Search results for "Bonding"
showing 10 items of 996 documents
Structures of yeast peroxisomal Δ(3),Δ(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks f…
2015
Δ3,Δ2-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomalSaccharomyces cerevisiaeECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3′,5′-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bo…
Alkali metal mediated resorcarene capsules: An ESI-FTICRMS study on gas-phase structure and cation binding of tetraethyl resorcarene and its per-meth…
2002
AbstractElectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) with additional ab initio calculations were used to examine the alkali metal cation binding selectivity (i.e., molecular recognition) and host properties of tetraethyl resorcarene (1) and its per-methylated derivative (2). The significance of intramolecular hydrogen bonding for the crown conformation was demonstrated. The presence of intramolecular flip-flop hydrogen bonding in 1 was confirmed both with calculations and in ND3-exchange experiments. All the alkali metal cations formed host–guest complexes by docking inside the cavity of the host. Complexation with the larger cations, esp…
Ion-Pair Recognition of Tetramethylammonium Salts by Halogenated Resorcinarenes
2011
The non-covalent interactions of different upper-rim-substituted C(2)-resorcinarenes with tetramethylammonium salts were analyzed in the gas phase in an Electrospray Ionization Fourier-transform ion-cyclotron-resonance (ESI-FTICR) mass spectrometer and by (1)H NMR titrations. The order of binding strengths of the hosts towards the tetramethylammonium cation in the gas phase reflects the electronic nature of the substituents on the upper rim of the resorcinarene. In solution, however, a different trend with particularly high binding constants for halogenated resorcinarenes has been observed. This trend can be explained by a synergetic effect originating from the interaction of the halogenate…
Experimental and Computational Studies of Hydrogen Bonding and Proton Transfer to [Cp*Fe(dppe)H]
2005
The present contribution reports experimental and computational investigations of the interaction between [Cp*Fe(dppe)H] and different proton donors (HA). The focus is on the structure of the proton transfer intermediates and on the potential energy surface of the proton transfer leading to the dihydrogen complex [Cp*Fe(dppe)(H2)]+. With p-nitrophenol (PNP) a UV/Visible study provides evidence of the formation of the ion-pair stabilized by a hydrogen bond between the nonclassical cation [Cp*Fe(dppe)(H2)]+ and the homoconjugated anion ([AHA]-). With trifluoroacetic acid (TFA), the hydrogen-bonded ion pair containing the simple conjugate base (A-) in equilibrium with the free ions is observed…
A synthetic method for diversification of the P1′ substituent in phosphinic dipeptides as a tool for exploration of the specificity of the S1′ bindin…
2007
Abstract A novel, general, and versatile method of diversification of the P1′ position in phosphinic pseudodipeptides, presumable inhibitors of proteolytic enzymes, was elaborated. The procedure was based on parallel derivatization of the amino group in the suitably protected phosphinate building blocks with appropriate alkyl and aryl halides. This synthetic strategy represents an original approach to phosphinic dipeptide chemistry. Its usefulness was confirmed by obtaining a series of P1′ modified phosphinic dipeptides, inhibitors of cytosolic leucine aminopeptidase, through computer-aided design basing on the structure of homophenylalanyl-phenylalanine analogue (hPheP[CH 2 ]Phe) bound in …
Six amino acids define a minimal dimerization sequence and stabilize a transmembrane helix dimer by close packing and hydrogen bonding
2013
AbstractDistinct amino acid sequences have been described to mediate oligomerization of transmembrane α-helices. However, as the sequence context is crucial to determine specificity in transmembrane helix–helix interaction, the question arises how small a sequence can be without losing specificity. In the present analysis, six amino acids have been identified in the PsbF transmembrane helix dimer, which form the contact region of two interacting helices and are directly involved in helix–helix interactions. However, individual amino acids within the complex sequence pattern only together ensure sequence specificity of the analyzed transmembrane helix–helix interactions by mediating close pa…
Recognition of G-quadruplex DNA by triangular star-shaped compounds: with or without side chains?
2011
International audience; We report the synthesis of two new series of triangular aromatic platforms, either with three aminoalkyl side chains (triazatrinaphthylene series, TrisK: six compounds), or without side chains (triazoniatrinaphthylene, TrisQ). The quadruplex-DNA binding behavior of the two series, which differ essentially by the localization of the cationic charges, was evaluated by means of FRET-melting and G4-FID assays. For the trisubstituted triazatrinaphthylenes (TrisK), the length of the substituents and the presence of terminal hydrogen-bond-donor groups (NH(2)) were shown to be crucial for ensuring a high quadruplex affinity (ΔT(1/2) values of up to 20 °C at 1 μM for the best…
Dibutyltin(IV) complexes containing arylazobenzoate ligands: chemistry, in vitro cytotoxic effects on human tumor cell lines and mode of interaction …
2009
Dibutyltin(IV) complexes of composition Bu2Sn (LH)2, where LH is a carboxylate residue derived from 2-[(E)- (5-tert-butyl-2- hydroxyphenyl)diazenyl]benzoate (L1H) with water molecule (1), 4-[(E)-(5-tert-butyl-2-hydroxyphenyl) diazenyl]benzoate (L2H) (2) and 4-[(E)-(4-hydroxy-5- methylphenyl)diazenyl]benzoate (L3H) (3), were synthesized and characterized by spectroscopic (1H, 13C and 119Sn NMR, IR, 119Sn Mössbauer) techniques. A full characterization was accomplished from the crystal structure of complex 1. The molecular structures and geometries of the complexes (1a i.e. 1 without water molecule and 3) were fully optimized using the quantum mechanical method (PM6). Complexes 1 and 3 were fo…
Solvent effects on the conformational preferences of model peptoids. MP2 study.
2014
The influence of aqueous environment on the main-chain conformation (ω0, ϕ, and ψ dihedral angles) of two model peptoids: N-acetyl-N-methylglycine N’-methylamide (Ac-N(Me)-Gly-NHMe) (1) and N-acetyl-N-methylglycine N’,N’-dimethylamide (Ac-N(Me)-Gly-NMe2) (2) was investigated by MP2/6-311++G(d,p) method. The Ramachandran maps of both studied molecules with cis and trans configuration of the N-terminal amide bond in the gas phase and in water environment were obtained and all energy minima localized. The polarizable continuum model was applied to estimate the solvation effect on conformation. Energy minima of the Ac-N(Me)-Gly-NHMe and Ac-N(Me)-Gly-NMe2 have been analyzed in terms of the possi…
Conformational investigation of ?,?-dehydropeptides.N-acetyl-(E)-dehydrophenylalanineN?-methylamide: conformational properties from infrared and theo…
2005
N-Acetyl-(E)-dehydrophenylalanine N'-methylamide [Ac-(E)-DeltaPhe-NHMe], one of a few representative (E)-alpha,beta-dehydroamino acids, was studied by FTIR in dichloromethane and acetonitrile. To support spectroscopic interpretations and to gain some deeper insight into the Ac-(E)-DeltaPhe-NHMe molecule, the Ramachandran potential energy surface was calculated by the B3LYP/6-31G*//HF/3-21G method and the conformers localized were fully optimized at the B3LYP/6-31 + G** level. The spectra and calculations were compared with those of the related molecules Ac-DeltaAla-NHMe and Ac-(Z)-DeltaPhe-NHMe. The title compound assumes two conformational states in equilibrium in dichloromethane solution …