Cysteamine Chemisorption at Mercury-Solution Interfaces in the Context of Redox and Microdissociation Equilibria.

The redox behavior and chemisorption of cysteamine (CA) at a charged mercury surface are described, with an emphasis on its acid-base properties supported by molecular dynamics and quantum mechanical calculations. It was found that CA forms chemisorbed layers on the surface of the mercury electrode. The formation of Hg-CA complexes is connected to mercury disproportionation, as reflected in peaks SII and SI at potentials higher than the electrode potential of zero charge (p.z.c.). Both the process of chemisorption of CA and its consequent redox transformation are proton-dependent. Also, depending on the protonation of CA, the formation of typical populations of chemisorbed conformers can be observed. In addition, cystamine (CA disulfide dimer) can be reduced on the mercury surface. Between the potentials of this reduction and peak SI, the p.z.c. of the electrode used can be found. Furthermore, CA can serve as an LMW catalyst for hydrogen evolution. The mechanistic insights presented here can be used for follow-up research on CA chemisorption and targeted modification of other metallic surfaces.

Synthesis and Profiling of Highly Selective Inhibitors of Methyltransferase DOT1L Based on Carbocyclic C-Nucleosides.

Histone methyltransferase DOT1L is an attractive therapeutic target for the treatment of hematological malignancies. Here, we report the design, synthesis, and profiling of new DOT1L inhibitors based on nonroutine carbocyclic C-nucleoside scaffolds. The experimentally observed SAR was found to be nontrivial as seemingly minor changes of individual substituents resulted in significant changes in the affinity to DOT1L. Molecular modeling suggested that these trends could be related to significant conformational changes of the protein upon interaction with the inhibitors. The compounds 22 and (-)-53 (MU1656), carbocyclic C-nucleoside analogues of the natural nucleoside derivative EPZ004777, and the clinical candidate EPZ5676 (pinometostat) potently and selectively inhibit DOT1L in vitro as well as in the cell. The most potent compound MU1656 was found to be more metabolically stable and significantly less toxic in vivo than pinometostat itself.

Oxalic Acid Adsorption on Rutile: Molecular Dynamics and ab Initio Calculations.

Detailed analysis of the adsorption of oxalic acid ions, that is, oxalate and hydrogenoxalate, on the rutile (110) surface was carried out using molecular dynamics augmented by free energy calculations and supported by ab initio calculations. The predicted adsorption on perfect nonhydroxylated and hydroxylated surfaces with surface charge density from neutral to +0.208 C/m2 corresponding to pH values of about 6 and 3.7, respectively, agrees with experimental adsorption data and charge-distribution multisite ion complexation model predictions obtained using the most favorable surface complexes identified in our simulations. We found that outer-sphere complexes are the most favorable, owing to strong hydrogen binding of oxalic acid ions with surface hydroxyls and physisorbed water. The monodentate complex, the most stable among inner-sphere complexes, was about 15 kJ/mol higher in energy, but separated by a large energy barrier. Other inner-sphere complexes, including some previously suggested in the literature as likely adsorption structures such as bidentate and chelate complexes, were found to be unstable both by classical and by ab initio modeling. Both the surfaces and (hydrogen)oxalate ions were modeled using charges scaled to 75% of the nominal values in accord with the electronic continuum theory and our earlier parameterization of (hydrogen)oxalate ions, which showed that nominal charges exaggerate ion-water interactions.

Oxalic Acid Adsorption on Rutile: Experiments and Surface Complexation Modeling to 150 °C.

