β-Carotene encapsulation into single-walled carbon nanotubes: a theoretical study

Recently, the encapsulation of β-carotene molecules into carbon nanotubes has been achieved. In this work, we report molecular dynamics simulations and tight-binding density functional-based results for a theoretical study of the encapsulation processes. Our results show that the molecules undergo geometrical deformations when encapsulated with significant changes in their electronic structure. Based on these results, we propose a new interpretation to the changes associated with the β-carotene absorption bands experimentally observed.     

Biogas upgrading using single-walled carbon nanotubes by molecular simulation

Abstract

Biogas from anaerobic digestion of biological wastes is a renewable energy resource that mainly contains CH₄, CO₂, trace amounts of H₂S and a fraction of H₂O vapour. In order to transfer biogas into biomethane to meet the standards for use as vehicle fuel or for injection in the natural gas grid, removing H₂S from biogas in advance is necessary. In addition, biogas is usually saturated with water vapour. It is significant to study the effect of the presence of H₂O on the biogas separation performance. Adsorption of H₂S/CO₂/CH₄ and H₂O/CO₂/CH₄ ternary mixtures using single-walled carbon nanotubes (SWCNT) were investigated via the Grand Canonical Monte Carlo (GCMC) method. We studied the effects of carbon nanotube diameter, –COOH modification, temperature and pressure on H₂S adsorption. The results indicate that the presence of hydrophilic –COOH groups does affect the separation of H₂S/CO₂/CH₄ mixtures. Temperature swing adsorption is more suitable than pressure swing adsorption for the separation of H₂S/CO₂/CH₄ mixtures. The effect of water vapour on the separation of CO₂/CH₄ was also investigated. The result shows that the presence of H₂O has little effect on the selectivity of CO₂/CH₄ in pristine CNT, but the selectivity of CO₂/CH₄ with the presence of H₂O is markedly enhanced after modification in –COOH modified SWCNT with specific modification degree. It is expected that this work could provide some useful information for biogas upgrading.     

Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion

Carbon nanotubes have been proposed to be efficient nanovectors able to deliver genetic or therapeutic cargo into living cells. However, a direct evidence of the molecular mechanism of their translocation across cell membranes is still needed. Here, we report on an extensive computational study of short (5 nm length) pristine and functionalized single-walled carbon nanotubes uptake by phospholipid bilayer models using all-atom molecular dynamics simulations. Our data support the hypothesis of a direct translocation of the nanotubes through the phospholipid membrane. We find that insertion of neat nanotubes within the bilayer is a "nanoneedle" like process, which can often be divided in three consecutive steps: landing and floating, penetration of the lipid headgroup area and finally sliding into the membrane core. The presence of functional groups at moderate concentrations does not modify the overall scheme of diffusion mechanism, provided that their deprotonated state favors translocation through the lipid bilayer.     

Formation of binocular-like structure using graphene nanosheet and carbon nanotubes

Binocular-like carbon structure was successfully fabricated using forced-field-based molecular dynamics simulations. The mechanism for the self-scrolling of graphene sheet using carbon nanotubes as template was analysed. By analysing the self-scrolling process, it was found that the van der Waals interactions were responsible for the formation of the binocular-like carbon nanostructures. Furthermore, the position and number of carbon tubes influenced the self-scrolling process. Moreover, the mechanism was also discussed. Our theoretical results will provide researchers a powerful guide and helpful assistance in designing better targeted programmes in experiments.     

Molecular dynamics simulation of single-walled carbon nanotubes inside liquid crystals

Molecular dynamic simulations of systems of single-walled carbon nanotubes (CNTs) in liquid crystalline solvents were performed, in order to investigate the effect of the molecular structure and phase of the liquid crystal (LC) on the interactions between the CNTs. Three different LC molecules (5CB, 8CB and 5CF) were considered in our study. Our results with 5CB and 8CB suggest that increasing the chain length of the hydrophobic part of the LC molecule by three carbon atoms is insufficient to decrease the tendency for the CNTs to aggregate in the LCs. Additionally, varying the phase of the LC is also insufficient to decrease the aggregation tendency of the CNTs. However, simulations with 5CF (which has fluorine atoms in the head group of the LC molecule) suggest that this LC solvent can decrease the tendency of the CNTs to aggregate. This study is relevant to assist experimentalists with the development of high-quality dispersions of large concentrations of CNTs in the LCs.     

