Conformation Analysis (conformation + analysis)

Distribution by Scientific Domains
Distribution within Chemistry


Selected Abstracts


Conformation Analyses, Dynamic Behavior and Amide Bond Distortions of Medium-Sized Heterocycles.

CHEMINFORM, Issue 24 2005
Part 1.
No abstract is available for this article. [source]


Conformation Analyses, Dynamic Behavior, and Amide Bond Distortions of Medium-Sized Heterocycles.

CHEMINFORM, Issue 24 2005
Part 2.
No abstract is available for this article. [source]


Synthesis and Conformation Analysis of New Perphosphorylated Calix[4]resorcinarenes

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 23 2004
Vera I. Maslennikova
Abstract The octaphosphorylation of calix[4]resorcinarenes 1 by 2-dialkylamino-1,3,2-diheterophosphorinanes 2 is described, and the effect of different factors on the structures of the resulting perphosphorylated products 3,5 was studied. Conformation analysis of these compounds by correlated 2D NMR spectroscopy and X-ray diffraction analysis was performed, and it was found that compounds 3,5, like the initial resorcinarenes 1, each have the all - cis configuration of the R groups in the methylidene bridges of the calixarene system, but different orientations of benzene rings and phosphorinane fragments with respect to one another and to the macrocycle plane. Perphosphorylated resorcinarenes 3a,c, 4a and 5a with R = alkyl exist in flattened cone conformations with the phosphorinane fragments on the same side of the macrocycle plane. The conformations of the perphosphorylated resorcinarenes 3d, 4b and 5b with R = Ph change to forms intermediate between flattened cone and 1,3 - alternate. The phosphorus fragments in these compounds are located on opposite sides of the macrocycle plane. It was shown that the oxidation and sulfurisation of phosphocalixarenes 3 proceed without any change in the spatial organisation of the macrocyclic system. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]


,- O -Linked Glycopeptide Mimetics: Synthesis, Conformation Analysis, and Interactions with Viscumin, a Galactoside-Binding Model Lectin

CHEMISTRY - A EUROPEAN JOURNAL, Issue 40 2009
Jesús Jiménez-Barbero Prof.
Abstract Efficient cycloaddition of a silylidene-protected galactal with a suitable heterodiene yielded the basis for a facile diastereoselective route to a glycopeptide-mimetic scaffold. Its carbohydrate part was further extended by ,1,3-linked galactosylation. The pyranose rings retain their 4C1 chair conformation, as shown by molecular modeling and NMR spectroscopy, and the typical exo -anomeric geometry was observed for the disaccharide. The expected bioactivity was ascertained by saturation-transfer-difference NMR spectroscopy by using the galactoside-specific plant toxin viscumin as a model lectin. The experimental part was complemented by molecular docking. The described synthetic route and the strategic combination of computational and experimental techniques to reveal conformational properties and bioactivity establish the prepared ,- O -linked glycopeptide mimetics as promising candidates for further exploitation of this scaffold to give O -glycans for lectin blocking and vaccination. [source]


Synthesis and Conformation Analysis of New Perphosphorylated Calix[4]resorcinarenes

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 23 2004
Vera I. Maslennikova
Abstract The octaphosphorylation of calix[4]resorcinarenes 1 by 2-dialkylamino-1,3,2-diheterophosphorinanes 2 is described, and the effect of different factors on the structures of the resulting perphosphorylated products 3,5 was studied. Conformation analysis of these compounds by correlated 2D NMR spectroscopy and X-ray diffraction analysis was performed, and it was found that compounds 3,5, like the initial resorcinarenes 1, each have the all - cis configuration of the R groups in the methylidene bridges of the calixarene system, but different orientations of benzene rings and phosphorinane fragments with respect to one another and to the macrocycle plane. Perphosphorylated resorcinarenes 3a,c, 4a and 5a with R = alkyl exist in flattened cone conformations with the phosphorinane fragments on the same side of the macrocycle plane. The conformations of the perphosphorylated resorcinarenes 3d, 4b and 5b with R = Ph change to forms intermediate between flattened cone and 1,3 - alternate. The phosphorus fragments in these compounds are located on opposite sides of the macrocycle plane. It was shown that the oxidation and sulfurisation of phosphocalixarenes 3 proceed without any change in the spatial organisation of the macrocyclic system. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]


Enantioselective Recognition of Aliphatic Amino Acids by ,-Cyclodextrin Derivatives Bearing Aromatic Organoselenium Moieties on the Primary or Secondary Side

