Modeling the degradation of polypropylene and polystyrene under shock compression and mechanical cleaving using the ReaxFF force field

Polypropylene (PP) and polystyrene (PS) underwent a comprehensive investigation into their mechanical and chemical degradation through reactive molecular dynamics simulations. The simulations utilized the ReaxFF force field for CHO (carbon-hydrogen-oxygen) systems in the combustion branch. The study included equilibrium simulations to determine densities and melting temperatures, non-equilibrium simulations for stress-strain and Young moduli determination, mechanical cleaving to identify surface species resulting from material fragmentation, and shock compression simulations to elucidate chemical reactions activated by some external energy sources. The results indicate that material properties such as densities, phase transition temperatures, and Young moduli are accurately reproduced by the ReaxFF-CHO force field. The reactive dynamics analysis yielded crucial insights into the surface composition of fragmented polymers. Both polymers exhibited backbone breakage, leaving -CH2· and -CH·- radicals as terminals. PP demonstrated substantial fragmentation, while PS showed a tendency to develop crosslinks. A detailed analysis of chemical reactions resulting from increasing activation due to increasing value of compression pressure is presented and discussed.

Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene

The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3' and 5' ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3' and 5' ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure.

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.

Regulation of water access, storage, separation and release of drugs from the carbon nanotube functionalized by cytosine rich DNA fragments

We found that carmustine can be stored in the carbon nanotube (CNT) interior for a long time due to hydrophobic interactions. The access of water to carmustine phase in the CNT interior can be controlled by the state of cytosine rich DNA fragments covalently bound to the CNT tips and to the presence of doxorubicin molecules intercalated within bundles of DNA fragments. More effective control of water access and subsequent decomposition of carmustine due to the contact with water was observed when some small amount of doxorubicin molecules cork the CNT ends. Our analysis shows that carmustine decomposition products naturally separate when decomposition occurs within the CNT. The alkylating agent, chloroethyl carbonium cation, spontaneously escapes from the CNT but the carbamylation agent, chloroethyl isocyanate, is still kept within the nanotube interior. The separation process and release of the alkylating agent needs uncorking the nanotube by doxorubicin molecules. The latter process is likely to occur spontaneously at acidic pH when intercalation of doxorubicin within the DNA fragments becomes ineffective. The features of the proposed molecular model, obtained from molecular dynamics simulations, can be beneficial in design of novel smart drugs carriers to a tumor microenvironment revealing the reduced extracellular pH.

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.

Interaction of Human Telomeric i-Motif DNA with Single-Walled Carbon Nanotubes: Insights from Molecular Dynamics Simulations

This work deals with molecular dynamics simulations of human telomeric i-motif DNA interacting with functionalized single-walled carbon nanotubes. We study two kinds of i-motifs differing by the protonation state of cytosines, i.e., unprotonated ones representative to neutral pH and with half of the cytosines protonated and representative to acidic conditions. These i-motifs interact with two kinds of carbon nanotubes differing mainly in chirality (diameter), i.e., (10, 0) and (20, 0). Additionally, these nanotubes were on-tip functionalized by amino groups or by guanine- containing residues. We found that protonated i-motif adsorbs strongly, although not specifically, on the nanotube surfaces with its 3' and 5' ends directed toward the surface and that adsorption does not affect the i-motif shape and hydrogen bonds existing between C:C⁺ pairs. The functional groups on the nanotube tips have minimal effect either on position of i-motif or on its binding strength. Unprotonated i-motif, in turn, deteriorates significantly during interaction with the nanotubes and its binding strength is rather high as well. We found that (10, 0) nanotubes destroy the i-motif shape faster than (20, 0). Moreover the i-motif either tries to wrap the nanotube or migrates to its tip and becomes immobilized due to interaction with guanine residue localized on the nanotube tip and attempts to incorporate its 3' end into the nanotube interior. No hydrogen bonds exist within the unprotonated i-motif prior to and after adsorption on the nanotube. Thus, carbon nanotubes do not improve the stability of unprotonated i-motif due to simple adsorption or just physical interactions. We hypothesize that the stabilizing effect of carbon nanotubes reported in the literature is due to proton transfer from the functional group in the nanotube to cytosines and subsequent formation of C:C⁺ pairs.

