Suitability of the PM3-derived molecular electrostatic potentials

A systematic study of the suitability of PM3-derived molecular electrostatic potentials (MEPs) is presented. Forty-six MEP minima, 81 electrostatic charges, and 17 electrostatic dipoles were determined at the PM3 level and compared with those obtained from the ab initio 6-31G* wave function, as well as from the semiempirical MNDO and AM1 wave functions. The statistical results of the comparison analysis between semiempirical and ab initio 6-31G* MEPs show that PM3 is in general reliable for the study of the MEP minima but a mediocre method as a source of electrostatic charges. © 1993 John Wiley & Sons, Inc.     

Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials

The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.     

Electron donor-acceptor complexes: Evaluation of MNDO as a computational tool to probe intermolecular interactions

Donor-acceptor pairs form EDA complexes that exist as conformational isomers exhibiting different ground-state and photochemical properties. We have sought a rapid, general, and accurate quantum mechanical computational method to generate potential energy surfaces that are representative of the donor-acceptor intermolecular interactions at the self-consistent field (SCF) level. The semiempirical molecular orbital (MO) method MNDO has been compared to ab initio methods to assess its behavior with respect to energy, dipole moment and ionization potential shifts. MNDO correctly distinguishes between repulsive and bound EDA complex states at the SCF level and produces potential curves that are smooth and free of spurious minima or cusps. MNDO curves are systematically more repulsive than those for ab initio STO-3G calculations; calculated interaction energies exhibit a mean absolute deviation of 2.90 kcal/mol. MNDO appears to provide a reliable qualitative estimate of the nondispersion portion of the interaction energy. Limitations and errors arising from minimal basis sets, single determinants, and neglect of dispersion are discussed.     

Proton affinities of molecules containing nitrogen and oxygen: comparing ab initio and semiempirical results to experiments

We report a comparison of theoretical and experimental proton affinities at nitrogen and oxygen sites within a series of small molecules. The calculated proton affinities are determined using the semiempirical methods AM 1, MNDO , and PM 3; the ab initio Hartree–Fock method at the following basis levels: 3-21G //3-21G , 3-21+G //3-21G , 6-31G *//6-31G *, and 6-31+G (d, p)//6-31G *; and Møller–Plesset perturbation calculations: MP 2/6-31G *//6-31G *, MP 3/6-31G *//6-31G *, MP 2/6-31G +(d, p)//6-31G *, MP 3/6-31G +(d, p)//6-31G *, and MP 4(SDTQ )/6-31G +G (d, p)//6-31G *. The semiempirical methods have more nonsystematic scatter from the experimental values, compared to even the minimal 3-21G level ab initio calculations. The thermodynamically corrected 6-31G *//6-31G * proton affinities provide acceptable results compared to experiment, and we see no significant improvement over 6-31G *//6-31G * in the proton affinities with any of the higher-level calculations. © 1992 John Wiley & Sons, Inc.     

Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces

The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.     

Comparative semiempirical and ab initio study of the harmonic vibrational frequencies of aniline—I. The ground state

The harmonic vibrational frequencies of the ground state S₀ of aniline obtained from various ab initio methods [6-31G, 6-31G(*) and 6-31G* basis sets] and semiempirical methods (MINDO/3, MNDO, AM1 and PM3) have been compared to the experimental vibrational spectra. Detailed theoretical analyses of the atomic Cartesian displacements of all normal modes are presented. The semiempirical PM3 method reproduces the experimental frequencies of aniline with comparable accuracy to the ab initio methods. Ale PM3 method will be useful in predicting the vibrational spectra of larger aromatic amines.     

Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches

A semiempirical treatment of electrostatic potentials and partial charges is presented. These are the basic components needed for the evaluation of electrostatic interaction energies in combined quantum mechanical and molecular mechanical approaches. The procedure to compute electrostatic potentials uses AM1 and MNDO wave functions and is based on one previously suggested by Ford and Wang. It retains the NDDO approximation and is thus both easy to implement and computationally efficient. Partial atomic charges are derived from a semiempirical charge equilibration model, which is based on the principle of electronegativity equalization. Large sets of ab initio restricted Hartee-Fock (RHF/6-31G*) reference data have been used to calibrate the semiempirical models. Applying the final parameters (C, H, N, O), the ab initio electrostatic potentials are reproduced with an average accuracy of 20% (AM1) and 25% (MNDO), respectively, and the ab initio potential derived charges normally to within 0.1 e. In most cases our parameterized models are more accurate than the much more expensive quasi ab initio techniques, which employ deorthogonalized semiempirical wave functions and have generally been preferred in previous applications. © 1996 John Wiley & Sons, Inc.     

A theoretical study of the rotational isomers of nitrosomethanol by semiempirical (AM1) and ab initio methods

The conformational potential energy surface as a function of the two internal torsion angles in C-nitrosomethanol has been obtained using the semiempirical AM1 method. Optimized geometries are reported for the local minima on this surface and also for the corresponding points on the HF/6-31G, 6-31G*, and 6-31G** surfaces. All methods predict cis and trans minima which occur in degenerate pairs, each pair being connected by a transition state of C_s symmetry. The AM1 structures are found to compare well with the corresponding ab initio structures. Ab initio HF/6-31G and HF/6-31G* harmonic vibrational frequencies are reported for the cis and trans forms of nitrosomethanol. When scaled appropriately the calculated frequencies are found to compare well with experimental frequencies. The ab initio calculations predict the energy barrier for cis → trans isomerization to be between 5.8 and 6.5 kcal/mol with the trans → cis isomerization barrier lying between 2.3 and 6.5 kcal/mol. The corresponding AM1 energy barriers are around 1 kcal/mol lower in energy. The ab initio calculations predict the barrier to conversion between the two cis rotamers to be very small with the AM1 value being around 1 kcal/mol. Both AM1 and ab initio calculations predict interconversion between trans rotamers to require between 1.2 and 1.4 kcal/mol.     

