Electron paramagnetic resonance and Mössbauer spectroscopy and density functional theory analysis of a high-spin Fe(IV)-oxo complex

High-spin Fe(IV)-oxo species are known to be kinetically competent oxidants in non-heme iron enzymes. The properties of these oxidants are not as well understood as the corresponding intermediate-spin oxidants of heme complexes. The present work gives a detailed characterization of the structurally similar complexes [Fe(IV)H(3)buea(O)](-), [Fe(III)H(3)buea(O)](2-), and [Fe(III)H(3)buea(OH)](-) (H(3)buea = tris[(N'-tert-butylureaylato)-N-ethylene]aminato) using M?ssbauer and dual-frequency/dual-mode electron paramagnetic resonance (EPR) spectroscopies. The [Fe(IV)H(3)buea(O)](-) complex has a high-spin (S = 2) configuration imposed by the C(3)-symmetric ligand. The EPR spectra of the [Fe(IV)H(3)buea(O)](-) complex presented here represent the first documented examples of an EPR signal from an Fe(IV)-oxo complex, demonstrating the ability to detect and quantify Fe(IV) species with EPR spectroscopy. Quantitative simulations allowed the determination of the zero-field parameter, D = +4.7 cm(-1), and the species concentration. Density functional theory (DFT) calculations of the zero-field parameter were found to be in agreement with the experimental value and indicated that the major contribution to the D value is from spin-orbit coupling of the ground state with an excited S = 1 electronic configuration at 1.2 eV. (17)O isotope enrichment experiments allowed the determination of the hyperfine constants ((17)O)A(z) = 10 MHz for [Fe(IV)H(3)buea(O)](-) and ((17)O)A(y) = 8 MHz, ((17)O)A(z) = 12 MHz for [Fe(III)H(3)buea(OH)](-). The isotropic hyperfine constant (((17)O)A(iso) = -16.8 MHz) was derived from the experimental value to allow a quantitative determination of the spin polarization (ρ(p) = 0.56) of the oxo p orbitals of the Fe-oxo bond in [Fe(IV)H(3)buea(O)](-). This is the first experimental determination for non-heme complexes and indicates significant covalency in the Fe-oxo bond. High-field M?ssbauer spectroscopy gave an (57)Fe A(dip) tensor of (+5.6, +5.3, -10.9) MHz and A(iso) = -25.9 MHz for the [Fe(IV)H(3)buea(O)](-) complex, and the results of DFT calculations were in agreement with the nuclear parameters of the complex.     

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...     

Electron magnetic resonance and density functional theory study of room temperature X-irradiated β-D-fructose single crystals

Stable free radical formation in fructose single crystals X-irradiated at room temperature was investigated using Q-band electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three main crystallographic planes allowed an unambiguous determination of 12 proton HFC tensors. From the EIE studies, these hyperfine interactions were assigned to six different radical species, labeled F1-F6. Two of the radicals (F1 and F2) were studied previously by Vanhaelewyn et al. [Vanhaelewyn, G. C. A. M.; Pauwels, E.; Callens, F. J.; Waroquier, M.; Sagstuen, E.; Matthys, P. J. Phys. Chem. A 2006, 110, 2147.] and Tarpan et al. [Tarpan, M. A.; Vrielinck, H.; De Cooman, H.; Callens, F. J. J. Phys. Chem. A 2009, 113, 7994.]. The other four radicals are reported here for the first time and periodic density functional theory (DFT) calculations were used to aid their structural identification. For the radical F3 a C3 carbon centered radical with a carbonyl group at the C4 position is proposed. The close similarity in HFC tensors suggests that F4 and F5 originate from the same type of radical stabilized in two slightly different conformations. For these radicals a C2 carbon centered radical model with a carbonyl group situated at the C3 position is proposed. A rather exotic C2 centered radical model is proposed for F6.     

The importance of Colle–Salvetti for computational density functional theory

The purpose of this presentation is to show the importance of the Colle–Salvetti (Theor Chim Acta 37:329, 1975) paper in the development of modern computational density functional theory. To do this we cover the following topics (1) the Bright Wilson understanding (2) the Kohn–Sham equations (3) local density exchange (4) the exchange-hole (5) generalised gradient approximation for exchange (Becke and Cohen) (6) left–right correlation and dynamic correlation (7) the development of the Lee–Yang–Parr dynamic correlation functional from the Colle–Salvetti paper (8) the early success of GGA DFT. Finally we observe that the the BLYP and OLYP exchange-correlation functionals are not semi-empirical; this may explain their great success.     

