Molecular dynamics assessment of doxorubicin–carbon nanotubes molecular interactions for the design of drug delivery systems

Carbon nanotubes (CNTs) constitute an interesting material for nanomedicine applications because of their unique properties, especially their ability to penetrate membranes, to transport drugs specifically and to be easily functionalized. In this work, the energies of the intermolecular interactions of single-walled CNTs and the anticancer drug doxorubicin (DOX) were determined using the AMBER 12 molecular dynamics MM/PBSA and MM/GBSA methods with the aim of better understanding how the structural parameters of the nanotube can improve the interactions with the drug and to determine which structural parameters are more important for increasing the stability of the complexes formed between the CNTs and DOX. The armchair, zigzag, and chiral nanotubes were finite hydrogen-terminated open tubes, and the DOX was encapsulated inside the tube or adsorbed on the nanotube surface. Pentagon/heptagon bumpy defects and polyethylene glycol (PEG) nanotube functionalization were also studied. The best interaction occurred when the drug was located inside the cavity of the nanotube. Armchair and zigzag nanotubes doped with nitrogen, favored interaction with the drug, whereas chiral nanotubes exhibited better drug interactions when having bumpy defects. The π-π stacking and N-H…π electrostatic interactions were important components of the attractive drug-nanotube forces, enabling significant flattening of the nanotube to favor a dual strong interaction with the encapsulated drug, with DOX–CNT equilibrium distances of 3.1–3.9 Å. These results can contribute to the modeling of new drug-nanotube delivery systems.

     

Theoretical study on the electronic structure nature of single and double walled carbon nanotubes and its role on the electron transport

Density functional theory and molecular dynamics (MD) calculations were used to evaluate electronic structure properties in a series of nanotubes with smallest possible diameters (both types: armchair and zigzag), and the corresponding chiral nanotubes (8,m) for 0 ≤ m ≤ 8. The calculations were performed considering a length of 16.5 Å. We evaluated a set of 26 combinations of dual nanotubes (armchair/armchair, zigzag/zigzag, armchair/zigzag, and zigzag/armchair), where the first label corresponds to the outer tube. We extended our study with nine additional systems of double-walled carbon nanotubes (DWCNT) with semiconductor nature. In this regard, we gave insight into the semiconductive or metallic nature inherited to the dual tubes. DWCNT systems were possible to construct by maintaining a radial distance of 3.392 Å for the armchair/armchair arrangement and 3.526 Å for the zigzag/zigzag type. It was considered as a reference, the interplanar distance of graphite (3.350 Å). Electronic transport calculations were also performed on selected DWCNT systems in order to understand the role played by the different symmetries under study. It was evidenced that the electronic structure nature of the systems rules the ability to transport electrons through the DWCNT interface.     

Dynamics and density profile of water in nanotubes as one-dimensional fluid

The transport and structural properties of water confined in nanotubes with different diameters were studied by molecular dynamics (MD) simulation. The effects of pore size, molecule-wall interaction, and the helicity of CNT on the diffusivity, thermal conductivity, and shear viscosity as well as density profile were analyzed. For diffusivity, in model NT > in armchair CNT > in zigzag CNT at similar conditions. However in contrast to the diffusivity, the thermal conductivity and the shear viscosity increase as the pore size decreases, in zigzag CNT > in armchair CNT > (or approximately ) in model NT. The ordered layer distribution of water molecules in nanotubes is clear. It suggests the structure of fluid in the zigzag CNTs is more ordered, and more solidlike. In the nanotubes, where the molecule and the pore dimensions are of similar order of magnitude, the nature of water-water and water-wall interactions, the confinement effect of space, and the helicity of CNT become more significant.     

How a Zigzag Carbon Nanotube Grows

Owing to the unique structure of zigzag (ZZ) carbon nanotubes (CNTs), their ring‐by‐ring growth behavior is different from that of chiral or armchair (AC) CNTs, on the rims of which kinks serve as active sites for carbon attachment. Through first‐principle calculations, we found that, because of the high energy barrier of initiating a new carbon ring at the rim of a ZZ CNT, the growth rate of a ZZ CNT is proportional to its diameter and significantly (10–1000 times) slower than that of other CNTs. This study successfully explained the broad experimental observation of the lacking of ZZ CNTs in CNT samples and completed the theory of CNT growth.     

