Hydrogen dissociation on diene-functionalized carbon nanotubes

Chemical functionalization of a zigzag carbon nanotube (CNT) with 1, 3-cyclohexadiene (CHD), previously reported by experimentalists, has been investigated in the present study using density functional theory in terms of energetic, geometric, and electronic properties. Then, the thermodynamic and kinetic feasibility of H₂ dissociation on the pristine and functionalized CNTs have been compared. The dissociation energy of the H₂ molecule on the pristine and functionalized CNT has been calculated to be about ?1.00 and ?1.55 eV, while the barrier energy is found to be about 3.70 and 3.51 eV, respectively. Therefore, H₂ dissociation is thermodynamically more favorable on the CNT-CHD system than on the pristine tube, while the favorability of the dissociation on the pristine tube is higher in term of kinetics.     

A DFT study on the sensing behavior of a BC2N nanotube toward formaldehyde

We investigated the viability of using a BC₂N nanotube to detect formaldehyde (H₂CO) molecule by means of B3LYP and M06 density functionals. The results indicate that the molecule is weakly adsorbed on the intrinsic BC₂N nanotube releasing energy of 0.8 kcal mol^-1 (at B3LYP/6-31G(d)) without significant effect on the HOMO-LUMO energy gap and electrical conductivity of the tube. Thus, H₂CO cannot be detected using this intrinsic nanotube. To overcome this problem, a carbon atom of the tube wall was substituted by a Si atom. It was demonstrated that the Si-doped tube cannot only strongly adsorb the H₂CO molecule, but also may effectively detect its presence because of the increase in the electric conductivity of the tube.     

Tuning hydrogen storage of carbon nanotubes by mechanical bending: theoretical study

The effects of mechanical bending on tuning the hydrogen storage of titanium functionalised (4,0) carbon nanotube have been assessed using density functional theory calculations with reference to the ultimate targets of the US Department of Energy (DOE). The assessment has been carried out in terms of physisorption, gravimetric capacity, projected densities of states, statistical thermodynamic stability and reaction kinetics. The Ti atom binds at the hollow site of the hexagonal ring. The average adsorption energies (?0.54 eV) per hydrogen molecule meet the DOE target for physisorption (?0.20 to ?0.60 eV). The curvature attributed to the bending angle has no effect on the average adsorption energies per H₂ molecule. With no metal clustering, the system gravimetric capacities are expected to be as large as 9.0 wt%. The reactions of the deformed (bent) carbon nanotube have higher probabilities of occurring than those of the un-deformed carbon nanotube. The Gibbs free energies, enthalpies and entropies meet the ultimate targets of the DOE for all temperatures and pressures. The closest reactions to zero free energy occur at (378.15 K/2.961 atm.) and reverse at (340 and 360 K/1 atm.). The translational component is found to exact a dominant effect on the total entropy change with temperature. Favourable kinetics of the reactions at the temperatures targeted by DOE are reported regardless of the applied pressure. The more preferable thermodynamic properties assigned to the bending nanotube imply that hydrogen storage can be improved compared to the nonbending nanotube.     

Repair of DNA double-strand breaks in Escherichia coli, which requires recA function and the presence of a duplicate genome.

A method was devised for extracting, from cells of Escherichia coli K12, DNA molecules which sedimented on neutral sucrose gradients as would be expected for free DNA molecules approaching the genome in size. Gamma ray irradiation of oxygenated cells produced 0.20 DNA double-strand breaks per kilorad per 10⁹ daltons. Incubation after irradiation of cells grown in K medium, with four to five genomes per cell, showed repair of the double-strand breaks. No repair of double-strand breaks was found in cells grown in aspartate medium, with only 1.3 genomes per cell, although DNA single-strand breaks were still efficiently repaired. Cells which were recA^? or recA^?recB^? also did not repair double-strand breaks. These results suggest that repair of DNA double-strand breaks may occur by a recombinational event involving another DNA double helix with the same base sequence.     