Ultrafast excited state dynamics and spectroscopy of 13,13'-diphenyl-β-carotene

Ultrafast transient broadband absorption spectroscopy based on the Pump-Supercontinuum Probe (PSCP) technique has been applied to characterize the excited state dynamics of the newly-synthesized artificial β-carotene derivative 13,13'-diphenyl-β-carotene in the wavelength range 340-770 nm with ca. 60 fs cross-correlation time after excitation to the S(2) state. The influence of phenyl substitution at the polyene backbone has been investigated in different solvents by comparing the dynamics of the internal conversion (IC) processes S(2)→ S(1) and S(1)→ S(0)* with results for β-carotene. Global analysis provides IC time constants and also time-dependent S(1) spectra demonstrating vibrational relaxation processes. Intramolecular vibrational redistribution processes are accelerated by phenyl substitution and are also solvent-dependent. DFT and TDDFT-TDA calculations suggest that both phenyl rings prefer an orientation where their ring planes are almost perpendicular to the plane of the carotene backbone, largely decoupling them electronically from the polyene system. This is consistent with several experimental observations: the up-field chemical shift of adjacent hydrogen atoms by a ring-current effect of the phenyl groups in the (1)H NMR spectrum, a small red-shift of the S(0)→ S(2)(0-0) transition energy in the steady-state absorption spectrum relative to β-carotene, and almost the same S(1)→ S(0)* IC time constant as in β-carotene, suggesting a similar S(1)-S(0) energy gap. The oscillator strength of the S(0)→ S(2) transition of the diphenyl derivative is reduced by ca. 20%. In addition, we observe a highly structured ground state bleach combined with excited state absorption at longer wavelengths, which is typical for an "S* state". Both features can be clearly assigned to absorption of vibrationally hot molecules in the ground electronic state S(0)* superimposed on the bleach of room temperature molecules S(0). The S(0)* population is formed by IC from S(1). These findings are discussed in detail with respect to alternative interpretations previously reported in the literature. Understanding the dynamics of this type of artificial phenyl-substituted carotene systems appears useful regarding their future structural optimization with respect to enhanced thermal stability while keeping the desired photophysical properties.     

Raman spectroscopy and structural properties of InxBi40−xSe60 system

In_xBi_40−xSe₆₀ (x = 1.6, 4.4, 7, 10 and 13.2) alloys were synthesized by melt-quenching technique. The X-ray diffraction and Raman spectroscopy investigations confirm that the materials are in single phase. Archimedes method and Energy Dispersive Spectroscopy (EDS) have been used for density and chemical characterization of the obtained materials. Indium content dependences of different parameters such as the density (D), the compactness (δ), and the average coordination number (Z) have been investigated and discussed in light of chemical order network and topological models.     

Molecular dynamics, density functional and second-order Møller–Plesset theory study of the structure and conformation of acetylcholine in vacuo and in solution

 Molecular mechanics minimizations based on the CVFF force field and molecular dynamics simulation for a time of 2.5 ns were performed to examine the conformational behaviour and the molecular motion of acetylcholine in vacuo and in aqueous solution. Five low-lying conformations, namely the TT, TG, GG, G*G and GT, were obtained from molecular mechanics computations with the GT structure as the absolute minimum. Molecular dynamics trajectories in vacuo and in water show that only four (GT, GG, G*G and TG) and three (TG, TT and GT) conformations are present in the simulation time, respectively. Density functional B3LYP and second-order M?ller–Plesset (MP2) methods were then used to study all the five lowest-lying conformers of acetylcholine neurotransmitter in vacuo and in water by the polarizable continuum model approach. The B3LYP and MP2 computations show that in the gas phase all minima lie in a narrow range of energy with the G*G conformer as the most stable one. The relative minima GG, GT, TG and TT are located at 1.1 (3.3), 1.8 (4.2), 2.1 (4.5) and 4.3 (7.3) kcal/mol above the absolute one at the B3LYP (MP2) level. The preferred conformation in water is the TG. Solvation reduces the relative energy differences between the five minima in both computations. Received: 4 April 2001 / Accepted: 5 July 2001 / Published online: 30 October 2001     

Identifying promising metal–organic frameworks for heterogeneous catalysis via high-throughput periodic density functional theory

Metal–organic frameworks (MOFs) are a class of nanoporous materials with highly tunable structures in terms of both chemical composition and topology. Due to their tunable nature, high-throughput computational screening is a particularly appealing method to reduce the time-to-discovery of MOFs with desirable physical and chemical properties. In this work, a fully automated, high-throughput periodic density functional theory (DFT) workflow for screening promising MOF candidates was developed and benchmarked, with a specific focus on applications in catalysis. As a proof-of-concept, we use the high-throughput workflow to screen MOFs containing open metal sites (OMSs) from the Computation-Ready, Experimental MOF database for the oxidative C—H bond activation of methane. The results from the screening process suggest that, despite the strong C—H bond strength of methane, the main challenge from a screening standpoint is the identification of MOFs with OMSs that can be readily oxidized at moderate reaction conditions. © 2019 Wiley Periodicals, Inc.     

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.     

Structure–antioxidant activity relationships of dendrocandin analogues determined using density functional theory

Structural Chemistry - Quantum-chemical calculations based on the density functional theory (DFT) at the B3LYP/6–311?+?+?G(2d,2p)//B3LYP/6–31G(d,p) level were employed...     

