Synthesis, crystal structures and density functional theory study of dimeric copper(II) complexes of a tridentate Schiff-base ligand

Oxalate- or 4,4′-bipyridine-bridged dimeric copper(II) complexes, [Cu₂L₂(μ-ox)] (1) and [Cu₂L₂(μ-bipy)](BF₄)₂ (2) [where ox = oxalate, bipy = 4,4′-bipyridine, HL = N-(1H-pyrrol-2-ylmethylene)-2-pyridineethanamine, L⁻ = HL−H⁺], have been synthesised and characterised by elemental analysis, IR, UV-Vis and single crystal X-ray diffraction. Crystal structure determinations carried out on 1 and 2 reveal that 1 is an oxalate-bridged centrosymmetrical square pyramidal dimeric copper(II) complex while 2 is a 4,4′-bipyridine-bridged non-centrosymmetric square planar dinuclear copper(II) complex. Comparison of the optimised geometries with the corresponding crystal structures suggests that the B3LYP/LANL2DZ level can reproduce the structures of 1 and 2 on the whole. The electronic spectra of 1 and 2 predicted by B3LYP/LANL2DZ method show some blue shifts compared with their experimental data. Thermal analysis carried out on 1 shows that there is only one exothermal peak at about 260 °C and the residue is presumably Cu₂O₄N₆.     

Time-dependent density functional calculations of ligand K-edge X-ray absorption spectra

The Cl K-edge spectra of a series of metal tetrachloride complexes have been simulated using a simple TD-DFT based protocol. The influence of the chosen density functional, relativistics, basis set, and solvation has been systematically investigated. The results show that good agreement between the calculated spectra and the relative experimental energies and intensities can be achieved by using the BP86 functional with standard polarized triple-ζ basis sets (such as the TZVP basis of Ahlrichs’s and co-workers). Calculated energies and intensities are improved by using the more flexible CP(PPP) basis set on the metal atom. The inclusion of scalar-relativistic effects or solvation does not yield any significant improvement in the results. The subtleties arising from the incorporation of electric quadrupole and magnetic dipole intensity contributions into the calculations are discussed in some detail, and the contributions are shown to be negligible (∼1%) at the Cl K-edge.     

Theoretical studies on the absorption spectra of heteroleptic ruthenium polypyridyl dyes for nanocrystalline TiO2 solar cells: Revisited with transition-component analysis

The absorption spectra of Ru complexes of the type cis-[Ru(H₂dcbpy)(L)(NCS)₂], where H₂dcbpy = 4,4′-dicarboxy-2,2′-bipyridine and L = 1,10-phenanthroline (phen) (1) or dipyrido[3,2-a:2′,3′-c]phenazine (dppz) (2), in water were calculated by means of the time-dependent density functional theory, and the calculated spectra were subjected to transition-component analysis. Comparison of the calculated spectra of protonated, partially and fully deprotonated, and electrostatically non-compensated and fully compensated forms of 1 and 2 in water with the corresponding experimental absorption spectra in 0.01 M aqueous NaOH indicated that the predominant molecular structures are fully deprotonated anionic structures that are fully compensated with counter cations. The shapes of the calculated absorption spectra well reproduce the shapes of the corresponding experimental spectra in detail over the entire visible region. The calculated results indicated that the difference between the performances of 1- and 2-sensitized solar cells is due to differences in the contributions of the various electronic excitations that make up the absorption spectra. Transition-component analysis provided a detailed, quantitative explanation of the components of the absorption spectra of 1 and 2 and may be useful for the design and synthesis of improved sensitizers for high-performance dye-sensitized solar cells.     

