Conformational Behavior (conformational + behavior)

Distribution by Scientific Domains


Selected Abstracts


Synthesis and Conformational Behavior of New Intra-annularly Linked Cyclophane Possessing a 1,6-Dioxahexa-2,4-diyne Spacer.

CHEMINFORM, Issue 1 2003
Perumal Rajakumar
Abstract For Abstract see ChemInform Abstract in Full Text. [source]


ChemInform Abstract: Conformational Behaviors of Tetra-O-methylsulfinylcalix[4]arenes , An Approach to Control the Conformation of Thiacalix[4]arenes by Oxidizing Sulfur Bridges.

CHEMINFORM, Issue 5 2008
Hiroshi Katagiri
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]


C-Disaccharides as Probes for Carbohydrate Recognition , Investigation of the Conformational Requirements for Binding of Disaccharide Mimetics of Sialyl Lewis X

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 4 2007
Richard W. Denton
Abstract A set of C-disaccharide analogs was designed to probe the recognition of a known O-disaccharide mimetic of sialyl Lewis X, to P-selectin. The synthesis of the C-glycosides centered on the de novo construction of the galactose residue via an oxocarbenium ion/enol ether cyclization. Conformational analysis was performed by a combination of NMR spectroscopy and molecular mechanics (MM) and molecular dynamics (MD) calculations. The inhibition of P-selectin binding was evaluated in a P-selectin Biacore assay. At 12 mM, the O-glycoside showed 48,% inhibition of binding, while the C-glycoside analogs exhibited between 25,31,% inhibition. This data is discussed within the context of the active conformation of sLex and the conformational behavior of these ligands. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]


Molecular dynamics simulations of solvated UDP,glucose in interaction with Mg2+ cations

FEBS JOURNAL, Issue 20 2001
Pavla Petrová
,Glycosyltransferases are key enzymes involved in biosynthesis of oligosaccharides. Nucleotide-sugars, the glycosyltransferase substrates, serve as activated donors of sugar residues during the enzymatic reaction Although very little is known about the catalytic mechanism of these enzymes, it appears that the catalytic activity in most glycosyltransferases is dependent upon the presence of a divalent cation, for example Mn2+ or Mg2+. It is not known whether the ion is bound to the enzyme before its interaction with the substrate, or if it binds the substrate before the enzymatic reaction to modify its conformation to fit better the active site of the enzyme. We have inspected the latter possibility by running four 2-ns molecular dynamics trajectories on fully solvated UDP-glucose in the presence of Mg2+ ions. Our results indicate that the divalent cation interacts strongly with the nucleotide-sugar in solution, and that it can alter its conformational behavior. It is also shown that a conformation of the pyrophosphate moiety that results in an eclipsed or almost eclipsed orientation of two of the oxygen atoms, and which is found in protein interacting with a nucleotide di- or tri-phosphate X-ray data, is energetically favored. The results are also discussed in light of existing NMR data, and are found to be in a good agreement with them. [source]


Ab initio calculations of intramolecular parameters for a class of arylamide polymers

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2006
Satyavani Vemparala
Abstract Using DFT methods, we have determined intramolecular parameters for an important class of arylamide polymers displaying antimicrobial and anticoagulant inhibitory properties. A strong link has been established between these functions and the conformation that the polymers adopt in solution and at lipid bilayer interfaces. Thus, it is imperative for molecular dynamics simulations designed to probe the conformational behavior of these systems to accurately describe the torsional degrees of freedom. Standard force fields were shown to be deficient in this respect. Therefore, we have computed the relevant torsional energy profiles using a series of constrained geometry optimizations. We have also determined electrostatic parameters using our results in combination with standard RESP charge optimization. Force constants for bond and angle potentials were calculated by iteratively matching quantum and classical normal modes via a Monte Carlo scheme. The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 693,700, 2006 [source]