Vibrational spectroscopy investigation using ab initio and density functional theory on 3′-chloropropiophenone and 3′-nitropropiophenone

The FTIR and FT Raman spectra of 3′-chloropropiophenone and 3′-nitropropiophenone have been recorded in the regions 4000–400 and 3500–100 cm^?1 respectively. The optimized geometry, frequency and intensity of the vibrational bands of 3′-chloropropiophenone and 3′-nitropropiophenone were obtained by ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-31G (d,p) basis set. A complete vibrational assignment aided by the theoretical harmonic frequency analysis has been proposed. The harmonic vibrational frequencies calculated have been compared with experimental FTIR and FT Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed simulated spectrograms.     

Probing the metal-to-ligand charge transfer first excited state in (η6-naphthalene)Cr(CO)3 and (η6-phenanthrene)Cr(CO)3 by resonance Raman spectroscopy and density functional theory calculations

The nature of the lowest energy optical transition for the complexes (η(6)-naphthalene)Cr(CO)(3) and (η(6)-phenanthrene)Cr(CO)(3) in the solid state has been investigated by Raman spectroscopy using a range of different excitation wavelengths progressively approaching the resonant condition. Examination of the resonantly enhanced Raman modes confirms that the first absorption is attributed predominantly to a metal-to-arene charge transfer transition for both complexes. A notable difference in the photochemistry of the two complexes was observed. In the case of the phenanthrene complex, population of the lowest energy excited state leads to a photochemical process which resulted in the loss of the arene ligand and formation of Cr(CO)(6).     

Molecular electronegativity in density functional theory (II) --Direct calculation of group electronegativity and the atomic charges in a group

On the basis of a more precise expression of the atomic effective electronegativity deduced from the density functional theory and electronegativity equalization principle, a new scheme for calculating the group electronegativity and the atomic charges in a group is proposed and programed, and various parameters of electronegativity and hardness are given for some common atoms. Through calculation, analysis and comparison of more than one hundred groups, it is shown that the results from this scheme are reasonable and may be extended.     

Effects of H-bonding and structural constituents on the acidity and potential "anticancer activity" of D-mandelonitrile-β-D-glucuronic acid by density functional theory

Research on Chemical Intermediates - Laetrile (D-mandelonitrile-β-D-glucuronic acid, 1COOH) is being promoted, more and more, as an alternate cancer treatment, in many countries. Here we show...     

Assessment of the Van Voorhis–Scuseria exchange–correlation functional for predicting excitation energies using time-dependent density functional theory

We assess the performance of the Van Voorhis–Scuseria exchange–correlation functional (VSXC), a kinetic-energy-density-dependent exchange–correlation functional recently developed in our group, for calculating vertical excitation energies using time-dependent density functional theory in a benchmark set of molecules. Overall, VSXC performs very well, with accuracy similar to that of hybrid functionals such as the hybrid Perdew–Burke–Ernzerhof functional and Becke's three parameter hybrid method with the Lee, Yang, and Parr correlation functional, which contain a portion of Hartree–Fock exchange. Received: 29 December 1999 / Accepted: 5 June 2000 / Published online: 11 September 2000     

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.     

Surface-enhanced Raman scattering of M2–pyrazine–M2 (M = Cu,Ag, Au): Analysis by natural perturbation orbitals and density functional theory functional dependence

Here, we propose a new method to analyze various electronic properties of molecules based on natural perturbation orbitals (NPOs). We applied the proposed method to chemical enhancement of the surface-enhanced Raman scattering (SERS) intensity of M₂–pyrazine–M₂ (M = Cu, Ag, Au) complexes. The SERS intensity can be effectively decomposed into the contributions of four NPO pairs (1σ–1σ*, 2σ–2σ*, 1π–1π*, and 2π–2π*), so NPO analysis makes the SERS intensity much easier to understand than by conventional canonical molecular orbitals. Moreover, we analyzed the dependence of the density functional theory functional on the SERS intensity. For the Ag₂–pyrazine–Ag₂ complex, the BP86 functional overestimates the Raman intensity by about 23 times compared with coupled-cluster singles and doubles level of theory, while the CAM-B3LYP functional gives moderately accurate values. This overestimation arises from the inaccuracy of the energy derivative along the normal vibrational mode.     

A density functional theory investigation of CrSin (n=1–6) clusters

Clusters of the form CrSi_n (n=1–6) were investigated computationally using a density functional approach. In particular, geometry optimizations were carried out under the constraint of well-defined point group symmetries at the B3LYP level employing a pseudopotential method in conjunction with double zeta basis sets. In this article, the resulting total energies, Mulliken atomic net populations, overlap populations, fragmentation energies and geometries of CrSi_n (n=1–6) are presented and discussed, together with natural populations and natural electron configurations. In addition, we comment on the charge transfer within the clusters. From this analysis, the 3d orbital of the Cr atom in CrSi_n (n=1–6) cluster absorbs electrons. From this tendency, conclusions are drawn with respect to the electronic populations and the chemical bond between Si and Cr as well as Si and Si.     

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.