van der Waals potential barrier for cobaltocene encapsulation into single-walled carbon nanotubes: classical molecular dynamics and ab initio study

In this work, we carried out geometry optimisations and classical molecular dynamics for the problem of cobaltocene (CC) encapsulation into different carbon nanotubes (CNTs) ((7,7), (8,8), (13,0) and (14,0) tubes were used). CCs are molecules composed of two aromatic pentagonal rings (C5H5) sandwiching one cobalt atom. From our simulation results, we observed that CC was encapsulated into CNTs (8,8), (13,0) and (14,0). However, for CNT (7,7), the encapsulation could not occur, in disaggrement with some previous works in the literature. Our results show that the encapsulation process is mainly governed by van der Waals potential barriers.     

Modeling the interaction between anti-cancer drug penicillamine and pristine and functionalized carbon nanotubes for medical applications: density functional theory investigation and a molecular dynamics simulation

Abstract

The present study focuses on the prediction and investigation of binding properties of penicillamine with pure (5,5) single-walled carbon nanotube (SWCNT) and functionalized SWCNT (f-SWCNT) through the B3LYP and M06-2X functionals using the 6-31G** basis set. The electronic and structural properties, adsorption energy and frontier molecular orbitals of various configurations are examined. Our theoretical results indicated that the interaction of the nanotubes with penicillamine molecule is weak so that the drug adsorption process is typically physisorption. Also, results of theoretical calculations show that the adsorption of the drug molecule on f-SWCNT is stronger with shorter intermolecular distances in comparison to pure SWCNT. The natural bond orbital (NBO) analysis of studied systems demonstrates that the charge is transferred from penicillamine molecule to the nanotubes. Furthermore, molecular dynamics (MD) simulation is employed to evaluate the dynamic and diffusion behavior of drug molecule on SWCNT and f-SWCNT. Energy results show that drug molecule spontaneously moves toward the carriers, and the van der Waals energy contributions in drug adsorption are more than electrostatic interaction. The obtained results from MD simulation confirm that the functionalization of SWCNT leads to increase in the solubility of the carrier in aqueous solution.

Communicated by Ramaswamy H. Sarma     

One-pot fluorescence detection of multiple analytes in homogenous solution based on noncovalent assembly of single-walled carbon nanotubes and aptamers

We have developed a new multicolor fluorescent sensing system to detect multiple analytes in one pot. This design is based on the noncovalent assembly of dye-labeled aptamer with single-walled carbon nanotubes (SWNTs) by π-stacking between the nucleotide bases and the SWNTs sidewalls. In the presence of the targets, the aptamer-target binding separates the assembly of dye-labeled aptamers and SWNTs, resulting in the restoration of fluorescence signal of the dye labeled with aptamers. As a proof of concept, we demonstrate that a two-color fluorescent system can simultaneously and selectively detect two targets (thrombin and adenosine triphosphate) in a single solution. Since the method is mix-and-detect manner, the present strategy is simple and cost-effective.     

Predicting doxorubicin drug delivery by single-walled carbon nanotube through cell membrane in the absence and presence of nicotine molecules: a molecular dynamics simulation study

Abstract

In order to study the interaction of the anticancer agent Doxorubicin with the single-walled carbon nanotubes with different diameters as drug delivery systems, the molecular dynamics (MD) simulations have been used. Also, for design and development of intracellular Doxorubicin drug delivery systems, a series of steered MD simulations are applied to explore the possibility of encapsulated Doxorubicin–carbon nanotube penetration through a lipid bilayer in presence and absence of Nicotine molecules at different pulling rates. Our simulation results showed that in spite of the adsorption of drug molecules on the outer sidewall of the nanotubes, the spontaneous localization of one Doxorubicin molecule into the cavity of the nanovectors with larger diameters is observed. It is found that the presence of Nicotine molecules in extracellular medium increases the required force for pulling nanotube-encapsulated drug as well as the required time for penetration process, especially at higher velocity. Also, the entering process of the Nicotine molecules into the carbon nanotube causes that the encapsulated drug molecule is fully released in the hydrophobic phase of the lipid bilayer.