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8 2003
Yu Liu
Abstract Spectrophotometric titrations have been performed in order to determine the stability constants of inclusion complexation of some aliphatic amino acids with four structurally related organoselenium-modified ,-cyclodextrins: mono(6-phenylseleno-6-deoxy)-,-cyclodextrin (1a), mono[6-(p -methoxyphenylseleno)-6-deoxy]-,-cyclodextrin (1b), mono(2-phenylseleno-2-deoxy)-,-cyclodextrin (2a), and mono[2-(p -methoxyphenylseleno)-2-deoxy]-,-cyclodextrin (2b). Conformation analysis by circular dichroism and 2D NMR spectroscopic studies revealed that the aryl-substituted ,-cyclodextrins gave self-inclusion intramolecular complexes in aqueous solution, while the extent of penetration depended both on the positions and on the structures of substituents. Quantitative investigation on the binding ability of the hosts with amino acids showed that they were able to recognize the size and the shape of guests, affording supramolecular complexes with quite small stability constants ranging from 24 to 355 M,1. The molecular recognition abilities are discussed from the viewpoints of induced-fitting mechanisms, geometric complementary, and cooperative binding processes. Furthermore, these ,-cyclodextrin derivatives displayed considerable enantioselectivity towards L/D -amino acid isomers, giving the highest L -enantioselectivity (up to 8.4) for inclusion complexation between leucine and 2a. The binding modes of L/D -leucine with 1b were elucidated from NOESY studies and the chiral recognition phenomena were interpreted accordingly. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source]


Conformation analysis and molecular mobility of ethylene and tetrafluoroethylene copolymer using solid-state 19F MAS and 1H , 19F CP/MAS NMR spectroscopy

MAGNETIC RESONANCE IN CHEMISTRY, Issue 7 2004
Keitaro Aimi
Abstract The changes in the conformation and molecular mobility accompanied by a phase transition in the crystalline domain were analyzed for ethylene (E) and tetrafluoroethylene (TFE) copolymer, ETFE, using variable-temperature (VT) solid-state 19F magic angle spinning (MAS) and 1H , 19F cross-polarization (CP)/MAS NMR spectroscopy. The shifts of the signals for fluorines in TFE units to higher frequency and the continuing decrease and increase in the T1,F values suggest that conformational exchange motions exist in the crystalline domain between 42 and 145 °C. Quantum chemical calculations of magnetic shielding constants showed that the high-frequency shift of TFE units should be induced by trans to gauche conformational changes at the CH2CF2 linkage in the E,TFE unit. Although the 19F signals of the crystalline domain are substantially overlapped with those of the amorphous domain at ambient probe temperature (68 °C), they were successfully distinguished by using the dipolar filter and spin-lock pulse sequences at 145 °C. The dipolar coupling constants for the crystalline domain, which can be estimated by fitting the dipolar oscillation behaviors in the 1H , 19F CP curve, showed a significant decrease with increasing temperature from 42 to 145 °C. This is due to the averaging of 1H19F dipolar interactions originating from the molecular motion in the crystalline domain. The increase in molecular mobility in the crystalline domain was clearly shown by VT T1,F and 1H , 19F CP measurements in the phase transition temperature range. Copyright © 2004 John Wiley & Sons, Ltd. [source]


Archazolid-7- O -,- D -glucopyranoside , Isolation, Structural Elucidation and Solution Conformation of a Novel V-ATPase Inhibitor from the Myxobacterium Cystobacter violaceus

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 7 2007
Dirk Menche
Abstract The novel polyketide macrolide archazolid-7- O -,- D -glucopyranoside (3) has been isolated from the myxobacterium Cystobacter violaceus and the structure of this first archazolid-glycoside has been determined by spectroscopic and degradative methods. A synthesis of simplified 7- O analogues, based on regioselective derivatisation of archazolid A, was elaborated. These structurally novel archazolids of natural and synthetic origin were evaluated in detail for V-ATPase inhibition and their biological activities are discussed in terms of their solution conformations, as determined by high-field NMR studies, including J -based conformation analysis and constrained molecular dynamics simulations. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]


Controlled Release of Perfumery Alcohols by Neighboring-Group Participation.

