Theoretical Evidence for the Stronger Ability of Thymine to Disperse SWCNT than Cytosine and Adenine: self-stacking of DNA bases vs their cross-stacking with SWCNT

Self-stacking of four DNA bases, adenine (A), cytosine (C), guanine (G) and thymine (T), and their cross-stacking with (5,5) as well as (10,0) single walled carbon nanotubes (SWCNTs) were extensively investigated with a novel hybrid DFT method, MPWB1K/cc-pVDZ. The binding energies were further corrected with MP2/6-311++G(d,p) method in both gas phase and aqueous solution, where the solvent effects were included with conductor-like polarized continuum model (CPCM) model and UAHF radii. The strongest self-stacking of G and A takes displaced anti-parallel configuration, but un-displaced or "eclipsed" anti-parallel configuration is the most stable for C and T. In gas phase the self-stacking of nucleobases decreases in the sequence G>A>C>T, while because of quite different solvent effects their self-stacking in aqueous solution exhibits a distinct sequence A>G>T>C. For a given base, cross-stacking is stronger than self-stacking in both gas phase and aqueous solution. Binding energy for cross-stacking in gas phase varies as G>A>T>C for both (10,0) and (5,5) SWCNTs, and the binding of four nucleobases to (10,0) is slightly stronger than to (5,5) SWCNT by a range of 0.1-0.5 kcal/mol. The cross-stacking in aqueous solution varies differently from that gas phase: A>G>T>C for (10,0) SWCNT and G>A>T>C for (5,5) SWCNT. It is suggested that the ability of nucleobases to disperse SWCNT depends on relative strength [Formula: see text] of self-stacking and cross-stacking with SWCNT in aqueous solution. Of the four investigated nucleobases thymine (T) exhibits the highest [Formula: see text] which can well explain the experimental finding that T more efficiently functionalizes SWCNT than C and A.     

Theoretical investigation of the stability,electronic and magnetic properties of thiolated single‐wall carbon nanotubes

The addition of SH and OH groups to single‐wall carbon nanotubes (SWCNTs) was investigated employing first principles calculations. In the case of the semiconducting (10, 0) SWCNT the SWCNT‐SH binding energy is weak, 2–4 kcal/mol. However, for the metallic (5, 5) SWCNT it is larger, 7–9 kcal/mol. Thus metallic SWCNTs seem to be more reactive to SH than the semiconducting ones. Indeed, the (6, 6) SWCNT is more reactive to SH than the (10, 0) SWCNT, by 2–3 kcal/mol, something that can be explained only considering the electronic structure of the tube, because the (6, 6) has a larger diameter. The binding energies are larger for the addition of the OH group, 25 and 30 kcal/mol for the (10, 0) and (5, 5) SWCNTs, respectively. When a single OH or SH group is attached to the metallic SWCNTs, we observe important changes in the DOS at the Fermi level. However, when multiple SH groups are attached, the changes in the electronic and magnetic properties depend on the position of the SH groups. The small binding energy found for the SH addition indicates that the successful functionalization of SWCNTs with SH, SCH₃, and S(CH₂)_nSH groups is mostly due to the presence of defects created after acid treatment and to a minor extent by the metallic tubes present in the samples. Perfect semiconducting SWCNTs showed very low reactivity against the SH group. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Carbon chains and the (5,5) single-walled nanotube: structure and energetics versus length

Reliable thermochemistry is computed for infinite stretches of pure-carbon materials including acetylenic and cumulenic carbon chains, graphene sheet, and single-walled carbon nanotubes (SWCNTs) by connection to the properties of finite size molecules that grow into the infinitely long systems. Using ab initio G3 theory, the infinite cumulenic chain (:C[double bond]C[double bond]C[double bond]C:) is found to be 1.9+/-0.4 kcal/mol per carbon less stable in free energy at room temperature than the acetylenic chain (.C[triple bond]C-C[triple bond]C.) which is 24.0 kcal/mol less stable than graphite. The difference between carbon-carbon triple, double, and single bond lengths (1.257, 1.279, and 1.333 A, respectively) in infinite chains is evident but much less than with small hydrocarbon molecules. These results are used to evaluate the efficacy of similar calculations with the less rigorous PM3 semiempirical method on the (5,5) SWCNT, which is too large to be studied with high-level ab initio methods. The equilibrium electronic energy change for C(g)-->C[infinite (5,5) SWCNT] is -166.7 kcal/mol, while the corresponding free energy change at room temperature is -153.3 kcal/mol (6.7 kcal/mol less stable than graphite). A threefold alternation (6.866, 6.866, and 6.823 A) in the ring diameter of the equilibrium structure of infinitely long (5,5) SWCNT is apparent, although the stability of this structure over the constant diameter structure is small compared to the zero point energy of the nanotube. In general, different (n,m) SWCNTs have different infinite tube energetics, as well as very different energetic trends that vary significantly with length, diameter, and capping.     

