The Comparison of Catalytic Activity of Carbimazole and Methimazole on Electroreduction of Zinc (II) in Chlorates (VII): Experimental and Molecular Modelling Study.

With the help of electrochemical methods, including CV and EIS, the influence of methimazole, carbimazole, and the concentration of the supporting electrolyte on the kinetics and mechanism of zinc electroreduction on a mercury electrode was compared and analyzed. Moreover, molecular dynamics simulations of zinc/carbimazole and zinc/methimazole solutions were carried out to determine the effect of drugs on the hydration sphere of Zn2+ ions. It was shown that the electroreduction of Zn2+ in the presence of methimazole and carbimazole occurs in two steps and the first one determines the kinetics of the entire process. The presence of both drugs in the solution and the increase in the concentration of the supporting electrolyte reduce the degree of hydration of the depolarizer ions and the hydration of the electrode surface, what is a factor favoring the rate of electroreduction. Based on theoretical studies, the formation of stable complexes between Zn2+ and the molecules of both drugs in a solution was considered unlikely. However, active complexes can be formed between depolarizer ions and molecules adsorbed at the electrode surface. They constitute a bridge facilitating charge exchange during the electrode reaction, revealing the catalytic abilities of methimazole and carbimazole. In the range of cdrug ≤ 1 × 10-3 mol dm-3, carbimazole is a better catalyst, whereas in the range of cdrug ≥ 5 × 10-3 mol dm-3, it is methimazole. The effectiveness of both compounds in catalyzing the first stage of the electrode reaction increases with the increase in the NaClO4 concentration.

Effect of Ionization Degree of Poly(amidoamine) Dendrimer and 5-Fluorouracil on the Efficiency of Complex Formation-A Theoretical and Experimental Approach.

Due to their unique structure, poly(amidoamine) (PAMAM) dendrimers can bind active ingredients in two ways: inside the structure or on their surface. The location of drug molecules significantly impacts the kinetics of active substance release and the mechanism of internalization into the cell. This study focuses on the effect of the protonation degree of the G4PAMAM dendrimer and the anticancer drug 5-fluorouracil (5FU) on the efficiency of complex formation. The most favorable conditions for constructing the G4PAMAM-5FU complex are a low degree of protonation of the dendrimer molecule with the drug simultaneously present in a deprotonated form. The fluorine components in the XPS spectra confirm the formation of the stable complex. Through SAXS and DLS methods, a decrease in the dendrimer's molecular size resulting from protonation changes at alkaline conditions was demonstrated. The gradual closure of the dendrimer structure observed at high pH values makes it difficult for the 5FU molecules to migrate to the interior of the support structure, thereby promoting drug immobilization on the surface. The 1H NMR and DOSY spectra indicate that electrostatic interactions determine the complex formation process. Through MD simulations, the localization profile and the number of 5FU molecules forming the complex were visualized on an atomic scale.

Interaction of Chondroitin and Hyaluronan Glycosaminoglycans with Surfaces of Carboxylated Carbon Nanotubes Studied Using Molecular Dynamics Simulations.

Interaction of ß-D-glucopyranuronic acid (GlcA), N-acetyl-ß-D-glucosamine (GlcNAc), N-acetyl-ß-D-galactosamine (GalNAc) and two natural decameric glycosaminoglycans, hyaluronic acid (HA) and Chondroitin (Ch) with carboxylated carbon nanotubes, were studied using molecular dynamics simulations in a condensed phase. The force field used for carbohydrates was the GLYCAM-06j version, while functionalized carbon nanotubes (fCNT) were described using version two of the general amber force field. We found a series of significant differences in carbohydrate-fCNT adsorption strength depending on the monosaccharide molecule and protonation state of surface carboxyl groups. GlcNAc and GalNAc reveal a strong adsorption on fCNT with deprotonated carboxyl groups, and a slightly weaker adsorption on the fCNT with protonated carboxyl groups. On the contrary, GlcA weakly adsorbs on fCNT. The change in protonation state of surface carboxyl groups leads to the reversal orientation of GlcNAc and GalNAc in reference to the fCNT surface, while GlcA is not sensitive to that factor. Adsorption of decameric oligomers on the surface of fCNT weakens with the increasing number of monosaccharide units. Chondroitin adsorbs weaker than hyaluronic acid and incorporation of four Ch molecules leads to partial detachment of them from the fCNT surface. The glycan-fCNT interactions are strong enough to alter the conformation of carbohydrate backbone; the corresponding conformational changes act toward a more intensive contact of glycan with the fCNT surface. Structural and energetic features of the adsorption process suggest the CH-π interaction-driven mechanism.

