Conformational analysis of 5,6-dihydropyrimidine and its derivatives

The equilibrium geometry and inversion barriers of 5,6-dihydropyrimidine, 6,7-dihydroazolopyrimidines with node nitrogen atoms and their alkyl (Me, Et, Prⁱ, Bu^t) and phenyl derivatives were calculated using a molecular mechanics approach. Annelation with azole cycles and the introduction of substituents have a slight effect on the equilibrium conformation of the dihydrocycle (distorted sofa). Alkyl substutuents at saturated carbons have an essentially equatorial orientation in 5,6-dihydropyridimine derivatives and are axial in the annelated analogs. On the other hand, the equatorial conformers are more stable in phenyl derivatives of dihydroazolopyrimidines. Factors determining the relative stability of conformers were analyzed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 487–491, March, 1995.     

Conformational analysis of 3,4-dihydropyridine and its alkyl derivatives

The geometry of dihydropyridine and its alkyl derivatives was studied by the molecular mechanics method. The dihydrocycle was found to be mobile; however, substituents exert little effect on its distorted sofa conformation. The alkyl groups attached to the saturated carbon atoms occupy pseudo-equatorial position in monosubstituted and pseudo-axial positions in disubstituted 3,4-dihydropyridines. Unusually high barriers to inversion of the dihydrocycle were observed incis-3,4-dialkyl-3,4-dihydropyridines caused by the eclipse of the substituents in the transition state.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1009–1012, June, 1994.     

Conformational analysis of sesquiterpene lactones of the germacrane type 1. 1(10)E,4E-Germacranolides

The structure of 1(10)E,4E-germacranolides was studied by a molecular mechanics method. Possible conformers, the probabilities of their occurrence, and the barriers to conformational transitions were determined.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No, 12, pp, 2890–2893, December, 1996.     

Conformational analysis of 2-oxo-1,2,3,4,-tetrahydropyridine and its alkyl- and phenyl-substituted derivatives

The molecular geometries and inversion barriers of the rings in 2-oxo-1,2,3,4-tetrahydropyridine and its alkyl-substituted (Me, Et, Prⁱ, or Bu^t) and phenyl-substituted derivatives were calculated by the molecular mechanics method. The introduction of substituents has no substantial effect on the equilibrium conformation of the heterocycle (a distorted sofa). For 4-alkyl- and 3-alkyl-substituted derivatives (except for 4-Me and 4-Et derivatives), an axial orientation of the alkyl group is more favorable. The phenyl substituents have equatorial and axial orientations at postions 4 and 3, respectively. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1584–1586, September, 1997.     

Conformational analysis and steric effects of substituents in derivatives of 3-oxo-, 3-imino-, and 3-methylenecyclohexene

The equilibrium conformations and the inversion barriers of the rings in 3-oxo-, 3-imino-, 3-methylenecyclohexenes and in their methyl,tert-butyl, and phenyl derivatives were calculated by molecular mechanics. The unsubstituted molecules adopt a sofa conformation. The nonbonded interactions between substituents at positions 2 and 4 and the exocyclic double bond lead to a change in the conformation of the ring to a half-chair. The effect is enhanced as the volume of the substituent increases in the series of the oxo, imino, and methylene derivatives. Substituents at other positions of the ring affect only slightly the equilibrium conformation. The results of calculations were confirmed by X-ray structural analysis of 2-(4-benzoyloxybenzyl)-6-isopropyl-3-methylcyclohex-2-enone. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1995–2000, November, 1997.     

Chain Conformations in the Crystalline Field of Syndiotactic Vinyl Polymers Deriving from 1,3‐Diene Monomers. Analysis by Molecular Mechanics

Summary: Conformational energy calculations on the chain conformation in the crystalline field have been performed for various syndiotactic vinyl polymers deriving from 1,3‐diene monomers. Energy maps as a function of the independent torsion angles have evidenced for all the polymers minima corresponding to highly extended and to helical chains. Energy minimizations as a function of all the internal parameters for the s(2/1)2 and t cm symmetries have allowed the evaluation of the energy differences between chains having the two symmetries and the prediction of the values of the conformational parameters for each polymer. The results have been compared with the experimental data reported in the literature for some of the studied polymers.