Prediction of the Frontier Electronic States in a Finite Single-wall Carbon Nanotube

A theoretical model is summarized into the shorter vector principle. It is used to predict the topological structure of wave function and the oscillation rule of energy gap in various types of finite carbon nanotubes (CNTs). The theoretical model indicates that the characteristics of the electronic states only depend on the nanotube size and its symmetry along the shorter vector direction. In this direction, the wave functions of the original 3m (or 3m/2) periodicity are also suitable for armchair, chiral and zigzag finite CNTs with the C2 (Cs), C1 and Cn point groups, respectively. Energy gaps present the oscillation with 3m (or 3m/2) or odd-even n. The first principle calculations for some prototype systems are performed. The results are consistent with the theoretical model.     

The Effects of the Formation of Stone–Wales Defects on the Electronic and Magnetic Properties of Silicon Carbide Nanoribbons: A First‐Principles Investigation

Detailed first‐principles density functional theory (DFT) computations were performed to investigate the geometries, the electronic, and the magnetic properties of both armchair‐edged silicon carbide nanoribbons (aSiCNRs) and zigzag‐edged silicon carbide nanoribbons (zSiCNRs) with Stone–Wales (SW) defects. SW defects in the center of aSiCNRs can remarkably reduce their band gaps, irrespective of the orientation of the defect, whereas zSiCNRs with SW defects in the center or at the edges exhibit degenerate energies of their ferromagnetic (FM) and antiferromagnetic (AFM) states, in which metallic and half‐metallic behavior can be observed, respectively; half‐metallic behavior can even be observed in both the FM and AFM states simultaneously. Further, it was shown that the formation energies of the SW defects in SiCNRs are orientation dependent, and the formation of edge defects is always favored over the formation of interior defects in zSiCNRs. The possible existence of SW defects in SiCNRs was further validated through exploring the kinetic process of their formation. These findings can be anticipated to provide valuable information in promoting the potential applications of SiC‐based nanomaterials in multifunctional and spintronic nanodevices.     

Impact of the Chirality and Curvature of Carbon Nanostructures on Their Interaction with Aromatics and Amino Acids

Understanding noncovalent interactions on the surfaces of carbon nanostructures (CNSs) is of fundamental importance and also has implications in nano‐ and biotechnology. The interactions of aromatic compounds such as benzene, naphthalene, and aromatic amino acids with CNSs of varying diameter, chirality, and curvature were systematically explored by using density functional theory. Planar graphene exhibits stronger binding affinity than curved carbon nanotubes (CNTs), whereas zigzag CNTs appear to show stronger binding affinity than armchair CNTs. For hydrocarbons, there exist two competing modes, namely, π–π stacking interactions and CH ??? π interactions, which bring the aromatic motifs into parallel and perpendicular dispositions with respect to the CNSs, respectively. Our results reveal that π–π stacking interactions override CH ??? π interactions in such cases. However, in the case of aromatic amino acids, π–π interactions can exist simultaneously along with a range of other interactions, including CH ??? π. The polarizability and HOMO energy of the CNSs were found to be the key factors that determine the binding energies. The HOMO–LUMO energy gaps of the CNSs were found to be undisturbed by the noncovalent functionalization of the aromatic molecules.     

Edge effects, electronic arrangement, and aromaticity patterns on finite-length carbon nanotubes

Previous investigations have revealed that even long carbon nanotubes (CNTs) retain bond patterns that are characterized by the localization of Clar rings. Even for CNTs with 10 nm length, an alternated, oscillating structure of Clar and Kekulé patterning was also found, indicating that these arrangements may possibly persist for even longer nanotubes, given that they are finite. In the present work, we perform a detailed and comprehensive theoretical study of this phenomenon, in order to find the causes that give rise to these patterns. A complete set of CNTs with different chiralities, diameters (up to 2 nm), lengths (up to 10 nm) and endings (capped, uncapped, and tailored endings) was considered for such purposes. The results indicate that the Clar patterning appears not only on armchair CNTs, but also on those with chiral angle values close to 30°, and this results in a stabilization of the structure, when compared with the uniform, zigzag CNTs. This stabilizing effect points to the causes that underlie the three Nakamura CNT types, resulting as the superposition of structures with a maximal number of Clar rings. Although there is a strict dependence on the border shape, the main cause of the bond patterning in long tubes is to be found in the intrinsic wrapping of each CNT, because the type and number of oscillations present in the longest structures do not depend on the particular length. Nevertheless, the three Nakamura types of armchair tubes appear to subsist beyond the appearance of oscillations, because each of these sets evolves in a different manner, and energy properties that link them together. Apart from the geometry, Clar patterning was investigated through NICS (Nucleus Independent Chemical Shifts) measures, which reveal a connection between the Clar rings and a local concentration of aromaticity.     

