Metal-ligand bonding in metallocenes: Differentiation between spin state, electrostatic and covalent bonding

We have analyzed metal-ligand bonding in metallocenes using density functional theory (DFT) at the OPBE/TZP level. This level of theory was recently shown to be the only DFT method able to correctly predict the spin ground state of iron complexes, and similar accuracy for spin ground states is found here. We considered metallocenes along the first-row transition metals (Sc-Zn) extended with alkaline-earth metals (Mg, Ca) and several second-row transition metals (Ru, Pd, Ag, Cd). Using an energy decomposition analysis, we have studied trends in metal-ligand bonding in these complexes. The OPBE/TZP enthalpy of heterolytic association for ferrocene (−658 kcal/mol) as obtained from the decomposition analysis is in excellent agreement with benchmark CCSD(T) and CASPT2 results. Covalent bonding is shown to vary largely for the different metallocenes and is found in the range from −155 to −635 kcal/mol. Much smaller variation is observed for Pauli repulsion (55-345 kcal/mol) or electrostatic interactions, which are however strong (−480 to −620 kcal/mol). The covalent bonding, and thus the metal-ligand bonding, is larger for low spin states than for higher spin states, due to better suitability of acceptor d-orbitals of the metal in the low spin state. Therefore, spin ground states of transition metal complexes can be seen as the result of a delicate interplay between metal-ligand bonding and Hund’s rule of maximum multiplicity.     

Density Functional Theory Calculations on Fe-O and O-O Cleavage of Ferric Hydroperoxide Species: Role of axial ligand and spin state

Density functional theory (DFT) calculations are performed on thiolate bound hydroperoxide complexes. O-O and Fe-O cleavage reaction coordinates, relevant to the active sites of cytochrome P450 and superoxide reductase enzymes, were investigated for both high and low spin states and for cis and trans orientations of the thiolate ligand with respect to the hydroperoxide ligand. The results indicate that the presence of a thiolate ligand produces significant elongation of the Fe-O bond and reduction of Fe-O vibrational frequency. While the fate of the O-O cleavage reaction is not significantly altered, the presence of a thiolate induces a heterolytic Fe-O cleavage irrespective of the spin state and orientation which is very different from results obtained with a trans ammine ligand.     

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations

The enzymatic cycle of hydroperoxidases involves the resting Fe(III) state of the enzyme and the high-valent iron intermediates Compound I and Compound II. These states might be characterized by X-ray crystallography and the transition pathways between each state can be investigated using atomistic simulations. Here we review our recent work in the modeling of two key steps of the enzymatic reaction of hydroperoxidases: the formation of Cpd I in peroxidase and the reduction of Cpd I in catalase. It will be shown that small conformational motions of distal side residues (His in peroxidases and His/Asn in catalases), not,or only partially, revealed by the available X-ray structures, play an important role in the catalytic processes examined.     

Ab initio analysis of the Cope rearrangement of germacrane sesquiterpenoids

The energetics of the Cope rearrangement of 17 germacrane sesquiterpenoids to their respective elemane forms have been calculated using both density functional theory (B3LYP/6-31G*) and post Hartee-Fock (MP2/6-31G**) ab initio methods. The calculations are in qualitative agreement with experimentally observed Cope rearrangements, but the two methods give slightly different results. MP2 calculations generally show more favorable elemene energies compared to the respective germacrenes (by around 3–4 kcal mol⁻¹) and smaller activation energies (by 2–3 kcal mol⁻¹). Additionally, neither method is accurate enough to consistently reproduce the germacrene/elemene equilibrium. Apparently, the generally small energy differences between the two forms in these sesquiterpenoids cannot be adequately reproduced at these levels of calculation. Figure The Cope rearrangement of the germacrane sesquiterpenoid bacchascandon to the elemane shyobunone     

Theoretical study of spin-spin coupling across the hydrogen (O-H⋯N) bond in adenosine derivatives

The study of spin-spin coupling constants across hydrogen bond provides useful information about configuration of complexes. The interesting case of such interactions was observed as a coupling across an intramolecular hydrogen bond in 8-bromo-2′,3′-O-isopropylideneadenosine between the -CH₂OH (at 5″ proton) group and the nitrogen atom of adenine. In this paper we report theoretical investigations on the ^4h J _NH coupling across the H″-C-O-H···N hydrogen bond in adenosine derivatives in various solvent models. Figure Coupling constants in 8-bromo-2′,3′-O-isopropylideneadenosine Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Conformational control of spin state in iron(II) tripodal imidazole complexes

