Norcaradiene-Cycloheptatriene Equilibrium: A Heavy-Atom Quantum Tunneling Case.

The equilibrium between norcaradiene and cycloheptatriene, which has captivated chemists for more than half a century, is revisited by state-of-the-art quantum chemical calculations. Our theoretical data significantly deviate from the experimental results (J. Am. Chem. Soc., 1981, 26, 7791-7792), especially at low temperatures, where isomerization is dominated by heavy-atom tunneling. This effect results in an extremely short half-life for norcaradiene, rendering it undetectable. This work sheds light on this equilibrium, updating the kinetic and thermodynamic data while also expanding the repertoire of organic reactions controlled by this exotic quantum effect.

Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation.

During translation, nascent polypeptide chains travel from the peptidyl transferase center through the nascent polypeptide exit tunnel (NPET) to emerge from 60S subunits. The NPET includes portions of five of the six 25S/5.8S rRNA domains and ribosomal proteins uL4, uL22, and eL39. Internal loops of uL4 and uL22 form the constriction sites of the NPET and are important for both assembly and function of ribosomes. Here, we investigated the roles of eL39 in tunnel construction, 60S biogenesis, and protein synthesis. We show that eL39 is important for proper protein folding during translation. Consistent with a delay in processing of 27S and 7S pre-rRNAs, eL39 functions in pre-60S assembly during middle nucleolar stages. Our biochemical assays suggest the presence of eL39 in particles at these stages, although it is not visualized in them by cryo-electron microscopy. This indicates that eL39 takes part in assembly even when it is not fully accommodated into the body of pre-60S particles. eL39 is also important for later steps of assembly, rotation of the 5S ribonucleoprotein complex, likely through long range rRNA interactions. Finally, our data strongly suggest the presence of alternative pathways of ribosome assembly, previously observed in the biogenesis of bacterial ribosomal subunits.

Synthesis of CxNy-rich polycyclic oligomers from primeval monomers in aqueous media.

A multichannel, non-thermolytic and efficient pathway is described toward the formation of functionalized carbon nitride-like oligomers, starting from readily available cyanamide and glyoxal (in ratios >2), in aqueous media under mild conditions. Such oligomers can be isolated as stable solids that result from structures involving cyanamide self-additions along with structures formally derived from the condensation of cyanamide, dicyandiamide or melamine with glyoxal, leading occasionally to oxygen-containing units. The oligomeric aggregates have masses up to 500 u, as inferred from mass spectra analyses, and their formation can be rationalized in terms of polyadditions of cyanamide (up to 10-mer) and glyoxal. The latter is not only a willing reaction partner, but also promotes facile condensation by enhancing the reactivity of nitrile fragments and inducing a significant lowering of the energy barriers. This mechanistic surmise is also supported by DFT calculations of the early condensation steps. As a result, melamine/triazine-type structures are obtained in aquatic environments under much milder conditions than those usually required by other synthetic procedures. Moreover, our results also help unveil the abiotic processes affording complex organic matter on celestial bodies and early earth.

From prebiotic chemistry to supramolecular oligomers: urea-glyoxal reactions.

A fundamental question in origin-of-life studies and astrochemistry concerns the actual processes that initiate the formation of reactive monomers and their oligomerization. Answers lie partly in the accurate description of reaction mechanisms compatible with environments plausible on early Earth as well as cosmological scenarios in planetary factories. Here we show in detail that reactions of urea-as archetypal prebiotic substance-and reactive carbonyls-exemplified by glyoxal-lead to a vast repertoire of oligomers, in which different five- and six-membered non-aromatic heterocycles self-assemble and insert into chains or dendritic-like structures with masses up to 1000 Da. Such regular patterns have been interpreted by experimental and computational methods. A salient conclusion is that such processes most likely occur through SN-type mechanisms on hydrated or protonated species. Remarkably, such supramolecular oligomeric mixtures can be easily isolated from organic solvents, thus opening the door to the generation of novel urea-containing polymers with potential applications in materials chemistry and beyond.

Interactions of Amino Acids and Aminoxazole Derivatives: Cocrystal Formation and Prebiotic Implications Enabled by Computational Analysis.

