Time filter

Source Type

Denis P.A.,Computational Nanotechnology | Denis P.A.,Centro Interdisciplinario En Nanotecnologia Y Quimica Fisica Of Materiales | Iribarne F.,Laboratorio Of Bioinformatica Y Farmacologia Molecular
Journal of Molecular Structure: THEOCHEM | Year: 2010

We investigated the adsorption of thiophene inside and outside Single Wall Carbon Nanotubes (SWCNTs) and onto graphene, employing periodic boundary conditions and the VDW-DF and LDA methodologies. The results indicate that thiophene adopts a nearly parallel configuration with respect to the graphene plane. The sulfur atom is 3.7Å above the sheet, whereas the two hydrogen atoms located in carbon atoms not bonded to sulfur are 3.45Å above it. The adsorption energy for this configuration is 8.9kcal/mol, smaller a value than the one determined for benzene. For the T-shaped configurations the potential energy surface is very flat showing different orientations with similar interaction energies. When two hydrogen atoms are positioned over a CC bond the binding energy is 5.2kcal/mol. However, when the sulfur atom is over a hexagon, the interaction energy reaches its minimum value. The vibrational frequencies of thiophene are red-shifted when it is adsorbed on graphene being the intensity of the most prominent peak in the IR spectra increased by 34% and red-shifted by 14cm-1. For the adsorption on carbon nanotubes, the internal adsorption energies are larger than the external ones, although the former decreases rapidly as the tube radius is increased. The orientation of the thiophene molecule inside a SWCNT strongly depends on the diameter of the tube. The charge transfer between thiophene and the carbon nanostructures is minimal thus the electronic properties are not affected by the adsorption. © 2010 Elsevier B.V.


Denis P.A.,Computational Nanotechnology | Denis P.A.,Centro Interdisciplinario En Nanotecnologia Y Quimica Fisica Of Materiales | Iribarne F.,Laboratorio Of Bioinformatica Y Farmacologia Molecular
Journal of Computational Chemistry | Year: 2011

We have performed a comparative study on the reactivity of metallic and semiconducting nanotubes using infinite and finite models. Infinite models were created using periodic boundary conditions while finite ones were constructed by means of hydrogen terminated nanotubes sections. Cluster models systematically underestimate the reactivity of metallic single wall carbon nanotube (SWCNT)s. We have confirmed that metallic nanotubes are more reactive than semiconducting species, in disagreement with previous works. The differences can be attributed to the presence of an instability in the singlet ground state of the wavefunction corresponding to semiconducting nanotubes clusters. When lower electronic states of the pristine cluster are considered, semiconducting nanotubes become less reactive as compared with metallic SWCNTs. Particularly, if an antiferromagnetic solution is considered for the semiconducting (10,0) SWCNT cluster, it becomes less reactive than the (5,5) SWCNT, as observed for infinite models. Because semiconducting nanotubes are less reactive than metallic counterparts, their reaction energies converge faster to the values observed for graphene. For a 1.6-nm diameter semiconducting nanotube, the addition energy is comparable with graphene. Thus, semiconducting nanotubes with diameters larger than 1.6 nm are going to be as reactive as graphene and the effects of curvature will be unimportant. © 2011 Wiley Periodicals, Inc.


Denis P.A.,Computational Nanotechnology | Denis P.A.,Centro Interdisciplinario en Nanotecnologia y Quimica | Iribarne F.,Laboratorio Of Bioinformatica Y Farmacologia Molecular
International Journal of Quantum Chemistry | Year: 2011

