Novel C3-Methylene-Bridged Indole Derivatives with and without Substituents at N1: The Influence of Substituents on Their Hemolytic, Cytoprotective, and Antimicrobial Activity

Alkaloids are natural compounds useful as scaffolds for discovering new bioactive molecules. This study utilized alkaloid gramine to synthesize two groups of C3-substituted indole derivatives, which were either functionalized at N1 or not. The compounds were characterized by spectroscopic methods. The protective effects of the new compounds against in vitro oxidative hemolysis induced by standard oxidant 2,2'-azobis(2-amidinopropane dihydro chloride (AAPH) on human erythrocytes as a cell model were investigated. Additionally, the compounds were screened for antimicrobial activity. The results indicated that most of the indole derivatives devoid of the N1 substitution exhibited strong cytoprotective properties. The docking studies supported the affinities of selected indole-based ligands as potential antioxidants. Furthermore, the derivatives obtained exhibited potent fungicidal properties. The structures of the eight derivatives possessing indole moiety bridged to the imidazole-, benzimidazole-, thiazole-, benzothiazole-, and 5-methylbenzothiazoline-2-thiones were determined by X-ray diffraction. The C=S bond lengths in the thioamide fragment pointed to the involvement of zwitterionic structures of varying contribution. The predominance of zwitterionic mesomers may explain the lack of cytoprotective properties, while steric effects, which limit multiple the hydrogen-bond acceptor properties of a thione sulfur, seem to be responsible for the high hemolytic activity.

Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations

The structures of three proton-bound dimers (Met₂H⁺, MetTrpH⁺, and Trp₂H⁺) are investigated in the gas phase with infrared multiple photon disassociation (IRMPD) spectroscopy in combination with quantum chemical calculations. Their IRMPD spectra in the range of 600–1850 cm^–1 are obtained experimentally using an FT-ICR mass spectrometer and the CLIO free electron laser as an IR light source. The most abundant conformers are elucidated by comparing the IRMPD spectra with harmonic frequencies obtained at the B3LYP-GD3BJ/6-311++G** level of theory. Discrepancies between the experimental and theoretical data in the region of 1500–1700 cm^–1 are attributed to the anharmonicity of the amino bending modes. We confirm the result of a previous IRMPD study that the structure of gas-phase Trp₂H⁺ is charge-solvated but find that there are more stable structures than originally reported (Feng, R.; Yin, H.; Kong, X. Rapid Commun. Mass Spectrom.2016, 30, 24–28). In addition, gas-phase Met₂H⁺ and MetTrpH⁺ have been revealed to have charge-solvated structures. For all three dimers, the most stable conformer is found to be of type A. The spectrum of Met₂H⁺, however, cannot be explained without some abundance of type B charge-solvated conformers as well as salt-bridged structures.

Intramolecular H⋯S interactions in metal di-(isopropyl)dithiocarbamate complexes

Intramolecular C–H⋯S interactions create restricted rotation of groups within di(isopropyl)dithiocarbate complexes.

A quantitative definition of hypervalency

The concept of hypervalency has had a long but troubled history. Although several attempts have been made to dispense with the concept altogether, it remains in widespread use. By developing a simple but quantitative measure of hypervalency, the concept can be rehabilitated to provide valuable chemical insights in the context of Lewis models.

From the inception of Lewis' theory of chemical bonding, hypervalency has remained a point of difficulty that has not been fully resolved by the currently accepted qualitative definition of this term. Therefore, in this work, a quantitative measure of hypervalency has been developed. The only required input is the atomic charge map, which can be obtained from either quantum calculations or from experiment. Using this definition, it is found that well-known species such as O₃, CH₂N₂ and ClO₄^–, are indeed hypervalent, whilst others such as XeF₄, PCl₅ and SO₄^2–, are not. Quantitative analysis of known species of general formulae XF_n^m–, XCl_n^m–, and XO_n^m– shows that there are no fundamental differences in chemical bonding for hypervalent and non-hypervalent species. Nevertheless, hypervalency is associated with chemical instability, as well as a high degree of covalent rather than ionic bonding. The implications for accepted Lewis structure conventions are discussed.

Robustness of a thioamide {⋯H–N–CS}2 synthon: synthesis and the effect of substituents on the formation of layered to cage-like supramolecular networks in coumarin–thiosemicarbazone hybrids

The study has been carried out to highlight the potential of thiosemicarbazones in crystal engineering.

Robustness of thioamide dimer synthon, carbon bonding and thioamide–thioamide stacking in ferrocene-based thiosemicarbazones

The role of thioureas in crystal engineering as robust supramolecular synthons is now recognized, but their analogs, namely thiosemicarbazones/N-iminothioureas, have not received the attention they deserve.

Crystal structure studies of RNA duplexes containing s(2)U:A and s(2)U:U base pairs

Structural studies of modified nucleobases in RNA duplexes are critical for developing a full understanding of the stability and specificity of RNA base pairing. 2-Thio-uridine (s²U) is a modified nucleobase found in certain tRNAs. Thermodynamic studies have evaluated the effects of s²U on base pairing in RNA, where it has been shown to stabilize U:A pairs and destabilize U:G wobble pairs. Surprisingly, no high-resolution crystal structures of s²U-containing RNA duplexes have yet been reported. We present here two high-resolution crystal structures of heptamer RNA duplexes (5′-uagcs²Ucc-3′ paired with 3′-aucgAgg-5′ and with 3′-aucgUgg-5′) containing s²U:A and s²U:U pairs, respectively. For comparison, we also present the structures of their native counterparts solved under identical conditions. We found that replacing O2 with S2 stabilizes the U:A base pair without any detectable structural perturbation. In contrast, an s²U:U base pair is strongly stabilized in one specific U:U pairing conformation out of four observed for the native U:U base pair. This s²U:U stabilization appears to be due at least in part to an unexpected sulfur-mediated hydrogen bond. This work provides additional insights into the effects of 2-thio-uridine on RNA base pairing.

