PM3 study of the proton affinities of 2-, 3-, and 4-monosubstituted pyridines in the gas phase

Heats of formation (ΔH_f) and proton affinities (PA) of 2-, 3-, and 4-monosubstituted pyridines in the gas phase are calculated using the AM1 and PM3 semiempirical methods. The following substitutents are considered: NO₂, CN, CF₃, CHO, F, Cl, COCH₃, H, CH₃, OCH₃, SCH₃, NH₂, and N(CH₃)₂. The results are compared with the experimental data. Both methods reproduce the ΔH_f with comparble accuracy; the rms deviations are 4.1 (AM1) and 4.5 kcal/mol (PM3) for the free bases and 9.5 (AM1) and 9.7 kcal/mol (PM3) for their conjugated acids. The PA are systematically underestimated by both methods, but AM1 appears to be clearly better than PM3 for reproducing the experimental values. The rms deviations for AM1 and PM3 are 5.1 and 9.6 kcal/mol, respectively. This is due to a cancellation of systematic errors in the calculated ΔH_f in the AM1 case and to a summation of the errors in the PM3 case. Both methods correctly reproduce conformations of the molecules under consideration.     

IR spectra simulation as auxiliary tool for gas chromatography/Fourier transform IR spectroscopy/mass spectrometry identification of unknown compounds. 2. PM3, AM1, MNDO and MINDO3 simulations for simple nitriles

A set of the semi-empirical methods (PM3, AM1, MNDO and MINDO3) supplied by the HyperChem™ package has been tested to find the best auxiliary tool for the gas chromatography/Fourier transform IR spectroscopy/mass spectrometry identification of nitriles, taking 23 relatively simple nitriles as test compounds. Of the four methods, MNDO can be considered as the most advantageous since: (1) for 17 compounds of 23 tested, the IR spectra simulated by this method best match the experimental spectra (and in additional 3 cases, the results are as good as those obtained by AM1 method); (2) within the range of experimental wavenumbers of 900–3100 cm⁻¹, MNDO provides the best linearity between the calculated and experimental values (with a correlation coefficient of 0.989). A scaling factor of 0.85 can be used to afford better correspondence between the calculated and experimental wavenumbers. A disadvantage of the MINDO simulations is underestimation of ν_CN (and sometimes ν_CH) band intensities.     

Correlation of singlet-triplet gaps for aryl carbenes calculated by MINDO/3, MNDO,AM1, and PM3 with Hammett-type substituent constants

Heats of formation, atomic charges, and geometries of some 110 structures involving substituted singlet and triplet phenyl and 4,4-dimethyl-1,4-dihydronaphthalene carbenes and the corresponding diazomethanes were calculated by MINDO/3, MNDO, AM1, and PM3 semiempirical molecular orbital methods. The singlet-triplet gaps for AM1 and PM3 calculations for the para derivatives in both systems have been successfully correlated with Brown σ⁺ constants. Good correlations with σ⁺ were found for the charges on the carbenic centers of the singlets as well as with the energy barrier for rotation of the aryl group about the C-C single bond in substituted singlet phenylcarbenes. Comparisons of these results with experimental data indicate that AM1 and PM3 are much better than MNDO and MINDO/3 in predicting the intrinsic substituent effects in singlet carbenes.     

The vibrational and NMR spectra,conformations and ab initio calculations of aminomethylene,propanedinitrile and itsN-methyl derivatives

The IR and Raman spectra of aminomethylene propanedinitrile (AM) [H₂N-CH=C(CN)₂], (methylamino)methylene propanedinitrile (MAM) [CH₃NH-CH=C(CN)₂] and (dimethylamino)methylene propanedinitrile (DMAM) [(CH₃)₂N-CH=C(CN)₂] as solids and solutes in various solvents have been recorded in the region 4000-50 cm^–1. AM and DMAM can exist only as one conformer. From the vibrational and NMR spectra of MAM in solutions, the existence of two conformers with the methyl group orientedanti andsyn toward the double C=C bond were confirmed. The enthalpy difference H ⁰ between the conformers was measured to be 3.7±1.4 kJ mol^–1 from the IR spectra in acetonitrile solution and 3.4±1.1 kJ mol^–1 from the NMR spectra in DMSO solution. Semiempirical (AM1, PM3, MNDO, MINDO3) and ab initio SCF calculations using a DZP basis set were carried out for all three compounds. The calculations support the existence of two conformersanti andsyn for MAM, withanti being 7.8 kJ mol^–1 more stable thansyn from ab initio and 8.6, 13.4, 11.6, and 10.8 kJ mor^–1 from AM1, PM3, MNDO, and MINDO3 calculations, respectively. Finally, complete assignments of the vibrational spectra for all three compounds were made with the aid of normal coordinate calculations employing scaled ab initio force constants. The same scale factors were optimized on the experimental frequencies of all three compounds, and a very good agreement between calculated and experimental frequencies was achieved.     