In Vitro Repair of Gaps in Bacteriophage T7 DNA

An in vitro system based upon extracts of Escherichia coli infected with bacteriophage T7 was used to study the mechanism of double-strand break repair. Double-strand breaks were placed in T7 genomes by cutting with a restriction endonuclease which recognizes a unique site in the T7 genome. These molecules were allowed to repair under conditions where the double-strand break could be healed by (i) direct joining of the two partial genomes resulting from the break, (ii) annealing of complementary versions of 17-bp sequences repeated on either side of the break, or (iii) recombination with intact T7 DNA molecules. The data show that while direct joining and single-strand annealing contributed to repair of double-strand breaks, these mechanisms made only minor contributions. The efficiency of repair was greatly enhanced when DNA molecules that bridge the region of the double-strand break (referred to as donor DNA) were provided in the reaction mixtures. Moreover, in the presence of the donor DNA most of the repaired molecules acquired genetic markers from the donor DNA, implying that recombination between the DNA molecules was instrumental in repairing the break. Double-strand break repair in this system is highly efficient, with more than 50% of the broken molecules being repaired within 30 min under some experimental conditions. Gaps of 1,600 nucleotides were repaired nearly as well as simple double-strand breaks. Perfect homology between the DNA sequence near the break site and the donor DNA resulted in minor (twofold) improvement in the efficiency of repair. However, double-strand break repair was still highly efficient when there were inhomogeneities between the ends created by the double-strand break and the T7 genome or between the ends of the donor DNA molecules and the genome. The distance between the double-strand break and the ends of the donor DNA molecule was critical to the repair efficiency. The data argue that ends of DNA molecules formed by double-strand breaks are typically digested by between 150 and 500 nucleotides to form a gap that is subsequently repaired by recombination with other DNA molecules present in the same reaction mixture or infected cell.     

A method for measuring the number of single- and double-strand breaks introduced into DNA molecules by the action of deoxyribonucleases.

A method is described for measuring the average number of nuclease-induced single- and double-strand breaks per DNA molecule. The procedure involves measuring the weight-average molecular weight of DNase I-digested DNA under neutral and alkaline conditions. A statistical equation is used to calculate the number of breaks per single- or double-stranded DNA molecule from the respective weight-average molecular weights. Enzymatic incorporation of³²P into the 5′-OH ends of DNase I-induced breaks gave an independent measurement of the number of breaks per DNA molecule. Results obtained by the two different methods were in good agreement. In agreement with earlier reports we find that magnesium-activated DNase catalyzes a high frequency of single-strand breaks in DNA. The frequency of double-strand breaks is low, but significantly higher than can be explained by random accumulation of single-strand breaks. Our data suggest that the frequency of double-strand scission is affected by DNase-metal ion interactions.     

C60 binds to and deforms nucleotides

Atomistic molecular dynamics simulations are performed for up to 20 ns to monitor the formation and the stability of complexes composed of single- or double-strand DNA molecules and C60 in aqueous solution. Despite the hydrophobic nature of C60, our results show that fullerenes strongly bind to nucleotides. The binding energies are in the range -27 to -42 kcal/mol; by contrast, the binding energy of two fullerenes in aqueous solution is only -7.5 kcal/mol. We observe the displacement of water molecules from the region between the nucleotides and the fullerenes and we attribute the large favorable interaction energies to hydrophobic interactions. The features of the DNA-C60 complexes depend on the nature of the nucleotides: C60 binds to double-strand DNA, either at the hydrophobic ends or at the minor groove of the nucleotide. C60 binds to single-strand DNA and deforms the nucleotides significantly. Unexpectedly, when the double-strand DNA is in the A-form, fullerenes penetrate into the double helix from the end, form stable hybrids, and frustrate the hydrogen bonds between end-group basepairs in the nucleotide. When the DNA molecule is damaged (specifically, a gap was created by removing a piece of the nucleotide from one helix), fullerenes can stably occupy the damaged site. We speculate that this strong association may negatively impact the self-repairing process of the double-strand DNA. Our results clearly indicate that the association between C60 and DNA is stronger and more favorable than that between two C60 molecules in water. Therefore, our simulation results suggest that C60 molecules have potentially negative impact on the structure, stability, and biological functions of DNA molecules.     

