1,556 research outputs found
FmocâRGDS based fibrils: atomistic details of their hierarchical assembly
We describe the 3D supramolecular structure of FmocâRGDS 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 Ă-sheet configurations. The proposed model, which closely resembles the cross-Ă core structure of amyloids, is stabilized by pâp stacking interactions between hydrophobic Fmoc groups. More specifically, in this organization, the Fmoc-groups of Ă-strands belonging to the same Ă-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 FmocÂżFmoc interactions, the hierarchical assembly of the constituent Ă-strands involves a rich variety of intra- and inter-strand interactions. Accordingly, hydrogen bonding, salt bridges and pâp stacking interactions coexist in the highly ordered packing network proposed for the FmocâRGDS amphiphile. Quantum mechanical calculations, which have been performed to quantify the above referred interactions, confirm the decisive role played by the pâp 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
Why 1,2âquinone derivatives are more stable than their 2,3âanalogues?
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 KohnâSham molecular orbital
theory. The results showed that we have to trace the origin
of 1,2-quinonesâ enhanced stability to the more efficient
bonding in the Ï-electron system due to more favorable
overlap between the SOMOÏ of the ·C4nâ2H2nâCH·· and
··CHâCOâCO· 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
Coordinatively unsaturated ruthenium complexes as efficient alkyne-azide cycloaddition catalysts
The performance of 16-electron ruthenium complexes with the general formula Cp*Ru(L)X (in which L = phosphine or N-heterocyclic carbene ligand; X = Cl or OCH2CF3) was explored in azideâalkyne cycloaddition reactions that afford the 1,2,3- triazole products. The scope of the Cp*Ru(PiPr3)Cl precatalyst was investigated for terminal alkynes leading to new 1,5-disubstituted 1,2,3-triazoles in high yields. Mechanistic studies were conducted and revealed a number of proposed intermediates. Cp*Ru- (PiPr3)(η2-HCCPh)Cl was observed and characterized by 1H, 13C, and 31P NMR at temperatures between 273 and 213 K. A rare example of N,N-Îș2-phosphazide complex, Cp*Ru(Îș2-iPr3PN3Bn)Cl, was fully characterized, and a single-crystal X-ray diffraction structure was obtained. DFT calculations describe a complete map of the catalytic reactivity with phenylacetylene and/or benzylazide.Publisher PDFPeer reviewe
Bonding in methylalkalimetals (CH(3)M)(n) (M = Li, Na, K; n = 1, 4). Agreement and divergences between AIM and ELF analyses
The chemical bonding in methylalkalimetals (C
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 Ï-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 Ï-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
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
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