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.

Multimodal, pH Sensitive, and Magnetically Assisted Carrier of Doxorubicin Designed and Analyzed by Means of Computer Simulations

This work deals with an analysis of drugs carriers based on the structure of a carbon nanotube using large-scale atomistic molecular dynamics simulations. The analyzed systems link several functions in a single architecture. They are as follows: (i) the sidewalls and tips of carbon nanotubes are covalently functionalized by polyethylene glycol-folic acid conjugates, and this approach allows for creation of hydrophytic and biocompatible systems; (ii) doxorubicin is kept in the internal space of a carbon nanotube as a mixture with dyes (p-phenylenediamine or neutral red)-it allows for pH-controlled release or alteration of the interaction topology; (iii) the mixture of doxorubicin and dyes in the nanotube interior is additionally sealed by fullerene nanoparticles which act as pistons at acidic pH and loosen the tangle of polyethylene glycol chains at the nanotube tips. This enhances the release of doxorubicin from the nanotube when compared to the analogous system but without the fullerene caps; (iv) another function of the carrier can be activated by filling of the fullerenes by magnetic material-then, the carrier can be visualized by means of magnetic resonance imaging, it can realize magnetic hyperthermia of tumor cells, and intense rotation of the nanoparticles can be induced by the application of an external magnetic field. That rotation enhances the release of doxorubicin from the nanotube and leads to the increase of the rotational temperature. The studies show that the proposed design of the drug-doxorubicin carrier reveals very promising properties. Its fabrication is absolutely feasible, as all individual stages necessary for its construction have been confirmed in the literature.

Pegylated and folic acid functionalized carbon nanotubes as pH controlled carriers of doxorubicin. Molecular dynamics analysis of the stability and drug release mechanism

This work deals with an analysis of the covalent functionalization of a carbon nanotube using polyethylene glycol chains terminated by folic acid fragments. The analysis is focused on theoretical predictions, using molecular dynamics simulations, of the properties of such constructs as pH controlled carriers of the anticancer drug doxorubicin. The analyzed systems are expected to hold the doxorubicin in the inner cavity of the carbon nanotube at neutral pH and unload the drug at slightly acidic pH. This property comes from incorporation into the nanotube of some dye molecules (p-phenylenediamine or neutral red) which undergo protonation at slightly acidic pH. We found that both dyes lead to the formation of a stable, co-absorbed phase of a doxorubicin-dye mixture inside the nanotube at physiological pH. At acidic pH we observed a spontaneous release of dyes from the nanotube, leading finally to the state with only doxorubicin encapsulated in the nanotube interior. Thus, the analyzed constructs can be considered as carriers of doxorubicin that are selective to tumor microenvironments (which exhibit reduced pH due to hypoxia and overexpression of folate receptors). However, we also found that the release of doxorubicin from the nanotube at acidic pH is kinetically blocked, at least in the case of the system sizes studied here. Thus, we also discussed some possible ways of reducing the activation barriers against doxorubicin release at acidic pH.

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. C2H6, CH4 adsorbed on silicalite and CO2, C2H6 adsorbed on NaX zeolite.

The calculations are relatively simple and can be applied industrially.

Application of the Dubinin–Radushkevich Equation for Describing Adsorption from Solutions on to Various Carbons

Dozens of papers have been published recently describing adsorption processes from solutions on to solid surfaces, but a certain lack of understanding of this problem is still observed. This article deals with the description of adsorption from binary solutions of non-electrolytes on to solids. This description covers adsorption both on homogeneous and heterogeneous surfaces from ideal and non-ideal liquid mixtures. Some important factors determining the adsorption process, i.e. the heterogeneity of the solid surface, interactions between the species in the bulk and surface phases, differences in molecular sizes of the adsorbate molecules, etc., have been discussed. The main attention has been focused on the Dubinin–Radushkevich equation and its application in the description of adsorption from solutions on to energetically, heterogeneous adsorbents. Numerous model calculations have been reported for this equation and several experimental systems have been analyzed. The application of the Dubinin–Radushkevich equation in characterizing liquid adsorption on to various carbons has been demonstrated.

