带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

平面五元水分子簇的量子化学研究

选用Gaussian03的B3LYP/6-31G(d,p)、DMol3的BLYP/DNP和deMon的BLYP/TZVP等方法计算了甲烷水合物(结构-1)中平面五元水分子簇的结合能和氢键能,作了基组重叠误差(BSSE)和色散能(dispersion)的修正,估算了次级相互作用的贡献.在DMol3程序中使用了大型数值基组DNP,将基组重叠误差降至最低.在Gaussi-an03的B3LYP/6-31G(d,p)计算中,采用平衡法(Counterpoise)校正基组重叠误差.两种计算方法给出了一致的结果,证实了在使用6-31G(d,p)基组时,一对水分子在平衡距离的基组重叠误差高达8 kJ/mol.为估算色散能的贡献,使用了新近发展的包含色散能的密度泛函的DFT程序deMon计算了五元水分子簇.用多种方法计算出了经基组重叠误差和色散能修正的五元水分子簇的分子间结合能和氢键能的较为精确的势能超曲面,为甲烷和其他气体水合物的分子动力学模拟提供了依据.     

6-烷基鸟嘌呤与DNA碱基间氢键作用的理论研究

用密度泛函B3LYP方法在6-311＋G**基组水平上对鸟嘌呤及顺(cis-)、反式(anti-)-6-烷基鸟嘌呤(O⁶-AlkylG)与DNA碱基(胸腺嘧啶T、胞嘧啶C、腺嘌呤A、鸟嘌呤G)的氢键二聚体结构进行了优化. 在MP2/cc-pVXZ(X＝D,T)// B3LYP/6-311＋G**水平上, 采用完全基组外推方法校正了氢键二聚体的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). 在B3LYP/6-311＋G**水平上计算了各氢键碱基对的全电子波函数, 并用分子中的原子理论(AIM)分析了碱基间的弱相互作用. 计算结果显示, 鸟嘌呤6-O烷基化改变了碱基间的氢键作用模式, 使碱基对发生了明显的螺旋桨式扭转和不同程度的位移, 碱基间的电子密度分布和氢键作用能明显减小. O⁶-AlkylG对DNA碱基间的氢键作用是去稳定化的, 去稳定化影响的顺序为GC＞GG＞GA≈GT. 计算结果与文献给出的实验结论基本一致.     

分子间相互作用研究的APF-D密度泛函SAM色散校正方法改进

APF密度泛函色散校正（APF-D）是由B3PW91和PBE0杂化的APF泛函,加上球形原子模型（SAM）色散校正构成的一种有别于Grimme经验色散校正的密度泛函理论色散校正（DFT-D）方法,计算稀有气体及其与小分子复合物结合能和势能面准确性很高,但对常见氢键、C―H…π和π…π等复合物结合能计算结果明显偏大,在一般性分子间相互作用问题研究中一直未被认可和采纳。我们发现APF-D结合能计算结果偏大的原因是APF泛函与SAM色散校正重复计入了一定量的长程色散能;通过引入不依赖于体系的SAM色散能阻力因子ζ,简单而有效地解决了APF-D色散能过度补偿问题,提出了APF-D改进方案APF-D^*;通过S66和L7标准测试集的对照计算表明,APF-D^*结合能准确性远高于原始APF-D,达到和超过目前常用的B3LYPD3和ωB97X-D方法水平,并具有较好的计算效率,期待在大体系分子间相互作用研究中得到广泛应用。     

B972-PFD:一种高精度的色散校正密度泛函方法

发现一种与球原子经验色散模型SAM深度契合的杂化泛函B972,组合成高精度的色散校正密度泛函B972-PFD。采用S66、S66x8和S22标准数据集以及大气氢键团簇、Adenine-Thymine的π…π堆叠、Watson-Crick氢键复合物和甲烷结合(H_2O)_(20)水簇等体系测试了B972-PFD的性能。测试结果显示:对于S66数据集B972-PFD方法的精度与Head-Gordon研究组的三个新泛函ωB97X-V、B97M-V和ωB97M-V处于同一水平,相对于CCSD(T)/CBS金质标准,结合能的RMSD小于1 k J?mol~(-1);在其它数据集的测试中,B972-PFD方法也表现出很好的计算精度。通过研究基函数效应,我们推荐Pople的6-311++G(2d,p)作为B972-PFD方法的最优性价比基组。     