On the applicability of cluster models to study the chemical reactivity of carbon nanotubes

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.     

A comparison of the effect of nanotube chirality and electronic properties on the π–π interaction of single‐wall carbon nanotubes with pyrazinamide antitubercular drug

Theoretical investigation on local electronic structure and stability of the π–π stacking interaction of pyrazinamide (PZA) with armchair (5,5) and zigzag (9,0) single‐walled carbon nanotubes (SWCNTs) is performed using density functional theory (DFT). PZA is physisorbed onto nanotube sidewall through interaction of π orbitals of PZA and SWCNT and the enhanced structural stability of PZA/SWCNT systems is due to weak side‐on rather than the head‐on π‐interactions. The physisorption of PZA onto SWCNT sidewall is thermodynamically favored; as a consequence, it modulates the electronic properties of pristine nanotube in the vicinity of Fermi region and π–π stacked interactions is stronger in (9,0) SWCNT compared to (5,5) SWCNT. The density of states (DOS) analysis show that PZA contributes toward the enhancement of electronic states. Projected DOS and frontier orbital analysis in the vicinity of Fermi level region suggest the electronic states to be contributed from SWCNT rather than PZA. In addition, hybrid DFT calculation which includes the dispersion correction is employed to explain the non‐covalent π–π stacking interaction between PZA and SWCNT. The local density approximation and GGA results are compared with DFT‐D to explain near about accurately the weak nonbonded van der Waals interactions between PZA and SWCNTs. © 2012 Wiley Periodicals, Inc.     

Mechanisms of water oxidation catalyzed by the cis,cis-[(bpy)2Ru(OH2)]2O4+ ion

The cis,cis-[(bpy)(2)Ru(III)(OH(2))](2)O(4+) micro-oxo dimeric coordination complex is an efficient catalyst for water oxidation by strong oxidants that proceeds via intermediary formation of cis,cis-[(bpy)(2)Ru(V)(O)](2)O(4+) (hereafter, [5,5]). Repetitive mass spectrometric measurement of the isotopic distribution of O(2) formed in reactions catalyzed by (18)O-labeled catalyst established the existence of two reaction pathways characterized by products containing either one atom each from a ruthenyl O and solvent H(2)O or both O atoms from solvent molecules. The apparent activation parameters for micro-oxo ion-catalyzed water oxidation by Ce(4+) and for [5,5] decay were nearly identical, with DeltaH(++) = 7.6 (+/-1.2) kcal/mol, DeltaS() = -43 (+/-4) cal/deg mol (23 degrees C) and DeltaH(++) = 7.9 (+/-1.1) kcal/mol, DeltaS(++) = -44 (+/-4) cal/deg mol, respectively, in 0.5 M CF(3)SO(3)H. An apparent solvent deuterium kinetic isotope effect (KIE) of 1.7 was measured for O(2) evolution at 23 degrees C; the corresponding KIE for [5,5] decay was 1.6. The (32)O(2)/(34)O(2) isotope distribution was also insensitive to solvent deuteration. On the basis of these results and previously established chemical properties of this class of compounds, mechanisms are proposed that feature as critical reaction steps H(2)O addition to the complex to form covalent hydrates. For the first pathway, the elements of H(2)O are added as OH and H to the adjacent terminal ruthenyl O atoms, and for the second pathway, OH is added to a bipyridine ring and H is added to one of the ruthenyl O atoms.     

Theoretical study of CO and H2O interaction on (110) and (101) Zirconia surfaces

Theoretical calculations of CO and H₂O adsorption on (110) and (101) tetragonal Zirconia surfaces were carried out using ONIOM2 methodology. The calculations showed that the adsorption processes are exothermic reactions with energy values of −28.4 kcal/mol for H₂O on the (110) surface, −51.0 kcal/mol for H₂O on the (101) surface, −21.7 kcal/mol for CO on (110) surface and −23.4 kcal/mol for CO on (101) surface. Analysis of the results suggest that different kinds of basic sites can be found on the (110) and (101) surfaces. In both (110) and (101) surfaces, CO adsorption is on bridged (bonded to two Zr atoms on the (110) surface, bonded to one Zr and O atoms on the (101) surface). The calculations showed that ONIOM can be a powerful tool to study structural and thermodynamics properties of solid surfaces.     

