A theoretical study of surface reduction mechanisms of CeO(2)(111) and (110) by H(2).

Reaction mechanisms for the interactions between CeO(2)(111) and (110) surfaces are investigated using periodic density functional theory (DFT) calculations. Both standard DFT and DFT+U calculations to examine the effect of the localization of Ce 4f states on the redox chemistry of H(2)-CeO(2) interactions are described. For mechanistic studies, molecular and dissociative local minima are initially located by placing an H(2) molecule at various active sites of the CeO(2) surfaces. The binding energies of physisorbed species optimized using the DFT and DFT+U methods are very weak. The dissociative adsorption reactions producing hydroxylated surfaces are all exothermic; exothermicities at the DFT level range from 4.1 kcal mol(-1) for the (111) to 26.5 kcal mol(-1) for the (110) surface, while those at the DFT+U level are between 65.0 kcal mol(-1) for the (111) and 81.8 kcal mol(-1) for the (110) surface. Predicted vibrational frequencies of adsorbed OH and H(2)O species on the surfaces are in line with available experimental and theoretical results. Potential energy profiles are constructed by connecting molecularly adsorbed and dissociatively adsorbed intermediates on each CeO(2) surface with tight transition states using the nudged elastic band (NEB) method. It is found that the U correction method plays a significant role in energetics, especially for the intermediates of the exit channels and products that are partially reduced. The surface reduction reaction on CeO(2)(110) is energetically much more favorable. Accordingly, oxygen vacancies are more easily formed on the (110) surface than on the (111) surface.     

密度泛函理论及其数值方法新进展

综述了密度泛函理论及其数值方法的最新进展.密度泛函理论的发展以寻找合适 的交换相关近似为主线,从最初的局域密度近似、广义梯度近似到现在的非局域泛函、自相 互作用修正,多种泛函形式的相继出现使得密度泛函理论可以提供越来越精确的计算结果. 除了交换相关近似的发展,近年来密度泛函理论向含时理论、相对论等方面的扩展也很活跃 .另外,在密度泛函理论体系发展的同时,相应的数值计算方法的发展也非常迅速.从古老 的有限差分、有限元到新兴的小波分析都被用来实现密度泛函理论的数值计算.与此同时, 线性标度的密度泛函理论算法日趋成熟,使得通过密度泛函理论研究诸如生物大分子之类的 体系成为可能.随着密度泛函理论本身及其数值方法的发展,它的应用也越来越广泛,一些新的应用领域和研究方向不断涌现.     

Assessment of Contemporary Theoretical Methods for Bond Dissociation Enthalpies

The density functional theory (DFT) is the most popular method for evaluating bond dis-sociation enthalpies (BDEs) of most molecules. Thus, we are committed to looking for alternative methods that can balance the computational cost and higher precision to the best for large systems. The performance of DFT, double-hybrid DFT, and high-level com-posite methods are examined. The tested sets contain monocyclic and polycyclic aromatic molecules, branched hydrocarbons, small inorganic molecules, etc. The results show that the mPW2PLYP and G4MP2 methods achieve reasonable agreement with the benchmark values for most tested molecules, and the mean absolute deviations are 2.43 and 1.96 kcal/mol after excluding the BDEs of branched hydrocarbons. We recommend the G4MP2 is the most appropriate method for small systems (atoms number ≤20); the double-hybrid DFT methods are advised for large aromatic molecules in medium size (20 ≤atoms number ≤50), and the double-hybrid DFT methods with empirical dispersion correction are recommended for long-chain and branched hydrocarbons in the same size scope; the DFT methods are advised to apply for large systems (atoms number ≥50), and the M06-2X and B3P86 methods are also favorable. Moreover, the di erences of optimized geometry of different methods are discussed and the effects of basis sets for various methods are investigated.     