Armchair型石墨纳米带的电子结构和输运性质

利用第一性原理的电子结构和输运性质计算方法, 研究了扶手椅(armchair)型单层石墨纳米带(具有锯齿边缘)的电子结构和输运性质及其边缘空位缺陷效应. 研究发现, 完整边缘的扶手椅型石墨纳米带是典型的金属性纳米带, 边缘空位缺陷的存在对扶手椅型纳米带能带结构有一定的影响,但并不彻底改变其金属性特征.     

Endohedral and exohedral complexes of 1-benzene with carbon nanotubes and high-density assembly of multiple benzenes inside of a carbon nanotube

The 1-benzene was put on the inside and surface of various armchair (n, n) (n = 6-12, 14) and zigzag (n, 0) (n = 10-17, 20) nanotubes of different diameters. The binding structure, binding energy, and effects on binding energy were analyzed. All interaction structures and the properties of the assembled complexes were investigated via density functional tight-binding method. Furthermore, we put multiple benzene molecules (2-18 benzenes) inside the armchair (10, 10), (9, 9), and (8, 8) carbon nanotubes (CNTs) and found that two types of structures were formed for the endohedral complexes of multiple benzenes-spiral symmetrical polygon and criss-crossed types, respectively. The detail of the binding energies and structure properties for (10, 10)/kBen (k = 1-6, 18), (9, 9)/kBen (k = 4, 5, 15), and (8, 8)/kBen (k = 1-8) were discussed. Furthermore, the HOMOs and LUMOs of the representative complexes were also studied to illustrate the interactions. This article offers a new assembly method to prepare a high density of benzenes inside of CNTs and offers a method for benzene adsorption by CNT.     

硼氮纳米管导电性与成键性的理论研究

用密度泛函的B3LYP方法对zigzag型(N,0)和armchair型(N,N)硼氮纳米管(N=4,5,6)进行了理论计算,根据其能带结构、态密度和健级讨论了四硼氮纳米管的成健作用和导电性,并与碳纳米管做比较.     

A dispersion-corrected density functional theory study of the noncovalent interactions between nucleobases and carbon nanotube models containing stone–wales defects

The noncovalent bonding between nucleobases (NBs) and Stone–Wales (SW) defect-containing closed-end single-walled carbon nanotubes (SWNTs) was theoretically studied in the framework of density function theory using a dispersion-corrected functional PBE-G06/DNP. The models employed in this study were armchair nanotube (ANT) (5,5) and zigzag nanotube (ZNT) (10,0), which incorporated SW defects in different orientations. In one of them, the (7,7) junction is tilted with respect to SWNT axis (ANT-t and ZNT-t), whereas in ANT-p and ZNT-p models the (7,7) junction is parallel and perpendicular to the axis, respectively. The binding energies for uracil, thymine, cytosine, 5-methylcytosine, adenine, and guanine interacting with the defect-containing nanotube models were compared to the values previously obtained with the same calculation technique for the case of defect-free SWNTs, both in the gas phase (vacuum) and in aqueous medium. For most models, the interaction strength tends to be higher for purine than for pyrimidine complexes, with a clear exception of the systems including ZNT-p, both in vacuum and in aqueous medium. As it could be expected, the binding strength in the latter case is lower as compared to that in vacuum, roughly by 2–4 kcal/mol, due to the implicit inclusion of a medium (i.e., water) via the conductor-like screening model model. The closest contacts between NBs and SWNT models, frontier orbital distribution, and highest-occupied molecular orbital–lowest-unoccupied molecular orbital gap energies are analyzed as well. © 2019 Wiley Periodicals, Inc.     