Action of Escherichia coli P1 restriction endonuclease on simian virus 40 DNA

The P1 restriction endonuclease (EcoP1) prepared from a P1 lysogen of Escherichia coli makes one double-strand break in simian virus (SV40) DNA. In the presence of cofactors S-adenosylmethionine and ATP the enzyme cleaves 70% of the closed circular SV40 DNA molecules once to produce unit-length linear molecules and renders the remaining 30% resistant to further cleavage. No molecules were found by electron microscopy or by gel electrophoresis that were cleaved more than once. It would appear that the double-strand break is made by two nearly simultaneous single-strand breaks, since no circular DNA molecules containing one single-strand break were found as intermediates during the cleavage reaction. The EcoP1 endonuclease-cleaved linear SV40 DNA molecules are not cleaved at a unique site, as shown by the generation of about 65% circular molecules after denaturation and renaturation. These EcoP1 endonuclease-cleaved, renatured circular molecules are resistant to further cleavage by EcoP1 endonuclease.The EcoP1 endonuclease cleavage sites on SV40 DNA were mapped relative to the partial denaturation map and to the EcoRI and HpaII restriction endonuclease cleavage sites. These maps suggest there are a minimum of four unique but widely spaced cleavage sites at 0.09, 0.19, 0.52, and 0.66 SV40 units relative to the EcoRI site. The frequency of cleavage at any particular site differs from that at another site. If S-adenosylmethionine is omitted from the enzyme reaction mix, SV40 DNA is cleaved into several fragments.An average of 4.6 ± 1 methyl groups are transferred to SV40 DNA from S-adenosylmethionine during the course of a normal reaction containing the cofactors. Under conditions which optimize this methylation, 7 ± 1 methyl groups can be transferred to DNA. This methylation protects most of the molecules from further cleavage. The methyl groups were mapped relative to the Hemophilus influenzae restriction endonuclease fragments. The A fragment receives three to four methyl groups and the B and G fragments each receive one to two methyl groups. These fragments correspond to those in which cleavage sites are located.     

Quantifying Double-Strand Breaks and Clustered Damages in DNA by Single-Molecule Laser Fluorescence Sizing

Fluorescence from a single DNA molecule passing through a laser beam is proportional to the size (contour length) of the molecule, and molecules of different sizes can be counted with equal efficiencies. Single-molecule fluorescence can thus determine the average length of the molecules in a sample and hence the frequency of double-strand breaks induced by various treatments. Ionizing radiation-induced frank double-strand breaks can thus be quantified by single-molecule sizing. Moreover, multiple classes of clustered damages involving damaged bases and abasic sites, alone or in combination with frank single-strand breaks, can be quantified by converting them to double-strand breaks by chemical or enzymatic treatments. For a given size range of DNA molecules, single-molecule sizing is as or more sensitive than gel electrophoresis, and requires several orders-of-magnitude less DNA to determine damage levels.     

Nitrous oxide adsorption on pristine and Si-doped AlN nanotubes

Using density functional theory, we studied the adsorption of an N₂O molecule onto pristine and Si-doped AlN nanotubes in terms of energetic, geometric, and electronic properties. The N₂O is weakly adsorbed onto the pristine tube, releasing energies in the range of ?1.1 to ?5.7 kcal mol^-1. The electronic properties of the pristine tube are not influenced by the adsorption process. The N₂O molecule is predicted to strongly interact with the Si-doped tube in such a way that its oxygen atom diffuses into the tube wall, releasing an N₂ molecule. The energy of this reaction is calculated to be about ?103.6 kcal mol^-1, and the electronic properties of the Si-doped tube are slightly altered.     