Here, we characterize oxalate adsorption by rutile in NaCl media (0.03 and 0.30 m) and between pH 3 and 10 over a wide temperature range which includes the near hydrothermal regime (10-150 °C). Oxalate adsorption increases with decreasing pH (as is typical for anion binding by metal oxides), but systematic trends with respect to ionic strength or temperature are absent. Surface complexation modeling (SCM) following the CD-MUSIC formalism, and as constrained by molecular modeling simulations and IR spectroscopic results from the literature, is used to interpret the adsorption data. The molecular modeling simulations, which include molecular dynamics simulations supported by free-energy and ab initio calculations, reveal that oxalate binding is outer-sphere, albeit via strong hydrogen bonds. Conversely, previous IR spectroscopic results conclude that various types of inner-sphere complexes often predominate. SCMs constrained by both the molecular modeling results and the IR spectroscopic data were developed, and both fit the adsorption data equally well. We conjecture that the discrepancy between the molecular simulation and IR spectroscopic results is due to the nature of the rutile surfaces investigated, that is, the perfect (110) crystal faces for the molecular simulations and various rutile powders for the IR spectroscopy studies. Although the (110) surface plane is most often dominant for rutile powders, a variety of steps, kinks, and other types of surface defects are also invariably present. Hence, we speculate that surface defect sites may be primarily responsible for inner-sphere oxalate adsorption, although further study is necessary to prove or disprove this hypothesis.

Modeling of solid-liquid interfaces using scaled charges: rutile (110) surfaces.

Electronic continuum correction (ECC) has been proven to bring significant improvement in the modeling of interactions of ions (especially multivalent) in aqueous solutions. We present a generalization and the first application of this approach to modeling solid-liquid interfaces, which are omnipresent in physical chemistry, geochemistry, and biophysics. Scaling charges of the top layer of surface atoms makes the existing solid models compatible with the ECC models of ions and molecules, allowing the use of modified force fields for a more accurate investigation of interactions of various metal and metal-oxide surfaces with aqueous solutions, including complex biomolecules and multivalent ions. We have reparametrized rutile (110) models with different surface charge densities (from 0 to -0.416 C m-2) and adopted/developed scaled charge force fields for ions, namely Na+, Rb+, Sr2+, and Cl-. A good agreement of the obtained molecular dynamics (MD) data with X-ray experiments and previously reported MD results was observed, but changes in the occupancy of various adsorption sites were observed and discussed in detail.

Structural Stability of Peptidic His-Containing Proton Wire in Solution and in the Adsorbed State.

Molecular wires are functional molecules applicable in the field of transfer processes in technological and biochemical applications. Besides molecular wires with the ability to transfer electrons, research is currently focused on molecular wires with high proton affinity and proton transfer ability. Recently, proposed peptidic proton wires (H wires) are one example. Their ability to mediate the transport of protons from aqueous solutions onto the surface of a Hg electrode in a catalytic hydrogen evolution reaction was investigated by constant-current chronopotentiometric stripping. However, elucidating the structure of H wires and rationalizing their stability are key requirements for their further research and application. In this article, we focus on the His (H) and Ala (A)-containing peptidic H wire A3-(H-A2)6 in solution and after its immobilization onto the electrode surface in the presence of the secondary structure stabilizer 2,2,2-trifluoroethanol (TFE). We found that the solvent containing more than 25% of TFE stabilizes the helical structure of A3-(H-A2)6 not only in solution but also in the adsorbed state. The TFE efficacy to stabilize α-helical structure was confirmed using high-resolution nuclear magnetic resonance, circular dichroism, and molecular dynamics simulation. Experimental and theoretical results indicated A3-(H-A2)6 to be a high proton-affinity peptidic H wire with an α-helical structure stabilized by TFE, which was confirmed in a comparative study with hexahistidine as an example of a peptide with a definitely disordered and random coil structure. The results presented here could be used for further investigation of the peptidic H wires and for the application of electrochemical methods in the research of proton transfer phenomena in general.

Force field parametrization of hydrogenoxalate and oxalate anions with scaled charges.