The role of fluctuations in both density functional and field theory of nanosystems

The role of fluctuations in both the density functional theory (DFT) and the field theory (FT) of nanosystems is studied. It turns out that although fluctuations are rigorously incorporated into the general formalism of DFT, they are often omitted in the choice of an approximate free energy functional that must be constructed in order to solve the basic integral equation appearing in DFT. Aside from the analytical discussion, it is demonstrated, in connection with a particular system (fluid in a nanopore) that the effects of fluctuation are missing when one of the most common functionals for this system is used. The demonstration involves a comparison of the results of Monte Carlo simulation with the predictions of DFT when this free energy functional is used. The applicability of FT and DFT in the context of the theory of nucleation is also discussed.     

A comparative relativistic DFT and ab initio study on the structure and thermodynamics of the oxofluorides of uranium(IV), (V) and (VI)

All the possible uranium(VI, V, IV) oxides, fluorides and oxofluorides were studied theoretically by using density functional theory (DFT) in the generalised gradient approximation (GGA), and three different relativistic methods (all-electron scalar four component Dyall RESC method (AE), relativistic small-core ECPs, and zeroth order regular approximation ZORA). In order to test different correlation methods, for the two former relativistic methods hybrid DFT, and, for the AE method, MP2 molecular orbital calculations were performed as well. Single-point AE-CCSD(T) energies were calculated on MP2 geometries as well. Energies of the uranium(VI) and (V) oxofluorides dissociation, uranium(VI) fluoride hydrolysis and oxofluoride disproportionation were calculated and compared against the available experimental thermochemical data. AE-CCSD(T) energies were the closest to the experiment. For GGA DFT methods, all the relativistic methods used yield similar results. For thermochemistry, the best quantitative agreement with the experimental and CCSD(T) values for both U=O and U-F bond strengths was obtained with hybrid DFT methods, provided that a reliable basis set was used. Both the GGA DFT and MP2 MO methods show overbinding of these bonds; moreover, this overbinding was found to be not uniform but strongly dependent on the coordination environment of the uranium atom in each case. U=O vibrational frequencies given by hybrid DFT, however, are systematically overestimated, and are better reproduced by GGA DFT; MP2 values usually fall in-between. Reaction enthalpies, U=O frequencies and complex geometries given by the PBE, MPBE, BPBE, BLYP and OLYP GGA functionals are quite similar, with OLYP performing slightly better than the others but still not as good as hybrid DFT. The geometries of the molecules are found to be influenced by the following factors: the inverse transinfluence (ITI) of the oxygen ligand and, for U(V), and U(IV), the Jahn-Teller distortion.     

Matrix-isolation FT-IR study and theoretical calculations of the vibrational, tautomeric and H-bonding properties of hypoxanthine

The neutral compound hypoxanthine is investigated using the technique of matrix-isolation FT-IR spectroscopy combined with density functional theory (DFT) and ab initio methods. Two theoretical methods (RHF and DFT/B3-LYP) are compared for vibrational frequency prediction, and four methods (RHF//RHF, MP2//RHF, DFT//DFT and MP2//DFT) for prediction of the relative energies of the tautomers and the interaction energies of the complexes. All the possible tautomeric forms have been considered theoretically, and the results indicate that two oxo forms (O17 and O19) and one hydroxy form (H9-r1) are the three most stable forms. The experimental FT-IR spectra are consistent with this prediction, and nearly all the characteristic spectral features of these forms have been identified in the spectrum. A theoretical study of the H-bonded complexes of these three tautomers with water is also performed. Several structures have been found for each form and the results demonstrate that the closed complexes with two H-bonds are the most stable systems due to the H-bond cooperative effect.     

Structural Characteristics of Graphane‐Type C and BN Nanostructures by Periodic Local MP2 Approach

The structural characteristics of fully‐hydrogenated carbon and boron nitride mono‐ and multilayer slabs, together with nanotubes derived from the slabs, are investigated mainly by means of periodic local second‐order Møller–Plesset perturbation (LMP2) calculations and the results are compared with Hartree–Fock (HF), density functional theory (DFT), and dispersion function‐augmented DFT (DFT‐D) obtained ones. The investigated systems are structurally analogous to (111) and (110) slabs of diamond, where the hydrogenated (111) slab of diamond corresponds to the experimentally known graphane. Multilayering of monolayers and nanotubes is energetically favorable at the LMP2 level for both C and BN, while HF and DFT are not able to reproduce this behavior for CH systems. The work highlights the importance of utilizing methods capable of properly describing weak interactions in the investigation of dispersively‐bound systems such as the multilayered graphanes and the corresponding nanotubes.     

