The energy landscape of a selective tumor-homing pentapeptide

Recently, a potentially powerful strategy based on phage-display libraries has been presented to target tumors via homing peptides attached to nanoparticles. The Cys-Arg-Glu-Lys-Ala (CREKA) peptide sequence has been identified as a tumor-homing peptide that binds to clotted plasmas proteins present in tumor vessels and interstitium. The aim of this work consists of mapping the conformational profile of CREKA to identify the bioactive conformation. For this purpose, a conformational search procedure based on modified simulated annealing combined with molecular dynamics was applied to three systems that mimic the experimentally used conditions: (i) the free peptide; (ii) the peptide attached to a nanoparticle; and (iii) the peptide inserted in a phage display protein. In addition, the free peptide was simulated in an ionized aqueous solution environment, which mimics the ionic strength of the physiological medium. Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems.     

Organocatalytic asymmetric synthesis of alpha,alpha-disubstituted alpha-amino acids and derivatives

It is shown that racemic oxazolones are excellent reagents for the synthesis of chiral quaternary amino acids and its derivatives by the diastereo- and enantioselective nucleophilic addition to alpha,beta-unsaturated aldehydes catalyzed by diarylprolinol silyl ethers. The scope of this new organocatalytic reaction is demonstrated for different oxazolones having aromatic and alkyl groups at the reactive carbon atom and different aromatic and aliphatic substituted alpha,beta-unsaturated aldehydes, for which the stereoselective reaction proceeds with good yield, moderate to good to very high diastereoselectivity, and very high enantioselectivity. The potential of the reaction is shown for the synthesis of optically active alpha,alpha-disubstituted alpha-amino acids, alpha-quaternary proline derivatives, amino alcohols, lactams, and tetrahydropyranes. Furthermore, we have calculated by DFT-methods the transition-state structures that account for both the diastereo- and enantioselectivity observed for the addition of oxazolones to the alpha,beta-unsaturated aldehydes. For one class of compounds, the stereoselectivity is controlled by a hydrogen-bonding interaction of the enolate-form of the oxazolone with an ortho-hydroxy-phenyl substituent of the alpha,beta-unsaturated aldehyde, whereas the benzhydryl-protecting group in the oxazolone determines the diastereo- and enantioselectivity in a more general manner for both aromatic and aliphatic alpha,beta-unsaturated aldehydes.     

Coarse-graining: a procedure to generate equilibrated and relaxed models of amorphous polymers

We present a coarse-graining procedure to construct models of amorphous polymers. The method, which was applied to polyethylene, is based on a generation-relaxation strategy previously developed to provide independent atomistic microstructures. The coarse-graining was performed by assigning positions to mesoscopic particles denoted blobs, which represent groups of atoms, through distance, angle and dihedral distribution functions. The interaction energy between pairs of blobs was evaluated through a soft potential, whose parameters were derived from atomistic models. Three levels of coarse-graining that differ in the number of atoms included in the blob have been considered. The structural and energy-related properties calculated using the coarse-grained models developed in this study are in good agreement with those obtained using atomistic simulations.     

Contraction process of an electroactive actuator based on a one microsecond atomistic molecular dynamics simulation

The contraction process of an electroactive actuator constituted by calix[4]arene units and quaterthiophene segments has been investigated at the microscopic level by using atomistic molecular dynamics simulations in dichloromethane solution using explicit solvent molecules. Results derived from a 1 mus trajectory of the oxidized and deprotonated actuator indicate that the contraction occurs through a non-concerted mechanism in which each actuating units present in the system behave independently. The efficiency of the contraction process can be reduced by the presence of secondary conformational transitions in the calix[4]arene scaffolds. Accordingly, the drastic reduction of the molecular length expected during the contraction process can be limited by such transitions, which involve the rotational isomerism of a phenolate ring. However, such type of conformational transitions does not compromise the actuator power due to its intrinsic capacity to adopt compact molecular arrangements. On the other hand, the rate of the contraction process is influenced by the presence of solvent molecules, which have been found to reduce it by a factor of about 1000.     

