Spatially restricted Double Z-Simplified Box Orbital basis sets: Optimization and comparison with some standard basis sets

As part of previous studies, we introduced a new type of basis function named Simplified Box Orbitals (SBOs) that belong to a class of spatially restricted functions which allow the zero differential overlap (ZDO) approximation to be applied with complete accuracy. The original SBOs and their Gaussian expansions SBO-3G form a minimal basis set, which was compared to the standard Slater-type orbital basis set (STO-3G). In the present paper, we have developed the SBO basis functions at double-zeta (DZ) level, and we have assessed the option of expanding the SBO-DZ as a combination of Gaussian functions. Finally, we have determined the quality of the new basis set by comparing the molecular properties calculated with SBO-nG with those achieved with some standard basis sets.     

Parallel Versus Antiparallel β-Sheet Structure in Cyclic Peptide Hybrids Containing γ- or δ-Cyclic Amino Acids

Cyclic peptides with disc-shaped structures have emerged as potent building blocks for the preparation of new biomaterials in fields ranging from biological to material science. In this work, we analyze in depth the self-assembling properties of a new type of cyclic peptides based on the alternation of α-residues and cyclic δ-amino acids (α,δ-CPs). To examine the preferred stacking properties adopted by cyclic peptides bearing this type of amino acids, we carried out a synergistic in vitro/in silico approximation by using simple dimeric models and then extended to nanotubes. Although these new cyclic peptides (α,δ-CPs) can interact either in a parallel or antiparallel fashion, our results confirm that although the parallel β-sheet is more stable, it can be switched to the antiparallel stacking by choosing residues that can establish favorable cross-strand interactions. Moreover, the subsequent comparison by using the same methodology but applied to α,γ-CPs models, up to the moment assumed as antiparallel-like d,l -α-CPs, led to unforeseen conclusions that put into question preliminary conjectures about these systems. Surprisingly, they tend to adopt a parallel β-sheet directed by the skeleton interactions. These results imply a change of paradigm with respect to cyclic peptide designs that should be considered for dimers and nanotubes.     

Photochemistry in Real Space: Batho- and Hypsochromism in the Water Dimer

The development of chemical intuition in photochemistry faces several difficulties that result from the inadequacy of the one-particle picture, the Born–Oppenheimer approximation, and other basic ideas used to build models. It is shown herein how real-space approaches can be efficiently used to gain valuable insights in photochemistry through a simple example of red and blue shift effects: the double hypso- and bathochromic shifts in the low-lying valence excited states of (H₂O)₂. It is demonstrated that 1) the use of these techniques allows the perturbative language used in the theory of intermolecular interactions, even in the strongly interacting short-range regime, to be maintained; 2) one and only one molecule is photoexcited in each of the addressed excited states and 3) the electrostatic interaction between the in-the-cluster molecular dipoles provides a fairly intuitive rationalisation of the observed batho- and hypsochromism. The methods exploited and illustrated herein are able to maintain the individuality and properties of the interacting entities in a molecular aggregate, and thereby they allow chemical intuition in general states, at any geometry and using a broad variety of electronic structure methods to be kept and built.     

Clar Goblet and Aromaticity Driven Multiradical Nanographenes

The Clar Goblet, the first radical bowtie nanographene proposed by Erich Clar nearly 50 years ago, was recently synthesized. Bowtie nanographenes present quasi-degenerate magnetic ground states, which make them so elusive as unique. A thorough analysis is presented of the spin-state energetics of Clar Goblet and bowtie nanographenes by a battery of existing and novel ab initio procedures ranging from density functional theory to complete active space Hamiltonians. With this, it was proven that π radicals of bowtie nanographenes sit on BP (Benzo[cd]Pyrene) moieties driven by their local aromaticity, a purely chemical concept, which confers global stability to the whole structure. Besides, a novel Pauli energy densities analysis provided a visual intuitive explanation for this preference. These findings allow envisioning that analogous bowtie nanographenes with arbitrary polyradical character are not only feasible at the molecular scale but will share Clar Goblet's peculiar properties.     

Measurement of the surface excitation parameter of Kapton,polyethylene (PE), polymethyl methacrylate (PMMA), polystyrene (PS) and polytetrafluoroethylene (PTFE)

Reflection electron energy loss spectra (REELS) were measured for five insulating organic compounds: Kapton, polyethylene (PE), poly(methyl methacrylate) (PMMA), polystyrene (PS) and polytetrafluoroethylene (PTFE), as well as for Ni and Si, in the energy range between 200 and 1600 eV. The average number of surface excitations for a single surface crossing were determined from the experimental data and were found to be considerably smaller than for earlier studied materials, which mainly consisted of elemental metals [Surf. Sci. 486(2001)L461]. The surface excitation parameter, a material parameter used to quantify the relative intensity of surface losses in (photo)electron spectroscopy, was extracted from the data and compared with values found in the literature. The results indicate that surface excitations only have a minor influence on quantification of XPS spectra of polymers. On the other hand, a correction for surface excitations turns out to be essential for measurements of the electron inelastic mean free path of polymers when a metal is used as reference material.     

