The original force field for clay materials (ClayFF) developed by Cygan et al. (J. Phys. Chem. B 2004, 108, 1255 is modified to describe negative charging of the (101) quartz surface above its point of zero charge (pH ≈ 2.0−4.5). The modified force field adopts the scaled natural bond orbital charges derived by the quantum mechanical calculations which are used to obtain the desired surface charge density and to determine the delocalization of the charge after deprotonation of surface silanol groups. Classical molecular dynamics simulations (CMD) of the ( 101) surface of α-quartz with different surface charge densities (0, −0.03, −0.06, and −0.12 C m −2 ) are performed to evaluate the influence of the negative surface charge on interfacial water and adsorption of Na + , Rb + , and Sr 2+ ions. The CMD results are compared with ab initio calculations, X-ray experiment, and the triple-layer model. The modified force field can be easily implemented in common molecular dynamics packages and used for simulations of interactions between quartz surfaces and various (bio)molecules over a wide range of pH values.

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) and adopted/developed scaled charge force fields for ions, namely Na, Rb, Sr, 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.

Molecular dynamics (MD) simulations of single-stranded (ss) and double-stranded (ds) oligonucleotides anchored via an aliphatic linker to a graphene surface were performed in order to investigate the role of the surface charge density in the structure and orientation of attached DNA. Two types of interactions of DNA with the surface are crucial for the stabilisation of the DNA-surface system. Whereas for a surface with a zero or low positive charge density the dispersion forces between the base(s) and the surface dominate, the higher charge densities applied on the surface lead to a strong electrostatic interaction between the phosphate groups of DNA, the surface and the ions. At high-charge densities, the interaction of the DNA with the surface is strongly affected by the formation of a low-mobility layer of counterions compensating for the charge of the surface. A considerable difference in the behaviour of the ds-DNA and ss-DNA anchored to the layer was observed. The ds-DNA interacts with the surface at low- and zero-charge densities exclusively by the nearest base pair. It keeps its geometry close to the canonical B-DNA form, even at surfaces with high-charge densities. The ss-DNA, owing to its much higher flexibility, has a tendency to maximise the attraction to the surface exploiting more bases for the interaction. The interaction of the polar amino group(s) of the base(s) of ss-DNA with a negatively charged surface also contributes significantly to the system stability.

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.

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/m 2 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.

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.

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.

We show that phase-sensitive vibrational sum frequency generation (SFG) spectra of solid/water and air/water interfaces, neutral and charged, can be successfully predicted using classical molecular dynamics (CMD) simulations in combination with simple nonpolarizable force fields (FFs). This can be achieved when employing velocity−velocity autocorrelation functions weighted by parameterized Raman and atomic polar tensors for the computation of the SFG. This procedure avoids computing polarizability tensors and dipole moments using either costly ab initio molecular dynamics (AIMD) simulations or CMD simulations with more complex and computationally demanding FFs. Such a methodology paves the way to a broad usage and computationally low-cost theoretical SFG spectroscopy, as even flexible nonpolarizable water models and common FFs for inorganic surfaces can provide good predictions of the SFG spectra, in rather good qualitative agreement with AIMD and/or experiments. The strongly reduced computational cost in our approach opens the possibility to study larger systems for long periods of time, for example, allowing a detailed characterization of the electric double-layer formation at interfaces with "environmentally relevant" ionic concentrations (mM), extracting fingerprints by theoretical CMD−SFG spectroscopy.