Scanning tunneling microscopy image simulation of the rutile (110) TiO2 surface with hybrid functionals and the localized basis set approach

In this work we present a simplified procedure to use hybrid functionals and localized atomic basis sets to simulate scanning tunneling microscopy (STM) images of stoichiometric, reduced and hydroxylated rutile (110) TiO2 surface. For the two defective systems it is necessary to introduce some exact Hartree-Fock exchange in the exchange functional in order to correctly describe the details of the electronic structure. Results are compared to the standard density functional theory and planewave basis set approach. Both methods have advantages and drawbacks that are analyzed in detail. In particular, for the localized basis set approach, it is necessary to introduce a number of Gaussian function in the vacuum region above the surface in order to correctly describe the exponential decay of the integrated local density of states from the surface. In the planewave periodic approach, a thick vacuum region is required to achieve correct results. Simulated STM images are obtained for both the reduced and hydroxylated surface which nicely compare with experimental findings. A direct comparison of the two defects as displayed in the simulated STM images indicates that the OH groups should appear brighter than oxygen vacancies in perfect agreement with the experimental STM data.     

Behavior of density functionals with respect to basis set. 3. Basis set superposition error

The impact of basis set superposition error (BSSE) upon molecular properties determined using the density functionals B3LYP, B3PW91, B3P86, BLYP, BPW91, and BP86 in combination with the correlation consistent basis sets [cc-pVnZ, where n = D(2), T(3), Q(4), and 5] for a set of first-row closed-shell molecules has been examined. Correcting for BSSE enables the irregular convergence behavior in molecular properties such as dissociation energies with respect to increasing basis set size, noted in earlier studies, to be improved. However, for some molecules and functional combinations, BSSE correction alone does not improve the irregular convergence behavior.     

Linear scaling calculation of maximally localized Wannier functions with atomic basis set

We have developed a linear scaling algorithm for calculating maximally localized Wannier functions (MLWFs) using atomic orbital basis. An O(N) ground state calculation is carried out to get the density matrix (DM). Through a projection of the DM onto atomic orbitals and a subsequent O(N) orthogonalization, we obtain initial orthogonal localized orbitals. These orbitals can be maximally localized in linear scaling by simple Jacobi sweeps. Our O(N) method is validated by applying it to water molecule and wurtzite ZnO. The linear scaling behavior of the new method is demonstrated by computing the MLWFs of boron nitride nanotubes.     

Behavior of density functionals with respect to basis set. VI. Truncation of the correlation consistent basis sets

Systematic truncation of the correlation consistent basis sets has been investigated in first and second row atoms and molecules to better understand basis set requirements for density functional theory, particularly the need for high angular momentum functions, as well as to understand possible computational cost savings that could be achieved by using reduced basis sets. The truncation scheme employed follows that recently introduced for ab initio methods [B. Mintz et al., J. Chem. Phys. 121, 5629 (2004)]. Properties examined in the current study include geometries, ionization potentials, electron affinities, and dissociation energies. In general, this investigation shows that a degree of truncation of higher angular momentum functions is possible with limited impact upon energetic properties, and does result in useful CPU time savings. However, not all properties investigated have the same level of dependence upon high angular momentum functions, and, thus, careful selection of truncated basis sets should be made.     

π和σ体系彻底分离的高度定域的键轨道基组的建立

高度定域的、对称的、键轨道基组的建立是一个多步的计算程序：(1)以定域片断轨道[φk,φi,φj]为基,对分子作有条件的RHF运算,算得FUL和DSI°态的片断分子轨道[Φ°l',Φ°n,Φ°m]和[Φl,Φn,Φm]。在基组[φk,φi,φj]中,φi∈双占据和空σ片断分子轨道(FMOs)组,φj∈πFMO组,φk∈单占据σFMO组,它们都精确地定域在各自的片断内;(2)利用Φ°l'与Φ°l间的重叠积分值(Sl'l>0.5),可以从DSI°态中,自动地选出Ns个对称的、由单占据轨道线性组合而成的分子轨道Φ°l'=Σakl'φk(k=1,2,…,Ns),接着,用Φ°l'取代FUL态中同类的、非对称轨道组Φl=Σaklφk(k=1,2,…,Ns);(3)以上述新的轨道组[Φ°l',Φn,Φm]为基(其中,Φ°l'∈DSI°态,它们离域于整个分子;双占据及空σFMO组Φm和πFMO组Φm属于FUL态),按FUL态的条件,再次对分子作有条件的RHF运算,从中得到一组对称的、闭壳层正则FMOs,而且每一个FMO均有正确的电子占据数;(4)利用Perkin原理,将第3步所得的正则FMO组定域成一个对称的键轨道基组[Φl',Φn',Φm']。在这个基组中,π体系Φm'与σ构架Φn'是彻底分离的,而且这两个轨道组始终精确地定域在各自的片断内。     

