Multicenter point charge model for high-quality molecular electrostatic potentials from AM1 calculations

The natural atomic orbital/point charge (NAO-PC) model based upon the AM1 wave function has been developed to calculate molecular electrostatic potentials (MEPs). Up to nine point charges (including the core charge) are used to represent heavy atoms. The positions and magnitudes of the eight charges that represent the atomic electron cloud are calculated from the natural atomic orbitals (NAOs) and their occupations. Each hybrid NAO is represented by two point charges situated at the centroid of each lobe. The positions of the centroids and the magnitudes of the charges were obtained by numerical integration of the Slater-type hybrids and the results used to set up polynomials and look-up tables that replace the integration step in the actual MEP calculation. The MEPs calculated using this method are found to be in better agreement with those obtained using RHF/6-31G* than those obtained from the AM1 wave function using Coulson charges or with MOPAC-ESP. The MEP calculations are extremely fast and have, for instance, been incorporated into an interactive graphics package. © 1993 John Wiley & Sons, Inc.     

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.     

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.     

Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations

Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.     

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。     

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.     

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     

Vibrational study of dialkylphosphonates: di-n-propyl- and di-i-propylphosphonates by semiempirical and ab initio methods

Fourier transform infrared and Fourier transform Raman spectra of n-C(3)H(7) and i-C(3)H(7) dialkylphosphonates have been obtained. Semiempirical AM1 and the ab initio orbital molecular RHF/6-31G* theories have been used to study the molecular geometry, and the harmonic vibrational spectra with the purpose to assist the experimental assignments of these compounds. An extensive discussion on the assignment of the C-C, C-O, P-O and P=O stretching is carried out based on experimental data of compounds which have the propyl and isopropyl groups, as well as comparing the vibrational spectra of propane. Most of the RHF/6-31G* and AM1 results, once applied the appropriate scaling factor, showed an excellent agreement with the experimental wavenumbers. A few calculated frequencies related to CC and CO stretching do not agree well with the experimental trends.     

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。     

2,3,7,8-四氯苯并二英分子结构与热力学性质的理论研究

用密度泛函理论(DFT)和从头算(ab initio)方法,在B3LYP/6-31G、 B3LYP/6-31G*、 B3LYP/6-311G*和MP2/6-31G*水平上全优化计算了2,3,7,8-四氯苯并二英(2,3,7,8-TCDD)的几何构型、电子结构和振动频率,并用校正后的频率计算了298～1500 K的标准热力学函数,同时用半经验的PM3 SCF-MO进行了同样的计算,计算结果与实验值及文献值较好地吻合.     

Binding energies of the proton-bound amino Acid dimers gly.gly, ala.ala, gly.ala, and lys.lys measured by blackbody infrared radiative dissociation

Arrhenius activation energies in the zero-pressure limit for dissociation of gas-phase proton-bound homodimers of N,N-dimethylacetamide (N,N-DMA), glycine, alanine, and lysine and the heterodimer alanine.glycine were measured using blackbody infrared radiative dissociation (BIRD). In combination with master equation modeling of the kinetic data, binding energies of these dimers were determined. A value of 1.25 +/- 0.05 eV is obtained for N,N-DMA and is in excellent agreement with that reported in the literature. The value obtained from the truncated Boltzmann model is significantly higher, indicating that the assumptions of this model do not apply to these ions. This is due to the competitive rates of photon emission and dissociation for these relatively large ions. The binding energies of the amino acid dimers are ~1.15 +/- 0.05 eV and are indistinguishable despite the difference in their gas-phase basicity and structure. The threshold dissociation energies can be accurately modeled using a range of dissociation parameters and absorption/emission rates. However, the absolute values of the dissociation rates depend more strongly on the absorption/emission rates. For N,N-DMA and glycine, an accurate fit was obtained using frequencies and transition dipole moments calculated at the ab initio RHF/2-31G* and MP2/2-31G* level, respectively. In order to obtain a similar accuracy using values obtained from AM1 semiempirical calculations, it was necessary to multiply the transition dipole moments by a factor of 3. These results demonstrate that in combination with master equation modeling, BIRD can be used to obtain accurate threshold dissociation energies of relatively small ions of biological interest.     

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     

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.     