Comparison of the use of the MNDO and MINDO/3 methods with ab initio methods to study tautomerism in histamine, 2- and 4-methylhistamine

The semiempirical MNDO and MINDO/3 methods are used to study the various tautomeric forms of histamine, 2-methylhistamine, and 4-methylhistamine. Comparisons of the optimized structures and tautomerization energies are made with values obtained from ab initio Hartree-Fock calculations using the 3-21G and STO-3G basis sets. Based on these results and previous comparisons of STO-3G results with x-ray structures, the present results indicate that while there are some differences in the values of the structural parameters, the changes in structure upon tautomerization and/or protonation are very similar. Further analysis of the MNDO and MINDO/3 structures by means of their utilization in 3-21G and STO-3G calculations indicates that either of these semiempirical methods provides reliable values for the structural parameters. Both methods give good qualitative agreement with the ab initio calculations for the relative energies of the various tautomers in the three compounds. In these studies the MNDO method appears to give better quantitative agreement with the 3-21G and STO-3G results than the MINDO/3 method.     

Stable conformations of CH3CH2OCH2CH2OH: A comparison of theoretical methods

This article presents the results of an extensive examination of the stable conformations of CH₃CH₂OCH₂CH₂OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN-3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO-3G and HF/3-21G levels using Gaussian 92. The optimized HF/3-21G structures are reoptimized at the HF/6-31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6-31G(d) level. In addition, single-point MP2/6-31G(d) calculations are performed using the HF/6-31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.     

Theoretical studies of [n]paracyclophanes and their valence isomers. I. Geometries,strain energies,and enthalpies of the inter-conversions of [n]paracyclophanes and their Dewar benzee isomers

Four semiempirical methods (AM1, MNDO, PM3, and MINDO/3) are used to calculate the deformation angles of [n]paracyclophanes and their Dewar benzene isomers for n = 3… 10. The results obtained by all these methods are in good agreement with data from X-ray studies. We have determined the strain energies that, in both series of compounds, are due to two components: (1) the strain energy of deformation of the cycle (aromatic or Dewar Benzene skeletons) and (2) the strain energy of the oligomethylene chain. In [6]paracyclophane, the strain energy [SE_ring(MNDO) ≈? 32.9 kcal/mol] almost compensates the resonance energy (E_resonance ≈ 36 kcal/mol) so that its chemical properties are closer to alkenes than to benzenic compounds. To better reproduce the enthalpy of the valence isomerization [n]Dewar bezene → [n]paracyclophane, which is poorly calculated with these methods, a correction is proposed and the reaction enthalpy of [6]paracyclophane is estimated to be about ΔH_r ≈ 15 ± 15 kcal/mol. It is found that MNDO and MINDO/3 need the smallest corrections, but MNDO leads to better geometries than MINDO/3. In conclusion, MNDO seems to be the best technique for further studies of these compounds. © 1992 by John Wiley & Sons, Inc.     

Mindo/3 and mndo calculations of closed- and open-shell cations containing C,H, N,and O

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.     