Sensing Abilities of Crown Ether Functionalized Polythiophenes

Tuning sensing abilities! The affinity of three different [15]crown‐5 ether functionalized polythiophenes for alkali ions has been explored (see figure). Ab initio and DFT quantum mechanical calculations show that the binding energy between neutral conducting polymers and metallic ions, which interact attractively, decreases as the size of the ion increases. Oxidation of these polythiophene derivatives significantly reduces their affinity towards alkali ions, becoming low or even nonexistent.

     

Trace determination of EDTA from water samples using dispersive liquid–liquid microextraction coupled with HPLC-DAD

Dispersive liquid–liquid microextraction (DLLME) in conjunction with high-performance liquid chromatography-diode array detection (HPLC-DAD) has been applied to the extraction and determination of EDTA in sediments and water samples. The effect of extraction, nature and volume of disperser solvent, pH value of sample solution, extraction time and extraction temperature were investigated. Under the optimal conditions the analytical range of EDTA was from 3.0 to 50.0 μg L^?1 with a correlation coefficient of 0.9982 and a detection limit of 1.7 μg L^?1. The relative standard deviation (RSD) was less than 5.4% (n?=?5), and the recovery values were in the range of 89–95%. The simplicity, high enrichment, high recovery and good repeatability are the main advantages of the method presented. The DLLME-HPLC-DAD method was successfully applied to the analysis of EDTA in aqueous samples.     

Theoretical investigation of the mechanism of primary amines reacting with hexamolybdate: an insight into the organoimido functionalization and related reactions of polyoxometalates

The functionalization of polyoxometalates (POMs), especially with an amino group to yield organonitrogenous derivatives of POMs, is an efficient approach to the enrichment of their structures and the diversification of their properties for various applications. The mechanism for the formation of organonitrogenous-derivatized hexamolybdates was explored by investigating the monofunctionalization of the [Mo(6)O(19)](2-) ion with methylamine using the density functional theory (DFT) method. The calculations show that the direct imidoylization of hexamolybdate with methylamine is both kinetically and thermodynamically unfavorable. However, this imidoylization was found to take place readily in the presence of dimethylcarbodiimide (DMC), for which the free-energy barrier was calculated to be +32.5 kcal mol(-1) in acetonitrile. Moreover, various factors controlling the efficiency of the imidoylization were examined. The calculations show that [W(5)MoO(19)](2-) has a relatively lower reactivity than [Mo(6)O(19)](2-), and that the imidoylization of [W(6)O(19)](2-) is an unfavorable process. With respect to the effect of carbodiimides, it is found that the catalytic activity is directly proportional to the electron-withdrawing effects of the substituents. As to the reactivity of R-NH(2) , the computation results indicate that the free-energy barriers of the substitution reactions are linearly correlated with the basicity constants (pK(b)) of the amino groups. It is noteworthy that the introduction of the proton dramatically decreases the free-energy barrier of the imidoylization of [Mo(6)O(19)](2-) catalyzed by DMC to 24.3 kcal mol(-1) in acetonitrile.     

Highly stereoselective synthesis of tertiary propargylic centers and their isomerization to enantiomerically enriched allenes

Center of attention: A new approach for the synthesis of enantiomerically enriched allenes by isomerization of 2-p-tolylsulfinylphenyl propargylic derivatives is presented, which in turn are prepared by reaction of sulfinylated lithium benzylcarbanions with arylsulfonylacetylenes. The high control of stereoselectivity in both steps is exerted by the sulfinyl group.     

Arylsulfonylacetylenes as alkynylating reagents of Csp2-H bonds activated with lithium bases

Chameleon: a new strategy for the synthesis of a wide variety of alkynyl derivatives by the reaction of substituted arylsulfonylacetylenes with organolithium species is described. The high yields, the simplicity of the experimental procedure, the broad scope of this reaction, and the formation of C(sp)-C(sp2) bonds without using transition metals are the main features of this methodology.