Solvation of Co(III)-cysteinato complexes in water: a DFT-based molecular dynamics study

Structural, dynamical, and vibrational properties of complexes made of metal cobalt(III) coordinated to different amounts of cysteine molecules were investigated with DFT-based Car-Parrinello molecular dynamics (CPMD) simulations in liquid water solution. The systems are composed of Co(III):3Cys and Co(III):2Cys immersed in liquid water which are modeled by about 110 explicit water molecules, thus one of the biggest molecular systems studied with ab initio molecular simulations so far. In such a way, we were able to investigate structural and dynamical properties of a model of a typical metal binding site used by several proteins. Cobalt, mainly a toxicological agent, can replace the natural binding metal and thus modify the biochemical activity. The structure of the surrounding solvent around the metal-ligands complexes is reported in detail, as well as the metal-ligands coordination bonds, using radial distribution functions and electronic analyses with Mayer bond orders. Structures of the Cocysteine complexes are found in very good agreement with EXAFS experimental data, stressing the importance of considering the surrounding solvent in the modeling. A vibrational analysis is also conducted and compared to experiment, which strengthens the reliability of the solvent interactions with the Cocysteine complexes from our molecular dynamics simulations, as well as the dynamics of the systems. From this preliminary analysis, we could suggest a vibrational fingerprint able to distinguish Co(III):2Cys from Co(III):3Cys. Our simulations also show the importance of considering a quantum explicit solvent, as solute-to-solvent proton transfer events have been observed.     

Toward a microscopic description of molecular electronic systems

The many-body perturbation theory is reformulated within the dielectric function method presented in the preceding paper [12]. The self-energy effects are explicitly considered. These corrections turn out to be important and are calculated to the same level of approximation as the corresponding local-field terms. The method is at the moment applicable to π-electron systems within the zero differential overlap approximation. Explicit calculations of the excitation energies for the benzene molecule, using different parametrizations, are presented. Comparison is made with the results obtained in the random phase approximation (RPA ) and other schemes.     

Toward a photochemical and thermal molecular machine: reversible ligand dissociation and binding in a ruthenium(II)-2,2'-bipyridine complex with tris(2-pyridylmethyl)amine

A Ru(II) complex having tris(2-pyridylmethl)amine (TPA) and 2,2'-bipyridine (bpy), [Ru(TPA)(bpy)]X(2) (X = ClO(4), PF(6)), exhibited a severe distortion of the coordination of the axial pyridine moiety of TPA due to steric hindrance. The complex showed interesting dissociation-binding behavior of the axial pyridine arm to form a solvent adduct with TPA ligation in a unique meridional tridentate fashion. The complex undergoes thermal dissociation to form solvent-coordinated species via an S(N)2-like mechanism with activation energy of 117 kJ/mol. In contrast, the complex showed reversible photochemical dissociation and rebinding via an S(N)1-like mechanism by MLCT irradiation. The photochemical dissociation was accelerated approximately 200-fold faster than the thermal process. The dissociation process involves selective binding behavior toward external ligands (solvents) with pi-acceptor character, which is indispensable, and no sigma-donating molecules could bind to the Ru(II) center. The guest molecule can be released upon photoirradiation after its thermal binding.     

Co(II) and Co(III) complexes of m-benziphthalocyanine

The syntheses and structural elucidations of three different cobalt complexes of m-benziphthalocyanine are reported; both Co(II) and Co(III) complexes can be generated, and the ring undergoes partial oxidation upon metalation with Co(OAc)2x4H2O.     

Potentiometric titration of Co(II) in presence of Co(III)

A potentiometric titration for cobalt(II) determination in the presence of Co(III) based on the oxidation of Co(II) with Na₂CrO₄ in ethylenediamine medium and back-titration of the oxidant excess with (NH₄)₂Fe(SO₄)₂ in acid medium is described. The titration is monitored with a Pt indicator electrode and carried out until the greatest jump of potential from one drop of titrant appears. A RSD smaller than 1.5% has been obtained for 50–300 μmol Co(II). The method proposed was applied in the analysis of a new type electroless copper plating solutions containing Co(II)-ethylenediamine complex compounds as reducing agents. Cu(II), Co(III) and Cr(III) do not interfere in the determination of Co(II).     

Co(II) and Co(III) macrocyclic boron-bearing dioximates

Syntheses are reported for CoD₃(BF)₂ and [CoD₃(BF)₂]BF₄,where H ₂ D is dimethylglyoxime, -benzyldioxime, or cyclohexanedione dioxime. The IR spectra at 400–4000 cm ^–1 have been measured, as have the electronic absorption spectra and the¹H,¹³C,and ¹¹BNMR spectra; a comparison is made with the spectra of the analogous iron(II) complexes.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 26, No. 3, pp. 375–377, May–June, 1990.     

