DFT performance for the hole transfer parameters in DNA π stacks

Recently, we showed that unoccupied Kohn‐Sham (KS) orbitals stemming from DFT calculations of a neutral system can be used to derive accurate estimates of the free energy and electronic couplings for excess electron transfer in DNA (Félix and Voityuk, J Phys Chem A 2008, 112, 9043). In this article, we consider the propagation of radical cation states (hole transfer) through DNA π‐stacks and compare the performance of different exchange‐correlation functionals to estimate the hole transfer (HT) parameters. Two different approaches are used: (1) calculations that use occupied KS orbitals of neutral π stacks of nucleobases, and (2) the time‐dependent DFT method which is applied to the radical cation states of these stacks. Comparison of the calculated parameters with the reference data suggests that the best results are provided by the KS scheme with hybrid functionals (B3LYP, PBE0, and BH&HLYP). The TD DFT approach gives significantly less accurate values of the HT parameters. In agreement with high‐level ab initio results, the KS scheme predicts that the hole in π stacks is confined to a single nucleobase; in contrast, the spin‐unrestricted DFT method considerably overestimates the hole delocalization in the radical cations. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Automatized Parameterization of the Density‐functional Tight‐binding Method. II. Two‐center Integrals

We present an efficient numerical integration scheme (TWOCENT) to be used in the context of automatized parameterization of the density‐functional tight‐binding (DFTB) method. The accuracy of the integration process is assessed and its range of applicability is discussed. The functionality of the developed code is tested by reproducing the electronic portion of the existing mio parameter sets and by reproducing a series of reference DFT band structures of elemental solids.     

Density functional LCAO calculations for solids: Comparison among Hartree–Fock,DFT local density approximation,and DFT generalized gradient approximation structural properties

In this article, the results of a recently implemented DFT a posteriori and Kohn-Sham (KS ) linear combination of atomic orbital computational scheme for solids are presented. The equilibrium lattice parameters, bulk moduli, and lattice energies are calculated for eight crystallized systems. Local density approximation (LDA ) and generalized gradient approximation (GCA ) functionals and potentials are used. The maps of the Hartree-Fock (HF ) and Ks electronic densities and band structures are depicted. The KS results confirm the trend of the a posteriori scheme. Very good agreement between calculated and experimental lattice energies has been found for GGA potentials. © 1995 John Wiley & Sons, Inc.     

DFT and MO calculations of atomic and molecular chemisorption energies on surface cluster models

Summary Density functional theory (DFT) (including gradient corrections) and MCPF calculations have been performed for atomic (H, C, N, O) and molecular CH _x (x = 1–3) chemisorption on cluster models of different sites of the Cu(100) surface. The DFT and MCPF results are in good agreement once the important effects of core-valence correlation have been accounted for in the MCPF calculations by including contributions from a core polarization potential (CPP); in the DFT approach the core-valence correlation is obtained directly from the total density using the functional. Very large effects on the four-fold hollow site binding energy from core-valence correlation are found for C, N and CH. Several different DFT functionals were employed and compared in the calculations.     

FT-IR,XPS, and DFT Study of Adsorption Mechanism of Sodium Acetohydroxamate onto Goethite or Hematite

The adsorption of sodium acetohydroxamate on the goethite or hematite surface was investi-gated by Fourier transform infrared spectroscopy (FT-IR), X-ray photoemission spectroscopy and periodic plane-wave density functional theory (DFT) calculations. The core-level shifts and charge transfers of the adsorbed surface iron sites calculated by DFT with periodic in-terfacial structures were confronted to the X-ray photoemission experiments. FT-IR results reveal that the interfacial structure of sodium acetohydroxamate adsorbed on the goethite or hematite surface may be assigned to a ve-membered ring complex. In agreement with the adsorption energies determined by the DFT calculations, a ve-membered ring complex is formed via bonding of one surface iron atom of goethite (101) or (100) to both oxygen atoms of hydroxamate group, and these two oxygen atoms of the hydroxamate group correspond-ingly attach to two neighboring iron atoms of the goethite surface. But a ve-membered ring complex between two oxygen atoms of the hydroxamate group and one surface iron atom of hematite (001) is formed without any extra attachments. The calculated core-level shifts of Fe2p for the interfacial structures are correspondingly in good agreement with the experimental observed one, which con rmed the reliability of the calculated results.     