Modeling the amide I bands of small peptides

In this paper different floating oscillator models for describing the amide I band of peptides and proteins are compared with density functional theory (DFT) calculations. Models for the variation of the frequency shifts of the oscillators and the nearest-neighbor coupling between them with respect to conformation are constructed from DFT normal mode calculations on N-acetyl-glycine-N(')-methylamide. The calculated frequencies are compared with those obtained from existing electrostatic models. Furthermore, a new transition charge coupling model is presented. We suggest a model which combines the nearest-neighbor maps with long-range interactions accounted for using the new transition charge model and an existing electrostatic map for long-range interaction frequency shifts. This model and others, which account for the frequency shifts by electrostatic maps exclusively, are tested by comparing the predicted IR spectra with those from DFT calculations on the pentapeptide [Leu]-enkephalin. The new model described above gives the best agreement and, after a systematic blueshift is accounted for, reproduces the DFT frequencies to within 3.5 cm(-1). The correlation of the intensities for this model with intensities from DFT calculations is 0.94.     

Solvent effects on the S(N)2 reaction: Application of the density functional theory-based effective fragment potential method

The performance of the density functional theory (DFT)-based effective fragment potential (EFP) method is assessed using the S(N)2 reaction: Cl- + nH2O + CH3Br = CH3Cl + Br- + nH2O. The effect of the systematic addition of water molecules on the structures and relative energies of all species involved in the reaction has been studied. The EFP1 method is compared with second-order perturbation theory (MP2) and DFT results for n = 1, 2, and 3, and EFP1 results are also presented for four water molecules. The incremental hydration effects on the barrier height are the same for all methods. However, only full MP2 or MP2 with EFP1 solvent molecules are able to provide an accurate treatment of the transition state (TS) and hence the central barriers. Full DFT and DFT with EFP1 solvent molecules both predict central barriers that are too small. The results illustrate that the EFP1-based DFT method gives reliable results when combined with an accurate quantum mechanical (QM) method, so it may be used as an efficient alternative to fully QM methods in the treatment of larger microsolvated systems.     

Assessing the accuracy of quantum Monte Carlo and density functional theory for energetics of small water clusters

We present a detailed study of the energetics of water clusters (H(2)O)(n) with n ≤ 6, comparing diffusion Monte Carlo (DMC) and approximate density functional theory (DFT) with well converged coupled-cluster benchmarks. We use the many-body decomposition of the total energy to classify the errors of DMC and DFT into 1-body, 2-body and beyond-2-body components. Using both equilibrium cluster configurations and thermal ensembles of configurations, we find DMC to be uniformly much more accurate than DFT, partly because some of the approximate functionals give poor 1-body distortion energies. Even when these are corrected, DFT remains considerably less accurate than DMC. When both 1- and 2-body errors of DFT are corrected, some functionals compete in accuracy with DMC; however, other functionals remain worse, showing that they suffer from significant beyond-2-body errors. Combining the evidence presented here with the recently demonstrated high accuracy of DMC for ice structures, we suggest how DMC can now be used to provide benchmarks for larger clusters and for bulk liquid water.     

Analysis of vibrational spectra of chlorotoluene based on density function theory calculations

The conformational behavior and structural stability of chlorotoluene were investigated by utilizing ab initio calculations with 6-31G* basis set at restricted Hartree-Fock (RHF) and density function theory (DFT) levels. The vibrational frequencies of chlorotoluene were computed at the RHF and DFT levels. Complete vibrational assignments were made on the basis of normal coordinate calculations for stable conformer of the molecule. RHF results without scaled quantum mechanical (SQM) force field procedure considered are in bad agreement with experimental values. Of the five DFT methods, BLYP reproduces the observed fundamental frequencies most satisfactorily with the mean absolute deviation of the non-CH stretching modes less than 10 cm(-1). Two hybrid DFT methods are found to yield frequencies, which are generally higher than the observed fundamental frequencies. When the calculated results are compared with 'experimental' frequencies, B3LYP method is found to be slightly more accurate for C-H stretching modes. The results indicate that BLYP calculation is a very promising approach for understanding the observed spectral features.     

