Structures and stabilities of Fe2+/3+ complexes relevant to Alzheimer's disease: an ab initio study

Iron is one of the most abundant metals found in senile plaques of post mortem patients with Alzheimer's disease. However, the interaction mode between iron ions and β-amyloid peptide as well as their precise affinity is unknown. In this study we apply ab initio computational methodology to calculate binding energies of Fe(2+/3+) with the His13-His14 sequence of Aβ, as well as other important ligands such as His6 and Tyr10. Calculations were carried out at the "MP2/6-311+G(2df,2p)"//B3LYP/6-31+G(d) level of theory and solvent effects included by the IEFPCM procedure. Several reaction paths for the binding of imidazole, phenol, and the His13-His14 fragment (modeled by N-(2-(1H-imidazol-4-yl)ethyl)-3-(1H-imidazol-4-yl)propanamide) were sequentially explored. The results show that the most stable complexes containing His13-His14 and phenolate of Tyr10 are the pentacoordinated [Fe(2+)(O-HisHis)(PhO(-))(H(2)O)](+) and [Fe(3+)(N-HisHis)(PhO(-))(H(2)O)](+) compounds and that simultaneous coordination of tyrosine and His13-His14 to Fe(2+/3+) is thermodynamically favorable in water at physiological pH. Computed Raman spectra confirm the conclusion obtained by Miura et al. ( Biochemistry 2000 , 39 , 7024 ) that tyrosine is coordinated to Fe(3+) but do not exclude coordination of imidazoles. Finally, calculations of standard reduction potentials indicate that phenol coordination reduces the redox activity of the iron/Aβ complexes.     

Cobalt(II) dioxygen carriers based on simple diamino ligands: kinetic and ab initio studies

The kinetics of the oxygenation reaction of CoL2(2+) complexes (L=ethylenediamine (en), N,N'-dimethylethylenediamnine (dmen)) have been investigated in dimethyl sulfoxide (dmso) at 298 K and in a medium adjusted to 0.1 mol dm(-3) with Et4NClO4 by means of a UV-vis spectrophotometric technique. The reaction mechanisms are consistent with the fast formation of superoxo 1:1 initial CoL2-O2 species (L=en, dmen), whereas the dimeric mu-peroxo (CoL2)2O2 adduct is formed only when L=en, in the rate determining step. The kinetic results are discussed taking into account the effects of ligand/solvent substitution. EPR results give information on the electronic structure and the coordination geometry of the Co(II) complexes and further confirm the stoichiometry of the species formed. Ab initio calculations provide insights on the geometrical parameters of all the complexes investigated and allow us to draw some hypotheses about the influence of H.H nonbonded interactions in the eventual formation of the dimeric mu-peroxo (CoL2)2O2 complexes. Solvational effects are also considered. The formation of the (CoL3)2O2 adduct is also proved when L=en by means of O2 volumetric absorption.     

Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self-consistent field supermolecular computations

Detailed investigations are performed of the binding energetics of Zn²⁺ to a series of neutral and anionic ligands making up the sidechains of amino acid residues of proteins, as well as ligands which can be involved in Zn²⁺ binding during enzymatic activation: imidazole, formamide, methanethiol, methanethiolate, methoxy, and hydroxy. The computations are performed using the SIBFA molecular mechanics procedure (SMM), which expresses the interaction energy under the form of four separate contributions related to the corresponding ab initio supermolecular ones: electrostatic, short-range repulsion, polarization, and charge transfer. Recent refinements to this procedure are first exposed. To test the reliability of this procedure in large-scale simulations of inhibitor binding to metalloenzyme cavities, we undertake systematic comparisons of the SMM results with those of recent large basis set ab initio self-consistent field (SCF) supermolecule computations, in which a decomposition of the total ΔE into its four corresponding components is done (N. Gresh, W. Stevens, and M. Krauss, J. Comp. Chem., 16 , 843, 1995). For each complex, the evolution of each individual SMM energy component as a function of radial and in- and out-of-plane angular variations of the Zn²⁺ position reproduces with good accuracy the behavior of the corresponding SCF term. Computations performed subsequently on di- and oligoligated complexes of Zn²⁺ show that the SIBFA molecular mechanics (SMM) functionals, E_pol and E_ct, closely account for the nonadditive behaviors of the corresponding second-order energy contributions determined from the ab initio SCF calculations on these complexes and their nonlinear dependence on the number of ligands. Thus, the total intermolecular interaction energies computed with this procedure reproduce, with good accuracy, the corresponding SCF ones without the need for additional, extraneous terms in the intermolecular potential of polyligated complexes of divalent cations. © 1995 by John Wiley & Sons, Inc.     

