硝酸酯几何构型,生成热和电子结构的PM3研究

用ＰＭ３ ＳＣＦ－ＭＯ方法，通过能量梯度全优化计算，得到３９个硝酸酯化合物的分子几何构型、生成热和电子结构。与实验结果和ＡＭ１计算结果进行了比较和评估。     

ClnAlNHn和HnAlNHn(n=1～3)的振动光谱与化学键性质的研究

用从头计算分子轨道法和密度泛函理论，在ＨＦ／６－３１Ｇ＊和Ｂ３ＬＹＰ／６－３１Ｇ＊水平上对ＣｌｎＡｌＮＨｎ和ＨａＡｌＮＨｎ（ｎ＝１～３）及其碎片分子的几何构型、电子结构、振动光谱和化学热力学性质进行了理论研究。结果表明，优化几何参数与实验值相。ＣｌＡｌＮＨ２和Ｈ２ＡｌＮＨ２分子中，Ａｌ－Ｎ键为由一个σ键和一个π键组成的双重键，旋转势垒分别为３４．１０和５４．３５ＫＪ．ｍｏｌ＾－１，而Ｃｌ３ＡｌＮＨ     

几个分子和负离子的QCI势能曲线

用ＱＣＩＳＤ（Ｔ）／６３１１＋Ｇ（３ｄｆ，２ｐ）（简称ＱＣＩ）计算了ＢＨ－（２Π），ＢＦ－（２Π），ＢＨ（１∑），ＢｅＨ－（１∑），ＢｅＦ－（１∑）和ＢＦ（１∑）的较完整的势能曲线，探讨了这些体系的稳定性和解离过程．同时用Ｍｏｒｓｅ函数和ＥＲ函数拟合得到势能曲线，用拟合结果计算谐性频率和非谐性频率，并与已有的实验数据（ＢＨ和ＢＦ分子）进行比较，由此考察了ＱＣＩ理论方法在远离平衡构型时的可靠性．对于因单参考态近似导致的反常势能曲线进行了ＣＡＳＳＣＦ计算．还比较了ＱＣＩ和Ｇ２理论中标准的ＭＰ２（ｆｕｌ）／６３１平衡几何构型及其对ＱＣＩ总能量的影响．     

丁二酰亚胺的结构、振动频率和热力学性质计算

用密度泛函理论（ＤＦＴ）和从头计算（ａｂ ｉｎｉｔｉｏ）方法,在Ｂ３ＬＹＰ／６－３１Ｇ、Ｂ３ＬＹＰ／６－３１１Ｇ和ＭＰ２／６－３１１Ｇ水平上,全优化计算了了二酰亚胺的分子几何构型和电子结构．进行了简正振动频率分析并用校正后的频率计算了２００－６００Ｋ温度范围的标准热力学函数,对计算结果进行了比较和讨论．     

NMR和分子力学法研究溶液中有机分子结构

在分子力学能量优化项中加入由ＮＭＲ实验得到的几何参数二面角（相应于~３Ｊ_（ＨＨ）耦合常数）及质子间距所构造的约束函数，使分子力学计算得到的能量极小点的分子构象，其耦合常数（~３Ｊ_（ＨＨ））及质子间距同ＮＭＲ实验结果相符合。文中以（±）－３－（４＇－甲苯基）－１－氮杂双环［２．２．２］－３－辛醇为例，采用自编的ＮＭＲ参数约束的分子力学计算程序ＭＭ２ＮＪ对其构象进行了计算。所得结果与Ｘ射线衍射法比较，有较好的一致性     

沙蚕毒系化合物的结构与生物活性关系

用ＭＮＤＯ－ＰＭ３方法对沙蚕毒系化合物二氢沙蚕毒，硫氰酸酯，巴丹，杀虫单及其异构件的几何构型进行了全自由度优化，并计算了其电子结构，讨论了生物活性与几何构型和电了结构的关系。     

应用分子图形学,分子力学,量子化学及静电势研究农药分？…

测定了标题化合物的晶体结构，它是由２个相似结构的化合物分子组成，晶体属单斜晶系，空间群为Ｐ２１，晶胞参数：ａ＝０．８４３１（３）ｎｍ，ｂ＝０．７２９７（１）ｎｍ，ｃ＝２．１８８０（７）ｎｍ，β＝１００．９０（３）°），Ｖ＝１．３２２（１）ｎｍ＾３，Ｚ＝２，应用分子力学程序ＭＭＸ及逐步旋转单键法探讨了它的构型和共它可能的优势构象，还应用ＭＮＤＯ方法计算了电荷分布及ＣＮＤＯ／２方法计算了静电势，结果有     

