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

Influence of Number of Ligands and Point Group on the Electronic Structure of Co2+ Aqua-Complexes

The nucleation process of zeolitic imidazolate frameworks (ZIFs) is, to date, not yet completely understood, making the search for tailored materials very difficult. Recently, it has been shown that, during the formation process, the symmetry of the precursors is reduced by ligand elimination and substitution reactions. The octahedral precursors with simple ligands, such as water, methanol, and/or NO₃^-, are transformed to five- and finally four-coordinated complexes with imidazole ligands. This reduction of symmetry, caused both by the changing coordination environment and distortions from the perfect symmetry leading to another point group, will have a large influence on the electronic structure and more specifically on the d-orbital splitting. This, in turn, will affect the d-d electronic excitations, which can be followed using UV-vis spectroscopy and which can help to unravel the formation process. In this work, we systematically investigate how the lowering of the number of ligands affects the symmetry and thus the geometry and electronic structure of Co²⁺ complexes with six, five, and four aqua ligands. Therefore, we first resort to qualitative techniques, such as crystal field theory (CFT) and ligand field theory (LFT), which reveal that the orbital splitting is characteristic for the number of ligands. However, as these techniques are not capable of providing quantitative results without the use of experimental data as input, we perform various computational calculations. Both average of configuration (AOC) and unrestricted density functional theory (UDFT) are thoroughly investigated, and we will determine which technique is the best suited to properly describe the ground state of these systems. To investigate the dependency on the d-orbital occupation, we also investigated V²⁺, Mn²⁺, and Ni²⁺ hexa-aqua-complexes and compared them to the Co systems.

Vacuolar H+ -ATPase is involved in preventing heavy metal-induced oxidative stress in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, vacuolar H⁺ -ATPase (V-ATPase) involved in the regulation of intracellular pH homeostasis has been shown to be important for tolerances to cadmium, cobalt and nickel. However, the molecular mechanism underlying the protective role of V-ATPase against these metals remains unclear. In this study, we show that cadmium, cobalt and nickel disturbed intracellular pH balance by triggering cytosolic acidification and vacuolar alkalinization, likely via their membrane permeabilizing effects. Since V-ATPase plays a crucial role in pumping excessive cytosolic protons into the vacuole, the metal-sensitive phenotypes of the Δvma2 and Δvma3 mutants lacking V-ATPase activity were supposed to result from highly acidified cytosol. However, we found that the metal-sensitive phenotypes of these mutants were caused by increased production of reactive oxygen species, likely as a result of decreased expression and activities of manganese superoxide dismutase and catalase. In addition, the loss of V-ATPase function led to aberrant vacuolar morphology and defective endocytic trafficking. Furthermore, the sensitivities of the Δvma mutants to other chemical compounds (i.e. acetic acid, H₂ O₂ , menadione, tunicamycin and cycloheximide) were a consequence of increased endogenous oxidative stress. These findings, therefore, suggest the important role of V-ATPase in preventing endogenous oxidative stress induced by metals and other chemical compounds.

Interaction between transition metals and phenylalanine: a combined experimental and computational study

Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M=Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal-oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal-nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV-vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d-d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic.

Mass spectrometric detection, identification, and fragmentation of arseno-phytochelatins

Phytochelatins (PC) are cystein-rich oligopeptides in plants for coordination with toxic metals and metalloids via their thiol groups. The composition, structure, and mass spectrometric fragmentation of arseno-PC (As-PC) with PC of different degree of oligomerization (PC2-PC5) in solution were studied using liquid chromatography coupled in parallel to inductively coupled plasma mass spectrometry and electrospray ionization quadrupole time-of-flight mass spectrometry. As-PC were detected from As(PC2) to As(PC5) with an increasing number of isomers that differ in the position of thiol groups bound to As. Thermodynamic modeling supported the identification process in case of these isomers. Mass spectrometric fragmentation of the As-PC does not follow the established pattern of peptides but is governed by the formation of series of As-containing annular cations, which coordinate to As via S, N, or O. Structure proposals for 30 As-PC fragment ions in the range m/z 147.92 to m/z 1290.18 are elaborated. Many of these fragment ions are characteristic to several As-PC and may be suited for a screening for As-PC in plant extracts. The mass spectrometric data offer the perspective for a future more sensitive determination of As-PC by means of liquid chromatography tandem mass spectrometry with multiple reaction monitoring.

What first principles molecular dynamics can tell us about EXAFS spectroscopy of radioactive heavy metal cations in water

In this paper we show how molecular dynamics simulation can improve comprehension of structure and dynamics of water solvent around heavy cations. In particular, metal-water radial distribution function obtained from molecular dynamics can be used into EXAFS equation to improve the experimental signal fitting. Here we show results on structure and dynamics of Co2+, that is a radiocontaminant cation in its isotopic form 60Co, and lanthanoids(III) that are the chemical analogues of actinides(III) in aqueous solution.

Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations

Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?

Structures and fragmentations of cobalt(II)-cysteine complexes in the gas phase

The electronebulization of a cobalt(II)/cysteine(Cys) mixture in water/methanol (50/50) produced mainly cobalt-cationized species. Three main groups of the Co-cationized species can be distinguished in the ESI-MS spectrum: (1) the cobalt complexes including the cysteine amino acid only (they can be singly charged, for example, [Co(Cys)n- H]+ with n = 1-3 or doubly charged such as [Co + (Cys)2]2+); (2) the cobalt complexes with methanol: [Co(CH3OH)n- H]+ with n = 1-3, [Co(CH3OH)4]2+; and (3) the complexes with the two different types of ligands: [Co(Cys)(CH3OH) - H]+. Only the singly charged complexes were observed. Collision-induced dissociation (CID) products of the [Co(Cys)2]2+, [Co(Cys)2 - H]+ and [Co(Cys) - H]+ complexes were studied as a function of the collision energy, and mechanisms for the dissociation reactions are proposed. These were supported by the results of deuterium labelling experiments and by density functional theory calculations. Since [Co(Cys) - H]+ was one of the main product ions obtained upon the CID of [Co(Cys)2]2+ and of [Co(Cys)2 - H]+ under low-energy conditions, the fragmentation pathways of [Co(Cys) - H]+ and the resulting product ion structures were studied in detail. The resulting product ion structures confirmed the high affinity of cobalt(II) for the sulfur atom of cysteine.

A Coupled Car-Parrinello Molecular Dynamics and EXAFS Data Analysis Investigation of Aqueous Co2+

We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.

Co2+ Binding Cysteine and Selenocysteine: A DFT Study

In this paper we report structural and energetic data for cysteine and selenocysteine in the gas phase and the effect of Co(2+) complexation on their properties. Different conformers are analyzed at the DFT/B3LYP level of both bound and unbound species. Geometries, vibrational frequencies, and natural population analysis are reported and used to understand the activity of these species. In particular, we have focused our attention on the role of sulfur and selenium in the metal binding process and on the resulting deprotonation of the thiol and seleniol functions. From the present calculations we are able to explain, both from electronic structure and thermochemical point of views, a metal-induced thiol deprotonation as observed in gas-phase experiments. A similar process is expected in the case of selenocysteine. In fact, cobalt was found to have a preferential affinity with respect to thiolate and selenolate functions. This can be related to the observation that only S and Se are able-in thiolate and selenolate states-to make a partial charge transfer to the cobalt thus forming very stable complexes. Globally, very similar results are found when substituting S with Se, and a very small difference in cobalt binding affinity is found, thus justifying the use of this substitution in X-ray absorption experiments done on biomolecules containing cysteine metal binding pockets.