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     

Fluorination of BC3 nanotubes: DFT studies

We have studied the adsorption of atomic and molecular fluorines on a BC₃ nanotube by using density functional calculations. It was found that the adsorption of atomic fluorine on a C atom of the tube surface is energetically more favorable than that on a B atom by about 0.97 eV. The adsorption of atomic fluorine on both C and B atoms significantly affects the electronic properties of the BC₃ tube. The HOMO-LUMO energy gap is considerably reduced from 2.37 to 1.50 and 1.14 eV upon atomic F adsorption on B and C atoms, respectively. Molecular fluorine energetically tends to be dissociated on B atoms of the tube surface. The associative and dissociative adsorption energies of F₂ were calculated to be about ?0.42 and ?4.79 eV, respectively. Electron emission density from BC₃ nanotube surface will be increased upon both atomic and molecular fluorine adsorptions due to work function decrement.     

Single-strand breakage on binding of DNA to cells in the genetic transformation of Diplococcus pneumoniae.

Mutants of Diplococcus pneumoniae that lack a membrane-localized DNAase are defective in transformation because entry of DNA into the cell is blocked. Such mutants still bind DNA on the outside of the cell. The bound DNA is double-stranded and its double-stranded molecular weight is unchanged. Its sedimentation behavior in alkali, however, shows that it has undergone single-strand breakage. The breaks are located randomly in both strands of the bound DNA at a mean separation of 2 × 10⁶ daltons of single-stranded DNA. Both binding and single-strand breakage occur in the presence of EDTA. Single-strand breaks are similarly formed on binding of DNA to normally transformable cells in the presence of EDTA. The single-strand breaks appear to be a consequence of attachment. DNA may be bound to the cell surface at the point of breakage.A mutant that is partially blocked in entry also binds DNA mainly on the outside of the cell. In the presence of EDTA, DNA bound by this mutant undergoes only single-strand breaks. In the absence of EDTA, however, double-strand breaks occur, apparently as a result of the initiation of entry. It is possible that the double-strand breaks arise from additional single-strand breaks opposite those that occurred on binding. The double-strand breaks presumably result from action of the membrane DNAase as it begins to release oligonucleotides from one strand segment while drawing the complementary strand segment into the cell.     

Induction of DNA damage, including abasic sites, in plasmid DNA by carbon ion and X-ray irradiation

DNA from plasmid pUC18 was irradiated with low-LET (13 keV/μm) or high-LET (60 keV/μm) carbon ions or X-rays (4 keV/μm) in solutions containing several concentrations of Tris (0.66–200 mM) to determine the yield of abasic (AP) sites and the effect of scavenging capacity. The yield of AP sites, detected as single-strand breaks (SSB) after digestion with E. coli endonuclease IV (Nfo), was compared with that of SSB and base lesions. At higher concentrations of Tris, the yields of single or clustered AP sites were significantly lower than those of single or clustered base lesions. The relative yields of single AP sites and AP clusters were less than 10 and 7 %, respectively, of the total damage produced at a scavenger capacity mimicking that in cells. The dependence of the yield of AP sites on scavenging capacity was similar to that of prompt strand breaks. The ratios of the yield of isolated AP sites to that of SSB induced by carbon ion or X-ray irradiation were relatively constant at 0.45 ± 0.15 over the tested range of scavenger capacity, although the ratio of SSB to double-strand breaks (DSB) showed the characteristic dependence on both scavenging capacity and radiation quality. These results indicate that the reaction of water radiolysis products, presumably OH radicals, with the sugar-phosphate moieties in the DNA backbone induces both AP sites and SSB with similar efficiency. Direct ionization of DNA is notably more involved in the production of DSB and base lesion clusters than in the production of AP site clusters.     

