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.     

Tautomerism of pyrimidine bases—uracil,cytosine, isocytosine: Theoretical study with complete optimization of geometry

The semiempirical MINDO /3 method with complete optimization of geometry is employed to calculate the electronic ground-state properties (dipole moments and ionization potentials) and the energies of various tautomeric forms of uracil, uracil monoanion, cytosine, and isocytosine. The results are shown to be consistent with most of the experimental data. Accuracy of various quantum–mechanical methods is discussed. Particular attention is paid to the influence of the geometry optimization on energy differences between various tautomers. Some qualitative conclusions of biological importance are drawn from these calculations.     

A semiempirical and ab initio MO study of the tautomers ofN-unsubstituted pyrazolones [hydroxy pyrazoles]

Semiempirical (MNDOC, MINDO/3, AM1, and MNDO) and ab initio (STO-3G and 4-31G basis sets) calculations on the relative stabilities, structures, and dipole moments of the 8 theoretically possible tautomeric forms of pyrazolone are reported. It is shown that MNDO + CI and MINDO/3 predict that 5-hydroxy pyrazole, 3-hydroxy pyrazole, and 2-pyrazolin-5-on are the most stable. These results correspond to the known experimental data. Of all used quantum chemical methods, the MINDO/3 results for the dipole moments of the investigated tautomers are in best agreement with the known experimental data. The electronic excitation energies were calculated using the CNDO/S-CI method. The results are in good agreement with the experimental UV spectra.     

Theoretical study of the N---H tautomerism in free base porphyrin

The N---H tautomerism of free base porphyrin is investigated at the semiempirical spin-unrestricted AM1 (UAM1) and ab initio RHF/3-21G levels. The UAM1 method provides delocalized geometries for all stationary structures without imposing any symmetry constraint. RHF/3-21G geometry optimizations have to be performed under symmetry restrictions to ensure that realistic delocalized structures are obtained. Both the semiempirical and the ab initio calculations predict that the interconversion between trans tautomers proceeds in an asynchronous two-step process via intermediate cis tautomers. The cis tautomers are characterized as minima in the potential energy surface and are 8–10 kcal mol⁻¹ higher in energy. The activation energy for the trans → cis interconversion is calculated to be approximately 23 kcal mol⁻¹ at the 3-21G level. The activation energy for the synchronous trans → trans interconversion is higher and has a value of 30.5 kcal mol⁻¹. The activation energies obtained at the semiempirical UAM1 level are twice as large as the ab initio values.     

A computational study of the reaction of methane with methyl radical

The activation energy and optimized transition-state geometry for the abstraction of a hydrogen atom from methane by methyl radical have been calculated by the semiempirical methods MINDO /3 and MNDO . These results are compared with other semiempirical and ab initio results. The MINDO /3 method, based upon accuracy of the computed energy of activation, appears to be the computational method of greatest reliability. A method of locating the transition state on semiempirical surfaces is demonstrated.     

Semiempirical implementation of strictly localized geminals for analysis of molecular electronic structure

Approximate electronic trial wave function taken as the antisymmetrized product of strictly localized geminals (APSLG) is implemented for semiempirical analysis of molecular electronic structure of “organic” compounds and for calculations of their heats of formation. This resulted in an O(N)‐scaling method. Using the MINDO/3 form of the semiempirical Hamiltonian with reparameterized β_AB values in combination with the APSLG form of the wave function yields the computational procedure BF'98. Calculations on the heats formation and the equilibrium geometries for a wide range of molecules show that the APSLG‐MINDO/3 approach is more favorable than its self‐consistent field‐based counterpart. Also, the APSLG formalism allows to interpret molecular electronic wave function in chemically sensible terms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 752–764, 2001     

