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.
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