Ab initio study of phenyl benzoate: structure,conformational analysis,dipole moment,IR and Raman vibrational spectra

The molecular structure (bond distances and angles), conformational properties, dipole moment and vibrational spectroscopic data (vibrational frequencies, IR and Raman intensities) of phenyl benzoate were calculated using Hartree–Fock (HF), density functional (DFT), and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6-31G* to 6-311++G**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2, B3LYP and B3PW91 levels with basis sets including diffuse functions. The B3LYP/6-31+G* theory level estimates the shape of the experimental functions for phenyl torsion around the Ph–O and Ph–C bonds well, but reproduces the height of the rotational barriers poorly. The B3LYP/6-31+G* harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported. They are in excellent agreement with experimental IR and Raman spectra.Figure Calculated and experimental (GED) potential energy functions for torsional motion of phenyl benzoate relative to the minimum value. a The potential function for torsion about the O₃–C₄ bond. b The potential function for torsion about the C₂–C₁₀ bond.     

Time-dependent density functional theory-assisted absolute configuration determination of cis-dihydrodiol metabolite produced from isoflavone by biphenyl dioxygenase

Escherichia coli cells containing the biphenyl dioxygenase genes bphA1A2A3A4 from Pseudomonas pseudoalcaligenes KF707 were found to biotransform isoflavone and produced a metabolite that was not found in a control experiment. Liquid chromatography/mass spectrometry (LC/MS) and ¹H and ¹³C nuclear magnetic resonance (NMR) analyses indicated that biphenyl dioxygenase induced 2′,3′-cis-dihydroxylation of the B-ring of isoflavone. In a previous report, the same enzyme showed dioxygenase activity toward flavone, producing flavone 2′,3′-cis-dihydrodiol. Due to growing interest in flavone chemistry and the absolute configuration of natural products, time-dependent density functional theory (TD-DFT) calculations were combined with circular dichroism (CD) spectroscopy to determine the absolute configuration of the isoflavone dihydrodiol. By computational methods, the structure of the isoflavone metabolite was determined to be 3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]-4H-chromen-4-one. This structure was confirmed further by the modified Mosher’s method. The same protocol was applied to the flavone metabolite, and the absolute configuration was determined to be 2-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]-4H-chromen-4-one. After determination of the absolute configurations of the biotransformation products, we suggest the binding mode of these substrate analogs to the enzyme active site.     

青蒿素及其类似物抗疟构效关系的DFT研究

为了从原子水平上揭示青蒿素及其类似物的结构与抗疟活性之间的关系,运用密度泛函理论DFT方法,在B3LYP/6-31G*水平上对青蒿素及其类似物二氢青蒿素、蒿甲醚和青蒿琥酯的结构和性质进行了理论计算。从分子的平衡构型、Wiberg键级、溶剂化能、偶极矩和静电势等方面分析了青蒿素及其类似物的抗疟构效关系。结果表明,青蒿素及其类似物结构中七元环上的过氧桥键、醚氧键以及六元环上的内酯结构是其抗疟作用的关键活性位,过氧桥键处负的静电势越多,青蒿素与血红素的相互作用越强,分子的抗疟活性越强。理论预测四个药物分子的抗疟活性顺序为:青蒿素<二氢青蒿素<蒿甲醚<青蒿琥酯,与实验活性结果一致。     

Mercaptoethanesulfonic acid (CoM imitator) interaction studies with nickel(II) complexes of pyridyl groups containing tetradentate ligands: Synthesis, structure, spectra and redox properties

Nickel(II) complexes of N,N′-dimethyl-N,N′-bis(pyridyl-2yl-methyl)ethylene-diamine (L¹), N,N′-dimethyl-N,N′-bis(pyridyl-2-ylmethyl)-1,2-diaminopropane (L²) and N,N′-dimethyl-N,N′-bis(pyridyl-2-ylmethyl)-1,3-diaminopropane (L³) were prepared and their spectroscopic and redox properties studied. The distorted octahedral structure was determined for [NiL³ClCH₃OH](ClO₄) by using X-ray crystallography. The electronic spectral behavior of the complexes at different pHs was analyzed; it is shown that a new band grew at the expense of the other band intensity in acid media. The redox properties of ligands and their complexes show the peaks of Ni(II) → Ni(III) and Ni(II) → Ni(0) as these were detected at low concentration while Ni(II) → Ni(I) process was detectable clearly at high concentration. Furthermore, the interaction studies of 2-mercaptoethanesulfonic acid as a simulator of coenzyme M reductase (CoM) with NiN₄ chromophores are discussed.     