In line with the postulated intermediacy of aminoxazoles derived from small sugars toward the direct assembly of nucleoside precursors, we show here a potential prebiotic scenario where aminoxazolines might have also played further roles as complexing and/or sequestering agents of other primeval blocks, namely amino acids. To this end, a bis-aminoxazoline derivative, generated from dihydroxyacetone and cyanamide, gives rise to stable co-crystal forms with dicarboxylic amino acids (Asp and Glu), while ionic interactions owing to proton transfer are inferred from spectroscopic data in aqueous solution. The structure of a 1:2 aminoxazoline: aspartic acid complex, discussed in detail, was elucidated by X-ray diffractometry. Optimized geometries of such ionic structures with bulk aqueous solvation were assessed by DFT calculations, which disclose preferential arrangements that validate the experimental data. Peripherally, we were able to detect in a few cases amino acid dimerization (i.e. dipeptide formation) after prolonged incubation with the bis-aminoxazole derivative. A mechanistic simulation aided by computation provides some predictive conclusions for future explorations and catalytic design.

Formation of Cyanamide-Glyoxal Oligomers in Aqueous Environments Relevant to Primeval and Astrochemical Scenarios: A Spectroscopic and Theoretical Study.

The condensation of cyanamide and glyoxal, two well-known prebiotic monomers, in an aqueous phase has been investigated in great detail, demonstrating the formation of oligomeric species of varied structure, though consistent with generalizable patterns. This chemistry involving structurally simple substances also illustrates the possibility of building molecular complexity under prebiotically plausible conditions, not only on Earth, but also in extraterrestrial scenarios. We show that cyanamide-glyoxal reactions in water lead to mixtures comprising both acyclic and cyclic fragments, largely based on fused five- and six-membered rings, which can be predicted by computation. Remarkably, such a mixture could be identified using high-resolution electrospray ionization (ESI) mass spectrometry and spectroscopic methods. A few mechanistic pathways can be postulated, most involving the intermediacy of glyoxal cyanoimine and further chain growth, thus increasing the diversity of the observed products. This rationale is supported by theoretical analyses with clear-cut identification of all of the stationary points and transition-state structures. The properties and structural differences of oligomers obtained under thermodynamic conditions in water as opposed to those isolated by precipitation from organic media are also discussed.

On the asymmetric autocatalysis of aldol reactions: The case of 4-nitrobenzaldehyde and acetone. A critical appraisal with a focus on theory.

Under neutral conditions, spontaneous mirror symmetry breaking has been occasionally reported for aldol reactions starting from achiral reagents and conditions. Chiral induction might be interpreted in terms of autocatalysis exerted by chiral mono-aldol or bis-aldol products as source of initial enantiomeric excesses, which may account for such experimental observations. We describe here a thorough Density Functional Theory (DFT) study on this complex and otherwise difficult problem, which provides some insights into this phenomenon. The picture adds further rationale to an in-depth analysis by Moyano et al, who showed the isolation and characterization of bis-aldol adducts and their participation in a complex network of reversible steps. However, the lack of enantiodiscrimination (ees vanish rapidly in solution) suggests, according to the present results, a weak association in complexes formed by the catalysts and substrates. The latter would also be consistent with almost flat transition states having similar heights for competitive catalyst-bound transition structures (actually, we were unable to locate them at the level explored). Overall, neither autocatalysis as once conjectured nor mutual inhibition of enantiomers appears to be operating mechanisms. Asymmetric amplification in early stages harnessing unavoidable enantiomeric imbalances in reaction mixtures of chiral products represents a plausible interpretation.

Prebiotic-Like Condensations of Cyanamide and Glyoxal: Revisiting Intractable Biotars.

We report a detailed investigation into the nature of products that are generated by the reactions of cyanamide and glyoxal, two small molecules of astrochemical and prebiotic significance, under different experimental conditions. The experimental data suggest that the formation of oligomeric structures is related in part to the formation of insoluble tholins in the presence of oxygen-containing molecules. Although oligomerization proceeds well in water, product isolation turned out to be impractical. Instead, solid precipitates were obtained easily in acetone. Crude mixtures have been thoroughly scrutinized by spectroscopic methods, in particular NMR and mass spectroscopy (ESI mode), which are all consistent with the generation of a few functional groups that are embedded into regular chains of five- and six-membered rings, thereby pointing to a supramolecular organization. Three different models of cross-condensation and chain growth are suggested. These synthetic explorations provide further insights into the formation of complex organic matter in interstellar scenarios and extraterrestrial bodies that might have played a pivotal role in chemical evolution.