受限于不同螺旋性的纳米碳管中水的分子动力学模拟

近年来将纳米碱米碳管引入到与生命过程息息相关的离子通道膜的研究逐渐成 为热点，而其中的关键就是要了解受限于膜孔道（碳管）中水分子的行为。采用分 子动力学模拟在300 K和1.01 * 10~5 Pa下对受限于（6，6）armchair型和（10， 0）zigzag型纳米碳管中的水进行了研究，得到了水分子在碳管中的局部密度分布 等静态性质以及水分子在碳管中的传递等动态性质，并对不同势能模型的模拟结果 作了比较。结果表明选择不同的势能模型并没有改变此体系的固有性质，即水分子 不仅能够进入到憎水性的（6，6）碳管中而且能形成一条稳定的由氢键相连的纵列 （single file），而且在管中以纵列的形式进行同歇传递。此外，碳管螺旋性对 受限水的静态性质影响不大但对动态性质则有一定程度的影响，水分子在（10，0 ）zigzag型碳管中的传递能力要强于在（6，6）armchair型碳管中的能力。     

接枝羧基对单壁碳纳米管弹性性质的影响

采用分子动力学方法对端口接枝不同数量羧基的扶手椅型和锯齿型单壁碳纳米管弹性模量进行了模拟研究. 结果表明, 扶手椅型(5, 5)、(10, 10)管和锯齿型(9, 0)、(18, 0)管在未接枝状态下杨氏模量分别为948、901GPa和804、860 GPa. 在接枝2-8个羧基情况下, 扶手椅型单壁碳纳米管拉伸杨氏模量基本不随接枝数量的增加而发生变化, 而锯齿型单壁碳纳米管则不同, 接枝状态下的弹性模量比未接枝状态小很多, 但随接枝数量的增加又呈略增趋势. 分别从接枝后碳纳米管变形电子密度等值线结构变化、键长变化和系统势能变化规律等方面, 对单壁碳纳米管弹性模量的接枝效应进行了分析.     

Computational studies of carbon nanotube-hydrocarbon bond strengths at nanotube ends: effect of link heteroatom and hydrocarbon structure

Semiempirical and density functional electronic structure theory methods were used to study SWNT-X--R bond strengths, where the single-walled carbon nanotube (SWNT) had an armchair or zigzag structure, the link heteroatom X was O, N(H), or S and the hydrocarbon chain R was CH(2)CH(3), CH(OH)CH(3), CHCH(2), or CH(CF(3))CH(3). In all systems the hydrocarbon was bonded to the end of the nanotube. The SWNT-X--R bond (that is, the bond joining the link atom to the hydrocarbon) is more than 0.4 eV stronger for armchair than for zigzag nanotubes with the same diameters, irrespective of whether O, N, or S are used as link atoms or whether OH, C==C, or CF(3) groups are present in the hydrocarbon chain. This raises the possibility for selective manipulation of armchair/zigzag nanotubes using a variety of link atoms and hydrocarbon structures. The SWNT-O--CH(CF(3))CH(3) bond is weaker than the SWNT-O--CH(2)CH(3) bond (for both armchair and zigzag nanotubes), while inclusion of a double bond in the ethyl chain increases the bond strengths. Also, SWNT-S--CH(2)CH(3) and SWNT-N(H)--CH(2)CH(3) bonds are stronger than SWNT-O--CH(2)CH(3) bonds.     

Theory of nitrogen doping of carbon nanoribbons: edge effects

Nitrogen doping of a carbon nanoribbon is profoundly affected by its one-dimensional character, symmetry, and interaction with edge states. Using state-of-the-art ab initio calculations, including hybrid exact-exchange density functional theory, we find that, for N-doped zigzag ribbons, the electronic properties are strongly dependent upon sublattice effects due to the non-equivalence of the two sublattices. For armchair ribbons, N-doping effects are different depending upon the ribbon family: for families 2 and 0, the N-induced levels are in the conduction band, while for family 1 the N levels are in the gap. In zigzag nanoribbons, nitrogen close to the edge is a deep center, while in armchair nanoribbons its behavior is close to an effective-mass-like donor with the ionization energy dependent on the value of the band gap. In chiral nanoribbons, we find strong dependence of the impurity level and formation energy upon the edge position of the dopant, while such site-specificity is not manifested in the magnitude of the magnetization.     