Application of the Dubinin–Astakhov Equation to the Study of the Geometric Structure, Energetic Surface Heterogeneity and Surface Topography of Carbonaceous Adsorbents

The new theoretical approach to multisite-occupancy adsorption on heterogeneous surfaces, developed recently by Rudziński and Everett, is generalized for the case of adsorption systems characterized by non-Gaussian adsorption energy distributions. Attention is focused on the adsorption energy distribution which, in the case of one-site-occupancy adsorption, leads to the Dubinin–Astakhov isotherm equation. In effect, a generalized form of that isotherm equation is developed for the common case of multisite-occupancy adorption in actual adsorption systems. The generalized equation is sensitive to surface topography; hence, fitting it to experimental adsorption isotherms creates a chance to study the surface topography of carbonaceous surfaces. An example of such computer exercises is reported here before a more systematic study is published.

Transitional hydrogen bonds in aqueous perchlorate solution

The water–perchlorate classical hydrogen bond can turn into a bifurcated or trifurcated one.

Alkane separation using nanoporous graphene membranes

The mechanism of alkane permeation across designed graphene nanopores has been studied using molecular dynamics simulations.

Theoretical prediction of gas adsorption kinetics based on equilibrium data

Based on the equilibrium adsorption isotherms, new expressions describing the rate of adsorption were developed. The theoretical model takes into account the influence of diffusional effects on the rate of adsorption. Other nonideal effects such as surface energetic heterogeneity or intermolecular interactions can be taken into account by using the adequate equilibrium isotherm. The accuracy of the presented rate equations was verified using real adsorption systems.

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.

Application of the vacancy solution theory to describe the enthalpic effects accompanying mixed-gas adsorption

The possibility of utilizing vacancy solution theory (VST) to study the enthalpic effects accompanying mixed-gas adsorption equilibria is presented. Besides heterogeneity, the interaction effects by using the regular adsorbed solution, Flory-Huggins, and Wilson models of nonideality in the adsorbed phase are taken into account. To predict adsorption phase diagrams and calorimetric effects in the mixed-gas adsorption system, only a knowledge of the single-gas adsorption isotherms and accompanying calorimetric effects is required. The possibility of simplification of the obtained theoretical expressions is shown. The obtained agreement between theory and experiment is very satisfactory.

Adsorption of Cytosine on a Mercury Electrode

The electrosorption behavior of cytosine at the mercury electrode/acetic buffer of pH 4 and 5 interfaces was determined from the double-layer differential capacity measurements extrapolated to zero frequency. Solutions of cytosine were prepared to cover the range from 1 × 10-4 to 6 × 10-3 mol dm-3. Adsorption of cytosine was described by the adsorption isotherms constants derived from the surface pressure data as a function of electrode charge density and bulk concentration. The obtained values of the relative surface excesses Γ′ were higher in the acetic buffer of pH 4 than of pH 5. Maximum of cytosine adsorption in the mentioned buffers was at -581 and -551 mV, respectively. The values of the standard Gibbs energy ∆G° obtained from the Frumkin isotherm were higher in the buffer of pH 4 than of pH 5. The values of the interaction parameter A indicated weaker repulsive interaction between adsorbed molecules of cytosine in the former buffer. The adsorption parameters obtained from the virial isotherm confirmed corresponding parameters obtained from the Frumkin isotherm. The dependences of ΦM-2 on the relative surface excess at a constant charge density were analyzed in order to calculate the electrostatic parameters of the inner layer.

Modeling of binary adsorption on heterogeneous surfaces characterized by a quasi-gaussian adsorption energy distribution

The integral equation (IE) approach coupled with a quasi-Gaussian adsorption energy distribution is used to model the adsorption of single gases and their binary mixture on a heterogeneous solid surface. The adsorbing surface is assumed to be characterized by two, generally different in width, quasi-Gaussian distribution functions, each of them related to a single component of the mixture. The influence of correlations between the distribution functions associated with different components on the corresponding adsorption isotherms and phase diagrams is discussed. In particular, it is demonstrated that a lack of microscopic correlations between the adsorption energies of the components may lead to the formation of an azeotropic mixture. The predictions of the theory are also compared with the results of the grand canonical Monte Carlo (GCMC) simulations carried out for the system studied.