Thermal oxidative degradation of additive-free polypropylene pellets investigated by multichannel Fourier-transform chemiluminescence spectroscopy

Thermal oxidative degradation of additive-free polypropylene pellets heated isothermally in dry air at 150 and 180 °C (below and above the melting point of 163 °C) was investigated by multichannel Fourier-transform chemiluminescence spectroscopy. The initial peak wavelength of chemiluminescence emission at 490 nm remained constant during the early stages of thermal degradation, but new emissions developed with time in the red spectral region over an extended oxidation period. The time-dependent luminescence spectra were deconvoluted into three emission bands by least-squares fitting using Gaussian curves. We concluded that at least three groups of luminescent species (luminophores), having different conjugation lengths, were generated by thermal oxidation over extended periods and show luminescence around 490, 660, and 740 nm.     

Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm

The Transition Rapidly exploring Random Eigenvector Assisted Tree (TRREAT) algorithm is introduced to perform searches along low curvature pathways on a potential energy surface (PES). The method combines local curvature information about the PES with an iterative Rapidly exploring Random Tree algorithm (LaValle, Computer Science Department, Iowa State University, 1998, TR98–11) that quickly searches high‐dimensional spaces for feasible pathways between local minima. Herein, the method is applied to identifying conformational changes of molecular systems using Cartesian coordinates while avoiding a priori definition of collective variables. We analyze the pathway identification problem for alanine dipeptide, cyclohexane and glycine using nonreactive and reactive forcefields. We show how TRREAT‐identified pathways can be used as valuable input guesses for double‐ended methods such as the Nudged Elastic Band when ascertaining transition state energies. This method can be utilized to improve/extend the reaction databases that lie at the core of automatic chemical reaction mechanism generator software currently developed to build kinetic models of chemical reactions. © 2013 Wiley Periodicals, Inc.     

Synthesis and conformational behavior of pseudopeptides containing δ-azaproline. A cis conformational preference for Xaa1–δ-azaPro bond

δ-Azaproline, a new bis-nitrogen proline surrogate has been used in order to control the conformation of an AA–ΨPro bond. Conformational analysis of Xaa₁–δ-azaPro–Xaa₃ performed by NMR, IR experiments, and molecular modeling revealed a preference for a trans conformation of the Xaa₁–δ-azaPro bond when δ-azaPro is protected by a Boc group. The removal of the Boc protection leads to the establishment of a C₁₀ pseudocycle via a hydrogen bond network favoring the cis conformation of the Xaa₁–δ-azaPro bond.     

Conformational change in a urea catalyst induced by sodium cation and its effect on enantioselectivity of a Friedel-Crafts reaction

While developing bis-camphorsulfonyl urea as a hydrogen-bonding catalysts, we discovered that the native conformation of the catalyst is unsuitable for inducing enantioselectivity. By complexing the catalyst with weakly Lewis acidic sodium cations, we were able to change the conformation of the catalyst and attain a significant improvement in the selectivity. We provide structural information from X-ray crystallography to show that the uncomplexed catalyst is indeed in an unfavorable conformation. Infrared and Raman spectroscopic studies show that sodium binds the catalyst through the carbonyl and sulfonyl groups. Simulated IR and Raman spectra match well with the experimentally recorded spectra, thereby corroborating the proposed conformational change. This result shows that weak Lewis acids can be used to tune the conformation of hydrogen-bonding catalysts and enhance the selectivity of reaction catalyzed by these systems.     

1′-Acetylferrocene amino acid esters and amides. A simple model for parallel β-helical peptides

In this study we present a synthesis and conformational analysis of 1′-acetylferrocene amino acid derivatives of type Ac–Fn–CO–AA–Y (Fn=ferrocene-1,1-diyl; AA=Gly, Ala or Val; Y=OMe or NHMe) as a simple model for parallel β-helical peptides. Derivatives with only one amino acid adopt a reduced number of total conformations and allow a more exact analysis of intramolecular hydrogen bonds (IHB) close to the ferrocene unit. Conformational analysis of these bioconjugates was performed by a combination of spectroscopic techniques (IR, NMR and CD) and corroborated by solution-phase DFT calculations. The investigation of ester conjugates 1–3 indicates the coexistence of non-bonded (an open forms) and hydrogen bonded NH_a group forming a 7-membered ring (γ-turn). The amide derivatives 4–6 with an additional NH_b hydrogen bond donor are mostly constituted of conformers with a 10-membered ring (β-turn) as a single IHB pattern or the β-turn accompanied by a 7-membered ring (γ-turn) containing NH_a group. The exchange of the amino acid side-chain does not significantly affect the conformational properties and IHB pattern of the studied conjugates 1–6.     