Near ab initio quality molecular electrostatic potential maps using hybridization displacement charges at PM3 level and effects of geometrical changes in amino groups

Charge distributions, dipole moments, and molecular electrostatic potentials (MEP) around several molecules consisting of carbon, nitrogen, oxygen, fluorine, sulfur, and chlorine atoms were studied using the PM3 semiempirical method and the results compared with those obtained using ab initio calculations at the RHF/6‐31G** level. Thus it is shown that relative MEP values near different atoms can be obtained using hybridization displacement charges (HDC) obtained by employing PM3 density matrices that usually agree quite satisfactorily with the ab initio ones. Further, positions of ab initio MEP minima are correctly located and the corresponding relative MEP values usually correctly predicted using the PM3(HDC) charges distributed continuously in three dimensions according to the forms of squares of valence s atomic orbitals. The necessary parameters for HDC calculations using the PM3 method were optimized. It is shown how within the frameworks of both PM3 and AM1 methods the π electrons or lone pairs associated with amino group nitrogen atoms and ring atoms can be satisfactorily treated in different situations. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 299–312, 2001     

Theoretical prediction on heats of formation for polyisocyanocubanes

The heats of formation (HOF) for all the 21 polyisocyanocubanes are calculated systematically with density functional theory (DFT) B3LYP and semiempirical MO(MINDO/3, MNDO, AM1 and PM3) methods. First, the accurate HOFs for the 8 title compounds are obtained by means of designed isodesmic reactions at DFT-B3LYP/6-31G* level, and the cubane cage skeleton has not been broken (i.e. choosing cubane as a reference compound) to produce more accurate and reliable results. It is found that there are good linear relationships between the HOFs calculated using the B3LYP/6-31G* and four semiempirical MO methods, respectively, and all of the linear correlation coefficients are more than 0.9971. The HOFs obtained from PM3 calculation are the best among the four semiempirical MO methods. Then, the accurate HOFs at B3LYP/6-31G* level of other 13 polyisocyanocubanes are obtained by systematically correcting their PM3-calculated HOFs. Polyisocyanocubanes have very high HOFs, and the HOFs increase linearly with the increasing of the number of isocyano groups in a molecule. The results show that polyisocyanocubanes are the new generation explosives with highly potential and exploitable value.     

Theoretical prediction on heats of formation for polyisocyanocubanes——Looking for typical high energetic density material(HEDM)

The heats of formation (HOP) for all the 21 polyisocyanocubanes are calculated systematically with density functional theory (DFT) B3LYP and semiempirical MO(MINDO/3, MNDO, AM1 and PM3) methods. First, the accurate HOFs for the 8 title compounds are obtained by means of designed isodesmic reactions at DFT-B3LYP/6-31G* level, and the cubane cage skeleton has not been broken (i.e. choosing cubane as a reference compound) to produce more accurate and reliable results. It is found that there are good linear relationships between the HOFs calculated using the B3LYP/6-31G* and four semiempirical MO methods, respectively, and all of the linear correlation coefficients are more than 0.9971. The HOFs obtained from PM3 calculation are the best among the four semiempirical MO methods. Then, the accurate HOFs at B3LYP/6-31G* level of other 13 polyisocyanocubanes are obtained by systematically correcting their PM3-calculated HOFs. Polyisocyanocubanes have very high HOFs, and the HOFs increase linearly with the increa     

1. 5-环辛二烯-3, 7-二炔(C~8H~4)结构和光谱性质的理论研究

采用量子化学从头算方法研究了1,5-环辛二烯-3,7-二炔(C~8H~4)的结构和光谱性质,根据等键反应分析和自然键轨道方法研究了它的稳定性、成键情况和共轭性。结果表明1,5-环辛二烯-3,7-二炔(C~8H~4)分子为平面刚性结构,可能稳定存在。分子中C≡C键与C=C键存在一定程度的共轭,可能具有芳香性。     

Effect of basic set quality and electron correlation on the scale factors of a harmonic force field

The completely optimized structure and harmonic force field of s-trans-buta-1,3-diene are reported at the MP2/6-31G and MP2/6-31G* levels of computation. Sets of empirical scale factors for the calculated force fields are derived and compared with the corresponding values computed at the RHF/4-31G and RHF/6-31G levels. Changes in the scale factors for this series of force fields are discussed. The vibrational frequencies are also reported for thirteen isotopomers of s-trans-buta-1,3-diene using the MP2/6-31G* force field. Some characteristics of the gauche and cis forms of buta-1,3-diene are also given.     

Experimental and Theoretical Conformational Analysis of Methylene- and Cyanophosphines and Their Oxides

The structure of a great number of methylenephosphine oxides 1-11 and cyanophosphines and their oxides 12-18 was studied by semiempirical PM3 and ab initio RHF/6-31G** calculations. Obtained results are in good agreement with experimental data (dipole moments, Kerr effect, IR spectroscopy). In 12-18 the contribution of interactions of CN group or Ph ring with lone pair of electrons (LPE) of the P atom, d-orbitals of the P atom, or P=O group is absent.