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.

Estimate of the experimental static hyperpolarizability of neon based on coupled cluster response calculations

Electrostatic interaction of the solvent with the solute and fluctuations of the solvent configurations may make excitation energies of the solute different from those in the gas phase. These effects may dominate photoinduced or chemical reaction dynamics in solution systems and can be observed as shifts or broadening of peaks in absorption spectra. In this work, the nitrogen K-edge X-ray absorption spectra were measured for pyridazine in the gas phase and in aqueous solution. The ultraviolet and X-ray absorption spectra of pyridazine in aqueous solution, as well as those in the gas phase, were then calculated with models based on the algebraic-diagrammatic construction through second order [ADC(2)] with the resolution-of-identity (RI) approximation and compared with the spectra obtained in experiments. For aqueous solution, explicit local solvation structures were extracted from an ab initio molecular dynamics (AIMD) trajectory of pyridazine in bulk water, and RI-ADC(2) was combined with the conductor-like screening model (COSMO). The experimental absorption spectra of pyridazine in aqueous solution were reproduced with good accuracy by theoretical treatment of an ensemble containing the explicit local solvation structures of pyridazine with relevant water molecules combined with the COSMO solvation model of water for long-range solvation.

Solvent Effects in the Ultraviolet and X-ray Absorption Spectra of Pyridazine in Aqueous Solution.

An implementation of a complex solver for the solution of the linear equations required to compute the complex response functions of damped response theory is presented for the resolution-of-identity (RI) coupled cluster singles and approximate doubles (CC2) method. The implementation uses a partitioned formulation that avoids the storage of double excitation amplitudes to make it applicable to large molecules. The solver is the keystone element for the development of the damped coupled cluster response formalism for linear and nonlinear effects in resonant frequency regions at the RI-CC2 level of theory. Illustrative results are reported for the one-photon absorption cross section of C60, the electronic circular dichroism of n-helicenes (n = 5, 6, 7), and the C6 dispersion coefficients of a set of selected organic molecules and fullerenes.

Damped (linear) response theory within the resolution-of-identity coupled cluster singles and approximate doubles (RI-CC2) method.

In frozen density embedding (FDE), the properties of a target molecule are computed in the presence of an effective embedding potential, which accounts for the attractive and repulsive contributions of the environment. The formally exact embedding potential, however, is in practice calculated using explicit kinetic-energy functionals for which the resulting potentials are in many cases not repulsive enough to account fully for Pauli repulsion by the electrons of the environment and to compensate thereby the strong electron-nuclear attraction. For the excited states on the target molecule, this leads to charge spill-out when diffuse basis functions are included, which allow that valence electrons are excited to those regions of the environment where the strong nuclear attraction is not sufficiently compensated by repulsive contributions. To reduce this insufficiency, we propose in the present work the inclusion of atomic all-electron pseudopotentials for all environment atoms on top of the conventional embedding potential. In the current work, the pseudopotentials are applied for computing vertical excitation energies of local excited states in complex systems employing the second-order algebraic diagrammatic construction (ADC(2)) scheme. The proposed approach leads to significantly reduced charge spill-out and an improved agreement of FDE and supermolecular calculations in the frozen solvent approximation. In particular, when diffuse functions are employed, the mean absolute deviation (MAD) is reduced from 0.27 to 0.05 eV for the investigated cases.

Christof Hättig

Papers

Estimate of the experimental static hyperpolarizability of neon based on coupled cluster response calculations

Solvent Effects in the Ultraviolet and X-ray Absorption Spectra of Pyridazine in Aqueous Solution.

Damped (linear) response theory within the resolution-of-identity coupled cluster singles and approximate doubles (RI-CC2) method.

Employing Pseudopotentials to Tackle Excited-State Electron Spill-Out in Frozen Density Embedding Calculations.

Comment on `Efficient calculation of canonical MP2 energies' [P. Pulay, S. Saebø, K. Wolinski, Chem. Phys. Lett. 344 (2001) 543–552]