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。     

甲烷与含氮有机杂环化合物吸附作用的DFT研究

根据煤中氮的存在形式,提炼出11种具有不同杂化方式及含氮量的有机环状化合物.应用密度泛函理论(DFT)模拟方法对甲烷在这11种含氮化合物上的吸附模型进行结构优化,并结合吸附能、电荷分布及静电势能面的分析,从微观角度考察了甲烷与这些化合物之间的相互作用.计算结果表明:甲烷与含氮化合物的相互作用能在3.81-6.82kJ·mol-1范围内,且通过氢键和静电力相互作用;当化合物中氮的杂化方式为sp2时,其与甲烷的作用能大于sp3杂化方式的;当化合物中的氮含量增加时,可以提供更多的甲烷吸附位点.     

双(3,4,5-取代吡唑基)甲烷衍生物高能量密度材料的分子设计（英文）

设计了一系列双(3,4,5-取代吡唑基)甲烷衍生物作为高能量密度材料的候选物.用密度泛函理论研究了它们的生成热、电子结构、能量特性和热稳定性.二氟氨基能增加目标化合物的电子结构、密度和爆轰性能的能隙.其中二[3,5-双(二氟氨基)-4-硝基吡唑]甲烷(C2)显示了优异的潜在高能量密度材料的性能,其晶体密度(2.11g/cm3)、冲击感度(h50,6.8 J)均高于六硝基六氮杂异伍兹烷(CL-20),而爆速(9.80 km/s)和爆压(46.62 GPa)与CL-20非常接近.     

密度泛函理论研究Al在丝光沸石骨架中的取代位置和NH_3的吸附(英文)

采用色散校正密度泛函方法(DFT-D2)计算了Al同晶取代进入H-[Al]MOR丝光沸石骨架中可能的位置及其对NH3分子吸附表征Brnsted酸性。热力学上,Al优先取代位是T2O5位,接着是T4O2、T1O7和T3O1位,能量差仅在0.03~0.07 eV,表明Al可能分布在四种非等价晶体T位。同时,电荷平衡质子的位置影响Al取代位的稳定性,数据表明电荷平衡质子与O5位结合的可能性最大。另外,用DFT和DFT-D2方法计算了NH3分子在每一个Al取代的T位的吸附能,通过比较,DFT低估了NH3吸附能0.41 eV,表明色散校正DFT-D2方法对于NH3吸附是很有必要的,T2O5位的Brnsted酸性最强。     

用GGA密度泛函及其长程、色散校正方法计算各类氢键的结合能

应用广义梯度近似(GGA) (PW91和PBE)、含动能密度的广义梯度近似(meta-GGA) (M06-L)、杂化泛函(hyper-GGA)(M06-2X、X3LYP和B3LYP)及其长程校正泛函LC-DFT(CAM-B3LYP、LC-ωPBE和ωB97X)和色散校正密度泛函(DFT-D)(ωB97X-D和B97-D),用多种基函数对15种不同强度的传统氢键和非传统氢键体系的结合能进行了系统的计算与分析.并与高精度的CCSD(T)/aug-cc-pVQZ结果比较发现:在上述各类泛函中,对于氢键结合能的计算M06-2X和ωB97X-D泛函较为精确与可靠,且没有必要使用过大的基函数,6-311++G(2d,2p)或aug-cc-pVDZ水平的基组就已足够,各类泛函所计算结合能的基组重叠误差(BSSE)均较小,除ωB97X和ωB97X-D外,其它9种泛函不经BSSE校正也能得到同样甚至更准确的结果.     

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.     

XYG3型双杂化密度泛函方法新进展：从能量到能量的解析梯度

本文回顾了现代密度泛函理论的基础,着重评述了XYG3型双杂化（XYG3typeofdoublyhybrid,xDH）泛函的最新进展,解析能量梯度的实现．XYG3是首个依照绝热途径理论建立的双杂化泛函,在具体实现上具有独特的构架．该类型泛函利用常用泛函（如B3LYP或PBE0等）作母泛函来进行自洽计算,以期获得更好的密度和轨道,然后将所得到的轨道和密度信息带入到xDH泛函中以得到最终能量．由于自洽泛函和最终能量泛函不同,因而在计算解析能量梯度时需要求解耦合微扰Kohn—Sham方程．在此基础上,还评述了xDH泛函在能量,尤其是构型优化方面的具体表现．测试的构型集包括以共价键键合的分子和非键相互作用体系的平衡结构,以及反应过渡态结构．结果表明,xDH双杂化泛函总体上给出了比母泛函更好的能量和几何构型．     

砷原子团簇结构的量子化学密度泛函理论研究

采用密度泛函理论的三种方法:局域自旋密度近似SVWN、梯度修正BLYP、杂化密度泛函B3LYP,优化了中性Asn、负离子Asn-(n=2～5)的结构,在优化结构基础上计算了它们的振动光谱,获得它们稳定的最低能量态的结构.其中中性Asn(n=2～5)的稳定结构的计算结果,与已有的理论结果以及实验数据进行了比较.而对负离子Asn-(n=2～5))的稳定结构作了预言.同时计算了Asn(n=2～5)的绝热电子亲和能(EAa),与有关光电子谱学的实验值符合较好.     

