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.     

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.     

Theoretical study on the adsorption of phenol on activated carbon using density functional theory

Density functional theory (DFT) calculations performed at the PBE/DZP level using the DFT-D2 method were utilized to investigate the adsorption of phenol on pristine activated carbon (AC) and on activated carbon functionalized with OH, CHO, or COOH groups. Over the pristine AC, the phenol molecule undergoes weak physical adsorption due to van der Waals interactions between the aromatic part of the phenol and the basal planes of the AC. Among the three functional groups used to functionalize the AC, the carboxylic group was found to interact most strongly with the hydroxyl group of phenol. These results suggest that functionalized AC-COOH has great potential for use in environmental applications as an adsorbent of phenol molecules in aqueous phases.     

Density functional theory study of epoxy polymer chains adsorbing onto single-walled carbon nanotubes: electronic and mechanical properties

We performed first principles calculations based on density functional theory (DFT) to investigate the effect of epoxy monomer content on the electronic and mechanical properties of single-walled carbon nanotubes (SWCNTs). Our calculation results reveal that interfacial interaction increases with increasing numbers of epoxy monomers on the surface of SWCNTs. Furthermore, density of states (DOS) results showed no orbital hybridization between the epoxy monomers and nanotubes. Mulliken charge analysis shows that the epoxy polymer carries a positive charge that is directly proportional to the number of monomers. The Young’s modulus of the nanotubes was also studied as a function of monomer content. It was found that, with increasing number of monomers on the nanotubes, the Young’s modulus first decreases and then approaches a constant value. The results of a SWCNT pullout simulation suggest that the interfacial shear stress of the epoxy/SWCNT complex is approximately 68 MPa. These results agreed well with experimental results, thus proving that the simulation methods used in this study are viable.     

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes

The adsorption of CO onto Ni-doped boron nitride nanotubes (BNNTs) was investigated using density functional theory at the B3LYP/LanL2DZ level of theory. The structures of the Ni-doped BNNTs and their CO-adsorbed configurations were obtained. It was found that the strength of adsorption of CO onto Ni-doped perfect BNNTs is higher than that on defective BNNTs. The electronic properties of all of the adsorption configurations of CO on Ni-doped BNNTs are reported.

Molecular insight into adsorption affinities of Carmustine drug on boron and nitrogen doped functionalized single-walled carbon nanotubes using density functional theory including dispersion correction calculations and molecular dynamics simulation

Abstract

We report a quantum mechanics calculation and molecular dynamics simulation study of Carmustine drug (BNU) adsorption on the surface of nitrogen (N) and boron (B) doped-functionalized single-walled carbon nanotubes. The stability of the optimized complexes is determined on the basis of relative adsorption energy (ΔE_ads). The ΔE_ads results claim that drug molecule tends to adsorb on the nitrogen and boron doped functionalized tubes with the energy values in the range of ?61.177 to ?95.806?kJ/mol. Based on the obtained results, it is observed that N-doping compared with B-doping has improved more effectively drug absorption on the surface of functionalized nanotube. The results of Atoms in Molecule calculations indicate that drug adsorbs molecularly via hydrogen bonds interactions on the surface doped-functionalized carbon nanotubes. Moreover, molecular dynamics simulation is performed to investigate the dynamics behavior of the drug molecules on the nitrogen-doped functionalized carbon nanotube (f-NNT) and functionalized carbon nanotube (f-CNT). The higher average calculated electrostatic and van der Waals energies as well as higher number of intermolecular hydrogen bonds in BNU-f-NNT in comparison with BNU-f-CNT model suggest the more effectual interaction between drug molecules and nitrogen-doped functionalized carbon nanotube.

Communicated by Ramaswamy H. Sarma     

Gas adsorption on the Zn-, Pd- and Os-doped armchair (5,5) single-walled carbon nanotubes

The adsorption of NO₂, NH₃, H₂O, CO₂ and H₂ gases on the undoped, Zn–, Pd– and Os–doped armchair (5,5) single–walled carbon nanotubes (SWCNTs) were studied using density functional method. The adsorptions of these five gases on the Zn–, Pd– and Os–doped SWCNTs are obviously stronger than on the undoped SWCNT and their adsorption abilities are in the same order: NO₂ > NH₃ > H₂O > CO₂ > H₂. Adsorption energies for all the studied gases on the undoped, Zn–, Pd– and Os–doped SWCNTs computed at the B3LYP/LanL2DZ level are reported.     

A density functional theory-based analysis of the structural,topological and electronic properties of gemcitabine drug adsorption on the pyrrolidine functionalized single-walled carbon nanotube

The stability of gemcitabine anticancer drug on the functionalized (8,0) zigzag carbon nanotube as a drug delivery vehicle is studied within the formalism of the density functional theory calculations to understand the role of the pyrrolidine functional group in binding the adsorbed molecule to the drug delivery system as well as improving water solubility. The binding energies, natural bond orbital calculations, and the quantum theory of atoms in molecules results are obtained to provide more evidences related to the intermolecular interaction between gemcitabine drug and the functionalized nanotube. The negative binding energy corresponds to favorable binding of gemcitabine drug to the functionalized nanotube and presence of the active sites available for hydrogen bond formation facilitates better drug binding to the nanotube sidewall. The results presented in this article indicate that pyrrolidine functionalized carbon nanotube seems to be a novel material for drug delivery applications.

