A density functional theory test study on the N2··· He dimer

 In the present contribution we report a study of the weakly bound van der Waals N₂–He molecule in the framework of the supermolecule approach by means of the PWPW and mPW1PW exchange–correlation functionals, using density functional theory local-spin-optimized atom-centered basis sets complemented with bond functions optimized at the mPW1PW level of theory. Calculations show that the mPW1PW functional using bond functions gives a realistic representation of the interaction-energy potentials for this van der Waals dimer, comparable to reference M?ller–Plesset perturbation theory calculations. In contrast, the PWPW functional is unable to describe the bonding properties of this system and all values of the bonding properties obtained at different geometries with this functional are considered out-of-scale compared with the rest of the calculations presented in this study. Received: 30 October 2000 / Accepted: 3 January 2001 / Published online: 3 April 2001     

Influence of impurity elements on the corrosion of α-uranium surface: a density functional theory study

Journal of Radioanalytical and Nuclear Chemistry - Influence of substitutional Fe, Al and Mg atoms on the corrosion of α-U(110) surface was studied by DFT?+?U method. The...     

A density functional theory study of the ��mythic�� Lindlar hydrogenation catalyst

A Lindlar catalyst is a popular heterogeneous catalyst that consists of 5?wt.% palladium supported on porous calcium carbonate and treated with various forms of lead and quinoline. The additives strategically deactivate palladium sites. The catalyst is widely used for the partial hydrogenation of acetylenic compounds in organic syntheses. Alkyne reduction is stereoselective, occurring via syn addition to give the cis-alkene. Even if it has been employed for about 60?years, there is a lack of molecular level understanding of the Lindlar catalyst. We have applied density functional theory simulations to understand the structure and the nature of the interplay between the multiple chemical modifiers in the Lindlar catalyst. Indeed, the poisons influence different parameters controlling selectivity to the alkene: Pb modifies the thermodynamic factor and hinders the formation of hydrides, while quinoline isolates Pd sites thus minimizing oligomerization.     

Calculation study on complex formation of catechins with β-cyclodextrin using density function theory

Journal of Inclusion Phenomena and Macrocyclic Chemistry - The inclusion of catechins with cyclodextrin (CD) is performed for the purpose of improving the water solubility and reducing the...     

Application of capillary affinity electrophoresis and density functional theory to the investigation of valinomycin–lithium complex

Capillary affinity electrophoresis (CAE) and quantum mechanical density functional theory (DFT) have been applied to the investigation of interactions of valinomycin (Val), a macrocyclic dodecadepsipeptide antibiotic ionophore, with lithium cation Li⁺. Firstly, from the dependence of effective electrophoretic mobility of Val on the Li⁺ ion concentration in the background electrolyte (BGE) (methanolic solution of 50 mM chloroacetic acid, 25 mM Tris, pH_MeOH 7.8, 0–40 mM LiCl), the apparent binding (stability) constant (K_b) of Val–Li⁺ complex in methanol was evaluated as log K_b = 1.50 ± 0.24. The employed CAE method include correction of the effective mobilities measured at ambient temperature, at different input power (Joule heating) and at variable ionic strength of the BGEs to the mobilities related to the reference temperature 25 °C and to the constant ionic strength 25 mM. Secondly, using DFT calculations, the most probable structures of the non-hydrated Val–Li⁺ and hydrated Val–Li⁺·3H₂O complex species were predicted.     

A theoretical study of CO adsorption on gold by Hückel theory and density functional theory calculations

It is crucial to understand the nature of CO adsorption on gold so as to elucidate the mechanism of low-temperature CO oxidation on nanogold catalysts. We performed theoretical analysis of CO adsorption on gold by using Hückel theory and density functional theory (DFT) calculations. Hückel theory indicates that CO adsorption on gold is dominated by the electron distribution at the Au atom, which is greatly affected by neighboring Au atoms, coadsorbed or doping species. The increase of σ-bonding electrons should weaken the CO adsorption, while the increase of π-electrons should strengthen the adsorption. DFT calculations proved this prediction quantitatively for various systems, including CO adsorption on a Au(100)-hex surface with locally varying subsurface configurations and CO coadsorption with acceptor or donor species.     