Interaction between alkyl radicals and single wall carbon nanotubes

The addition of primary, secondary, and tertiary alkyl radicals to single wall carbon nanotubes (SWCNTs) was studied by means of dispersion corrected density functional theory. The PBE, B97‐D, M06‐L, and M06‐2X functionals were used. Consideration of Van der Waals interactions is essential to obtain accurate addition energies. In effect, the enthalpy changes at 298 K, for the addition of methyl, ethyl, isopropyl, and tert‐butyl radicals onto a (5,5) SWCNT are: ?25.7, ?25.1, ?22.4, and ?16.6 kcal/mol, at the M06‐2X level, respectively, whereas at PBE/6‐31G* level they are significantly lower: ?25.0, ?19.0, ?16.7, and ?5.0 kcal/mol respectively. Although the binding energies are small, the attached alkyl radicals are expected to be stable because of the large desorption barriers. The importance of nonbonded interactions was more noticeable as we moved from primary to tertiary alkyl radicals. Indeed, for the tert‐butyl radical, physisorption onto the (11,0) SWCNT is preferred rather than chemisorption. The bond dissociation energies determined for alkyl radicals and SWCNT follow the trend suggested by the consideration of radical stabilization energies. However, they are in disagreement with some degrees of functionalization observed in recent experiments. This discrepancy would stem from the fact that for some HiPco nanotubes, nonbonded interactions with alkyl radicals are stronger than covalent bonds. © 2012 Wiley Periodicals, Inc.     

Theoretical proton affinity and fluoride affinity of nerve agent VX

Proton affinity and fluoride affinity of nerve agent VX at all of its possible sites were calculated at the RI-MP2/cc-pVTZ//B3LYP/6-31G* and RI-MP2/aug-cc-pVTZ//B3LYP/6-31+G* levels, respectively. The protonation leads to various unique structures, with H(+) attached to oxygen, nitrogen, and sulfur atoms; among which the nitrogen site possesses the highest proton affinity of -ΔE ～ 251 kcal/mol, suggesting that this is likely to be the major product. In addition some H(2), CH(4) dissociation as well as destruction channels have been found, among which the CH(4) + [Et-O-P(═O)(Me)-S-(CH(2))(2)-N(+)(iPr)═CHMe] product and the destruction product forming Et-O-P(═O)(Me)-SMe + CH(2)═N(+)(iPr)(2) are only 9 kcal/mol less stable than the most stable N-protonated product. For fluoridization, the S-P destruction channel to give Et-O-P(═O)(Me)(F) + [S-(CH(2))(2)-N-(iPr)(2)](-) is energetically the most favorable, with a fluoride affinity of -ΔE ～ 44 kcal. Various F(-) ion-molecule complexes are also found, with the one having F(-) interacting with two hydrogen atoms in different alkyl groups to be only 9 kcal/mol higher than the above destruction product. These results suggest VX behaves quite differently from surrogate systems.     

Electrostatic current switching and negative differential resistance behavior in a molecular device based on carbon nanotubes

The electronic transport properties of an all-carbon mechanically controlled molecular device based on carbon nanotubes are studied using non-equilibrium Green's function in combination with density functional theory. A segment of (10,0) single-walled carbon nanutube (SWCNT) is placed concentrically outside a (5,0) SWCNT, namely, a (5,0)@(10,0) double-walled carbon nanotube (DWCNT). It is found that the position, orientation and length scaling of the (10,0) SWCNT have crucial effects on the electronic transport properties of the system. When the (10,0) SWCNT is mechanically pushed forward along the axial direction, alternation of on/off switching behavior under low bias and negative differential resistance behavior under high bias are observed. Significant changes in the electronic transport properties arise when rotating the (10,0) SWCNT around the common axis or adding carbon atom layers in the transport direction. Theoretical explanations are proposed for these phenomena.     