On the Plausibility of Pseudosugar Formation in Cometary Ices and Oxygen-rich Tholins.

We revisit herein the formation and structure of dihydroxy dioxanes, which can be obtained from prebiotically available precursors and can be regarded as primeval sugar surrogates. Previous studies dealing with the heterogeneous composition of interstellar bodies point to the existence of significant amounts of small polyalcohols along with oxygen-containing oligomers. Even though such derivatives did not give rise to nucleosides and oligonucleotides, nor they were incorporated into subsequent metabolic routes, molecular chimeras based on sugar-like species could be opportunistic scaffolds in pre-evolutionary scenarios. We could figure out that pseudosugars, assembled by hemiacetalic bonds from available precursors in both interstellar and terrestrial scenarios, were presumably more abundant than thought. Moreover, these species share some key features with naturally-occurring sugar rings, such as anomeric preferences, coordinating ability, and the prevalent occurrence of racemic compounds.

Rethinking aromaticity in H-bonded systems. Caveats for transition structures involving hydrogen transfer and π-delocalization.

Monoaza- and diaza-derivatives of malondialdehydes, in short aminoacroleins and vinamidines, are prototypical examples of open-chain structures prone to π-electron delocalization, for which intramolecular hydrogen bonding enhances (or diminishes) their pseudoaromaticity depending on the substitution pattern. This interplay is illustrated herein by DFT-based calculations of aromaticity indices in the gas phase and polar solvents. Elucidation of transition structures involved in tautomeric conversions helps to solve how the intramolecular hydrogen transfer occurs. While TSs exhibit a high degree of aromaticity, the dichotomy between forward and backward pathways points to a complex trajectory. Addition of thermal corrections to the electronic energy decreases both the enthalpy and free energy leading to negative ΔH(‡) and ΔG(‡) values. This variational effect accounts for the otherwise elusive distinction between transition structures and saddle points (usually overlooked for high electronic barriers). Also, this rationale fits well within the framework of Marcus' theory.

Yeast polypeptide exit tunnel ribosomal proteins L17, L35 and L37 are necessary to recruit late-assembling factors required for 27SB pre-rRNA processing.

Ribosome synthesis involves the coordinated folding and processing of pre-rRNAs with assembly of ribosomal proteins. In eukaryotes, these events are facilitated by trans-acting factors that propel ribosome maturation from the nucleolus to the cytoplasm. However, there is a gap in understanding how ribosomal proteins configure pre-ribosomes in vivo to enable processing to occur. Here, we have examined the role of adjacent yeast r-proteins L17, L35 and L37 in folding and processing of pre-rRNAs, and binding of other proteins within assembling ribosomes. These three essential ribosomal proteins, which surround the polypeptide exit tunnel, are required for 60S subunit formation as a consequence of their role in removal of the ITS2 spacer from 27SB pre-rRNA. L17-, L35- and L37-depleted cells exhibit turnover of aberrant pre-60S assembly intermediates. Although the structure of ITS2 does not appear to be grossly affected in their absence, these three ribosomal proteins are necessary for efficient recruitment of factors required for 27SB pre-rRNA processing, namely, Nsa2 and Nog2, which associate with pre-60S ribosomal particles containing 27SB pre-rRNAs. Altogether, these data support that L17, L35 and L37 are specifically required for a recruiting step immediately preceding removal of ITS2.

Yeast ribosomal protein L7 and its homologue Rlp7 are simultaneously present at distinct sites on pre-60S ribosomal particles.

Ribosome biogenesis requires >300 assembly factors in Saccharomyces cerevisiae. Ribosome assembly factors Imp3, Mrt4, Rlp7 and Rlp24 have sequence similarity to ribosomal proteins S9, P0, L7 and L24, suggesting that these pre-ribosomal factors could be placeholders that prevent premature assembly of the corresponding ribosomal proteins to nascent ribosomes. However, we found L7 to be a highly specific component of Rlp7-associated complexes, revealing that the two proteins can bind simultaneously to pre-ribosomal particles. Cross-linking and cDNA analysis experiments showed that Rlp7 binds to the ITS2 region of 27S pre-rRNAs, at two sites, in helix III and in a region adjacent to the pre-rRNA processing sites C1 and E. However, L7 binds to mature 25S and 5S rRNAs and cross-linked predominantly to helix ES7(L)b within 25S rRNA. Thus, despite their predicted structural similarity, our data show that Rlp7 and L7 clearly bind at different positions on the same pre-60S particles. Our results also suggest that Rlp7 facilitates the formation of the hairpin structure of ITS2 during 60S ribosomal subunit maturation.