Communicated by Ramaswamy H. Sarma     

Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation

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Effect of chirality,length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study

We carried out molecular dynamics simulations to study the adsorption of all the 20 amino acids (AAs; aromatic, polar and non-polar) on the surface of chiral, zigzag and armchair single-walled carbon nanotubes. The adsorption was occurring in all systems. In the aromatic AAs, the π–π stacking and the semi-hydrogen bond formation cause a strong interaction with the carbon nanotubes (CNTs). We also investigated the chirality, length and diameter dependencies on adsorption energies. We found that all AAs have more tendency to adsorption on the chiral and zigzag CNTs over the armchair. The results show that increasing both the diameter and the length causes the enhancement of the adsorption energy. But, the effect of the length is more than of the diameter. For example, the adsorption energy of Trp on the surface of CNT (4,1), with 2 nm length, is 20.4 kcal/mol. When the length of CNT becomes twice, the adsorption energy increases by 24 ± 0.3%. But by doubling the diameter, the adsorption energy increased only by 9.8 ± 0.25%.     

Conformation of nifedipine in hydrated 1,2-di-myristoyl-sn-glycero-3-phosphorylcholine bilayer molecular dynamics simulation

The conformation of nifedipine, a cardiac and smooth muscle calcium ion channel antagonist is studied in a hydrated bilayer of forty nine 1,2-di-myristoyl-sn-glycero-3-phosphorylcho-line (DMPC) molecules using molecular dynamics (MD) simulation technique. The simulation was carried out in conditions of constant number, volume and temperature (NVT) at 310 K, which is above the liquid crystalline (Lα) transition temperature of DMPC. The periodic boundary conditions were applied in three-dimensions. Thus the model represented an infinite bilayer. The important geometric parameters characteristic to DMPC and nifedipine molecules were calculated and compared with other theoretical and experimental results pertaining to nifedipine and other related dihydrophyridine (DHP) analogues. Our results suggest that conformational parameters required for antagonist activity are fairly conserved during the interaction of nifedipine with DMPC bilary and bilayer stabilizes the drug conformation in the bioactive form.     

Neon atoms oscillating inside carbon and boron nitride nanotubes: a fully atomistic molecular dynamics investigation

In the present work, based on extensive fully atomistic molecular dynamics simulations, we discuss the dynamics of neon atoms oscillating inside (5,5) single-walled carbon nanotubes (CNTs) and boron nitride nanotubes (BNNTs). Our results show that sustained high-frequency oscillatory regimes are possible for a large range of temperatures. Our results also show that the general features of the oscillations are quite similar to those observed in CNT and BNNT, in contrast with some speculations in previous works in the literature about the importance of broken symmetry and chirality exhibited by BNNTs.     

Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen

In this research, for the first time, molecular dynamics (MD) method was used to simulate aspirin and ibuprofen at various concentrations and in neutral and charged states. Effects of the concentration (dosage), charge state, and existence of an integral protein in the membrane on the diffusion rate of drug molecules into lipid bilayer membrane were investigated on 11 systems, for which the parameters indicating diffusion rate and those affecting the rate were evaluated. Considering the diffusion rate, a suitable score was assigned to each system, based on which, analysis of variance (ANOVA) was performed. By calculating the effect size of the indicative parameters and total scores, an optimum system with the highest diffusion rate was determined. Consequently, diffusion rate controlling parameters were obtained: the drug–water hydrogen bond in protein-free systems and protein–drug hydrogen bond in the systems containing protein.     

Calculation of diffusion coefficient for supercritical carbon dioxide and carbon dioxide+naphthalene system by molecular dynamics simulation using EPM2 model

NVT ensemble molecular dynamics (MD) simulation has been applied to calculate the self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide. The simulation was carried out in the pressure range from 8 to 40 MPa. The elementary physical model proposed by Harris and Yung was adopted for carbon dioxide and some approximation models were used for naphthalene. The systems of MD simulation for carbon dioxide consist of 256 particles. One naphthalene molecule was added for carbon dioxide+naphthalene system. The system can be assumed to be an infinite dilution condition for carbon dioxide+naphthalene system and the mutual diffusion coefficients are equal to the tracer diffusion coefficients of naphthalene. The self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide can be calculated by mean square displacement. The calculated results of diffusion coefficients showed good agreement with the experimental data without adjustable parameters.     