Mechanism and kinetics of the reaction of the 2-propargyl radical with ammonia

Gas-phase mechanism and kinetics of the reactions of the 2-propargyl radical (H₂CCCH), an important intermediate in combustion processes, with ammonia were investigated using ab initio molecular orbital theory at the coupled-cluster CCSD(T)//B3LYP/6-311++G(3df,2p) method in conjunction with transition state theory (TST), variational transition state theory (VTST), and Rice–Ramsperger–Kassel–Macus (RRKM) calculations for rate constants. The potential energy surface (PES) constructed shows that the C₃H₃ + NH₃ reaction has four main entrances, including two H-abstraction and two addition channels in which the former are energetically more favorable. The H-abstraction channels occur via energy barriers of 24 (T0/P2) and 26 kcal/mol (T0/P3) forming loose van de Waals complexes, COM_1 (12 kcal/mol) and COM_2 (14 kcal/mol), respectively. These complexes can easily be decomposed via barrier-less processes resulting HCCCH₃ + NH₂ (P2, 14 kcal/mol) and HCCCH₃ + NH₂ (P3, 15 kcal/mol), respectively. The additional channels occur initially by formation of two intermediate states, H₂CCCHNH₃ (35 kcal/mol) and H₂CC(NH₃)CH (37 kcal/mol) via energy barriers of 37 and 40 kcal/mol at T0/1 and T0/5, respectively, followed by isomerization and decomposition yielding 21 different products. These processes are fully depicted in an as-complete-as-possible PES. The rate constants and product branching ratios for the low-energy channels calculated show that the C₃H₃ + NH₃ reaction is almost pressure-independent. For the temperature range of 300–2000 K, the HCCCH₃ + NH₂ is the major product, whereas the minor one, HCCCH₃ + NH₂, has more contribution when temperature increases. Theoretical results on the mechanism and kinetics of the reaction considered may be helpful for future experiments as well as for understanding the role of the propargyl radical in combustion chemistry.     

Nanotube-metal junctions: 2- and 3-terminal electrical transport

We address the quality of electrical contact between carbon nanotubes and metallic electrodes by performing first-principles calculations for the electron transmission through ideal 2- and 3-terminal junctions, thus revealing the physical limit of tube-metal conduction. The structural model constructed involves surrounding the tube by the metal atoms of the electrode as in most experiments; we consider metallic (5,5) and n-doped semiconducting (10,0) tubes surrounded by Au or Pd. In the case of metallic tubes, the contact conductance is shown to approach the ideal 4e2/h in the limit of large contact area. For three-terminals, the division of flux among the different transmission channels depends strongly on the metal material. A Pd electrode has nearly perfect tube-electrode transmission and therefore turns off the straight transport along the tube. Our results are in good agreement with some recent experimental reports and clarify a fundamental discrepancy between theory and experiment.     

Ab initio study of Pd-decorated single-walled carbon nanotube with C-vacancy as CO sensor

In this paper, the adsorption of CO onto Pd-decorated (5,5) single-walled carbon nanotube (Pd/SWCNT) and Pd-doped (5,5) single-walled carbon nanotube (Pd/SWCNT-V) has been investigated using ab initio studies. The larger binding energies and charges transfer show that the adsorption of CO onto Pd/SWCNT is more stable than that of CO onto Pd/SWCNT-V. The Pd/SWCNT can be utilized as good sensors for CO molecules due to strong binding energy and large electron charge transfer between the Pd/SWCNT and this molecule. Furthermore, the topological properties of the electron density distributions for intramolecular interactions have been analyzed in terms of the Bader theory of atoms in molecules. Finally, the natural population analysis method has been used to evaluate the Pd–C and Pd/CO interactions.     

Theoretical study of Au/SAPO-11 catalyst and its potential use in thiophene HDS

Quantum chemistry calculations were carried out, using ONIOM2 methodology, in order to investigate the thiophene interaction with gold supported on silicoaluminophospates molecular sieves (Au/SAPO-11) catalysts. Two models were studied, one containing one Au atom per site, and the other with two Au atoms per site. Thiophene adsorption was found to be η¹ type. This adsorption presents a ΔH of ?13.2 and ?9.7 kcal/mol, for the models with one Au atom (Au/SAPO-11), and two Au atoms (Au₂/SAPO-11), respectively. The partial hydrogenation of the thiophene–Au/SAPO-11 and thiophene–Au₂/SAPO-11 complexes gives 2,5-dihydrothiophene (DHT), with a ΔH of ?23.0 and ?36.8 kcal/mol, respectively. 2-Butene production was found in both models with further hydrogenation. Likewise the direct butadiene elimination is achieved, but only with the separated Au dimer (ΔH = ?17.5 kcal/mol).     