Photochemical and photophysical properties of ruthenium(II) bis-bipyridine bis-nitrile complexes: Photolability

The electrochemical and photophysical properties of two bis-nitrilo ruthenium(II) complexes formulated as [Ru(bpy)₂(L)₂](PF₆)₂, where bpy is 2,2′-bipyridine and L is AN = CH₃CN and sn = NC-CH₂CH₂-CN, have been investigated. Electrochemical data are typical of Ru-bpy complexes with two reversible reduction peaks located near −1.3 and −1.6 V assigned to each bipyridine ligand and one Ru^II/Ru^III oxidation wave centered at approximately +1.5 V. The sn derivative is both IR and Raman active with its coordinated CN stretch appearing at 2277 cm⁻¹ and 2273 cm⁻¹, respectively. The UV/Vis absorption spectrum of the sn derivative is dominated by an intense (ε_max ∼ 58700 M⁻¹ cm⁻¹) absorption band at 287 nm assigned as a LC (π → π∗) transition. The peak observed at 418 nm (ε ∼ 10 400 M⁻¹ cm⁻¹) is an MLCT band while the one at 244 nm (ε ∼ 23 600 M⁻¹ cm⁻¹) is of LMLCT character. The AN derivative behaves similarly. Both complexes show low-temperature emission at around 537 nm with a lifetime near 10.0 μs. ¹H and ¹³C assignments are consistent with the formulation of the complexes. The complexes undergo photosubstitution of solvent with quantum efficiencies near one. Calculated and experimental results support replacement of the nitrile ligands by solvent. Based on DFT calculations, the electron density of the HOMO lies on the metal center, the bipyridine ligands and the nitrile ligands and electron density of the LUMO resides primarily on the bipyridine ligands. The electronic spectra obtained from TDDFT calculations closely match the experimental ones.     

Theoretical Study on the Photophysical and Photochemical Properties of Elsinochrome A

Abstract

Elsinochrome A (EA) is one of the important perylenequinonoid photosensitizers (PQPs); however, its photophysical and photochemical properties were given less attention in comparsion with other PQPs. In view of the successful use of quantum chemical methods, especially time-dependent density functional theory (TD-DFT), in investigating the photo-physico- chemical characters of various photosensitizers, we attempt to explore the photophysical and photosensitive properties of EA by theoretical methods. Firstly, the absorption spectra and lowest-lying T₁ excitation energy of EA were estimated by TD-DFT calculations. Then, the photosensitizing mechanisms of EA were explored. It was found that EA can photo-generate ¹O₂ through energy transfer in both benzene and DMSO. However, EA gives birth to O₂ ^? only in DMSO, and it is E_A ^.- generated from autoionization reactions that is responsible for the O₂ ^.-- generation, which gains some deeper insights into the photosensitive behaviors of EA.     

Synthesis and density functional theoretical study of steroidal spiro-triazolidinone

The reaction of 3beta-chloro-5alpha-cholestan-6-one semicarbazone 1 with hydrogen peroxide at 0 degrees C gives 3beta-chloro-5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one 2 as a product. The structural assignment of the product was confirmed on the basis of its elemental, analytical and spectral data. The ab initio calculations were performed by using density functional theory (DFT) at B3LYP/6-31G* basis set in order to describe a free radical reaction mechanism. The reaction proceeds through two radical intermediates formation. The mechanism of the reaction was explained by using frontier molecular orbital (FMO), spin electronic density map, encoded electrostatic potential map and atomic charges. It was found that the localization of frontier orbitals and the flow of atomic charges of all the calculated structures support the present reaction mechanism. The molecular properties like total energy, dipole moment and hardness of each optimized structure, were also explained. Stability of all the optimized structures in this study was supported by their respective fundamental frequencies and energy minima.     