Pulay forces from localized orbitals optimized in situ using a psinc basis set

In situ optimization of a set of localized orbitals with respect to a systematically improvable basis set independent of the position of the atoms, such as psinc functions, would theoretically eliminate the correction due to Pulay forces from the total ionic forces. We demonstrate that for strict localization constraints, especially with small localization regions, there can be non-negligible Pulay forces that must be calculated as a correction to the Hellmann-Feynman forces in the ground state. Geometry optimization calculations, which rely heavily upon accurate evaluation of the total ionic forces, show much better convergence when Pulay forces are included. The more conventional case, where the local orbitals remain fixed to pseudo-atomic orbital multiple-ζ basis sets, also benefits from this implementation. We have validated the method on several test cases, including a DNA fragment with 1045 atoms.     

Transition levels of defects in ZnO: Total energy and Janak's theorem methods

Transition levels of defects are commonly calculated using either methods based on total energies of defects in relevant charge states or energy band single particle eigenvalues. The former method requires calculation of total energies of charged, perfect bulk supercells, as well as charged defect supercells, to obtain defect formation energies for various charge states. The latter method depends on Janak's theorem to obtain differences in defect formation energies for various charge states. Transition levels of V(Zn), V(O), and V(ZnO) vacancy defects in ZnO are calculated using both methods. The mean absolute deviation in transition level calculated using either method is 0.3 eV. Relative computational costs and accuracies of the methods are discussed.     

Procedure supplementing SCF interaction energies by dispersion term evaluated in dimer basis set within variation-perturbation approach

A variation-perturbation procedure for the evaluation of dispersion interaction, originally proposed by Jeziorski and van Hemert, has been reformulated to include basis set extension effects on an equal footing with the SCF interaction energy, corrected for basis set superposition error (BSSE). This approach has been tested for He₂, (H₂)₂, (H₂O)₂, and (C₂H₄)₂ complexes.The research was supported by ONR under contract N00014-80-C-0003 and in part by PAN within MR-I-9 project.     

Carbondioxide rare‐gas systems: Sensitivity of basis sets and double‐hybrid density functionals

This study emphasizes on the performance of six newly developed double‐hybrid density functionals (DHDF) in explaining the potential energy curves of different carbondioxide rare‐gas systems. The basis set sensitivity has also been explored with the use of three basis sets. Our results suggest that for lighter He/Ne‐CO₂ complexes, proper choice of DHDF and basis set lead to results those matches exactly with earlier calculations and also with the experiment. On the other hand, for heavier Ar/Kr‐CO₂ complexes although the equilibrium separation distance matches exactly with earlier observations, the interaction energy values lie far apart. The overall investigation emphasizes on the fact that one has to tune the methods and basis sets properly to achieve good and satisfactory results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Harmonic vibrational frequencies: scale factors for pure, hybrid, hybrid meta, and double-hybrid functionals in conjunction with correlation consistent basis sets

Scale factors for (a) low (<1000 cm(-1)) and high harmonic vibrational frequencies, (b) thermal contributions to enthalpy and entropy, and (c) zero-point vibrational energies have been determined for five hybrid functionals (B3P86, B3PW91, PBE1PBE, BH&HLYP, MPW1K), five pure functionals (BLYP, BPW91, PBEPBE, HCTH93, and BP86), four hybrid meta functionals (M05, M05-2X, M06, and M06-2X) and one double-hybrid functional (B2GP-PLYP) in combination with the correlation consistent basis sets [cc-pVnZ and aug-cc-pVnZ, n = D(2),T(3),Q(4)]. Calculations for vibrational frequencies were carried out on 41 organic molecules and an additional set of 22 small molecules was used for the zero-point vibrational energy scale factors. Before scaling, approximately 25% of the calculated frequencies were within 3% of experimental frequencies. Upon application of the derived scale factors, nearly 90% of the calculated frequencies deviated less than 3% from the experimental frequencies for all of the functionals when the augmented correlation consistent basis sets were used.     

Molecular properties and basis set quality: An approach based on information theory

Information theory can be used to evaluate the quality of a wave function by considering its ability to give values for some observables as close as possible to the experimental ones. A new method for improving the quality of a wave function is proposed. This paper deals exclusively with the HF (X ¹∑⁺) molecule.     

An application of the method of conjugate gradients to the calculation of minimal basis set localized orbitals

Using an STO -3G basis set, energy localized molecular orbitals (LMO ) were determined for the ten electron series HF, H₂O, NH₃, and CH₄ as well as for CH₃OH and C₂H₂F₂. The method of conjugate gradients is shown to be a viable alternative to other non-eigenvalue methods. The characterization of the LMO in terms of first and second moment measures indicates that the STO -3G basis set LMO may be accurately correlated to larger sp basis set LMO . Also, it is shown that the first and second moment measures display a good linear correlation with the classical concept of electronegativity.     

