Hydrogen Bonding between Metal‐Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies

The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal‐ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground‐state molecules, prior to interaction, can provide considerable insight into the interactions.     

Self-assembly of peptide porphyrin complexes: toward the development of smart biomaterials

The anionic porphyrin, meso-tetrakis(4-sulfonatophenyl)porphine, is found to tightly bind to an engineered 14-residue peptide, resulting in induced alpha-helix formation when mixed in aqueous solutions. The small porphyrin-peptide dissociation constant (2 muM) observed is related to the energetics of peptide helix formation coupled with electrostatic interactions between the anionic porphyrin and cationic residues in the coiled peptide. Analytical ultracentrifugation measurements indicate the porphyrin-peptide complexes dimerize, probably into a coiled coil, and weakly associate to form even higher order structures.     

Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods

We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim benzoate groups, OAM and OAH, respectively). We employed free-energy perturbation (FEP) for relative binding energies at the molecular mechanics (MM) and the combined quantum mechanical (QM) and MM (QM/MM) levels, the latter obtained with the reference-potential approach with QM/MM sampling for the MM → QM/MM FEP. The semiempirical QM method PM6-DH+ was employed for the ligand in the latter calculations. Moreover, binding free energies were also estimated from QM/MM optimised structures, combined with COSMO-RS estimates of the solvation energy and thermostatistical corrections from MM frequencies. They were performed at the PM6-DH+ level of theory with the full host and guest molecule in the QM system (and also four water molecules in the geometry optimisations) for 10–20 snapshots from molecular dynamics simulations of the complex. Finally, the structure with the lowest free energy was recalculated using the dispersion-corrected density-functional theory method TPSS-D3, for both the structure and the energy. The two FEP approaches gave similar results (PM6-DH+/MM slightly better for OAM), which were among the five submissions with the best performance in the challenge and gave the best results without any fit to data from the SAMPL5 challenge, with mean absolute deviations (MAD) of 2.4–5.2 kJ/mol and a correlation coefficient (R²) of 0.77–0.93. This is the first time QM/MM approaches give binding free energies that are competitive to those obtained with MM for the octa-acid host. The QM/MM-optimised structures gave somewhat worse performance (MAD?=?3–8 kJ/mol and R²?=?0.1–0.9), but the results were improved compared to previous studies of this system with similar methods.     

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking,MM/GBSA,QM/MM,and free-energy simulations

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970–1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.     

Kinetics and mechanism of biphasic substitution reactions of a platinum(II) complex with thioglycollic acid and 4-methyl-3-thiosemicarbazide in aqueous solution

The kinetics of interactions between cis-diaqua(2-aminomethylpyridine)platinum(II) perchlorate (1) [Pt(pic)(OH₂)₂](ClO₄)₂, thioglycollic acid (TGA), and 4-methyl-3-thiosemicarbazide (MTSC) have been studied spectrophotometrically in aqueous medium as a function of the [complex (1)] as well as [TGA] or [MTSC], pH and temperature at constant ionic strength. The observed pseudo-first-order rate constants were proportional to [TGA] or [MTSC]. At pH 4.0, the interactions of (1) with both TGA and MTSC show two distinct consecutive steps; the first step is dependent and second independent of [TGA] or [MTSC]. The association equilibrium constant (K _E) for the outer sphere complex formation has been evaluated, along with the rate constants for the two steps. The first step is assigned to ligand-assisted anation and the second to chelation of TGA or MTSC. The activation parameters for both the steps were evaluated using Eyring’s equation. On the basis of the kinetic observations and evaluated activation parameters, an associative mechanism is proposed for both the reactions.     