Modified MINDO/3 13C chemical shift calculations for simple hydrocarbons

Calculations of ¹³C chemical shifts in some simple hydrocarbons have been carried out using the GIAO approach in the MINDO/3 semiempirical formalism. In order to achieve reasonable agreement with experiment it is necessary to modify (increase) the vacant orbital energies in the MINDO/3 calculation in order to reduce the magnitude of the paramagnetic contribution, and to also modify this dominant term by generally reducing it as a function of the number of hydrogen and carbon atoms bonded to the resonant nucleus in question. For a set of 34 resonant nuclei of the simpler hydrocarbons, agreement with experiment of the order of 7.8 ppm is attained; however, pathological cases such as cyclopropane and some simple allenes continue to cause problems, increasing the standard deviation of the full set to 12.5 ppm. Our results indicate that the MINDO/3 approach is as viable for ¹³C chemical shift calculations as other semiempirical approaches, all of which seem currently to be limited to a standard deviation of the order of 10 ppm.     

Theoretical investigations on 1,2-ethanediol: The problem of intramolecular hydrogen bonds

The conformational space of 1,2-ethanediol is studied on the basis of ab initio and semiempirical calculations. All possible conformers are treated. The relative energies of the conformers are systematically studied using various basis sets up to 6–311 + G(3df, 3pd) in order to perform calculations as accurate as possible within a reasonable amount of computer time. Electron correlation is included using Møller-Plesset perturbation theory. We propose two methods to evaluate the basis set superposition error associated with the intramolecular hydrogen bond appearing in some of the conformers. The results of semiempirical calculations are compared with these ab initio calculations. © 1996 by John Wiley & Sons, Inc.     

All-valence MO study of hydrogen bonding in water

Theoretical hydrogen bond energies and proton barriers for water dimer and trimer calculated by semiempirical all-valence MO methods have been compared. The results of CNDO/2 and INDO calculations are more adequate than those obtained by the MINDO/1 approach.     

A theoretical study of bond energies in model Si–H–Cl molecules using density functional approaches for representing Si surface chemistry

The reliability of density functional theory (DFT) methods for calculating Si(SINGLE BOND)2H, Si(SINGLE BOND)Cl, and Si(SINGLE BOND)Si bond energies is examined in reactions involving molecules and small clusters representing various surface sites appropriate for Si surface chemistry. Results are presented for systematic studies using a valence double-zeta polarization basis for both all-electron calculations and valence–electron calculations employing effective core potentials (ECPs). All-electron DFT results are comparable to much more demanding MP4, G2, and MC–SCF–CI calculations for computed bond energies. Whereas the use of ECPs introduces systematic energy differences of ca. 3–5 kcal/mol compared to AE results, depending on the type of bond involved, the use of ECPs for carrying out calculations on larger clusters is discussed where AE calculations become more computationally demanding. The convergence of Si bond energies as a function of replacing hydrogens with silyl groups is examined. In constructing models to describe etching processes involving Cl species on Si surfaces, the need for incorporating differences in thermochemistries for one-, two-, and three-coordinate Si surface sites is emphasized. Comparisons of semiempirical approaches for thermochemistries of Si-containing species find these methods somewhat less reliable for obtaining reliable bond energies compared to computationally more demanding DFT and ab initio correlated models. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2075–2085, 1997     

Solvatons. II. Aqueous dissociation of hydrides in the MINDOS approximation

A simple electrostatic model of solvation is presented which allows the interaction with solvent to be included systematically within semiempirical SCF calculations. Solvent effects are incorporated into the Hamiltonian for a solute molecule through a series of imaginary particles, solvatons, which represent the oriented solvent distribution around the solute.The proposed model is based on an algorithm for approximating the enthalpy of solvation of each atomic center from its charge in the molecular system and the experimental hydration enthalpies of its various ions. The calculated atomic solvation energy of one center is then modified to include the interaction with other charged atomic centers in the molecule. The method, developed here for the MINDO/3 approximation, has been applied to the calculation of the aqueous dissociation of a series of hydrides. In general, it leads to fairly accurate solvation enthalpies andpK _a values when applied to systems with fixed molecular geometries. A general discussion of the problems associated with the development of a solvation model within a semiempirical framework is also presented.     