Toward the supramolecular structure of collagen: a molecular dynamics approach

The structure, stability, and conformational dynamics of an assembly of two pentameric bundles made of collagen-like triple helical segments are explored using 1.2 ns molecular dynamics simulations in three environments: 8.0% (v/v) formaldehyde/water solution, 1.4% (v/v) gallic acid/water solution, and pure water. Stable supramolecular arrangements, where the two collagen units are very close to each other at interacting distances, are identified via docking and energy minimization procedures. Analysis of the interaction with formaldehyde and gallic acid suggests that they perturb the protein in a similar way depending on hydrogen-bonding capability, hydrophobic association properties, and the size and concentration of the compound.     

Dinuclear [Co(II)(NCMe)5Co(II)(NCS)4] possessing octahedral and tetrahedral Co(II) sites

The structural and magnetic properties of dinuclear [Co(II)(NCMe)(5)Co(II)(NCS)(4)]·MeCN have been investigated. The structure consists of an octahedral Co(II)(NCMe)(5) center connected to a tetrahedral Co(II)(NCS)(4) center bridged by a μ(1,3)-NCS(-) ligand. The bridging NCS(-) weakly couples the pair of S = (3)/(2) Co(II) spin sites, as evidenced by the magnetic data being best fit by the Curie-Weiss expression with θ = -15.5 K.     

Effect of poly(ethylene glycol) (PEG) spacers on the conformational properties of small peptides: a molecular dynamics study

Poly(ethylene glycol) (PEG) is used as an inert spacer in a wide range of biotechnological applications such as to display peptides and proteins on surfaces for diagnostic purposes. In such applications it is critical that the peptide is accessible to solvent and that the PEG does not affect the conformational properties of the peptide to which it is attached. Using molecular dynamics (MD) simulation techniques, we have investigated the influence of a commonly used PEG spacer on the conformation properties of a series of five peptides with differing physical-chemical properties (YGSLPQ, VFVVFV, GSGGSG, EEGEEG, and KKGKKG). The conformational properties of the peptides were compared (a) free in solution, (b) attached to a PEG-11 spacer in solution, and (c) constrained to a two-dimensional lattice via a (PEG-11)(3) spacer, mimicking a peptide displayed on a surface as used in microarray techniques. The simulations suggest that the PEG spacer has little effect on the conformational properties of small neutral peptides but has a significant effect on the conformational properties of small highly charged peptides. When constrained to a two-dimensional surface at peptide densities similar to those used experimentally, it was found that the peptides, in particular the polar and nonpolar peptides, aggregated strongly. The peptides also partitioned into the PEG layer. Potentially, this means that at high packing densities only a small fraction of the peptide attached to the surface would in fact be accessible to a potential interaction partner.     

N-vinylcarbazole polymerization by 13X molecular sieve exchanged with Mn(II), Co(II), Ni(II), Cu(II) and Zn(II)

The polymerization of N-vinylcarbazole by 13X molecular sieves modified by five different transition metal ions, viz. Mn(II), Co(II), Ni(II), Cu(II) and Zn(II), has been studied under various conditions. The order of reactivity follows the trend: Mn(II) ≈ Cu(II) > Co(II) > Zn(II) > Ni(II) at pH ∼ 3.55 and an exchange level of 30% of the metal ion. The polymerizations are believed to occur by a dual-ion-initiation mechanism in which both metal ions and proton centres participate. The overall energy of activation (E_a) for each system decreases with decreasing pH of the exchanging salt solution. Average activation energy on proton centre (E_H) and that on metal ion centre (E_a) have been evaluated for each system. E_a, E_H and E_c have been shown to correlate with one another. The molecular weights and their distributions are affected by the nature of the metal ion and also by the protonic centres. The possibility of a correlation of the catalytic activity of the modified 13X with ionic radius, electronegativity and normal co-ordination number has been examined.     

Complexation of Co(II) Tetra-p-methoxyphenylporphine with molecular oxygen in the presence of unsaturated hydrocarbons

Conclusions It has been established that Co(II) porphyrins form five-coordinated complexes with olefins having a high level of donor capability, and six-coordinated complexes in the presence of oxygen. For these systems, we have found the equilibrium constants and the rate constant for the forward reaction of formation of the six-coordinated complex with oxygen in the example of 2-methyl-1-butene.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 533–536, March, 1984.     

Reexamination of lead(II) coordination preferences in sulfur-rich sites: implications for a critical mechanism of lead poisoning

Recent studies suggest that the developmental toxicity associated with childhood lead poisoning may be attributable to interactions of Pb(II) with proteins containing thiol-rich structural zinc-binding sites. Here, we report detailed structural studies of Pb(II) in such sites, providing critical insights into the mechanism by which lead alters the activity of these proteins. X-ray absorption spectroscopy of Pb(II) bound to structural zinc-binding peptides reveals that Pb(II) binds in a three-coordinate Pb(II)-S(3) mode, while Zn(II) is known to bind in a four-coordinate mode in these proteins. This Pb(II)-S(3) coordination in peptides is consistent with a trigonal pyramidal Pb(II)-S(3) model compound previously reported by Bridgewater and Parkin, but it differs from many other reports in the small molecule literature which have suggested Pb(II)-S(4) as a preferred coordination mode for lead. Reexamination of the published structures of these "Pb(II)-S(4)" compounds reveals that, in almost all cases, the coordination number of Pb is actually 5, 6, or 8. The results reported herein combined with this new review of published structures suggest that lead prefers to avoid four-coordination in sulfur-rich sites, binding instead as trigonal pyramidal Pb(II)-S(3) or as Pb(II)-S(5-8). In the case of structural zinc-binding protein sites, the observation that lead binds in a three-coordinate mode, and in a geometry that is fundamentally different from the natural coordination of zinc in these sites, explains why lead disrupts the structure of these peptides and thus provides the first detailed molecular understanding of the developmental toxicity of lead.     