Evaluation of MINDO/3 calculated structures. II. Branching errors in alkanes and cycloalkanes

MINDO/3 calculations have been carried out for a series of branched chain alkanes in order to assess effects of branching on calculated geometries and heats of formation (ΔH_f). With vicinal branching, MINDO/3 calculates the central C? C bond to be too long. Bond angles are also found to be distorted. Errors in calculated heats of formation are large when geminal branching is present and significant with vicinal branching. Branching error corrections for ΔH_f have been derived and applied to a separate series of branched acyclic and cyclic compounds. For the test sample, application of the branching error corrections gave calculated structures of acyclic branched hydrocarbons with heats of formation having an average absolute error of 1.3 kcal/mole rather than 17.3 kcal/mole before correction. Cyclic branched hydrocarbons are shown to be less well corrected. Calculations of heats of reaction have also been carried out for some isomerization and cyclization reactions using the MINDO/3 and MNDO methods. It is clear from the comparisons that MNDO calculations give less severe errors for highly branched compounds but the errors are still substantial. For prediction of heats of reaction, the error-corrected calculations are shown to be superior to the “raw” calculations obtained by MINDO/3 or MNDO.     

Stereoelectronic effects and the problem of the choice of model compounds for organic derivatives of a pentacoordinated silicon atom (taking silatranes as an example)

Anomeric effects at the silicon atom in silatranes XSi(OCH₂CH₂)₃N and model trimethoxysilanes XSi(OMe)₃ (X=H, Me, SiH₃, F, Cl) containing a tetracoordinated silicon atom were studied by the MNDO and AM1 methods. Unlike silatranes, the nature of substituent X pronouncedly affects the type and degree of stereoelectronic effects on the values of X−Si−O−C dihedral angles, X−Si bond lengths, and proton affinities of trimethoxysilanes. The results obtained indicate the necessity of modifying the set of spectral and structural indications of pentacoordination of the anomeric silicon atom established previously and observing the principle of conformational similarity for compared compounds. Bicyclic organosilicon ethers XSi(OCH₂)₃CH were proposed to be used as models of corresponding silatranes. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1061–1065, June, 1999.     

Hydrocarbon acidities calculated with MINDO/3, MNDO,and AM1

Acidities of 32 hydrocarbons have been calculated using MINDO/3, MNDO, and AM1. All three semiempirical procedures have systematic errors and reproduce experimental acidities poorly. A linear correlation, however, does exist between the calculated and experimental results. Correction of the AM1 or MNDO acidities leads to good agreement with literature values even for acids, such as methane and ethylene, whose conjugate bases are small localized anions. Predictions for several hydrocarbons are given.     

Structures and stabilities of [C3H3O]+ ions in the gas phase: A molecular orbital study

The relative energies of 11 [C₃H₃O]⁺ ions are calculated by different molecular orbital methods (MINDO/3, MNDO, ab initio with 3-21G and 4-31G* basis set and configuration interaction). The four most stable structures are: a ([CH₂?CH? CO]⁺), b c ([CH?C? CHOH]⁺) and d ([CH₂?C?COH]⁺); their relative energies at the CI/4-31G*//3-21G level are 0, 117, 171 and 218 kJ mol^?1, respectively. The isomerizations c→[CH?CH? CHO]⁺→[CH₂?C? CHO]⁺→ a and dissociations into [C₂H₃]⁺+CO and [HCO]⁺+C₂H₂ are explored. The calculated potential energy profile reveals that the energy-determining step is the 1,3-H migration c→[CH?CH? CHO]⁺. This explains the value of unity of the branching ratio and the spread of kinetic energy released for the two dissociation channels.     

Proton-coupled 13C NMR spectra of 2- and 3-substituted pyridines

The proton-coupled ¹³C NMR and PMR spectra of pyridine and the 2- and 3-monosubstituted pyridines NC₅H₄X [where X=CH₃, CN, COCH₃, COOCH₃, N(CH₃)₂, NO₂, OCH₃, Cl, or Br] for one-molar solutions of the compounds in DMSO-D₆, have been analyzed. The signs and values of the ¹³C-¹H HSSCs have been determined. Equations have been obtained connecting the ¹³C-¹H SSCCs in the 2- and 3-substituted pyridines and the monosubstituted benzenes. A satisfactory correlation of ¹JCH with the F and R constants of the substituents has been shown.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1223–1230, September, 1984.     