(Co,P)双掺杂MgF2电子结构和光学性质的第一性原理研究

基于密度泛函理论(DFT)的第一性原理平面波超软赝势方法,计算了纯MgF2晶体、Co掺杂MgF2晶体、P掺杂MgF2晶体和(Co,P)双掺杂MgF2晶体的电子结构和光学特性.结果表明,掺杂后的MgF2晶体发生了畸变,原子之间的键长也有所变化.(Co,P)双掺杂后,由于非金属原子p态和金属原子d态之间的轨道杂化,在MgF...     

分子筛限域孔道中吡啶的吸附结构和能量

以吸附于ZSM-5孔道中的吡啶分子为例,利用量子化学理论方法考察了计算模型和密度泛函方法的选择对吡啶吸附结构和吸附能的影响,从而为准确计算分子筛限域孔道中客体分子吸附态结构和能量参数提供了依据.计算结果表明,吡啶吸附能随着所选用的分子筛的计算模型(从8T到128T)增大而增大,当选用的孔道结构能够将整个分子筛的孔道结构完全包括进来的时候(72T)达到收敛.与常规的密度泛函方法(B3LYP和M06-2X)相比较,考虑到色散作用校正的B97D泛函方法能够很好地处理分子筛体系中主客体间的长程相互作用和弱相互作用,计算得到的能量数据与实验结果符合得很好.     

Performance of dispersion-corrected density functional theory for the interactions in ionic liquids

Potential energy curves for the dissociation of cation-anion associates representing the building units of ionic liquids have been computed with dispersion corrected DFT methods. Non-local van der Waals density functionals (DFT-NL) for the first time as well as an atom pair-wise correction method (DFT-D3) have been tested. Reference data have been computed at the extrapolated MP2/CBS and estimated CCSD(T)/CBS levels of theory. The investigated systems are combined from two cations (1-butyl-3-methylimidazolium and tributyl(methyl)posphonium) and three anions (chloride, dicyanamide, acetate). We find substantial stabilization from London dispersion energy near equilibrium of 5-7 kcal mol(-1) (about 5-6% of the interaction energy). Equilibrium distances are shortened by 0.03-0.09 ? and fundamental (inter-fragment) vibrational frequencies (which are in the range 140-180 cm(-1)) are increased by typically 10 cm(-1) when dispersion corrections are made. The dispersion-corrected hybrid functional potentials are in general in excellent agreement with the corresponding CCSD(T) reference data (typical deviations of about 1-2%). The DFT-D3 method performs unexpectedly well presumably because of cancellation of errors between the dispersion coefficients of the cations and anions. Due to self-interaction error, semi-local density functionals exhibit severe SCF convergence problems, and provide artificial charge-transfer and inaccurate interaction energies for larger inter-fragment distances. Although these problems may be alleviated in condensed phase simulations by effective Coulomb screening, only dispersion-corrected hybrid functionals with larger amounts of Fock-exchange can in general be recommended for such ionic systems.     

Assessment of density functional theory to calculate the phase transition pressure of ice

To assess the accuracy of density functional theory (DFT) methods in describing hydrogen bonding in condensed phases, we benchmarked their performance in describing phase transitions among different phases of ice. We performed DFT calculations of ice for phases Ih, II, III, VI and VII using BLYP, PW91, PBE, PBE-D, PBEsol, B3LYP, PBE0, and PBE0-D, and compared the calculated phase transition pressures between Ih-II, Ih-III, II-VI, and VI-VII with the 0 K experimental values of Whalley [J. Chem. Phys., 1984, 81, 4087]. From the geometry optimization of many different candidates, we found that the most stable proton orientation as well as the phase transition pressure does not show much functional dependence for the generalized gradient approximation and hybrid functionals. Although all these methods overestimated the phase transition pressure, the addition of van der Waals (vdW) correction using PBE-D and PBE0-D reduced the transition pressure and improved the agreement for Ih-II. On the other hand, energy ordering between VI and VII reversed and gave an unphysical negative transition pressure. Binding energy profiles of a few conformations of water dimers were calculated to understand the improvement for certain transitions and failures for others with the vdW correction. We conclude that vdW dispersion forces must be considered to accurately describe the hydrogen bond in many different phases of ice, but the simple addition of the R(-6) term with a small basis set tends to over stabilize certain geometries giving unphysical ordering in the high density phases.     