The addition of oxygen-centered radicals to fullerenes has been intensively studied due to their role in cell protection against against hydrogen peroxide induced oxidative damage. However, the analogous reaction of sulfur-centered radicals has been largely overlooked. Herein, we investigate the addition of S-centered radicals to C50, C60, C70, and C100 fullerenes by means of DFT calculations. The radicals assayed were: S, SH, SCH3, SCH2CH3, SC 6H5, SCH2C6H5, and the open-disulfide SCH2CH2CH2CH2S. Sulfur, the most reactive species, prefers to be attached to a 66-bond of C 60 with a binding energy (Ebind) of 2.4 eV. For the SR radicals the electronic binding energies to C60 are 0.77, 0.74, 0.58, 0.67, and 0.35 eV for SH, SCH3, SCH2CH3, SCH2C6H5, and SC6H5, respectively. The reactivity of C60 toward SR radicals can be increased by lithium doping. For Li@C60, the Ebind is increased by 0.65 eV with respect to C60, but only by 0.33 eV for the exohedral doping. Fullerenes act like free radical sponges. Indeed, the C 60-SR Ebind can be duplicated if two radicals are added in ortho or para positions. The enhanced reactivity because of multiple additions is mostly a local effect, although the addition of one radical makes the whole cage more reactive. Therefore, as observed for hydroxylated fullerenes, they should protect cells from oxidative damage. However, the thiolated fullerenes have one advantage, they can be easily attached to gold nanoparticles. For the addition on pentagon junctions smaller fullerenes like C50 are more reactive than C60. Interestingly, C70 is as reactive as C60, even for the addition on the equatorial belt. For larger fullerenes like C100, reactivity decreases for the carbon atoms belonging to hexagon junctions. © 2010 Wiley Periodicals, Inc.


Denis P.A.,Computational Nanotechnology | Iribarne F.,Laboratorio Of Bioinformatica Y Farmacologia Molecular
Journal of Materials Chemistry | Year: 2012

Herein, we study [2 + 2] cycloadditions reactions onto graphene. We have found that owing to stacking, CH-π interactions and steric hindrance existing between the aromatic rings, the addition of benzyne molecules follows a characteristic pattern. For a 4 × 4 graphene unit cell, the optimum level of functionalization is achieved when one benzyne group per 4.0 carbon atoms is attached. Although the addition of benzyne molecules does not result in unpaired electrons (as observed for free radicals), the attachment of benzyne molecules in pairs on opposite sides of the sheet and on neighboring carbon atoms dramatically increases binding energies. We observed that reaction energies were increased by more than three times, as compared with the addition of an isolated benzyne molecule. The preferred structure has a band gap close to 1.5 eV. The uniformity of the properties found for aryne modified graphene, the ease whereby this is achieved (due to non bonded interactions, cooperative effects and steric hindrance between the benzyne molecules) and the fact that the reaction occurs in solution, turns the nanomaterial into a very attractive species for electronics. Lastly, we have shown that the addition of larger benzyne molecules as well as the addition of biscyclopropyl alkenes is favored from a thermodynamical stand point. © The Royal Society of Chemistry 2012.


Denis P.A.,Computational Nanotechnology | Iribarne F.,Laboratorio Of Bioinformatica Y Farmacologia Molecular
International Journal of Quantum Chemistry | Year: 2010

Herein, we perform a comparative study on the addition of azomethine ylides to graphene, carbon nanotubes, C60, ethene, pyrene and a C 48H18 hydrocarbon. The calculated binding energies and free energy corrections suggest that the addition of azomethine ylide to perfect graphene is not spontaneous (ΔG > 0). However, the presence of Stones-Wales defects significantly increases reactivity: the binding energy between SW-defective graphene and the azomethine ylide is 0.83 eV, close to that determined for a (5,5) SWCNT. The electronic properties of the sheet are not modified by the 1,3 cycloaddition. The binding energies determined for the addition of an azomethine ylide to a (5,5) SWCNT are significantly lower than previously reported. © 2009 Wiley Periodicals, Inc.