Graphene功能分子在HOPG上自组装结构的密度泛函研究

Graphene自组装超分子结构,是指FTBC-Cn(n=4,6,8,12)分子有序自组装在高定向裂解石墨(HOPG)上形成的自组装超分子结构,是一种新型二维固体表面材料.其中FTBC-Cn分子是由三角形扶手椅型graphene每边添加2条含有n(n=4,6,8,12)个C原子的烷基链所形成具有曲面结构的一种分子.采用...     

SERS and DFT study of nitroarenes adsorbed on metal nanoparticles

A combined SERS and DFT investigation has been performed for 2-amino,5-nitropyridine (ANP) adsorbed on silver colloidal nanoparticles in order to get a better insight into the adsorption mechanism of ANP on the silver surface. Both B3LYP and B3PW91 functionals were used in the DFT calculations on ANP in the anionic form (ANP⁻) and on different models of ANP⁻/silver surface complexes. A mixed basis set 6-311++G^**/LANL2DZ was used in the case of the ANP⁻/Ag⁺ complexes. From the comparison between the experimental and the computational data, it was evinced that ANP is adsorbed on the silver surface in the anionic form with a quinonoid electronic structure through the nitrogen atom of the imino group.     

Towards the versatile DFT and MP2 computational schemes for 31P NMR chemical shifts taking into account relativistic corrections

The main factors affecting the accuracy and computational cost of the calculation of ³¹P NMR chemical shifts in the representative series of organophosphorous compounds are examined at the density functional theory (DFT) and second‐order Møller–Plesset perturbation theory (MP2) levels. At the DFT level, the best functionals for the calculation of ³¹P NMR chemical shifts are those of Keal and Tozer, KT2 and KT3. Both at the DFT and MP2 levels, the most reliable basis sets are those of Jensen, pcS‐2 or larger, and those of Pople, 6‐311G(d,p) or larger. The reliable basis sets of Dunning's family are those of at least penta‐zeta quality that precludes their practical consideration. An encouraging finding is that basically, the locally dense basis set approach resulting in a dramatic decrease in computational cost is justified in the calculation of ³¹P NMR chemical shifts within the 1–2‐ppm error. Relativistic corrections to ³¹P NMR absolute shielding constants are of major importance reaching about 20–30 ppm (ca 7%) improving (not worsening!) the agreement of calculation with experiment. Further better agreement with the experiment by 1–2 ppm can be obtained by taking into account solvent effects within the integral equation formalism polarizable continuum model solvation scheme. We recommend the GIAO‐DFT‐KT2/pcS‐3//pcS‐2 scheme with relativistic corrections and solvent effects taken into account as the most versatile computational scheme for the calculation of ³¹P NMR chemical shifts characterized by a mean absolute error of ca 9 ppm in the range of 550 ppm. Copyright © 2014 John Wiley & Sons, Ltd.     

The structure of the chiral Pt531 surface: a combined LEED and DFT study

The structure of the chiral kinked Pt531 surface has been determined by low-energy electron diffraction intensity-versus-energy (LEED-IV) analysis and density functional theory (DFT). Large contractions and expansions of the vertical interlayer distances with respect to the bulk-terminated surface geometry were found for the first six layers (LEED: d12 = 0.44 A, d23 = 0.69 A, d34 = 0.49 A, d45 = 0.95 A, d56 = 0.56 A; DFT: d12 = 0.51 A, d23 = 0.55 A, d34 = 0.74 A, d45 = 0.78 A, d56 = 0.63 A; dbulk = 0.66 A). Energy-dependent cancellations of LEED spots over unusually large energy ranges, up to 100 eV, can be explained by surface roughness and reproduced by applying a model involving 0.25 ML of vacancies and adatoms in the scattering calculations. The agreement between the results from LEED and DFT is not as good as in other cases, which could be due to this roughness of the real surface.     

