Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.     

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.     

Solvation of ligandopentaamminecobalt (III) complexes in dimethyl sulfoxide–water mixtures

The rate constants for the replacement of water from the inner-coordination shell of Co(NH₃)₅OH₂³⁺, I, by dimethyl sulfoxide (DMSO) as DMSO gradually replaced water in the solvation shell of I were found to approach, and finally equal, the water-exchange rate constant of I in aqueous media in accordance with expectation for a dissociative mechanism. Also the rate constants for the replacement of DMSO from the innercoordination shell of Co(NH₃)₅DMSO³⁺, II, by water as water replaced DMSO in the solvation shell of II were found to approach, and approximately equal, the DMSO-exchange rate constant for II in liquid DMSO in accordance with expectation for a dissociative mechanism. The DMSO-exchange rate constant for II in liquid DMSO was determined and found to be equal to (3.6 ± 0.8) × 10^?4 sec^?1 at 45°C. The dissociation quotient, [II] [NO₃^?]/[Co(NH₃)₅NO₃²⁺], was found to be equal to 0.28 ± 0.11 M at 45°C by NMR methods. The pseudo first-order rate constants for anation of II by NO₃^? and the solvation of Co(NH₃)₅NO₃ ²⁺ by DMSO were determined at various temperatures.     

Dinuclear Co(II)Co(III) mixed-valence and Co(III)Co(III) complexes with N- and O-donor ligands: characterization and water oxidation studies

The tridentate ligand N-methyl-N,N-bis(2-pyridylmethyl)amine (L) has been employed to synthesize a dinuclear Co(II)Co(III) mixed-valence complex containing μ-methoxo and μ-carboxylato bridging ligands, [LCo(II)(μ-carboxylato)bis(μ-methoxo)Co(III)L](ClO(4))(2). In this complex, the two pseudo-octahedral Co centers have an identical ligand environment, yet the average Co-N and Co-O bond distances at the two Co ions differ significantly. Electrochemical, spectroscopic, and magnetic susceptibility measurements confirm that it belongs to a localized Class II mixed-valence system, despite the presence of a short Co···Co distance of 3.021 ?. Oxidation of this Co(II)Co(III) complex leads to formation of the corresponding Co(III)Co(III) complex that was characterized structurally and spectroscopically. In addition, dinuclear and trinuclear μ-hydroxo Co(III) complexes have been obtained in the presence of phosphate anions and absence of methanol, respectively, suggesting that an additional bridging ligand is needed to stabilize the Co(III)bis(μ-hydroxo)Co(III) fragment. Moreover, the ability of the mixed-valence Co(II)Co(III) complex and the three related Co(III) complexes to electrocatalytically oxidize water was also investigated. The observed limited water oxidation catalytic ability for these systems suggests that a multinuclear Co cluster and/or presence of O-rich ligands may be needed for the generation of efficient molecular Co-based water oxidation catalysts.     

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.     

Solvation of transmembrane proteins by isotropic membrane mimetics: a molecular dynamics study

Mixtures of organic solvents are often used as membrane mimetics in structure determination of transmembrane proteins by solution NMR; however, the mechanism through which these isotropic solvents mimic the anisotropic environment of cell membranes is not known. Here, we use molecular dynamics simulations to study the solvation thermodynamics of the c-subunit of Escherichia coli F1F0 ATP synthase in membrane mimetic mixtures of methanol, chloroform, and water with varying fractions of components as well as in lipid bilayers. We show that the protein induces a local phase separation of the solvent components into hydrophobic and hydrophilic layers, which provides the anisotropic solvation environment to stabilize the amphiphilic peptide. The extent of this effect varies with solvent composition and is most pronounced in the ternary methanol-chloroform-water mixtures. Analysis of the solvent structure, including the local mole fraction, density profiles, and pair distribution functions, reveals considerable variation among solvent mixtures in the solvation environment surrounding the hydrophobic transmembrane region of the protein. Hydrogen bond analysis indicates that this is primarily driven by the hydrogen-bonding propensity of the essential Asp(61) residue. The impact of the latter on the conformational stability of the solvated protein is discussed. Comparison with the simulations in explicit all-atom models of lipid bilayer indicates a higher flexibility and reduced structural integrity of the membrane mimetic solvated c-subunit. This was particularly true for the deprotonated form of the protein and found to be linked to solvent stabilization of the charged Asp(61).     