甲烷晶体的晶格能和弹性性质: 不同方法及泛函的评估

通过对甲烷晶体进行结构、晶格能和弹性特性的研究, 评估了不包含和包含色散能量修正的密度泛函理论的性能. 我们分别利用不包含色散能量修正的密度泛函理论(DFT) (包含不同的标准泛函和杂化泛函)和包含色散能量修正的密度泛函理论(DFT-D)计算了甲烷晶体特性, 并与实验作对比. 尽管DFT-D 与传统密度泛函理论及杂化密度泛函理论相比, 修正了甲烷晶体中的范德华(vdW)相互作用, 但是一些修正方案过分修正了这种相互作用. 因此, 人们在使用DFT-D方法时务必谨慎.     

An assessment of density functional methods for studying molecular adsorption in cluster models of zeolites

The performance of six density functional theory (DFT) methods has been tested for a zeolite cluster containing three tetrahedral atoms (3T) and the complexes it forms with water and methanol molecules. The DFT methods (BLYP, BP86, BPW91, B3LYP, B3P86, B3PW91) give results in good agreement with second-order perturbation theory (MP2). The results in this paper provide evidence of the suitability of DFT methods for studying hydrogen-bonded adsorption complexes in zeolites. Generally, the hybrid DFT methods are in closer agreement with experiment and MP2 than the pure DFT methods for geometrical parameters. The only exception is the Z⁻ geometry, perhaps due to its anionic character. All DFT methods give results in good overall agreement with MP2 for intramolecular geometrical parameters of the adsorption complexes, intramolecular vibrational frequencies, and adsorption energies. The B3LYP method gives intermolecular geometries and intermolecular vibrational frequencies which are closest to those obtained from the MP2 method. Thus, the B3LYP method seems to be the best choice for a density functional treatment of molecular adsorption in zeolite systems.     

Theoretical investigation of CO interaction with copper sites in zeolites: periodic DFT and hybrid quantum mechanical/interatomic potential function study

Periodic DFT and combined quantum mechanics/interatomic potential function (QM-pot) models were used to describe the interaction of CO with the Cu+ sites in FER. The CO stretching frequencies were calculated using omega(CO)(CCSD(T))/r(CO)(DFT) scaling method relating frequencies determined using a high-level quantum-chemical (coupled clusters) method for simple model carbonyls to CO bond lengths calculated using periodic DFT and QM-pot methods for the Cu+-zeolite system. Both periodic DFT and QM-pot models together with omega(CO)/r(CO) scaling describe the CO stretching dynamics with the "near spectroscopic accuracy", giving nu(CO) = 2156 cm(-1) in excellent agreement with experimental data. Calculations for various Cu+ sites in FER show that both types of Cu+ sites in FER (channel-wall sites and intersection sites) have the same CO stretching frequencies. Thus, the CO stretching frequencies are not site-specific in the CO/Cu+/FER system. The convergence of the results with respect to the model size was analyzed. When the same exchange-correlation functional is used the adsorption energies from periodic DFT and QM-pot are in good agreement (about 2 kcal/mol difference) but substantially larger than those of the experiment. The adsorption energy calculated with the B3LYP functional agrees with available experimental data. The overestimation of the adsorption energy in DFT calculations (periodic or QM-pot) is related to a red-shift of the CO stretching mode, both result from an underestimation of the HOMO(5sigma)-LUMO(2pi) gap of CO and the consequent overestimation of the Cu(+)(d)-CO(2pi*) back-donation. For the adsorption energy, this can be overcome by the use of hybrid B3LYP exchange-correlation functional. For the frequency calculations, the DFT problem can be overcome by the use of the omega(CO)(CCSD(T))/r(CO)(DFT) correlation.     