From Cyclo[18]carbon to the Novel Nanostructures-Theoretical Predictions.

In this paper, we present a number of novel pure-carbon structures generated from cyclo[18]carbon. Due to the very high reactivity of cyclo[18]carbon, it is possible to link these molecules together to form bigger molecular systems. In our studies, we generated new structures containing 18, 36 and 72 carbon atoms. They are of different shapes including ribbons, sheets and tubes. All these new structures were obtained in virtual reactions driven by external forces. For every reaction, the energy requirement was evaluated exactly when the corresponding transition state was found or it was estimated through our new approach. A small HOMO-LUMO gap in these nanostructures indicates easy excitations and the multiple bonds network indicates their high reactivity. Both of these factors suggest that some potential applications of the new nanostructures are as components of therapeutically active carbon quantum dots, terminal fragments of graphene or carbon nanotubes obtained after fracture or growing in situ in catalytic reactions leading to the formation of carbonaceous materials.

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.

Molecular Dynamics Study of the Interaction of Carbon Nanotubes With Telomeric DNA Fragment Containing Noncanonical G-quadruplex and i-Motif Forms.

This work deals with molecular dynamics simulations of systems composed of telomeric dsDNA fragments, iG, and functionalized carbon nanotubes, fCNT. The iG contains 90 nucleotides in total and in its middle part the noncanonical i-motif and G-quadruplex are formed. Two chiralities of the fCNT were used, i.e., (10,0) and (20,0) and these nanotubes were either on-tip functionalized by guanine containing functional groups or left without functionalization. We proposed a dedicated computational procedure, based on the replica exchange concept, for finding a thermodynamically optimal conformation of iG and fCNT without destroying the very fragile noncanonical parts of the iG. We found that iG forms a V-shape spatial structure with the noncanonical fragments located at the edge and the remaining dsDNA strands forming the arms of V letter. The optimal configuration of iG in reference to fCNT strongly depends on the on-tip functionalization of the fCNT. The carbon nanotube without functionalization moves freely between the dsDNA arms, while the presence of guanine residues leads to immobilization of the fCNT and preferential location of the nanotube tip near the junction between the dsDNA duplex and i-motif and G-quadruplex. We also studied how the presence of fCNT affects the stability of the i-motif at the neutral pH when the cytosine pairs are nonprotonated. We concluded that carbon nanotubes do not improve the stability of the spatial structure of i-motif also when it is a part of a bigger structure like the iG. Such an effect was described in literature in reference to carboxylated nanotubes. Our current results suggest that the stabilization of i-motif is most probably related to easy formation of semiprotonated cytosine pairs at neutral pH due to interaction with carboxylated carbon nanotubes.

Carbon nanotube bottles for incorporation, release and enhanced cytotoxic effect of cisplatin.

Carbon nanotubes (CNTs) have emerged as promising drug delivery systems particularly for cancer therapy, due to their abilities to overcome some of the challenges faced by cancer treatment, namely non-specificity, poor permeability into tumour tissues, and poor stability of anticancer drugs. Encapsulation of anticancer agents inside CNTs provides protection from external deactivating agents. However, the open ends of the CNTs leave the encapsulated drugs exposed to the environment and eventually their uncontrolled release before reaching the desired target. In this study, we report the successful encapsulation of cisplatin, a FDA-approved chemotherapeutic drug, into multi-walled carbon nanotubes and the capping at the ends with functionalised gold nanoparticles to achieve a "carbon nanotube bottle" structure. In this proof-of-concept study, these caps did not prevent the encapsulation of drug in the inner space of CNTs; on the contrary, we achieved higher drug loading inside the nanotubes in comparison with data reported in literature. In addition, we demonstrated that encapsulated cisplatin could be delivered in living cells under physiological conditions to exert its pharmacological action.

Self-Assembled Supramolecular Ribbon-Like Structures Complexed to Single Walled Carbon Nanotubes as Possible Anticancer Drug Delivery Systems.