Concurrent cyclopropanation by carbenes and carbanions? A density functional theory study on the reaction pathways

The mechanisms for the addition reactions of phenylhalocarbenes and phenyldihalomethide carbanions with acrylonitrile (ACN) and trimethylethylene (TME) have been investigated using an ab initio BH and HLYP/6-31G (d, p) level of theory. Solvent effects on these reactions have been explored by calculations that included a polarizable continuum model (PCM) for the solvent (THF). These model calculations show that for the addition of phenylhalocarbenes, a TME species may readily undergo addition reactions with carbenes while ACN has a high-energy barrier to overcome. It was also found that phenyldihalomethide carbanions do not readily add to the electron-rich TME. The cyclopropane yields only appear to occur via addition of PhCBr to TME. However, the cyclopropanation proceeds not only via slow addition of phenylhalocarbenes to ACN but also forms through the stepwise reaction of phenyldihalomethide carbanions with ACN. Our calculation results are in good agreement with experimental observations (Moss, R.A.; Tian, J.-Z. J. Am. Chem. Soc. 2005, 127, 8960) that indicate that the cyclopropanation of phenylhalocarbenes and phenyldihalomethide carbanions with ACN are concurrent in THF.     

Comparison study of several numerical integration schemes used in calculations of density functional theory

Several numerical integration schemes for the evaluation of matrix elements in density functional theory calculations have been studied and compared by computational practice. The best scheme was found to be the combination of the atomic partition function proposed by Becke with the scaled generalized Gauss-Laguerre quadrature formula for radial integration suggested by Yang, which achieve the highest convergence rate to the numerical integration. With the same number of integration points, the accuracy of the calculated results by this scheme is higher by 1 to 2 orders of magnitudes than that by other schemes. The reason for achieving higher accuracy by this scheme has been proposed preliminarily.     

Fluorine as a Lewis acid: A symmetry-adapted perturbation theory based on density functional theory and interacting quantum atoms study of noncovalent interactions in the NCF⋯NH3 complex

Different computational methods are used to investigate the nature of interaction in the NCF⋯NH₃ model complex, in which the fluorine atom acts as a Lewis acid and forms a noncovalent bond with the ammonia (Lewis base). Symmetry-adapted perturbation theory based on density functional theory (SAPT(DFT)) indicates that the noncovalent interaction in the NCF⋯NH₃ complex is mainly electrostatics. However, dispersion and induction terms also play important roles. Although fluorine noncovalent interactions are typically classified as halogen bonds, they are somewhat different from the well-known halogen bonds of iodine, bromine, and chlorine. The halogen bonds of NCCl⋯NH₃ and NCBr⋯NH₃ are directional and the C  X  N (X = Cl or Br) angle tends to be linear. In contrast, the fluorine interaction in NCF⋯NH₃ is not directional; the interaction energy shows no sensitivity to the angular (C  F  N ) distortions, and the energy profile is flat over a wide angular range (from 180° to about 140° ). However, for the angles less than 130° , the energy curve shows a clear angular dependence and the interaction between NCF and NH₃ becomes stronger as the C  F  N angle decreases. It seems that at the tighter angles, a tetrel-bonded NCF⋯NH₃ complex is preferred. Moreover, interacting quantum atoms (IQA) analysis shows that the competition between different intra-atomic and interatomic interactions determines the geometry of NCF⋯NH₃ complex.     

A DFT study on the effect of hydrogen bonding on the reaction of a μ-benzoquinone diruthenium complex with acetylene

A DFT study was carried out to investigate the reaction mechanisms of a model μ-benzoquinone diruthenium complex {CpRu(μ-H)}₂(μ-η²:η²-C₆H₄O₂), derived from the experimental compound {Cp*Ru(μ-H)}₂(μ-η²:η²-C₆H₃RO₂) (R = H or R = Me, Cp* = η⁵-C₅Me₅), with acetylene both in aprotic and protic solvents. Results of calculations show that the influence of the solvent methanol on the reaction is mainly on the step of acetylene coordination. Enhanced hydrogen bonding is the reason for acceleration of the reaction in protic solvent, which is supported by NBO charge analysis.     

Ab initio density functional theory: the best of both worlds?

Density functional theory (DFT), in its current local, gradient corrected, and hybrid implementations and their extensions, is approaching an impasse. To continue to progress toward the quality of results demanded by today's ab initio quantum chemistry encourages a new direction. We believe ab initio DFT is a promising route to pursue. Whereas conventional DFT cannot describe weak interactions, photoelectron spectra, or many potential energy surfaces, ab initio DFT, even in its initial, optimized effective potential, second-order many-body perturbation theory form [OEP (2)-semi canonical], is shown to do all well. In fact, we obtain accuracy that frequently exceeds MP2, being competitive with coupled-cluster theory in some cases. Furthermore, this is accomplished within a relatively fast computational procedure that scales like iterative second order. We illustrate our results with several molecular examples including Ne2,Be2,F2, and benzene.     

