Search results for "conformation"
showing 10 items of 1414 documents
Reinvestigation of the Pd-catalysed bis(silylation) of alkynes with 1,1,2,2-tetramethyl-1,2-bis(phenylthiomethyl)disilane: Unexpected formation of th…
2013
International audience; The bis(silylated) alkenes Z-(PhSCH2)Me2SiC(H)=C(Fc)SiMe2(CH2SPh) (2) and Z-(PhSCH2)Me2SiC(H)=C(bipheny)SiMe2(CH2SPh) (3) have been prepared by Pd-catalysed double silylation of ethynylferrocene and 4-ethynyl-1,1'-biphenyl in the presence of 1,1,2,2-tetramethyl-1,2-bis(phenylthiomethyl)disilane (1). A reinvestigation on the interaction of 1 with [PdCl2(PhCN)2] in technical-grade CH2Cl2 as solvent revealed competition between reduction to elemental palladium (due to oxidative addition of the Si-Si bond across Pd(II) and subsequent reductive elimination) and formation of an unusual eight-membered chelate complex cis-[PdCl2{(PhSCH2SiMe2)2O}] (4), which is fluxional in s…
Computing the Arrangement of Circles on a Sphere, with Applications in Structural Biology
2009
International audience; Balls and spheres are the simplest modeling primitives after affine ones, which accounts for their ubiquitousness in Computer Science and Applied Mathematics. Amongst the many applications, we may cite their prevalence when it comes to modeling our ambient 3D space, or to handle molecular shapes using Van der Waals models. If most of the applications developed so far are based upon simple geometric tests between balls, in particular the intersection test, a number of applications would obviously benefit from finer pieces of information. Consider a sphere $S_0$ and a list of circles on it, each such circle stemming from the intersection between $S_0$ and another spher…
The crystal structure of bacteriophage Qβ at 3.5 å resolution
1996
Abstract Background: The capsid protein subunits of small RNA bacteriophages form a T=3 particle upon assembly and RNA encapsidation. Dimers of the capsid protein repress translation of the replicase gene product by binding to the ribosome binding site and this interaction is believed to initiate RNA encapsidation. We have determined the crystal structure of phage Qβ with the aim of clarifying which factors are the most important for particle assembly and RNA interaction in the small phages. Results The crystal structure of bacteriophage Qβ determined at 3.5 a resolution shows that the capsid is stabilized by disulfide bonds on each side of the flexible loops that are situated around the fi…
Structure, stability, and fragmentation of sodium bis(2-ethylhexyl)sulfosuccinate negatively charged aggregates in vacuo by MD simulations.
2014
Negatively charged supramolecular aggregates formed in vacuo by n bis(2-ethylhexyl)sulfosuccinate (AOT(-)) anions and n + n(c) sodium counterions (i.e., [AOT(n) Na(n+nc)](nc)) have been investigated by molecular dynamics (MD) simulations for n = 1 to 20 and n(c) = -1 to -5. By comparing the maximum excess charge values of negatively and positively charged AOTNa aggregates, it is found that the charge storage capability is higher for the latter systems, the difference decreasing as the aggregation number increases. Statistical analysis of physical properties like gyration radii and moment of inertia tensors of aggregates provides detailed information on their structural properties. Even for …
A topology-constrained distance network algorithm for protein structure determination from NOESY data.
2005
This article formulates the multidi- mensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-con- strained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology-constrained distance net- work analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DY- ANA. The minimum input for AutoStructure in- cludes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStru…
The influence of solvent on conformational properties of peptides with Aib residue—a DFT study
2017
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results,…
Structural study of oxalamide compounds: 1H, 13C, and DFT calculations
2011
Abstract The conformational properties of some N-alkyl, N,N′-dialky, and tetraalkyloxalamides have been investigated, in vacuo and in solvent using DFT methods at the B3LYP/6-31G∗∗ computational level. Special emphasis has been given on oxalamides with substituents of the type –CH2CH2OH. In oxalamides with the N–H group (N-alkyl and N,N′-dialky), the most stable conformations are those in which the oxalamide moiety adopts a planar s-trans arrangement and the amide bonds are trans. A different situation appears in the case of tetraalkyloxalamides, in which the oxalamide moiety always adopts a skewed arrangement and there are conformations with similar energy. A careful study of 13C and 1H NM…
Identification of Three-Way DNA Junction Ligands through Screening of Chemical Libraries and Validation by Complementary in Vitro Assays
2019
International audience; The human genome is replete with repetitive DNA sequences that can fold into thermodynamically stable secondary structures such as hairpins and quadruplexes. Cellular enzymes exist to cope with these structures whose stable accumulation would result in DNA damage through interference with DNA transactions such as transcription and replication. Therefore, the chemical stabilization of secondary DNA structures offers an attractive way to foster DNA transaction-associated damages to trigger cell death in proliferating cancer cells. While much emphasis has been recently given to DNA quadruplexes, we focused here on three-way DNA junctions (TWJ) and report on a strategy t…
Synthesis, electrochemical and theoretical studies of the Au(i)-Cu(i) heterometallic clusters bearing ferrocenyl groups
2009
Treatment of the polymeric alkynyl compounds (AuC2R)n (R = Fc, C6H4Fc; Fc = ferrocenyl) with the diphosphine PPh2C6H4PPh2 gave complexes (RC2Au)PPh2C6H4PPh2(AuC2R) (1, R = Fc; 2, R = C6H4Fc) with end-capped ferrocenyl groups. The reactions of 1 or 2 with Cu(NCMe)4PF6 result in formation of the heterotrimetallic aggregates [{Au3Cu2(C2R)6}Au3(PPh2C6H4PPh2)3](PF6)2 (3, R = Fc; 4, R = C6H4Fc), which consist of the alkynyl clusters [Au3Cu2(C2R)6]−“wrapped” by the cationic [Au3(PPh2C6H4PPh2)3]3+“belt”. The novel compounds were characterized by NMR spectroscopy and ESI-MS measurements. The solid state structure of 3 is reported. Electrochemical properties of the complexes 1–4 have been studied. Th…
Entrapment of amino acids in gas phase surfactant assemblies: The case of tryptophan confined in positively charged (1R,2S)-dodecyl (2-hydroxy-1-meth…
2017
The ability of positively charged aggregates of the surfactant (1R,2S)‐dodecyl (2‐hydroxy‐1‐methyl‐2‐phenylethyl))dimethylammonium bromide (DMEB) to incorporate D-tryptophan or L-tryptophan in the gas phase has been investigated by electrospray ion mobility mass spectrometry (ESIâIMâMS). Strongly impacted by the pH of the electrosprayed solutions, both protonated (T+) and deprotonated (T-) tryptophan are effectively included into the aggregates, whereas, tryptophan in zwitterionic (T0) form is practically absent in singly charged DMEB aggregates but can be found in multiply charged ones. The ability to incorporate tryptophan increases with the aggregation number and charge state of aggr…