Dennis R. Salahub

Bio: Dennis R. Salahub is an academic researcher from University of Calgary. The author has contributed to research in topics: Density functional theory & QM/MM. The author has an hindex of 39, co-authored 132 publications receiving 9259 citations. Previous affiliations of Dennis R. Salahub include Henan University of Technology & Université de Montréal.

Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: Characterization and correction of the time-dependent local density approximation ionization threshold

Abstract: This paper presents an evaluation of the performance of time-dependent density-functional response theory (TD-DFRT) for the calculation of high-lying bound electronic excitation energies of molecules. TD-DFRT excitation energies are reported for a large number of states for each of four molecules: N2, CO, CH2O, and C2H4. In contrast to the good results obtained for low-lying states within the time-dependent local density approximation (TDLDA), there is a marked deterioration of the results for high-lying bound states. This is manifested as a collapse of the states above the TDLDA ionization threshold, which is at ??HOMOLDA (the negative of the highest occupied molecular orbital energy in the LDA). The ??HOMOLDA is much lower than the true ionization potential because the LDA exchange-correlation potential has the wrong asymptotic behavior. For this reason, the excitation energies were also calculated using the asymptotically correct potential of van Leeuwen and Baerends (LB94) in the self-consistent field step. This was found to correct the collapse of the high-lying states that was observed with the LDA. Nevertheless, further improvement of the functional is desirable. For low-lying states the asymptotic behavior of the exchange-correlation potential is not critical and the LDA potential does remarkably well. We propose criteria delineating for which states the TDLDA can be expected to be used without serious impact from the incorrect asymptotic behavior of the LDA potential

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Abstract: Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP-and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, s(R), scaling globally the vdW radii. For good results, a basis set of at least triple-zeta quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively.

Charge-transfer correction for improved time-dependent local density approximation excited-state potential energy curves: Analysis within the two-level model with illustration for H2 and LiH

Abstract: Time-dependent density-functional theory (TDDFT) is an increasingly popular approach for calculating molecular excitation energies However, the TDDFT lowest triplet excitation energy, ωT, of a closed-shell molecule often falls rapidly to zero and then becomes imaginary at large internuclear distances We show that this unphysical behavior occurs because ωT2 must become negative wherever symmetry breaking lowers the energy of the ground state solution below that of the symmetry unbroken solution We use the fact that the ΔSCF method gives a qualitatively correct first triplet excited state to derive a “charge-transfer correction” (CTC) for the time-dependent local density approximation (TDLDA) within the two-level model and the Tamm-Dancoff approximation (TDA) Although this correction would not be needed for the exact exchange–correlation functional, it is evidently important for a correct description of molecular excited state potential energy surfaces in the TDLDA As a byproduct of our analysis, we sh

Hydrated proton clusters and solvent effects on the proton transfer barrier: A density functional study

Abstract: The density functional calculations using the Perdew nonlocal corrections to exchange and correlation have been carried out for a sequence of hydrated proton clusters. The optimized structures were obtained up to H13O+6. It is found that H3O+ is indeed the central unit in all the lowest energy structures we found. Our results support the argument that the structure with a four‐coordinate first solvation shell is very unlikely in small hydrated proton clusters. The density functional calculations with the Perdew nonlocal corrections to exchange and correlation give somewhat shorter hydrogen bond lengths, but slightly longer chemical bond lengths as compared with the post‐Hartree–Fock calculations. The harmonic vibrational frequencies and IR intensities of various vibrational modes have been generated for all the structures optimized. Results for small clusters are compared with the high resolution experimental spectroscopy studies of Yeh et al. and Begemann et al. Results for larger clusters are used to in...

Nuclear magnetic resonance spin-spin coupling constants from density functional theory: Problems and results

Abstract: Our recently developed method for the calculation of indirect nuclear spin–spin coupling constants is studied in more detail. For the couplings between nuclei other than N, O, and F (which have lone pairs) the method yields very reliable results. The results for 1J(Si–H) couplings are presented and their dependence on the basis set quality is analyzed. Also, 2J(H–H) and 1J(X–H) couplings (X=C, Si, Ge, Sn) in XH4 molecules are presented and the relativistic effects on 1J(X–H) are discussed. The limitations of the method, which is based on density functional theory, are connected with the inability of the present LDA and GGA exchange‐correlation functionals to describe properly the spin‐perturbations (through the Fermi‐contact mechanism) on atoms to the right of the periodic table (containing lone pairs). However, the deviations from experiment of the calculated couplings for such nuclei are systematic, at least for one‐bond couplings, and therefore these calculated couplings should still be useful for NMR ...

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

Abstract: 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.

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

Abstract: 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.

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

Abstract: 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。

Effect of the damping function in dispersion corrected density functional theory

Abstract: 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.

Toward reliable density functional methods without adjustable parameters: The PBE0 model

Abstract: We present an analysis of the performances of a parameter free density functional model (PBE0) obtained combining the so called PBE generalized gradient functional with a predefined amount of exact exchange. The results obtained for structural, thermodynamic, kinetic and spectroscopic (magnetic, infrared and electronic) properties are satisfactory and not far from those delivered by the most reliable functionals including heavy parameterization. The way in which the functional is derived and the lack of empirical parameters fitted to specific properties make the PBE0 model a widely applicable method for both quantum chemistry and condensed matter physics.