Conformational energy map of sPBD12.     

Configuration and conformation of alfentanil hydrochloride. Conformational study by NMR and theoretical calculations

The configurational and conformational structure of alfentanil hydrochloride (1) was studied by nuclear magnetic resonance and theoretical calculations. Compound 1 is best described by equilibrium between two stereoisomeric piperidinium rings with the N‐substituent always being in equatorial position. Nuclear magnetic resonance spectra demonstrate that, depending on the solvent, 1 adopts the conformation with an axial methoxymethylene group. Computations were crucial in determining the importance of the transannular attractive interaction between the positive charge at the piperidinium N‐atom and the methoxymethyl group in position 4. Copyright © 2014 John Wiley & Sons, Ltd.     

Conformational mobility of the six-membered ring in 5-oxo-1,3-cyclohexadiene and its derivatives

Molecular mechanics and MNDO calculations showed that the six-membered ring in the molecule of 5-oxo-1,3-cyclohexadiene possesses high conformational mobility. The transition from a planar equilibrium conformation to a distorted sofa conformation in which the C(sp²)-C(=O)-C(sp³)-C(sp²) torsion angle is equal to ±30° increases the energy of the molecule by less than 1 kcal mol^–1. The influence of steric (R = Me, Et, Prⁱ, Bu^t) and electronic (R = NH₂, NO₂) effects of substituents R on the equilibrium conformation and mobility of the carbocycle has been analyzed. Both types of substituents at unsaturated C atoms do not change the equlibrium conformation or flexibility of the six-membered ring. Substituents at saturated C atoms cause the transition of the carbocycle to the distorted sofa conformation and significantly restrict its mobility. The electronic structures of 5-oxo-1,3-cyclohexadiene and its amino and nitro derivatives have been analyzed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 849–854, May, 1995.     

Models of Adjacent Re‐Entry Folds in the β Form of Syndiotactic Polystyrene. Conformational and Packing Analysis by Molecular Mechanics

The adjacent re‐entry folds of chains of syndiotactic polystyrene crystallized in the β form have been investigated by molecular mechanics. Various models of fold of chains along bilayers have been found. The results are in agreement with the literature experimental data indicating that the fold surface is irregular. Both the conformational and the packing energy of folded chains have been minimized by various techniques using several set of potential functions. A theoretical prediction of the work of fold is given.     

The effect of substituents on the conformational mobility of the heterocycle in 1,4-dihydropyrimidine and its derivatives

The equilibrium geometry of 1,4-dihydropyrimidine, 4,7-dihydro-1,2,4-triazolo[1,5-a]pyrimidine, and their alkyl (Me, Et, Prⁱ, Bu^t) and phenyl derivatives has been calculated by molecular mechanics method. The equilibrium conformation of unsubstituted molecules is planar, but it is easily transformed to the boat conformation with a small change in the conformational energy. The effect of substituents on the geometry and conformational mobility of the dihydropyrimidine ring has been studied.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1394–1397, August, 1994.     

Pyrrolizidine alkaloids necine bases: II. Conformational analysis of free bases

Molecular mechanics calculations were applied to the conformational analysis of two diasteroisomers, the pyrrolizidine alkaloids (PAs) retronecine and heliotridine. The application of reoptimized parameters for H bonding corrected the tendency of MM3(92) calculations to give unrealistic H(DOTTED BOND)O distances for intramolecular OH interactions occurring in both diasterisomers. Inversions in the H-bond direction of exo-retronecine and in the relative stability of heliotridine endo–exo conformers were also observed with the application of the new parameters. A set of probable conformers was obtained for each diasterisomer, based on conformational and Boltzmann population analysis. Only exo-puckered conformers were found in the retronecine set, whereas both exo- and endo-puckered conformers were obtained for heliotridine. Transition state conformations supplied arguments supporting the design of models for H-bond interconversion in the case of exo-retronecine and for the exo–endo interconversion of heliotridine. Reactivity behaviors and ¹H-NMR data of both diasterisomers were elucidated in light of the theoretical results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1853–1861, 1998     

