Synthesis of Pyrimidines and Triazines in Ice: Implications for the Prebiotic Chemistry of Nucleobases

From urea to nucleobases : Freeze–thaw cycles in urea ( 1 ) solutions under methane/nitrogen atmospheres lead, with application of an energy source, to the synthesis of pyrimidines (mainly cytosine ( 2 ) and uracil ( 3 )), triazines (such as cyanuric acid ( 4 )), and adenine. This synthesis appears to be dependent on the atmosphere and the freezing conditions. At room temperature, hydantoin ( 5 ) is obtained. However, a freezing urea/water system subjected to an energy source under an inert atmosphere generates s‐triazines.

     

Synthesis and Crystal Structures of the Five-Coordinate Diorganotin(IV) Complex [Ph<Subscript>2</Subscript>Sn(L)]·DMF and its 5-Hydroxypyrazoline Ligand (H<Subscript>2</Subscript>L)

Abstract  

A five-coordinate diorganotin(IV) complex [Ph₂Sn(L)]·DMF and its ligand, 5-hydroxy-3-methyl-5-phenyl-(N ⁴-phenylthiosemicarbazone)pyrazoline (H₂L), were synthesized and characterized by elemental analysis, IR, NMR (¹H, ¹³C) spectroscopies and X-ray crystallography techniques. Our studies revealed that H₂L has formed as 5-hydroxy-4,5-dihydropyrazoline derivative in orthorhombic, Pbca space group with a = 15.4330(3) ?, b = 11.5427(2) ?, c = 18.1440(3) ? whereas [Ph₂Sn(L)]·DMF crystallizes with two independent molecules (a and b) in the asymmetric unit in triclinic system, Pī space group with a = 9.2795(1) ?, b = 15.8315(2) ?, c = 19.9895(3) ?, α = 100.855(1)°, β = 92.985(1)°, γ = 102.243(1)°. In molecule a, the central Sn(IV) atom adopts a distorted tetragonal–pyramidal (TTP) geometry with N2 atom at apical position, while in molecule b the Sn(IV) occupies the centre of a trigonal-bipyramid (TBP) with N2 atom of the ONS-tridentate ligand and both Ph groups occupying equatorial positions. One molecule of DMF (crystallization solvent) helps in stabilizing the crystal structure.     

Synthesis and Molecular Structure Investigation by DFT and X-Ray Diffraction of ARNO

Abstract  

We report here the synthesis of (Z)-5-(4-nitrobenzyliden)-3-N(2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one (ARNO) compound. The crystal structure has been determined by X-ray diffraction. The compound crystallizes in the triclinic system with space group P[`1] P\bar{1} and cell parameters: a = 9.1289(19), b = 9.3717(7), c = 12.136(3) ?, α = 102.133(11)°, β = 90.99(2)°, γ = 117.165(9)°, V = 895.4(3) ?³ and Z = 2. The structure has been refined to a final R = 0.05 for 2591 observed reflections. The refined structure was found to be significantly non planar. The molecule exhibits intermolecular hydrogen bond of type C–H⋯O and C–H⋯S. ab initio calculations were also were performed at Hartree–Fock and density functional theory levels. The full HF and DFT geometry optimization was carried out using LANL2DZ, 6-31G* and B3LYP/6-31+G** basis sets. The optimized geometry of the title compound was found to be consistent structure determined by X-ray diffraction. The minimum energy of geometrical structure is obtained by using level HF/LANL2DZ basis sets.     

Distonoid ions

By Yates, Bouma, and Radom's definition, distonic radical ions are those formally arising by ionization of diradicals or zwitterionic molecules (including ylides). These ions differ, therefore, from conventional radical ions by displaying the charge site and unpaired electron site (spin) localized mandatorily on separate atoms or group of atoms; that is, these sites are separated in all of their major resonance forms. Many conventional radical ions with a major resonance form in which charge and spin sites reside formally on the same atom or group of atoms display, however, high degree of discretionary (non-mandatory) charge-spin separation. By analogy with the metal/metalloid terminology, we propose that these distonic-like radical ions be classified as distonoid ions. Radical ions would, therefore, be divided into three sub-classes: conventional, distonic, and distonoid ions. B3LYP/6-311 + G(d,p) calculations for a proof-of-principle set of radical cations are used to demonstrate the existence of many types of distonoid ions with a high degree of discretionary charge-spin separation. Reliable calculations are indispensable for probing distonoid ions, since an ion that was expected to be distonoid (by the analysis of its resonance forms) is shown by the calculations to display a characteristic conventional-ion electronic distribution. Similarly to many distonic radical ions, and in sharp contrast to a conventional radical ion (ionized 1,4-dioxane), the gas-phase intrinsic bimolecular reactivity with selective neutrals of a representative distonoid ion, ionized 2-methylene 1,3-dioxolane, is found to include dual ion-radical type reactions.     