Synthesis and Structural Characterization of 1-Arylimidazole-2-thiones and N,N'-Aryldiethoxyethylthioureas with Electronically Diverse Substituents: A Manifold of Hydrogen Bonding Networks

The 1-arylimidazole-2-thiones, (HmimAr) [Ar = 3,4,5-C6H2(OMe)3, 2,4-C6H3(NO2)(OMe), 2,4,6-C6H2Cl3 and 3,5-C6H3(CF3)2], which feature electronically diverse substituents, may be obtained via acid-catalyzed ring closure of the corresponding N,N'-aryldiethoxyethylthiourea derivatives, ArN(H)C(S)N(H)CH2CH(OEt)2, (H2detuAr), which in turn are obtained via treatment of aminoacetaldehyde diethyl acetal, H2NCH2CH(OEt)2, with the respective arylisothiocyanates (ArNCS). The molecular structures of all of the above N,N'-aryldiethoxyethylthioureas and 1-arylimidazole-2-thiones have been determined by X-ray diffraction, thereby demonstrating that the substituents have a profound effect on the crystal structures. For example, each of the N,N'-aryldiethoxyethylthiourea derivatives adopts a different hydrogen bonding pattern. Specifically, the hydrogen-bonding network in (i) H2detuArCl3 consists of chains of 9-membered rings, with an [ [Formula: see text](9)] motif, that feature one N-H ⋯ O and one N-H ⋯ S interaction, (ii) H2detuArOMe,NO2 consists of chains of 6-membered rings, with an [ [Formula: see text](6)] motif, that feature two head-to-tail N-H ⋯ S interactions, (iii) H2detuAr(CF3)2 consists of a dimer that features two pairs of N-H ⋯ O interactions, of which each pair is a component of an 8-membered ring with an [ [Formula: see text](8)] motif, and (iv) H2detuAr(OMe)3 consists of a chain of head-to-head dimeric rings with a basic [ [Formula: see text](16)] motif, a notable feature of which is that sulfur does not play a role as a hydrogen bond acceptor. Each of the 1-arylimidazole-2-thiones exists as a "head-to-head" hydrogen-bonded dimer in the solid state, with an [ [Formula: see text](8)] motif. However, while the hydrogen-bonded motifs for HmimArCl3 and HmimAr(OMe)3 are planar, those for HmimAr(CF3)2 and HmimArOMe,NO2 are extremely puckered, with fold angles of 24.2° (mean value) and 45.7°, respectively.

SO2-catalyzed steam pretreatment enhances the strength and stability of softwood pellets

Densification can partially resolve the logistical challenges encountered when large volumes of biomass are required for bioconversion processes to benefit from economies-of-scale. Despite the higher bulk density of pellets, their lower mechanical strength and sensitivity to moisture are still recurring issues hindering long term transportation and storage. In this study, we have evaluated the potential benefits of SO(2)-catalyzed steam treatment to achieve both the needed size reduction prior to pelletization while improving the stability of the produced pellets. This pretreatment substantially reduced the particle size of the woodchips eliminating any further grinding. The treated pellets had a higher density and exhibited a two-time higher mechanical strength compared to untreated pellets. Despite a higher moisture adsorption capacity, treated pellets remained intact even under highly humid conditions. The high heating values, low ash content and good overall carbohydrate recovery of treated pellets indicated their potential suitability for both biochemical and thermochemical applications.

Advances in understanding of chemical bonding: inputs from experimental and theoretical charge density analysis

The development of charge density analysis has undergone a major renaissance in the last two decades. In recent years, the characterization of bonding features associated with atoms in molecules and in crystals has been explored using high-resolution X-ray diffraction data (laboratory or synchrotron) complemented by high level ab initio theoretical calculations. The extraction of one electron topological properties, namely, electrostatic charges, dipole moment and higher moments, electrostatic potential, electric field gradients, in addition to evaluation of the local kinetic and potential energy densities, have contributed toward an understanding of the electron density distributions in molecular solids. New topological descriptors, namely, the source function (SF) and electron localization function (ELF) provide additional information as regards characterization of the topology of the electron density. In addition, delocalization indices have also been developed to account for bonding features pertinent to M-M bonds. The evaluation of these properties have contributed significantly toward the understanding of intra- and intermolecular bonding features in organic, inorganic, and biomolecules in the crystalline phase, with concomitant applications in the understanding of chemical reactivity and material/biological properties. In recent years, the focus has strongly shifted toward the understanding of structure-property relationships in organometallic complexes containing labile M-C bonds in the crystal structure with subsequent implications in catalysis. This perspective aims to highlight the major developments in electron density measurements in the past few years and provides pointers directed toward the potential use of this technique in future applications for an improved understanding of chemical bonding in systems that have been unexplored.