Syntheses,characterization and thermal properties of lanthanide complexes with 2-mercaptonicotinic acid

Fourteen new complexes with the general formula of Ln(Hmna)₃·nH₂O (n=2 for Ln=La-Ho and n=1 for Er-Lu, H₂mna=2-mercaptonicotinic acid) were synthesized and characterized by elemental analyses, IR spectra and thermogravimetric analyses. In addition, molar specific heat capacities were determined by a microcalorimeter at 298.15 K. The IR spectra of the prepared complexes revealed that carboxyl groups of the ligands coordinated with Ln(III) ions in bidentate chelating mode. Hydrated complexes lost water molecules during heating in one step and then the anhydrous complexes decomposed directly to oxides Ln₂O₃, CeO₂, Pr₆O₁₁ and Tb₄O₇. The values of molar specific heat capacities for fourteen solid complexes were plotted against the atomic numbers of lanthanide, which presented as ‘tripartite effect’. It suggested a certain amount of covalent character existed in the bond of Ln³⁺ and ligands, according with nephelauxetic effect of 4f electrons of rare earth ions.     

Molecular mechanics,quantum mechanics,potentiometric, and conductometric studies on the complexes of some rare earth metals with 5‐azorhodanine derivatives

The geometry of metal ions (La³⁺, Ce³⁺, UO, and Th⁴⁺) complexes with 5‐azorhodanine derivatives was optimized at the level of molecular mechanics. Two stoichiometric ratios of metal to ligand (i.e., 1:1 and 1:2) were investigated. Tetracoordinate and hexacoordinate of each stoichiometric ratio have been studied. Effect of substitution in the ligand on the geometry of the complexes was discussed in the light of electron donating–accepting properties of these substituents. The influence of the nuclear effective charge of the central metal ions on the metal–ligand (M–L) bonding was discussed and the effect of the number of ligands on the M–L bond length was also discussed and correlated to the experimental results. The total energies of the different metal complexes were computed using the extended Huckel method. The effect of substituents in ligand, metal type, and stoichiometry of the complexes on the complex total energies were discussed. Stability constant of (La³⁺, Ce³⁺, UO, and Th⁴⁺) metal ions with 5‐azorhodanine derivaties have been determined potentiometrically in 0.1 M KCl and 50% (v/v) ethanol–water mixture. The order of the stability constants of the formed complexes was found to be La³⁺ < Ce³⁺ < UO < Th⁴⁺. The influence of substituents on the stability of the complexes was examined on the basis of electron‐repelling property of the substituent. The effect of temperature on the stability of the complexes formed was studied and the corresponding thermodynamic parameters (ΔG, ΔH, and ΔS) were derived and discussed. The stoichiometries of these complexes were determined conductometrically and indicated the formation of 1:1 and 1:2 (metal:ligand) complexes. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Pyridine-type complexes of transition-metal halides. III: Structural and thermal relationships among the cobalt(II) complexes with halide ions and 2-, 3-, and 4-Methylpyridine,the crystal structure of dibromotetrakis (3-methylpyridine)cobalt(II)

The correlation between structure and thermal properties of halogeno methylpyridine cobalt(II) is described. The ternary mixed tetrakis-derivatives and the tetrahedral bis-complexes of cobalt(II) chlorides and bromides formed with picolines are structurally very similar to the cadmium(II) and nickel(II) analogues, the iodides are somewhat different, however. On the basis of the characteristic correlation between the densities calculated from powder diffraction data and the molecular weights, the densities of a few thermal intermediates, which have not yet been prepared, are predicted. The square bipyramidal structure of dibromotetrakis(3-methylpyridine)cobalt(II) is described, and the deformation of the octahedra is discussed in detail. Structural study was extended by molecular mechanics (MM+ and MMX) and molecular orbital (SINDO1) calculations.     

