Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly

We describe the 3D supramolecular structure of Fmoc–RGDS fibrils, where Fmoc and RGDS refer to the hydrophobic N-(fluorenyl-9-methoxycarbonyl) group and the hydrophilic Arg-Gly-Asp-Ser peptide sequence, respectively. For this purpose, we performed atomistic all-atom molecular dynamics simulations of a wide variety of packing modes derived from both parallel and antiparallel ß-sheet configurations. The proposed model, which closely resembles the cross-ß core structure of amyloids, is stabilized by p–p stacking interactions between hydrophobic Fmoc groups. More specifically, in this organization, the Fmoc-groups of ß-strands belonging to the same ß-sheet form columns of p-stacked aromatic rings arranged in a parallel fashion. Eight of such columns pack laterally forming a compact and dense hydrophobic core, in which two central columns are surrounded by three adjacent columns on each side. In addition to such Fmoc¿Fmoc interactions, the hierarchical assembly of the constituent ß-strands involves a rich variety of intra- and inter-strand interactions. Accordingly, hydrogen bonding, salt bridges and p–p stacking interactions coexist in the highly ordered packing network proposed for the Fmoc–RGDS amphiphile. Quantum mechanical calculations, which have been performed to quantify the above referred interactions, confirm the decisive role played by the p–p stacking interactions between the rings of the Fmoc groups, even though both inter-strand and intra-strand hydrogen bonds and salt bridges also play a non-negligible role. Overall, these results provide a solid reference to complement the available experimental data, which are not precise enough to determine the fibril structure, and reconcile previous independent observations.Peer ReviewedPostprint (published version

Aromaticity determines the relative stability of kinked vs. straight topologies in polycyclic aromatic hydrocarbons

It is well-known that kinked phenacenes are more stable than their isomeric linear acenes, the archetypal example being phenanthrene that is more stable than anthracene by about 4-8 kcal/mol. In previous studies, the origin of the higher stability of kinked polycyclic aromatic hydrocarbons (PAHs) was found to be better π-bonding interactions, i.e., larger aromaticity, in kinked as compared to linear PAHs. Some years ago, however, Dominikowska and Palusiak (2011) found that dicationic linear anthracene is more stable than the dicationic kinked phenanthrene. Therefore, these authors showed that, in some cases, the linear topology in PAHs can be preferred over the kinked one. Our results using energy decomposition analyses in combination with the turn-upside-down approach show that the origin of the higher stability of dicationic anthracene is the same as in the neutral species, i.e., better π-bonding interactions. A similar result is found for the kinked and straight pyrano-chromenes. We conclude that the aromaticity is the driving force that determines the relative stability of kinked vs. straight topologies in PAHs

Why 1,2‑quinone derivatives are more stable than their 2,3‑analogues?

In this work, we have studied the relative stability of 1,2- and 2,3-quinones. While 1,2-quinones have a closed-shell singlet ground state, the ground state for the studied 2,3-isomers is open-shell singlet, except for 2,3-naphthaquinone that has a closed-shell singlet ground state. In all cases, 1,2-quinones are more stable than their 2,3-counterparts. We analyzed the reasons for the higher stability of the 1,2-isomers through energy decomposition analysis in the framework of Kohn–Sham molecular orbital theory. The results showed that we have to trace the origin of 1,2-quinones’ enhanced stability to the more efficient bonding in the π-electron system due to more favorable overlap between the SOMOπ of the ·C4n−2H2n–CH·· and ··CH–CO–CO· fragments in the 1,2-arrangement. Furthermore, whereas 1,2-quinones present a constant trend with their elongation for all analyzed properties (geometric, energetic, and electronic), 2,3-quinone derivatives present a substantial breaking in monotonicity.European Union in the framework of European Social Fund through the Warsaw University of Technology Development Programme. O.A. S., H. S. and T.M. K

Planar vs. three-dimensional X-6(2-), X2Y42-, and X3Y32- (X, Y = B, Al, Ga) metal clusters: an analysis of their relative energies through the turn-upside-down approach

Despite the fact that B and Al belong to the same group 13 elements, the B-6(2-) cluster prefers the planar D-2h geometry, whereas Al-6(2-) favours the Oh structure. In this work, we analyse the origin of the relative stability of D2h and Oh forms in these clusters by means of energy decomposition analysis based on the turn-upside-down approach. Our results show that what causes the different trends observed is the orbital interaction term, which combined with the electrostatic component do (Al-6(2-) and Ga-6(2-)) or do not (B-6(2-)) compensate the higher Pauli repulsion of the Oh form. Analysing the orbital interaction term in more detail, we find that the preference of B-6(2-) for the planar D-2h form has to be attributed to two particular molecular orbital interactions. Our results are in line with a dominant delocalisation force in Al clusters and the preference for more localised bonding in B metal clusters. For mixed clusters, we have found that those with more than two B atoms prefer the planar structure for the same reasons as for B-6(2-)

