Crystal Structure and Conformation of a 10-Thiabilirubin

 A crystal structure determination of a bilirubin analog with a sulfur instead of a C(10)–CH₂ linking the two dipyrrinones is reported. Conformation-determining torsion angles and key hydrogen bond distances and angles are compared to those obtained from molecular dynamics calculations as well as to the corresponding data from X-ray determinations and molecular dynamics calculations of bilirubin. Like other bilirubins, the component dipyrrinones of the analog are present in the bis-lactam form with (Z)-configurated double bonds at C(4) and C(15). Despite the large differences in bond lengths and angles at –S–vs.–CH₂–, the crystal structure shows considerable similarity to bilirubin: both pigments adopt a folded, intramolecularly hydrogen-bonded ridge-tile conformation stabilized by six hydrogen bonds – although the interplanar angle of the ridge-tile conformation of the title compound is smaller (∼ 86°) than that of bilirubin (∼ 98°). The collective data indicate that even with long C–S bond lengths and a smaller C–S–C bond angle at the pivot point on the ridge-tile seam, intramolecular hydrogen bonding persists.     

Crystal Structure and Conformation of a 10-Thiabilirubin

Summary.  A crystal structure determination of a bilirubin analog with a sulfur instead of a C(10)–CH₂ linking the two dipyrrinones is reported. Conformation-determining torsion angles and key hydrogen bond distances and angles are compared to those obtained from molecular dynamics calculations as well as to the corresponding data from X-ray determinations and molecular dynamics calculations of bilirubin. Like other bilirubins, the component dipyrrinones of the analog are present in the bis-lactam form with (Z)-configurated double bonds at C(4) and C(15). Despite the large differences in bond lengths and angles at –S–vs.–CH₂–, the crystal structure shows considerable similarity to bilirubin: both pigments adopt a folded, intramolecularly hydrogen-bonded ridge-tile conformation stabilized by six hydrogen bonds – although the interplanar angle of the ridge-tile conformation of the title compound is smaller (∼ 86°) than that of bilirubin (∼ 98°). The collective data indicate that even with long C–S bond lengths and a smaller C–S–C bond angle at the pivot point on the ridge-tile seam, intramolecular hydrogen bonding persists. Received August 16, 2001. Accepted September 12, 2001     

A simple procedure for estimating changes in the nuclear configuration of molecules in the excited ππ*-electronic state

A simple procedure is suggested for estimating changes in the bond lengths q and angles a between them in the excited ππ states of molecules avoiding calculations of molecular vibrations. The distances q and the angles a are estimated for the triplet state B_1u (ππ*) of the tetm-β-chlomdioxin molecule. Translated from Zhumal Struktumoi Khimii, Vol. 41, No. 1, pp. 149-156, January–February, 2000.     

Ab initio Study of Malonaldehyde Rotamers

 Malonaldehyde rotamer geometries were optimized using ab initio calculations at the HF level with STO-3G^** and 6-21G^** basis sets. The most stable rotamer is the ω-shaped one with cyclic structure and intramolecular hydrogen bond. The most unstable rotamer is that obtained by rotation of the ω-rotamer around the CO single bond by 180° due to the loss of the additional stabilization contributed by the intramolecular H-bond. The energy barriers separating the different rotamers vary between 13 and 233 kJċmol⁻¹. The structure of the transition states is non-planar with rotation angles varying between 72 and 98°.     

Ab initio Study of Malonaldehyde Rotamers

Summary.  Malonaldehyde rotamer geometries were optimized using ab initio calculations at the HF level with STO-3G^** and 6-21G^** basis sets. The most stable rotamer is the ω-shaped one with cyclic structure and intramolecular hydrogen bond. The most unstable rotamer is that obtained by rotation of the ω-rotamer around the CO single bond by 180° due to the loss of the additional stabilization contributed by the intramolecular H-bond. The energy barriers separating the different rotamers vary between 13 and 233 kJċmol⁻¹. The structure of the transition states is non-planar with rotation angles varying between 72 and 98°. Received January 18, 1999. Accepted (revised) August 4, 1999     

Molecular structure of 2-phenyl-2-selenoxo-2-phosphabicyclo[4.4.0]decan-5-one

This paper reports on an X-ray diffraction study of one of the stereoisomers of 2-phenyl-2-selenoxo-2-phosphabicyclo[4.4.0]decan-5-one. The effect of the nature of the atom (O, S, Se) on bond lengths, bond angles, and conformation parameters in the series of stereoisomer heteroanalogs is considered. Deceased. Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 3, pp. 547–553, May–June, 1997.     