Novel cellulose derivatives. III. Thermal analysis of mixed esters with butyric and hexanoic acid

Cellulose derivatives with low degrees of substitution (i.e., DS < 1.5) often fail to reveal glass transition temperatures (T_g) by virtue of their tenacious adherence to moisture, thus preventing systematic analysis of substituent effects (size and DS) on T_g and T_m transitions. On the other hand, cellulose triesters have T_ms that decline with acyl substituent size except when the substituent size becomes very large (i.e., > C₆), and they have T_gs within 5–20°C of their T_ms. This proximity is unusual for a semicrystalline material, and it interferes with the crystallization process that occurs between T_m and T_g. Triesters of cellulose with mixed acyl substituents (one smaller and one larger) allow not only unambiguous observation of T_gs and T_ms but also an adjustable Δ(T_m ? T_g) window that depends upon the size and the DS of the larger substituent. The materials studied including cellulose acetate butyrate triesters (DS_bu 0.8–2.6), cellulose acetate hexanoate triesters (DS_hex 0–3.0), and cellulose acetate (DS_ac 2.44), revealed that only the mixed esters, in which the bulkier acyl group is in the range of DS 0.3–1.0, had a Δ(T_m ? T_g) value in excess of 40°C. Although the T_m of cellulose acetate hexanoate declined by ca. 150°C per unit of DS_hex as DS_hex rose from 0 to 1, this was only ca. 25°C between DS_hex of 1 and 3. Frequently observed dual-melt endotherms were attributed to two separate crystal morphologies. ©1995 John Wiley & Sons, Inc.     

The use of 3,3-bis(2-imidazolyl) propionic acid (bip-OH) as a new chelating ligand for Re(CO)3 and Ru complexes: Formation of organometallic PNA oligomers with (bip)Re(CO)3 and their interaction with complementary DNA

We report the use of 3,3-bis(2-imidazolyl) propionic acid (bip-OH, 1) as a new chelating bis(imidazole) ligand. The synthesis and full characterization of complexes Re(bip-O)(CO)₃2 and [Ru(bpy)₂(bip-OH)]²⁺3 is reported. Both complexes show interesting spectroscopic properties, namely IR for compound 2 and ¹H NMR for 3, respectively. The free carboxylic acid functionality of 1 may be used for the coupling to biomolecules. We have prepared two peptide nucleic acid (PNA) decamers to which the rhenium complex 2 is coupled. All reactions were carried out by solid phase synthesis methods. The Re-PNA oligomer conjugates Re(CO)₃(bip- tgt cta gca a -NH₂) 4 and Re(CO)₃(bip- agg agc aac t-Lys-NH₂) 5 were obtained in good yield and high purity after HPLC purification and identified by their mass spectra. The interaction of 5 with complementary DNA yields a melting temperature of (53.9 ± 1) °C. This is the first DNA melting temperature reported for an organometallic metal-PNA conjugate.     

Binding interactions of mixed ligand copper(II) amino acid Schiff base complexes with biological targets: Spectroscopic evaluation and molecular docking