Insights into aggregation dynamics of NACore peptides from coarse-grained simulations

Alpha(α)-synuclein is closely related to the pathogenesis of Parkinson's disease (PD). The NACore, a fragment of α-synuclein, is considered to be the key region of α-synuclein that causes PD. The aggregation dynamics of NACores are studied via coarse-grained molecular dynamics simulations. We find that NACores can self-assemble into a large cluster at high concentrations. The aggregation dynamics can be divided into three stages. The growth kinetics for the first and second stages follows the power law, S_max ~ t^γ, with the second stage faster than the first one. The characteristic lifetime for the high concentration is 40 times larger than that for the low concentration, implying the low fluidity. Understanding the aggregation dynamics of NACores is helpful to develop drugs for therapeutic prevention and intervention.     

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer

The bacterial outer membrane protein OmpA is one of the few membrane proteins whose structure has been solved both by X-ray crystallography and by NMR. Crystals were obtained in the presence of detergent, and the NMR structure is of the protein in a detergent micelle. We have used 10 ns duration molecular dynamics simulations to compare the behaviour of OmpA in a detergent micelle and in a phospholipid bilayer. The dynamic fluctuations of the protein structure seem to be ca 1.5 times greater in the micelle environment than in the lipid bilayer. There are subtle differences between the nature of OmpA-detergent and OmpA-lipid interactions. As a consequence of the enhanced flexibility of the OmpA protein in the micellar environment, side-chain torsion angle changes are such as to lead to formation of a continuous pore through the centre of the OmpA molecule. This may explain the experimentally observed channel formation by OmpA.     

Self-diffusivity,hydrogen bonding and density of different water models in carbon nanotubes

In this paper, the density, hydrogen bonding and self-diffusivity of water confined in carbon nanotubes are investigated. Molecular dynamics is used to simulate a large variety of nanotubes with various water models. Our results produce, for the first time, the complete trend of these properties from narrow nanotubes, where water shows particularly anomalous behaviour, to large ones where its characteristics are similar to those of bulk.     

Molecular dynamics simulations of heat conduction in multi-walled carbon nanotubes

Heat conduction in multi-walled carbon nanotubes (MWNTs) was studied using non-equilibrium molecular dynamics simulations. This research focuses on the effects of the multi-wall structure of the MWNTs on the heat conduction. The results show that the thermal conductivity of a MWNT is almost the same as that of the corresponding single-walled carbon nanotubes (SWNTs) rather than much smaller as has been suggested. Thus, the multi-wall structure does not significantly affect the thermal conduction in the MWNTs. Analysis of the temperature profiles and the phonon density of states confirms that there is almost no heat transport between the MWNT layers and that each layer conducts heat nearly independently along parallel channels. This is physically reasonable since the weak inter-wall interactions and large interfacial thermal resistances make the MWNT layers behave like parallel thermal circuits.     

A study of comparative modelling,simulation and molecular dynamics of CXCR3 receptor with lipid bilayer

The G-coupled receptors seen on the cell surface are composites with a lipid bilayer. The chemokines are kind of G-coupled receptor which majorly involved in the activation and downstream signalling of the cell. In general, many G-coupled receptors lack their 3D structures which become a hurdle in the drug designing process. In this study, comparative modelling of the CXCR3 receptor was carried out, structure evaluation was done using various tools and softwares. Additionally, molecular dynamics and docking were performed to prove the structural quality and architecture. Interestingly, the studies like toggle switch mechanism, lipid dynamics, virtual screening were carried out to find the potent antagonist for the CXCR3 receptor. During virtual screening 14,303 similar molecules were retrieved among them only four compounds have an ability to interact with a crucial amino acid residue of an antagonist. Hence, these screened compounds can serve as a drug candidate for a CXCR3 receptor, but further in vitro and in vivo studies are ought to do to prove its same efficacy.