Three new iron(II) N₆ tripodal complexes provide information on the role of ligand conformation on spin crossover behavior. The ligands (generated in situ) are the Schiff base condensate of tris(2-aminoethyl)amine (tren) with three equivalents of 4-methyl-5-imidazolecarboxaldehyde, H₃(1), and the condensates of tris(2-aminoethyl)methylammonium ion (N(Me)tren⁺) with three equivalents of 4-methyl-5-imidazolecarboxaldehyde, N(Me)H₃(1)⁺, or with 2-imidazole carboxaldehyde, N(Me)H₃(3)⁺. The structures of [FeH₃(1)](ClO₄)₂, [FeN(Me)H₃(1)](ClO₄)₃ and [FeN(Me)H₃(1)](ClO₄)₃ are reported. The central tren nitrogen atom in these complexes exhibits three different geometries, pyramidal with the nitrogen pointed toward the iron (“N in”, Fe-N distance of 3.050 Å), planar (Fe-N distance of 3.527 Å), and pyramidal with the nitrogen pointed away from the iron atom (“N out”, Fe-N distance of 3.921 Å). With iron(II) the “N in” geometry is high spin while the planar and “N out” geometries are low spin. [FeH₃(1)](ClO₄)₂ exhibits spin crossover behavior between room temperature and 77 K as determined by Mössbauer spectroscopy and also exhibits a conformational change from “N in” to planar over this same temperature range. The structures of [FeN(Me)H₃(1)](ClO₄)₃ and [FeN(Me)H₃ (3)](ClO₄)₃ are locked into the “N out” geometry due to the quaternary nitrogen atom and are low spin even at room temperature. The LS planar and “N out” conformations place a strain on the bond angles of the aliphatic arms of the ligand, which are more pronounced in the “N out” case. The HS “N in” geometry lacks this strain.     

Deformability of Fe(II)CO and Fe(III)CN groups in heme protein models: nonlocal density functional theory calculations

 High-quality nonlocal density functional calculations have been carried out on the deformability of Fe(II)CO and Fe(III)CN units in model compounds of heme proteins. The results confirm our previous finding with a local functional that the Fe(II)CO unit is significantly deformable with respect to tilting and bending. This deformability stems in large part from a large, negative interaction constant between the FeC tilt and FeCO bend coordinates. The Fe(III)CN unit is also significantly deformable, but in this case the deformability results from a very small Fe(III)CN bend force constant and the ability of the cyano nitrogen to act as a hydrogen bond acceptor. The prediction that the energetic penalty associated with deforming the Fe(II)CO unit is relatively modest indicates that such deformations are unlikely to be the dominant contributor to myoglobin's discrimation against CO in favor of O₂. Received, accepted: 16 June 1997     

Excretory-secretory antigen is better than crude antigen for the serodiagnosis of clonorchiasis by ELISA

Although stool examination is the standard diagnostic method of clonorchiasis, serodiagnosis by ELISA using crude antigen is now widely used because of its convenience. However, ELISA diagnosis still suffers from cross-reactions, and therefore there is a need to improve the present conventional ELISA. The present study was undertaken to evaluate the diagnostic value of ELISA using excretory-secretory antigen (ESA) instead of crude antigen (CA) of Clonorchis sinensis. The diagnostic sensitivity of ELISA using excretory-secretory antigen was 92.5%, which was higher than that of ELISA using crude Clonorchis sinensis antigen (88.2%). In addition, the specificity of excretory-secretory antigen was found 93.1% while that of crude antigen was 87.8%. In summary, Clonorchis sinensis ESA was found to be a better serodiagnostic antigen than CA for ELISA.     

On the complex formation of iron(III) bromide in the space-demanding solvent N,N′-dimethylpropyleneurea and the structure of the trisbromoiron(III) complex in solution and crystalline state

The complex formation between iron(III) and bromide has been studied calorimetrically in N,N′-dimethylpropyleneurea (DMPU), and the structure of the DMPU solvated tribromoiron(III) complex has been studied in solution by extended X-ray absorption fine structure (EXAFS) and large angle X-ray scattering (LAXS), and in solid state by EXAFS and single crystal X-ray diffraction. The calorimetric study showed that iron(III) forms three medium strong bromide complexes in DMPU, and the thermodynamic pattern strongly indicates that all complexes are formed in entropy driven substitution reactions. In DMPU solution, the tribromoiron(III) complex has a regular trigonal planar configuration with a mean Fe-Br bond distance of 2.36 Å, and without any solvent molecules strongly bound to iron(III). In the solid state, however, the structure is a slightly distorted trigonal bipyramid, with one short and two slightly longer Fe-Br bonds, 2.37 and 2.44 Å, respectively, in a somewhat distorted trigonal plane, and two DMPU solvent molecules (mean Fe-O bond distance 1.98 Å) in the apical positions. The DMPU solution of iron(III) bromide and the [FeBr₃(dmpu)₂] crystals are both blackish red.     