A theoretical study of tautomerism: 2- and 4-oxopyrimidine and some of their derivatives

Here we present a detailed study of the theoretical approach to the tautomerization processes considering 2- and 4-oxo-pyrimidine and several of their derivatives. We look into molecular relaxation, suitability of semiempirical methods, and the effect of basis sets size in pseudopotential ab initio calculations. We found that no semiempirical method is suited for studying the relative stability of the tautomers, even ab initio calculations with minimal basis sets. On the other hand MNDO appears to be very useful for molecular relaxation and can be used, as well as Ab initio calculations, for reasonable estimates of relative tautomerization. We also considered the quality of prediction of other parameters, in particular the ionization potentials. We considered the correlation of experimental and theoretical values as a means to adjust the theoretical results to obtain more reliable predictions.     

The Electronic Structure of Phenylene and Naphthylene Bicyclobutanes. Photoelectron spectroscopy and model calculations

The photoelectron (PE.) spectra of 1,2,3-methenoindane ( 2 ), 1,2,3-metheno-2,3-dihydro-1H-cyclopenta [b]naphthalene ( 3 ) and 1,2,3-metheno-2,3-dihydro-1H-phenalene ( 4 ) are investigated. The PE. spectrum of 1,3-methano-2,3-dihydrophenalene ( 7 ) is reported and compared with that of 4 . The experimental results are analyzed in terms of empirical correlation diagrams and the results of semiempirical MINDO/3 and CNDO/S calculations. The analysis indicates that the strong impact of the bicyclobutylene group on the spectroscopic properties of the aromatic π-systems in 2 , 3 and 4 is due to hyperconjugative interactions involving bicyclobutane Walsh orbitals.     

Treatment of hydrogen bonding within CNDO/2 and MINDO/3: CNDO/2H and MINDO/3H

A formalism has been developed to treat hydrogen-bonded A—H…?B systems within the CNDO /2 and the MINDO /3 methodologies. In this formalism the interactions are divided into three distinct classes; those between (a) two hydrogen-bonded atoms, (b) one hydrogen-bonded and non-hydrogen-bonded atom, and (c) two non-hydrogen-bonded atoms. The last class of interactions is treated solely by the existing CNDO /2 or MINDO /3 method. For A –H…?B systems, the core resonance integrals are individually parametrized depending upon the class of the interaction. Three types of A—H…?B systems have been thus far parametrized. Nine hydrogen-bonded dimers have been studied using the new formalism and the current CNDO /2 and the MINDO /3 methods. MINDO /3 predicts very large interatomic (A –B) distances for the equilibrium geometry, and relatively small stabilization values for the hydrogen-bond energies. CNDO/2 predicts the reverse. The new formalism for both CNDO /2 and MINDO /3 predicts accurate geometries as well as energies for all nine dimers. The new formalisms are called CNDO /2H and MINDO /3H. A general discussion of the nature of hydrogen bonding as exhibited by CNDO /2H and MINDO /3H is presented.     

Quantenchemische untersuchungen zum mechanismus der elektrophilen substitution. I. Zur potentialhyperfläche des systems benzol/h+

Results of semiempirical calculations (CNDO/2-FK and MINDO/2 methods) for the σ-π complex problem on protonated benzene are given and compared with previous ones. The semiempirical methods were chosen according to the agreement of their results with new theoretical energy data (E_HF + E_korrel) concerning the classical–nonclassical problem of protonated ethylene. By these methods the corresponding part of the energy surface of the benzene/H⁺ system is simulated. The stationary points of this surface are found by a gradient method with complete optimization of the geometry. On the basis of this method we determined the energy profile of a reaction coordinate between the classical (σ-complex) and nonclassical (π-complex) cation. The so called strong π-complex is a saddle point between two σ-complex minima and can be interpreted as transition state of 1,2-proton shifts. Hypotheses for possible minimum energy paths of electrophilic attacks in the given region of the surface are discussed.     