Palladium(II) complex taken as a model of an antitumour agent: Synthesis and equilibrium investigation involving biologically relevant ligands

Pd(DHP)Cl₂ and Pd(DHP)(CBDCA) complexes (DHP = 1,3-diamino-2-hydroxopropane and CBDCA = 1,1-cyclobutanedicarboxylate), were synthesized and characterized by elemental analysis, IR and NMR spectral measurements. The coordination of [Pd(DHP)(H₂O)₂]²⁺ with some selected bio-relevant ligands, containing different functional groups was investigated. The ligands used are amino acids, peptides, DNA constituents and dicarboxylic acids. Stoichiometry and stability constants of the complexes formed are reported at 25 °C and 0.1 M ionic strength. The results show the formation of 1:1 complexes with amino acids and dicarboxylic acids. DNA constituents form 1:1 and 1:2 complexes. Peptides form both 1:1 complexes and the corresponding deprotonated amide species. The effect of chloride ion concentration and dioxane on the acid dissociation constants of 1,1-cyclobutane dicarboxylic acid (CBDCAH₂) and the formation constant of its complex with Pd(DHP)²⁺ was reported. The equilibrium constants for the displacement of coordinated ligands as uracil, glycine or methionine by cysteine are calculated. The results are expected to contribute to the chemistry of antitumour agents.     

Spectroscopic and magnetic properties of Cu(II) complexes with selected biologically important ligands

The aim of this work was to study the spectroscopic and magnetic properties of copper(II) o-, m-, p-aminobenzoates, o-, m-, p-methoxybenzoates and o-, m- and p-nitrobenzoates. The complexes were synthesized and their compositions were evaluated by elementary analysis. The infrared and Raman spectra for Cu(II) aminobenzoates, methoxybenzoates and nitrobenzoates were recorded and assigned. The obtained data were compared with those previously published for aminobenzoic, methoxybenzoic and nitrobenzoic acids and their sodium salts. The structures of Cu(II) o-, m-, p-aminobenzoates, o-, m-, p-methoxybenzoates and o-, m- and p-nitrobenzoates as well as the change in the electronic charges distribution caused by Cu(II) complex formation were discussed.     

From pure C(60) to silicon carbon fullerene-based nanotube: an ab initio study

The energetics, geometrical, and electronic properties of the silicon carbon fullerene-based materials, obtained from C(60) by replacing 12 carbon atoms of the C(60) cage with silicon atoms, are studied based on ab initio calculations. We have found that, of the two C(48)Si(12) isomers obtained, the one with the carbon atoms and the silicon atoms located in separated region, i.e., with a phase-separated structure is more stable. Fullerene-based C(36)Si(24) cluster, C(36)Si(24)-C(36)Si(24) dimer, and the nanotube constructed from the clusters are then studied. The calculations on the electronic properties of these silicon carbon fullerene-based nanomaterials demonstrate that the energy gaps are greatly modified and show a decreasing trend with increasing the size of the clusters. The silicon carbon fullerene-based nanotube has a narrow and direct energy band gap, implying that it is a narrow gap semiconductor and may be a promising candidate for optoelectronic devices.     

Histidine-rich branched peptides as Cu(II) and Zn(II) chelators with potential therapeutic application in Alzheimer's disease

Two histidine-rich branched peptides with one lysine as a branching unit have been designed and synthesized by solid-phase peptide synthesis. Their complex formation with Cu(II) and Zn(II) as well as their ability to attenuate the metal-ion induced amyloid aggregation has been characterized. Both peptides can keep Cu(II) and Zn(II) in complexed forms at pH 7.4 and can bind two equivalents of metal ions in solutions with excess metal. The stoichiometry, stability and structure of the complexes formed have been determined by pH potentiometry, UV-Vis spectrophotometry, circular dichroism, EPR and NMR spectroscopy and ESI-MS. Both mono- and bimetallic species have been detected over the whole pH range studied. The basic binding mode is either a tridentate {N(amino), N(amide), N(im)} or a histamine-type of coordination which is complemented by the binding of far imidazole or amino groups leading to macrochelate formation. The peptides were able to prevent Cu(II)-induced Aβ(1-40) aggregation but could not effectively compete for Zn(II) in vitro. Our results suggest that branched peptides containing potential metal-binding sites may be suitable metal chelators for reducing the risk of amyloid plaque formation in Alzheimer's disease.     