Interpolating DFT Data for 15D Modeling of Methane Dissociation on an fcc Metal

Detailed simulation of reactions occurring on and with the surfaces of crystalline materials usually require a continuous representation of the potential energy surface that describes the adsorbate–surface interaction. Only a few techniques are available to describe interactions with polyatomic adsorbates that respect all of the symmetries of the interactions. The modified Shepard interpolation has recently been reformulated to ensure symmetries are rigorously imposed. In this work, the modified Shepard interpolation is used to construct a 15D potential energy surface for the reaction of methane with the {100} surface of a face‐centered cubic metal, in the Born‐‐Oppenheimer static surface (BOSS) approximation. The energy of the system is calculated using density functional theory (DFT), and the geometries around which the potential is expanded are selected by quasi‐classical trajectory calculations. The energy of the resulting continuous potential energy surface exactly matched the DFT energy at these points; there is no fitting error. It is demonstrated that the classical reaction probability converges with a reasonable number of interpolation points for this 15D system.     

O2 induced Cu surface segregation in Au-Cu alloys studied by angle resolved XPS and DFT modelling

Surface segregation effects on polycrystalline Au-Cu alloys (Au(0.80)Cu(0.20), Au(0.85)Cu(0.15) and Au(0.90)Cu(0.10)) were studied at room temperature by angle resolved XPS (ARXPS) and density functional theory (DFT) before and after exposure to O(2). Au surface enrichment was found as predicted from calculations showing that this process is energetically favourable, with a segregation energy for Au in a Cu matrix of -0.37 eV atom(-1). Surface enrichment with Cu was observed after exposure to O(2) due to its dissociative adsorption, in agreement with DFT calculations that predicted an energy gain of -1.80 eV atom(-1) for the transfer of Cu atoms to a surface containing adsorbed oxygen atoms, thus leading to an inversion in surface population.     

An ONIOM and DFT study of water adsorption on rutile TiO2 (110) cluster

Density functional theory (DFT) calculations performed at ONIOM DFT B3LYP/6‐31G**‐MD/UFF level are employed to study molecular and dissociative water adsorption on rutile TiO₂ (110) surface represented by partially relaxed Ti₂₅O₃₇ ONIOM cluster. DFT calculations indicate that dissociative water adsorption is not favorable because of high activation barrier (23.2 kcal/mol). The adsorption energy and vibration frequency of both molecularly and dissociatively adsorbed water molecule on rutile TiO₂ (110) surface compare well with the values reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Carbonyl-ene reactions catalyzed by bis(oxazoline) copper (II) complexes proceed by a facile stepwise mechanism: DFT and ONIOM (DFT:PM3) studies

The mechanism of a carbonyl-ene addition reaction catalyzed by a bis(oxazoline) copper (II) complex has been studied using DFT methods. We find that the reaction proceeds by a stepwise mechanism with very low barriers and have identified the role of the metal catalyst. We find that the more computationally economic ONIOM method gives accurate geometries for the stationary structures on the potential energy surface but that accurate energetics must be calculated at the full DFT level.     

De novo prediction of the ground state structure of transition metal complexes using semiempirical and ab initio quantum mechanics. Coordination isomerism

The ground state coordination isomers for 30 different trigonal bipyramidal transition metal complexes have been predicted using different levels of quantum mechanics: semiempirical (PM3(tm)), ab initio (MP2//HF), pure (BPW91) and hybrid (B3PW91) density functional theory (DFT) methods. For species where these methods failed to reproduce crystallographic data, hybrid quantum mechanics/molecular mechanics (QM/MM) methods were used to study more exact experimental models. Literature deficiencies regarding ground state multiplicity of these species were supplemented by spin predictions using previously tested PM3(tm) methods. Geometry optimization calculations were performed for each possible coordination isomer. The predicted ground state minima provided by the different methods are compared to each other and with crystallographic data. Pure DFT functionals outperformed hybrid functionals and MP2//HF. The very rapid PM3(tm) parameterization method provided accurate predictions in comparison to other levels of theory. An integrated MM/PM3(tm)/DFT de novo scheme accurately reproduced crystallographic data for species where the individual methods failed.     