Models of the hydrogenoxalate (bioxalate, charge -1) and oxalate (charge -2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with water were described using charges scaled according to the electronic continuum correction approach with rescaling of nonbonded parameters (ECCR), and those descriptions of anion interactions were found to agree well with relevant AIMD and experimental results. The models with full RESP charges showed excessively strong electrostatic interactions between the solute and water molecules, leading to an overstructured solvation shell around the anions and thus to a diffusion coefficient that was much too low. The effect of charge scaling was more evident for the oxalate dianion than for the hydrogenoxalate anion. Our work provides CMD models for ions of oxalic acid and extends previous studies that showed the importance of ECCR for modeling divalent ions and ions of organic compounds. Graphical abstract The radial distribution function between a water oxygen (Ow) and an oxygen of the oxalate dianion (Ox) significantly improved when scaled charges were applied to the anion.

Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study.

Hydrogenoxalate (charge -1) and oxalate (charge -2) anions and their solvated forms were studied by various computational techniques. Ab initio quantum chemical calculations in gas phase, in implicit solvent and microsolvated (up to 32 water molecules) environment were performed in order to explore a potential energy surface of both anions. The solvation envelope of water molecules around them and the role of water on the conformation of the anions was revealed by means of Born-Oppenheimer molecular dynamics simulations and optimization procedures. The structure of the anions was found to be dependent on the number of water molecules in the solvation shell. A subtle interplay between intramolecular and intermolecular hydrogen bonding dictates the final conformation and thus an explicit solvent model is necessary for a proper description of this phenomena. Graphical Abstract Solvated hydrogenoxalate and oxalate anions.

Pt···H Nonclassical Interaction in Water-Dissolved Pt(II) Complexes: Coaction of Electronic Effects with Solvent-Assisted Stabilization.

The structure of the hydration shell of cisplatin, cis-[Pt(NH3)2Cl2], and its aquated derivatives cis-[Pt(NH3)2Cl(H2O)](+), cis-[Pt(NH3)2OH(H2O)](+), and cis-[Pt(NH3)2(H2O)2](2+) were studied by a number of density functional molecular dynamics (DFT-MD) simulations (from 30 to 250 ps) in which Pt(II) complexes were immersed in a periodic box with 72 explicit water molecules. Furthermore, Pt(II) complex-water binding energy curves and full DFT optimizations of clusters derived from the lowest potential energy DFT-MD frames offered a deeper insight into the structure of the first hydration shell and electronic changes connected with the formation of a nonclassical Pt···H-O-H (Pt···Hw) hydrogen bond (inverse hydration). The probability of a Pt···Hw interaction decreases with increasing charge of the platinum complex due to disadvantageous electrostatics. The main stabilization comes from the charge transfer being followed by polarization and dispersion. Ligands form a framework for the network of H-bond interactions between the solvent molecules, which play an important role in the promotion/suppression of the formation of the Pt···Hw interactions. In the +2 charged diaqua complex the Pt···Hw interaction is still attractive but cannot compete with classical H bonds between solvent molecules. Thus, the formation of a Pt···Hw interaction is the result of a suitable solvent H-bonding network and the probability of its incidence decreases with increasing flexibility of the solvent.

Cy3 and Cy5 dyes terminally attached to 5'C end of DNA: structure, dynamics, and energetics.

Cy3 and Cy5 cyanine dyes terminally attached to the 5'C end (C1) of the DNA oligonucleotide were studied by metadynamics (MTD), molecular dynamics (MD), and density-functional methods with dispersion corrections (DFT-D). MTD simulations explored the free energy surface (FES) of the dye-DNA interactions, which included stacking and major groove binding motifs and unstacked structures. Dynamics of the stacked structures was studied by the MD simulations. All possible combinations of stacking interactions between the two indole rings of the dyes and the neighbor guanine and cytosine rings were observed. The most probable interaction included the stacking between the dye's distal indole ring and the guanine base. In ∼10% of the structures the delocalized π-electrons of the dyes' polymethine linkers played a key role in the dye-DNA dispersion interactions. The stacked conformers of the Cy3 dye were confirmed as true minima by DFT-D full optimizations. The stacked dye decreased flexibility up to two neighbor base pairs.