2-Methylthio-imidazolins: a rare case of different tautomeric forms in solid state and in solution

Structural Chemistry - The synthesis and structure elucidation of two new compounds, 2-(methylthio)-1,3-diazaspiro[4.4]non-2-ene-4-one (1) and 2-(methylthio)-1,3-diazaspiro[4.4]non-2-ene-4-thione...     

Two similar dibenzo cyclic ethers with dissimilar conformations

Two dibenzo cyclic ether compounds, 6,12‐dibromodibenzo[d,i]‐1,2,3,6,7,8‐hexahydro‐1,3‐dioxecin (systematic name: 8,16‐dibromo‐2,4‐dioxatricyclo[12.4.0.0^5,10]octadeca‐5,7,9,14,16,18‐hexaene), C₁₆H₁₄Br₂O₂, (II), and 8,14‐dibromodibenzo[f,k]‐1,5‐dioxa‐1,2,3,4,5,8,9,10‐octahydrocyclododecene (systematic name: 7,19‐dibromo‐11,15‐dioxatricyclo[14.4.0.0^5,10]icosa‐5,7,9,16,18,20‐hexaene), C₁₈H₁₈Br₂O₂, (III), were prepared as scaffolding for phosphate‐anion receptors. In both compounds, the two aromatic rings are linked by three methylene units ortho to the oxygen substituent of each ring. The only difference between the two compounds is the number of methylene units linking the two ether O atoms. The dibenzo cyclic ether with an ether linkage of one methylene unit adopts a chair‐like conformation, where the two aromatic rings are parallel to each other. On the other hand, the dibenzo cyclic ether with an oxygen linkage of three methylene units adopts a bowl‐like conformation. The latter scaffold configuration is the only structure of the two that would allow for the placement of convergent functional groups necessary for the establishment of an anion‐selective binding pocket.     

Molecular surface-volume and property matching to superpose flexible dissimilar molecules

Summary Steric complementarity is a prerequisite for ligand-receptor recognition; this implies that drugs with a common receptor binding site should possess sterically similar binding surfaces. This principle is used as the basis for an automatic and unbiased method that superposes molecules. One molecule is rotated and translated to maximize the overlap between the two molecular surface volumes. A fast grid-based method is used to determine the extent of this overlap, and this is optimized using simulated annealing. Matches with high steric similarity scores are then sorted on the basis of both hydrogen-bond and electrostatic similarity between the matched molecules. Flexible molecules are treated as a set of rigid representative conformers. The algorithm has correctly predicted superpositions between a number of pairs of molecules, according to crystallographic data from ligands that have been co-crystallized at common enzyme binding sites.     

Two dimeric CuII benzoate derivatives solvated with aceto­nitrile

The title compounds, tetrakis(μ‐benzoato‐O:O′)­bis(2,6‐di­amino­pyridine)‐1κN,2κN‐dicopper(II)–aceto­nitrile (1/2), [Cu₂(C₇H₅O₂)₄(C₅H₇N₃)₂]·2C₂H₃N, (I), and bis­(aceto­nitrile)‐1κN,2κN‐tetrakis(μ‐benzoato‐O:O′)­dicopper(II)–aceto­nitrile (1/1.5), [Cu₂(C₇H₅O₂)₄(C₂H₃N)₂]·1.5C₂H₃N, (II), crystallize as aceto­nitrile solvates exhibiting different stability. They have similar molecular structures with discrete dimeric units located at crystallographic inversion centres. The copper ions are bridged by four benzoate groups and neutral N‐donor ligands, viz. 2,6‐di­amino­pyridine in (I) and aceto­nitrile in (II), are coordinated at apical positions. The diverse stability is probably due to hydrogen‐bond interactions of the solvated aceto­nitrile mol­ecules with neighbouring dimers in compound (I).     

Two new dimeric naphthoquinones with neuraminidase inhibitory activity from Lithospermum erythrorhizon

The crude methanol extract of roots of Lithospermum erythrorhizon was subjected to successive chromatographic fractionation which afforded two new dimeric naphthoquinone derivatives shikometabolin E (2) and shikometabolin F (3) as well as one known compound shikometabolin A (1). The structures of compounds 1–3 were elucidated by using UV, MS, 1D and 2D NMR spectroscopic analysis. The two new dimeric naphthoquinone derivatives showed significant neuraminidase inhibitory activities.     

