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.     

Theoretical studies on the structure and electronic properties of aryl sulfides and sulfones

Molecular orbital calculations are reported on the structure and electronic properties of diphenyl sulfide using both semiempirical and ab initio methods. Neither the MNDO nor AM1 methods give satisfactory structures, but better results are obtained with the PM3 method. At the ab initio level, the 4-31G basis set with polarization functions on sulfur alone (4-31G/S*) gives comparable results to those obtained with the 6-31G** basis set. The corresponding bond lengths and angles at the sulfur atom of 4-aminophenyl-4′-nitrophenyl sulfide and related derivatives of diphenyl sulfone, diphenyl disulfide, and phenylthiosulfonate calculated at the 4-31 G/S* level show a good correlation with crystallographic data where available. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 141–147, 1998     

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.     

A comparison of semiempirical and ab initio transition states for HF elimination in unimolecular decompositions

The transition states for unimolecular HF elimination from a series of methylene halides and vinyl halides have been located and properly characterized at the AM 1, MNDO , PM 3, RHF /6-311G (d, p), and MP 2/6-311G (d, p) levels. Whereas the semiempirical MO methods deal well with the structures of the stable molecules, the structural differences between the ab initio and semiempirical transition states are considerably larger. The AM 1 and PM 3 activation energies appear to be relatively more accurate. © 1994 John Wiley & Sons, Inc.     

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.     

Conformational energetics of 1,3-dichloropropane as predicted by several calculations methods

Two semiempirical methods (MNDO and AM1), a molecular mechanics technique (MM2) and two ab initio approaches (6–31G* full optimization and 3–21G/6–31G*) were used to calculate the ordering of and energy difference between conformers in 1,3-dichloropropane. The semiempirical methods did not order the conformers properly or predict correct energy differences. Both ab initio methods ordered the conformers and predicted energy differences correctly, with the 6–31G* full optimization performing slightly better. The MM2 results were presented for calculations involving a force field with no hydrogens and a full force field of all atoms. The full force field properly ordered the conformers but did not correctly predict the energy differences. The nonhydrogen field ordered the conformers based on the Cl…Cl nonbonded distance. The data show that conformer stability is not a simple matter of maximizing the Cl…Cl nonbonded distance, but is also related to some other stabilizing interaction(s).     

A new scaling procedure to correct semiempirical MEP and MEP-derived properties

Summary The MNDO, AM1, PM3, and ab initio 6–31G^* and 6–31+G^* MEPs for 21 neutral and 12 charged molecules were computed in layers ranging from 1.2 to 2.0 times the van der Waals radii of atoms. Semiempirical and ab initio MEPs for each layer and two groups of layers were compared to gain insight into the relationships between semiempirical and ab initio MEPs. A detailed statistical study allowed us to obtain a new set of scaling coefficients able to correct the semiempirical MEPs to provide better representations of the ab initio values. The corrected semiempirical MEPs were used to obtain electrostatic charges, whose quality was tested by the comparison between semiempirical Coulombic MEPs and ab initio quantum mechanical MEPs.     

On the conformation of the propranolol molecule

The structure of the propranolol molecule has been optimized within the AM1 and PM3 semiempirical framework followed by ab initio HF/6-31G^* refinement. On each calculation level the conformational space was sampled to search for the lowest-energy conformer(s) from among a few hundreds of conformers at the semiempirical step and next from among a few dozens of conformers at the ab initio level. Finally, five stable conformers were found; each stabilized by one or two of the three possible hydrogen bonds. The geometrical and electronic parameters were established and found to differ only slightly in the structures with the hydrogen bond either present or not.     

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg²⁺ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.     

Performance of semiempirical methods in fullerene chemistry: relative energies and nucleus-independent chemical shifts

Semiempirical MNDO, AM1, and PM3 calculations are reported for 153 fullerene isomers in an attempt to assess the reliability of these methods through comparisons with ab initio and density functional results. B3LYP/6-31G^* relative energies are generally reproduced quite well by these calculations. Qualitative trends in ab initio nucleus-independent chemical shifts at the cage centers are captured by the semiempirical GIAO-MNDO approach while underestimating their absolute values. The agreement between the semiempirical results and the ab initio or density functional reference data is generally better for the larger fullerenes (C₆₀–C₁₀₂) than for the smaller ones (C₂₀–C₅₀). These systematic comparisons clarify the accuracy that may be expected from semiempirical computations in fullerene chemistry.     

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.     

Si~2Cl~6分子的内旋转能垒和振动基频的理论研究

用从头算方法HF/6-31G^*^*和密度函方法B3LYP/6-31G^*^*,对Si~2Cl~6分子的平衡几何构型进行优化,优化的结果与实验结果吻合得较好.并用上述两种不同的方法计算Si~2Cl~6分子的内旋转能垒,结果分别为8.786和6.694kJ/mol,其中DFT方法的计算结果与实验结果4.18kJ/mol吻合得较好.对Si~2Cl~6分子的振动基频进行计算.用HF/6-31G^*^*SQM力场所计算的频率理论值与实验值的平均误差为7.3cm^-^1,用B3LYP/6-31G^*^*未标度的力场所计算的频率理论值与实验值的平均误差为6.0cm^-^1.该密度泛函方法(B3LYP/~6-31G^*^*)的理论计算值比用HF/6-31G^*^*标度后的SQM力场计算的频率与实验值(除Si--Si键扭转振动基频之外的11条振动基频)吻合得更好.并给出了Si--Si键扭转振动基频的预测值。     

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.     

