Molecular orbital and DFT studies of the alimemazine radical cation

Semiempirical molecular orbital methods including CNDO, MNDO, AM1 and PM3, and density function theory method B3LYP/3-21G(d) were employed in the study of the alimemazine radical cation. It was found that PM3 was much better than CNDO, MNDO and AM1 in the structural optimization. The bond lengths and bond angles by PM3 were close to the experimental data, and comparable with the results by the density function theory method.     

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.     

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     

Molecular modeling of oxaphosphetane intermediates of wittig olefination reactions

The literature reveals that the structures of four unusual oxaphosphetanes have been established by x-ray diffraction studies, and the structure of one mythical oxaphosphetane ( 6 ) has been deduced by theoretical calculations. We have used these known structures to calibrate the MMX87 force field, the only necessary modification being the stretching term for the P-O bond. The bond length, 1_o, was set at 1.80Å, which is an “average” of the P-O axial bond distances of the stable oxaphosphetanes. The AMPAC (Ver. 1.0) molecular orbital package utilizing the MNDO hamiltonian was also applied to the same problem, starting with the minimized geometries of the modified MMX87 force field. Fixed bond lengths and full minimizations were performed. The computed geometries of the four-member ring of each of the four oxaphosphetanes of known structures were found to be in very good agreement with the values obtained by x-ray diffraction. Furthermore, the method was applied to the mythical oxaphosphetane, and the results of MMX87 and MNDO calculations were found to be in very good agreement with the results of ab initio calculations. The MMX force field and the MNDO semiempirical method have been used to calculate the geometries and the steric energies (or heats of formation) of diastereomeric oxaphosphetanes formed in a theoretically real Wittig reaction.     

A quantum chemical study on structure of 1,2-bis(diphenylphosphinoyl)ethane and phenol cocrystal

The cocrystal of 1,2-bis(diphenylphosphinoyl)ethane (DPPEO) with phenol (1:1) were studied theoretically with AM1, PM3, MNDO and MINDO/3 semi-empirical methods to elucidate its structure. The bond lengths and angles from theoretical studies of molecule DPPEO/phenol (1:1) were found to be as expected. Theoretical results, concerning with intermolecular van der Waals forces in cocrystal, were compared with the previously obtained experimental data and AM1 results were found to be the best fit for bond lengths and angles of DPPEO/phenol.     

A combined quantum chemical/molecular mechanical study of hydrogen-bonded systems

A computational approach, which involves the combination of the OPLS force field and molecular orbital MNDO , AM 1, and PM 3 methods, has been developed to describe the effects of a large, molecular mechanically simulated environment on the Hamiltonian of a quantum chemical system. To test the validity of the combined quantum mechanical/molecular mechanical (QM /MM ) potential, a systematic study of the structures and energies of neutral and charged hydrogen-bonded complexes has been carried out, including comparisons with pure semiempirical calculations and available experimental and ab initio data. It is shown that, in many cases, the hybrid QM /MM potential behaves better than do related MNDO /M , AM 1, and PM 3 methods. As a case in point, the draw-back of AM 1 favoring bifurcated H-bonded structures over single ones is not presented in the combined AM 1/OPLS scheme. Possible ways of improvement of the combined QM /MM potential are discussed. © 1992 John Wiley & Sons, Inc.     

Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

共轭烯烃的分子几何构型、电子结构和生成热的DMM和AM1、PM3的比较研究

运用Ｄｅｌｆｔ分子力学（ＤＭＭ）力场和程序以及半经验分子轨道ＡＭ１和ＰＭ３方法计算研究了丁二烯、苯、甲苯、联苯、苯乙烯、富烯、、环辛四烯、［２，２］对环烷和菲等１０个共轭烯烃分子的几何构型、电子结构和生成热．ＤＭＭ计算的几何构型和生成热与实验结果相吻合，电荷分布结果与从头计算结果较接近．ＡＭ１和ＰＭ３计算的几何构型较好，但计算的生成热与实验结果偏差较大．ＰＭ３计算值比ＡＭ１的稍好．     