Oxidation of mixed-valence Co(III)/Fe(II) complexes reversed at high pH: a kinetico-mechanistic study of water oxidation

The outer-sphere oxidation of Fe(II) in the mixed-valence complex trans-[L(14S)Co(III)NCFe(II)(CN)(6)](-), being L(14S) an N(3)S(2) macrocylic donor set on the cobalt(III) center, has been studied. The comparison with the known processes of N(5) macrocycle complexes has been carried out in view of the important differences occurring on the redox potential of the cobalt center. The results indicate that the outer-sphere oxidation reactions with S(2)O(8)(2-) and [Co(ox)(3)](3-) involve a great amount of solvent-assisted hydrogen bonding that, as a consequence from the change from two amines to sulfur donors, are more restricted. This is shown by the more positive values found for DeltaS(#) and DeltaV(#). The X-ray structure of the oxidized complex has been determined, and it is clearly indicative of the above-mentioned solvent-assisted hydrogen bonding between nitrogen and cyanide donors on the cobalt and iron centers, respectively. trans-[L(14S)Co(III)NCFe(III)(CN)(6)], as well as the analogous N(5) systems trans-[L(14)Co(III)NCFe(III)(CN)(6)], trans-[L(15)Co(III)NCFe(III)(CN)(6)], and cis-[L(13)Co(III)NCFe(III)(CN)(6)], oxidize water to hydrogen peroxide at pH > 10 with a rather simple stoichiometry, i.e., [L(n)()Co(III)NCFe(III)(CN)(5)] + OH(-) --> [L(n)()Co(III)NCFe(II)(CN)(5)](-) + (1)/(2)H(2)O(2). In this way, the reversibility of the iron oxidation process is achieved. The determination of kinetic and thermal and pressure activation parameters for this water to hydrogen peroxide oxidation leads to the kinetic determination of a cyanide based OH(-) adduct of the complex. A second-order dependence on the base concentration is associated with deprotonation of this adduct to produce the final inner-sphere reduction process. The activation enthalpies are found to be extremely low (15 to 35 kJ mol(-1)) and responsible for the very fast reaction observed. The values of DeltaS(#) and DeltaV(#) (-76 to -113 J K(-1) mol(-1) and -5.5 to -8.9 cm(3) mol(-1), respectively) indicate a highly organized but not very compressed transition state in agreement with the inner-sphere one-electron transfer from O(2-) to Fe(III).     

Solvation of the Whelk-O1 chiral stationary phase: a molecular dynamics study

Density functional theory calculations and molecular dynamics simulations are employed to explore the solvation of the Whelk-O1 chiral stationary phase. First, a semi-flexible representation of the Whelk-O1 selective molecule is extracted from an extensive series of B3LYP/6-311+ G(2d,p) calculations. The resulting model is used to build a chiral surface, including end-caps, for molecular dynamics study of the interface between solvent and Whelk-O1. Three solvent environments in common use for Whelk-O1 HPLC have been examined: a normal-phase solvent of n-hexane/2-propanol; a reversed-phase solvent of water/methanol; and a supercritical solvent of CO(2) and methanol. In each case, we analyze the interface with an emphasis on solvent composition and solvent hydrogen bonding to the Whelk-O1 selector.     