Resonance energy transfer and competing processes in donor–acceptor of sodium zinc (II)-2,9,16,23-phthalocyanine tetracarboxylate molecule

An important issue that should be taken into consideration when applying the molecules in photodynamic therapy (PDT) of cancer is the occurrence of homo-resonance energy transfer process between them. We have determined the probability of energy transfer for sodium zinc (II)-2,9,16,23-phthalocyanine tetracarboxylate (ZnPc(COONa)₄) molecules in aqueous NaOH solution. The homo-quenching effect of the molecule was also measured by calculating the diffusion controlled bimolecular rate constant of k _q = 6.5?×?10⁹ M^?1s^?1, which did not show a significant competition with the rate constant of homo-resonance energy transfer process at the applied concentration of the molecules (6 μM). The Förster radius (R? ₀) for ZnPc(COONa)₄ molecules was calculated to be 42 Å. The availability of these calculations should facilitate the potential application of ZnPc(COONa)₄ molecule as an anticancer drug in PDT.     

Simple benzene derivatives adsorption on defective single-walled carbon nanotubes: a first-principles van der Waals density functional study

We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp ²-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The ?0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems.

Interaction of a Ti-doped semi-fullerene (TiC<Subscript>30</Subscript>) with molecules of CO and CO<Subscript>2</Subscript>

Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C₆₀ fullerene (i.e., C₃₀), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titanium atom on C₃₀ occurs in the concave surface of the molecule. Afterward, we investigated the interaction of the system C₃₀-titanium with carbon monoxide and carbon dioxide molecules, respectively. We found that each of these molecules is chemisorbed, with no dissociation. The value of the adsorption energy for the carbon monoxide molecule varies from ?0.897 to ?1.673 eV, and for the carbon dioxide molecule, it is between ?1.065 and ?1.274 eV. These values depend on the initial orientation of these molecules with respect to TiC₃₀.

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Graphical Abstract The TiC₃₀ system chemisorbs CO or CO₂?with no dissociation at atmospheric pressure and 300K

     

Driving force of water entry into hydrophobic channels of carbon nanotubes: entropy or energy?

Spontaneous entry of water molecules inside single-wall carbon nanotubes (SWCNTs) has been confirmed by both simulations and experiments. Using molecular dynamics simulations, we have studied the thermodynamics of filling of a (6,6) carbon nanotube in a temperature range from 273 to 353 K and with different strengths of the nanotube–water interaction. From explicit energy and entropy calculations using the two-phase thermodynamics method, we have presented a thermodynamic understanding of the filling behaviour of a nanotube. We show that both the energy and the entropy of transfer decrease with increasing temperature. On the other hand, scaling down the attractive part of the carbon–oxygen interaction results in increased energy of transfer while the entropy of transfer increases slowly with decreasing the interaction strength. Our results indicate that both energy and entropy favour water entry into (6,6) SWCNTs. Our results are compared with those of several recent studies of water entry into carbon nanotubes.     

Repair of MMS-induced DNA double-strand breaks in haploid cells of Saccharomyces cerevisiae, which requires the presence of a duplicate genome.

Summary The formation and repair of double-strand breaks induced in DNA by MMS was studied in haploid wild type and MMS-sensitive rad6 mutant strains of Saccharomyces cerevisiae with the use of the neutral and alkaline sucrose sedimentation technique. A similar decrease in average molecular weight of double-stranded DNA from 5–6x10⁸ to 1–0.7x10⁸ daltons was observed following treatment with 0.5% MMS in wild type and mutant strains. Incubation of cells after MMS treatment in a fresh drug-free growing medium resulted in repair of double-strand breaks in the wild type strain, but only in the exponential phase of growth. No repair of double-strand breaks was found when cells of the wild type strain were synchronized in G-1 phase by treatment with factor, although DNA single-strand breaks were still efficiently repaired. Mutant rad6 which has a very low ability to repair MMS-induced single-strand breaks, did not repair double-strand breaks regardless of the phase of growth.These results suggest that (1) repair of double-strand breaks requires the ability for single-strand breaks repair, (2) rejoining of double-strand breaks requires the availability of two homologous DNA molecules, this strongly supports the recombinational model of DNA repair.