Structure and dynamics of self-assembled poly(ethylene glycol) based coiled-coil nano-objects.

Herein we describe the structure and dynamics of self-assembled nano-objects generated from poly(ethylene glycol) based (PEG-ylated) coiled-coil hybrid block copolymers. Electron paramagnetic resonance (EPR) experiments on spin-labeled samples provided a strong indication for a parallel alignment of the peptide helices in at least the dimeric coiled-coil nano-object and indicated that the PEG chains are folded rather closely around the peptide core of the nano-objects. The EPR results were supported by AFM studies, which revealed the presence of discrete nanosized objects in thin, spin cast films of the block copolymers on mica substrates. Since their size and structure may be engineered via directed mutations in the amino acid sequence, these nano-objects may be interesting building blocks for the development of supramolecular materials with various potential applications.     

Generation of Molecular Fields, Quantum Similarity Measures and Related Questions

A straightforward discussion on how to generate molecular fields is developed within the postulates of quantum mechanics. The theoretical formalism points towards the generalization and extension of the well-known molecular field forms, associated to density function and electrostatic molecular potential (EMP), including another category of fields associated to quantum molecular similarity measures. The results show that the new formalism can be easily applied to obtain an unlimited number of new information about molecular behavior.     

Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces

The conformational change of the 39-43 residues of the amyloid beta-peptide (Abeta) toward a beta-sheet enriched state promotes self-aggregation of the peptide molecules and constitutes the major peptide component of the amyloid plaques in Alzheimer patients. The crucial question behind the self-aggregation of Abeta is related to the different pathways the peptide may take after cleavage from the amyloid precursor proteins at cellular membranes. This work is aiming at determining the conformation of the Abeta (1-40) adsorbed on hydrophobic Teflon and hydrophilic silica particles, as model sorbent surfaces mimicking the apolar transmembrane environment and the polar, charged membrane surface, respectively. The mechanism by which the Abeta interacts with solid surfaces strongly depends on the hydrophobic/hydrophilic character of the particles. Hydrophobic and electrostatic interactions contribute differently in each case, causing a completely different conformational change of the adsorbed molecules on the two surfaces. When hydrophobic interactions between the peptide and the sorbent prevail, the adsorbed Abeta (1-40) mainly adopts an alpha-helix conformation due to H-bonding in the apolar part of the peptide that is oriented towards the surface. On the other hand, when the peptide adsorbs by electrostatic interactions beta-sheet formation is promoted due to intermolecular association between the apolar parts of the adsorbed peptide. Irrespective of the characteristics of the solid sorbent, crowding the surface results in intermolecular association between adsorbed molecules leading to a strong aggregation tendency of the Abeta (1-40). [Diagram: see text] CD spectra of Abeta (1-40) at pH 7: A) in solution ([Abeta]=0.2 mg.ml(-1)) freshly prepared (line) and after overnight incubation (symbols);B) on Teflon (Gamma=0.5 mg.m(-2)).     

Nanotechnology with soft materials.

Nature exploits self-organization of soft materials in many ways, to produce cell membranes, biopolymer fibers and viruses, to name just three. Mankind is now able to design materials at the nanoscale, whether through atom-by-atom or molecule-by-molecule methods (top-down) or through self-organization (bottom-up). The latter method encompasses soft nanotechnology. Self-organization of soft materials can be exploited to create a panoply of nanostructures for diverse applications. The richness of structures results from the weak ordering because of noncovalent interactions. Thus, thermal energy is important as it enables transitions between phases with differing degrees of order. The power of self-organization may be harnessed most usefully in a number of nanotechnology applications, which include the preparation of nanoparticles, the templating of nanostructures, nanomotor design, the exploitation of biomineralization, and the development of functionalized delivery vectors.     

氢甲酰化反应溶剂效应的量子化学研究

在B3LYP/6-31G(d, p)(Rh和P采用LANL2DZ + Polar)水平下,利用自洽反应场（SCRF）的Onsager模型,系统研究了C6H12、C6H6、THF、CH2Cl2、CH3OH和H2O（相对介电常数ε分别为2.02、2.25、7.58、8.93、32.63和78.39）六种溶剂对乙烯氢甲酰化反应中各驻点的结构和反应机理的影响.分别在上述溶剂中优化了反应物、产物、中间体和过渡态的结构,并计算了自由能和活化自由能.计算结果表明,不同溶剂对反应势能面上各驻点的结构和能量均有一定的影响,而且随着相对介电常数ε的增加,反应的活化自由能下降.水是以上六种溶剂中最佳的溶剂,这与大量的实验研究结果一致.     

