Molecular dynamics simulation of an aqueous Na2SO4 solution

The structure of sodium sulfate in tip3p water solution with the concentration of 0.1191 mol/dm3 was studied by means of classical molecular dynamics. Both ions have clear hydration shells. The comparison between radial distribution functions and cumulative numbers of selected atoms around the reference one makes it possible to precisely describe the structure of investigated system. Applying such tools geometrical parameters of the hydrogen bond of the dimer SO42-/H2O have been obtained.

Application of the Integral Equation Approach to the Study of Enthalpic Effects Accompanying Mixed-Gas Adsorption on Heterogeneous Solid Surfaces

The possibilities of the Integral Equation approach for describing mixed-gas adsorption equilibria are presented. In this study, the energetic heterogeneity was described through the use of the Gaussian-like adsorption energy distribution function. As a result, very simple equations describing the isosteric heats of mixture components were obtained. The advantage of the model presented is the possibility of predicting the phase diagrams and enthalpic effects accompanying mixed-gas adsorption from a theoretical viewpoint based on pure-component adsorption data. New equations for isosteric heats of component mixtures were examined using the experimental data obtained by Dunne et al . (1996a, b, 1997), i.e. C 2 H 6 , CH 4 adsorbed on silicalite and CO 2 , C 2 H 6 adsorbed on NaX zeolite. The calculations are relatively simple and can be applied industrially

The inhibition effect of water on the purification of natural gas with nanoporous graphene membranes

Molecular dynamics simulations are used to investigate the inhibiting effect of water on the natural gas separation with nanoporous graphene. The membrane separation process involves CH4 + N2 mixtures with and without the addition of water. The results show that water is able to form hydrogen bonds with nitrogen atoms located in a nanopore rim. This effect causes a decrease of separation selectivity as well as a reduction of gas permeation. In the extreme case, when the nanopore rim contains only nitrogen atoms, water agglomerates at the center of the nanopore and effectively closes down the permeation path. The conclusions are confirmed by the analysis of stability and kinetics of hydrogen bonds

Validation of Simple Equations Describing the Adsorption of Binary Gas Mixtures onto Surfaces with an Asymmetric Distribution of Adsorption Energy

The Monte Carlo simulation method was used to test the accuracy of approximate equations derived for binary gas adsorption onto a heterogeneous surface characterized by a Dubinin-Astakhov adsorption energy distribution (AED) function. In particular, the Condensation Approximation (CA) was applied to obtain simple equations for the partial adsorption isotherms and phase diagrams in the system for which a separate AED was assumed for each component of the mixture. A few cases involving different relationships between the AEDs associated with the adsorbing components were discussed. Additionally, the results of the proposed theory were compared with exact numerical solutions obtained using the Integral Equation method. From both simulations and numerical calculations, it follows that, in general, the CA is not appropriate for the prediction of binary adsorption equilibria when the individual AEDs are of an entirely different shape. On the other hand, when the AEDs were microscopically correlated, i.e. when the adsorption energy of one component on every site was shifted by a constant value compared to that of the other, the phase diagrams obtained were found to be in a very good agreement with their simulated counterparts

Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields

Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems

Cytosine-Rich DNA Fragments Covalently Bound to Carbon Nanotube as Factors Triggering Doxorubicin Release at Acidic pH. A Molecular Dynamics Study

This works deals with analysis of properties of a carbon nanotube, the tips of which were functionalized by short cytosine-rich fragments of ssDNA. That object is aimed to work as a platform for storage and controlled release of doxorubicin in response to pH changes. We found that at neutral pH, doxorubicin molecules can be intercalated between the ssDNA fragments, and formation of such knots can effectively block other doxorubicin molecules, encapsulated in the nanotube interior, against release to the bulk. Because at the neutral pH, the ssDNA fragments are in form of random coils, the intercalation of doxorubicin is strong. At acidic pH, the ssDNA fragments undergo folding into i-motifs, and this leads to significant reduction of the interaction strength between doxorubicin and other components of the system. Thus, the drug molecules can be released to the bulk at acidic pH. The above conclusions concerning the storage/release mechanism of doxorubicin were drawn from the observation of molecular dynamics trajectories of the systems as well as from analysis of various components of pair interaction energies