Performance of ab initio and density functional methods for conformational equilibria of CnH2n+2 alkane isomers (n=2-8)

Conformational energies of n-butane, n-pentane, and n-hexane have been calculated at the CCSD(T) level and at or near the basis set limit. Post-CCSD(T) contribution were considered and found to be unimportant. The data thus obtained were used to assess the performance of a variety of density functional methods. Double-hybrid functionals like B2GP-PLYP and B2K-PLYP, especially with a small Grimme-type empirical dispersion correction, are capable of rendering conformational energies of CCSD(T) quality. These were then used as a `secondary standard' for a larger sample of alkanes, including isopentane and the branched hexanes as well as key isomers of heptane and octane. Popular DFT functionals like B3LYP, B3PW91, BLYP, PBE, and PBE0 tend to overestimate conformer energies without dispersion correction, while the M06 family severely underestimates GG interaction energies. Grimme-type dispersion corrections for these overcorrect and lead to qualitatively wrong conformer orderings. All of these functionals also exhibit deficiencies in the conformer geometries, particularly the backbone torsion angles. The PW6B95 and, to a lesser extent, BMK functionals are relatively free of these deficiencies. Performance of these methods is further investigated to derive conformer ensemble corrections to the enthalpy function, $H_{298}-H_0$, and the Gibbs energy function, ${\rm gef}(T)\equiv - [G(T)-H_0]/T$, of these alkanes. While $H_{298}-H_0$ is only moderately sensitive to the level of theory, ${\rm gef}(T)$ exhibits more pronounced sensitivity. Once again, double hybrids acquit themselves very well.Comment: J. Phys. Chem. A, revised [Walter Thiel festschrift

Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections

In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the basis set superposition error and the inclusion of the deformation energies (for the S12L set) have been crucial for obtaining precise DLPNO-CCSD(T)/CBS interaction energies. Among the density functionals evaluated, the double-hybrid revPBE0-DH-NL and B2PLYP-NL with the three-body dispersion correction provide remarkably accurate association energies very close to the chemical accuracy. Overall, the NL van der Waals approach combined with proper density functionals can be seen as an accurate and affordable computational tool for the modeling of large weakly bonded supramolecular systems.Financial support by the “Ministerio de Economía y Competitividad” (MINECO) of Spain and European FEDER funds through projects CTQ2011-27253 and CTQ2012-31914 is acknowledged. The support of the Generalitat Valenciana (Prometeo/2012/053) is also acknowledged. J.A. thanks the EU for the FP7-PEOPLE-2012-IEF-329513 grant. J.C. acknowledges the “Ministerio de Educación, Cultura y Deporte” (MECD) of Spain for a predoctoral FPU grant

Elastic and vibrational properties of alpha and beta-PbO

The structure, electronic and dynamic properties of the two layered alpha (litharge) and beta (massicot) phases of PbO have been studied by density functional methods. The role of London dispersion interactions as leading component of the total interaction energy between layers has been addressed by using the Grimme's approach, in which new parameters for Pb and O atoms have been developed. Both gradient corrected and hybrid functionals have been adopted using Gaussian-type basis sets of polarized triple zeta quality for O atoms and small core pseudo-potential for the Pb atoms. Basis set superposition error (BSSE) has been accounted for by the Boys-Bernardi correction to compute the interlayer separation. Cross check with calculations adopting plane waves that are BSSE free have also been performed for both structures and vibrational frequencies. With the new set of proposed Grimme's type parameters structures and dynamical parameters for both PbO phases are in good agreement with experimental data.Comment: 8 pages, 5 figure

Spin states of zigzag-edged Mobius graphene nanoribbons from first principles

Mobius graphene nanoribbons have only one edge topologically. How the magnetic structures, previously associated with the two edges of zigzag-edged flat nanoribbons or cyclic nanorings, would change for their Mobius counterparts is an intriguing question. Using spin-polarized density functional theory, we shed light on this question. We examine spin states of zigzag-edged Mobius graphene nanoribbons (ZMGNRs) with different widths and lengths. We find a triplet ground state for a Mobius cyclacene, while the corresponding two-edged cyclacene has an open-shell singlet ground state. For wider ZMGNRs, the total magnetization of the ground state is found to increase with the ribbon length. For example, a quintet ground state is found for a ZMGNR. Local magnetic moments on the edge carbon atoms form domains of majority and minor spins along the edge. Spins at the domain boundaries are found to be frustrated. Our findings show that the Mobius topology (i.e., only one edge) causes ZMGNRs to favor one spin over the other, leading to a ground state with non-zero total magnetization.Comment: 17 pages, 4 figure

Excited States of Ladder-type Poly-p-phenylene Oligomers

Ground state properties and excited states of ladder-type paraphenylene oligomers are calculated applying semiempirical methods for up to eleven phenylene rings. The results are in qualitative agreement with experimental data. A new scheme to interpret the excited states is developed which reveals the excitonic nature of the excited states. The electron-hole pair of the S1-state has a mean distance of approximately 4 Angstroem.Comment: 24 pages, 21 figure

Quasiparticle bandgap engineering of graphene and graphone on hexagonal boron nitride substrate

