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1.
Implementation of empirical dispersion corrections to density functional theory for periodic systems
Werner Reckien Florian Janetzko Michael F. Peintinger Thomas Bredow 《Journal of computational chemistry》2012,33(25):2023-2031
A recently developed empirical dispersion correction (Grimme et al., J. Chem. Phys. 2010, 132, 154104) to standard density functional theory (DFT‐D3) is implemented in the plane‐wave program package VASP. The DFT‐D3 implementation is compared with an implementation of the earlier DFT‐D2 version (Grimme, J. Comput. Chem. 2004, 25, 1463; Grimme, J. Comput. Chem. 2006, 27, 1787). Summation of empirical pair potential terms is performed over all atom pairs in the reference cell and over atoms in shells of neighboring cells until convergence of the dispersion energy is obtained. For DFT‐D3, the definition of coordination numbers has to be modified with respect to the molecular version to ensure convergence. The effect of three‐center terms as implemented in the original molecular DFT‐D3 version is investigated. The empirical parameters are taken from the original DFT‐D3 version where they had been optimized for a reference set of small molecules. As the coordination numbers of atoms in bulk and surfaces are much larger than in the reference compounds, this effect has to be discussed. The results of test calculations for bulk properties of metals, metal oxides, benzene, and graphite indicate that the original parameters are also suitable for solid‐state systems. In particular, the interlayer distance in bulk graphite and lattice constants of molecular crystals is considerably improved over standard functionals. With the molecular standard parameters (Grimme et al., J. Chem. Phys. 2010, 132, 154104; Grimme, J. Comput. Chem. 2006, 27, 1787) a slight overbinding is observed for ionic oxides where dispersion should not contribute to the bond. For simple adsorbate systems, such as Xe atoms and benzene on Ag(111), the DFT‐D implementations reproduce experimental results with a similar accuracy as more sophisticated approaches based on perturbation theory (Rohlfing and Bredow, Phys. Rev. Lett. 2008, 101, 266106). © 2012 Wiley Periodicals, Inc. 相似文献
2.
The reaction energies of 275 elementary reactions from the hydrocarbon combustion model GRI-Mech 3.0 were evaluated by electronic structure calculations using both localized Gaussian basis and plane wave basis sets. In the Gaussian basis calculations, the d-polarization function on C, N, and O elements reduces the mean absolute deviation (MAD) from the experimental value by 53%, a significant improvement in computational accuracy. In the plane wave basis calculation using different exchange-correlation (XC) functionals, the MAD values were 0.316–0.426 eV when non-hybrid type XC functionals such as RPBE, PBE, PW91, revPBE, and PBEsol were used. On the other hand, hybrid functionals like B3LYP and HSE06 reduced the MAD values significantly down to 0.182 and 0.233 eV, respectively. The B3LYP results have 49% less MAD compared to the PBE results. These demonstrated the strong advantage of the hybrid functional for calculating gas-phase reaction energies. The present comprehensive benchmarks will be crucial for future microkinetics as well as machine learning studies on the catalytic reactions. © 2019 Wiley Periodicals, Inc. 相似文献
3.
Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients 下载免费PDF全文
Roman Łazarski Asbjörn Manfred Burow Lukáš Grajciar Marek Sierka 《Journal of computational chemistry》2016,37(28):2518-2526
A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian‐type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange‐correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn–Sham matrix formation. © 2016 Wiley Periodicals, Inc. 相似文献
4.
Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density‐functional tight‐binding theory and particle mesh Ewald method 下载免费PDF全文
A quantum mechanical/molecular mechanical (QM/MM) approach based on the density‐functional tight‐binding (DFTB) theory is a useful tool for analyzing chemical reaction systems in detail. In this study, an efficient QM/MM method is developed by the combination of the DFTB/MM and particle mesh Ewald (PME) methods. Because the Fock matrix, which is required in the DFTB calculation, is analytically obtained by the PME method, the Coulomb energy is accurately and rapidly computed. For assessing the performance of this method, DFTB/MM calculations and molecular dynamics simulation are conducted for a system consisting of two amyloid‐β(1‐16) peptides and a zinc ion in explicit water under periodic boundary conditions. As compared with that of the conventional Ewald summation method, the computational cost of the Coulomb energy by utilizing the present approach is drastically reduced, i.e., 166.5 times faster. Furthermore, the deviation of the electronic energy is less than . © 2016 Wiley Periodicals, Inc. 相似文献
5.
A full implementation of the analytical stress tensor for periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian-type orbitals as basis functions. It is the extension of the implementation of analytical energy gradients (Lazarski et al., Journal of Computational Chemistry 2016, 37, 2518–2526) to the stress tensor for the purpose of optimization of lattice vectors. Its key component is the efficient calculation of the Coulomb contribution by combining density fitting approximation and continuous fast multipole method. For the exchange-correlation (XC) part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097–3104) is extended to XC weight derivatives and stress tensor. The computational efficiency and favorable scaling behavior of the stress tensor implementation are demonstrated for various model systems. The overall computational effort for energy gradient and stress tensor for the largest systems investigated is shown to be at most two and a half times the computational effort for the Kohn–Sham matrix formation. © 2019 Wiley Periodicals, Inc. 相似文献
6.