Addition of anions to carbonyl compounds: an ab initio study

Energies for the addition of anionic nucleophiles, Z(-), to carbonyl compounds, XYCO, are calculated at the G2(MP2) level of theory. The substituents X, Y, and Z are taken from the set {H, CH3, NH2, OH, F, CF3, CHCH2, CHO, CCH, and CN}. The basicity and, to a lesser extent, ionization potential of Z(-) were found to correlate with the enthalpy of addition of Z(-) to H2CO. The enthalpy of addition of Z(-) to XYCO relative to H2CO is largely independent of Z. The ordering of the enthalpies of addition for the series of XYCO's is rationalized. By using a thermodynamic cycle, the independence of this ordering from Z is attributed to the additivity of the inductive stabilization of XYZCO(-) by X and Y versus H2ZCO(-). A method for estimating the enthalpy of addition for nucleophile/carbonyl combinations not studied above is described and shown to give good results on a model system.     

Computational studies of Cu(II)/Met and Cu(I)/Met binding motifs relevant for the chemistry of Alzheimer's disease

A systematic study of the binding motifs of Cu(II) and Cu(I) to a methionine model peptide, namely, N-formylmethioninamide 1, has been carried out by quantum chemical computations. Geometries of the coordination modes obtained at the B3LYP/6-31G(d) level of theory are discussed in the context of copper coordination by the peptide backbone and the S atom of a methionine residue in peptides with special emphasis on Met35 of the amyloid-beta peptide (Abeta) of Alzheimer's disease. The relative binding free energies in the gas phase, DeltaG(g), are calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level of theory, and the solvation affects are included by means of the COSMO model to obtain the relative binding energies in solution, DeltaG(aq). A free energy of binding, DeltaG(aq) = -19.4 kJ mol(-1), relative to aqueous Cu(II) and the free peptide is found for the most stable Cu(II)/Met complex, 12. The most stable Cu(I)/Met complex, 23, is bound by -15.6 kJ mol(-1) relative to the separated species. The reduction potential relative to the standard hydrogen electrode is estimated to be E degrees (12/23) = 0.41 V. On the basis of these results, the participation of Met35 as a low affinity binding site of Cu(II) in Abeta, and its role in the redox chemistry underlying Alzheimer's disease is discussed.     

Thermal decomposition of decalin: an ab initio study

Density functional theory calculations (B3LYP and BH&HLYP functionals) of the potential energy surface have been performed to investigate the mechanisms of decalin breakdown, and the Rice-Ramsperger-Kassel-Marcus and transition state theory methods have been used to compute the high-pressure limit thermal rate constants for the new reaction pathways. The new pathways connect decalin to five primary monoaromatic species: benzene, toluene, styrene, ethylbenzene, and xylene. The reactions used for the new routes are carbon-carbon bond cleavage reaction, dissociation reaction, and hydrogen abstraction and addition reactions. A kinetic analysis was performed for pyrolytic conditions, and benzene, toluene, and xylene were identified as major products.     

Kinetics and mechanism of the reactions of Ru(II)-arene complex with some biologically relevant ligands

The reactions of ruthenium(II)-arene complex [Ru^II(η⁶-p-cym)(pydc)Cl] (where p-cym = p-isopropyl toluene, pydc = 2,3-pyridinedicarboxylato) with biologically nitrogen-donor nucleophiles, such as guanosine-5′-monophosphate (5′-GMP), guanosine (Guo) and l-histidine (l-His) were studied by UV-Vis spectrophotometry and ¹H NMR spectroscopy. The reactions were studied at pH 2.5 and at 7.2. All reactions were followed under pseudo-first order conditions with large excess of the nucleophiles. The selected nucleophiles have a high affinity for Ru(II)-arene complex. The reactivity of the used ligands follow the same order at both pH values: Guo > 5′-GMP > l-His, while the reactions at pH 7.2 are always faster. The negative entropies of activation (ΔS^≠) support an associative mode of activation. However, the rate constants obtained by ¹H NMR at 295 K in D₂O follow the same order of the ligand reactivity. The hydrolysis of the [Ru^II(η⁶-p-cym)(pydc)Cl] complex was very fast and completed by the time the first spectrum was measured. Addition of excess of NaCl to equilibrium solutions reversed the hydrolysis.     

