Search results for "Conformational analysis"

Toward engineering efficient peptidomimetics. Screening conformational landscape of two modified dehydroaminoacids

2013

Effective peptidomimetics should posses structural rigidity and appropriate interaction pattern leading to potential spatial and electronic matching to the target receptor site. Rational design of such small bioactive molecules could push chemical synthesis and molecular modeling toward faster progress in medicinal chemistry. Conformational properties of N-t-butoxycarbonyl-glycine-(E/Z)-dehydrophenylalanine N′,N′-dimethylamides (Boc-Gly-(E/Z)-ΔPhe-NMe2) in chloroform were studied by NMR and IR spectroscopy. The experimental findings were supported by extensive calculations at DFT(B3LYP, M06-2X) and MP2 levels of theory and the β-turn tendency for both isomers of the studied dipeptide were d…

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,…

Ferrocenyl-Labeled Sugar Amino Acids: Conformation and Properties

2012

Novel organometallic sugar amino acid conjugates 1–5 have been prepared by amide coupling of O-protected N-acetylmuramic acid and iso-muramic acid (2-[3-amino-2, 5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxypropanoic acid) with 1-aminoferrocene, 1-aminoferrocene-1′-carboxylic acid (H-Fca-OH), or 1, 1′-diaminoferrocene, respectively. The influence of the ferrocenyl moiety and presence of additional remote potential hydrogen atom acceptors and donors at the ferrocenyl core on the conformation and lipophilicity is investigated by TLC, IR, NMR, and CD spectroscopic methods augmented by density functional calculations. Furthermore, the redox potential of the ferrocene/ferrocenium couple is tuned by…

l-Arabinose Conformers Adsorption on Ruthenium Surfaces: A DFT Study

2012

Adsorption of 5 L-arabinose tautomers – one acyclic and four cyclic (α and β, pyranose and furanose) species – on a ruthenium surface was studied as a precursor-process of the, nowadays more and more, industrially important sugar catalytic hydrogenation on metal surfaces in water medium. The study was mostly referred to a 37-atom metal catalyst fragment, even though border-effects on the adsorption processes were also checked employing a 61-atom metal fragment. In order to figure out conformational effects on the title process the tautomer flexibility was, at first, investigated by the genetic-algorithm based code Balloon, considering the conformational spaces of the different aquo tautomer…

STUDIO QUANTOMECCANICO STRUTTURALE E CONFORMAZIONALE DELL'INSETTICIDA ROTENONE

2008

Effetto della flessibilità conformazionale sull'equilibrio di interconversione tra aldosi e chetosi

2008

Le reazioni di interconversione tra gli aldosi e i chetosi sono importanti trasformazioni, di interesse biochimico, che si presentano in parecchi stadi sia del catabolismo (glicolisi, via dei pentosofosfati) che dell'anabolismo (ciclo di Calvin) dei glucidi. Il meccanismo di reazione accettato, che coinvolge intermedi 1,2-endiolici, è talvolta riferito come una doppia tautomeria acido-catalizzata. Poiché, d'altro canto, reagenti, prodotti ed intermedi presentano tutti un'elevata flessibilità molecolare, ogni indagine computazionale sufficientemente accurata deve comprendere necessariamente l'analisi conformazionale di ciascun substrato coinvolto nell'equilibrio chimico. Tale analisi è stata…

The effect of β‐methylation on the conformation of α, β‐dehydrophenylalanine: a DFT study

2009

Dehydroamino acids are non‐coded amino acids that offer unique conformational properties. Dehydrophenylalanine (ΔPhe) is most commonly used to modify bioactive peptides to constrain the topography of the phenyl ring in the side chain, which commonly serves as a pharmacophore. The Ramachandran maps (in the gas phase and in CHCl3 mimicking environments) of ΔPhe analogues with methyl groups at the β position of the side chain as well as at the C‐terminal amide were calculated using the B3LYP/6‐31 + G** method. Unexpectedly, β‐methylation alone results in an increase of conformational freedom of the affected ΔPhe residue. However, further modification by introducing an additional methyl group a…