Predicting whether aromatic molecules would prefer to enter a carbon nanotube: A density functional theory study

The interaction of a carbon nanotube (CNT) with various aromatic molecules, such as aniline, benzophenone, and diphenylamine, was studied using density functional theory able to compute intermolecular weak interactions (B3LYP-D3). CNTs of varying lengths were used, such as 4-CNT, 6-CNT, and 8-CNT (the numbers denoting relative lengths), with the lengths being chosen appropriately to save computation times. All aromatic molecules were found to exhibit strong intermolecular binding energies with the inner surface of the CNT, rather than the outer surface. Hydrogen bonding between two aromatic molecules that include N and O atoms is shown to further stabilize the intermolecular adsorption process. Therefore, when benzophenone and diphenylamine were simultaneously allowed to interact with a CNT, the aromatic molecules were expected to preferably enter the CNT. Furthermore, additional calculations of the intermolecular adsorption energy for aniline adsorbed on a graphene surface showed that the concavity of graphene-like carbon sheet is in proportion to the intermolecular binding energy between the graphene-like carbon sheet and the aromatic molecule.     

Formaldehyde encapsulated in lithium-decorated metal-organic frameworks: a density functional theory study

The stability of monomeric formaldehyde encapsulated in the lithium-decorated metal-organic framework Li-MOF-5 was investigated by means of density functional calculations with the M06-L functional and the 6-31G(d,p) basis set. To assess the efficiency of Li-MOF-5 for formaldehyde preservation, we consider the reaction kinetics and the thermodynamic equilibrium between formaldehyde and its trimerized product, 1,3,5-trioxane. We propose that trimerization of encapsulated formaldehyde takes place in a single reaction step with an activation energy of 34.5 kcal mol(-1). This is 17.2 kcal mol(-1) higher than the corresponding activation energy in the bare system. In addition, the reaction energy of the system studied herein is endothermic by 6.1 kcal mol(-1) and the Gibbs free energy (ΔG) of the reaction becomes positive (11.0 kcal mol(-1)). Consequently, the predicted reverse rate for the trimerization reaction in the Li-MOF-5 is significantly faster than the forward rate. The calculations show that the oligomerization of formaldehyde in Li-MOF-5 is a reversible reaction, suggesting that such a zeolite might be a good candidate material for preserving formaldehyde in its monomeric form.     

Regional self-interaction correction of density functional theory

We propose a new simple scheme for self-interaction correction (SIC) of exchange functionals in the density functional theory. In the new scheme, exchange energies are corrected by substituting exchange self-interactions for exchange functionals in regions of self-interaction. To classify the regions of self-interaction, we take advantage of the property of the total kinetic energy density approaching the Weizs?cker density in the case of electrons in isolated orbitals. The scheme differs from conventional SIC methods in that it produces optimized molecular structures. Applying the scheme to the calculation of reaction energy barriers showed that it provides a clear improvement in cases where the barriers are underestimated by conventional "pure" functionals. In particular, we found that this scheme even reproduces a transition state that is not given by pure functionals.     

Large‐compound vesicle‐encapsulated multiwalled carbon nanotubes: A unique route to nanotube composites

A simple and unique strategy for preparation of large‐compound vesicle (LCV)‐encapsulated multiwalled carbon nanotubes (MWCNTs) has been developed, and this involves dispersion of MWCNTs in H‐shaped copolymers solution in DMF and encapsulation of MWCNTs with LCVs formed from hydrolysis and polycondensation of ? Si(OCH₃)₃ groups in the amphiphilic H‐shaped copolymers, (PTMSPMA)₂PEG(PTMSPMA)₂. This unique noncovalent approach is nondestructive, and the original structure of MWCNTs remains in the resultant MWCNTs/LCVs nanocomposites. The morphologies of nanocomposites LCVs/MWCNTs are controlled by the chain length ratio (N_PTMSPMA/N_PEG) of PTMSPMA to PEG. For the H‐shaped copolymers with N_PMSPMA/N_PEG ≤ 1.7, they self‐assembled to form LCVs with dense cavities in the presence of MWCNTs in a mixture of DMF/H₂O. When this ratio was more than 2.0, the large‐compound micelle‐wrapped MWCNTs were produced. This approach is potentially useful for preparation of MWCNTs encapsulated with various morphologies of polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3669–3679, 2009     

Spin‐orbit ab initio and density functional theory investigation of bismuth monoboronyl,BiBO

