The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.

http://dns2.asia.edu.tw/~ysho/YSHO-English/1000%20WC/PDF/J%20Che%20Phy132,%20154104.pdf

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

/pdf/the-m06-suite-of-density-functionals-for-main-group-1748swzp1l.pdf

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.

Effect of the damping function in dispersion corrected density functional theory

An essay on the theory and calculations of intermolecular interactions

Electron correlation corrections have a considerable influence on the relative stabilities of lithium isocyanide (1), lithium cyanide (2), and the bridged form, 3. While Hartree-Fock theory finds 1 to be most stable and 3 not to be a minimum, MP2/6-31G* optimization indicates 3 to be the global minimum. At higher levels employing full fourth-order Moller-Plesset theory and a quadruply split valence and polarized basis set (MP4STDQ/6-311+G*), 2 is only about 2 kcal/mol less stable than 1 and 3, which are indicated to have nearly the same energy. LiNC thus is similar to C(Na)N and C(K)N, both of which are known to prefer T-shaped (bridged) structures in the gas phase. However, to an even greater extent than formerly realized, rotation of the lithium cation around the cyanide anion nucleus should be practically free. ΔH (LiCN) = 32.8 kcal/mol is estimated from the calculated lithium cation affinity of 151.2 kcal/mol. In addition, we find at the MP4SDTQ/6-31+G*//MP2/6-31G* level that the bridged form of NaCN is favored by 2–3 kcal/mol over the corresponding linear forms, which have nearly the same energy.

The Remarkable Structure of Lithium Cyanide/Isocyanide

To contribute to the understanding of noncovalent binding of halogenated molecules with biological activity, electrostatic potential (ESP) maps of more than 2500 compounds were thoroughly analysed. A peculiar region of positive ESP, called the σ-hole, is a concept of central importance for halogen bonding. We aim to simplify the view on σ-holes and to provide general trends in organic drug-like molecules. The results are in fair agreement with crystallographic surveys of small molecules as well as biomolecular complexes and may help to improve the intuition of chemists when dealing with halogenated compounds.

Statistical analysis of σ-holes: a novel complementary view on halogen bonding

An ab initio quantum chemical analysis of the close amino group contacts, existing in many DNA crystal structures, is presented. The calculations are made at the Hartree-Fock (HF) level with medium 6–31G* and 6–31 G(NH2*) basis sets as well as with inclusion of correlation energy using the second order Moller-Plesset theory (MP2) with the 6–31G* basis set. We demonstrate that the model system (methylamine dimer, cytosine dimer) amino groups are forced to adopt significantly non-planar geometry to stabilize their mutual interaction. Comparison is made with a representative set of empirical potentials including AMBER, CHARMM and GROMOS. The empirical potentials are not reliable enough to analyze the amino group contacts occurring in the DNA double helices. We propose that the mutual amino group interactions contribute to the conformational variability of the CpG and ApT B-DNA steps.

Pavel Hobza

Papers

An essay on the theory and calculations of intermolecular interactions

The Remarkable Structure of Lithium Cyanide/Isocyanide

Statistical analysis of σ-holes: a novel complementary view on halogen bonding

Interactions between amino groups in DNA. An Ab initio study and a comparison with empirical potentials.

Applicability of the supermolecule MP2 approach to intermolecular interactions: He2 and Ne2