Coordination mode of nitrate in uranyl(VI) complexes: a first-principles molecular dynamics study

According to Car-Parrinello molecular dynamics simulations for [UO(2)(NO(3))(3)](-), [UO(2)(NO(3))(4)](2-), and [UO(2)(OH(2))(4-)(NO(3))](+) complexes in the gas phase and in aqueous solution, the nitrate coordination mode to uranyl depends on the interplay between ligand-metal attractions, interligand repulsions, and solvation. In the trinitrate, the eta(2)-coordination is clearly favored in water and in the gas phase, leading to a coordination number (CN) of 6. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, a change in free energy of +6 kcal/mol is predicted for eta(2)- to eta(1)-transition of one of the three nitrate ligands in the gas phase. In the gas phase, the mononitrate-hydrate complex also prefers a eta(2)-binding mode but with a CN of 5, one H(2)O molecule being in the second shell. This contrasts with the aqueous solution where the nitrate binds in a eta(1)-fashion and uranyl coordinates to four H2O ligands. A driving force of ca. -3 kcal/mol is predicted for the eta(2)- to eta(1)- transition in water. This structural preference is interpreted in terms of steric arguments and differential solvation of terminal vs uranyl-coordinated O atoms of the nitrate ligands. The [UO(2)(NO(3))(4)](2-) complex with two eta(2)- and two eta(1)- coordinated nitrates, observed in the solid state, is stable for 1-2 ps in the gas phase and in solution. In the studied series, the modulation of uranyl-ligand distances upon immersion of the complex in water is found to depend on the nature of the ligand and the composition of the complex.     

Dinuclear Co(III)/Co(III) and Co(II)/Co(III) mixed-valent complexes: synthetic control of the cobalt oxidation level

The reactivity of cobalt(II) salts towards H(3)L (2-(2-hydroxyphenyl)-1,3-bis[4-(2-hydroxyphenyl)-3-azabut-3-enyl]-1,3-imidazolidine) was studied in different reaction conditions. Accordingly, the interaction of cobalt(II) acetate with H(3)L in methanol gives rise to the discrete complex [Co(III)(2)L(OAc)(2)(OMe)]*1.5H(2)O.MeOH, 1. Reaction of cobalt(II) acetylacetonate with H(3)L in the presence of dicarboxylic acids was also investigated. Thus, when cobalt(II) acetylacetonate and H(3)L are mixed with terephthalic or malonic acid in 4 : 2 : 1 molar ratios, the mixed valent [Co(II/III)(2)L(acac)(p-O(2)CC(6)H(4)CO(2)H)][Co(II/III)(2)L(acac)(OH)]*2H(2)O*2MeOH, 2 and [Co(II/III)(2)L(acac)(O(2)CCH(2)CO(2)H)][Co(II/III)(2)L(acac)(OH)]*7H(2)O, complexes are isolated. Decreasing the pH of the medium, by addition of a second mol of dicarboxylic acid, leads to [Co(II/III)(2)L(O(2)CCH(2)CO(2))(MeOH)]*2MeOH, 4, while the reaction with terephthalic acid does not proceed. 1, 2 and 4 were crystallographically characterised and all the complexes are dinuclear, with hydrogen bonds that expand the initial nodes. The magnetic characterisation, as well as the NMR spectroscopy, indicates a diamagnetic nature for 1, in agreement with the presence of Co(III), showing the aerial oxidation suffered by the cobalt(II) ions. Nevertheless, are paramagnetic. Temperature variable magnetic measurements were recorded for the crystallographically characterised complexes 2 and 4 and these studies confirm the mixed valence Co(II)/Co(III) nature of the compounds. The best fits of the magnetic data give an axial distortion parameter Delta = 628.7 cm(-1) for 2 and 698.8 cm(-1) for 4, and spin-orbit coupling constant lambda = -117.8 cm(-1) for 2 and -107.0 cm(-1) for 4. Therefore, this study shows that the oxidation degree of the initial cobalt(ii) salt by atmospheric oxygen can be controlled according to the pH of the medium.     

Solvation of inorganic complexes: transfer chemical potentials for mono- and bi-nuclear cobalt(III) complexes to methanol + water mixtures

Solubilities in MeOH--H₂O mixtures at 298.2 K are reported for a number of salts of mono- and bi-nuclear cobalt(III) complexes. From these solubilities and published single ion transfer chemical potentials, on the TPTB (Ph₄P⁺ = BPh^– ₄ ) assumption, transfer chemical potentials have been derived for these mono- and bi-nuclear cobalt(III) complexes. The results and trends are discussed in relation to those for other complexes and ions in these binary aqueous solvent mixtures.     