The molecular properties of bismuth monoboronyl, BiBO, were investigated using high‐level ab initio and density functional theory calculations by including the effect of spin‐orbit coupling (SOC). SOC does not cause any change in the Bi? B bond length of BiBO, by contrast it causes significant elongation of the Bi? B bond of BiBO^?, by ～0.03 Å. The Bi? B bond length of BiBO^? that is calculated by considering SOC is almost identical to that of BiBO; this result is consistent with a recent experimental study. The term values of excited states of BiBO calculated by including SOC are in good agreement with the experimental results. One excited state which was not assigned in the previous experimental study is the Ω = 0⁺ state generated by strong SOC. In the theoretical calculations on molecules containing 6p‐block elements, including SOC is crucial for obtaining results that are consistent with the corresponding experimental results.     

Electric field amplification of plasmon-molecule hybrids revealed by first-principles time dependent density functional theory calculations

Using first-principles quantum mechanical calculations, we investigate the electric field amplification in hybrid nanostructures composed of few-atom Ni linear chains attached to an organic molecule. We found that the pristine Ni linear chains exhibit localized plasmons and produce nanoscale hotspot regions, acting as a plasmon-like nanoantenna. We demonstrate that localized plasmons provide massive electric field amplification in the vicinity of the molecule. Besides, we also investigated the active modulation of the optical absorption spectra due to the inclusion of a positive and/or negative electric field in the Hamiltonian. We believe that the results presented in this work are important for the emerging field of cavity induced photo-catalysis and will aid in the realization of new quantum nano-optic devices.     

Role of electron–electron coalescence density in density functional theory

An expression for the evaluation of electron–electron coalescence density as a functional of the density for any electron system is proposed. The formula, clarifies previously advanced upper bounds for this quantity and provides a method to independently estimate the system‐averaged on‐top exchange–correlation hole. The relationship with the on‐top pair density shows that producing the true electron–electron coalescense should be considered as a leading physical requirement for trial wave functions in any energy minimization scheme. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Dissociation of sulfur oxoacids by two water molecules studied using ab initio and density functional theory calculations

Using ab initio [SCS‐MP2 and CCSD(T)] and density functional theory (M062X) calculations, we have studied the geometries and energies of sulfur oxoacids H₂S_mO₆ (m = 2–4) and their monohydrated and dihydrated clusters. When including the results from previously reported disulfuric acid (H₂S₂O₇) cases, the gas phase acidity is ordered as H₂S₂O₆ < H₂S₃O₆ < H₂S₂O₇ < H₂S₄O₆. The intramolecular H‐bonding, which may indicate the degree of structural flexibility in this molecular series, is an important factor for the order of the gas phase acidity. All these sulfur oxoacids show dissociated (or deprotonated) geometries with only two water molecules, although the energies of the dissociated conformers are ranked differently. All of the dissociated conformers form a unique H‐bonding network structure in which the protonated first water (H₃O⁺) is triply H‐bonded to each oxygen atom of two SO₃ moieties as well as the second water, which in turn is H‐bonded to a SO₃ moiety. H₂S₃O₆ has the best molecular flexibility for adopting such an H‐bonding network structure, and thereby all the low‐lying conformers of H₂S₃O₆(H₂O)₂ are dissociated. In contrast, the least flexible H₂S₂O₆ forms such a structure with a high strain, and dissociation of H₂S₂O₆(H₂O)₂ is found from the third lowest conformer. Although the gas phase acidity of H₂S₄O₆ is the highest in this series, the lowest dissociated conformer and the lowest undissociated conformer of H₂S₄O₆(H₂O)₂ are very close in energy. This is because forming the H‐bonding network structure is somewhat difficult due to the large distance between the two SO₃ moieties.     

A solvation‐free‐energy functional: A reference‐modified density functional formulation

The three‐dimensional reference interaction site model (3D‐RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation‐free‐energy (SFE) for large solute molecules in water. To improve the free‐energy density functional for the SFE of solute molecules, we propose a reference‐modified density functional theory (RMDFT) that is a general theoretical approach to construct the free‐energy density functional systematically. In the RMDFT formulation, hard‐sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction‐site‐model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side‐chain analogues as well as for 504 small organic molecules. © 2015 Wiley Periodicals, Inc.     

