Data related to conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation.

In this data article, M06-2X/6-31G(d) level optimized geometries of complexes of tyrosine conformers binding with graphene sheets are shown in top and side views with selected non-bonding distances. The images of frontier molecular orbitals from HOMO-15 to LUMO+15 of the complexes involving graphene with tyrosine conformers are presented and the isovalue is 0.003 au. For some complexes involving small graphene, the orbitals are from HOMO-5 to LUMO+5. The molecular orbitals highlighted with frames show obvious overlaps between the fragments. Total energies of small and large graphene (G S and G L ) and selected tyrosine conformers in gas and aqueous phases obtained at M06-2X/6-31G(d) level are given. The data also include total energies of all complexes in the gas phase and the aqueous phase, binding energies, BSSE (basis set superposition error) correction, and BSSE-corrected binding energies in gas phase and solvation effect on the binding energies obtained at M06-2X/6-31G(d) level. Mulliken charges of tyrosine conformers in gas and aqueous phases, and the deformation energy for tyrosine and graphene in the gas phase complexes are provided. The values of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) and HOMO-LUMO energy gaps for some of graphene-tyrosine complexes that were not reported in the article [1] are given. The data is related to the research article "Conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation" [1].

Computational investigation of double nitrogen doping on graphene.

Density functional theory (DFT) calculations were performed to study doping of two nitrogen atoms at different positions on a finite-sized graphene model of C82H24. We examined 21 structures of double nitrogen doped graphene to calculate their relative stabilities. The structure with two nitrogen atoms located apart is the most stable among the positional isomers considered in this study. For double nitrogen doping within a six-membered ring, the 1,4-position is more preferred than 1,3- or 1,2-positions for the finite-sized single layer graphene sheet. Our computational study supports the experimental observation of two nitrogen atoms at the 1,3- and 1,4-positions in a single six-membered ring of graphene. Furthermore, the structures with N-N bond are the least stable among two nitrogen doped graphene structures. The effects of nitrogen doping and the positions of two nitrogen atoms on the HOMO-LUMO energy gap of pristine graphene were analyzed.

Binding of Alkali Metal Ions with 1,3,5-Tri(phenyl)benzene and 1,3,5-Tri(naphthyl)benzene: The Effect of Phenyl and Naphthyl Ring Substitution on Cation-π Interactions Revealed by DFT Study.

The effect of substitution of phenyl and naphthyl rings to benzene was examined to elucidate the cation-π interactions involving alkali metal ions with 1,3,5-tri(phenyl)benzene (TPB) and 1,3,5-tri(naphthyl)benzene (TNB). Benzene, TPB, and four TNB isomers (with ααα, ααß, αßß, and ßßß types of fusion) and their complexes with Li+, Na+, K+, Rb+, and Cs+ were optimized using DFT approach with B3LYP and M06-2X functionals in conjunction with the def2-QZVP basis set. Higher relative stability of ß,ß,ß-TNB over α,α,α-TNB can be attributed to peri repulsion, which is defined as the nonbonding repulsive interaction between substituents in the 1- and the 8-positions on the naphthalene core. Binding energies, distances between ring centroid and the metal ions, and the distance to metal ions from the center of other six-membered rings were compared for all complexes. Our computational study reveals that the binding affinity of alkali metal cations increases significantly with the 1,3,5-trisubstitution of phenyl and naphthyl rings to benzene. The detailed computational analyses of geometries, partial charges, binding energies, and ligand organization energies reveal the possibility of favorable C-H···M+ interactions when a α-naphthyl group exists in complexes of TNB structures. Like benzene-alkali metal ion complexes, the binding affinity of metal ions follows the order: Li+ > Na+ > K+ > Rb+ > Cs+ for any considered 1,3,5-trisubstituted benzene systems. In case of TNB, we found that the strength of interactions increases as the fusion point changes from α to ß position of naphthalene.

Toward selection of efficient density functionals for van der Waals molecular complexes: comparative study of C-H···π and N-H···π interactions.