A semiempirical SCF-MO study of the tautomeric forms of 3-acetyl tetronic- and tetramic acids

Summary A number of tautomeric geometries of 3-acetyl tetramic acid and 3-acetyl tetronic acid were examined using the AM1 and PM3 methods. The results are compared with experimental data and with studies using MNDO and older methods, with the conclusion that both AM1 and PM3 provide satisfactory models of the behaviour of these species.     

Gas-phase tautomeric equilibrium of 4-hydroxypyrimidine with its ketonic forms: a free jet millimeterwave spectroscopy study

4-Hydroxypyrimidine (4HP) has two conformational forms (the hydroxyl hydrogen cis or trans with respect to the adjacent nitrogen), which are in tautomeric equilibrium with two ketonic forms, 4-pyrimidinone (4PO) and 6-pyrimidinone (6PO). We have investigated the free jet absorption millimeterwave spectrum of this system, assigning the rotational spectra of 4HPcis and 4PO; the latter species is more stable by 2.0(9) kJ/mol. No lines corresponding to the trans isomer of 4-hydroxypyridine and to 6PO have been observed.     

Two tautomeric forms of 2‐amino‐5,6‐dimethylpyrimidin‐4‐one

Derivatives of 4‐hydroxypyrimidine are an important class of biomolecules. These compounds can undergo keto–enol tautomerization in solution, though a search of the Cambridge Structural Database shows a strong bias toward the 3H‐keto tautomer in the solid state. Recrystallization of 2‐amino‐5,6‐dimethyl‐4‐hydroxypyrimidine, C₆H₉N₃O, from aqueous solution yielded triclinic crystals of the 1H‐keto tautomer, denoted form (I). Though not apparent in the X‐ray data, the IR spectrum suggests that small amounts of the 4‐hydroxy tautomer are also present in the crystal. Monoclinic crystals of form (II), comprised of a 1:1 ratio of both the 1H‐keto and the 3H‐keto tautomers, were obtained from aqueous solutions containing uric acid. Forms (I) and (II) exhibit one‐dimensional and three‐dimensional hydrogen‐bonding motifs, respectively.     

A comprehensive conformational analysis of tryptophan,its ionic and dimeric forms

Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan ( W ) and its ionized counterparts cations (WC) , anions (WA) , and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH‐π, NH‐π, CH‐π, CH‐O, and π‐π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH‐O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T‐shaped orientations (CH‐π interactions) are more prevalent, while stacked orientations (π‐π interactions) are predominant at a smaller distance. © 2013 Wiley Periodicals, Inc.     

Two forms of complexes of heteroonium salts with amines

Heteroonium salts form molecular compounds of two forms with amines: true complexes (charge-transfer complexes) and complexes with a localized bond between the components.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 663–667, May, 1973.     

Theoretical and experimental study of the vertical excitation energies in the ionic and tautomeric forms of 4-aminomethylpyridine

4-Aminomethylpyridine (4-PAM) has been widely used as a model compound to elucidate the mechanisms of biological and biomedical action of the amino derivatives of vitamin B₆. By virtue of the presence of two ionizable groups (viz. a pyridine nitrogen and an amino function) in its structure, 4-PAM in solution occurs as various ionic and tautomeric forms in equilibrium. In this work, we optimized the geometries of such forms and found the protonation status of the ionizable groups in 4-PAM to affect the molecular geometry and frontier orbitals. In addition, we determined the experimental electronic excitation energies for each molecular species of 4-PAM from deconvoluted UV–vis spectra. The results thus obtained were compared with their theoretical counterparts as determined from TD-DFT calculations. Based on the outcome, the theoretical methodology used affords correct simulation of electronic excitation energies. The theoretical and experimental results showed that the deprotonation of the pyridine nitrogen has no effect on the energy of the first electronic transition, however it affects its intensity. Additionally, the deprotonation of both pyridine nitrogen and methylamino group increases the number of bands, by increasing the n–π^* transitions.     