A systematic study of rare gas atoms encapsulated in small fullerenes using dispersion corrected density functional theory

The most stable fullerene structures from C₂₀ to C₆₀ are chosen to study the energetics and geometrical consequences of encapsulating the rare gas elements He, Ne, or Ar inside the fullerene cage using dispersion corrected density functional theory. An exponential increase in stability is found with increasing number of carbon atoms. A similar exponential law is found for the volume expansion of the cage due to rare gas encapsulation with decreasing number of carbon atoms. We show that dispersion interactions become important with increasing size of the fullerene cage, where Van der Waals forces between the rare gas atom and the fullerene cage start to dominate over repulsive interactions. The smallest fullerenes where encapsulation of a rare gas element is energetically still favorable are He@C₄₈, Ne@C₅₂, and Ar@C₅₈. While dispersion interactions follow the trend Ar > Ne > He inside C₆₀ due to the trend in the rare gas dipole polarizabilities, repulsive forces become soon dominant with smaller cage size and we have a complete reversal for the energetics of rare gas encapsulation at C₅₀. © 2014 Wiley Periodicals, Inc.     

Thermodynamic and kinetic study of ibuprofen with hydroxyl radical: A density functional theory approach

Ibuprofen, a frequently detected pharmaceutical in natural and engineered waters, was studied in both neutral and anionic forms using density functional theory at the B3LYP/6‐311++G**//B3LYP/6‐31G* level of theory in its reaction with hydroxyl radical ( ? OH). The reaction pathways included ? OH addition to aromatic ring, abstraction of a H‐atom, and nucleophilic attack on the carbonyl group. The results showed that H‐atom abstraction pathways are the most favorable. The free energy change for H‐atom abstraction reaction ranges from ?37.8 to ?15.9 kcal/mol; for ? OH addition ranges from ?3.85 to ?1.23 kcal/mol; and for nucleophilic attack on the carbonyl group is 13.9 kcal/mol. The calculated rate constant between neutral ibuprofen and ? OH, 6.72 × 10⁹ M^?1s^?1, is consistent with the experimental value, 6.5 ± 0.2 × 10⁹ M^?1s^?1. Our results provide direct evidence for byproduct formation and identification on the molecular level. © 2013 Wiley Periodicals, Inc.     

Mechanism for the reaction of 2-naphthol with N-methyl-N-phenyl-hydrazine suggested by the density functional theory investigations

For the first time the computed mechanisms for the novel reaction of 2-naphthol with N-methyl-N-phenylhydrazine, leading to 1-amino-2-naphthol (Tang et al., J Am Chem Soc 2008, 130, 5840), have been investigated using the density functional theory. Four distinct possible pathways were evaluated: two amination mechanisms with the attack of NH(2) group respectively at the α-position C1 and β-position C3 atoms of 2-naphthol (pathways 1 and 2) as well as two rearrangement processes with displacement of the phenolic hydroxyl group followed by the benzidine-like rearrangement at the α-position C1 and β-position C3 atoms of 2-naphthol, respectively (pathways 3 and 4). Solvent effect has been tested based on the optimized geometries of the stationary points in solution at the B3LYP/PCM/6-31+G(d,p) level of theory with an averaged dielectric constant of binary solvent. Single-point energies of the optimized structures have been calculated using three hybrid density functionals, B3LYP, MPW3LYP, and B3PW91 with the 6-311++G(3df,2p) basis set. Our computed results clearly manifest that pathway 1 (α-amination) has the highest possibility to occur, with the Gibbs free energies being lower by 6 to 20 kcal/mol compared with the other three pathways, which leads to 1-amino-2-naphthol and N-methylaniline as products. It is in excellent agreement with the experimental observation.     

A density functional theory study of van der Waals interaction in carbon nanotubes

In this article, we investigate the effect of van der Waals force in zigzag carbon nanotubes (CNTs) including single-wall CNT (SWCNT) and double-walled CNT (DWCNT) structures with several interaction configurations. The solid-state density functional theory is employed to calculate the geometric optimization, normal mode frequencies, and IR and Raman spectra with the periodic boundary condition. For SWCNTs, we find that the Raman intensity is not affected by the tube diameter or the electronic structure. The IR absorption, however, increases with the tube diameter. We find that the close metallicity of the electronic structure has a significant impact on the IR simulations. When the van der Waals force is applied outside the CNTs at a distance longer than 3.0, the effect on Raman spectra is minimal but some effects can still be confirmed by IR absorption. When the van der Waals force acts inside the CNTs, the effect on the spectrum can be observed, especially at a distance of 2.8 Å, both IR and Raman can be significantly enhanced in many modes.     