UV-laser photoisomerization of fumaryl chloride: the first identification of maleoyl chloride: matrix isolation infrared and ab initio studies

Fourier transform infrared spectra of fumaryl chloride 1 isolated in an argon matrix at 10 K have been analyzed. The comparison between the ab initio HF/6-31G calculated infrared spectra with the experimental ones reveals the existence of three planar conformers, the cis cis 1a, the cis trans 1b and the trans trans 1c. Laser UV irradiation of 1 at lambda = 340 nm yields maleoyl chloride 2 by a carbon carbon double bond photoisomerization process. The first identification of this compound was performed by comparison of the experimental infrared spectra with the calculated ones at the MP2/6-1G** level. AM1 semiempirical and ab initio calculations were used to calculate the structure and the relative stability of the three non planar maleoyl chloride conformers.     

Conformational behavior of some hydroxamic acids

The conformational preferences of a few hydroxamic acids are investigated by the density functional B3LYP/6-311++G**//B3LYP16-31G* and semiempirical AM1 and PM3 methods in this work. It is found that both semiempirical methods give satisfactory results in comparison with sophisticated DFT and ab initio calculations, except for the activation barriers, which are overestimated. Of the two semiempirical methods, while the PM3 method gives better results for relative stabilities, AM1 geometries are in slightly better agreement with the experiments. The keto forms are found to be most stable and the reaction pathways for the interconversion between the keto and enol forms have been deduced. The effect of solvation on the reaction has also been investigated, as has the effect of methyl substitution at the carbon and nitrogen atoms. All the investigated acids exhibit N-acid behavior.     

Semiempirical (AM1) and ab initio calculations of 2-X-adenine (X = H, F, Cl) and β-D-1-amino-2,3-didehydro-1,2,3-trideoxyribofuranose

We performed semiempirical (AM1) and ab initio (3-21G and 4-31G^**) calculations, with complete optimization of geometry, for 2-X-adenine (X = H, F, Cl) and selected conformers of β-D-1-amino-2,3-didehydro-1,2,3-trideoxyribo-furanose. Together (as 2-X-2',3'-didehydro-2',3'-dideoxyadenosine), or in separate conjunction with similar fragments, these structures belong to a group of 2',3'-dideoxynucleosides with potential anti-HIV activity.

The 2-X-adenine molecules are basically flat. For the halogenated species, especially the chlorine derivative, the results of the semiempirical method differ from the ab initio findings more widely than for adenine.

The results for the ribose derivative show the existence of conformers differing very little in energy. Ring puckering does not appear to depend on exocyclic torsion angles, structures with different conformations around the exocyclic C-C bond having similar ring conformations in all the cases analysed. The AMI method yielded geometries similar to those obtained ab initio with 3-21G.     

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.     

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: comparison of semiempirical, ab initio, and density functional results

The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium-bacteriochlorin, magnesium-chlorin, magnesium-porphin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree-Fock/6-31G* ab initio and density functional B3LYP/6-31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c(1), and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self-consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6-31G* or Hartree-Fock/6-31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree-Fock/6-31G* and B3LYP/6-31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin-like molecules.     

Ab initio and semiempirical study of structure and electronic spectra of hydroxy substituted naphthoquinones

The geometries of hydroxy derivatives of 1,4-naphthoquinone (NQ), viz., 2-hydroxy-1,4-naphthoquinone (2HNQ), 5-hydroxy-1,4-naphthoquinone (5HNQ), and 5,8-dihydroxy-1,4-naphthoquinone (DHNQ), have been optimized using the semiempirical and ab initio theoretical methods. Semiempirical methods used for the optimization are Austin Model 1 (AM1) and Zerner's Intermediate Neglect of Differential Overlap/1(ZINDO/1). For ab initio calculations the 6-31G* basis set is used. The electronic spectra of 1,4-naphthoquinone and its hydroxy derivatives are calculated using the semiempirical Zerner's Intermediate Neglect of Differential Overlap/Spectroscopy (ZINDO/S) method employing the geometries optimized at AM1, ZINDO/1 and ab initio levels and compared with their electronic absorption spectra measured by us. For hydroxy substituted systems, such calculations for spectral assignments are made for the first time. It is found that though the predictions of the three theoretical methods for the geometries are similar, the predictions of the ZINDO/S method using the ZINDO/1 optimized geometries, are better for the transition wavelengths in the visible region of the hydroxy substituted naphthoquinones, especially for 5HNQ and DHNQ.     

2-丁基-四氢噻吩亚砜13C-NMR的理论研究

在RHF/6-31G和B3LYP/6-31G水平上对顺式(Cis-)与反式(Trans-)2-丁基-四氢噻吩亚砜(BTHTO)进行几何优化,应用规范不变原子轨道法(GIAO)在6-31G、6-31+G、6-31++G和6-31+G(2d,p)水平上计算了Cis-和Trans-BTHTO的13C-NMR,对13C-NMR谱进行了归属。结果表明,BTHTO噻吩五元环的稳定构象呈半椅式,Cis-和Trans-BTHTO中与硫原子直接碳原子13C-NMR的显著差异主要是由于空间构型不同引起分子的静电势场对相应碳原子的屏蔽作用不同所致。