Stepwise formation of 1,3-diazolium-4-thiolates by münchnone cycloadditions: promising candidates for nonlinear optics.

An improved preparation of mesoionic heterocycles 1,3-diazolium-4-thiolates by [3 + 2] cycloadditions of münchnones with aryl isothiocyanates is reported. The process takes place with high or complete regioselectivity, and fast and clean transformations are observed under microwave heating in DMF. DFT calculations support that this cycloaddition proceeds preferably through a stepwise mechanism. Given the pattern substitution around the mesoionic ring resulting in a push-pull system, theoretical estimations predict large hyperpolarizabilities in some cases, which is typical of molecules exhibiting nonlinear optical responses.

Pseudo-cyclic structures of mono- and di-azaderivatives of malondialdehydes. Synthesis and conformational disentanglement by computational analyses.

Mono- and diaza-derivatives of malondialdehydes, namely 3-alkyl(aryl)amino-2-arylacroleins and 1,5-dialkyl(aryl)-3-arylvinamidines are open-chain systems in which extended electron delocalization and pseudoaromaticity can be envisaged. A set of diversely functionalized compounds has been synthesized and characterized by spectroscopic data and X-ray diffractometry. Quantum-chemical calculations were performed for all possible neutral tautomers and conformers in the gas phase and compared to those in polar solvents (CHCl3, DMSO, and EtOH) at the M06-2X/6-311++G(d,p) level. Tautomeric equilibria and conformational preferences can be rationalized in terms of structural factors, which can be roughly estimated as summation or subtractions of intramolecular interactions. As expected, a key role is played by intramolecular hydrogen bonds whose strength varies from the gas phase to polar ethanol. This issue also delves into the concept of resonance-assisted H-bond, where the donor and acceptor atoms are connected by a π-conjugated system. The most stable conformers (structures a and c) possess a high degree of pseudoaromaticity as inferred from HOMA indexes and other delocalization parameters.

A new series of acylhydrazones derived from metribuzin with modulated herbicidal activity.

This paper reports the preparation and herbicidal evaluation of a small library of acylhydrazones based on the synthetic herbicide metribuzin. The hydrazone linkage easily obtained by reaction of metribuzin with aliphatic and aromatic aldehydes, masks efficiently the exocyclic amino group, thereby altering significantly H-bonding with the receptor and increasing the lipophilicity relative to the parent herbicide. The structures of all compounds, including key stereochemical issues on conformation and E/Z configuration around the C[bond, double bond]N bond were thoroughly elucidated by spectroscopic methods, and unambiguously corroborated by X-ray diffraction analysis. The herbicidal assays using an aliphatic and an aromatic acylhydrazone were performed on tomato and rapeseed plants grown in greenhouse. Our results demonstrate, regardless of rate application, that such acylhydrazone formulations do not alter the selectivity of metribuzin. Moreover, the herbicide activity was even higher in the alkyl derivative than that achieved by commercial metribuzin, thus suggesting that this substance can be applied with no need of combination with chemical coadjuvants, unlike most formulations of commercially available herbicides. Therefore, the study shows the promising effect of chemical derivatization of a common herbicide as metribuzin, to improve the herbicide activity without compromising selectivity, and allowing the farmers its use in crop protection safely and effectively.

On the prebiotic synthesis of D-sugars catalyzed by L-peptides: assessments from first-principles calculations.

What accounts for a particular chiral selection in the case of a few sugars of prebiotic relevance, thereby mirroring the asymmetry observed in nature? By using first-principles calculations, the generation of pentoses from glycolaldehyde (the initial product of the autocatalytic formose reaction), which has been detected in outer space), has been modeled by using L-Val-L-Val as a primeval catalyst. Our theoretical study provides insight into the mechanism of this reaction and satisfactorily explains a few key molecular events. Our rationale agrees with the reported experimental data and shows that the D-configuration is only favored for ribose. L-pentoses are usually favored in the presence of L-configured dipeptides, as observed experimentally, although no chiral selection could be observed in the case of xylose. These results confirm that a prebiotic sugar soup could be fine-tuned in the presence of shorter peptides as catalysts and that D-ribose would have also resulted in an advantageous imbalance for further amplification and chemical evolution.