Insight into the copper coordination environment in the prion protein through density functional theory calculations of EPR parameters

Density functional theory (DFT) calculations of Cu(II) electron paramagnetic resonance (EPR) parameters for the octarepeat unit of the prion protein were conducted. Model complexes were constructed and optimized using the crystal structure of the octarepeat unit of the prion protein. Copper g and A tensors and nitrogen hyperfine and quadrupole coupling constants were calculated using DFT. Solvent effects were incorporated using the conductor-like screening model as well as through the inclusion of explicit water molecules. Calculations using the model with an additional axial water molecule added to the coordination sphere of the Cu(II) metal center give the best qualitative agreement for the copper g and A tensors. The S-band experimental EPR spectra were interpreted in light of the DFT calculations of the directly coordinated nitrogen hyperfine coupling constants which indicate that the three directly coordinated nitrogen atoms in the octarepeat unit are not equivalent. These results demonstrate that DFT calculations of EPR parameters can provide important insight with respect to the structural interpretation of experimental EPR data. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A DFT study on the second-order nonlinear optical properties of the plenary mixed-metal polyoxometalate

The redox and second-order nonlinear optical (NLO) properties of organic–inorganic hybrid polyoxoanions [LNbOEMe₃]^3 ? , [LNbOEPh₃]^3 ?  (L = α-{PW₁₁O₃₉}^7 ? , E = Si, Ge, Sn, Pb) are investigated by density functional theory method. The element substitution effects on the molecular nonlinear response have been analysed. The results show that the computed β₀ values depend on both E (E = Si < Ge < Sn < Pb) and the organic groups connected with E. For [LNbOEPh₃]^3 ?  (L = α-{PW₁₁O₃₉}^7 ? , E = Si, Ge, Sn, Pb), the analysis of major contributions to β₀ value suggests that the charge transfer from organic group to Keggin polyanion plays the key role in NLO response; the polyanion acts as a donor, whereas the organic group acts as an acceptor in [LNbOEPh₃]^3 ? . Our results show that this kind of organic–inorganic hybrid compound possesses larger molecular second-order polarisability and might be a potential NLO material.     

Conformational preferences of 1,4,7-trithiacyclononane: a molecular mechanics and density functional theory study

Conformational preferences of 1,4,7-trithiacyclononane were studied using a highly efficient sampling technique based on local nonstochastic deformations and the MM2(91) force field. The results show that conformers that the molecule adopts in the crystal state were found to be low-energy conformers (LECs) within 5 kcal mol(-1) of the global minimum. A conformation with C1 symmetry was the global minimum and the C3 and C2 conformations were calculated to be 0.03 and 1.78 kcal mol(-1) higher in energy, respectively. The structures were further minimized using Density Functional Theory (DFT) calculations with two different functionals. The C2 and the C1 conformations were found to be LECs with the C3 conformation more than 4.0 kcal mol(-1) above the global minimum. The relative energies and structural ordering obtained using the BP86 functional are in agreement with the previously reported relative energies calculated using second-order Moller-Plesset (MP2) ab initio calculations. With the energy ordering being dependent on the molecular mechanics force field used, the approach of MM-->DFT (searching exhaustively the available conformational space at the MM level followed by generating the energy ordering through DFT calculations) appears to be appropriate for thiacrown ethers.     

First-principles investigation on structural,elastic, electronic and thermodynamic properties of filled skutterudite PrFe4P12 compound for thermoelectric applications

Filled skutterudite compound PrFe₄P₁₂ is studied using the full potential linear muffin-tin orbital method with the local density approximation for the exchange correlation potential to investigate the systematic trends for structural and elastic properties of the cubic PrFe₄P₁₂ skutterudite. The calculated ground state quantities such as the lattice constant and internal free parameters are in fairly good agreement with the available experimental data. The elastic constants and their pressure dependence are obtained by calculating the total energy versus volume-conserving strains using the Mehl model. Pressure and temperature effects on the lattice constant, bulk modulus, thermal expansion coefficient, Debye temperature and heat capacity are obtained in the range of 0–30 GPa and 0–1000 K. Reduction of bulk modulus and Debye temperature with temperature essentially indicates the thermal softening of the rare earth-filled skutterudites lattice.     

