DensToolKit2: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields.

In this article, we provide details of the suite DensToolKit-v2, which consists of a set of cross-platform, optionally parallelized programs for analyzing the molecular electron density (ρ), as well as different fields and chemical indices derived from it. Notably, with this version, the user can compute the Non-Covalent Interaction index, the Density Overlap Regions Index, and fields related to single-spin-type molecular orbitals, such as the spin density. In addition, DensToolKit-v2 includes several programs for analyzing other less-known fields, such as the Density Matrix of order 1, the two-electron pair density function, and the Fourier transforms of these fields, that is, functionals in momentum space.

Ferrier Glycosylation Mediated by the TEMPO Oxoammonium Cation.

The TEMPO oxoammonium cation has been proven to be both an efficient oxidizing reagent and an electrophilic substrate frequently found in organic reactions. Here, we report that this versatile chemical reagent can also be used as an efficient promoter for C- and N-glycosylation reactions through a Ferrier rearrangement with moderate to high yields. This unprecedented reactivity is explained in terms of a Lewis acid activation of glycal by TEMPO forming a type of glycal-TEMPO mesomeric structure, which occurs through an extended vinylogous hyperconjugation toward the π* orbital [LP → π*, π* → σ*, and LP → π*].

Stabilizing Effect of a 4c/6e Hypervalent Bond in Dinitrodiphenyl Disulfides and Their Thermochemical Properties: Experimental and Computational Approach.

Thermochemical properties and intramolecular interactions of 2,2'-dinitrodiphenyl disulfide (2DNDPDS) and 4,4'-dinitrodiphenyl disulfide (4DNDPDS) were determined and analyzed. Their standard molar formation enthalpies in the gas phase (Δ(g)'s) were experimentally determined; theoretically, they were computed using the G4 composite method and atomization reactions. Specifically, Δ(g)'s were obtained by combining formation enthalpies in the condensed phase and enthalpies of phase change.

Accelerated Dimerization of α,β-Unsaturated D--Hexofurano-5-ulose Derivatives through Asynchronous Hetero-Diels-Alder Reaction.

While some hetero-Diels-Alder (HDA) reactions are accelerated by either carbonyl or phosphate groups attached directly to the heterodiene moiety, the alkyl or aryl groups, on the other hand, have minimal influence. However, in this article, we demonstrate that aryl groups have a significant effect on the spontaneous dimerization reaction of α,β-unsaturated D-xylo-hexofurano-5-ulose derivatives to their respective pyrano adducts via intermolecular HDA reaction. Experimental and computational studies provide strong evidence that dimerization follows the Woodward-Katz two-stage mechanism reaction (asynchronous process), from which the aryl/aryl π-stacking interaction is mainly responsible for the rate-determining step (RDS) and electrostatic interaction for the second bond formation.

Homochiral bifunctional L-prolinamide- and L-bis-prolinamide-catalyzed asymmetric aldol reactions performed in wet solvent-free conditions.

In this study, the novel bifunctional homochiral thiourea-L-prolinamides 1-4, tertiary amino-L-prolinamide 5, and bis-L-prolinamides 6 and 7 were prepared from enantiomerically pure (11R,12R)-11,12-diamino-9,10-dihydro-9,10-ethanoanthracene 8 and (11S,12S)-11,12-diamino-9,10-dihydro-9,10-ethanoanthracene ent-8. Highly enantioselective and diastereoselective aldolic intermolecular reactions (up to 95% enantiomeric excess, 93:7 anti/syn) between aliphatic ketones (20 equiv) and a range of aromatic aldehydes (1 equiv) were successfully carried out in the presence of water (10 equiv) and monochloroacetic acid (10 mol%), solvent-free conditions, at room temperature over 24 h using organocatalysts 1-7 (5 mol%). Stereoselective induction using density functional theory-based methods was consistent with the experimental data.

Porphyrin Supramolecular Arrays Formed by Weakly Interacting Meso-Functional Groups on Au(111).

The formation of a binary porphyrinic self-assembled system between meso-tetrakis(4-carboxyphenyl) porphyrin (TCPP) and meso-tetrakis(4-dimethyl amino) porphyrin (TDAP) was easily designed through non-covalent interactions in solution and adsorbed on a gold substrate. It was found that non-covalent interactions and geometrical conformations between porphyrins allow their self-assembly into a well-defined arrangement, which was confirmed by UV-Vis spectroscopy, electrochemistry, atomic force microscopy and density functional theory (DFT) studies.