Denis P.A.,Computational Nanotechnology | Iribarne F.,Laboratorio Of Bioinformatica Y Farmacologia Molecular
Chemistry - A European Journal | Year: 2012

The interaction between alkyl radicals and graphene was studied by means of dispersion-corrected density functional theory. The results indicate that isolated alkyl radicals are not likely to be attached onto perfect graphene. It was found that the covalent binding energies are low, and because of the large entropic contribution, ΔG° 298 is positive for methyl, ethyl, isopropyl, and tert-butyl radicals. Although the alkylation may proceed by moderate heating, the desorption barriers are low. For the removal of the methyl and tert-butyl radicals covalently bonded to graphene, 15.3 and 2.4 kcal mol -1 are needed, respectively. When alkyl radicals are agglomerated, the binding energies are increased. For the addition in the ortho position and on opposite sides of the sheet, the graphene-CH 3 binding energy is increased by 20 kcal mol -1, whereas for the para addition on the same side of the sheet, the increment is 9.4 kcal mol -1. In both cases, the agglomeration turns the ΔG° 298<0. For the ethyl radical, the ortho addition on opposite sides of the sheet has a negative ΔG° 298, whereas for isopropyl and tert-butyl radicals the reactions are endergonic. The attachment of the four alkyl radicals under consideration onto the zigzag edges is exergonic. The noncovalent adsorption energies computed for ethyl, isopropyl, and tert-butyl radicals are significantly larger than the graphene-alkyl-radical covalent binding energies. Thus, physisorption is favored over chemisorption. As for the ΔG° 298 for the adsorption of isolated alkyl radicals, only the tert-butyl radical is likely to be exergonic. For the phenalenyl radical we were not able to locate a local minimum for the chemisorbed structure since it moves to the physisorbed structure. An important conclusion of this work is that the consideration of entropic effects is essential to investigate the interaction between graphene and free radicals. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Denis P.A.,Computational Nanotechnology | Iribarne F.,Laboratorio Of Bioinformatica Y Farmacologia Molecular
Chemistry - A European Journal | Year: 2011

By means of first principle calculations we have investigated a set of molecules that are presumed to contain carbon-sulfur triple bonds, namely HCSOH, H 3SCH, cis-FCSF, F 3CCSF 3, and F 5SCSF 3. For HCSOH, FCSF, and H 3SCH we used the CCSD(T) methodology and the correlation-consistent basis sets. On the other hand, F 3CCSF 3 and F 5SCSF 3 were studied at the B3LYP, M06-2X, MP2, and G3 levels of theory. We found that none of these molecules display a carbon-sulfur adiabatic bond dissociation energy (ABDE) as strong as diatomic CS (170.5a kcalmol -1), or a diabatic bond dissociation energy (DBDE) larger than the one found in SCO (212.0a kcalmol -1), although the DBDE of FCSF comes quite close at 208.3a kcalmol -1. The CS ABDEs of F 3CCSF 3, F 5SCSF 3, and H 3SCH are comparable to that of a single C-S bond. In contrast with the experimental results, F 3CCSF 3 and F 5SCSF 3 are predicted to be linear with C 3v and C s symmetry, respectively, at the B3LYP/6-311+G(3df,2p) level. MP2/6-311+G(2df,2p) calculations support the C 3v symmetry for F 3CCSF 3, despite F 5SCSF 3 not having a perfect linear structure; the CSC angle is 174.6°, which is nearly 20° larger than the experimental value. The analysis of the carbene structures of HCSOH and H 3SCH revealed that they are not significant, because the triplet state is dissociative in these cases. However, for F 3CCSF 3 and F 5SCSF 3, the carbene triplet states lie 0.81 and 0.77a eV above the singlet state, respectively. In the same vein, our investigation supports the presence of a strong double bond for HCSOH. The conflicting evidence available for F 3CCSF 3 and F 5SCSF 3 makes it very difficult to determine the nature of the CS bonds. However, the bond dissociation energies and the singlet-triplet splittings clearly suggest that these compounds should be considered as masked sulfinylcarbenes. The analysis of the bond dissociation energies challenges the existence of a triple bond in these five molecules, but from a strictly thermodynamic standpoint, cis-FCSF is found to be the candidate most likely to exhibit triple-bond character. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Loading Laboratorio Of Bioinformatica Y Farmacologia Molecular collaborators
Loading Laboratorio Of Bioinformatica Y Farmacologia Molecular collaborators