The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study

We report the performance of eight density functionals (B3LYP, BPW91, OLYP, O3LYP, M06, M06-2X, PBE, and SVWN5) in two Gaussian basis sets (Wachters and Partridge-1 on iron atoms; cc-pVDZ on the rest of atoms) for the prediction of the isomer shift (IS) and the quadrupole splitting (QS) parameters of M?ssbauer spectroscopy. Two sources of geometry (density functional theory-optimized and X-ray) are used. Our data set consists of 31 iron-containing compounds (35 signals), the M?ssbauer spectra of which were determined at liquid helium temperature and where the X-ray geometries are known. Our results indicate that the larger and uncontracted Partridge-1 basis set produces slightly more accurate linear correlations of electronic density used for the prediction of IS and noticeably more accurate results for the QS parameter. We confirm and discuss the earlier observation of Noodleman and co-workers that different oxidation states of iron produce different IS calibration lines. The B3LYP and O3LYP functionals have the lowest errors for either IS or QS. BPW91, OLYP, PBE, and M06 have a mixed success whereas SVWN5 and M06-2X demonstrate the worst performance. Finally, our calibrations and conclusions regarding the best functional to compute the M?ssbauer characteristics are applied to candidate structures for the peroxo and Q intermediates of the enzyme methane monooxygenase hydroxylase (MMOH), and compared to experimental data in the literature.     

The impact of dihydrogen phosphate anions on the excited-state proton transfer of harmane. Effect of β-cyclodextrin on these photoreactions

Photoinduced proton transfer reactions of harmane (1-methyl-9H-pyrido[3,4-b]indole) (HAR) in the presence of a proton donor/acceptor such as dihydrogen phosphate anions in aqueous solution have been studied by stationary and time-resolved fluorescence spectroscopy. The presence of high amounts of dihydrogen phosphate ions modifies the acid/base properties of this alkaloid. Thus, by keeping the pH constant at pH 8.8 and by increasing the amount of NaH(2)PO(4) in the solution, it is possible to reproduce the same spectral profiles as those obtained in high alkaline solutions (pH >12) in the absence of NaH(2)PO(4). Under these conditions, a new fluorescence profile appears at around 520 nm. This result could be related to the results of a recent investigation which suggests that a high intake of phosphates may promote skin tumorigenesis. The presence of β-cyclodextrin (β-CD) avoids the proton transfer reactions in this alkaloid by means the formation of an inclusion complex between β-CD and HAR. The formation of this complex originates a remarkable enhancement of the emission intensity from the neutral form in contrast to the cationic and zwitterionic forms. A new lifetime was obtained at 360 nm (2.5 ns), which was associated with the emission of this inclusion complex. At this wavelength, the fluorescence intensity decay of HAR can be described by a linear combination of two exponentials. From the ratio between the pre-exponential factors, we have obtained a value of K = 501 M for the equilibrium of formation of this complex.     

Effect of intermolecular O-H ⋯ O hydrogen bonding on the molecular structure of phenol: An ab initio molecular orbital study

The effect of intermolecular O-H O hydrogen bonding on the molecular structure of phenol has been studied by SCF ab initio MO calculations at the HF/6-31G * level. The systems investigated are eight phenol-water complexes and the dimer and trimer of phenol. Optimized geometries show that hydrogen bond formation causes a consistent pattern of changes in the structure of the molecule. When phenol acts as a proton donor, the expected increase ofr (O-H) is accompanied by a slight decrease ofr(C-O) and of the internal ring angles at theipso andpara positions, and by an increase ofr(C _ipso © _ortho ). These changes suggest that the relative contribution of polar canonical forms to the electronic structure of the molecule increases upon hydrogen bond formation, since this enhances the strength of the interaction. The opposite changes occur when phenol acts as a proton acceptor, except forr(O-H), which is the same as in the free molecule. If phenol acts as a proton donorand as a proton acceptor, the two hydrogen bonds become stronger due to a synergic effect. In this case, however, the structural deformation of the molecule is less pronounced than in the previous cases, due to the opposite effect of the two hydrogen bonds. The available experimental evidence on gas-crystal structural differences for phenol is critically reviewed, also in the light of the present results on gas-phase complexes.     