Transition-Metal-Free Deconstructive Lactamization of Piperidines.

One of the major challenges in organic synthesis is the activation or deconstructive functionalization of unreactive C(sp )-C(sp ) bonds, which requires using transition or precious metal catalysts. We present here an alternative: the deconstructive lactamization of piperidines without using transition metal catalysts. To this end, we use 3-alkoxyamino-2-piperidones, which were prepared from piperidines through a dual C(sp )-H oxidation, as transitory intermediates.

Can an n → π* Interaction Provide Thermodynamic Stability to Naturally Occurring Cephalosporolides?

The stereocontrolled synthesis of naturally occurring products containing a 5,5-spiroketal molecular structure represents a major synthetic problem. Moreover, in a previous work, the stereocontrolled synthesis of cephalosporolide E (ceph E), which presumably was obtained from its epimer congener (ceph F) through an acid-mediated equilibration process, was reported. Consequently, we performed a theoretical investigation to provide relevant information regarding the title question, and it was found that the higher thermodynamic stability of ceph E, relative to ceph F, is caused by an n → π* interaction between a lone electron pair of the oxygen atom of the spiroketal ring (n) and the antibonding orbital of the carbonyl group (π*).

The Intramolecular Hydrogen Bond N-H···S in 2,2'-Diaminodiphenyl Disulfide: Experimental and Computational Thermochemistry.

The intramolecular hydrogen bond of the N-H···S type has been investigated sparingly by thermochemical and computational methods. In order to study this interaction, the standard molar enthalpies of formation in gaseous phase of diphenyl disulfide, 2,2'-diaminodiphenyl disulfide and 4,4'-diaminodiphenyl disulfide at T = 298.15 K were determined by experimental thermochemical methods and computational calculations.

Looking Inside the Intramolecular C-H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine.

Recently, strong evidence that supports the presence of an intramolecular C-H···O hydrogen bond in amides derived from the chiral auxiliary α-methylbenzylamine was disclosed. Due to the high importance of this chiral auxiliary in asymmetric synthesis, the inadvertent presence of this C-H···O interaction may lead to new interpretations upon stereochemical models in which this chiral auxiliary is present. Therefore, a series of lactams containing the chiral auxiliary α-methylbenzylamine (from three to eight-membered ring) were theoretically studied at the MP2/cc-pVDZ level of theory with the purpose of studying the origin and nature of the C-Hα···O interaction.

In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae.

The Stabilizing Role of the Intramolecular C-H···O Hydrogen Bond in Cyclic Amides Derived From α-Methylbenzylamine.

A series of five-, six-, seven-, and eight-membered lactams containing the chiral auxiliary α-methylbenzylamine were structurally analyzed and further studied by DFT calculations with the purpose to examine with detail the previously detected intramolecular C-H···O hydrogen-bonding interaction formed between the hydrogen atom of the α-methylbenzylamine and the carbonyl group of the cyclic amide. The main objective was to establish whether its presence does have a tangible relevance in their spatial arrangement in solution and in the solid state or is a simple and not stabilizing interaction.

Experimental and Computational Thermochemistry of 3- and 4-Nitrophthalic Anhydride.

In order to understand the influence that the position of the nitro group on the aromatic ring has on the relative stability of two isomers, the standard enthalpies of formation of 3- and 4-nitrophthalic anhydride in the gaseous phase, at T = 298.15 K, were obtained by experimental thermochemistry and theoretical studies. The standard enthalpies of formation in the crystalline phase, at T = 298.

β-Oxygen effect in the Barton-McCombie deoxygenation reaction: further experimental and theoretical findings.

The chemistry of (S)-methyl xanthates derived from xylo- and ribo-furanose derivatives in the presence of the stannyl radical is investigated. Xanthate derived from β-xylo-furanose affords exclusively a deoxygenated product; whereas, under the same reaction conditions, the α-ribo-furanose xanthate derivative produces quantitatively a hemithioacetal compound. We reasoned that in the case of the β-xylo-furanose derivative, a favorable β-oxygen effect in the Barton-McCombie deoxygenation reaction is operating where, according to theoretical calculations, unusual molecular orbital interactions (and not strain, as previously proposed) are present.