Three mixed ligand copper(II) complexes [Cu(o ‐vanillin‐l ‐tryptophan Schiff base)(diimine)] (diimine =2,2′‐bipyridine ( 1 ), 1,10‐phenanthroline ( 2 ) and 5,6‐dimethyl‐1,10‐phenanthroline( 3 )) were synthesized and characterized using analytical and spectral methods. The molecular structures of 1 – 3 were optimized using density functional theory (DFT) at B3LYP/LanL2DZ levels in the gas phase. Spectral and DFT studies suggest a distorted square pyramidal geometry around the copper ion. Binding interactions of 1 – 3 with calf thymus DNA and bovine serum albumin protein were studied using UV–visible and fluorescence spectroscopies, viscometric titrations and cyclic voltammetry and also using molecular docking analysis. Studies of the binding of the complexes with calf thymus DNA reveal intercalation, which is supported by molecular docking simulation. The DNA cleavage nature of 1 – 3 with pUC19 DNA shows that the complexes can cleave DNA without any external agents, and the efficiency follows the order 1  >  3  >  2 . Synchronous and three‐dimensional fluorescence spectral studies suggest that the secondary structures of the protein are altered by the complexes. Antioxidant studies reveal that the complexes have significant radical scavenging activity against DPPH. In vitro cytotoxic activity of the complexes was evaluated against breast cancer cells (MCF‐7), revealing that complex 2 exhibits higher cytotoxicity than the other complexes. Nuclear chromatin condensation and fragmentation were observed with DAPI staining assay. The mitochondrial membrane potential damage was studied by FITC staining assay. Flow cytometric analysis suggests that all the metal complexes induce cell apoptosis.     

Synthesis and structural and DNA binding studies of mono‐ and dinuclear copper(II) complexes constructed with ─O and ─N donor ligands: Potential anti‐skin cancer drugs

Mononuclear and dinuclear copper(II) complexes with thiophenecarboxylic acid, [Cu(3‐TCA)₂(2,2′‐bpy)] ( 1 ), [Cu(3‐Me‐2‐TCA)₂(H₂O)(2,2′‐bpy)] ( 2 ), [Cu(5‐Me‐2‐TCA)₂(H₂O)(2,2′‐bpy)] ( 3 ) and [Cu₂(2,5‐TDCA)(DMF)₂(H₂O)₂(2,2′‐bpy)₂](ClO₄)₂ ( 4 ) (where 3‐TCA = 3‐thiophenecarboxylic acid; 3‐Me‐2‐TCA = 3‐methyl‐2‐thiophenecarboxylic acid; 5‐Me‐2‐TCA = 5‐methyl‐2‐thiophenecarboxylic acid; 2,5‐TDCA = thiophene‐2,5‐dicarboxylic acid; 2,2′‐bpy = 2,2′‐bipyridyl; DMF = N,N‐dimethylformamide), were synthesized. Compounds 1 – 4 were extensively characterized using both analytical and spectroscopic methods. Additionally, the solid‐state structures of 1 and 4 were unambiguously established from single‐crystal X‐ray diffraction studies. The hexacoordinated Cu(II) centre in 1 (CuO₄N₂) is a distorted octahedral geometry whereas the pentacoodinated 4 (CuO₃N₂) has distorted square pyramidal geometry. Compounds 1 and 4 exhibit intermolecular hydrogen bonding which leads to the formation of two‐ and three‐dimensional supramolecular architectures, respectively. Spectrophotometric and computational investigations suggest that these compounds bind with DNA in minor groove binding such that K_b = 4.9 × 10⁵ M^?1 and K_sv = 3.4 × 10⁵ M^?1, and binding score of ?5.26 kcal mol^?1. The binding affinity of these complexes to calf thymus DNA is in the order 2 > 3 > 4 > 1 . Methyl‐substituted thiophene ring increases the DNA binding affinity whereas unsubstituted thiophene ring DNA binding rate is reduced. The methyl group on the thiophene ring would sterically hinder π–π stacking of the ring with DNA base pairs, and subsequently they are involved in hydrophobic interaction with the DNA surface rather than partial intercalative interaction. Compounds 1 – 4 show pronounced activity against B16 mouse melanoma skin cancer cell lines as measured by MTT assay yielding IC₅₀ values in the micromolar concentration range. The compounds could prove to be efficient anti‐cancer agents, since at a concentration as low as 2.1 μg ml^?1 they exerted a significant cytotoxic effect in cancer cells whereas cell viability was not affected in normal cells.