Binding of Cu(II) to poly(methacrylic acid)

The binding of Cu(II) ions to partly neutralized poly(methacrylic acid) (PMA) has been investigated by potentiometric titration and dialysis to determine the stoichiometry the Cu–PMA complexes formed. Partly ionized PMA was titrated with solutions of the metal ion to enable a large range of metal ion/polymer ratios to be studied. Combination of the results from these two techniques at ionic strength 0.1 indicates that at very low Cu(II)/polymer ratios, a 4:1 complex exists, but at higher ratios the complex breaks down to give a mainly 2:1 coordination with some 1:1 binding. Conductance titrations support these results. Viscometric titrations show strong interactions between the metal and polymer, preventing the full extension of the polyion at high degrees of ionization, and spectrophotometric titrations support the existence of at least two types of complexes in the solution.     

Binding of Co(II) and Cu(II) cations to chemically modified wool fibres: an IR investigation

Wool fibres were modified by treatment with tannic acid (TA) solution or by acylation with ethylenediaminetetraacetic (EDTA) dianhydride. The unmodified and modified fibres were subsequently treated with Cu²⁺ and Co²⁺ solutions, at alkaline pH, and analysed by Attenuated Total Reflectance, ATR/IR spectroscopy to evaluate the changes induced in the structure of the fibre by metal binding. The spectral changes were correlated to metal adsorption results obtained by Inductive Coupled Plasma-Atomic Emission Spectrometry (ICP-AES).

The IR results were discussed in relation to our previous findings on the metal binding mode of Bombyx mori and Tussah silk fibres; the changes observed in the spectra were explained by considering the different affinity of the fibres for the modifying reagent and the amount of the metal absorbed. More relevant spectral changes were observed upon Cu²⁺ complexation rather than Co²⁺ complexation, according to the metal absorption results. The most relevant changes were observed for the EDTA-modified wool sample treated with Cu²⁺, according to the higher affinity of wool for EDTA. The IR spectra were quantitatively evaluated by the intensity ratio between the Amide I and Amide II bands (I_AmideI/I_AmideII) and its trend as a function of metal absorption was reported.

The present investigation demonstrated that the interaction between fibre and metal and the subsequent fibre modification depend on the chemical nature of the fibre, the metal cation and the modifying reagent.     

Binding of pi-acceptor ligands to (triamine)iron(II) complexes

A series of (Me3TACN)FeII derivatives with soft coligands have been investigated, where Me3TACN is N,N',N"-trimethyl-1,4,7-triazacyclononane. Treatment of Me3TACN with FeCl2 afforded a compound with the empirical formula (Me3TACN)FeCl2 (1). Compound 1, which is a versatile precursor reagent, was shown by single-crystal X-ray diffraction to be the salt [(Me3TACN)2Fe2Cl3][(Me3TACN)FeCl3], containing isolated [(Me3TACN)2Fe2Cl3]+ and [(Me3TACN)FeCl3]- subunits. Treatment of 1 with NaBPh4 gave the known [(Me3TACN)2Fe2Cl3]BPh4, while the addition of Me3TACN to FeCl4(2-) gave [(Me3TACN)FeCl3]-. Oxygenation of 1 afforded [(Me3TACN)FeCl2]2(mu-O), which was shown crystallographically to be centrosymmetric with a pair of distorted octahedral Fe centers. The Fe-N bond trans to the Fe-O bond is elongated by 02 A relative to the other Fe-N distances. Solutions of 1 and thiolates absorb CO to give [(Me3TACN)Fe(SPh)(CO)2]BPh4 and (Me3TACN)Fe(S2C2H4)(CO) (nu CO = 1896 cm-1). Treatment of 1 with excess CN- afforded [(Me3TACN)Fe(CN)3]-, isolated as its PPh4+ salt 5. Crystallographic and spectroscopic studies show that 5 is low spin with a C3v structure; its Fe-N distances contracted by 023 A relative to those in [(Me3TACN)FeCl3]-. Aqueous solutions of 1 bind CO upon the addition of CN- to produce (Me3TACN)Fe(CN)2(CO) (6) Analogous to 6 is (Me3TACN)Fe(CN)2(CNMe), prepared by methylation of 5. The metastable dicarbonyl [(Me3TACN)FeI(CO)2]I was prepared by treatment of FeI2(CO)4 with Me3TACN and was crystallographically characterized as its BPh4- salt. Values of E1/2 for [(Me3TACN)FeCl3]-, 5, and 6 are -0409, -0640, and 0533 V vs Fc/Fc+, respectively.     

