甲烷晶体的晶格能和弹性性质: 不同方法及泛函的评估

通过对甲烷晶体进行结构、晶格能和弹性特性的研究, 评估了不包含和包含色散能量修正的密度泛函理论的性能. 我们分别利用不包含色散能量修正的密度泛函理论(DFT) (包含不同的标准泛函和杂化泛函)和包含色散能量修正的密度泛函理论(DFT-D)计算了甲烷晶体特性, 并与实验作对比. 尽管DFT-D 与传统密度泛函理论及杂化密度泛函理论相比, 修正了甲烷晶体中的范德华(vdW)相互作用, 但是一些修正方案过分修正了这种相互作用. 因此, 人们在使用DFT-D方法时务必谨慎.     

Accurate Structure and Bonding Description of the Transition Metal‐Disulfur Monoxide Complexes [(PMe3)2M(S2O)] (M = Ni,Pd, Pt): Grimme Dispersion Corrected DFT Study

Geometry and bonding energy analysis of M–S₂O bonds in the metal‐disulfur monoxide complexes [(PMe₃)₂M(S₂O)] of nickel, palladium, and platinum were investigated at DFT, DFT‐D3, and DFT‐D3(BJ) methods using three different functionals (BP86, PBE, and TPSS). The TPSS/DFT‐D3(BJ) yields better geometry, while the BP86 geometry is least accurate for studied complexes. The geometry of platinum complex optimized at TPSS/DFT‐D3(BJ) level is in excellent agreement with the available experimental values. The M–S bonds are shorter than the M–S(O) bonds. The Mayer bond orders suggest the presence of M–S and M–S(O) single bonds. Both the M–S and M–S(O) bond lengths vary with the density functionals as TPSS‐D3(BJ) < TPSS < PBE < BP86. The Hirshfeld charge distribution indicates that the overall charge flows from metal fragment to [S₂O]. The Ni–S₂O bond has greater degree of covalent character than the ionic. The contribution of dispersion interactions is large in computing accurate bond dissociation energies between the interacting fragments. The BDEs are largest for the functional TPSS and smallest for the functional BP86. The DFT‐D3 dispersion corrections to the BDEs between the metal fragments [(PMe₃)₂M] and ligand fragment [(S₂O)] for the TPSS functional are in the range 7.1–7.3 kcal · mol^–1, which are smaller than the corresponding DFT‐D3(BJ) dispersion corrections (9.4–10.6 kcal · mol^–1).     

Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): a promising tool for studying isolated small peptides

Resolution of identity standard density functional theory augmented with a damped empirical dispersion term (RI-DFT-D) calculations have been carried out on a set of lowest energy minima of tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides. RI-DFT-D (TPSS/TZVP) results are in excellent agreement with benchmark data based on the CCSD(T) method. Experimental spectra could be assigned according to the calculated IR frequencies. Central processing unit (CPU) time requirements are only slightly higher than those needed for the DFT calculations. Consequently, RI-DFT-D theory seems to be a promising methodology for studying oligopeptides with accuracy comparable to ab initio quantum chemical calculations.     

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.     

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.     

Reparameterization of a meta-generalized gradient approximation functional by combining TPSS exchange with τ1 correlation

We present a new local meta-GGA exchange-correlation density functional by combining the TPSS meta-GGA exchange and the τ1 meta-GGA correlation functionals. The TPSS meta-GGA exchange-correlation and the τ1 meta-GGA correlation functionals have been implemented in the deMon code. The parameters in the τ1 meta-GGA correlation model are reoptimized in a synchronized way to match the original TPSS meta-GGA exchange counterpart. This reparametrized meta-GGA functional is referred to as “TPSSτ3”. The TPSSτ3 and TPSSτ1 meta-GGAs are validated using a test set that consists of covalent molecules, hydrogen-bonded complexes, and van der Waals interactions. The calculated results from TPSSτ1 and TPSSτ3 are analyzed and compared with reliable experimental data and theoretical data, as well as with those from Bmτ1 and TPSS calculations. The τ1 correlation model describes the aromatic compounds better than TPSS. TPSSτ3 yields satisfactory results for the covalent molecules, the hydrogen-bonded complexes, and the van der Waals complexes in the test set compared with TPSS, Bmτ1 and TPSSτ1. Contribution to the Serafin Fraga Memorial Issue.     

Comparison of intermolecular interaction energies from SAPT and DFT including empirical dispersion contributions

The dispersion correction based on damped atom-atom long-range interaction contributions has been tested for an extended S22 database of intermolecular complexes using density functional theory (DFT) and symmetry adapted perturbation theory (SAPT) to account for the remaining interaction energy contributions. In the case of DFT, the dispersion correction of Grimme (J. Comput. Chem. 2006, 27, 1787) was used, while for SAPT, another damping function has been developed that has been optimized particularly for the database. It is found that both approaches yield about the same accuracy for the mixed-type complexes, while the DFT plus dispersion method performs better for the hydrogen-bridged systems and the SAPT plus dispersion approach is better for the dispersion-dominated complexes if compared with coupled cluster singles-doubles with perturbative triples interaction energies as a reference.     