Synthesis and conformational analysis of new troponyl aromatic amino acid

Synthetic peptides are in huge demand in expansion of potential peptide mimics, which may have improved or comparable function as natural one. With these concerns, phenyl bearing aromatic amino acids and peptides has extensively explored, because phenyl residue has high probability in forming stable secondary structure, owing to the presence of an extra stabilizing factor as π–π non-covalent interactions. Apart from phenyl bearing benzenoid aromatic amino acids, a few non-benzenoid aromatic derivatives such as tropolone and related compounds are also occurred in nature, but troponyl containing amino acids and peptides are very poorly understood. Tropolonyl derivatives also contain carbonyl functional group, which may play an important role to provide stable conformation in peptide. Herein we report the synthesis, and conformational analysis of rationally designed new unnatural δ-amino acid, troponyl aminoethylglycine (Tr-aeg), which contains troponyl residue as side chain in flexible aminoethylglycine (aeg) amino acid backbone. We also demonstrate the role of troponyl carbonyl of Tr-aeg residue in hydrogen bonding with adjacent amide NH of their hybrid di/tri-peptides with NMR methods and DFT calculations. In future, Tr-aeg amino acid would be a potential building block in development of promisable peptide mimics.     

Structure-based study of antiamyloidogenic cyclic d,l-α-peptides

Protein misfolding and aggregation are the hallmarks of many devastating diseases. We have previously shown that cyclic d,l-α-peptide CP-2 reacts and stabilizes less toxic forms of amyloid β (Aβ), and protects the cells from Aβ-induced toxicity. Here, we performed extensive structure-based studies on CP-2 to elucidate the contribution of each residue to the total antiamyloidogenic activity and determine the interactions that are involved between CP-2 and Aβ. We showed that the hydrophobicity of CP-2 analogs correlates with their antiamyloidogenic potency, however, aromatic interactions are even more important for this activity. The antiamyloidogenic activity of CP-2 analogs also correlates with their ability to self-assemble, as shown by the critical micelle concentration measurements. The cell survival studies performed on rat pheochromocytoma PC-12 cells suggest that incorporation of an additional aromatic residue to the CP-2's sequence increases its protective effect against Aβ42-induced toxicity.     

A comprehensive conformational analysis of tryptophan,its ionic and dimeric forms

Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan ( W ) and its ionized counterparts cations (WC) , anions (WA) , and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH‐π, NH‐π, CH‐π, CH‐O, and π‐π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH‐O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T‐shaped orientations (CH‐π interactions) are more prevalent, while stacked orientations (π‐π interactions) are predominant at a smaller distance. © 2013 Wiley Periodicals, Inc.     

GPCR A2A AR腺苷受体蛋白的激动剂结合及其诱导的蛋白活性开关构象变化

运用分子动力学模拟,研究了腺苷酸（激动剂）与A2AAR腺苷受体蛋白的相互作用和配体结合诱导的蛋白动力学变化．识别了与腺苷酸结合力强于0．5kcal／mol的关键基团：A63^2．61,I66^2．64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52和N253^6.55,观察到腺苷酸没有与L167^5.28相互作用,这一结果支持了L167^5.28是抑制剂特异性结合位点,不与激动剂结合．未结合配体（激动剂或抑制剂）的单体A2AAR和腺苷酸结合后的A2AAR在构象上有三个不同功能性开关．腺苷酸结合可以诱导A2AAR腺苷受体蛋白的构象调整,使得三个功能性开关器件的构象与单体A2AAR不同．     

You cannot fight the pressure: Structural rearrangements of active pharmaceutical ingredients under magic angle spinning

Although solid-state nuclear magnetic resonance (NMR) is a versatile analytical tool to study polymorphs and phase transitions of pharmaceutical molecules and products, this work summarizes examples of spontaneous and unexpected (and unwanted) structural rearrangements and phase transitions (amorphous-to-crystalline and crystalline-to-crystalline) under magic angle spinning (MAS) conditions, some of them clearly being due to the pressure experienced by the samples. It is widely known that such changes can often be detected by X-ray powder diffraction (XRPD); here, the capability of solid-state NMR experiments with a special focus on ¹H-¹³C frequency-switched Lee–Goldburg heteronuclear correlation (FSLG HETCOR)/MAS NMR experiments to detect even subtle changes on a molecular level not observable by conventional 1D NMR experiments or XRPD is presented. Furthermore, it is shown that a polymorphic impurity combined with MAS can induce a crystalline-to-crystalline phase transition. This showcases that solid-state NMR is not always noninvasive and such changes upon MAS should be considered in particular when compounds are studied over longer time spans.