Designing an effective targeted anticancer drug delivery method is still a big challenge, since chemotherapeutics often cause a variety of undesirable side effects affecting normal tissues. This work presents the research on a novel system consisting of single walled carbon nanotubes (SWNT), dispersed with Congo Red (CR), a compound that forms self-assembled ribbon-like structures (SRLS) and anticancer drug doxorubicin (DOX). SWNT provide a large surface for binding of planar aromatic compounds, including drugs, while CR supramolecular ribbon-like assemblies can be intercalated by drugs, like anthracycline rings containing DOX. The mechanism of interactions in SWNT-CR-DOX triple system was proposed based on electrophoretic, spectral, Dynamic Light Scattering and scanning electron microscopy analyzes. The profile of drug release from the investigated system was evaluated using dialysis and Differential Scanning Calorimetry. The results indicate that ribbon-like supramolecular structures of CR bind to SWNT surface forming SWNT-CR complexes which finally bind DOX. The high amount of nanotube-bound CR greatly increases the capacity of the carrier for the drug. The high capacity for drug binding and possible control of its release (through pH changes) in the analyzed system may result in prolonged and localized drug action. The proposed SWNT-CR-DOX triple system meets the basic criteria that justifies its further research as a potential drug carrier.

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.

Coadsorption of Doxorubicin and Selected Dyes on Carbon Nanotubes. Theoretical Investigation of Potential Application as a pH-Controlled Drug Delivery System.

This work shows results of a theoretical survey, based on molecular dynamics simulation, of potential applicability of doxorubicin coadsorption with various dyes molecules on/in carbon nanotubes as a drug delivery system. The central idea is to take advantage of the dyes charge distribution change upon switching the pH of the environment from neutral (physiological 7.4) to acidic one (∼5.5 which is typical for tumor tissues). This work discusses results obtained for four dye molecules revealing more or less interesting behavior. These were bromothymol blue, methyl red, neutral red, and p-phenylenediamine. All of them reveal pKa in the range 5-7 and thus will undergo protonation in that pH range. We considered coadsorption on external walls of carbon nanotubes and sequential filling of the nanotubes inner hollow space by drug and dyes. The latter approach, with the application of neutral red and p-phenylenediamine as blockers of doxorubicin, led to the most promising results. Closer analysis of these systems allowed us to state that neutral red can be particularly useful as a long-term blocker of doxorubicin encapsulated in the inner cavity of (30,0) carbon nanotube at neutral pH. At acidic pH we observed a spontaneous release of neutral red from the nanotube and unblocking of doxorubicin. We also confirmed, by analysis of free energy profiles, that unblocked doxorubicin can spontaneously leave the nanotube interior at the considered conditions. Thus, that system can realize pH controlled doxorubicin release in acidic environment of tumor tissues.

In vivo biodistribution of platinum-based drugs encapsulated into multi-walled carbon nanotubes.

Carbon nanotubes (CNTs) are promising drug delivery systems due to their external functionalizable surface and their hollowed cavity that can encapsulate several bioactive molecules. In this study, the chemotherapeutic drug cisplatin or an inert platinum(IV) complex were entrapped inside functionalized-multi-walled-CNTs and intravenously injected into mice to investigate the influence of CNTs on the biodistribution of Pt-based molecules. The platinum levels in vital organs suggested that functionalized-CNTs did not affect cisplatin distribution, while they significantly enhanced the accumulation of Pt(IV) sample in some tissues (e.g. in the lungs, suggesting their potential application in lung cancer therapy) and reduced both kidney and liver accumulation (thus decreasing eventual nephrotoxicity, a typical side effect of cisplatin). Concurrently, CNTs did not induce any intrinsic abnormal immune response or inflammation, as confirmed by normal cytokine levels and histological evaluations. Therefore, functionalized nanotubes represent an efficient nano-carrier to improve accumulation of Pt species in targeted tissues/organs. From the clinical editor: In this preclinical study functionalized carbon nanotubes are reported to be safe and efficient for targeted delivery of platinum-containing compounds in rodents. Approaches like this may improve the treatment of specific cancers, since platinum based chemotherapies are commonly used, yet limited by toxicity and relatively poor target tissue concentration.

Insight Into Interfacial Behaviors between Doxorubicin and Zwitterion/PAMAM/CQD Hybrid Nanocarrier. A Molecular Dynamics Simulations Study.

Poly(amidoamine) dendrimer (PAMAM)/carbon quantum dot (CQD) nanohybrids are promising candidates for many biomedical applications, including drug delivery. Effectively designing a hybrid nanocarrier requires a deep understanding of the interactions of the hybrid nanoparticle with the drug to ensure drug stability and therapeutic efficiency. In this study, we utilized fully atomistic molecular dynamics (MD) simulations to investigate the adsorption behavior of a doxorubicin (DOX) anticancer drug onto a zwitterion/PAMAM/CQD hybrid nanocarrier. The hybrid nanoparticles were composed of CQD, at two oxidation levels, grafted with PAMAM dendrimers of generation 3 (G3) or 4 (G4) decorated with zwitterion monomers. Our work reveals that the generation of the grafted dendrimer was the primary determinant of efficient adsorption of DOX, unlike the oxidation level of CQD or dendrimer surface chemistry. After grafting, the G4 dendrimers assume a more stretched conformation compared to the G3 dendrimers. This allowed DOX molecules to penetrate inside the dendritic cavities of G4 dendrimers, resulting in enhanced drug protection. The hydrophobic interaction, between the aromatic structure of DOX molecules and the nonpolar parts of dendrimers, has been proven to play a crucial role in mediating the adsorption of drug molecules. These findings provide valuable insights to assist in the design of a zwitterion/PAMAM/CQD hybrid nanoplatform for drug delivery applications.

