Complex Networks Analyses of Antibiofilm Peptides: An Emerging Tool for Next-Generation Antimicrobials' Discovery.

Microbial biofilms cause several environmental and industrial issues, even affecting human health. Although they have long represented a threat due to their resistance to antibiotics, there are currently no approved antibiofilm agents for clinical treatments. The multi-functionality of antimicrobial peptides (AMPs), including their antibiofilm activity and their potential to target multiple microbes, has motivated the synthesis of AMPs and their relatives for developing antibiofilm agents for clinical purposes.

Exploring the Non-Covalent Bonding in Water Clusters.

QTAIM and source function analysis were used to explore the non-covalent bonding in twelve different water clusters (HO) obtained by considering = 2-7 and various geometrical arrangements. A total of seventy-seven O-H⋯O hydrogen bonds (HBs) were identified in the systems under consideration, and the examination of the electron density at the bond critical point (BCP) of these HBs revealed the existence of a great diversity of O-H⋯O interactions. Furthermore, the analysis of quantities, such as |V(r)|/G(r) and H(r), allowed a further description of the nature of analogous O-H⋯O interactions within each cluster.

A Theoretical Study of the C-X Bond Cleavage Mediated by Cob(II)Aloxime.

The C-X bond cleavage in different methyl halides (CHX; X = Cl, Br, I) mediated by 5,6-dimethylbenzimidazole-bis(dimethylglyoximate)cobalt(II) (CoCbx) was theoretically investigated in the present work. An S2-like mechanism was considered to simulate the chemical process where the cobalt atom acts as the nucleophile and the halogen as the leaving group. The reaction path was computed by means of the intrinsic reaction coordinate method and analyzed in detail through the reaction force formalism, the quantum theory of atoms in molecules (QTAIM), and the calculation of one-electron density derived quantities, such as the source function (SF) and the spin density.

Dehydrochlorination of PCDDs on SWCN-Supported Ni and Ni Clusters, a DFT Study.

Polychlorinated dibenzo-p-dioxins (PCDDs) are known to be a group of compounds of high toxicity for animals and, particularly, for humans. Given that the most common method to destroy these compounds is by high-temperature combustion, finding other routes to render them less toxic is of paramount importance. Taking advantage of the physisorption properties of nanotubes, we studied the reactions of atomic hydrogen on physisorbed PCDDs using DFT; likewise, we investigated the reaction of molecular hydrogen on PCDDs aided by Ni and Ni clusters adsorbed on single-wall carbon nanotubes.

The closed-edge structure of graphite and the effect of electrostatic charging.

The properties of graphite, and of few-layer graphene, can be strongly influenced by the edge structure of the graphene planes, but there is still much that we do not understand about the geometry and stability of these edges. We present an experimental and theoretical study of the closed edges of graphite crystals, and of the effect of an electric field on their structure. High-resolution transmission electron microscopy is used to image the edge structure of fresh graphite and of graphite that has been exposed to an electric field, which experiences a separation of the graphene layers.

When global and local molecular descriptors are more than the sum of its parts: Simple, But Not Simpler?

In this report, we introduce a set of aggregation operators (AOs) to calculate global and local (group and atom type) molecular descriptors (MDs) as a generalization of the classical approach of molecular encoding using the sum of the atomic (or fragment) contributions. These AOs are implemented in a new and free software denominated MD-LOVIs ( http://tomocomd.com/md-lovis ), which allows for the calculation of MDs from atomic weights vector and LOVIs (local vertex invariants).

Stability of "No-Pair Ferromagnetic" Lithium Clusters.

High-spin lithium clusters, Li ( = 2-21), have been systematically studied by using density functional theory. Although these high-spin clusters have no bonding electron pairs, they are stable with respect to isolated atoms. A set of 42 density functional theory functionals were benchmarked against CCSD(T)/cc-pVQZ results for clusters from the dimer to the hexamer.

Higher-Order and Mixed Discrete Derivatives such as a Novel Graph- Theoretical Invariant for Generating New Molecular Descriptors.

Background: Recently, some authors have defined new molecular descriptors (MDs) based on the use of the Graph Discrete Derivative, known as Graph Derivative Indices (GDI). This new approach about discrete derivatives over various elements from a graph takes as outset the formation of subgraphs. Previously, these definitions were extended into the chemical context (N-tuples) and interpreted in structural/physicalchemical terms as well as applied into the description of several endpoints, with good results.

Theoretical investigation of the mechanism for the reductive dehalogenation of methyl halides mediated by the Co-based compounds cobalamin and cobaloxime.

Theoretical calculations focusing on the cleavage of the C-X bond in methyl halides (CHX; X = Cl, Br, I) as mediated by Co-based systems have been carried out using the hybrid functional ωB97-XD together with the basis set 6-311++G(2d,2p). A total of seven Co-based compounds were evaluated: cob[I]alamin (CoCbl) in its base-on form and cobaloxime (CoCbx) with either no ligand or different ligands (either pyridine (PYR), tributylphosphine (TBP), dimethyl sulfide (DMS), cyclohexylisocyanide (CI), or 5,6-dimethylbenzimidazole (DMB)) at the lower axial position. For the large CoCbl system, an ONIOM scheme was employed, where the high layer was described at the DFT level and the low layer was computed using the semi-empirical method PM6.

Generalized Molecular Descriptors Derived From Event-Based Discrete Derivative.

In the present study, a generalized approach for molecular structure characterization is introduced, based on the relation frequency matrix (F) representation of the molecular graph and the subsequent calculation of the corresponding discrete derivative (finite difference) over a pair of elements (atoms). In earlier publications (22- 24), an unique event, named connected subgraphs, (based on the Kier-Hall's subgraphs) was systematically employed for the computation of the matrix F. The present report is a generalization of this notion, in which eleven additional events are introduced, classified in three categories, namely, topological (terminal paths, vertex path incidence, quantum subgraphs, walks of length k, Sach's subgraphs), fingerprints (MACCs, E-state and substructure fingerprints) and atomic contributions (Ghose and Crippen atom-types for hydrophobicity and refractivity) for F generation.

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms.

This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms).

2,2,3,3'-Tetra-phenyl-7,7'-biquinoxaline.

In the crystal structure of the title compound, C(40)H(26)N(4), mol-ecules reside on crystallographic centers of inversion and are linked via C-H⋯N inter-actions about inversion centers into one-dimensional chains: longer C-H⋯π(arene) inter-actions complete the inter-molecular inter-actions.