Charles W. Bauschlicher Jr. 《International journal of quantum chemistry》2009,109(2):357-361
The convergence of the binding energy of oxygen on Cu(100) as a function of the k‐points, energy cutoff for the inclusion of plane waves, surface model, and oxygen coverage is studied. Overall the convergence is good, with an accuracy of 0.1 eV obtained for an affordable level of treatment. Published 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 相似文献
7.
Yu W Liang L Lin Z Ling S Haranczyk M Gutowski M 《Journal of computational chemistry》2009,30(4):589-600
Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-311++G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-311++G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-311++G(d,p), aug-cc-pVDZ, 6-311++G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds. 相似文献
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9.
《International journal of quantum chemistry》2018,118(15)
The enzyme nitrogenase contains a complicated MoFe7CS9 cofactor with 35 possible broken‐symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one‐electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Likewise, the effect of the surrounding protein is restricted, up to 10 and 7 kJ/mol for the electrostatic and van der Waals energy terms. Single‐point energies calculated on a single geometry give a good correlation (R2 = 0.92‐0.98) to energies calculated after geometry optimization, but some BS states may be disfavored by up to 37 kJ/mol. A change from the pure TPSS functional to the hybrid B3LYP functional may change the relative energies by up to 58 kJ/mol and the correlation between the two results is only 0.57‐0.72. Both functionals agree that BS7 is the most stable BS state and that the ground spin state is the quartet for the resting state and the quintet for the reduced state. With the TPSS functional, the BS6 state is the second most stable state, always at least 21 kJ/mol less stable than the BS7 state. However, with the B3LYP functional, BS10 is the second most stable state and for the protonated state it comes close in energy. Based on these results, we suggest a procedure how to consider the 35 BS states in future investigations of the nitrogenase reaction mechanism. 相似文献
10.
Benchmarking dispersion and geometrical counterpoise corrections for cost‐effective large‐scale DFT calculations of water adsorption on graphene 下载免费PDF全文
Marco Lorenz Bartolomeo Civalleri Lorenzo Maschio Mauro Sgroi Daniele Pullini 《Journal of computational chemistry》2014,35(24):1789-1800
The physisorption of water on graphene is investigated with the hybrid density functional theory (DFT)‐functional B3LYP combined with empirical corrections, using moderate‐sized basis sets such as 6‐31G(d). This setup allows to model the interaction of water with graphene going beyond the quality of classical or semiclassical simulations, while still keeping the computational costs under control. Good agreement with respect to Coupled Cluster with singles and doubles excitations and perturbative triples (CCSD(T)) results is achieved for the adsorption of a single water molecule in a benchmark with two DFT‐functionals (Perdew/Burke/Ernzerhof (PBE), B3LYP) and Grimme's empirical dispersion and counterpoise corrections. We apply the same setting to graphene supported by epitaxial hexagonal boron nitride (h‐BN), leading to an increased interaction energy. To further demonstrate the achievement of the empirical corrections, we model, entirely from first principles, the electronic properties of graphene and graphene supported by h‐BN covered with different amounts of water (one, 10 water molecules per cell and full coverage). The effect of h‐BN on these properties turns out to be negligibly small, making it a good candidate for a substrate to grow graphene on. © 2014 Wiley Periodicals, Inc. 相似文献
11.
We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense. 相似文献
12.
Noriyuki Yoshii Yoshimichi Andoh Susumu Okazaki 《Journal of computational chemistry》2020,41(9):940-948
We derived a new expression for the electrostatic interaction of three-dimensional charge-neutral systems with two-dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells are expressed as a sum of real and reciprocal space terms, and a self-interaction term. The reciprocal space contribution consists of two parts: zero and nonzero terms of the absolute value of the reciprocal lattice vector. To test the new expressions, electrostatic interactions were calculated for a randomly placed charge distribution in a cubic box and liquid water produced by molecular dynamics calculation. The accuracy could be controlled by the degree of expansion of the FMM. In the present expression, the computational complexity of the electrostatic interaction of N-particle systems is order N, which is superior to that of the conventional two-dimensional periodic Ewald method for a slab geometry and the particle mesh Ewald method with a large empty space at an interface of the unit cell. © 2020 Wiley Periodicals, Inc. 相似文献
13.
Plane-wave density functional theory has been applied to determine the strengths of hydrogen bonds in the phase I crystal structures of ammonia and urea. For ammonia, each component of the trifurcated hydrogen bond has been found to be almost as strong as a standard N-H.N interaction, and for urea the strengths of the two different N-H.O interactions have been determined by a quantum mechanical technique for the first time. 相似文献
14.