The effect of 3d-metal intercalation on the electronic structure of metallic and semiconducting nanotubes

The electronic structure of 3d-metal-intercalated metallic (5,5) and semiconducting (10,0) nanotubes has been studied by quantum-chemical methods. The total and partial densities of states of nanotubes as a function of metal concentration and nature and the carbon-shell structure have been calculated by the linear augmented-cylindrical-wave method. Metalized nanowires based on armchair (5,5) and zigzag (10,0) nanotubes with one, two, three, and four metal atoms in the cross-section have been calculated. The introduction of the metal is accompanied by a sharp increase in the density of states at the Fermi level of the nanowire, which determines the concentration of free electrons involved in charge transfer in the nanotube. The 3d electrons of the metal and the carbon shell are nearly equally involved in electron transport in intercalated wires. Both the 3d electrons of a metal and the carbon shell should be nearly equally involved in electron transport in intercalated wires. The introduction of metals not only affects the conductive state of the carbon nanotube but also changes the entire pattern of its valence band, in particular, increases the valence band width of the nanotube by 5–10 eV owing to the low-energy shift of the 2s(C) states.     

CO2 adsorption by nitrogen-doped carbon nanotubes predicted by density-functional theory with dispersion-correcting potentials

The interaction of CO(2) to the interior and exterior walls of pristine and nitrogen-doped single-walled carbon nanotubes (SWNT) has been studied using density-functional theory with dispersion-correcting potentials (DCPs). Our calculations predict Gibbs energies of binding between SWNT and CO(2) of up to 9.1 kcal mol(-1), with strongest binding observed for a zigzag [10,0] nanotube, compared to armchair [6,6] (8.3 kcal mol(-1)) and chiral [8,4] (7.0 kcal mol(-1)). Doping of the [10,0] tube with nitrogen increases the Gibbs energies of binding of CO(2) by ca. 3 kcal mol(-1), but slightly reduced binding is found when [6,6] and [8,4] SWNT are doped in similar fashion. The Gibbs energy of binding of CO(2) to the exterior of the tubes is quite small compared to the binding that occurs inside the tubes. These findings suggest that the zigzag SWNT show greater promise as a means of CO(2) gas-capture.     

The non-covalent functionalisation of carbon nanotubes studied by density functional and semi-empirical molecular orbital methods including dispersion corrections

Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added empirical dispersion correction have been used to study the binding of a series of small molecules and planar aromatic molecules to single-walled carbon nanotubes (CNTs). For the small molecule set, the PM3-D method gives a mean unsigned error (MUE) in the binding energies of 1.2 kcal mol(-1) when judged against experimental reference data for graphitic carbon. This value is close to the MUE for this method compared to high-level ab initio data for biological complexes. The PM3-D and DFT-D calculations describing the adsorption of the planar organic molecules (benzene, bibenzene, naphthalene, anthracene, TCNQ and DDQ) on the outer-walls of both semi-conducting and metallic CNTs give similar binding energies for benzene and DDQ, but do not display a stronger adsorption on [6,6] compared to [10,0] structures shown by another DFT study.     

A quick solvation energy estimator based on electronegativity equalization

ESE-EE (Easy Solvation Estimation with Electronegativity equalization) is a quick method for estimation of solvation-free energies ΔGº_solv, which uses a thoroughly fitted electronegativity equalization (EE) scheme to obtain atomic charges, which are further employed in a scaled noniterative COSMO-like calculation to evaluate the electrostatic component of ΔGº_solv. Nonelectrostatic corrections including adjustable parameters are also added. For neutral solutes, ESE-EE yields a mean absolute error (MAE) in ΔG_solv° of 1.5 kcal/mol for aqueous solutions; 1.0 kcal/mol for nonaqueous polar protic solvents; 0.9 kcal/mol for polar aprotic solvents; and about 0.6 kcal/mol for nonpolar solvents. Since ESE-EE only requires a molecular geometry as input for a ΔGº_solv prediction, it can be utilized for a rapid screening of ΔGº_solvfor large neutral molecules. However, for ionic solutes, ESE-EE yields larger errors (typically several kcal/mol) and is recommendable for preliminary estimations only. Upon a special refitting, ESE-EE is able to yield partition coefficients with a good accuracy.