Computational Investigations of the Chalcogen-Substituted Carboxylic Acids RC(=O)XH and RC(=X)OH and their Dimers [RC(=O)XH]2 and [RC(=X)OH]2 (X=S, Se, Te)

Semiempirical and ab initio theoretical methods have been used to investigate molecular structures of the chalcogen-substituted carboxylic acid isomers RC(=O)XH (chalcogenol acid) and RC(=X)OH (chalcogenon acid). A recent experimental report suggests that the chalcogenon isomers, although less stable at room temperature, predominate at low temperature in polar solvents and that there is only a small barrier to isomerization between the isomers. Theoretical calculations have been used to locate minimum energy structures of chalcogen-substituted carboxylic acid isomers and to calculate energy differences between pairs of isomers. Carboxylic acids are well known to dimerize, especially in the gas phase and in non-polar solvents. We have, therefore, also calculated energies of dimerization of the chalcogen-substituted acids by optimizing the geometries of the symmetric dimers. We note that the PM3 level of theory is only qualitatively correct for sulfur- and selenium-containing species but fails even qualitatively for the tellurium-containing compounds. Ab initio results confirm the experimental observations and provide good estimates of both isomerization and dimerization energies. We conclude that for many functional groups with tautomers RC(=X)YH and RC(=Y)XH, the more acidic tautomer is the one with the acid proton on the smaller, more electronegative atom, although in many cases this may not be the more stable tautomer.Electronic Supplementary Material available.     

Structural and electronic properties of diazonium functionalized (4, 4) single walled carbon nanotube: an ab initio study

In this work, ab initio density functional theory (DFT) calculations are performed to study the structural and electronic properties of diazonium reagent functionalized (4, 4) single-walled carbon nanotube (SWCNT). We find the aryl group covalently bonds with SWCNT and prefers to be perpendicular to the side wall of nanotube. It has a rotational barrier of 0.35 eV around the formed aryl-tube bond axis and should be thermodynamically stable at room temperature. Additionally, new peaks appeared around the Fermi energy in the density of state (DOS) due to the weak band dispersion. Increasing of the coverage of the functional group will result in significant upshift of the Fermi level.     

A structural study of the hydrated and the dimethylsulfoxide, N,N′-dimethylpropyleneurea, and N,N-dimethylthioformamide solvated iron(II) and iron(III) ions in solution and solid state

The structures of the solvated iron(II) and iron(III) ions have been studied in solution and solid state by extended X-ray absorption fine structure (EXAFS) in three oxygen donor solvents, water, dimethylsulfoxide (Me₂SO), N,N′-dimethylpropyleneurea (DMPU), and one sulfur donor solvent, N,N-dimethylthioformamide (DMTF); these solvents have different coordination and solvation properties. In addition, the structure of hexakis(dimethylsulfoxide)iron(III) perchlorate has been determined crystallographically to support the determination of the corresponding solvate in solution. The hydrated, the dimethylsulfoxide and N,N-dimethylthioformamide solvated iron(II) ions show regular octahedral coordination in both solution and solid state with mean Fe-O, Fe-O, and Fe-S bond distances of 2.10, 2.10, and 2.52 Å, respectively, whereas the N,N′-dimethylpropyleneurea iron(II) solvate is five-coordinated, d(Fe-O) = 2.06 Å. The compounds vary in color from light green (hydrate) to dark orange or red (DMPU). The hydrated iron(III) ion in aqueous solution and the dimethylsulfoxide solvated iron(III) ions in solution and solid state show the expected octahedral coordination, the Fe-O bond distances are 2.00 Å for both, whereas the N,N′-dimethylpropyleneurea iron(III) solvate is found to be five-coordinated with a mean Fe-O bond distance of 1.99 Å. The N,N-dimethylthioformamide solvated iron(III) ion in the solid perchlorate salt is tetrahedrally four-coordinated, the mean Fe-S bond distance is 2.20 Å. Iron(III) is reduced with time to iron(II) in N,N-dimethylthioformamide solution. The compounds vary in color from pale yellow (hydrate) to blackish red (DMPU).     