Benchmark calculations on the electron detachment energies of MO3* and M2O6* (M = Cr, Mo, W)

Neutral and anionic molecules of the monomers and dimers of the group VIB transition metal oxides (MO3 and M2O6) were studied with density functional theory (DFT) and coupled cluster CCSD(T) theory. Franck-Condon simulations of the photoelectron spectra were carried out for the transition from the ground state of the anion to that of the neutral molecule. Molecular structures from the DFT and CCSD(T) methods are compared. Electron detachment energies reported in the literature were evaluated. The calculated adiabatic and vertical electron detachment energies (ADEs and VDEs) were compared with the experimental results. CCSD(T) gives results within 0.12 eV for the ADEs. CCSD(T) predicts VDEs that are in error by as much as 0.3 eV for M = Cr. DFT hybrid functionals were found to give poor results for the ADEs and VDEs for M = Cr due to the substantial amount of multireference character in the wavefunction, whereas the pure DFT functionals give superior results. For M = Mo and W, excellent agreement was found for both CCSD(T) and many DFT fucntionals. The BP86 functional yields the best overall results for the VDEs of all the metal oxide clusters considered. Heats of formation calculated at the CCSD(T) level extrapolated to the complete basis set limit are also in good agreement with available experimental data.     

CASCI-DFT study of the phenalenyl radical system

We present ab initio complete-active-space configuration interaction (CASCI) density functional theory (DFT) study of the phenalenyl radical systems. Our approach employed in this study is based on the assumption that one-electron per one phenalenyl unit is responsible for magnetic properties of the phenalenyl radical dimeric compounds and that the residual correlation effects can be covered by DFT correlation potential for CASCI[2,2] wavefunction. The effective exchange integrals and lowest-lying excited energies of several phenalenyl dimeric compounds are calculated by CASCI[2,2]-DFT method. The implication of the computational results are discussed in relation with those of spin unrestricted Hartree–Fock (UHF), hybrid DFT, and pure DFT, and the experimental ones.     

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.     

QM/MM study of the absorption spectra of DsRed.M1 chromophores

We report geometries and vertical excitation energies for the red and green chromophores of the DsRed.M1 protein in the gas phase and in the solvated protein environment. Geometries are optimized using density functional theory (DFT, B3LYP functional) for the isolated chromophores and combined quantum mechanical/molecular mechanical (QM/MM) methods for the protein (B3LYP/MM). Vertical excitation energies are computed using DFT/MRCI, OM2/MRCI, and TDDFT as QM methods. In the case of the red chromophore, there is a general blue shift in the excitation energies when going from the isolated chromophore to the protein, which is caused both by structural changes and by electrostatic interactions with the environment. For the lowest ππ* transition, these two factors contribute to a similar extent to the overall DFT/MRCI shift of 0.4 eV. An enlargement of the QM region to include active‐site residues does not change the DFT/MRCI excitation energies much. The DFT/MRCI results are closest to experiment for both chromophores. OM2/MRCI and TDDFT overestimate the first vertical excitation energy by 0.3–0.5 and 0.2–0.4 eV, respectively, relative to the experimental or DFT/MRCI values. The experimental gap of 0.35 eV between the lowest ππ* excitation energies of the red (cis‐acylimine) and green (trans‐peptide) forms is well reproduced by DFT/MRCI and TDDFT (0.32 and 0.37 eV, respectively). A histogram spectrum for an equal mixture of the two forms, generated by OM2/MRCI calculations on 450 snapshots along molecular dynamics trajectories, matches the experimental spectrum quite well, with a gap of 0.23 eV and an overall blue shift of about 0.3 eV. DFT/MRCI appears as an attractive choice for calculating excitation energies in fluorescent proteins, without the shortcomings of TDDFT and computationally more affordable than CASSCF‐based approaches. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010