Theoretical studies on heats of formation for cubylnitrates using density functional theory B3LYP method and semiempirical MO methods

The heats of formation (HOF) have been calculated for all the 21 cubylnitrate compounds using the semiemprical molecular orbital (MO) methods (MINDO/3, MNDO, AM1, and PM3) and for 8 of 21 cubylnitrates containing 1–4 ? ONO₂ groups using the density functional theory (DFT) method at the B3LYP/6‐31G* level by means of designed isodesmic reactions. The cubane cage skeletons in cubylnitrate molecules have been kept in setting up isodesmic reactions to produce more accurate and reliable results. It is found that there are good linear relationships between the HOFs of the 8 cubylnitrates calculated using B3LYP/6‐31G* and two semiempirical MO (PM3 and AM1) methods, and the linear correlation coefficients of PM3 and AM1 methods are 0.9901 and 0.9826, respectively. Subsequently, the accurate HOFs at B3LYP/6‐31G* level of other 13 cubylnitrates containing 4–8 ? ONO₂ groups are obtained by systematically correcting their PM3‐calculated HOFs. Compared with noncaged nitrates, all the 21 cubylnitrates have high heats of formation implying that they may be very powerful energetic materials and have highly exploitable value. The relationship between the HOFs and the molecular structures of cubylnitrates has been discussed. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Study of hydrogen bonding interactions relevant to biomolecular structure and function

Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO-3G, 3-21G, 6-31G*, and MP2/6-31G* levels (geometries were fully optimized at each level). For anionic species, 6-31 + G* and MP2/6-31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for O? H-O and N? HO types of hydrogen bonds, but not for hydrogen bonds involving O-H? S and S-H? O, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.     

Tautomerism of rhodanine

Semiempirical (MINDO/3, AM1, PM3, MNDO) and ab initio (4-31G and 4-3IG + dAO/S basis sets) calculations on the relative stabilities and structures of the five potential tautomeric forms of rhodanine are reported. It is shown that all methods (excepting PM3) predict as most stable 2-thioxo-4-thiazolidinone. These results correspond to the known experimental data. The infrared spectrum of rhodanine was recorded for the region 4000-150 cm^–1, and the characteristic bands were compared with AM1 and 4-31G + dAO/S calculated frequencies. The transition states between five pairs of all possible tautomeric forms of the rhodanine were found by the AM1 method.     

Molecular enthalpies 3: Ground-state thermodynamic and computed enthalpies of the valence isomers of benzene

This paper is a study of benzene, Dewar benzene, benzvalene, [3]prismane, and 3,3-bicyclopropenyl by the MM2, MM3, MNDO, AM1, and PM3 calculational methods. Comparisons are made with experimental results and ab initio molecular orbital calculations from the literature.     

Theoretical calculations of the structure of a donor—acceptor stilbene, azobenzene and related molecules

The structures of a substituted stilbene, azobenzene, and two isomeric benzylidene anilines containing the 4-dimethyl-amino group at one end of the molecule and the 4′-nitro group at the other, have been calculated using the semiempirical MNDO, AM1, and PM3 methods and the ab initio HF/3-21G method. The results are compared with experimental data where available. The MNDO method gives a very poor account of the geometry of the stilbene, but both the AM1 and PM3 methods correctly predict the planarity of the substituted stilbene and nitrobenzylidene aniline but erroneously predict a non-planar structure for the azobenzene. In contrast, the ab initio method predicts planar structures for the substituted stilbene, azobenzene, and nitrobenzylidene aniline, and a twisted structure for the isomeric benzylidene nitroaniline, in line with crystallographic data. This loss of planarity for the benzylidene nitroaniline is almost certainly responsible for its smaller non-linear activity and for the hypsochromic shift observed in its low energy absorption band relative to the other molecules.     