An improved OPLS,AA force field for carbohydrates

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2002
D. Kony
Abstract This work describes an improved version of the original OPLS,all atom (OPLS,AA) force field for carbohydrates (Damm et al., J Comp Chem 1997, 18, 1955). The improvement is achieved by applying additional scaling factors for the electrostatic interactions between 1,5- and 1,6-interactions. This new model is tested first for improving the conformational energetics of 1,2-ethanediol, the smallest polyol. With a 1,5-scaling factor of 1.25 the force field calculated relative energies are in excellent agreement with the ab initio -derived data. Applying the new 1,5-scaling makes it also necessary to use a 1,6-scaling factor for the interactions between the C4 and C6 atoms in hexopyranoses. After torsional parameter fitting, this improves the conformational energetics in comparison to the OPLS,AA force field. The set of hexopyranoses included in the torsional parameter derivation consists of the two anomers of D -glucose, D -mannose, and D -galactose, as well as of the methyl-pyranosides of D -glucose, D -mannose. Rotational profiles for the rotation of the exocyclic group and of different hydroxyl groups are also compared for the two force fields and at the ab initio level of theory. The new force field reduces the overly high barriers calculated using the OPLS,AA force field. This leads to better sampling, which was shown to produce more realistic conformational behavior for hexopyranoses in liquid simulation. From 10-ns molecular dynamics (MD) simulations of ,- D -glucose and ,- D -galactose the ratios for the three different conformations of the hydroxymethylene group and the average 3JH,H coupling constants are derived and compared to experimental values. The results obtained for OPLS,AA,SEI force field are in good agreement with experiment whereas the properties derived for the OPLS,AA force field suffer from sampling problems. The undertaken investigations show that the newly derived OPLS,AA,SEI force field will allow simulating larger carbohydrates or polysaccharides with improved sampling of the hydroxyl groups. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1416,1429, 2002 [source]


Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2002
Caterina Benzi
The conformational behavior of the title compounds has been investigated by Hartree,Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed , turn (,l), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4,0.5 kcal/mol for helical structures and about 2 kcal/mol for ,l structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for ,l structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 341,350, 2002 [source]


Structural characterization of a neurotoxic threonine-rich peptide corresponding to the human prion protein ,2-helical 180,195 segment, and comparison with full-length ,2-helix-derived peptides,

JOURNAL OF PEPTIDE SCIENCE, Issue 10 2008
Luisa Ronga
Abstract The 173,195 segment corresponding to the helix 2 of the globular PrP domain is a good candidate to be one of the several ,spots' of intrinsic structural flexibility, which might induce local destabilization and concur to protein transformation, leading to aggregation-prone conformations. Here, we report CD and NMR studies on the ,2-helix-derived peptide of maximal length (hPrP[180,195]) that is able to exhibit a regular structure different from the prevalently random arrangement of other ,2-helix-derived peptides. This peptide, which has previously been shown to be affected by buffer composition via the ion charge density dependence typical of Hofmeister effects, corresponds to the C -terminal sequence of the PrPC full-length ,2-helix and includes the highly conserved threonine-rich 188,195 segment. At neutral pH, its conformation is dominated by ,-type contributions, which only very strong environmental modifications are able to modify. On TFE addition, an increase of ,-helical content can be observed, but a fully helical conformation is only obtained in neat TFE. However, linking of the 173,179 segment, as occurring in wild-type and mutant peptides corresponding to the full-length ,2-helix, perturbs these intrinsic structural propensities in a manner that depends on whether the environment is water or TFE. Overall, these results confirm that the 180,195 parental region in hPrPC makes a strong contribution to the chameleon conformational behavior of the segment corresponding to the full-length ,2-helix, and could play a role in determining structural rearrangements of the entire globular domain. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source]


Syntheses, spectroscopic study and X-ray crystallography of some new phosphoramidates and lanthanide(III) complexes of N -(4-nitrobenzoyl)- N,,N,,-bis(morpholino)phosphoric triamide

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2010
Khodayar Gholivand
New phosphoramidates with the formula RC(O)N(H)P(O)X2, R = 2-NO2,C6H4, 3-NO2,C6H4 and 4-NO2,C6H4, X = N(CH2CH3) (1),(3), NC4H8 (4),(6), and NC4H8O (7),(9) were synthesized and characterized by 1H, 13C, 31P NMR and IR spectroscopy, and elemental analysis. The reaction of (9) with hydrated lanthanide(III) nitrate leads to ten- or nine-coordinated complexes, (10),(13). The crystal structure has been determined for (3), (5), (9), (10) and (13). In contrast to all of the previously reported similar phosphoramidate compounds, the ,C(O),N(H),P(O) skeleton in the free ligand (9) shows a cisoid conformation, with the C=O and P=O double bonds adopting a nearly syn conformation. Quantum chemical calculations were applied for clarifying this exceptional conformational behavior. The monodentate neutral ligand (9) is coordinated to the metal ions via the phosphoryl O atom, adopting the usual anti conformation between the C=O and P=O groups. [source]