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1.
Int J Mol Sci ; 24(1)2023 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-36614260

RESUMEN

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.


Asunto(s)
Dendrímeros , Fluorouracilo , Dendrímeros/química , Dispersión del Ángulo Pequeño , Difracción de Rayos X
2.
Molecules ; 28(2)2023 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-36677880

RESUMEN

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.


Asunto(s)
Condroitín , Nanotubos de Carbono , Glicosaminoglicanos , Ácido Hialurónico , Simulación de Dinámica Molecular , Nanotubos de Carbono/química , Monosacáridos , Ácidos Carboxílicos
3.
Int J Mol Sci ; 23(21)2022 Oct 26.
Artículo en Inglés | MEDLINE | ID: mdl-36361747

RESUMEN

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.


Asunto(s)
Grafito , Nanoestructuras , Nanotubos de Carbono , Puntos Cuánticos , Nanotubos de Carbono/química , Nanoestructuras/química , Catálisis
4.
Molecules ; 27(15)2022 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-35956863

RESUMEN

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.


Asunto(s)
ADN , Simulación de Dinámica Molecular , Citosina/química , ADN/química , Cinética , Telómero
5.
Int J Mol Sci ; 22(16)2021 Aug 06.
Artículo en Inglés | MEDLINE | ID: mdl-34445172

RESUMEN

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.


Asunto(s)
Antibióticos Antineoplásicos/administración & dosificación , Citosina/análogos & derivados , Preparaciones de Acción Retardada/química , Doxorrubicina/administración & dosificación , Nanotubos de Carbono/química , Antibióticos Antineoplásicos/química , ADN/química , Doxorrubicina/química , Liberación de Fármacos , Concentración de Iones de Hidrógeno , Simulación de Dinámica Molecular
6.
Int J Mol Sci ; 21(6)2020 Mar 11.
Artículo en Inglés | MEDLINE | ID: mdl-32168928

RESUMEN

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.


Asunto(s)
ADN/química , Nanotubos de Carbono/química , Telómero/genética , Citosina/química , G-Cuádruplex , Concentración de Iones de Hidrógeno , Modelos Moleculares , Simulación de Dinámica Molecular , Telómero/química , Termodinámica
7.
Carbon N Y ; 50(4): 1625-1634, 2019 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-31105316

RESUMEN

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.

8.
Int J Mol Sci ; 20(9)2019 Apr 26.
Artículo en Inglés | MEDLINE | ID: mdl-31027351

RESUMEN

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.


Asunto(s)
Antibióticos Antineoplásicos/química , Antineoplásicos/química , Sistemas de Liberación de Medicamentos/métodos , Nanotubos de Carbono/química , Rojo Congo , Doxorrubicina/química , Liberación de Fármacos , Dispersión Dinámica de Luz , Electroforesis
9.
Langmuir ; 34(7): 2543-2550, 2018 02 20.
Artículo en Inglés | MEDLINE | ID: mdl-29376380

RESUMEN

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.


Asunto(s)
Simulación por Computador , Doxorrubicina/química , Portadores de Fármacos , Magnetismo , Portadores de Fármacos/química , Concentración de Iones de Hidrógeno , Nanotubos de Carbono/química
10.
Phys Chem Chem Phys ; 19(13): 9300-9312, 2017 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-28323298

RESUMEN

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.


Asunto(s)
Antineoplásicos/administración & dosificación , Doxorrubicina/administración & dosificación , Liberación de Fármacos , Nanotubos de Carbono/química , Antineoplásicos/química , Doxorrubicina/química , Portadores de Fármacos , Ácido Fólico/química , Simulación de Dinámica Molecular , Polietilenglicoles/química
11.
Langmuir ; 32(19): 4719-28, 2016 05 17.
Artículo en Inglés | MEDLINE | ID: mdl-27133585

RESUMEN

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.

12.
Nanomedicine ; 10(7): 1465-75, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-24486857

RESUMEN

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.


Asunto(s)
Antineoplásicos/farmacocinética , Nanotubos de Carbono , Compuestos de Platino/farmacocinética , Animales , Portadores de Fármacos , Femenino , Ratones , Ratones Endogámicos BALB C , Distribución Tisular
13.
Chemosphere ; 357: 142056, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38641294

RESUMEN

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.


Asunto(s)
Polipropilenos , Poliestirenos , Poliestirenos/química , Polipropilenos/química , Simulación de Dinámica Molecular , Presión , Modelos Químicos
14.
J Phys Chem B ; 126(35): 6671-6681, 2022 09 08.
Artículo en Inglés | MEDLINE | ID: mdl-36036695

RESUMEN

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.


Asunto(s)
Grafito , Simulación de Dinámica Molecular , Aminas , ADN/química , Grafito/química , Humanos , Telómero
15.
Biomater Adv ; 137: 212835, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35929267

RESUMEN

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.