Comparison of the performance of dispersion-corrected density functional theory for weak hydrogen bonds

Potential energy curves for five complexes with weak to medium strong hydrogen bonds have been computed with dispersion corrected DFT methods. The electronic density based vdW-DF2 and VV10 van der Waals density functionals have been tested, as well as an atom pair-wise correction method (DFT-D3). The short-range exchange-correlation components BLYP and rPW86-PBE together with the extended aug-cc-pVQZ basis sets have been employed. Reference data have been computed at the estimated CCSD(T)/CBS(aQ-a5) level of theory. The investigated systems are CH(4)·NH(3), Cl(3)CH·NH(3), NH(3)·NH(3), CH(3)F·C(2)H(2) and CH(3)F·H(2)O with binding energies ranging from -0.7 kcal mol(-1) to -5.5 kcal mol(-1). We find that all dispersion corrected methods perform reasonably well for these hydrogen bonds, but also observe distinct differences. The BLYP-D3 method provides the best results for three out of five systems. For the fluorinated complexes, the VV10 method gives remarkably good results. The vdW-DF2 method yields good interaction energies similar to the other methods (mean average deviation of 0.2-0.3 kcal mol(-1)), but fails to provide accurate equilibrium separations. Based on these results and previous experience with the computation of non-covalent interactions, for large-scale applications we can recommend DFT-D3 based structure optimizations with subsequent checking of interaction energies by single-point VV10 computations. Comparison of the DFT-D3 and VV10 results leads to the conclusion that the short-range exchange-correlation functional and not the dispersion correction mainly determines the achievable accuracy.     

The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations

The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and graphene has been studied using post Hartree-Fock wave function theory (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE, vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene-M (M = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively. We found that the nature of binding of the three metals is different: While silver binds predominantly through dispersion interactions, the binding of palladium has a covalent character, and the binding of gold involves a subtle combination of charge transfer and dispersion interactions as well as relativistic effects. We demonstrate that the CCSD(T) benchmark binding energies for benzene-M complexes can be reproduced in plane-wave density functional theory calculations by including a fraction of the exact exchange and a nonempirical van der Waals correction (EE+vdW). Applying the EE+vdW method, we obtained binding energies for the graphene-M (M = Pd, Au, Ag) complexes of 17.4, 5.6, and 4.3 kcal/mol, respectively. The trends in binding energies found for the benzene-M complexes correspond to those in coronene and graphene complexes. DFT methods that use empirical corrections to account for the effects of vdW interactions significantly overestimate binding energies in some of the studied systems.     

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.     

Benchmarking density functional methods against the S66 and S66x8 datasets for non-covalent interactions

Dispersion-corrected density functional theory is assessed on the new S66 and S66x8 benchmark sets for non-covalent interactions. In total, 17 different density functionals are evaluated. Two flavors of our latest additive London-dispersion correction DFT-D3 and DFT-D3(BJ), which differ in their short-range damping functions, are tested. In general, dispersion corrections are again shown to be crucial to obtain reliable non-covalent interaction energies and equilibrium distances. The corrections strongly diminish the performance differences between the functionals, and in summary most dispersion-corrected methods can be recommended. DFT-D3 and DFT-D3(BJ) also yield similar results but for most functionals and intermolecular distances, the rational Becke-Johnson scheme performs slightly better. Particularly, the statistical analysis for S66x8, which covers also non-equilibrium complex geometries, shows that the Minnesota class of functionals is also improved by the D3 scheme. The best methods on the (meta-)GGA or hybrid- (meta-)GGA level are B97-D3, BLYP-D3(BJ), PW6B95-D3, MPW1B95-D3 and LC-ωPBE-D3. Double-hybrid functionals are the most accurate and robust methods, and in particular PWPB95-D3 and B2-PLYP-D3(BJ) can be recommended. The best DFT-D3 and DFT-D3(BJ) approaches are competitive to specially adapted perturbation methods and clearly outperform standard MP2. Comparisons between S66, S22 and parts of the GMTKN30 database show that the S66 set provides statistically well-behaved data and can serve as a valuable tool for, for example, fitting purposes or cross-validation of other benchmark databases.     

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.