O6-鸟嘌呤和O4-胸腺嘧啶甲基化与DNA碱基异常氢键作用的理论研究

用密度泛函B3LYP方法在6-311＋G**基组水平上对顺(cis-)、反式(anti-)O⁶-甲基鸟嘌呤(O⁶-MeG)和O⁴-甲基胸腺嘧啶(O⁴-MeT)与DNA碱基(腺嘌呤A、鸟嘌呤G)的非Watson-Crick氢键二聚体进行了优化. 在MP2/cc-pVXZ (X＝D,T)//B3LYP/6-311＋G**水平上, 采用完全基组外推方法校正了氢键二聚体的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). 此外, 在B3LYP/6-311＋G**水平上计算了各氢键碱基对的全电子波函数, 并用分子中的原子理论(AIM)和电子密度拓扑方法分析了碱基间的弱相互作用. 计算结果显示, 甲基化使碱基对间的氢键作用模式发生了明显的扭转和不同程度的位移, 碱基间的电子密度分布和氢键作用能明显减小, 甲基化对O⁶-MeG和O⁴-MeT与DNA碱基间的氢键作用是去稳定化的, 这种影响主要来自于大体积的甲基的空间效应和给电子效应, 且对顺式的影响明显大于反式. 计算结果与文献给出的实验结论基本一致.     

采用12种密度泛函理论方法表征三种三价铀复合物

比较了BP86、PBE、B3LYP、B3PW91、BHandHLYP、PBE0、X3LYP、CAM-B3LYP、TPSS、M06L、M06和M06-2X等12种采用了广义梯度近似(GGA、hybrid GGA、meta-GGA和hybrid meta-GGA)的密度泛函理论(DFT)方法在三个三价铀复合物表征中的应用. 研究模型采用铀复合物催化CO₂和CS₂官能团化反应中的三个中间体(Tp^*)₂U- η¹-CH₂Ph (Cpd2), (Tp^*)₂U- κ²-O₂CCH₂Ph (Cpd3) 和(Tp^*)₂U- κ²-S₂CCH₂Ph (Cpd4). 研究发现, B3LYP 和B3PW91 在几何结构和电子结构方面优于其它方法. 基于分子轨道理论的MP2 方法在Cpd2 和Cpd3 的表征中给出与DFT方法相近的结果, 而在Cpd4 的表征中表现出较大的差异. 这可能是由于同样是单参考态方法的MP2捕捉到了与DFT方法不同的电子结构. 同时, 通过对比分别采用小核赝势(5f-in-valence)和大核赝势(5f-in-core)基组处理铀原子的计算结果, 发现对测试的模型体系, 两种处理方法可获得相近的热力学能量. 与以往主要关注高价态锕系复合物的处理方法的评估工作不同, 本项工作适应逐渐增加的对低价态锕系分子体系的研究的需求, 对12 种常用的密度泛函理论方法在低价态锕系复合物研究中的应用进行了评估, 期望为处理类似体系的研究工作提供参考.     

TATB与二氟甲烷以及与聚偏二氟乙烯的分子间相互作用

动用密度泛函理论(SFT)B3LYP方法,取3－21G*基组,求得TATB(1,3,5-三氨基-2,4,6-三硝基苯)与CH~2F~2混合体系的三种优化构型以Boys-Bernardi方案校正基组叠加误差求得结合能。在B3LYP/6----311G*//B3LYP/3---21G*水TATB与CH~2F~2间的最大结合能为4.62kJ·mol^-1,还用MO－PM3方法计算TATB与---（CF~2CH~2}－(N=1,2,3,4,5,)的混合体系,由色散校正电子相关近似地求得其结合能力。当n＝5时,求得TATB与－（CF~2CH~2）--~n的最大结合能约为52.97kJ·MOL^-1。此外,自然键轨道分析用于讨论TATB与CH~2F~2之间的电荷转移。     