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.

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.

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.

Enhanced skin penetration of berberine from proniosome gel attenuates pain and inflammation in a mouse model of osteoarthritis.

Dermal delivery of bioactive molecules remains an attractive route of administration in osteoarthritis (OA) due to the local accumulation of drugs while avoiding their systemic side effects. In this study we propose a proniosome gel comprising non-ionic surfactants that self-assemble into de-hydrated vesicles for the delivery of the natural anti-inflammatory compound berberine. By modulating the hydrating ability of the proniosome gel, berberine can be efficiently released with minimal mechanical force. A combination of sorbitan oleate (S80) and polyethlene glycol sorbitan monolaurate (T20) in a sorbitan stearate (S60)-based proniosome enables a readily hydrated gel to deliver berberine into the skin, as confirmed by ex vivo skin permeation studies. Concurrently, an in vitro model of OA using primary mouse chondrocytes demonstrated that the release of berberine at a concentration as low as 1 µg mL-1 is sufficient to restore the production of sulphated glycosaminoglycans (sGAG) to levels comparable to healthy chondrocytes while avoiding the cytotoxic concentrations (IC50 = 33 µg mL-1) on skin keratinocytes. In a mouse model of OA, the optimized formulation is able to attenuate inflammation and pain and minimize cartilage degeneration. Taken together, these data demonstrate the feasibility of adopting proniosome gels as a suitable platform to deliver active molecules for the management of osteoarthritis.

Protonation of Cytosine-Rich Telomeric DNA Fragments by Carboxylated Carbon Nanotubes: Insights from Computational Studies.

In this work, we studied, using computational methods, the protonation reactions of telomeric DNA fragments being due to interaction with carboxylated carbon nanotubes. The applied computational methodology is divided into two stages. (i) Using classical molecular dynamics, we generated states in which carboxyl groups are brought to the vicinity of nitrogen atoms within the cytosine rings belonging to the DNA duplex. (ii) From these states, we selected two systems for systematic quantum chemical studies aimed at the analysis of proton-transfer reactions between the carboxyl groups and nitrogen atoms within the cytosine rings. Results of molecular dynamics calculations led to the conclusion that sidewall-functionalized carbon nanotubes deliver carboxyl groups slightly more effectively than the on-tip-functionalized ones. The latter can provide carboxyl groups in various arrangements and more diverse quality of approach of carboxyl groups to the cytosines; however, the differences between various arrangements of carboxyl groups are still not big. It was generally observed that narrow nanotubes can access the cytosine pocket easier than wider ones. Quantum chemical calculations led however to the conclusion that a direct proton transfer from the carboxyl group to the nitrogen atom within the cytosine ring is impossible under normal conditions. Precisely, we detected either very high activation barrier for the proton-transfer reaction or instability of the reaction product, i.e., its spontaneous decomposition toward reaction substrates.

Influence of the rotational degrees of freedom on the initial sticking probability of water on Pt{110}-(1 x 2): a molecular dynamics study.

This work focuses on a molecular dynamics (MD) study of the initial sticking probability of water on the Pt{110}-(1 x 2) surface. Previous studies of the system [T. Panczyk et al., J. Chem. Phys. 131, 064703 (2009)] led to the following conclusions: (i) adsorption of water is controlled by the efficiency of the dissipation of the initial kinetic energy during collision with the surface and (ii) the process is probably dominated by the electron-hole pair excitation mechanism. In the current work, we extend this study to understand the influence of the orientation of the water molecule and its rotational energy on the probability of the energy exchange during collision. The simulated MD trajectories correspond to various orientations of water molecule at different rotational energies. We found that assuming the angular dependence on the probability of the energy exchange can explain the experimental results obtained using supersonic molecular beams, especially for high incident molecular beam energies. For low beam energies, dispersion of the incident kinetic energy must be incorporated into the model. These are the key factors that enable to model the experimental results on a good qualitative level.