High pressure investigations of the photo-stimulated orientational ordering transition in a liquid crystal with photoactive dimeric molecules

High pressure investigations have been carried out on the photo-stimulated phase transition exhibited by a guest–host system, where the host is a non-photoactive liquid crystal. As guest molecules we chose successive homologues of a dimeric photoactive azobenzene liquid crystalline molecule to understand the influence of the length and parity of the alkylene spacer on such a transition. Our studies show that application of pressure as well as the parity of the spacer has a drastic influence both on the static and dynamic characters of the photo-stimulated phase transition.     

Identification of derivatives of 2H-chromenes and their acyclic tautomeric forms in the gas phase by mass spectrometry

It was established that mass spectrometry makes it possible to identify in the gas phase molecular ions with both the 2H-chromene structure and their acyclic tautomers from the characteristic (M-OH)⁺ and (M-ArNH)⁺ fragment ions, respectively. The fragmentation scheme was confirmed by methods involving dissociation of ions activated by collision and deuterium labeling. Measurement of the ionization energies of the investigated compounds makes it possible to exclude the possibility of the existence in the gas phase of a tautomeric form with an o-quinoid structure.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 6, pp. 746–750, June, 1988.     

Quantum-chemical calculations of the tautomeric forms of azo derivatives of acetylacetone and determination of the stability constants of their complexes with rare-earth metals

The effective atomic charges in the tautomeric forms (enol-azo, keto-azo, and hydrazo) of 3-(2-hydroxy-5-nitro-3-sulfophenylazo)pentane-2,4-dione (L¹), 3-(2-hydroxy-3,5-disulfophenylazo)pentane-2,4-dione (L²), 3-(5-chloro-2-hydroxy-3-sulfophenylazo)pentane-2,4-dione (L³), 3-(2-hydroxy-4-nitrophenylazo)pentane-2,4-dione (L⁴), and 3-(2-hydroxyphenylazo)pentane-2,4-dione (L⁵) were calculated by the Hückel method (MO LCAO). It was found that the hydrazo form is most reactive for meta- and meta’-substituted derivatives (L^1–3) and the keto-azo form is most reactive for para-substituted (L⁴) and unsubstituted ones (L⁵). The stability constants of complexes of rare-earth metals (La, Ce, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) with L^1–5 determined by potentiometric titration decrease in the order: Lu > Yb > Tm > Er > Ho > Dy > Tb > Gd > Eu > Sm > Nd > Ce > La. Functionalization of the aromatic part of ligands L affected neither the rare-earth metal: L ratio (1: 2) nor the above order of the stability constants.     

Structure of zinc complexes with 3-(pyridin-2-yl)-5-(arylideneiminophenyl)-1H-1,2,4-triazoles in different tautomeric forms: DFT and QTAIM study

On the basis of X-ray crystallographic data on molecular crystals of zinc complexes with 3-(pyridin-2-yl)-5-(arylideneiminophenyl)-1H-1,2,4-triazoles, quantum-chemical analysis of the electron density distribution function for these complexes has been performed by Bader’s atoms in molecules method. Topological parameters of electron density at the critical points of coordination and noncovalent bonds have been interpreted, and the bond energies have been estimated using the Espinosa equation. For the solvated complex Zn[(L3)(OAc)₂] · i-PrOH (L3 = 3-(pyridin-2-yl)-5-(benzylideneiminophenyl)-1H-1,2,4-triazole), a variable coordination number of the Zn²⁺ ion has been predicted as a result of dynamic dissociation/formation of an unstable Zn-O coordination bond. For the binuclear [Zn₂(L2)₂] complex (L2 = 3-(pyridin-2-yl)-5-(salicylideneiminophenyl)-1H-1,2,4-triazole), an orbital interpretation of the decrease in the fluorescence quantum yield in tetrahydrofuran and dimethyl sulfoxide as compared with free L2 ligand is presented.     

Chemiluminescence change of polyphenol dendrimers with different core molecules

Second generation polyphenol dendrimers (PDs) with different core molecules were synthesized, and their chemiluminescence (CL) was measured by reacting the PDs with H2O2 under alkaline conditions. All of the PDs showed a strong CL, more than 120-fold greater than that of gallic acid. Various CL intensities of the PDs were obtained using different core molecules in the PDs. The distance between each dendron in the PD structure is crucial in the PD CL intensity.