Quantum-chemical analysis of the tautomerisim of 1,2,4-triazole and its amino and diamino derivatives

Calculation of the dipole moments and heats of formation for 1,2,4-triazole confirmed that it exists primarily in the unsymmetrical form, while similar calculations for 3-amino- and 3,5-diamino-1,2,4-triazoles showed that the amino tautomers with a hydrogen atom attached to the N-N bond are the preferred forms.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 540–545, April, 1977.The authors thank S. P. Zacheslavskii for providing the program to determine optimization of geometry for the MINDO/2 method.     

Tautomeric equilibria of heterocyclic molecules. A test of the semiempirical AM1 and MNDO-PM3 methods

Tautomeric equilibria (mainly of the lactam-lactim type) for a rather large number of six-membered heterocyclic molecules are calculated by the semiempirical AM1, MNDO-PM3, and MNDO methods. Except for compounds with adjacent pyridine-like lone pairs both AM1 as well as MNDO-PM3 give rather reliable predictions for relative stabilities of the various tautomeric species–comparable to quite high level ab initio calculations. The known errors associated with MNDO in the treatment of heterocyclic tautomerism are thus largely corrected in AM1 as well as MNDO-PM3. For 2-hydroxypyridine-pyrid-2(1H)-one the effect of self-association is less satisfactorily described by MNDO-PM3 than by AM1. MNDO-PM3 calculated relative stabilities of methylated derivatives are, however, in considerably closer agreement with experimental values than those obtained by AM1. Ionization potentials, especially those for lone-pair orbitals, are overestimated by all three semiempirical methods. MNDO-PM3 results for nitrogen lone-pair orbital energies are slightly better than those obtained by the AM1 or MNDO method.     

Optimum geometries and relative energies for cytosine,thymine, uracil,the imino tautomer of cytosine,the enol tautomer of thymine,and the enol tautomer of uracil by the MINDO/2 SCF MO method

A MINDO /2 SCF MO geometry optimization of cytosine (C), thymine (T), uracil (U), the imino tautomer of cytosine (C*), the enol tautomer of thymine (T*), and the enol tautomer of uracil (U*)was made. The optimized geometries for cytosine, thymine, and uracil agree well with crystallographic data. The optimized geometries for the tautomers show the correct trends in bond lengthening and bond angle except for the C4—O4 length and C4—O4—H angle of T* and U*. The energies of tautomerization were found to be 10.3, ?9.0, and ?14.2 kcal/mol for C?C*, T?T*, and U?U*, respectively, when optimized geometries are used. The overestimation of the C4—O4—H angle is speculated to arise because of an inadequacy in the parametrization of the one-center integrals in MINDO /2.     

Numerical sensitivity of trajectories across conformational energy hypersurfaces from geometry optimized molecular orbital calculations: AM1, MNDO,and MINDO/3

The monocyclic β-lactam [[4(S)-methyl-2-oxo-1-azetidinyl]thia]acetic acid was studied by the semiempirical molecular orbital methods AM1, MNDO, and MINDO/3. Using the reaction coordinate option in the program MOPAC on VAX and Cray X-MP computers, the potential energy curve was calculated for rotation of the C2-N1-S-C torsional angle in the conformationally flexible side chain while optimizing all other geometrical variables in the molecule. The trajectory taken during geometry optimization was found to be sensitive to the computer, the program version, the convergence criteria, and the degree of code optimization used in the calculation. In order to reduce the likelihood of spurious results, conformational or reaction energy hypersurfaces need to be calculated with the more precise SCF convergence and minimization criteria available in programs for MINDO/3, MNDO, and AM1 calculations. The nitrogen in the model β-lactam antibiotic is predicted to invert periodically as the dihedral angle to the exocyclic N-substituent sweeps through 360°.