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

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

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

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

/pdf/quantum-mechanical-continuum-solvation-models-3edv963g14.pdf

Quantum mechanical continuum solvation models.

Understanding deactivation mechanisms of functional groups is a key step to design novel photo-active devices and molecular imaging agents. Here, we elucidate the photochemistry of linear triazenes, an extended analogue of the photo-switchable azo group, exemplarily for the widely used DNA-minor-groove binder berenil. Combining ultrafast spectroscopy and ab initio calculations unveils that the E-azo,s-trans structure of berenil predominates in the gas phase and in aqueous solution, and ADC(2) intrinsic reaction coordinate calculations disclose that the excited-state relaxation to the S1 minima/conical intersections follows a two-step mechanism: NN bond stretching followed by a bicycle-pedal rotation in the triazene bridge. Furthermore, studying the ground-state pathways shows that a fraction of the molecules relaxes back to the E-azo,s-trans isomer while the other part photoisomerizes to the Z-azo,s-trans via a hula-twist motion, as evidenced by experimental quantum yields of Φ ≈ 0.5 found for berenil in water, ethylene glycol, or bound to β-trypsin. Moreover, our studies show that while the excited-state relaxation is insensitive to the environment, the ground-state dynamics depend on biomolecular binding partners.

How a linear triazene photoisomerizes in a volume-conserving fashion

Erratum to: ``Coupled cluster calculations of Verdet constants'' [Chem. Phys. Lett. 281 (1997) 445]

Cobalt ferrite, CoFe2O4 (CFO), nanocrystals are efficient and competitive anode materials in the field of electrochemical water splitting. Using density functional theory with on-site Hubbard U cor...

Structure and Reactivity of Pristine and Reduced Spinel CoFe2O4 (001)/(100) Surfaces

The frequency-dependent electric field-induced second harmonic generation (ESHG) second hyperpolarizabilities γ of neon, argon, and krypton are calculated using the approximate coupled cluster triples model CC3. Systematic basis set investigations are carried out to establish basis set limits, and scalar relativistic effects are accounted for by direct perturbation theory. To estimate higher-order correlation effects, full configuration-interaction results are used to benchmark the accuracy of CC3. The best theoretical estimates obtained thereby for the static second hyperpolarizabilities γ0 are 107.4, 1159, and 2589 a.u. for neon, argon, and krypton, respectively. These values as well as the results for the dispersion curve of the parallel component γ‖ agree well with the latest experimental values from electric field-induced second harmonic generation. In addition, the dispersion of the perpendicular component γ⊥ and the hyperpolarizability ratios γ‖∕γ⊥ has been studied for the first time on a consisten...

Frequency-dependent hyperpolarizabilities of the Ne, Ar, and Kr atoms using the approximate coupled cluster triples model CC3.

The adsorption of N2 on the rutile TiO2 (110) surface in the limit of low coverage has been studied as a prototype example for the adsorption of non-polar molecules on strongly ionic oxide surfaces. We employed for this study an embedded cluster ansatz in combination with density functional theory and wavefunction methods. Both, clusters saturated with hydrogen atoms and electrostatically embedded clusters have been applied and methods and basis sets have been varied to test their reliability and accuracy for describing the electrostatic potential on the surface and its interaction with the non-polar N2 molecule. Quantum clusters consisting of up to 342 atoms have been used to converge the results with respect to the cluster size. For electrostatically embedded clusters, the convergence can considerably be enhanced by optimizing the charges for the point charge embedding. On the rutile (110) surface an accurate account of the long ranging interaction of the adsorbate with the bridging oxygen atoms is important for quantitative adsorption energies of weakly bound molecules. In addition the geometric relaxation of the surface has a marked influence on the results, whereas the basis set–dependence is small. Of all methods investigated (HF, DFT/PBE, DFT/B3LYP, MP2), only MP2 and DFT/B3LYP were able to describe the adsorption of N2 on the rutile surface properly. After including the zeropoint vibrational energy, the calculated adsorption energy is close to experimental results. The approach is thus promising for future investigations on adsorption energies and structures of non-polar molecules on ionic oxide surfaces.

Christof Hättig

Papers

How a linear triazene photoisomerizes in a volume-conserving fashion

Erratum to: ``Coupled cluster calculations of Verdet constants'' [Chem. Phys. Lett. 281 (1997) 445]

Structure and Reactivity of Pristine and Reduced Spinel CoFe2O4 (001)/(100) Surfaces

Frequency-dependent hyperpolarizabilities of the Ne, Ar, and Kr atoms using the approximate coupled cluster triples model CC3.

Embedded cluster density functional and second-order Møller-Plesset perturbation theory study on the adsorption of N2 on the rutile (110) surface.