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.     

Assessment of the PW86+PBE+XDM density functional on van der Waals complexes at non-equilibrium geometries

The deficiency of conventional density-functional theory (DFT) in properly describing van der Waals (vdW) (especially dispersion-bound) complexes has been extensively addressed in the past decade. There are now several new methods published in the literature that are capable of accurately capturing weak dispersion interactions in complexes at equilibrium geometries. However, the performance of these new methods at non-equilibrium geometries remains to be assessed. We have previously published [F. O. Kannemann and A. D. Becke, J. Chem. Theory Comput. 6, 1081 (2010); A. D. Becke, A. A. Arabi, and F. O. Kannemann, Can. J. Chem. 88, 1057 (2010)] that the functional PW86+PBE+XDM for exchange + correlation + dispersion, respectively, is a highly accurate functional for general thermochemistry and vdW complexes at equilibrium geometries. Here, we show that this nonempirical, except for two parameters in the dispersion damping part, functional also performs well for vdW complexes at compressed and stretched intermonomer separations. The mean absolute relative error (MARE) is 9.4% overall for vdW complexes in the "S22×5" database incorporating compressed and stretched geometries [J. Rezac, K. E. Riley, and P. Hobza, J. Chem. Theory Comput. 7, 2427 (2011)]. Our largest MARE on the S22×5 database is 13.3% on the compressed geometry set.     

Evaluation of DFT methods for computing the interaction energies of homomolecular and heteromolecular dimers of monosubstituted benzene

We present density functional theory (DFT) interaction energies for the sandwich and T‐shaped conformers of substituted benzene dimers. The DFT functionals studied include TPSS, HCTH407, B3LYP, and X3LYP. We also include Hartree–Fock (HF) and second‐order Møller–Plesset perturbation theory calculations (MP2), as well as calculations using a new functional, P3LYP, which includes PBE and HF exchange and LYP correlation. Although DFT methods do not explicitly account for the dispersion interactions important in the benzene–dimer interactions, we find that our new method, P3LYP, as well as HCTH407 and TPSS, match MP2 and CCSD(T) calculations much better than the hybrid methods B3LYP and X3LYP methods do. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

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.     

Is the uniform electron gas limit important for small Ag clusters? Assessment of different density functionals for Ag(n) (n < or = 4)

Twenty-three density functional theory (DFT) methods, including the second- and the third-generation functionals, are tested in conjunction with two basis sets (LANL2DZ and SDD) for studying the properties of neutral and ionic silver clusters. We find that DFT methods incorporating the uniform electron gas limit in the correlation functional, namely, those with Perdew's correlation functionals (PW91, PBE, P86, and TPSS), Becke's B95, and the Van Voorhis-Scuseria functional VSXC, generally perform better than the other group of functionals, e.g., those incorporating the LYP correlation functional and variations of the B97 functional. Strikingly, these two groups of functionals can produce qualitatively different results for the Ag3 and Ag4 clusters. The energetic properties and vibrational frequencies of Ag(n) are also evaluated by the different functionals. The present study shows that the choice of DFT methods for heavy metals may be critical. It is found that the exact-exchange-incorporated PBE functional (PBE1PBE) is among the best for predicting the range of properties.     

Assessing the performance of density functional theory for the dynamic polarizabilities of amino acids: Treatment of correlation and role of exact exchange

The theoretical determination of electric response properties of the biological systems is a field where the application of density functional theory (DFT) appears to be quite promising. In this work, the performance of 41 density functional methods is evaluated in predicting dynamic polarizabilities of an experimental benchmark set of 20 proteinogenic amino acids. The behavior of a large number of density functionals, including various types of the local spin density approximation (LSDA), generalized gradient approximation (GGA), meta‐GGA (m‐GGA), hybrid‐GGA (h‐GGA), hybrid meta‐GGA (hm‐GGA), and range‐separated hybrid‐GGA (rsh‐GGA), has been assessed for the purpose. Analyzing the results of our DFT benchmarking, we found that these computationally economical methods show very diverse predictive capability and a careful selection of DFT functionals is very important in the polarizability calculations. Considering the role of exchange, correlation, dispersion and long‐range corrections, it turned out that in the LSDA class, SVWN3 gives better results than SPL and SVWN5 toward the reference values. Of the GGA methods, OPBE outperforms all other functionals. The M06‐L is the best method of m‐GGA class. The B3LYP and TPSSh are the best functionals of h‐GGA and hm‐GGA lineages, respectively. Finally, CAM‐B3LYP is the best method of rsh‐GGA functionals that predicts the most accurate polarizability for amino acids by a large margin with respect to others. Overall, the best performing functionals turn out to be hm‐GGAs TPSSh, TPSS1KCIS, M05, tau‐HCTHhyb, and h‐GGA B3LYP. Hopefully, the results of this investigation might provide the useful guidance to propose a new exchange‐correlation functional for calculating the optical properties of biomolecular materials. © 2013 Wiley Periodicals, Inc.     

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.