The electronic structure of Ti(BH4)3: Photoelectron spectra and calculation of vertical ionization energies

He I and He II PE spectra of Ti(BH₄)₃ are reported and assigned by reference to density functional calculations on the molecule and cation. The performance of different functionals in predicting the first vertical ionization energy is assessed. Calculations based on hybrid functionals are found to give ionisation energies closer to the experimental value than those using pure density functionals. The accuracy of the ΔSCF method and time dependent density functional theory in calculating higher vertical ionization energies is also examined.     

The role of axial ligands for the structure and function of chlorophylls

We have studied the effect of axial ligation of chlorophyll and bacteriochlorophyll using density functional calculations. Eleven different axial ligands have been considered, including models of histidine, aspartate/glutamate, asparagine/glutamine, serine, tyrosine, methionine, water, the protein backbone, and phosphate. The native chlorophylls, as well as their cation and anion radical states and models of the reaction centres P680 and P700, have been studied and we have compared the geometries, binding energies, reduction potentials, and absorption spectra. Our results clearly show that the chlorophylls strongly prefer to be five-coordinate, in accordance with available crystal structures. The axial ligands decrease the reduction potentials, so they cannot explain the high potential of P680. They also redshift the Q band, but not enough to explain the occurrence of red chlorophylls. However, there is some relation between the axial ligands and their location in the various photosynthetic proteins. In particular, the intrinsic reduction potential of the second molecule in the electron transfer path is always lower than that of the third one, a feature that may prevent back-transfer of the electron.     

Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G^** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO₂ group substituted molecules, the N–N bond distance increases with the increase of NO₂ groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρ_bcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO₂ groups in the nitramine molecules. The Laplacian of electron density ▽²ρ_bcp(r) of N–NO₂ bonds [DMNA: ? 16.7 eÅ^? 5, MDA: ? 12.8 eÅ^? 5 and TNA: ? 7.9 eÅ^? 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO₂ groups; this implies that the charge concentration decreases with the increase of NO₂ groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO₂ groups. The oxygen balance OB₁₀₀ of the molecules increases as the number of NO₂ group increases in the molecules, in which, the TNA molecule having maximum OB₁₀₀ value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO₂ group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.     

Tuning of redox potential and visible absorption band of ruthenium(II) complexes of (benzimidazolyl) derivatives: Synthesis, characterization, spectroscopic and redox properties, X-ray structures and DFT calculations

Six ruthenium(II) complexes have been prepared using the tridentate ligands 2,6-bis(benzimidazolyl) pyridine and bis(2-benzimidazolyl methyl) amine and having 2,2′-bipyridine, 2,2′:6′,2″-terpyridine, PPh₃, MeCN and chloride as coligands. The crystal structures of three of the complexes trans-[Ru(bbpH₂)(PPh₃)₂(CH₃CN)](ClO₄)₂ · 2H₂O (2), [Ru(bbpH₂)(bpy)Cl]ClO₄ (3) and [Ru(bbpH₂)(terpy)](ClO₄)₂ (4) are also reported. The complexes show visible region absorption at 402-517 nm, indicating that it is possible to tune the visible region absorption by varying the ancillary ligand. Luminescence behavior of the complexes has been studied both at RT and at liquid nitrogen temperature (LNT). Luminescence of the complexes is found to be insensitive to the presence of dioxygen. Two of the complexes [Ru(bbpH₂)(bpy)Cl]ClO₄ (3) and [Ru(bbpH₂)(terpy)](ClO₄)₂ (4) show RT emission in the NIR region, having lifetime, quantum yield and radiative constant values suitable for their application as NIR emitter in the solid state devices. The DFT calculations on these two complexes indicate that the metal t_2g electrons are appreciably delocalized over the ligand backbone.