HELVETICA CHIMICA ACTA, Issue 8 2003
2-(Hydroxymethyl)-, 2-Carbamoylbenzoates, Comparison of the Rate Constants for the Alkaline Hydrolysis of 2-Acyl-
A series of 2-acylbenzoates 1 and 2, 2-(hydroxymethyl)benzoates 3, 2-carbamoylbenzoates 4,6, as well as the carbamoyl esters 7 or 8 of maleate or succinate, respectively (see Fig.,2), were prepared in a few reaction steps, and the potential use of these compounds as chemical delivery systems for the controlled release of primary, secondary, and tertiary fragrance alcohols was investigated. The rate constants for the neighboring-group-assisted alkaline ester hydrolysis were determined by anal. HPLC in buffered H2O/MeCN solution at different pH (Table,1). The rates of hydrolysis were found to depend on the structure of the alcohol, together with the precursor skeleton and the structure of the neighboring nucleophile that attacks the ester function. Primary alcohols were released more rapidly than secondary and tertiary alcohols, and benzoates of allylic primary alcohols (e.g., geraniol) were hydrolyzed 2,4 times faster than their homologous saturated alcohols (e.g., citronellol). For the same leaving alcohol, 2-[(ethylamino)carbonyl]benzoates cyclized faster than the corresponding 2-(hydroxymethyl)benzoates, and much faster than their 2-formyl and 2-acetyl analogues (see, e.g., Fig.,4). Within the carbamoyl ester series, 2-[(ethylamino)carbonyl]benzoates were found to have the highest rate constants for the alkaline ester hydrolysis, followed by unsubstituted 2-(aminocarbonyl)benzoates, or the corresponding isopropyl derivatives. To rationalize the influence of the different structural changes on the hydrolysis kinetics, the experimental data obtained for the 2-[(alkylamino)carbonyl]benzoates were compared with the results of density-functional computer simulations (Table,2 and Scheme,4). Based on a preliminary semi-empirical conformation analysis, density-functional calculations at the B3LYP/6-31G** level were carried out for the starting precursor molecules, several reaction intermediates, and the cyclized phthalimides. For the same precursor skeleton, these simple calculations were found to model the experimental data correctly. With an understanding of the influence of structural parameters on the rate constants obtained in this work, it is now possible to influence the rates of hydrolysis over several orders of magnitude, to design tailor-made precursors for a large variety of fragrance alcohols, and to predict their efficiency as controlled-release systems in practical applications. [source]


A search for cyclophilin-A gene (PPIA) variation and its contribution to the risk of atherosclerosis and myocardial infarction

INTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2008
M. Palacín
Summary Cyclophilin A is secreted by vascular smooth muscle cells in response to inflammatory stimuli, and could thus contribute to atherosclerosis. We hypothesized that the genetic variation at the cyclophilin A gene (PPIA) could affect the risk for developing atherosclerosis and myocardial infarction. This study included 250 myocardial infarction patients (all male and < 60 years; 95% are smokers). All these cases had at least one atherosclerotic diseased coronary vessel. DNA was obtained from patients and from 250 healthy controls. The variation at the PPIA gene was determined in the patients through single-strand conformation analysis and direct sequencing of seven polymerase chain reaction fragments. Allele and genotype frequencies were compared between patients and controls. The effect of a promoter polymorphism (,11 G/C) on gene expression was in vitro analysed with luciferase-reporter assays. We found two common polymorphisms in the PPIA promoter (,11 G/C) and the 5, non-translated (+36 G/A) regions. Cells transfected with luciferase-plasmids containing the ,11 G had significantly higher luciferase activity. Genotype frequencies for these polymorphisms did not differ between patients and controls. In conclusion, we reported a functional variant in the PPIA promoter. However, the PPIA variation did not significantly contribute to the risk of suffering from myocardial infarction among patients with atherosclerotic diseased vessels. [source]


New oxidized sterols from Aspergillus awamori and the endo -boat conformation adopted by the cyclohexene oxide system

MAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2010
Hao Gao
Abstract Two new oxidized sterols 1 and 2 were obtained from the active fraction of a mangrove fungus Aspergillus awamori isolated from the soils around the mangrove plant Acrostichum speciosum. Their structures were elucidated using spectroscopic methods as 22E -7,-methoxy-5,,6,-epoxyergosta-8(14),22-dien-3,-ol (1) and 22E -3,-hydroxy-5,,6,,8,,14,-diepoxyergosta-22-en-7-one (2). The NMR data and complete assignments for both DMSO- d6 and CDCl3 were given. Their cytotoxic activity against A549 cell line was evaluated. Furthermore, the detailed conformation analysis for ring B (cyclohexene oxide system) of sterol 1 was given on the basis of NOEs. The endo -boat conformation was considered as the preferred conformation for ring B rather than half-chair conformation. Copyright © 2009 John Wiley & Sons, Ltd. [source]


