Comparison of semiempirical calculations for silicon compounds

A comparison is made of the performance of the MINDO/3, MNDO, AM1, and PM3 methods in calculating the nature of the dimer reconstruction observed on the silicon (100) crystal surface. Based on this case study we conclude that MINDO/3 gives the most realistic results, with PM3 calculations being quite similar but both MNDO and AM1 missing some key features of this system and giving rather unrealistic charge distributions. Hence use of PM3 is recommended for Si containing molecules where a lack of parameters or other restrictions prevent the use of MINDO/3.     

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.     

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.     

Variation of calculated single bond lengths in saturated hydrocarbon and silicon hydride molecules

A series of saturated X_nH_m (X being either C or Si) molecules is studied using the MINDO /3 and MNDO quantum-chemistry procedures. We find that the proximity of H atoms tends to shorten X? X bonds, and that this effect is (especially for MINDO /3) much larger than a similar trend in experimental values. The connection between this and hybridization values calculated from localized orbitals is investigated. It is found that the hybridization model works well for X? H bonds, whereas for X? X bonds non-σ-bond effects also play a significant role. It is shown that the changes in electronic structure may be directly connected to differences in X and H atomic levels, so that similar bond length differences may be expected in other molecular orbital calculations.     

Calculations on the diphenylmethyl anion

Semiempirical and ab initio calculations for the diphenylmethyl anion and related species are reported. MINDO/3 calculations indicate a coplanar anion with an enlarged bond angle of ～139° to counteract the steric repulsions. MNDO calculations reveal an expanded bond angle with somewhat greater twist (21°). The ab initio calculations (STO -3G level) reveal an expanded central bond angle with an intermediate degree of phenyl twist. The results are compared with experimental data for this and related anions.     

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.     

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.     

SINDO1 II. Application to ground states of molecules containing carbon,nitrogen and oxygen atoms

Molecular geometries, binding energies, ionization potentials and dipole moments are calculated by the SINDO1 method for a large number of molecules containing C, N and O atoms. Comparison is made with MINDO/3, MNDO and where possible with STO-3G results. The explicit data and an error statistics show the relative merits of SINDO1.     

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.     

Calculations of molecular vibrational frequencies using semiempirical methods

MINDO/3, MNDO, AM1, and PM3 calculations of molecular vibrational frequencies are reported for 61 molecules. All techniques were applied to both well-behaved and badly behaved systems. Overall, MINDO/3 and MNDO were found to contain rather large errors whereas AM1 and PM3 were relatively accurate. Since no technique does well for all molecules, the technique used should be chosen based on the molecular vibration of interest. In general, AM1 and PM3 together provide fairly accurate results.     

Quantum chemical study of the structure of thioformaldehyde S,S-dioxide and the possibility of its isomerization into an ylid

Thioformaldehyde S,S-dioxide (sulfene) has a highly reactive C=S bond. The estimation of the length and strength of this bond depends largely on the quantum chemical approximation selected. In comparison with ab initio schemes, the use of semiempirical MINDO/3, MNDO, AM1, and PM3 schemes involves difficulties related to the parameters for sulfur. Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 35, No. 1, pp. 35–38, January–February, 1999.     

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.     

Extension of MNDO to d orbitals: Parameters and results for the halogens

A recently proposed extension of the MNDO formalism to d orbitals has been parameterized for the halogens CI, Br, and I. Extensive test calculations indicate slight consistent improvements for normalvalent molecules and dramatic improvements for hypervalent molecules, in comparison with established MNDO -type methods without d orbitals. The mean absolute errors in calculated heats of formation are 3.9 kcal/mol for 155 normalvalent compounds and 2.8 kcal/mol for 23 hypervalent compounds. The predicted structures of the hypervalent molecules are qualitatively correct, with a mean absolute error of 2° in 19 bond angles.     

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。     

Coupling of stereochemistry and proton donor-acceptor properties of a schiff base,a model of a light-driven proton pump

On the basis of MINDO/3, MINDO/3 CI and MNDO calculations it is demonstrated that the (photo-)isomerization (single and double bond rotations) of a Schiff base polyene depends strongly on the protonation state. The results are pertinent to the ground state behaviour and the photobehaviour of retinal in bacteriorhodopsin, a protein which acts as a light-driven proton pump in Halobacterium halobium.     

硝酸酯化合物生成热的分子轨道研究

用MINDO/3, MNDO和AM1三种SCF-MO方法, 在全优化分子几何构型的基础上, 系统地计算研究了32个硝酸酯化合物的生成热, 与实验值相比, MNDO计算结果偏大很多; MINDO/3计算值与凝聚相实验值符合较好, 由于克服了MNDO法过高地估算原子之间Van der Waals核排斥能的缺点, AM1法给出了较满意的结果: 与七个气态实验值之间存在良好的线性关系(相关系数为0.992), 其间的平均绝对差值和平均差值分别只有10.28和-1.01kJ/mol。     

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 calculations of internal barriers to rotation and ring puckering: II. Amindo/3 study

The MINDO/3 technique is examined for its applicability to rotational barriers and ring puckering of strained-ring compounds. Comparisons are made with MINDO/2' and INDO on the compounds ethane, acetone, isobutylene, 3-oxetanone, cyclobutane, cyclobutanone, methylenecyclobutane, and 1,1-difluorocyclobutane. The MINDO/3 method improperly predicts all ring compounds to energetically favor the planar conformation as does its predecessor. Some improvement in bond lengths and bond angles is observed by MINDO/3 but the rotational barriers are still underestimated.     

A MINDO/3 MO study of oxidized flavins

The use of semi-empirical molecular orbital methods for the study of biologically important molecules has increased in recent years. The validity of well-known approximate Hartree-Fock molecular orbital methods such as MINDO/3 and MNDO still remains largely untested for biological molecules. Here we report its first application to the study of the electronic structures of isoalloxazines. Electronic charge distribution, variation of dipole moment, first ionization potential, electron affinity, orbital energies and electronic transitions are examined. Some of these results are compared with experiments. Good correlations with experiments were generally found in net atomic charge distributions, ionization potentials and electronic transitions. As a result of relatively good correlations with experiment application of the MINDO/3 method for extended study of biologically important coenzymes is promising.     

多原子分子力场的模型势函法与MNDO,MINDO／3方法的研究

用量子力学方法获得分子的模型力场现已占有很重要的位置.然而由于理论上很难获得体系高精度解析势能面,使力场的理论计算遇到了困难.直到Pulay提出梯度法后,量子化学方法才被广泛用于多原子分子的振动分析.但由于该方法采用数值微分通过能量的第二阶导数所获得的力场矩阵对角元误差很大,需将其伸缩、变角对角力常数分别扣除10％、20％,才能获得与观测值相近的结果;且ab initio计算花机时太多,应用于大分子计算存在一定的困难.为此本文把前文提出的确定力常数的模型势函法与MNDO、MINDO/3等半经验方法结合起来,构造多原子分子的力场,并用于振动分析,获得了满意的结果.