Communicated by Heidar Moradnia     

Dinitroamino benzene derivatives: a class new potential high energy density compounds

Dinitroamino benzene derivatives are designed and studied in detail with quantum chemistry method. The molecular theory density, heats of formation, bond dissociation energies, impact sensitive and detonation performance are investigated at DFT-B3LYP/6-311G** level. The results of detonation performance indicated most of the compounds have better detonation velocity and pressure than RDX and HMX. The N-N bond can be regard as the trigger bond in explosive reaction, and the bond dissociation energies of trigger bond are almost not affected by the position and number of substituent group. The impact sensitive are calculated by two different theory methods. It is found that the compounds, which can become candidates of high energy materials, have smaller H₅₀ values than RDX and HMX. It is hoped that this work can provide some basis information for further theory and experiment studies of benzene derivatives.     

Molecular modeling of dissociative and non-dissociative chemisorption of nitrosamine on close-ended and open-ended pristine and Stone-Wales defective (5,5) armchair single-walled carbon nanotubes

The nitrosamine adsorbed on close-ended and open-ended pristine and Stone-Wales defective (5,5) armchair single-walled carbon nanotubes (SWCNTs) was studied using the B3LYP/6-31G(d) method. Structure optimization of all possible adsorption configurations based on the combination of two nitrosamine (amino- and imino-) isomers and four types of nanotubes was carried out. The most stable configuration for the nitrosamine adsorbed on the (5,5) armchair SWCNTs was found to be dissociative chemisorption. The adsorption energies of the most stable structures of the adsorption complexes of close-ended and open-ended pristine SWCNTs with the imino isomer of nitrosamine were −127.15 and −137.14 kcal mol⁻¹, respectively.     

Amino acid adsorption on anatase (101) surface at vacuum and aqueous solution: a density functional study

The adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO₂) has been investigated under the scheme of density functional theory. Through the analysis of adsorption geometries, amino group and side chains of AAs have been identified as the major side to adsorb on TiO₂, while the carboxyl group prefers to stay outside to avoid the repulsion between negatively charged oxygen from TiO₂ and AAs. On the surface, two-coordinated oxygen is the major site to stabilize AAs through O–H interactions. The above conclusion does not change when it is in the aqueous solution based on the calculations with AAs surrounded by explicit water molecules. The above knowledge is helpful in predicting how AAs and even peptides adsorb on inorganic materials.

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Graphical abstract The adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO₂) has been investigated under the scheme of density functional theory.

     

Triplex inducer-directed self-assembly of single-walled carbon nanotubes: a triplex DNA-based approach for controlled manipulation of nanostructures

As a promising strategy for artificially control of gene expression, reversible assembly of nanomaterials and DNA nanomachine, DNA triplex formation has received much attention. Carbon nanotubes as gene and drug delivery vector or as 'building blocks' in nano/microelectronic devices have been successfully explored. Therefore, studies on triplex DNA-based carbon nanotube hybrid materials are important for development of smart nanomaterials and for gene therapy. In this report, a small molecule directed single-walled carbon nanotubes (SWNTs) self-assembly assay has been developed by disproportionation of SWNTs-dT(22)·dA(22) duplex into triplex dT(22)·dA(22)·dT(22) and dA(22) by a triplex formation inducer, coralyne. This has been studied by circular dichroism, light scattering (LS) spectroscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), electrophoretic mobility shift assay and supported by using DNA random sequence. In contrast, SWNTs do not aggregate under the same experimental conditions when the small molecules used can not induce dT(22)·dA(22)·dT(22) triplex formation. Therefore, this novel small molecule-directed SWNTs self-assembly assay has also been used for screening of triplex inducers in our studies.     

On the importance of van der Waals interaction in the groove binding of DNA with ligands: restrained molecular dynamics study

Comparison of interaction energy between an oligonucleotide and a DNA-binding ligand in the minor and major groove modes was made by use of restrained molecular dynamics. Distortion in DNA was found for the major groove mode whereas less significant changes for both ligand and DNA were detected for the minor groove binding after molecular dynamics simulation. The conformation of the ligand obtained from the major groove mode resembles that computed with the ligand soaked in water. The van der Waals contact energy was found to be as significant as electrostatic energy and more important for difference in binding energy between these two binding modes. The importance of van der Waals force in groove binding was supported by computations on the complex formed by the repressor peptide fragment from the bacteriophage 434 and its operator oligonucleotide.     

Thiophenic compounds adsorption on Na(I)Y and rare earth exchanged Y zeolites: a density functional theory study

We have theoretically investigated the adsorption of thiophene, benzothiophene, dibenzothiophene on Na(I)Y and rare earth exchanged La(III)Y, Ce(III)Y, Pr(III)Y Nd(III)Y zeolites by density functional theory calculations. The calculated results show that except benzothiophene adsorbed on Na(I)Y with a stand configuration, the stable adsorption structures of other thiophenic compounds on zeolites exhibit lying configurations. Adsorption energies of thiophenic compounds on the Na(I)Y are very low, and decrease with the increase of the number of benzene rings in thiophenic compounds. All rare earth exchanged zeolites exhibit strong interaction with thiophene. La(III)Y and Nd(III)Y zeolites are found to show enhanced adsorption energies to benzothiophene and Pr(III)Y zeolites are favorable for dibenzothiophene adsorption. The analysis of the electronic total charge density and electron orbital overlaps show that the thiophenic compounds interact with zeolites by π-electrons of thiophene ring and exchanged metal atom. Mulliken charge populations analysis reveals that adsorption energies are strongly dependent on the charge transfer of thiophenic molecule and exchanged metal atom.     

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%.