The water exchange process of tetraaquaplatinum(II): density-functional theory and ab initio computational study

The water exchange process of square planar tetraaquaplatinum(II) was computationally investigated at the Hartree-Fock, density-functional theory (B3LYP, PW91PW91, and mPW1PW91) and the second-order Moller-Plesset perturbation theory of levels of calculation. The stationary points on the gas phase and on the reaction field potential-energy surface were fully optimized and characterized. The self-consistent reaction field (SCRF) methods were also applied on the same system. The structures and energetic processes of all the species involved were investigated. The kinetic and thermodynamic properties for the gas phase and SCRF model data were compared with the available experimental data. The rate constants in MP2 level of theory and B3LYP isodensity polarized continuum model reaction field are in good agreement with the experimental data.     

Be(II) in aqueous solution--an extended ab initio QM/MM MD study

An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation at double-zeta restricted Hartree-Fock (RHF) level was performed at 293.15 K, including first and second hydration shell in the QM region to study the structural and dynamical properties of the Be(II)-hydrate in aqueous solution. The first tetrahedrally arranged hydration shell, with the four water molecules located at a mean Be-O distance of 1.61 A, is highly inert with respect to ligand exchange processes. The second shell, however, consisting in average of approximately 9.2 water ligands at a mean Be-O distance of 3.7 A and the third shell at a mean Be-O distance of 5.4 A with approximately 19 ligands rapidly exchange water molecules between them and with the bulk, respectively. Other structural parameters such as radial and angular distribution functions (RDF and ADF) and tilt- and theta-angle distributions were also evaluated. The dynamics of the hydrate were studied in terms of ligand mean residence times (MRTs) and librational and vibrational frequencies. The mean residence times for second shell and third shell ligands were determined as 4.8 and 3.2 ps, respectively. The Be-O stretching frequency of 658 cm(-1), associated with a force constant of 147 N m(-1) could be overestimated but it certainly reflects the exceptional stability of the ion-ligand bond in the first hydration shell.     

An equilibrium ab initio atomistic thermodynamics study of chlorine adsorption on the Cu(001) surface

The effect of chlorine (Cl) chemisorption on the energetics and atomic structure of the Cu(001) surface over a wide range of chlorine pressures and temperatures has been studied using equilibrium ab initio atomistic thermodynamics to elucidate the formation of cuprous chloride (CuCl) as part of the Deacon reaction on copper metal. The calculated surface free energies show that the 1/2 monolayer (ML) c(2 × 2)-Cl phase with chlorine atoms adsorbed at the hollow sites is the most stable structure for a wide range of Cl chemical potential, in agreement with experimental observations. It is also found that at very low pressure and exposure, but elevated temperature, the 1/9 ML and 1/4 ML phases become the most stable. By contrast, a high coverage of Cl does not lead to thermodynamically stable geometries. The subsurface adsorption of Cl atoms, however, dramatically increases the stability of the 1 ML and 2 ML adsorption configurations providing a possible pathway for the formation of the bulk-chloride surface phases in the kinetic regime.     

On the structure and torsional potential of trifluoromethoxybenzene: an ab initio and density functional study

The torsional potential of trifluoromethoxybenzene around the aryl–O bond was investigated with the aid of large-scale ab initio calculations performed at the Møller–Plesset second order (MP2) level, with several post-MP2 methods, and with a hybrid density functional method (B3LYP). Contrary to several recent reports, we do not find substantial qualitative differences between MP2 and B3LYP results, provided sufficiently large basis sets are used. The results are confronted with analogous MP2 and B3LYP data for methoxybenzene, for hypothetical anions as obtained by deprotonation at the para-position, and for ethylbenzene. The trends in the calculated torsional potentials, barrier heights and energy differences between conformers are discussed and correlated with selected structural parameters.     

An ab initio intermolecular potential energy surface for the F(2) dimer

Two analytical representations for the potential energy surface of the F(2) dimer were constructed on the basis of ab initio calculations up to the fourth-order of M?ller-Plesset (MP) perturbation theory. The best estimate of the complete basis set limit of interaction energy was derived for analysis of basis set incompleteness errors. At the MP4/aug-cc-pVTZ level of theory, the most stable structure of the dimer was obtained at R = 6.82 au, theta(a) = 12.9 degrees , theta(b) = 76.0 degrees , and phi = 180 degrees , with a well depth of 716 microE(h). Two other minima were found for canted and X-shaped configurations with potential energies around -596 and -629 microE(h), respectively. Hexadecapole moments of monomers play an important role in the anisotropy of interaction energy that is highly R-dependent at intermediate intermolecular distances. The quality of potentials was tested by computing values of the second virial coefficient. The fitted MP4 potential has a more reasonable agreement with experimental values.