimers by the method of molecular orbitals in CNDO/2H, MINDO/3, MINDO/3H, MNDO, MNDO/H, AM1, and PM3 approximations showed that the PM3 was the most suitable method for the description of geometrical and thermodynamic characteristics of hydrogen bonds between their amide groups. The calculation of the H-bound dimers of N-acetylalanine methylamide, which mimicked the beta structure of protein macromolecule, showed that the antiparallel conformation of the dimer is by 2.85 kcal/mol more stable than the parallel conformation.
View Article and Find Full Text PDFBiophys Chem
January 1996
B. Verkin Institute for Low Temperature Physics and Engineering of the Academy of Sciences of Ukraine, Lenin Ave. 47, Kharkov 310164, Ukraine.
Structural and electronic parameters of the chemotherapeutic alkylating drug thiotepa obtained by MNDO and MINDO/3 quantum mechanical calculations are used to explain some physical, chemical and biological properties of this compound. On the basis of the revealed difference between the preferential conformations of the thiotepa molecule in crystal and vacuum, a conclusion is made concerning the precautions in the choice of the appropriate molecular geometry in the search of structure-activity correlations. The theoretical data are also applied to the explanation of some peculiarities of soft ionization mass spectra of thiotepa, in particular its sensitivity to high field effects and the absence of protonation.
View Article and Find Full Text PDFThe considerable antibacterial activity of [[3(S)-(acylamino)-2-oxo-1-azetidinyl]oxy]acetic acids (oxamazins) in contrast to the lack of activity of the corresponding sulfur analogues (thiamazins) is examined in terms of physicochemical parameters, including electronegativity, IR carbonyl stretching frequencies, base hydrolysis rates, and three-dimensional molecular geometries. An X-ray structure determination of a protected thiamazin together with molecular graphics and molecular orbital calculations on model structures reveals that thiamazins would not fit as well as oxamazins in the active site of target bacterial transpeptidases. As a result of thiamazins' long N-S and S-C bond lengths, the pharmacophoric beta-lactam ring and carboxylate functionality cannot adopt the spatial relationship they have in penicillins and cephalosporins.
View Article and Find Full Text PDFJ Comput Chem
April 1986
Institut für Organische Chemie, Technische Universität Berlin, Straße des 17. Juni 135, D-1000 Berlin 12, West Germany.
Heats of formation of 119 closed- and open-shell carbocations calculated by the semiempirical quantum chemical methods MINDO/3 and MNDO are reported and compared with experimental data. With proper consideration of failures in specific areas, both methods can be used for the thermodynamics of carbocations containing C, H, N, and O. MINDO/3 predicts unrealistic values for nitrogen containing cations with nitrogen multiple bonds and is not suited for closed-shell cations containing oxygen.
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