The reactivity of defects at the sidewalls of single-walled carbon nanotubes: the Stone-Wales defect

The reactivity of 5/7/7/5 (Stone-Wales, SW) defects is compared to that of the pristine sidewalls of (5,5) and (10,0) carbon nanotubes (CNTs) using density functional theory (PBE). Infinite tube models (periodic boundary conditions) are used to investigate the reaction energy for CH(2) addition to the ten [5,6], [5,7], [6,7], and [7,7] C-C junctions resulting from SW rotations of the two unique bonds in (5,5) and (10,0) CNTs. In all cases, at least one of the junctions associated with the SW defects is more highly reactive than the pristine tubes. The orientation of these junctions with respect to the tube axis mainly determines the exothermicity. The [7,7] junctions are not the most reactive sites in SW defects of (5,5) and (10,0) CNTs.     

A theoretical study on the chirality detection of serine amino acid based on carbon nanotubes with and without Stone-Wales defects

In the present study, the interaction of serine (SER) amino acid (AA) with the pristine and defected carbon nanotubes (CNTs) has been investigated by employing the molecular dynamics (MD) and the density functional theory (DFT) approaches. Furthermore, the potential application of CNTs with and without the Stone-Wales (SW) defects in sensing of SER chirality has been studied. Our results confirm that introducing the chiral l and d SERs (LSER and DSER) exerts a significant effect on the electronic and optical properties of the CNTs with and without the SW defect. According to the MD results, it is observed that for all the structures, the obtained minimum distance is among the SER aliphatic segments and the tube atoms. The calculated structural and electronic properties of pristine and defected CNT are in good agreement with the reported research studies. The results indicate that pyramidalization angles (θ_p) at C atoms are altered in the presence of the SW defects. The overall increment of θ_p suggests that the reactivity has increased at the defective regions. In the case of CNT with one SW defect (CNTSW1), the central C–C bond of the SW defect is the most chemically reactive site. Our results establish that pristine CNT is a semiconductor when the LSER and DSER are adsorbed (with the band gap of 0.30 eV and 0.32 eV, respectively). The LSER-adsorbing CNT with two SW defects (CNTSW2) is a semiconductor with a reduced band gap (0.41 eV), while the DSER-adsorbing CNTSW2 is an n-type semiconductor (with a band gap of 0.70 eV). The optical properties are inferred from the dielectric functions of the CNTs. The most remarkable result belongs to the CNTSW2; the imaginary part of the CNTSW2 dielectric function can sensitively distinguish the chirality of the SER amino acid.

     

Boron Nitride Nanotubes as Novel Vectors for Drug Delivery of Amino Acids:A First Principles Simulation

The first principles calculations based on density functional theory(DFT) were performed for investigating the interaction of amino acids with(5, 5) armchair and(8, 0) zigzag boron nitride nanotubes(BNNTs). Findings showed that the adsorption and solvation energies were negative for(5, 5)/(8,0) BNNTs-amino acid complexes, implying the thermodynamic favorability and spontaneous interactions of amino acids with BNNTs sidewall. Based on calculated results, the BNNTs are expected to be a potential efficient adsorbent as well as a suitable drug delivery vehicle for the adsorption of amino acids within biological systems.     

DFT studies of functionalized zigzag and armchair boron nitride nanotubes as nanovectors for drug delivery of collagen amino acids

The interaction of collagen amino acids with (5, 5) armchair and (9, 0) zigzag single-walled boron nitride nanotubes (BNNTs) are studied using density functional theory. Our results show that the BNNTs can act as a suitable drug delivery vehicle of collagen amino acids within biological systems. DFT-LDA/DNP calculations revealed that the binding and solvation energies were negative for (5, 5)/(9, 0) BNNTs–collagen amino acid complexes implying the thermodynamic favorability and spontaneous interactions of collagen amino acids with BNNTs sidewall. These results were extremely relevant in order to identify the potential applications of functionalized BNNTs as drug delivery systems.