A density functional theory study of the Cu+·(CO)n (n = 1–3) complexes

Density functional theory calculations, with an effective core potential for the copper ion, and large polarized basis set functions have been used to construct the potential energy surface of the Cu⁺·(CO)_n (n = 1–3) complexes. A linear configuration is obtained for the global minimum of the Cu⁺·CO and Cu⁺·(CO)₂ complexes with a bond dissociation energy (BDE) of 35.9 and 40.0 kcal mol^-1, respectively. For the Cu⁺·(CO)₃ complex, a trigonal planar geometry is obtained for the global minimum with a BDE of 16.5 kcal mol^?1. C-coordinated copper ion complexes exhibit stronger binding energy than O-coordinated complexes as a result of C_lp → 4s σ-donation. The computed sequential BDEs of Cu⁺·(CO)_n (n = 1–4) complexes agree well with experimental findings, in which the electrostatic energy and σ-donation play an important role in the observed trend.     

Excited-state N-H···S hydrogen bond between indole and dimethyl sulfide: time-dependent density functional theory study

The intermolecular hydrogen bond N-H···S between indole and dimethyl sulfide is theoretically investigated. The formation of N-H···S hydrogen bonds between indole and dimethyl sulfide in ground and excited states is confirmed by the analysis of geometric structure, Mulliken charge, and infrared spectra. The result shows that the S(1) state of hydrogen bonded indole-Me(2)S is mainly a charger transfer state, while the S(2) state is a local excited state and also the state corresponding to the experiment. More importantly, it is demonstrated that the intermolecular hydrogen bond N-H···S of indole-Me(2)S is strengthened in the S(1) and S(2) states compared to that in ground state. Moreover, the strengthening of intermolecular N-H···S hydrogen bond in excited state induces the fluorescence emission peak of indole shifts to the red. These findings may provide insights for further study of N-H···S hydrogen bonds existing in many biomolecular systems.     

Modelling the metal atom positions of the Photosystem II water oxidising complex: a density functional theory appraisal of the 1.9 Å resolution crystal structure

Density functional theory (DFT) calculations are reported for a set of model compounds intended to represent the structure of the Photosystem II (PSII) water oxidising complex (WOC) as determined by the recent 1.9 ? resolution single crystal X-ray diffraction (XRD) study of Umena et al. In contrast with several other theoretical studies addressing this structure, we find that it is not necessary to invoke photoreduction of the crystalline sample below the S(1)'resting state' in order to rationalise the observed WOC geometry. Our results are consistent with crystallised PSII in the S(1) state, with S(1) corresponding to either (Mn(III))(4) or (Mn(III))(2)(Mn(IV))(2) as required by the two competing paradigms for the WOC oxidation state pattern. Of these two paradigms, the 'low-oxidation-state' paradigm provides a better match for the crystal structure, with the comparatively long Mn(2)-Mn(3) distance in particular proving difficult to reconcile with the 'high-oxidation-state' model. Best agreement with the set of metal-metal distances is obtained with a S(1) model featuring μ-O, μ-OH bridging between Mn(3) and Mn(4) and deprotonation of one water ligand on Mn(4). Theoretical modelling of the 1.9 ? structure is an important step in assessing the validity of this recent crystal structure, with implications for our understanding of the mechanism of water oxidation by PSII.     

Intermolecular potentials of the methane dimer calculated with Møller-Plesset perturbation theory and density functional theory

We have calculated the intermolecular interaction potentials of the methane dimer at the minimum-energy D(3d) conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order M?ller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with the Perdew-Wang (PW91) functional as the exchange or the correlation part. The HF calculations yield unbound potentials largely due to the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater-type orbitals fitted with Gaussian functions (STO-nG) (n=3-6) [Quantum Theory of Molecular and Solids: The Self-Consistent Field for Molecular and Solids (McGraw-Hill, New York, 1974), Vol. 4], Pople's medium size basis sets of Krishnan et al. [J. Chem. Phys. 72, 650 (1980)] [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets [J. Chem. Phys. 90, 1007 (1989)] (cc-pVXZ and aug-cc-pVXZ) (X=D, T, and Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(2d,2p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy (approximately 0.01 kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the destined C6 value from molecular polarizability calculations. The slow convergence could indicate the inefficacy of using the MP2 calculations with Gaussian-type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the destined potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energy calculated using the PW91PW91 functional and the equilibrium bond length calculated using the PW91VP86 functional are close to the MP2 results at the basis set limit.     

Application of density functional theory and optical spectroscopy for the prediction of the photophysical properties of Р-pyridylphospholanes

Russian Chemical Bulletin - The spatial and electronic structure of a series of pyridyl-containing phospholanes, which are potential ligands for the synthesis of luminescent transition metal...