The mechanistic aspects of iron(III) porphyrin catalyzed oxidation reactions in mixed solvents

In the iron(III) porphyrin catalyzed oxidation reactions, the formation of various reactive intermediates have been observed to depend upon the nature of the catalyst, the oxidant and the solvent used for the study. The various iron(III) porphyrin catalysts such as F₂₀TPPFeCl, F₁₆TPPFeCl, F₁₂TPPFeCl and F₈TPPFeCl have been used in the present study to understand the effect of solvent system in the activation of the catalysts. As the terminal oxidant t-BuOOH has been used. It has been observed that acetonitrile contaminated with water activates all the catalysts. It has been noted that ∼9% of water in acetonitrile is the best solvent system for the activation of all the catalysts. The results obtained have been applied to successfully oxidize cyclohexene and cyclohexane by these oxidizing systems. It has also been observed that CH₃OH mixed with CH₂Cl₂ play a very important role in the activation of catalyst in hydroperoxide oxidizing system. The 33 ± 3% ratio of CH₃OH in CH₂Cl₂ acts as the most suitable solvent system to convert organopalladium compound 1a-c to 2a-c.     

Chiral-at-metal tetrahydrosalen complexes of resolved titanium(IV) sec-butoxides: Ligand wrapping and multiple asymmetric catalytic induction

The reaction of the racemic and resolved tetrahydrosalen derivative LH₂ (LH₂ = N,N’-bis(3,5-dichloro-2-hydroxybenzyl)-trans-1,2-diaminocyclohexane) with the resolved titanium(IV) sec-butoxides Ti(O^R-2Bu)₄ or Ti(O^S-2Bu)₄ yielded a series of four compounds, LTi(O²Bu)₂ (1-4), which have been characterized by IR, elemental analysis, ¹H and ¹³C NMR and X-ray crystallography. X-ray crystallography revealed the co-crystallization of two pseudo-C₂-symmetric products from racemic LH₂, whereas a perfect chiral induction of the ligand to the metal occurred when resolved (R,R)-LH₂ was used, resulting in a Δ fac-fac wrapping mode of the tetradentate ligand about the titanium center. Ab initio electronic structure calculations (DFT) are in agreement that the lowest energy isomer is that which is experimentally observed. Catalysis screenings show that Ti(O^S-2Bu)₄, in conjunction with (R,R)-LH₂, forms a matched pair that catalyzes the addition of dimethyl zinc to benzaldehyde with higher enantioselectivity than that observed for resolved (R,R)-LH₂ with Ti(O^R-2Bu)₄ or achiral Ti(OⁱPr)₄. Increasing the temperature of the system results in slightly increased enantiomeric excess.     

Computational study on the mechanisms of action of the potential anticancer drug trans-isopropylaminedimethylaminedichloroplatinum (trans-IPADMADP) and its cis isomer with DNA purine bases

The monofunctional and bifunctional bindings of the potential anticancer drug trans-isopropylaminedimethylaminedichloroplatinum (trans-IPADMADP) and its cis isomer to purine base in DNA are explored by using density functional theory and IEF-PCM solvation models. The computed lowest free energy barrier in the aqueous solution is 14.0/11.6 kcal/mol (from trans-Pt-chloroaqua complex to trans-/cis-monoadduct) for guanine(G), and 11.7/13.3 kcal/mol (from trans-Pt-chloroaqua complex to trans-/cis-monoadduct) for adenine(A). Our calculations demonstrate that the trans reactant complexes (or isolated reactants) can generate trans- or cis-monoadducts via similar trigonal bipyramidal transition state structures, suggesting that the monoadducts can subsequently close to form the bifunctional intrastrand Pt-DNA adducts and simultaneously distort DNA in the similar way as cisplatin. Our calculations show that Pt(isopropylamine)(dimethylamine)G₂²⁺ head-to-head path has the lowest free energy of activation at 17.6 kcal/mol, closely followed by the Pt(isopropylamine)(dimethylamine)GA²⁺ head-to-head path at 19.6 kcal/mol when the monofunctional cis-Pt-G complex serves as the reactant; while the Pt(isopropylamine)(dimethylamine)G₂²⁺ head-to-tail adduct has the lowest barrier of 20.5 kcal/mol, closely followed by the Pt(isopropylamine)(dimethylamine)GA²⁺ head-to-tail adduct at 23.0 kcal/mol if the monofunctional trans-Pt-G complex is the reactant.The calculated relatively lower activation energy barrier than that of cisplatin theoretically confirm that trans-[PtCl₂(isopropylamine)(dimethylamine)] is a potential anticancer drug as described by experiment.     

Commensal Leucothoidae (Crustacea, Amphipoda) of the Ryukyu Archipelago, Japan. Part III: coral rubble-dwellers

Commensal leucothoid amphipods have been collected from coral rubble samples throughout the Ryukyu Archipelago, Japan. Seven new species are described in two generawith valuable location data. A new locality is presented for Paranamixis misakiensis Thomas, 1997. An identification key to all described Leucothoidae of the Ryukyu Archipelago is provided.     

