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 (ΔfHm°(g)'s) were experimentally determined; theoretically, they were computed using the G4 composite method and atomization reactions. Specifically, ΔfHm°(g)'s were obtained by combining formation enthalpies in the condensed phase and enthalpies of phase change. Formation enthalpies in the condensed phase were determined experimentally through combustion energies, which in turn were found by means of a rotatory bomb combustion calorimeter. Sublimation enthalpies were derived from thermogravimetric experiments, measuring the rate of mass loss and using Langmuir and Clausius-Clapeyron equations. Fusion enthalpies and heat capacities of the solid and liquid phases were measured as functions of temperature by differential scanning calorimetry, and the heat capacities of the gas phase were calculated via molecular orbital calculations. Theoretical and experimental ΔfHm°(g)'s differed by <5.5kJ·mol-1, and isomerization enthalpies are discussed. In addition, using theoretical tools [natural bond orbitals (NBO) and quantum theory of atoms in molecules (QTAIM)], intramolecular interactions were analyzed. An uncommon hypervalent four-center six-electron interaction of type O···S-S···O was found in 2DNDPDS. This hypervalent interaction, in addition to the extent of conjugation between the aryl and NO2 moieties and the formation of intramolecular C-H···S hydrogen bonds, counteracts the repulsion caused by steric repulsions. Hydrogen bonding was confirmed through geometric parameters as well as QTAIM.

Accelerated Dimerization of α,ß-Unsaturated D-Xylo-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,ß-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. Since the latter interaction is highly affected by dipolar moment, 5-ulose derivative having a strong electron-withdrawing group (R = CN; µ = 14.3 D) is spontaneously dimerized more than 15 times faster than 5-ulose that possesses an electron-donating group (R = OMe; µ = 2.1 D).

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.

Can an n(O) → 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 (nO) and the antibonding orbital of the carbonyl group (π*C=O). Although similar stereoelectronic interactions have been disclosed in other molecular structures, its presence in ceph E, and very likely in other related naturally occurring products, represents a novel nonanomeric stabilizing effect that should be introduced into the chemical literature.

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(sp3 )-C(sp3 ) 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(sp3 )-H oxidation, as transitory intermediates. Experimental and theoretical studies confirm that this unprecedented lactamization occurs in a tandem manner involving an oxidative deamination of 3-alkoxyamino-2-piperidones to 3-keto-2-piperidones, followed by a regioselective Baeyer-Villiger oxidation to give N-carboxyanhydride intermediates, which finally undergo a spontaneous and concerted decarboxylative intramolecular translactamization.

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. The experimental enthalpies of formation in gas-phase were obtained from enthalpies of formation in crystalline phase and enthalpies of sublimation. Enthalpies of formation in crystalline phase were obtained using rotatory bomb combustion calorimetry. By thermogravimetry, enthalpies of vaporization were obtained, and by combining them with enthalpies of fusion, the enthalpies of sublimation were calculated. The Gaussian-4 procedure and the atomization method were applied to obtain enthalpies of formation in gas-phase of the compounds under study. Theoretical and experimental values are in good agreement. Through natural bond orbital (NBO) analysis and a topological analysis of the electronic density, the intramolecular hydrogen bridge (N-H···S) in the 2,2'-diaminodiphenyl disulfide was confirmed. Finally, an enthalpic difference of 11.8 kJ·mol-1 between the 2,2'-diaminodiphenyl disulfide and 4,4'-diaminodiphenyl disulfide was found, which is attributed to the intramolecular N-H···S interaction.

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. NBO analysis revealed that rehybridization at C atom of the C-Hα bond (s-character at C is ~23%) and the subsequent bond polarization are the dominant effect over the orbital interaction energy n(O)→σ*C-Hα (E(2) < 2 kcal/mol), causing an important shortening of the C-Hα bond distance and an increment in the positive charge in the Hα atom.

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.

Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units.

Using a grid-based method to search the critical points in electron density, we show how to accelerate such a method with graphics processing units (GPUs). When the GPU implementation is contrasted with that used on central processing units (CPUs), we found a large difference between the time elapsed by both implementations: the smallest time is observed when GPUs are used. We tested two GPUs, one related with video games and other used for high-performance computing (HPC). By the side of the CPUs, two processors were tested, one used in common personal computers and other used for HPC, both of last generation. Although our parallel algorithm scales quite well on CPUs, the same implementation on GPUs runs around 10× faster than 16 CPUs, with any of the tested GPUs and CPUs. We have found what one GPU dedicated for video games can be used without any problem for our application, delivering a remarkable performance, in fact; this GPU competes against one HPC GPU, in particular when single-precision is used.

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 = 298.15 K, were obtained by combustion calorimetry and the enthalpies of sublimation by the Knudsen method. For the theoretical calculations, a standard ab initio molecular orbital method at the G3 level was used. The enthalpies of formation in the gaseous phase were obtained from atomization and isodesmic reactions. A theoretical study of the molecular and electronic structures of these compounds was also performed. Differences of -9.7 kJ·mol-1, for 3-nitrophthalic anhydride, and -2.6 kJ·mol-1 for 4-nitrophthalic anhydride, were found from a comparison between our theoretical and experimental results.

ß-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 ß-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 ß-xylo-furanose derivative, a favorable ß-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. These orbital interactions involve the SOMO (intermediary generated from the stannyl radical addition) with the σ* orbital of the bond undergoing cleavage and this with the two C-O antibonding orbitals anti oriented. Such molecular orbital interactions are not present in the α-ribo-furanose; therefore, the ß-scission is highly delayed, and due to the reversibly nature of the stannyl radical addition, the ribo-furanose xanthate is forced to take an alternative route: the homolytic substitution (S(H)2) of the sulfide sulfur by stannyl radical. This radical addition gives the alkoxythiocarbonyl radical, which is trapped by Bu3SnH before the elimination of carbonyl sulfide; subsequently, radical stannyl addition followed by radical reduction produces the hemithioacetal.

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. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability, physicochemical properties and spatial organization in comparison to the NMD factor depicted for Homo sapiens. These observations strongly support the notion that human and fungal UPF1 could perform equivalent biological activities.