Synthesis of Co(III) molybdoheteropolyanions using carbonato-ammine Co(III) complexes as starting materials

The preparation of two cobalt(III) molybdoheteropolyanions, [CoMo₆O₂₄H₆]³⁻ and [Co₂Mo₁₀O₃₈H₄]⁶⁻, was systematically studied using some carbonato-ammine cobalt(III) complexes as starting materials. The selectivity and yields of products were significantly influenced by the number of ammine ligands and the charge on the complexes.     

Structure and dynamics of water surrounding the poly(methacrylic acid): a molecular dynamics study

All-atom molecular dynamics simulations are used to study a single chain of poly(methacrylic acid) in aqueous solutions at various degrees of charge density. Through a combination of analysis on the radial distribution functions of water and snapshots of the equilibrated structure, we observe that local arrangements of water molecules, surrounding the functional groups of COO- and COOH in the chain, behave differently and correlated well to the resulting chain conformation behavior. In general, due to strong attractive interactions between water and charged COO- via the formation of hydrogen bonds, water molecules tend to form shell-like layers around the COO- groups. Furthermore, water molecules often act as a bridging agent between two neighboring COO- groups. These bridged water molecules are observed to stabilize the rodlike chain conformation that the highly charged chain reveals, as they significantly limit torsional and bending degrees of the backbone monomers. In addition, they display different dynamic properties from the bulk water. Both the resulting oxygen and hydrogen spectra are greatly shifted due to the presence of strong H-bonded interactions.     

Solvation of xyloglucan in water/alcohol systems by molecular dynamics simulation

Xyloglucan in water solution turns into a gel with addition of alcohol such as methanol and ethanol. In regard to this phenomenon, we investigated the adhesive property of alcohol to xyloglucan and proposed the mechanism of the gelation by molecular dynamics (MD) simulation of a xyloglucan in water, water/methanol, and water/ethanol solution for 10 ns. The alcohol molecules showed its adhesive property to the xyloglucan and made the swelling-shrinking motion of the xyloglucan slow. Alcohol molecules solvated to the xyloglucan mainly in hydrophobic way so as to fill the void of water hydration shell, resulting in reformation of the hydrogen-bond network of water molecules around the solute. We also found that alcohol molecules have strong tendency to hydrogen-bond on xylose O3 in xyloglucan. According to these results, we proposed the gelation mechanism of xyloglucan in water/alcohol solution.     

Solvation of sodium chloride in the 1-butyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide ionic liquid: a molecular dynamics study

We report molecular dynamics studies on the solvation of sodium chloride in the 1-butyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide ionic liquid ([BMI][Tf2N] IL). We first consider the potential of mean force for dissociating a single Na+Cl- ion pair, showing that the latter prefers to be undissociated rather than dissociated (by ca. 9 kcal/mol), with a free energy barrier of ca. 5 kcal/mol (at d approximately 5.2 A) for the association process. The preference for Na+Cl- association is also observed from a 100 ns molecular dynamics simulation of a concentrated solution, where the Na+Cl- ions tend to form oligomers and microcrystals in the IL. Conversely, the simulation of Na13Cl14- and Na14Cl13+ cubic microcrystals (with, respectively, Cl- and Na+ at the vertices) does not lead to dissolution in the IL. Among these, Na14Cl13+ is found to be better solvated than Na13Cl14-, mainly due to the stronger Na+...Tf2N- interactions as compared to the Cl-...BMI+ interactions at the vertices of the cube. We finally consider the solid/liquid interface between the 100 face of NaCl and the IL, revealing that, in spite of its polar nature, the crystal surface is solvated by the less polar IL components (CF3(Tf2N) and butyl(BMI) groups) rather than by the polar ones (O(Tf2N) and imidazolium(BMI) ring). Specific ordering at the interface is described for both Tf2N- anions and BMI+ cations. In the first IL layer, the ions are rather parallel to the surface, whereas in the second "layer" they are more perpendicular. A similar IL structure is found at the surface of the all-neutral Na0Cl0 solid analogue, confirming that the solvation of the crystal is rather "apolar", due to the mismatch between the IL and the crystal ions. Several comparisons with water, methanol, or different BMI+-based ILs as solvents are presented, allowing us to better understand the specificity of the ionic liquid-NaCl interactions.     