《Journal of computational chemistry》2018,39(2):105-116
A low‐computational‐cost algorithm and its parallel implementation for periodic divide‐and‐conquer density‐functional tight‐binding (DC‐DFTB) calculations are presented. The developed algorithm enables rapid computation of the interaction between atomic partial charges, which is the bottleneck for applications to large systems, by means of multipole‐ and interpolation‐based approaches for long‐ and short‐range contributions. The numerical errors of energy and forces with respect to the conventional Ewald‐based technique can be under the control of the multipole expansion order, level of unit cell replication, and interpolation grid size. The parallel performance of four different evaluation schemes combining previous approaches and the proposed one are assessed using test calculations of a cubic water box on the K computer. The largest benchmark system consisted of 3,295,500 atoms. DC‐DFTB energy and forces for this system were obtained in only a few minutes when the proposed algorithm was activated and parallelized over 16,000 nodes in the K computer. The high performance using a single node workstation was also confirmed. In addition to liquid water systems, the feasibility of the present method was examined by testing solid systems such as diamond form of carbon, face‐centered cubic form of copper, and rock salt form of sodium chloride. © 2017 Wiley Periodicals, Inc. 相似文献
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16.
《Journal of computational chemistry》2017,38(13):949-956
We present a computational study of magnetic‐shielding and quadrupolar‐coupling tensors of 43Ca sites in crystalline solids. A comparison between periodic and cluster‐based approaches for modeling solid‐state interactions demonstrates that cluster‐based approaches are suitable for predicting 43Ca NMR parameters. Several model chemistries, including Hartree–Fock theory and 17 DFT approximations (SVWN, CA‐PZ, PBE, PBE0, PW91, B3PW91, rPBE, PBEsol, WC, PKZB, BMK, M06‐L, M06, M06‐2X, M06‐HF, TPSS, and TPSSh), are evaluated for the prediction of 43Ca NMR parameters. Convergence of NMR parameters with respect to basis sets of the form cc‐pVXZ (X = D, T, Q) is also evaluated. All DFT methods lead to substantial, and frequently systematic, overestimations of experimental chemical shifts. Hartree–Fock calculations outperform all DFT methods for the prediction of 43Ca chemical‐shift tensors. © 2017 Wiley Periodicals, Inc. 相似文献
17.
《International journal of quantum chemistry》2018,118(2)
To achieve the necessary accuracy when calculating the electronic structures of materials, for example, for surface or bulk models, we propose a combined plane wave (PW) and localized orbital (LO) electronic structure calculation approach. A high level theory calculation based on the LO approach can be used to describe chemical reactions and other electronic processes using a cluster model. Conversely, the electronic structure of a surface or bulk model is best calculated using a PW approach. In this study, we analyzed the potential energy surface of a hydrogen atom adsorption on a Pd(111) surface using our proposed combined PW and LO approach. We clearly demonstrate that the combined PW and LO approach is both effective and necessary to determine local surface phenomena. We expect that the proposed approach will be effective for a broad range of applications in the material science field. 相似文献
18.
Fernanda S. Tiago Pedro H.O. Santiago Marília M.P. Amaral 《Journal of Coordination Chemistry》2016,69(2):330-342
This work describes the synthesis and the crystal structure of a copper(II) complex – [Cu(HL)(NO3)2]·H2O – based on 2-acetylpyridine-benzoylhydrazone ligand (HL). In the complex, copper(II) is five-coordinate with two nitrate ligands and a tridentate NNO-donor. The copper center has square pyramidal geometry with an axial nitrate and the equatorial positions occupied by another nitrate and the hydrazone. Besides X-ray studies, the complete structural characterization includes elemental analysis, IR, and UV–vis spectroscopy. Plane wave and localized basis set calculations support the distorted square pyramidal geometry. Theoretical calculations using several DFT functionals were used to study the performance of functionals for this complex. Solvent effect was studied on optimized geometries allowing better support to its spectroscopic data. Noncovalent π?π stacking interactions were also analyzed. 相似文献
19.
Effect of differently terminal groups of poly(amido‐amine) dendrimers on dispersion stability of nano‐silica and ab initio calculations 下载免费PDF全文
To investigate the effect of differently terminal groups of the lowest‐order generation poly(amido‐amine) dendrimers on dispersion stability of nano‐silica, the four types of G0‐CH2CH3 (G0E), G0‐CH2CH2CH2CH3 (G0B), G0‐NH2 (G0N), and G0‐COOH (G0C) dendrimer molecules are used to modify the silica based on the dry modification. The zeta potential, the surface charge density, and the storage stability of kinds of modified SiO2 dispersion systems have been studied. The results show that the effect of carboxyl groups on dispersion stability is stronger than that of the other groups such as the amine and alkyl groups. Mulliken charge distributions of the main active sites are analyzed through the conductor‐like polarizable calculation model (CPCM) on basis of the density functional theory (DFT) method, indicating the formation of chemical bonding between the modifiers and SiO2 particles. The most stable SiO2 dispersion system modified by G0‐COOH dendrimer molecule is obtained due to the combined effect including the hydrogen bonding, electrostatic repulsive force, and the steric hindrance of the terminal groups. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献