Stereochemical studies. XXXIV. Quantitative description of ring puckering via torsional angles. The case of six-membered rings

2,3,4,6,7,8,9,10-Octahydropyrimido[1,2-a]azepin-1-ium 2-cyano-1-(2,6-dimethylanilino)-2-(phenylsulfonyl)ethenethiolate

In the title compound, C₉H₁₇N₂⁺·C₁₇H₁₅N₂O₂S₂⁻, the Csp²—N bonds in the tetra­hydro­pyrimidine ring of the cation are delocalized. The negative charge is localized on the S atom of the thione group. Cations and anions are linked by N—H⋯S inter­molecular hydrogen bonds.

Are Isolated Nucleic Acid Bases Really Planar? A Car−Parrinello Molecular Dynamics Study

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.

Heterocyclic Analogues of Cyclohexene: Theoretical Studies of the Molecular Structures and Ring-Inversion Processes

The equilibrium geometry, ring-inversion barrier, and pathway for heterocyclic analogues of cyclohexene have been studied using the MP2/6-311G(d,p) level of theory. It is concluded that the replacement of one methylene group in cyclohexene by heteroatom results in significant changes in the character of the potential-energy surface in comparison with cyclohexene. The equilibrium conformation of ring strongly depends on the position of the heteroatom due to the existence of the n-pi conjugation. However, the character of the ring-inversion process is determined by the nature of the heteroatom. In the case of sulfur- and selenium-containing rings, the boat or twist-boat conformation corresponds to an additional minimum on the potential-energy surface. Moreover, the barriers of the conformational transition from this conformer to two different half-chair forms are significantly different. Nitrogen-containing heterocycles possess two pairs of minima corresponding to the different configurations of the nitrogen atom. However, the transition between the two minima with the same configuration of the heteroatom proceeds only in two steps that include ring inversion and nitrogen inversion.

5-Cinnamoyl- and 5-(Ethoxycarbonyl)-6-styryl Derivatives of 4-Aryl-3,4-dihydropyrimidin-2(1H)-ones

Several 5-cinnamoyl- and 5-(ethoxycarbonyl)-6-styryl derivatives of 4-aryl-3,4-dihydropyrimidin-2(1H)-ones were obtained and their physicochemical properties were investigated. The introduction of alkyl substituent in position 1 of dihydropyrimidine ring was shown to promote the Claisen-Schmidt reaction on acetyl group only; without the alkyl both acetyl and 6-methyl groups participate in the reaction.