Hydrogen/deuterium adsorption and absorption properties on and in palladium using a combined plane wave and localized basis set method

Detailed information on the H/D isotope effects for adsorption on the surface and absorption in the bulk is important for understanding the nuclear quantum effect. To achieve this, we developed a new theoretical approach, namely, the combined plane wave and localized basis set (CPLB) method. By using the multicomponent quantum chemical method, which takes into account the quantum effect of a proton or deuteron, with the localized part of the CPLB method, direct analysis of the H/D isotope effect about adsorption and absorption is carried out. In this study, we performed a theoretical investigation of the H/D isotope effects for adsorption on a Pd(111) surface and absorption in bulk Pd. We clearly showed an H/D isotope effect on geometry during adsorption and absorption. Our developed CPLB approach is a powerful tool for analyzing the quantum nature of H/D in surface, bulk, and inhomogeneous systems.     

Many-electron self-interaction and spin polarization errors in local hybrid density functionals

Errors for systems with noninteger occupation have been connected to common failures of density functionals. Previously, global hybrids and pure density functionals have been investigated for systems with noninteger charge and noninteger spin state. Local hybrids have not been investigated for either of those systems to the best of our knowledge. This study intends to close this gap. We investigate systems with noninteger charge to assess the many-electron self-interaction error and systems with noninteger spin state to assess the spin polarization error of recently proposed local hybrids and their range-separated variants. We find that long-range correction is very important to correct for many-electron self-interaction error in cations, whereas most full-range local hybrids seem to be sufficient for anions, where long-range-corrected density functionals tend to overcorrect. On the other hand, while all hitherto proposed long-range-corrected density functionals show large spin polarization errors, the Perdew-Staroverov-Tao-Scuseria (PSTS) functional performs best of all local hybrids in this case and shows an outstanding behavior for the dependence of the energy on the spin polarization.     

Electrochemical approach to the development of a photoelectrode on the basis of photosynthetic reaction centers

Experimental approaches to the coupling of photoinduced charge separation in reaction centers (RCs) of the photosynthetic bacterium Rhodobacter sphaeroides R-26 with electron transfer to an electrode are discussed. Exogenous quinones are used as an electron transfer mediator. With the use of photopolarography it is shown that water-soluble ubiquinone can serve as a diffusionally mobile mediator of electron transfer. Some methods of quinone immobilization at an electrode have been developed to obtain a non-diffusional mediator of electron transfer. Quasi-reversible electrochemical kinetics were observed for aminonaphthoquinone immobilized as a monolayer at a Pt electrode. The ubiquinone-depleted RCs were subjected to affinity immobilization at these chemically modified electrodes probably due to the insertion of the immobilized quinone into the primary quinone Q_A binding site. The quantum efficiency of photocurrent formation was ca. 5% for the photoelectrode obtained. The electrochemical process of the immobilized quinone is shown to be the stage that limits electron transfer from RCs to the electrode.     

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: benchmarks approaching the complete basis set limit

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Moller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.     

Molecular energies and properties from density functional theory: Exploring basis set dependence of Kohn—Sham equation using several density functionals

The performance of four commonly used density functionals (VWN, BLYP, BP91, and Becke's original three-parameter approximation to the adiabatic connection formula, referred to herein as the adiabatic connection method or ACM) was studied with a series of six Gaussian-type atomic basis sets [DZP, 6–31G**, DZVP, TZVP, TZ2P, and uncontracted aug-cc-pVTZ (UCC)]. The geometries and dipole moments of over 100 first-row and second-row molecules and reaction energies of over 300 chemical reactions involving such molecules were computed using each of the four density functionals in combination with each of the six basis sets. The results were compared to experimentally determined values. Based on overall mean absolute theory versus experiment errors, it was found that ACM is the best choice for predictions of both energies of reaction [overall mean absolute theory versus experiment error (MATvEE) of 4.7 kcal/mol with our most complete (UCC) basis set] and molecular geometries (overall MATvEE of 0.92 pm for bond distances and 0.88° for bond angles with the UCC basis set). For routine calculations with moderate basis sets (those of double-ζ type: DZP, 6–31G**, and DZVP) the DZVP basis set was, on average, the best choice. There were, however, examples of reactions where significantly larger basis sets were required to achieve reasonable accuracy (errors ≤ 5 kcal/mol). For dipole moments, ACM, BP91, and BLYP performed comparably (overall MATvEE of 0.071, 0.067, and 0.059 debye, respectively, with the UCC basis set). Basis sets that include additional polarization functions and diffuse functions were found to be important for accurate density functional theory predictions of dipole moments. © 1997 by John Wiley & Sons, Inc.     

Adsorption of small aromatic molecules on gold: a DFT localized basis set study including van der Waals effects

Schrödinger equation for harmonium and related models may be transformed to the biconfluent Heun equation. The solubility of this equation and its applications in quantum chemistry are briefly discussed.