Self-organized patterning on Si(001) by ion sputtering with simultaneous metal incorporation

This report focuses on the effect of simultaneous Fe incorporation in the self-organized pattern formation on Si(001) by low-energy ion-beam sputtering. Experimental observations giving evidence for the correlation between different ion-beam parameters, Fe concentration on the substrate, and the resulting topography are shown. It was observed that the incorporation of Fe affects the evolution of the topography and it is a requisite for the formation of ripples at near-normal incidence. It is shown also that Fe is not homogeneously distributed on the surface, but there is a higher concentration at the crests of the ripples than at the valleys. For the experimental setup used for this study, the Fe flux that reaches the surface is determined mainly by the acceleration voltage (U _acc), while the ion energy (E _ion) and ion-beam incidence angle (α) control the concentration of Fe in the steady state. The adjustment of these operational parameters of the ion source enables the fine-tuning of surface patterns.     

Helix propensity of highly fluorinated amino acids

Highly fluorinated amino acids have been used to stabilize helical proteins for potential application in various protein-based biotechnologies. To gain further insight into the effect of these highly fluorinated amino acids on helix formation exclusively, we measured the helix propensity of three highly fluorinated amino acids: (S)-5,5,5,5',5',5'-hexafluoroleucine (Hfl), (S)-2-amino-4,4,4-trifluorobutyric acid (Atb), and (S)-pentafluorophenylalanine (Pff). We have developed a short chemoenzymatic synthesis of Hfl with extremely high enantioselectivity (>99%). To measure the helix propensity (w) of the amino acids, alanine-based peptides were synthesized, purified, and investigated by circular dichroism spectroscopy (CD). On the basis of the CD data, the helix propensity of hydrocarbon amino acids can decrease up to 24-fold (1.72 kcal.mol-1.residue-1) upon fluorination. This difference in helix propensity has previously been overlooked in estimating the magnitude of the fluoro-stabilization effect (which has been estimated to be 0.32-0.83 kcal.mol-1.residue-1 for Hfl), resulting in a gross underestimation. Therefore, the full potential of the fluoro-stabilization effect should provide even more stable proteins than the fluoro-stabilized proteins to date.     

Kinetics and Mechanism of the Interaction of Di-μ-hydroxobis(1,10-phenanthroline)dipalladium(II) Perchlorate with Thioglycolic Acid and Glutathione in Aqueous Solution

The kinetics of interaction between di-μ-hydroxobis(1,10-phenanthroline)dipalladium(II) perchlorate and thioglycolic acid and with glutathione has been studied spectrophotometrically in aqueous medium as a function of the complex concentration as well as the ligand concentrations, pH, and temperature at constant ionic strength. The observed pseudo-first-order rate constants k _obs (s^?1) obeyed the equation k _obs = k ₁[Nu] (Nu = nucleophile). At pH = 6.5, the interaction with thioglycolic acid shows two distinct consecutive steps and both steps are dependent on the concentration of thioglycolic acid. The rate constants for the process are: k ₁ ≈ 10^?5 s^?1 and k ₂ ≈ 10^?3 dm³ · mol^?1 · s^?1. The association equilibrium constant (K _E) for the outer sphere complex formation has been evaluated together with the rate constants for the two subsequent steps. The other bio-active ligand, glutathione, showed a single step reaction depending on [ligand] with a second-order anation rate constant: the 10² (k ₂) values are (61.72, 79.20, 109.24 and 154.33) dm³ · mol^?1 · s^?1 at 20, 25, 30 and 35 °C, respectively. On the basis of the kinetic observations and evaluated activation parameters, plausible associative mechanisms are proposed for both interaction processes.     

<Emphasis Type="Italic">Rhodobacter capsulatus</Emphasis> porphobilinogen synthase,a high activity metal ion independent hexamer

Background  

The enzyme porphobilinogen synthase (PBGS), which is central to the biosynthesis of heme, chlorophyll and cobalamins, has long been known to use a variety of metal ions and has recently been shown able to exist in two very different quaternary forms that are related to metal ion usage. This paper reports new information on the metal ion independence and quaternary structure of PBGS from the photosynthetic bacterium Rhodobacter capsulatus.