Path-dependency of energy decomposition analysis & the elusive nature of bonding

Here, we provide evidence of the path-dependency of the energy components of the energy decomposition analysis scheme, EDA, by studying a set of thirty-one closed-shell model systems with the D2h symmetry point group. For each system, we computed EDA components from nine different pathways and numerically showed that the relative magnitudes of the components differ substantially from one path to the other. Not surprisingly, yet unfortunately, the most significant variations in the relative magnitudes of the EDA components appear in the case of species with bonds within the grey zone of covalency and ionicity. We further discussed that the role of anions and their effect on arbitrary Pauli repulsion energy components affects the nature of bonding defined by EDA. The outcome variation by the selected partitioning scheme of EDA might bring arbitrariness when a careful comparison is overlooked

Exploring the validity of the Glidewell-Lloyd extension of Clar's pi-sextet rule: assessment from polycyclic conjugated hydrocarbons

The Clar pi-sextet rule was formulated as a tool to qualitatively assign the local aromatic character of six-membered rings in benzenoid species. This simple rule has been widely validated both experimentally and theoretically. In 1984, Glidewell and Lloyd reported an extension of this rule to polycyclic conjugated hydrocarbons having rings with any even number of carbon atoms in their structure. In this work, we assess the validity of the Glidewell-Lloyd extension in 69 polycyclic conjugated hydrocarbons composed of different combinations of four-, six-, and eight-membered rings. Our results support the validity of this extension with some exceptions that are discussed. Finally, a minor modification to the rule is proposed

Complexes of adamantane-based group 13 Lewis acids and superacids: Bonding analysis and thermodynamics of hydrogen splitting

The electronic structure and chemical bonding in donor-acceptor complexes formed by group 13 element adamantane and perfluorinated adamantane derivatives EC9R15 (E=B, Al; R=H, F) with Lewis bases XR3 and XC9H15 (X=N, P; R= H, CH3) have been studied using energy decomposition analysis at the BP86/TZ2P level of theory. Larger stability of complexes with perfluorinated adamantane derivatives is mainly due to better electrostatic and orbital interactions. Deformation energies of the fragments and Pauli repulsion are of less importance, with exception for the boron-phosphorus complexes. The MO analysis reveals that LUMO energies of EC9R15 significantly decrease upon fluorination (by 4.7 and 3.6 eV for E=B and Al, respectively) which results in an increase of orbital interaction energies by 27-38 (B) and 15-26 (Al) kcal mol(-1). HOMO energies of XR3 increase in order PH3<NH3<PMe3<PC9H15<NMe3<NC9H15. For the studied complexes, there is a linear correlation between the dissociation energy of the complex and the energy difference between HOMO of the donor and LUMO of the acceptor. The fluorination of the Lewis acid significantly reduces standard enthalpies of the heterolytic hydrogen splitting H-2+D+A=[HD](+)+[HA](-). Analysis of several types of the [HD](+)center dot center dot center dot[HA](-) ion pair formation in the gas phase reveals that structures with additional H center dot center dot center dot F interactions are energetically favorable. Taking into account the ion pair formation, hydrogen splitting is predicted to be highly exothermic in case of the perfluorinated derivatives both in the gas phase and in solution. Thus, fluorinated adamantane-based Lewis superacids are attractive synthetic targets for the construction of the donor-acceptor cryptands

Testing the effectiveness of the isoelectronic substitution principle through the transformation of aromatic osmathiophene derivatives into their inorganic analogues

The objective of the current work is to evaluate the effectiveness of the isoelectronic substitution (IS) principle on a series of complexes with the general formula OsCl2(SX3H3)(PH3)(2), where X-3 represents the moieties CCC, CCB, CCN, CBN, CNB or NCB, formed by substitution of the carbon atoms in CCC by either the isoelectronic B- or N+ separately, or by both. The SX3H3 moiety forms, together with Os, an aromatic five-membered ring (5-MR) called osmathiophene. The preservation of stability and aromaticity in the resulting systems is used to indicate the effectiveness of the IS principle. The aromaticity of the proposed molecules is analyzed according to the magnetic (induced magnetic field (B-ind)) and electronic (through the multicenter index (MCI)) criteria. In addition a chemical bonding analysis on selected species is performed by the adaptive natural density partitioning (AdNDP) method