Graphene holds great promise for post-silicon electronics, however, it faces two main challenges: opening up a bandgap and finding a suitable substrate material. In principle, graphene on hexagonal boron nitride (hBN) substrate provides potential system to overcome these challenges. Recent theoretical and experimental studies have provided conflicting results: while theoretical studies suggested a possibility of a finite bandgap of graphene on hBN, recent experimental studies find no bandgap. Using the first-principles density functional method and the many-body perturbation theory, we have studied graphene on hBN substrate. A Bernal stacked graphene on hBN has a bandgap on the order of 0.1 eV, which disappears when graphene is misaligned with respect to hBN. The latter is the likely scenario in realistic devices. In contrast, if graphene supported on hBN is hydrogenated, the resulting system (graphone) exhibits bandgaps larger than 2.5 eV. While the bandgap opening in graphene/hBN is due to symmetry breaking and is vulnerable to slight perturbation such as misalignment, the graphone bandgap is due to chemical functionalization and is robust in the presence of misalignment. The bandgap of graphone reduces by about 1 eV when it is supported on hBN due to the polarization effects at the graphone/hBN interface. The band offsets at graphone/hBN interface indicate that hBN can be used not only as a substrate but also as a dielectric in the field effect devices employing graphone as a channel material. Our study could open up new way of bandgap engineering in graphene based nanostructures.Comment: 8 pages, 4 figures; Nano Letters, Publication Date (Web): Oct. 25 2011, http://pubs.acs.org/doi/abs/10.1021/nl202725

Formation and destruction of polycyclic aromatic hydrocarbon clusters in the interstellar medium

The competition between the formation and destruction of coronene clusters under interstellar conditions is investigated theoretically. The unimolecular nucleation of neutral clusters is simulated with an atomic model combining an explicit classical force field and a quantum tight-binding approach. Evaporation rates are calculated in the framework of the phase space theory and are inserted in an infrared emission model and compared with the growth rate constants. It is found that, in interstellar conditions, most collisions lead to cluster growth. The time evolution of small clusters (containing up to 312 carbon atoms) was specifically investigated under the physical conditions of the northern photodissociation region of NGC 7023. These clusters are found to be thermally photoevaporated much faster than they are reformed, thus providing an interpretation for the lowest limit of the interstellar cluster size distribution inferred from observations. The effects of ionizing the clusters and density heterogeneities are also considered. Based on our results, the possibility that PAH clusters could be formed in PDRs is critically discussed.Comment: 14 pages, 14 figures. Astronomy & Astrophysics, accepted for publicatio

Supramolecular architecture of [AsPh2Br2]2[(Br3)−…(Br2)…(Br3)−] obtained by bromination of (AsPh2)2S

Bromination of (AsPh2)2S leads to cleavage of the sulfide bridge to give AsPh2Br when 1 mol of bromine is used but with 2 mols the product is the polybromide, [AsPh2Br2]2[Br8], containing the previously unknown [AsPh2Br2]+ cation and a rare [(Br3)−…(Br2)…(Br3)−] ensemble whose short (yet not covalent) Br2…Br3 contacts have previously supported tentative description as an octabromide Br82− anion. X-ray crystallography shows that the compound has a three dimensional supramolecular structure based on cooperativity of weak intermolecular Csingle bondH…π, Csingle bondH…Br hydrogen bonds and secondary Br…Br interactions in the solid state. The electronic structure and the stability of the [AsPh2Br2]2[Br8] are rationalized using DFT and HF calculations and molecular orbital considerations

Unraveling the performance of dispersion-corrected functionals for the accurate description of weakly bound natural polyphenols

Long-range non-covalent interactions play a key role in the chemistry of natural polyphenols. We have previously proposed a description of supramolecular polyphenol complexes by the B3P86 density functional coupled with some corrections for dispersion. We couple here the B3P86 functional with the D3 correction for dispersion, assessing systematically the accuracy of the new B3P86-D3 model using for that the well-known S66, HB23, NCCE31, and S12L datasets for non-covalent interactions. Furthermore, the association energies of these complexes were carefully compared to those obtained by other dispersion-corrected functionals, such as B(3)LYP-D3, BP86-D3 or B3P86-NL. Finally, this set of models were also applied to a database composed of seven non-covalent polyphenol complexes of the most interest.FDM acknowledges financial support from the Swedish Research Council (Grant No. 621-2014-4646) and SNIC (Swedish National Infrastructure for Computing) for providing computer resources. The work in Limoges (IB and PT) is supported by the “Conseil Régional du Limousin”. PT gratefully acknowledges the support by the Operational Program Research and Development Fund (project CZ.1.05/2.1.00/03.0058 of the Ministry of Education, Youth and Sports of the Czech Republic). IB gratefully acknowledges financial support from “Association Djerbienne en France”

Asymmetric triplex metallohelices with high and selective activity against cancer cells

Small cationic amphiphilic α-helical peptides are emerging as agents for the treatment of cancer and infection, but they are costly and display unfavourable pharmacokinetics. Helical coordination complexes may offer a three-dimensional scaffold for the synthesis of mimetic architectures. However, the high symmetry and modest functionality of current systems offer little scope to tailor the structure to interact with specific biomolecular targets, or to create libraries for phenotypic screens. Here, we report the highly stereoselective asymmetric self-assembly of very stable, functionalized metallohelices. Their anti-parallel head-to-head-to-tail ‘triplex’ strand arrangement creates an amphipathic functional topology akin to that of the active sub-units of, for example, host-defence peptides and ​p53. The metallohelices display high, structure-dependent toxicity to the human colon carcinoma cell-line HCT116 ​p53++, causing dramatic changes in the cell cycle without DNA damage. They have lower toxicity to human breast adenocarcinoma cells (MDA-MB-468) and, most remarkably, they show no significant toxicity to the bacteria methicillin-resistant Staphylococcus aureus and Escherichia coli. At a glanc