超价化合物NLi4^n＋和OLi4^n＋电子结构和性质

以６－３１Ｇ＾＊基组利用ＨＦ、ＭＰ２和ＤＦＴ方法优化了超价化合物ＮＬｉ４＾ｎ＋和ＯＬｉ４＾ｎ－的几何构型。研究结果表明，ＭＰ２和ＤＦＴ法计算出的ＯＬｉ４分子解离出Ｌｉ和Ｌｉ２的反应能与已有的实验值吻合，对于ＮＬｉ４分子，得到其解离出Ｌｉ和Ｌｉ２的反应能分别为１９１．７８和５１５．３７ｋＪ／ｍｏｌ（ＭＰ２值）。并预测了ＯＬｉ４＾ｎ＋和ＮＬｉ４＾ｎ＋分子的基振动频率。     

RS－联萘酚膦酰胺晶体结构及与其SS体分子力学计算结果的比较

测定了Ｏ，Ｏ（２，２′－联萘基）－Ｎ－（α－苯基乙基）膦酰胺（简称联萘酚膦酰胺，ＤＮＰＡ）ＲＳ体与乙醇形成的分子化合物晶体结构。晶体学数据为：Ｃ＿（２８）Ｈ＿（２２）ＮＯ＿３Ｐ·Ｃ＿２Ｈ＿５ＯＨ，Ｍｒ＝４９７．５，单斜晶系，Ｐ２＿１空间群，α＝９．３５９（２），ｂ＝１２．８０６（３），ｃ＝１１．６４１（Ａ），β＝１１１．６２（３）°，Ｚ＝２，Ｖ＝１２９４．０（５）（Ａ）３，Ｄｃ＝１．２７７ｇ／ｃｍ￣３，ＭｏＫａ（λ＝０．７１０７３Ａ）射线，μ＝０．１３６ｍｍ￣（－１），可观测数据３８７１个，Ｆ（０００）＝５２４，Ｒ＝０．０３５，Ｒｗ＝０．０４２。分子间以氢键相连接。ＲＳ体晶体结构与分子力学方法计算得到的ＳＳ体构象比较，发现这一对非对映体构象的差别由联萘基一边的构型决定。     

4—（H酸偶氮）—1—苯基—3—甲基吡唑酮光度法测定铝

研究了新试剂４－（Ｈ酸偶氮）－１－苯基－３－甲基吡唑酮（ＨＡＰＭＰ）与铝的显色反应，在ｐＨ４．６的ＨＡｃ－ＮａＡｃ缓冲介质中，ＣＴＭＡＢ存在下，ＨＡＰＭＰ和Ａｌ（Ⅲ）反应生成２：１红色络合物，铝的含量在０￣３．５μｇ／２５ｍＬ内符合比尔定律，方法已用于天然水样中铝的测定。     

Comparison of semiempirical MO methods applied to large molecules

The heats of formation for 19 molecules have been calculated with PM3 and AM1 semiempirical methods. The values obtained have been compared with experimental heats of formation. With PM3 and AM1 the average differences between calculated and experimental heats of formation are 8.45 and 12.34 kcal mol^?1 respectively. There are significant differences when large molecules are considered: this suggests that the parameterization should be done including larger molecules.     