We have evaluated the performance of two of the recently developed density functionals (M06-2X and B2PLYP-D), which are widely used, by considering three important prototype systems, including benzene-acetylene, benzene-methane, and benzene-ammonia, possessing C-H···π or N-H···π interactions. Computational results are compared with the available experimental data. Considered density functionals are from two different classes: hybrid meta density functional (M06-2X) and double hybrid density functional (B2PLYP-D). The performance of a range of basis sets (6-31G(d), 6-31+G(d), 6-31+G(d,p), 6-311G(d,p), 6-311+G(d,p), aug-cc-pVXZ (X = D, T, Q)) with the above-mentioned two density functionals was evaluated. Comparison of the results includes Pople's basis sets versus Dunning's correlation consistent basis sets with the M06-2X and B2PLYP-D functionals considered in this study. The basis set effect on geometrical parameters, dissociation energies, and selected vibrational frequency shifts was thoroughly analyzed. We have addressed whether the counterpoise corrections with geometry optimizations and vibrational frequencies are important. Our computational study reveals that calculations carried out with smaller basis sets very well reproduce the reported experimental values of dissociation energies. The present study also shows that using the very large Dunning's correlation consistent basis set worsens the results. The necessity of including counterpoise correction for binding energies depends on the system and the type of method used. In general, vibrational frequency calculations using these DFT functionals generate characteristic red shifts for the C-H···π or N-H···π interactions in the complexes.

Structural, energetic, spectroscopic and QTAIM analyses of cation-π interactions involving mono- and bi-cyclic ring fused benzene systems.

The effect of increasing the number of monocyclic six-membered rings or bicyclic rings of bicyclo[2.1.1]hexenyl fused to benzene on cation-π interactions involving alkali metal ions (Li(+), Na(+), and K(+)) has been investigated. The binding energy data at the B3LYP/6-311+G(2d,2p) level clearly indicate that the binding affinity of the metal ion with benzene is enhanced by increasing the number of rings fused irrespective of a monocyclic or a bicyclic ring. Calculated binding energies are in good agreement with the available experimental results. The binding strength of cations with ligands decreases in the order Li(+) > Na(+) > K(+). Our study establishes that trisannelation of bicyclo[2.1.1]hexene to benzene facilitates a very strong interaction between benzene and cations. Infrared (IR) frequencies and nuclear magnetic resonance (NMR) chemical shifts are shown to be valuable in characterizing cation-π interactions. The C-C bonds of the central six-membered rings are weakened due to metal ion binding. Based on the Quantum Theory of Atoms in Molecules (QTAIM), we have observed the presence of stabilizing H∙∙∙H interactions in two of the considered systems as opposed to the frequent description of these interactions as non-bonded repulsive interactions. Alkali metal ion binding with those two ligands slightly reduces the strength of such H∙∙∙H interactions.

Computational study on C-H...π interactions of acetylene with benzene, 1,3,5-trifluorobenzene and coronene.

Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C-H(…)π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals that the C-H(...)π interaction complex where acetylene located above to the center of benzene ring (classical T-shaped) is the lowest energy structure. This structure is twice more stable than the configuration characterized by H atom of benzene interacting with the π-cloud of acetylene. The binding energy of 2.91 kcal/mol calculated at the M06-2X/6-311+G(d,p) level for the lowest energy configuration (1A) is in very good agreement with the experimental binding energy of 2.7 ± 0.2 kcal/mol for benzene-acetylene complex. Interestingly, the C-H(...)π interaction of acetylene above to the center of the aromatic ring is not the lowest energy configuration for 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. The lowest energy configuration (2A) for the former complex possesses both C-H(...)π interaction and C-H(...)F hydrogen bond, while the lowest energy structure for the coronene-acetylene complex involves both π-π and C-H(...)π interactions. C-H stretching vibrational frequencies and the frequency shifts are reported and analyzed for all of the configurations. We observed red-shift of the vibrational frequency for the stretching mode of the C-H bond that interacts with the π-cloud. Acetylene in the lowest-energy structures of the complexes exhibits significant red-shift of the C-H stretching frequency and change in intensity of the corresponding vibrational frequency, compared to bare acetylene. We have examined the molecular electrostatic potential on the surfaces of benzene, 1,3,5-trifluorobenzene, coronene and acetylene to explain the binding strengths of various complexes studied here.

Advancing risk assessment of engineered nanomaterials: application of computational approaches.

Nanotechnology that develops novel materials at size of 100nm or less has become one of the most promising areas of human endeavor. Because of their intrinsic properties, nanoparticles are commonly employed in electronics, photovoltaic, catalysis, environmental and space engineering, cosmetic industry and - finally - in medicine and pharmacy. In that sense, nanotechnology creates great opportunities for the progress of modern medicine. However, recent studies have shown evident toxicity of some nanoparticles to living organisms (toxicity), and their potentially negative impact on environmental ecosystems (ecotoxicity). Lack of available data and low adequacy of experimental protocols prevent comprehensive risk assessment. The purpose of this review is to present the current state of knowledge related to the risks of the engineered nanoparticles and to assess the potential of efficient expansion and development of new approaches, which are offered by application of theoretical and computational methods, applicable for evaluation of nanomaterials.