Synthesis,spectroscopic, XRPD and computational study of transition metal-organic frameworks (TMOFs) derived from (6R)-6-(α-phenyl-D-glycylamino) penicillanic acid

Transition metal-organic frameworks (TMOFs) of (6R)-6-(α-phenyl-D-glycylamino) penicillanic acid (L = ligand) with Mn(II), Co(II), and Ni(II) were prepared and characterized by various physiochemical and spectroscopic measurements viz. IR, ¹H NMR, EPR, UV-vis, XRPD. Molecular modeling was also used to detect bond lengths, bond angles, atomic coordinates through molecular models. The article is published in the original.     

Three-dimensional configurations of organic/inorganic hybrid nanostructural blocks (I). A quantum mechanical investigation for ladder-like structure of vinylsilsesquioxane

Silsesquioxanes (SSO) or polyhedral oligomericsilsesquioxanes (POSS) are generally prepared frommolecular precursors using the hydrolytic condensa-tion of trialkoxysilane, RSi(OR')3. They are organic/inorganic hybrid nanostructural blocks with theircomplete general formula Tn(T = RSiO1.5, n = 1,2, …), and the incomplete generic formula is Tn-(OH)x(OR')y[x, y = 0, 1, 2, …, T= RSiO1.5 ?(x+y)/2n][1,2].Each VSSO, possessing a certain structural formulaand molecular weight, may h…     

Structural features of <Emphasis Type="Italic">N</Emphasis>-acylcytisines

N-Acyl cytisine derivatives were synthesized by acylation with acetic anhydride; benzoyl and o-bromo- and p-nitrobenzoyl chlorides; and crotonyl and cinnamoyl chlorides. The structures of the synthesized compounds were studied using IR, PMR, and x-ray structure analysis (XSA). PMR spectra of the N-acylcytisines in solution typically had two rotational isomers around the N12–CO bond. Conformational analysis was performed using XSA for the position of the acyl group relative to the cytisine core. Bond lengths and angles of the acyl groups involved in the conjugation were analyzed.     

Verification of the correlation between geometric parameters of molecules and the parameters of their 1H NMR spectra

The dihedral and bond direction angles between all pairs of vicinal protons of the arabinofuranose residue were calculated from the coordinatees of the hydrogen atoms found by an X-ray study of 3-O-acetyl-β-L -arabinofuranose 1,2,5-orthobenzoate. The values found were compared with those calculated with the help of correlation equations previously proposed by Karplus and recently by the authors, linking the values of those angles with the spin-spin coupling constants of vicinal protons [³J(H,H′)]. It has been found that the best agreement between the angles found crystallographically and calculated from the ¹H NMR data can be achieved using the equation which includes bond direction angles and the sum of the chemical shifts of the protons involved.     

Crystal structures of [Hg(<Emphasis Type="Italic">N</Emphasis>-ethylthiourea)<Subscript>2</Subscript>(CN)<Subscript>2</Subscript>] and [Hg(<Emphasis Type="Italic">N</Emphasis>-propylthiourea)<Subscript>2</Subscript>(CN)<Subscript>2</Subscript>]

Two mercury(II) cyanide complexes of N-ethylthiourea (Ettu) and N-propylthiourea (Prtu) ligands, [Hg(Ettu)₂(CN)₂] (1) and [Hg(Prtu)₂(CN)₂] (2), were prepared and their crystal structures were determined by X-ray crystallography. In both structures, the mercury atom is coordinated to two sulfur atoms of thioureas and two cyanide carbon atoms in a pseudo-tetrahedral mode with the bond angles in the range of 90.52(11)–162.2(3)°. The structures are stabilized by N-H—S, N-H—N, and C-H—N intramolecular and intermolecular hydrogen bonds.     

Structures of the racemate and (S)-enantiomer of 7,8-difluoro-3-methyl-2,3-dihydro-4H-[1,4]benzoxazine

The comparative X-ray diffraction study of racemic and (S)-enantiomer of 7,8-difluoro-3-methyl-2,3-dihydro-4H-[1,4]benzoxazine was carried out. The both forms of benzoxazine are crystallized in the orthorhombic crystal system, the (S)-enantiomer is crystallized in the chiral space group P2₁2₁2₁, while the racemate is crystallized in the centrosymmetric Pbca space group. The bond lengths and bond and torsional angles in the both molecules are almost equal. The packing of the racemate is characterized by a closer interaction of polar NH…O groups.     

Structure of N-chloromethyllactams and features of the interaction of atoms in them as a result of ab initio calculations

Quantum-chemical calculations have been carried out by the RHF/6-31G(d) and MP2/6-31+G(d) methods of molecules of N-chloromethylpyrrolidone, N-chloromethylcaprolactam, N-chloromethyl-succinimide, and N-chloromethylphthalimide with full optimization of their geometry, and also N-chloromethylpyrrolidone molecule by the RHF/6-31G(d) method at various angles of rotation of the CH₂Cl group around the C―N bond. It was shown that the lower frequencies of the ³⁵Cl NQR of the first two molecules in comparison with the later are mainly determined by the high populations of the p _σ -orbitals of their Cl atoms. The population of the orbitals of the unshared electron pair of the N atom is practically unchanged on rotating the CH₂Cl group, but the N atom polarizes the C―Cl bond in the indicated molecule. This does not confirm the supposed p,σ*-conjugation in the Cl―C―N grouping. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1537–1544, October, 2008.     