Phenolate and phenoxyl radical complexes of Co(II) and Co(III)

The new phenol-imidazole pro-ligands (R)LH react with Co(BF(4))(2).6H(2)O in the presence of Et(3)N to form the corresponding [Co(II)((R)L)(2)] compound (R = Ph (1), PhOMe (2), or Bz (3)). Also, (Bz)LH, reacts with Co(ii) in the presence of Et(3)N and H(2)O(2) to form [Co(III)((Bz)L)(3)](4). The structures of 1.2.5MeCN, 2.2DMF, 3.4MeOH, and 4.4DMF have been determined by X-ray crystallography. 1, 2, and 3 each involve Co(II) bound to two N,O-bidentate ligands with a distorted tetrahedral coordination sphere; 4 involves Co(III) bound to three N,O-bidentate ligands in a mer-N(3)O(3) distorted octahedral geometry. [Co(II)((R)L)(2)](R = Ph or PhOMe) undergo two, one-electron, oxidations. The products of the first oxidation, [1](+) and [2](+), have been synthesised by the chemical oxidation of 1 and 2, respectively; these cations, formulated as [Co(II)((R)L*)((R)L)(2)](+), comprise one phenoxyl radical and one phenolate ligand bound to Co(II) and are the first phenoxyl radical ligand complexes of tetra-coordinated Co(II). 4 undergoes two, one-electron, ligand-based oxidations, the first of which produces [4](+), [Co(III)((Bz)L*)((Bz)L)(2)](+). Unlike [1](+) and [2](+), product of the one-electron oxidation of [Co(II)((Bz)L)(2)], [3](+), is unstable and decomposes to produce [4](+). These studies have demonstrated that the chemical properties of [M(II)((R)L*)((R)L)(2)](+)(M = Co, Cu, Zn) are highly dependent on the nature of both the ligand and the metal centre.     

Dinuclear triple helical Mn(III), Fe(III) and Co(III) complexes

Synthesis, characterization and physical properties of the dinuclear triple helical complexes [Mn₂(μ-L)₃] (1), [Fe₂(μ-L)₃] (2) and [Co₂(μ-L)₃] (3) with the tetradentate Schiff base (H₂L) derived from 1 mol equiv. of hydrazine and 2 mole equiv. of 2-hydroxy-1-naphthaldehyde are described. Triple helical molecular structures of 2 and 3 have been confirmed by X-ray crystallography. Magnetic susceptibility measurements reveal complex 3 is diamagnetic while a weak antiferromagnetic interaction is operative between the metal centres in both 1 and 2.     

Solvation phenomena of a tetrapeptide in water/trifluoroethanol and water/ethanol mixtures: a diffusion NMR,intermolecular NOE,and molecular dynamics study

Solvation of a tetrapeptide, NAc-Ser-Phe-Val-Gly-OMe (1), in water and in water/alcohol mixtures with 2,2,2-trifluoroethanol (TFE)/water or ethanol (ETH)/water has been studied by diffusion NMR and intermolecular NOE measurements. The experimental results were compared with those obtained from detailed Molecular Dynamics (MD) calculations. Independently, all three methods revealed preferential solvation on the surface of the peptide by TFE in the water/TFE mixtures, but not by ETH in the water/ETH mixtures. The MD calculations show that the TFE concentration coating the peptide is higher than that in the bulk, while for ethanol, the concentration is nearly equal to that in the bulk. Calculated site-specific preferential solvation data between TFE, ETH, and water with the different peptide groups have been compared with the NMR data and shown to be in general agreement with the experimental facts.