H-ZSM-5催化环己酮肟制ε-己内酰胺反应机理的ONIOM研究

采用ONIOM和DFT方法研究了H-ZSM-5分子筛催化环己酮肟制ε-己内酰胺的贝克曼重排反应机理.所有的构型优化使用ONIOM(B3LYP/6-31+G(d):PM3)方法进行,并在此基础上对得到的最优构型应用多种密度泛度方法,如B3LYP/6-31+G(d),PBE/6-31+G(d),M062X/6-31+G(d)和ωB97XD/6-31+G(d)进行完整46T簇模型的单点能计算.B3LYP,PBE和M062X泛函使用dftd3程序计算了额外色散校正,以考虑分子筛内部的弱相互作用.计算结果显示,经色散校正的DFT方法的计算精度被大大提高,达到一个与MP2方法相媲美的精度.反应的决速步是由第一步1,2-H转移和重排步共同决定,内部反应能垒为44.5 kcal/mol.反应速率常数表明,在293~393 K时,在H-ZSM-5上贝克曼重排反应进行得相当缓慢;当温度达到423 K时,正逆反应速率相当,反应开始发生;当达到623 K时,反应速率常数为130 1/s.     

硝酸甲酯分子间相互作用的DFT和ab initio比较

用密度泛函理论(DFT)和从头算(ab initio)方法,分别在B3LYP/6 31G和HF/6 31G水平上求得硝酸甲酯三种二聚体的全优化几何构型和电子结构,并用6 311G和6 311＋＋G基组进行总能量计算.对HF/6 31G计算结果进行MP4SDTQ电子相关校正.在各基组下均进行基组叠加误差(BSSE)和零点能(ZPE)校正求得结合能.对6 31G优化构型作振动分析并基于统计热力学求得200～600 K温度下单体和二聚体的热力学性质.详细比较两种方法的相应计算结果,发现DFT求得的分子间距离较短,分子内键长较长,所得结合能均小于相应ab initio计算值.     

Nickel-catalyzed alkyl coupling reactions: evaluation of computational methods

The B3LYP, M06, M06L, M062X, MPW1K, and PBE1PBE DFT methods were evaluated for modeling nickel-catalyzed coupling reactions. The reaction consists of a nucleophilic attack by a carbanion equivalent on the nickel complex, S(N)2 attack by the anionic nickel complex on an alkyl halide, and reductive elimination of the coupled alkane product, regenerating the nickel catalyst. On the basis of CCSD(T)//DFT single-point energies, the B3LYP, M06, and PBE1PBE functionals were judged to generate the best ground state geometries. M06 energies are generally comparable or superior to B3LYP and PBE1PBE energies for transition state calculations. The MP2 and CCSD methods were also evaluated for single-point energies at the M06 geometries. The rate-determining step of this reaction was found to be nucleophilic attack of a L(2)NiR anion on the alkyl halide.     

Basis set convergence of indirect spin-spin coupling constants in the Kohn-Sham limit for several small molecules

The performance of more than 40 density functionals in predicting indirect spin-spin coupling constants (SSCCs) in the Kohn-Sham basis set limit was tested. For comparison, similar calculations were performed using the RHF, SOPPA, SOPPA(CC2), and SOPPA(CCSD) methods, and the results were estimated toward the complete basis set (CBS) limit. The SSCCs of nine small molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6), and C(6)H(6)) were calculated using the dedicated Jensen pcJ-n polarization-consistent basis sets and used for the CBS limit estimations within the Kohn-Sham limit. These CBS results were compared with calculations using the aug-cc-pVTZ-J basis set. Among the 41 studied DFT methods, the tHCTHhyb, HSEh1PBE, HSE2PBE, wB97XD, wB97, and wB97X functionals reproduced accurately the experimental (1)J(XH) SSCCs and (3)J(HH60) and (2)J(HH(gem)) in ethane. Similarly, the functionals HSEh1PBE, HSE2PBE, wB97XD, wB97, and wB97X predicted accurately (1)J(CC), and B98, B97-1, B97-2, PBE1PBE, B1LYP, and O3LYP provided accurate (1)J(CO) results in the CO molecule. A very good performance for the calculation of the SSCCs based on the use of the relatively small basis set aug-cc-pVTZ-J was observed.     