A computational investigation of sulfur-containing heterocyclic components from the anal sac secretions of Mustela species

A computational investigation of the sulfur-containing heterocyclic components (substituted thietanes and 1,2-dithiolanes) of Mustela anal sac secretions has been carried out. A cluster analysis of the chemical compositions of Mustela anal sac volatiles reveals little similarity with established phylogenetic relationships between members of the genus. Ab initio calculations [MP2/6–311++G(2df,2p)//B3LYP/6–311++G**] show the lowest-energy C₅H₁₀S isomeric thietane to be 2,2-dimethylthietane, which is also the most abundant of the Mustela thietanes. Similarly, 3,3-dimethyl-1,2-dithiolane is the lowest-energy C₅H₁₀S₂ compound. 2-n-Propylthietane is the highest-energy C₆H₁₂S compound, but the most abundant Mustela C₆H₁₂S compound produced, whereas cis-2-ethyl-4-methylthietane, the lowest-energy C₆H₁₂S thietane, has never been observed in Mustela anal sac secretions. A molecular docking analysis of the Mustela sulfur-containing heterocycles into both porcine and bovine odorant binding proteins reveals the interactions of the docked ligands with the proteins to be largely hydrophobic, and have binding energies generally lower than typical odorant molecules such as linalool or eugenol. Figure Mustela anal sac volatile components, 2,2-dimethylthietane and cis-3,4-dimethyl–1,2-dithiolane.     

Photothermal studies of the room temperature photo-induced spin state change in the Fe(III)(salten)(mepepy) complex

The complex [Fe(III)(salten)(mepepy)]BPh₄ (salten = 4-azaheptamethylene-1,7-bis(salicylideneiminate; mepepy = 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)-ethene; BPh₄ = tetraphenyl borate) has been investigated to determine the volume and enthalpy changes associated with the room temperature photo-induced spin crossover. Here we report the photophysical properties of the trans to cis isomerization of the mepepy ligand as well as the spin crossover of the Fe(III)(salten)(mepepy) complex in acetonitrile:water mixtures using photoacoustic calorimetry (PAC). The PAC studies indicate that the trans to cis transition of the mepepy ligand occurs faster than the ∼20 ns response time of the acoustic detector and gives rise to a negligible volume change (0.7 ± 0.3 mL mol⁻¹) and an enthalpy change of 33 ± 10 kcal mol⁻¹. These results are consistent with the loss of a charge assisted hydrogen bond between a water molecule and the pyridyl ring of the mepepy upon photoisomerization. In the case of Fe(III)(salten)(mepepy) photoexcitation, PAC results indicate that the high-spin to low-spin transition, also occurring in ?20 ns, gives rise to small volume and enthalpy changes (0.9 mL mol⁻¹ and 4 kcal mol⁻¹). Analysis of the results indicate that the observed thermodynamics are related to a distortion of the Fe(II)(salten)(mepepy) complex associated with the cleavage of an Fe?N bond upon spin conversion.     

Synthesis, structure and catalytic activity of low-spin dicyano iron(III) complexes of N,N-bis(quinolyl)malonamide derivatives

Two low-spin Fe(III) dicyano-dicarboxamido complexes have been prepared from N,N^′-bis(8-quinolyl)malonamide derivatives. Crystal structures show that the four nitrogen donors available to complex the metal are arranged in the equatorial plane with the two cyanides trans to each other in the axial positions when the malonyl moiety is disubstituted. In contrast, the unsubstituted malonyl results in only three nitrogens in the equatorial plane with the fourth in an apical position and the two cyanides occupying cis sites, one equatorial and the other axial. NMR analyses show that the solid state structure of both complexes is retained in solution. Both types of configurational complexes catalyze cyclic olefin oxidations with H₂O₂ but only the cis-dicyano complex catalyzes stilbene oxidation with formation of epoxides, diols and benzaldehyde.     

Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex

Theoretical calculations of structural parameters, 57Fe, 14N and 17 O electric field gradient (EFG) tensors for full size-hemin group have been carried out using density functional theory. These calculations are intended to shed light on the difference between the geometry parameters, nuclear quadrupole coupling constants (QCC), and asymmetry parameters (eta Q) found in three spin states of hemin; doublet, quartet and sextet. The optimization results reveal a significant change for propionic groups and porphyrin plane in different spin states. It is found that all principal components of EFG tensor at the iron site are sensitive to electronic and geometry structures. A relationship between the EFG tensor at the 14N and 17 O sites and the spin state of hemin complex is also detected.