Search results for "BOND"

1995

Supramolecular structures based on 4-(3,5-dioxo-1,2,4-triazolidin-4-yl) benzoic acid (U4A) units act as effective junction zones in functionalized polybutadienes, resulting in the formation of thermoplastic elastomers. The dynamics on a molecular scale of the phenyl rings have been probed by 2H-NMR. In the polymeric system, there are three spatially separated environments, which are reflected in the mobility of the polar units. Phenyl rings which are incorporated in the structures are either rigid or undergo 180° phenyl flips. The small fraction of free functional groups move isotropically and their mobility is coupled to the dynamics of the polybutadiene matrix. In two model compounds, whe…

Molecular aggregation in selected crystalline 1:1 complexes of hydrophobicD- andL-amino acids. IV. TheL-phenylalanine series

2009

The amino acid L-phenylalanine has been cocrystallized with D-2-aminobutyric acid, C(9)H(11)NO(2).C(4)H(9)NO(2), D-norvaline, C(9)H(11)NO(2).C(5)H(11)NO(2), and D-methionine, C(9)H(11)NO(2).C(5)H(11)NO(2)S, with linear side chains, as well as with D-leucine, C(9)H(11)NO(2).C(6)H(13)NO(2), D-isoleucine, C(9)H(11)NO(2).C(6)H(13)NO(2), and D-allo-isoleucine, C(9)H(11)NO(2).C(6)H(13)NO(2), with branched side chains. The structures of these 1:1 complexes fall into two classes based on the observed hydrogen-bonding pattern. From a comparison with other L:D complexes involving hydrophobic amino acids and regular racemates, it is shown that the structure-directing properties of phenylalanine closel…

Two penta­de­hydro­peptides with different configurations of the ΔPhe residues

2009

Comparison of the crystal structures of two pentadehydropeptides containing DeltaPhe residues, namely (Z,Z)-N-(tert-butoxycarbonyl)glycyl-alpha,beta-phenylalanylglycyl-alpha,beta-phenylalanylglycine (or Boc(0)-Gly(1)-Delta(Z)Phe(2)-Gly(3)-Delta(Z)Phe(4)-Gly(5)-OH) methanol solvate, C(29)H(33)N(5)O(8) x CH(4)O, (I), and (E,E)-N-(tert-butoxycarbonyl)glycyl-alpha,beta-phenylalanylglycyl-alpha,beta-phenylalanylglycine (or Boc(0)-Gly(1)-Delta(E)Phe(2)-Gly(3)-Delta(E)Phe(4)-Gly(5)-OH), C(29)H(33)N(5)O(8), (II), indicates that the Delta(Z)Phe residue is a more effective inducer of folded structures than the Delta(E)Phe residue. The values of the torsion angles phi and psi show the presence of two …

Spectrophotometric determinations of binding constants between cyclodextrins and aromatic nitrogen substrates at various pH values

2001

The inclusion capacity of native β-cyclodextrin (1) and mono-(6-amino-6-deoxy)-β-cyclodextrin (2) versus aromatic compounds having a nitro or an amino group or both has been investigated at three different pH values. Molecular interactions in inclusion complexes have also been investigated by means of molecular mechanics (MM2/QD) models. Electrostatic and van der Waals interactions and the formation of a hydrogen bond between the donor amino group and the oxygen atom of the secondary hydroxyl group seem to be the more important contributions in determining complex stability. The inclusion capacity of two different cyclodextrins versus aromatic compounds has been investigated at three differ…

Estimation of pKa shifts in weak polyacids using a simple molecular model: effects of strong polybases, hydrogen bonding and divalent counterion bind…

2004

Abstract The pKa values of ionizable groups in macromolecules can be significantly different than those of the isolated groups in solution. We have estimated theoretically the changes in the dissociation constant of a weak acid (a) in the vicinity of another ionizable group (b) on the basis of the theoretical approach by Hill (J. Am. Chem. Soc. 78 (1956) 3330) for matching pairs of interacting sites on two large molecules. Three cases are considered for group b: the strong base, the same weak acid as group a with hydrogen bonding between them, and the same weak acid as group a with divalent counterion binding. The pKa shifts are evaluated in each case as a function of the interaction energy…

Electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in rat and chicken tissues and its partial characterisation i…

2010

Electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in rat and chicken tissues and its partial characterisation in rat liverTightly bound to DNA proteins (TBP) are a protein group that remain attached to DNA with covalent or non-covalent bonds after its deproteinisation. The distribution of TBP in genes reflects the type of cell differentiation. It has been hypothesised that TBP binding is involved in regulation of gene expression. Early studies reported uniformity of the TBPs from different sources. Later it was shown that TBPs obtained from DNA, isolated in mild conditions from evolutionary distant species, are different. Application of chloroform DNA e…

2014

The interest in RNA modification enzymes surges due to their involvement in epigenetic phenomena. Here we present a particularly informative approach to investigate the interaction of dye-labeled RNA with modification enzymes. We investigated pseudouridine (Ψ) synthase TruB interacting with an alleged suicide substrate RNA containing 5-fluorouridine (5FU). A longstanding dogma, stipulating formation of a stable covalent complex was challenged by discrepancies between the time scale of complex formation and enzymatic turnover. Instead of classic mutagenesis, we used differentially positioned fluorescent labels to modulate substrate properties in a range of enzymatic conversion between 6% and…

N-Methyldehydroamino acids promote a configuration cis of N-methylamide bond

2008

Abstract Dehydroamino acids with a methylated N-terminal tertiary amide bond occur in natural small cyclic peptide toxins. To investigate their conformational preferences a systematic theoretical analysis was performed on N ′-methylamides of N -acetyl- N -methyldehydroamino acids (Ac-Δ(Me)Xaa-NHMe, where Xaa = ( Z )-Abu, ( E )-Abu, Val, ( Z )-Phe, and ( E )-Phe) considering the configuration trans and cis of the tertiary amide bond. The ϕ , ψ potential energy surfaces were calculated at the B3LYP/6-31+G ∗∗ //HF/3-21G level with inclusion of the solvent (water) effect (SCRF method). The conformers localised were fully optimised at the B3LYP/6-31+G ∗∗ in vacuo. The accessible areas of the pot…

On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes

2020

AbstractThe problem of aromaticity in heterocyclic rings of uracil and its 5-halogenoderivatives (5XU) was analyzed theoretically by calculating modified harmonic oscillator model of aromaticity (HOMA) for Heterocycle Electron Delocalization (HOMHED), nucleus-independent chemical shift parameters (NICS) and the so-called scan experiments, using helium-3 atom as a magnetic probe. The impact of halogen electronegativity on C5 atom’s NBO charges was also investigated. Water, as a polar environment, has a negligible impact on 5XU aromaticity. The most stable diketo tautomer shows a very low aromaticity while the “rare” dihydroxy form (tautomer No 6) is aromatic and resembles benzene. This is in…

ChemInform Abstract: Preparation and Structural Characterization of (Me3SiNSN)2Se, a New Synthon for Sulfur-Selenium Nitrides.

2010

The reaction of (Me(3)SiN)(2)S with SeCl(2) (2:1 ratio) in CH(2)Cl(2) at -70 degrees C provides a route to the novel mixed selenium-sulfur-nitrogen compound (Me(3)SiNSN)(2)Se (1). Crystals of 1 are monoclinic and belong the space group P2(1)/c, with a = 7.236(1) A, b = 19.260(4) A, c = 11.436(2) A, beta = 92.05(3) degrees, V = 1592.7(5) A(3), Z = 4, and T = -155(2) degrees C. The NSNSeNSN chain in 1 consists of Se-N single bonds (1.844(3) A) and S=N double bonds (1.521(3)-1.548(3) A) with syn and anti geometry at the N=S=N units. The N-Se-N bond angle is 91.8(1) degrees. The EI mass spectrum shows a molecular ion with good agreement between the observed and calculated isotopic distributions…