Performance of Density Functional Theory for Transition Metal Oxygen Bonds

The accuracy of density functional theory (DFT) limits predictions in theoretical catalysis, and strong chemical bonds between transition metals and oxygen pose a particular challenge. We benchmarked 30 diverse density functionals against the bond dissociation enthalpies (BDE) of the 30 MO and 30 MO⁺ diatomic systems of all the 3d, 4d, and 5d metals, to test universality across the d-block as required in comparative studies. Seven functionals, B98, B97-1, B3P86, B2PLYP, TPSSh, B3LYP, and B97-2, display mean absolute errors (MAE) <30 kJ/mol. In contrast, many commonly used functionals such as PBE and RPBE overestimate M−O bonding by +30 kJ/mol and display MAEs from 48–76 kJ/mol. RPBE and OPBE reduce the over-binding of PBE but remain very inaccurate. We identify a linear relationship (p-value 7.6 ⋅ 10⁻⁵) between the precision and accuracy of DFT, i. e. inaccurate functionals tend to produce larger, unpredictable random errors. Some functionals commonly deviate from this relationship: Thus, M06-2X is very precise but not very accurate, whereas B3LYP* and MN15-L are more accurate but less precise than M06-2X. The best-performing hybrids have 10–30 % HF exchange, but this can be relieved by double hybrids (B2PLYP). Most functionals describe trends well, but errors comparing 5d to 4d/3d are ∼10 kJ/mol larger than group-wise errors, due to uncertainties in the spin-orbit coupling corrections for effective core potentials, affecting e. g. Pt/Pd or Au/Ag comparisons.     

The accuracy of DFT-optimized geometries of functional transition metal compounds: a validation study of catalysts for olefin metathesis and other reactions in the homogeneous phase

We have investigated the performance of eight popular density functionals, four of which are "standard" functionals not including dispersion (B3LYP, BP86, PBE, and TPSS) and four of which have been constructed to account for dispersion (B97D, wB97XD, M06, and M06L), in reproducing 18 molecular structures derived from single-crystal X-ray diffraction experiments on ruthenium-based olefin metathesis catalyst precursors. Our analysis of all the internuclear distances reveals that standard DFT predicts systematically expanded structures. In contrast, all the methods accounting for dispersion give rise to more compact structures, removing the systematic overestimation of internuclear distances. The contracting effect of dispersion is general and also affects chemical bonds, thus reducing the general overestimation of bond lengths. The best overall performance is observed for wB97XD, which offers relatively small statistical errors when considering the overall structure as well as selected distances. Only for the coordination center geometry is the accuracy of wB97XD matched by standard functionals such as PBE and TPSS, whereas M06 and M06L are associated with larger errors. At the other end of the scale, B3LYP is seen to give the largest statistical errors in general, both when considering the complete structures and the geometries of the coordination centers alone. For the organic ligands, however, B3LYP performs clearly better than the other standard functionals although not as well as the functionals accounting for dispersion. Extending the basis sets is seen to improve the structures in particular of the coordination center, thus underlining the importance of using sufficiently flexible basis sets if highly accurate geometries are to be obtained. Similar conclusions to those obtained for the ruthenium catalysts can be drawn from comparisons of the X-ray crystal structures of 10 other organometallic complexes of relevance to homogeneous catalysis, covering first (Ti, Fe, Co, Ni), second (Zr, Mo, Rh, Pd) and third (W, Ir) row transition metals, with those of DFT. The latter analyses thus offer a first indication that the picture obtained for the ruthenium alkylidene complexes may be extended to other classes of relatively large transition metal complexes.     

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: benchmarks approaching the complete basis set limit

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Moller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.     

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O[ellipsis (horizontal)]N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95?? to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).     

A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error

We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP.     

Hydrogen bonding in the urea dimers and adenine–thymine DNA base pair: anharmonic effects in the intermolecular H-bond and intramolecular H-stretching vibrations

The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different (cyclic and asymmetric) urea dimers and for the adenine–thymine DNA base pair system have been studied using the second-order Møller–Plesset perturbation theory (MP2) method and different density functional theory (DFT) exchange–correlation (XC) functionals (BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V++** basis sets. The widely used a posteriori Boys–Bernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.