MNDO calculations of proton and methyl-and ethyl-cation affinities of neutral carbon,nitrogen, and oxygen bases

Proton affinities (PA) of 80 neutral bases were calculated using the semiempirical molecular orbital procedure MNDO. These were compared with the corresponding experimental and, where available, ab initio STO-3G and 4-31G data. For the 12 bases studied which led to ions which were not hyperconjugatively stabilized, the mean absolute error between the calculated and experimental values was 7.2 kcal mol^?1. However, a plot of these data revealed a clear tendency of MNDO to underestimate the PAs of the more basic molecules. Where hyperconjugative stabilization of the ion was possible, the calculated PAS were underestimated by a further 7–10 kcal mol^?1 for each attached alkyl group. Calculated and observed methyl-and ethyl-cation affinities were compared for 18 bases with qualitatively similar results.     

Dipole moment derivatives from MINDO/3 semi-empirical MO calculations

Dipole moment derivatives for CO, NO, CO₂, H₂O, HCN, BF₃, CH₄, C₂H₄, C₂H₆, CH₃F, F₂CO and H₂CO molecules have been evaluated using MINDO/3 MO calculations. The values are compared with those obtained by other semi-empirical MO methods.     

Conformations and electronic properties of alkyl peroxides,alkylperoxy radicals and alkoxy radicals

The equilibrium geometric parameters have been determined for peroxides (H₂O₂, CH₂O₂H, and CH₃O₂CH₃), alkylperoxy radicals (HO₂, CH₃O₂), and C₂H₅O₂), and alkoxy radicals (HO, CH₃O, and C₂H₅O) by means of the semiempirical MINDO/2' method. The predicted bond lengths were found to be more reasonable than those estimated by the CNDO/2 and INDO methods, but the bond angles were predicted too large because of the insufficient parametrizations for such heteroatoms as oxygen. The electronic properties of the above species are also discussed in connection with their physicochemical constants.     

Calculation of harmonic force constants,vibrational frequencies and integrated intensities of some organic molecules using the MINDO—Forces method

The harmonic force constants, vibrational frequencies and integrated intensity ratios of CH₂, H₂O, CH₂O, C₂H₂, CO₂, HCN, CH₃, CH₄, and C₂H₄ have been calculated using the MINDO—FORCES program and the Pulay method for the calculation of the molecular force constants. The results obtained are in general quite satisfactory when compared with available literature values. The results are, however, not as satisfactory in case of molecules containing heteroatoms, due to the neglect of some dipolar repulsion integrals for the heteroatoms by the MINDO/3 method. Calculated integrated intensities for CH₃ and C₂H₄ agree well with experimental results. The calculated integrated intensities for other molecules are obtained for the first time and no comparison with published data is therefore possible.Part of the M.Sc. Thesis of K. H. A. 1978.     

PM3 semiempirical calculations of lithium-cation and proton affinities for XYZPO and XYSO2 compounds

Proton affinities (PAs) of a series of phosphorous compounds bearing the phosphoryl function have been calculated using AM1 and PM3, as well as lithium-cation affinities (LCAs) using the recent PM3 lithium parametrization. Sulfonyl derivatives PAs and LCAs have been also calculated using PM3. The Li⁺ cation can be bonded in a “chelate” form with the two oxygens of the sulfonyl group. Nevertheless, the “linear” adduct, with the lithium-oxygen bond collinear with one of the SO bonds, is more stable. This is confirmed by ab initio calculations on Me₂SO₂ Li⁺ adducts. © 1996 John Wiley & Sons, Inc.     

Theoretical calculations of β-lactam antibiotics. III. AM1, MNDO,and MINDO/3 calculations of hydrolysis of β-lactam compound (azetidin-2-one ring)

Semiempirical AM1, MINDO/3, and MNDO methods have been used in the study of the alkaline hydrolysis of β-lactam antibiotics through a base-catalyzed, acyl-cleavage, bimolecular mechanism. In this work, the hydroxyl ion has been chosen as nucleophilic agent and the azetidin-2-one ring like a model of β-lactam antibiotic. The MINDO/3 method does not predict correctly the energies of small rings. This, together with the fact that, like MNDO, it cannot detect the occurrence of hydrogen bonds, gives rise to uncertain estimates of energy barriers. The AM1 method can be considered the most suitable for studying the hydrolysis of β-lactam compounds.