Structural and electronic effects involving pyridine rings in 4-methylpyridine Cu4OX6L4 complexes. II. Correlations based on molecular structure of the Cu4OCl6(4-Mepy)4 complex

Correlations involving bond lengths and bond angles in the molecular structure of the Cu₄OCl₆(4-Mepy)₄ complex (4-Mepy = 4-methylpyridine) with four symmetrically independent molecules present in the unit cell showed that the donor-acceptor behavior involving the π-back donation into the pyridine rings of the 4-Mepy ligands is most effectively stimulated by a suitable orientation of the pyridine rings in the trigonal bipyramidal geometry. The pyridine ring planes are almost in parallel orientation with one of the three Cu-Cl bonds. The bond lengths of these Cu-Cl bonds are in a significant linear correlation with the Cu-N bond lengths and the bonds lengths of the pyridine rings. The pyridine rings orientation is affected by distortion of the trigonal bipyramidal geometry to tetragonal pyramidal coordination, by out-of plane pyridine rings deviation and in-plane pyridine rings tilting, by puckering of the pyridine rings and by the effects of the methyl groups. The pyridine rings in at least seven of the sixteen trigonal bipyramidal coordinations exhibit an orientation supporting the π-back bonding between the Cu(II) atoms and the pyridine rings.     

ESR study of structural characteristics and intramolecular motions of tris(3,5-di-<Emphasis Type="Italic">tert</Emphasis>-butyl-4-hydroxybenzyl)amine free radical in toluene

The magnetic and dynamic properties of tris(2,6-di-tert-butyl-4-hydroxybenzyl)amine free radical was studied by ESR spectroscopy in the temperature range from 170 to 350 K in toluene. Symmetrical conformers in the rigid toluene matrix with characteristic angles θ₁ = 26° and θ₂ = 60° between the symmetry axis of the 2p _z -orbital on the C_α atom of the phenoxyl ring and the direction of the C_α-C_β bond of the CH₂ fragment were determined. The activation energy of transition between the conformers was determined to be 8.2 kcal mol⁻¹. The correlation time of transition between the conformers was established as 8.2·10⁻¹ s.     

Synthesis and structure of tetra- and triphenylbismuth arenesulfonates

Tetraphenylbismuth arenesulfonates were synthesized by the reaction of pentaphenylantimony of-bismuth with triphenylbismuth bis(arenesulfonates). Triphenylbismuth bis(arenesulfonates) were synthesized by the reaction of triphenylbismuth with arenesulfonic acids in the presence of hydrogen peroxide. The crystal structures of the tetraphenylbismuth 2,5-dimethylbenzenesulfonate crystal hydrate (1), tetraphenylbismuth 3-carboxy-4-hydroxybenzenesulfonate (2), and triphenylbismuth bis(2,5-dimethylbenzenesulfonate) (3) were determined by X-ray diffraction analysis. The Bi atom in1 has a tetrahedral coordination (bond angles vary from 106.6(6) to 111.9(10)^o). The Bi coordination observed in2 is intermediate between tetrahedral and trigonal-bipyramidal, and that in structure3 is trigonal-bipyramidal, with the oxygen atoms in the axial positions. The Bi−O bond lengths are 2.19(2) and 2.27(2) Å. In the crystal of2, the anions form an infinite hydrogen-bonded chain. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2350–2354, December, 1999.     

Towards an Understanding of the Carbon-Carbon Bond

In this essay, the classical question of “the influence of the number and kind of substituents on the strength of the C? C bond”, is pursued with the modern tools of contemporary physical organic chemistry. Based on the work of Karl Ziegler, the products and kinetics of thermolysis of a large number of highly branched aliphatic hydrocarbons and phenyl- or cyano-substituted derivatives were investigated. For each class of compounds, a linear relationship was found between the free enthalpy of activation of the homolytic cleavage of the weakest C? C bond and the strain energy in the ground state. These relationships permitted a quantitative separation of steric and electronic effects on the cleavage of C? C bonds. The influence of the size of the substituent groups on bond angles, bond lengths, and the conformational behavior of model compounds was studied by means of experimental structure determinations and force field calculations. C? C bond lengths up to 164 pm, bond angles at tetracoordinate carbon as large as 126°, and unusual eclipsed and gauche preferred conformations were found.     

Dynamic behavior of polymer surface and the time dependence of contact angle

The increased attention has been focused on the re-searches of soft materials proposed by Pierre-Gilles de Gennes, a Nobel Prize Laureate in Physics. A special issue of “Science” on soft surfaces was published in 2002 to review specific surface properti…