Ribosomal protein L35 is required for 27SB pre-rRNA processing in Saccharomyces cerevisiae.

Ribosome synthesis involves the concomitance of pre-rRNA processing and ribosomal protein assembly. In eukaryotes, this is a complex process that requires the participation of specific sequences and structures within the pre-rRNAs, at least 200 trans-acting factors and the ribosomal proteins. There is little information on the function of individual 60S ribosomal proteins in ribosome synthesis. Herein, we have analysed the contribution of ribosomal protein L35 in ribosome biogenesis. In vivo depletion of L35 results in a deficit in 60S ribosomal subunits and the appearance of half-mer polysomes. Pulse-chase, northern hybridization and primer extension analyses show that processing of the 27SB to 7S pre-rRNAs is strongly delayed upon L35 depletion. Most likely as a consequence of this, release of pre-60S ribosomal particles from the nucleolus to the nucleoplasm is also blocked. Deletion of RPL35A leads to similar although less pronounced phenotypes. Moreover, we show that L35 assembles in the nucleolus and binds to early pre-60S ribosomal particles. Finally, flow cytometry analysis indicated that L35-depleted cells mildly delay the G1 phase of the cell cycle. We conclude that L35 assembly is a prerequisite for the efficient cleavage of the internal transcribed spacer 2 at site C(2).

On the enhanced reactivity and selectivity of triazole formation in molecular flasks. A theoretical rationale.

The azide-alkyne cycloaddition assisted by a self-assembled molecular flask developed by Rebek and coworkers (Org. Lett., 2002, 4, 327) has been simulated by means of the ONIOM methodology, thereby evidencing the reliability of this theoretical approach to model such large encapsulated systems. Experimental evidences accounting for this transformation within the supramolecular assembly such as the significant rate enhancement, complete regioselectivity, and product inhibition as the reaction proceeds have been qualitatively disentangled through estimation of the energy barriers and the structural characteristics of the corresponding host-guest complexes.

Assessing the whole range of CuAAC mechanisms by DFT calculations--on the intermediacy of copper acetylides.

The archetypal Cu(I)-catalyzed alkyne-azide click cycloaddition (CuAAC) has been explored thoroughly via density functional calculations, modeling copper nuclei with the LANL2DZ basis set and aqueous environments with CPCM solvation. All the mechanistic proposals, ranging from the intermediacy of copper acetylides to π-complexes and multinuclear clusters have been compared. The known features of the CuAAC reaction such as the observed second order kinetics for the Cu(I) species and the marked regioselectivity have been taken into account. The calculated energy barriers point to the intermediacy of copper(i) acetylides with two metal centers, in agreement with the observed kinetics, which exhibit barriers of 10.1 kcal mol(-1) and 13.7 kcal mol(-1) for the 1,4- and 1,5-regiochemistries, respectively, thus accounting for the marked regioselectivity of the copper catalyzed azide-alkyne cycloaddition. The copper acetylide versus π-complexes dilemma has also been experimentally addressed through the click reaction of benzyl azide and isotopically labeled phenylacetylene. The total proton/deuterium exchange in the afforded triazole demonstrates the formation of a copper acetylide intermediate during the transformation.

Tautomerism in Schiff bases. The cases of 2-hydroxy-1-naphthaldehyde and 1-hydroxy-2-naphthaldehyde investigated in solution and the solid state.

Schiff bases derived from hydroxyl naphthaldehydes and o-substituted anilines have been prepared and their tautomerism assessed by spectroscopic, crystallographic, and computational methods. Tautomeric equilibria have also been studied and reveal in most cases a slight preference of imine tautomers in solution; a fact supported by DFT calculations in the gas phase as well as incorporating solvent effects through the SMD model. To simulate the effect exerted by the crystal lattice on tautomer stability, we have developed a computational protocol in the case of 1-tert-butyl-2-(2-hydroxy-1-naphthylmethylene)aminobenzene whose data have been obtained experimentally at 120 K. Although a rapid imine-enamine interconversion may be occurring in the solid state, the imine tautomer becomes the most stable form and the energy difference should be related to the difference in the packing of the molecules.