Electrophilic aromatic nitration: understanding its mechanism and substituent effects

Theoretical calculations and gas-phase mass spectrometric studies were performed for the reaction of the naked (NO2+) and monosolvated (CH3NO2.NO2+) nitronium ion with several monosubstituted aromatic compounds. From these studies, we propose a general model for regioselectivity based on the single-electron transfer (SET) mechanism and an alternative mechanistic scheme for electrophilic aromatic nitration. This scheme considers the SET and the polar (Ingold-Hughes) mechanisms as extremes in a continuum pathway, the occurrence and extents of both mechanisms being governed mainly by the ability, or lack of ability, of the aromatic compound to transfer an electron to NO2+.     

Imbibition, desiccation and mechanical deformations of zein pills in relation to their porosity

This paper deals with the interaction between zein (the main protein component of corn grain) and water. It induces macroscopic properties changes and may allow for the understanding of the basis of zein endosperm structure: vitreous endosperm is compact and floury endosperm is porous, giving the endosperm its hard and soft textures, respectively. In that aim porous pills made by compaction of zein powder submitted to different hydration/dehydration processes have been prepared and studied. In particular, imbibition measurements of a pure-water drop deposited onto a zein pill were performed. Also, desiccation of a zein pill previously imbibed induces strong mechanical stresses leading to crack formation and/or large deformations.     

Absolute configuration of strictosidinic acid

The absolute configuration of strictosidinic acid, (2S,3R,4S)‐3‐ethenyl‐2‐(β‐d ‐glucopyranosyloxy)‐4‐{[(1S)‐2,3,4,9‐tetrahydro‐1H‐pyrido[3,4‐b]indol‐1‐yl]methyl}‐3,4‐dihydro‐2H‐pyran‐5‐carboxylate, was determined from its sodium chloride trihydrate, poly[[diaqua((2S,3R,4S)‐3‐ethenyl‐2‐(β‐d ‐glucopyranosyloxy)‐4‐{[(1S)‐2,3,4,9‐tetrahydro‐1H‐pyrido[3,4‐b]indol‐2‐ium‐1‐yl]methyl}‐3,4‐dihydro‐2H‐pyran‐5‐carboxylate)sodium] chloride monohydrate], {[Na(C₂₆H₃₂N₂O₉)(H₂O)₂]Cl·H₂O}_n. The strictosidinic acid molecule participates in intermolecular hydrogen bonds of the O—H...O and O—H...Cl types. The solid‐state conformation was observed as a zwitterion, based on a charged pyridine N atom and a carboxylate group, the latter mediating the packing through coordination with the sodium cation.     

Analysis of Bile Acids Profile in Human Serum by Ultrafiltration Clean-up and LC-MS/MS

Bile acids (BAs) are useful biomarkers for the diagnosis of many diseases. The pathologies related to bile acid synthesis are often expressed in the first years of life and may lead to serious liver injury. Here we present a sensitive and rapid method for the analysis of the main 14 bile acids in human serum by liquid chromatography-tandem mass spectrometry. The chromatographic separation is performed using a core–shell column which provides improved separation, highly desirable considering the small structural differences among the analytes. All isomeric BAs of interest were resolved in less than 9 min. Sample pretreatment consisted in ultrafiltration of serum after addition of methanol by means of centrifugal filter devices. The calculated LOQs ranged between 2 and 5 ng mL⁻¹ with linearity of the calibration curves in the 5–5,000 ng mL⁻¹ range for all the BAs. The extraction recoveries for all the analytes were higher than 80 %. Intra-day and inter-day coefficients of variation were all below 15 %. The method proposed has been validated and has been applied for the analysis of serum of pediatric patients. This simple procedure allowed minimal consumption of serum sample (about 100 μL) and a rapid assay, easily implementable in routine analysis.

     

Von Willebrand Factor Multimers and the Relaxation Response: A One-Year Study

Background and aim: Mental stress represents a pivotal factor in cardiovascular diseases. The mechanism by which stress produces its deleterious ischemic effects is still under study but some of the most explored pathways are inflammation, endothelial function and balancing of the thrombotic state. In this scenario, von Willebrand factor (vWF) is a plasma glycoprotein best known for its crucial hemostatic role, also acting as key regulatory element of inflammation, being released by the activated vascular endothelium. Antistress techniques seem to be able to slow down inflammation. As we have recently verified how the practice of the Relaxation Response (RR), which counteracts psychological stress, causes favorable changes in some inflammatory genes’ expressions, neurotransmitters, hormones, cytokines and inflammatory circulating microRNAs with coronary endothelial function improvement, we aimed to verify a possible change even in serum levels of vWF. Experimental procedure: We measured vWF multimers and the total protein carbonyl contents in the sera of 90 patients with ischemic heart disease (and 30 healthy controls) immediately before and after an RR session, three times (baseline, 6 months, 12 months), during a one-year follow-up study. Results: According to our data, large vWF multimers decrease during the RR, as does the plasma total carbonyl content. Conclusion: vWF levels seem to vary rapidly between anti-inflammatory and antithrombotic behaviors dependent on psychological activity, leading to relaxation and also possibly changes in its quaternary structure.