Correlation of the acidity of substituted phenols,anilines, and benzoic acids calculated by MNDO,AM1, and PM3 with Hammett-type substituent constants

Heats of formation and net atomic charges of some 120 structures involving substituted phenols, anilines, and benzoic acids and the corresponding anions were calculated by MNDO, AM1, and PM3 semiempirical methods. The gas phase acidities of substituted phenols and anilines and the net atomic charges on the anionic heteroatoms of the corresponding anions have been successfully correlated with σ^? constants. Moreover, good correlations with σ were found for the charges on the acidic hydrogens of substituted phenols and anilines. In contrast, the gas phase acidities of substituted benzoic acids and the charges on the anionic oxygens of the corresponding anions are better correlated with Taft σ° constants. Comparisons of these results with experimental data and ab initio theoretical calculations indicate that AM1 and PM3 methods are much better than MNDO in predicting the acidity of aromatic compounds.     

Comparative parametric method 5 (PM5) study of trans-stilbene

In this work we report a comparative Austin method 1 (AM1), parametric method 3 (PM3), and parametric method 5 (PM5) studies for trans-stilbene in its ground, excited (singlet and triplet), and ionic (positive and negative polarons and bipolarons) states. We evaluated the accuracy of the recently developed PM5 method. PM5 and AM1 predict a non-planar ground and singlet states for trans-stilbene, while PM3 predicts planar ones, which is in agreement with the available experimental data. In general the PM3 and PM5 bond lengths are superior to AM1 while AM1 bond angles are superior to PM3 and PM5 when compared with available experimental data. The PM5 underestimates the cis–trans isomerization energy and and it is not a quite reliable method for the calculation of relative IP values. The presumed PM5 superior performance against AM1 and PM3 was not observed for the stilbene structures.     

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.     

The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials

The natural atomic orbital/point (NAO-PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO-PC/PM3 reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO-PC are found to be in better agreement with those given by RHF/6-31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAO-PC model is often slightly worse then the method implemented in MOPAC-ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6-31G* than those obtain with AM1. © 1994 by John Wiley & Sons, Inc.     

NDDO semiempirical approximations coupled with Green's function technique—a reliable approach for calculating ionization potentials

The ionization potentials of different molecules have been calculated with the outer valence Green's function (OVGF) technique, coupled with semiempirical MNDO, AM1 and PM3 methods. It is found that the OVGF method gives significantly better agreement with the experimental data than do results obtained with semiempirical calculations using Koopman's theorem including a new SAM1 and MNDO/d methods. Of the three semiempirical methods tested (MNDO, AM1, PM3) the OVGF (AM1) method gives the best agreement with experiment.     

Evaluation of PM3, AM1, and MNDO for calculation of higher energy ionization potentials

Higher ionization energies were calculated with PM3, AM1, and MNDO for three series of molecules, representative small molecules, molecules containing heteroatoms, and sterically congested alkenes. Values from PM3, AM1, and MNDO were compared to experimental values. In most instances, the semiempirical calculations correctly predict the ordering of higher ionization energies. In the absence of steric hindrance, MNDO is the method of choice. Within groups of molecules, AM1 performs better on hydrocarbons, especially twisted hydrocarbons, than PM3. PM3 commonly gives sigma orbitals which are too high in energy compared to related pi orbitals. PM3 performed better than AM1 with molecules containing oxygen, but failed to give the correct geometry for hydrogen peroxide.     

硝酸酯分子几何构型的量子化学研究

运用MINDO / 3、MNDO 和AM1 三种半经验分子轨道(MO)方法, 通过SCF计算, 首次系统地获得了32个硝酸酯化合物分子的全优化几何构型。三种方法的计算结果与已报道的四个化合物(硝酸甲酯、吉纳、硝化甘油和太安)的实验结果相比, AM1法较好。所有硝酸酯的酯基(-ONO~2)具有近似不变的几何参数。直链烷基硝酸酯的键长和键角极为相近, 全部重原子均共平面。二元直链和四元硝酸酯具有对称的分子构型。