Semiempirical NDDO calculations with STO-3G and 4-31G basis sets

Possible refinements of semiempirical methods include the use of larger basis sets and of correlated wave functions. These possibilities are investigated in semiempirical NDDO SCF calculations with the STO-3G and 4-31G basis sets, and in correlated calculations at the STO-3G level. The present approach is characterized by the analytical evaluation of all one-center terms and two-electron integrals, and the semiempirical adjustment of the remaining one-electron integrals and the nuclear repulsions. The NDDO SCF results tend to reproduce the correspondingab initio results more closely than experimental data, even if they are parametrized with respect to experiment. The explicit inclusion of electron correlation at the STO-3G level improves the calculated results only slightly.     

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.     

On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges

A new strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point-charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO-3G and 6-31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6-31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6-31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6-31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrostatic charges.     

Improvement of the hydrogen bonding correction to MNDO for calculations of biochemical interest

Recent suggestions for correcting H? Acceptor interactions within MNDO, together with results of crystallographic analysis, were used to modify this SCF semiempirical calculation for multiple hydrogen bonded associations. Thermodynamic profiles for model systems of biochemical interest such as H₂O? H₂O, hydration of neutral and charged molecules, dimerizations and proton transfers show the advantages of this method. Its treatment of charges, bonding, geometries, energetics and vibrational frequencies is shown to be comparable to ab initio calculations with various basis sets. However, basic MNDO deficiencies and criteria applied for H-bonding result in some too high barriers for proton transfers.     

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.     

Atomic charges derived from semiempirical methods

It is demonstrated that semiempirical methods give electrostatic potential (ESP) derived atomic point charges that are in reasonable agreement with ab initio ESP charges. Furthermore, we find that MNDO ESP charges are superior to AM1 ESP charges in correlating with ESP charges derived from the 6-31G* basis set. Thus, it is possible to obtain 6-31G* quality point charges by simply scaling MNDO ESP charges. The charges are scaled in a linear (y = Mx) manner to conserve charge. In this way researchers desiring to carry out force field simulations or minimizations can obtain charges by using MNDO, which requires much less computer time than the corresponding 6-31G* calculation.     

Pyrrolizidine alkaloids necine bases: Ab initio,semiempirical, and molecular mechanics approaches to molecular properties

The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and ¹H-NMR (nuclear magnetic resonance) studies in D₂O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.     

Ab initio molecular orbital study of 1-fluorosilatrane

The molecular geometry of 1-fluorosilatrane was optimized fully by restricted Hartree–Fock (HF) calculations using the 3-21G, 3-21G(d) and 6-31G(d) basis sets, with the aim of locating the positions of the local minima on the energy hypersurface. The optimized geometries were compared with available experimental (X-ray and ED) and semiempirical data. The ab initio calculations using polarized basis sets are in good agreement with those of previously reported semiempirical calculations, giving a slightly longer equilibrium Si? N distance (～ 256 pm) in the case of the endo minimum. However, the exo minimum predicted by the semiempirical methods is not supported. There was no experimental evidence for the existence of this exo minimum, and the present ab initio calculations suggest that it is highly unstable. There is considerable disagreement among the experimental results in the C? N and C? C bond lengths in various silatranes, their differences being as large as 13 pm. The present calculations predict that these differences may appear because the silatrane skeleton is flexible with low-energy, large-amplitude internal motions which introduce considerable uncertainties into the position of ring carbon atoms. © 1994 by John Wiley & Sons, Inc.     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

An investigation of the relative stabilities of the isomers of CF2N2: Comparison of ab initio and MNDO calculations

Ab initio SCF calculations at the HF/3-21G level and semi-empirical MNDO calculations have been used to locate the stationary points on the CF₂N₂ energy surface. Perfluorodiazomethane is predicted to be most stable isomer, but perfluorodiazirine is predicted to lie only ca 41 kJ higher in energy at the SCF level. There are significant differences between the ab initio and MNDO results for the ordering of some of the isomers. Frequency calculations give results in good agreement with the limited experimental data on these molecules.     

Theoretical Modeling of the Stereoisomerization of Tetracoordinated Be(II) Bis(chelate) Complexes

Quantum-chemical (semiempirical MNDO and ab initio RHF SCF with an STO-3G basis set) calculations were performed for stereoisomerization of tetracoordinated Be(II) bis(chelate) complexes with BeN₂O₂ coordination unit. The most probable pathway for their monomolecular isomerization was found to involve, in agreement with experimental data, cleavage of a Be–N coordination bond to form a tricoordinated Be intermediate (dissociation–recombination mechanism) rather than a competitive polytopal rearrangement. The planar structure of the intermediate detected upon thermo- and photoexcitation of the complexes was predicted from our calculations.