A novel mixed-valence complex containing Co(II)(2)Co(III)(2) molecular squares with 4,5-imidazoledicarboxylate bridges

A heterometallic complex, Na(2)[Co(II)(2)Co(III)(2)(IDC(3-))(4)(bipy)(4)].12H(2)O (bipy = 2,2'-bipyridine), in which mixed-valence tetranuclear squares with imidazoledicarboxylate (IDC(3-)) linkers are tethered into a unique chain through disodium units, is hydrothermally synthesized and structurally and magnetically characterized.     

Mechanism of copper(II) inhibiting Alzheimer's amyloid beta-peptide from aggregation: a molecular dynamics investigation

The aggregation of an amyloid beta peptide (Abeta) into fibrils is a key pathological event in Alzheimer's disease (AD). Under certain conditions, Cu2+ markedly inhibits Abeta from aggregation and is considered as a potential factor in the normal brain preventing Abeta from aggregation. The possible mechanism of the inhibitory effect of Cu2+ was investigated for the first time by molecular dynamics (MD) simulations. On the basis of the radial distribution function analysis of the MD data, a novel strategy, the Q function, was proposed to explore the binding sites of Cu2+ by evaluating the coordination priority of atoms in Abeta, and the [6-5-5] tri-ring 4N binding mode of the Cu2+-Abeta complexes was found. The mechanism of the conformational transition of Abeta from the beta conformation to distorted beta conformations, which destabilizes the aggregation of Abeta into fibrils, was also revealed. All the results provide helpful clues for an improved understanding of the role of Cu2+ in the pathogenesis of AD and contribute to the development of an anti-amyloid therapeutic strategy.     

Template synthesis and physicochemical studies of 14-membered hexaazmacrocyclic complexes with Co(II), Ni(II), Cu(II) and Zn(II): a comparative spectroscopic approach on DNA binding with Cu(II) and Ni(II) complexes

A new series of 14-membered pendant arm hexaazamacrocyclic complexes of the type [MLX₂] · [M = Co(II), Ni(II), Cu(II) or Zn(II) for X = Cl; Co(II), Ni(II), Cu(II) or Zn(II) for X = NO₃] has been synthesized by metal template condensation of 1,2-phenylenediamine and 1,4-phenylenediamine with formaldehyde in methanol. The mode of bonding and overall geometry of these complexes have been deduced by elemental analyses, molar conductance values, FT-IR, ¹H-NMR, ¹³C-NMR, EPR, ESI-mass and UV–VIS along with magnetic measurement studies. The fluorescence and UV–VIS studies revealed a significant binding ability to DNA.     

Formation of unusual molecular rectangles and squares containing low spin and high spin Co(II) and Fe(II) centers

The ditopic carbohydrazide and thiocarbohydrazide based ligands H?L1 and H?L2 react with Co(II)(OAc)? to produce the homoleptic Co(II) molecular rectangles 1 and 2, containing either a mixture of high spin and low spin Co(II) sites or exclusively low spin Co(II) centers, respectively, with two mono-deprotonated ligands in a syn-conformation, and the other two doubly-deprotonated ligands in an anti-arrangement. The Co(II) centers are bridged by μ-O/S and μ-N-N groups, respectively. Magnetic susceptibility measurements indicate weak antiferromagnetic coupling between metal centers in 1 and 2, with room temperature magnetic moments of 6.6 and 3.4 μ(B), respectively, in good agreement with two S = 3/2 and two S = 1/2 centers for 1 and four S = 1/2 centers for 2. Reaction of H?L1 and H?L2 with Fe(II)(CF?SO?)? in the presence of a base leads to the formation of μ-O/S bridged homoleptic molecular squares 3 and 4, with the Fe(II) centers in high spin and low spin configurations, respectively at room temperature, as indicated from X-ray structural data and magnetic susceptibility measurements. However, in 3 one Fe(II) site undergoes spin crossover to a low spin state at about 150 K, while 4 stays diamagnetic in the full 2-300 K temperature range. Electrochemistry of 4 showed four distinct reversible red-ox waves associated with step-by-step one electron processes in the molecular square [-0.643 (ΔE(p) = 81 mV), -0.278 (ΔE(p) = 70 mV), +0.565 (ΔE(p) = 65 mV), ~1.1 V], associated with the Fe(II)/Fe(III) red-ox couples.