Asunto(s)
Nanotubos de Carbono , Alquilantes , Carmustina , Citosina , ADN , Doxorrubicina/química , Simulación de Dinámica Molecular , Nanotubos de Carbono/química , Agua/química , Abastecimiento de Agua
16.
Biomater Sci ; 10(7): 1752-1764, 2022 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-35199120

RESUMEN

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.


Asunto(s)
Berberina , Osteoartritis , Animales , Berberina/farmacología , Berberina/uso terapéutico , Condrocitos , Geles/farmacología , Inflamación , Ratones , Osteoartritis/tratamiento farmacológico , Dolor , Absorción Cutánea
17.
J Phys Chem B ; 125(21): 5526-5536, 2021 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-34009989

RESUMEN

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.


Asunto(s)
Citosina , Nanotubos de Carbono , ADN , Simulación de Dinámica Molecular , Telómero/genética
18.
J Chem Phys ; 133(3): 034708, 2010 Jul 21.
Artículo en Inglés | MEDLINE | ID: mdl-20649351

RESUMEN

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.

19.
Pharmaceutics ; 12(7)2020 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-32635253

RESUMEN

The controlled delivery and release of drug molecules at specific targets increases the therapeutic efficacy of treatment. This paper presents a triple complex which is a new potential drug delivery system. Triple complex contains single-walled carbon nanotubes, Congo red, and doxorubicin. Nanotubes are built of a folded graphene layer providing a large surface for binding Congo red via "face-to-face" stacking which markedly increases the binding capacity of the carrier. Congo red is a compound that self-associates to form supramolecular ribbon-like structures, which are able to bind some drugs by intercalation. The nanotube-Congo red complex can bind the model drug doxorubicin. Thus, a new triple carrier system was obtained. The aim of this paper is to present studies on the controlled release of a model anticancer drug from a triple carrier system through pH changes. The specific aim of the study was to model the structure of the obtained experimental systems and to compare the changes in the average energy of interaction between its components induced by pH changes. The studies also aimed to compare the intensity of pH-dependent changes in hydrodynamic diameters of individual components of the triple carrier system. The effect of pH changes on the stability of the analyzed systems was examined using the molecular modeling method and dynamic light scattering. The decrease in pH influenced the structure and stability of the analyzed triple systems and ensured efficient drug release. The changes in hydrodynamic diameters of the obtained fractions were examined with the use of dynamic light scattering and were confirmed by computer simulation methods. The formulation presented in this paper shows potential for a therapeutic application owing to its high drug binding capacity and pH-dependent release. This ensures prolonged local action of the drug. The results reveal that the studied complex fulfills the basic requirements for its potential use as drug carrier, thus reducing side effects and enhancing pharmacological efficacy of drugs.

20.
J Chem Phys ; 131(6): 064703, 2009 Aug 14.
Artículo en Inglés | MEDLINE | ID: mdl-19691399

RESUMEN

Recent experimental studies of water adsorption on Pt{110}-(1x2) using supersonic molecular beams [F. R. Laffir et al., J. Chem. Phys. 128, 114717 (2008)] have revealed that the translational energy dependence of the initial sticking probability is a stepwise function with a threshold energy of 5 kJ/mol. The initial sticking probability increases sixfold from approximately 0.1 (at translational energies less than 5 kJ/mol) to approximately 0.64 (at translational energies greater than 10 kJ/mol). The aim of this work is to study the adsorption dynamics of water using classical molecular dynamics simulation in order to assess what physical factors are responsible for the observed behavior of the initial sticking probability. The simulations were performed using a purpose-designed code; water molecules were modeled using the well-known TIP4P water model, whereas the water-platinum potential energy function was determined using the ab initio density functional theory calculations. We conclude that the main factor controlling the initial sticking probability is a relatively weak energy transfer between the water molecule and the surface substrate during collision. This energy transfer is enhanced when the total energy of the water molecule increases. The assumption of an exponential increase of the probability of the energy transfer as a function of total energy of water molecule gives initial sticking probabilities very similar to those experimentally obtained. The same model was applied for the simulation of the coverage dependent sticking probability using a hybrid method comprising molecular dynamics and kinetic Monte Carlo approaches. We found a reasonable agreement between our results and the experimental data. The sticking probability as a function of coverage initially increases due to an increasing amount of the adsorbate island edges; it reaches a maximum and finally decreases as the islands merge together at high coverage. The saturation coverage was determined to be 2.8 ML at surface temperature 165 K, where water forms a puckered almost regular lattice with each water molecule having four nearest neighbors. At the studied temperature we did not observe the existence of stable water multilayers on the surface which is consistent with the experimental findings.

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