A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites

The development of novel anti-infectives requires unprecedented strategies targeting pathways which are solely present in pathogens but absent in humans. Following this principle, we developed inhibitors of lipoic acid ( LA ) salvage, a crucial pathway for the survival of LA auxotrophic bacteria and parasites but non-essential in human cells. An LA -based probe was selectively transferred onto substrate proteins via lipoate protein ligase (LPL) in intact cells, and their binding sites were determined by mass spectrometry. Probe labeling served as a proxy of LPL activity, enabling in situ screenings for cell-permeable LPL inhibitors. Profiling a focused compound library revealed two substrate analogs ( LAMe and C3 ) as inhibitors, which were further validated by binding studies and co-crystallography. Importantly, LAMe exhibited low toxicity in human cells and achieved killing of Plasmodium falciparum in erythrocytes with an EC₅₀ value of 15 μM, making it the most effective LPL inhibitor reported to date.     

Synthesis of Ir Catalysts Featuring Amide-functionalized NHC Ligands and Survey of their Activity on Formic Acid Dehydrogenation

2 a and 2 b , [Ir(CI)(COD)(NHC)] (COD=1,5-cyclooctadiene), have been prepared via transmetallation from NHC−Ag complexes. [Rh(CI)(COD)(NHC)] ( 4 ) was prepared analogously. [Ir({κ-C,N-(NHC-acetamide−1H)}(COD)] ( 3 c ) has been synthesized via transmetallation from the deprotonated NHC−Ag complex. [IrCp*({κ-C,N-(NHC-acetamide−1H)}] ( 5 ) (Cp*=pentamethylcyclopentadienyl), has been obtained analogously. [Ir(CI)(CO)₂(NHC)] ( 6 ) and [Ir({κ-C,N-(NHC-acetamide−1H)}(CO)₂] ( 7 ) have been prepared by carbonylation of 2 b and 3 c , respectively. The catalytic activity of these complexes has been evaluated in the dehydrogenation of formic acid, under solventless conditions, in the presence of water as a cosolvent, and in a 5 : 2 HCOOH/Et₃N mixture, with the best TOF values being obtained in the case of the latter. Stoichiometric experiments suggest COD hydrogenation as the preactivation step.     

The Role of Mechanical Properties and Structure of Type I Collagen Hydrogels on Colorectal Cancer Cell Migration

Mechanical interactions between cells and their microenvironment play an important role in determining cell fate, which is particularly relevant in metastasis, a process where cells invade tissue matrices with different mechanical properties. In vitro, type I collagen hydrogels have been commonly used for modeling the microenvironment due to its ubiquity in the human body. In this work, the combined influence of the stiffness of these hydrogels and their ultrastructure on the migration patterns of HCT-116 and HT-29 spheroids are analyzed. For this, six different types of pure type I collagen hydrogels by changing the collagen concentration and the gelation temperature are prepared. The stiffness of each sample is measured and its ultrastructure is characterized. Cell migration studies are then performed by seeding the spheroids in three different spatial conditions. It is shown that changes in the aforementioned parameters lead to differences in the mechanical stiffness of the matrices as well as the ultrastructure. These differences, in turn, lead to distinct cell migration patterns of HCT-116 and HT-29 spheroids in either of the spatial conditions tested. Based on these results, it is concluded that the stiffness and the ultrastructural organization of the matrix can actively modulate cell migration behavior in colorectal cancer spheroids.     

Ruthenium‐Catalyzed Oxidative Coupling of Primary Amines with Internal Alkynes through CH Bond Activation: Scope and Mechanistic Studies

The oxidative coupling of primary amines with internal alkynes catalyzed by Ru complexes is presented as a general atom‐economy methodology with a broad scope of applications in the synthesis of N‐heterocycles. Reactions proceed through regioselective C?H bond activation in 15 minutes under microwave irradiation or in 24 hours with conventional heating. The synthesis of 2,3,5‐substituted pyridines, benzo[h]isoquinolines, benzo[g]isoquinolines, 8,9‐dihydro‐benzo[de]quinoline, 5,6,7,8‐tetrahydroisoquinolines, pyrido[3,4g]isoquinolines, and pyrido[4,3g]isoquinolines is achievable depending on the starting primary amine used. DFT calculations on a benzylamine substrate support a reaction mechanism that consists of acetate‐assisted C?H bond activation, migratory‐insertion, and C?N bond formation steps that involve 28–30 kcal mol^?1. The computational study is extended to additional substrates, namely, 1‐naphthylmethyl‐, 2‐methylallyl‐, and 2‐thiophenemethylamines.