Structure determination and conformation analysis of symmetrical dimers

MAGNETIC RESONANCE IN CHEMISTRY, Issue 3 2005
Alexei V. Buevich
Abstract Conformational and stereochemical analysis of six new symmetrical dimers was performed using proton,proton vicinal coupling measured from 1H NMR and 13C satellites of 1H NMR signals, natural abundance 13C-edited nuclear overhauser effect (NOE) experiments, comprehensive NOE analysis and molecular modeling. The 13C satellite analysis and 13C-edited NOE experiments were carried out to extract spectral information between equivalent protons. Molecular modeling was applied for estimations of three-dimensional parameters of the studied dimers, which were subsequently used to generate a set of theoretical NOE for each possible conformation. The J -coupling, 13C-edited NOE and quantitative NOE analyses showed the predominance of gauche conformation for three dimers, whereas a mixture of gauche and anti conformations (45:55) for three other dimers was established by quantitative NOE analysis. X-ray crystallographic study confirmed the stereochemistry of one of the dimers and revealed a discrepancy in conformation stability between liquid and solid states. Copyright © 2004 John Wiley & Sons, Ltd. [source]


Circular Dichroism of Designed Peptide Helices and ,-Hairpins: Analysis of Trp- and Tyr-Rich Peptides

CHEMBIOCHEM, Issue 12 2005
Radhakrishnan Mahalakshmi
VCD versus ECD spectroscopy. Peptides rich in aromatic residues yield anomalous far-UV electronic circular dichroism (ECD) spectra that preclude secondary structure assignment. The utility of vibrational circular dichroism (VCD) in conformation analysis is demonstrated by using a set of well-defined peptide helices and hairpins containing proximal aromatic residues. [source]


Preferred Conformations of Peptides Containing tert -Leucine, a Sterically Demanding, Lipophilic ,-Amino Acid with a Quaternary Side-Chain C, Atom

CHEMISTRY - A EUROPEAN JOURNAL, Issue 8 2005
Fernando Formaggio Prof.
Abstract Terminally protected homopeptides of tert -leucine, from the dimer to the hexamer, co-oligopeptides of tert -leucine in combination with ,-aminoisobutyric acid or glycine residues up to the hexamer level, and simple dipeptides representing known scaffolds for catalysts in asymmetric organic reactions were prepared by solution methods and fully characterized. The results of conformation analysis, performed by use of FT-IR absorption, NMR, CD, and X-ray diffraction techniques, indicate that this hydrophobic ,-amino acid with tetrasubstitution at the C, atom is structurally versatile. We show that it prefers extended or semiextended conformations, but can also be accommodated in folded structures, provided that these are biased by the presence of helicogenic residues. The current large-scale production of Tle, combined with its conformational preferences unravelled in this work, should make this bulky, hydrophobic, C, -trisubstituted ,-amino acid a regular building block of any strategy seeking to tailor peptides with improved catalytic and pharmacological properties. [source]


De novo duplication of MECP2 in a girl with mental retardation and no obvious dysmorphic features

CLINICAL GENETICS, Issue 2 2010
P Makrythanasis
Makrythanasis P, Moix I, Gimelli S, Fluss J, Aliferis K, Antonarakis SE, Morris MA, Béna F, Bottani A. De novo duplication of MECP2 in a girl with mental retardation and no obvious dysmorphic features. Loss-of-function mutations of MECP2 are responsible for Rett syndrome (RTT), an X-linked neurodevelopmental disorder affecting mainly girls. The availability of MECP2 testing has led to the identification of such mutations in girls with atypical RTT features and the recognition of milder forms. Furthermore, duplication of the entire gene has recently been described in boys with mental retardation and recurrent infections. We describe a girl with a heterozygous de novo MECP2 duplication. The patient, at the age of 19, has mental retardation with no autistic features. She is friendly but gets frequently anxious. She has neither dysmorphic features nor malformations. Her motor development was delayed with walking at 20 months. Speech is fluid with good pronunciation but is simple and repetitive. Diagnosis was made after single-strand conformation analysis (SSCA) and multiplex ligation-dependent probe amplification (MLPA) analysis of MECP2. Array comparative genomic hybridization (aCGH) analysis showed a duplication of 29 kb including MECP2 and part of IRAK1. Fluorescent in situ hybridization (FISH) has revealed that the duplicated region is inserted near the telomere of the short arm of chromosome 10. X-chromosome inactivation in leukocyte DNA was not skewed. We conclude that it is likely that this MECP2 duplication is responsible for the mental retardation in this patient. This case broadens the phenotypic spectrum of MECP2 abnormalities with consequent implication in diagnosis and genetic counselling of girls with non-syndromic mental retardation. [source]