An ONIOM and DFT study of water and ammonia adsorption on anatase TiO2 (001) cluster

Density functional theory (DFT) calculations at ONIOM DFT B3LYP/ 6‐31G**‐MD/UFF level are employed to study molecular and dissociative water and ammonia adsorption on anatase TiO₂ (001) surface represented by partially relaxed Ti₂₀O₃₅ ONIOM cluster. DFT calculations indicate that water molecule is dissociated on anatase TiO₂ (001) surface by a nonactivated process with an exothermic relative energy difference of 58.12 kcal/mol. Dissociation of ammonia molecule on the same surface is energetically more favorable than molecular adsorption of ammonia (?37.17 kcal/mol vs. ?23.28 kcal/mol). The vibration frequency values also are computed for the optimized geometries of adsorbed water and ammonia molecules on anatase TiO₂ (001) surface. The computed adsorption energy and vibration frequency values are comparable with the values reported in the literature. Finally, several thermodynamical properties (ΔH°, ΔS°, and ΔG°) are calculated for temperatures corresponding to the experimental studies. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

FT-IR、XPS和DFT研究水杨酸钠在针铁矿或赤铁矿上的吸附机理

采用傅里叶变换红外(FT-IR)光谱、X射线光电子能谱(XPS)以及基于周期平面波的密度泛函理论(DFT)分别研究了水杨酸钠在针铁矿或赤铁矿表面上的吸附结构,并将计算得到的光电子能谱移动(CLS)和电荷转移与实验得到的XPS结果进行对比。FT-IR结果表明,水杨酸钠可能以双齿双核(V)和双齿单核(IV)的形式分别吸附于针铁矿或赤铁矿表面。由DFT计算结果可知,水杨酸钠在针铁矿(101)晶面上形成双齿双核化合物(V)的吸附能为-5.46 eV。而水杨酸钠在针铁矿(101)晶面上形成双齿单核化合物(IV)的吸附能为3.80 eV,因此水杨酸钠在针铁矿上基本不以双齿单核化合物(IV)构型存在。水杨酸钠在赤铁矿(001)晶面上形成双齿单核化合物(IV)时吸附能为-4.07 eV,说明水杨酸钠在赤铁矿(001)晶面上形成了双齿单核化合物(IV)。另外,理论计算的针铁矿(101)晶面上吸附位点铁原子的Fe 2p的CLS值(-0.68 eV)与实验观察到的Fe 2p的CLS值(-0.5 eV)吻合。理论计算的赤铁矿(001)晶面上吸附位点铁原子的Fe 2p的CLS值(-0.80 eV)与实验观察到的Fe 2p的CLS值(-0.8 eV)吻合。因此,水杨酸钠吸附在针铁矿表面时能够通过羧酸基团上一个氧原子和酚羟基上的氧原子与针铁矿(101)表面上的两个铁原子形成双齿双核(V)结构,而在赤铁矿(001)表面上,水杨酸钠中羧酸基团上一个氧原子和酚羟基上的氧原子与赤铁矿(001)表面上的一个铁原子形成了双齿单核(IV)结构。     

On the accuracy factors and computational cost of the GIAO–DFT calculation of 15N NMR chemical shifts of amides

The main factors affecting the accuracy and computational cost of Gauge‐independent Atomic Orbital–density functional theory (GIAO–DFT) calculation of ¹⁵N NMR chemical shifts in the benchmark series of 16 amides are considered. Among those are the choice of the DFT functional and basis set, solvent effects, internal reference conversion factor and applicability of the locally dense basis set (LDBS) scheme. Solvent effects are treated within the polarizable continuum model (PCM) scheme as well as at supermolecular level with solvent molecules considered in explicit way. The best result is found for Keal and Tozer's KT3 functional used in combination with Jensen's pcS‐3 basis set with taking into account solvent effects within the polarizable continuum model. The proposed LDBS scheme implies pcS‐3 on nitrogen and pc‐2 elsewhere in the molecule. The resulting mean average error for the calculated ¹⁵N NMR chemical shifts is about 6 ppm. The application of the LDBS approach tested in a series of 16 amides results in a dramatic decrease in computational cost (more than an order of magnitude in time scale) with insignificant loss of accuracy.