Molecular dynamics simulation and density functional theory insight into the cocrystal explosive of hexaazaisowurtzitane/nitroguanidine

Theoretical methods involving molecular dynamics (MD) simulation and density functional theory were performed to investigate the different molecular ratios, mechanical Properties, structure, trigger bond, and intermolecular interaction of hexaazaisowurtzitane (CL‐20)/nitroguanidine (NQ) cocrystal explosive. Results of MD simulation show that CL‐20 and NQ packed in ratios of 1:1 present the larger binding energy and better mechanical properties than any other molecular ratios, which indicates 1:1 cocrystal can form the stable crystal structure. Shorter length and larger dissociation energy of trigger bond in composite structure than in isolated CL‐20 component suggests that the cocrystal may exhibit less sensitive than CL‐20. Analyses of atoms in molecules, reduced density gradient, and natural bond orbital confirm that intermolecular interactions are mainly derived from a series of weak hydrogen bond and strong vdW forces, involving of NH···O, CH···O, CH···N, O···N, and O···O. Additionally, composite structures of 2 and 3 bringing us more attractive performance will act as a key role in constructing of CL‐20/NQ cocrystal explosive. © 2015 Wiley Periodicals, Inc.     

Performance of density functional theory in computing nonresonant vibrational (hyper)polarizabilities

A set of exchange‐correlation functionals, including BLYP, PBE0, B3LYP, BHandHLYP, CAM‐B3LYP, LC‐BLYP, and HSE, has been used to determine static and dynamic nonresonant (nuclear relaxation) vibrational (hyper)polarizabilities for a series of all‐trans polymethineimine (PMI) oligomers containing up to eight monomer units. These functionals are assessed against reference values obtained using the Møller–Plesset second‐order perturbation theory (MP2) and CCSD methods. For the smallest oligomer, CCSD(T) calculations confirm the choice of MP2 and CCSD as appropriate for assessing the density functionals. By and large, CAM‐B3LYP is the most successful, because it is best for the nuclear relaxation contribution to the static linear polarizability, intensity‐dependent refractive index second hyperpolarizability, static second hyperpolarizability, and is close to the best for the electro‐optical Pockels effect first hyperpolarizability. However, none of the functionals perform satisfactorily for all the vibrational (hyper)polarizabilities studied. In fact, in the case of electric field‐induced second harmonic generation all of them, as well as the Hartree–Fock approximation, yield the wrong sign. We have also found that the Pople 6–31+G(d) basis set is unreliable for computing nuclear relaxation (hyper)polarizabilities of PMI oligomers due to the spurious prediction of a nonplanar equilibrium geometry. © 2013 Wiley Periodicals, Inc.     

Reaction mechanism of palladium‐catalyzed silastannation of allenes by density functional theory

The reaction mechanism of Pd(0)‐catalyzed allenes silastannation reaction is investigated by the density functional method B3LYP. The overall reaction mechanism is examined. For the allene insertion step, the Pd Si bond is preferred over the Pd Sn bond. The electronic mechanism of the allene insertion into Pd Si bond to form σ‐vinylpalladium (terminal‐insertion) and σ‐allylpalladium (internal‐insertion) insertion products is discussed in terms of the electron donation and back‐donation. It is found that the electron back‐donation is significant for both terminal‐ and internal‐insertion. During allene insertion into Pd Si bond, internal‐insertion is preferred over terminal‐insertion. By using methylallene, the regio‐selectivity for the monosubstituted allene insertion into Pd Si and Pd Sn bond is analyzed. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Elucidation of the methyl transfer mechanism catalyzed by chalcone O-methyltransferase: a density functional study

The mechanism of the methyl transfer catalyzed by chalcone O-methyltransferase has been computationally investigated by employing the hybrid functional B3LYP. Two models are constructed based on the two conformations of the substrate isoliquiritigenin in the X-ray structure. Our calculations show that the overall reaction is divided into two elementary steps: the water-assisted deprotonation of the substrate by His278 as a catalytic base, followed by the methyl transfer from S-adenosyl-L-methionine (SAM) to the substrate. The calculated rate-limiting barriers for the methyl-transfer step indicate that the catalytic reactions are energetically feasible for both conformations adopted by the substrate.