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods

Two new semiempirical methods employing a Pairwise Distance Directed Gaussian modification have been developed: PDDG/PM3 and PDDG/MNDO; they are easily implemented in existing software, and yield heats of formation for compounds containing C, H, N, and O atoms with significantly improved accuracy over the standard NDDO schemes, PM5, PM3, AM1, and MNDO. The PDDG/PM3 results for heats of formation also show substantial improvement over density functional theory with large basis sets. The PDDG modifications consist of a single function, which is added to the existing pairwise core repulsion functions within PM3 and MNDO, a reparameterized semiempirical parameter set, and modified computation of the energy of formation of a gaseous atom. The PDDG addition introduces functional group information via pairwise atomic interactions using only atom-based parameters. For 622 diverse molecules containing C, H, N, and O atoms, mean absolute errors in calculated heats of formation are reduced from 4.4 to 3.2 kcal/mol and from 8.4 to 5.2 kcal/mol using the PDDG modified versions of PM3 and MNDO over the standard versions, respectively. Several specific problems are overcome, including the relative stability of hydrocarbon isomers, and energetics of small rings and molecules containing multiple heteroatoms. The internal consistency of PDDG energies is also significantly improved, enabling more reliable analysis of isomerization energies and trends across series of molecules; PDDG isomerization energies show significant improvement over B3LYP/6-31G* results. Comparison of heats of formation, ionization potentials, dipole moments, isomer, and conformer energetics, intermolecular interaction energies, activation energies, and molecular geometries from the PDDG techniques is made to experimental data and values from other semiempirical and ab initio methods.     

硝酸酯几何构型、生成热和电子结构的PM3 研究

用PM3 SCF-MO方法,通过能量梯度全优化计算,得到39个硝酸酯化合物的分子几何构型、生成热和电子结构。与实验结果和AM₁计算结果进行了比较和评估。     

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 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.     

Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules

Extensive testing of the SCC-DFTB method has been performed, permitting direct comparison to data available for NDDO-based semiempirical methods. For 34 diverse isomerizations of neutral molecules containing the elements C, H, N, and O, the mean absolute errors (MAE) for the enthalpy changes are 2.7, 3.2, 5.0, 5.1, and 7.2 kcal/mol from PDDG/PM3, B3LYP/6-31G(d), PM3, SCC-DFTB, and AM1, respectively. A more comprehensive test was then performed by computing heats of formation for 622 neutral, closed-shell H, C, N, and O-containing molecules; the MAE of 5.8 kcal/mol for SCC-DFTB is intermediate between AM1 (6.8 kcal/mol) and PM3 (4.4 kcal/mol) and significantly higher than for PDDG/PM3 (3.2 kcal/mol). Similarly, SCC-DFTB is found to be less accurate for heats of formation of ions and radicals; however, it is more accurate for conformational energetics and intermolecular interaction energies, though none of the methods perform well for hydrogen bonds with strengths under ca. 7 kcal/mol. SCC-DFTB and the NDDO methods all reproduce MP2/cc-pVTZ molecular geometries with average errors for bond lengths, bond angles, and dihedral angles of only ca. 0.01 A, 1.5 degrees , and 3 degrees . Testing was also carried out for sulfur containing molecules; SCC-DFTB currently yields much less accurate heats of formation in this case than the NDDO-based methods due to the over-stabilization of molecules containing an SO bond.     

Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens

The new semiempirical methods, PDDG/PM3 and PDDG/MNDO, have been parameterized for halogens. For comparison, the original MNDO and PM3 were also reoptimized for the halogens using the same training set; these modified methods are referred to as MNDO' and PM3'. For 442 halogen-containing molecules, the smallest mean absolute error (MAE) in heats of formation is obtained with PDDG/PM3 (5.6 kcal/mol), followed by PM3' (6.1 kcal/mol), PDDG/MNDO (6.6 kcal/mol), PM3 (8.1 kcal/mol), MNDO' (8.5 kcal/mol), AM1 (11.1 kcal/mol), and MNDO (14.0 kcal/mol). For normal-valent halogen-containing molecules, the PDDG methods also provide improved heats of formation over MNDO/d. Hypervalent compounds were not included in the training set and improvements over the standard NDDO methods with sp basis sets were not obtained. For small haloalkanes, the PDDG methods yield more accurate heats of formation than are obtained from density functional theory (DFT) with the B3LYP and B3PW91 functionals using large basis sets. PDDG/PM3 and PM3' also give improved binding energies over the standard NDDO methods for complexes involving halide anions, and they are competitive with B3LYP/6-311++G(d,p) results including thermal corrections. Among the semiempirical methods studied, PDDG/PM3 also generates the best agreement with high-level ab initio G2 and CCSD(T) intrinsic activation energies for S(N)2 reactions involving methyl halides and halide anions. Finally, the MAEs in ionization potentials, dipole moments, and molecular geometries show that the parameter sets for the PDDG and reoptimized NDDO methods reduce the MAEs in heats of formation without compromising the other important QM observables.     

RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I

Twenty years ago, the landmark AM1 was introduced, and has since had an increasingly wide following among chemists due to its consistently good results and time-tested reliability--being presently available in countless computational quantum chemistry programs. However, semiempirical molecular orbital models still are of limited accuracy and need to be improved if the full potential of new linear scaling techniques, such as MOZYME and LocalSCF, is to be realized. Accordingly, in this article we present RM1 (Recife Model 1): a reparameterization of AM1. As before, the properties used in the parameterization procedure were: heats of formation, dipole moments, ionization potentials and geometric variables (bond lengths and angles). Considering that the vast majority of molecules of importance to life can be assembled by using only six elements: C, H, N, O, P, and S, and that by adding the halogens we can now build most molecules of importance to pharmaceutical research, our training set consisted of 1736 molecules, representative of organic and biochemistry, containing C, H, N, O, P, S, F, Cl, Br, and I atoms. Unlike AM1, and similar to PM3, all RM1 parameters have been optimized. For enthalpies of formation, dipole moments, ionization potentials, and interatomic distances, the average errors in RM1, for the 1736 molecules, are less than those for AM1, PM3, and PM5. Indeed, the average errors in kcal x mol(-1) of the enthalpies of formation for AM1, PM3, and PM5 are 11.15, 7.98, and 6.03, whereas for RM1 this value is 5.77. The errors, in Debye, of the dipole moments for AM1, PM3, PM5, and RM1 are, respectively, 0.37, 0.38, 0.50, and 0.34. Likewise, the respective errors for the ionization potentials, in eV, are 0.60, 0.55, 0.48, and 0.45, and the respective errors, in angstroms, for the interatomic distances are 0.036, 0.029, 0.037, and 0.027. The RM1 average error in bond angles of 6.82 degrees is only slightly higher than the AM1 figure of 5.88 degrees, and both are much smaller than the PM3 and PM5 figures of 6.98 degrees and 9.83 degrees, respectively. Moreover, a known error in PM3 nitrogen charges is corrected in RM1. Therefore, RM1 represents an improvement over AM1 and its similar successor PM3, and is probably very competitive with PM5, which is a somewhat different model, and not fully disclosed. RM1 possesses the same analytical construct and the same number of parameters for each atom as AM1, and, therefore, can be easily implemented in any software that already has AM1, not requiring any change in any line of code, with the sole exception of the values of the parameters themselves.     

Prediction of geometries and interaction energies of complexes formed by small molecules using semiempirical and ab initio methods

The accuracy of the semiempirical quantum mechanics methods (AM1 and PM3), and the ab initio methods (6-31G^** and MP2/6-31G^**) in predicting intermolecular geometries and interaction energies have been evaluated by detailed studies of 17 bimolecular complexes formed by small molecules. Comparisons between calculated and experimental geometries for 12 complexes are presented. It was found that AM1 gave reasonably good predictions of the geometries of complexes such as CH₄ · CH₄, which have very weak interactions, but it is not as good as other methods in predicting intermolecular geometry for complexes where hydrogen bonding interactions play an important role. This is consistent with its inability to reproduce the charge transfer in the formation of hydrogen bonds in these complexes.

PM3 is able to predict intermolecular geometries for most complexes, including those with hydrogen bonding; its major flaw is its tendency to overestimate the strength of the interactions between hydrogen atoms. Care should be taken therefore in using PM3 to study complicated molecular systems with multiple hydrogen atom interactions and the method's weakness in handling complexes in which electrostatic forces are important should also be noted.

Among ab initio methods, both the 6-31G^** and the MP2/6-31G^** were found to outperform AM1 and PM3 in prediction of intermolecular geometry. Both of these ab initio methods showed excellent consistency in geometry prediction for most of the complexes studied, although MP2/6-31G^** is better than 6-31G^**. It is noted that the MP2/6-31G^** did not produce the correct geometry for the CO₂· HF complex.

For 12 complexes for which experimental geometry data are available, AM1, PM3, 6-31G^**, and MP2/6-31G^** successfully predicted the geometry in 10, 12, 12, and 11 cases, respectively. The average errors given by AM1 in the predicted intermolecular distances were 0.264, 0.272, 0.091, and 0.061 Å, respectively. In comparison to the ab initio methods, AM1 and PM3 commonly underestimated the molecular interaction energy in such complexes by ˜ 1–2 kcal mol⁻¹.