Two‐ and Three‐Dimensional Molecular Organization of Schiff‐Base Derivatives

We have designed and synthesized a series of Schiff base derivatives, and studied their structural features in two‐dimensional (2D) and three‐dimensional (3D) states by combining scanning tunneling microscopy (STM) and X‐ray diffraction experiments. The Schiff‐base derivatives with short alkyl chains crystallize easily, which allows a detailed structural analysis by X‐ray diffraction. Due to the strong adsorbate–substrate interactions, those bases with long alkyl chains easily form 2D assemblies on highly oriented pyrolytic graphite (HOPG). The STM images indicate also that the introduction of two methoxy groups into the molecule can change the structure of these 2D assemblies as a result of the increased steric hindrances, for example: the Schiff‐base derivative, bearing both methoxy groups and C₁₆H₃₃ tails, forms 2D Moiré patterns, and an alignment of pairing Schiff‐base molecules may be easily resolved. Conversely, the Schiff base derivative, bearing solely C₁₆H₃₃ tails, forms 2D non‐Moiré patterns. It is demonstrated that the 3D structural features result from the compromise of intermolecular interactions of different molecular moieties. However, there is one more factor, which also governs the 2D structure: the adsorbate‐substrate interaction. The 3D crystal structure may thus help to understand many factors involved in the formation of 2D structures, and would be helpful for designing new molecular assemblies with tailoring functions.     

Role of the special pair in the charge-separating event in photosynthesis

We synthesized special-pair/electron-acceptor systems consisting of a complementary slipped cofacial dimer of imidazolyl-substituted zinc porphyrin, bearing pyromellitdiimide as the electron acceptor. In the case of the dimer, the first and second oxidation potentials were split into a total of four peaks in the differential pulse voltammetry measurement. Furthermore, the shift values of the first oxidation potentials obtained by changing the solvent polarity for the dimer were almost half of those observed for the monomer. These results indicate that the radical cation is delocalized over the whole pi system of the dimer. Time-resolved transient absorption measurements revealed that, relative to the corresponding monomer, the dimer accelerated the charge separation rate, but decelerated the charge recombination rate. The smaller reorganization energy of the slipped cofacial dimer relative to that of the monomeric system demonstrates the significance of the special-pair arrangement for efficient charge separation in photosynthesis.     

Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR

Comparative molecular similarity indices analysis (CoMSIA), a three-dimensional quantitative structure activity relationship (3D QSAR) paradigm, was used to examine the correlations between the calculated physicochemical properties and the in vitro activities (3'-processing and 3'-strand transfer inhibition) of a series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors. The training set consisted of 34 molecules from five structurally diverse classes: salicylpyrazolinones, dioxepinones, coumarins, quinones, and benzoic hydrazides. The data set was aligned using extrema of molecular electrostatic potentials (MEPs). The predictive ability of the resultant model was evaluated using a test set comprised of 7 molecules belonging to a different structural class of thiazepinediones. A CoMSIA model using an MEP-based alignment showed considerable internal as well external predictive ability (r2(cv) = 0.821, r2(pred) = 0.608 for 3'-processing; and r2(cv) = 0.759, r2(pred.) = 0.660 for 3'-strand transfer).     

Self‐Assembly of Dialkyltin Moieties and Mercaptobenzoic Acid into Macrocyclic Complexes with Hydrophobic “Pseudo‐Cage” or Double‐Cavity Structures: Supramolecular Infrastructures Involving Intermolecular C?H⋅⋅⋅S Weak Hydrogen Bonds and π–π Interactions

Four novel organotin complexes of two types—[R₂Sn(o‐SC₆H₄CO₂)]₆ (R=Me, 1 ?H₂O; nBu, 2 ) and {[R₂Sn(m‐CO₂C₆H₄S)R₂Sn(m‐SC₆H₄CO₂)SnR₂]O}₂ (R=Me, 3 ; nBu, 4 )—have been prepared by treatment of o‐ or m‐mercaptobenzoic acid and the corresponding R₂SnCl₂ (R=Me, nBu) with sodium ethoxide in ethanol (95 %). All the complexes were characterized by elemental analysis, FT‐IR and NMR (¹H, ¹³C, ¹¹⁹Sn) spectroscopy, TGA, and X‐ray crystallography diffraction analysis. The molecular structure analyses reveal that both 1 and 2 are hexanuclear macrocycles with hydrophobic “pseudo‐cage” structures, while 3 and 4 are hexanuclear macrocycles with double‐cavity structures. Furthermore, the supramolecular structure analyses show that looser and more intriguing supramolecular infrastructures were also found in complexes 1 – 4 , which exist either as one‐dimensional chains of rings or as two‐dimensional networks assembled from the organometallic subunits through intermolecular C? H???S weak hydrogen bonds (WHBs) and π–π interactions.     

Dipyrrolyldiketone difluoroboron complexes: novel anion sensors with C-H...X- interactions

1,3-Dipyrrolyl-1,3-propanediones, synthesized from pyrroles and malonyl chloride, form BF2 complexes, which represent a new class of naked-eye sensors for halide and oxoanions. The association mode for the interactions of both the pyrrolyl NH and bridging CH protons with anions was confirmed by 1H NMR chemical shifts in CD2Cl2 and supported by theoretical studies. The binding constants (Ka) were estimated as 8.1x10(4), 2.0x10(3), 3.3x10(2), 1.3x10(4), and 80 M(-1) for F-, Cl-, Br-, H2PO4(-), and HSO4(-) by UV/Vis absorption spectral changes in CH2Cl2. Augmentation of Ka compared with dipyrrolylquinoxaline for H2PO4(-) is much larger than those for other anions. Contrary to other anions, F- quenches the emission almost completely, which was detected by the fluorescence spectrum as well as the naked-eye. In the case of the chloride anion complex, the formation of Cl(-)-bridged 1D networks, in which anion is associated with two BF2 complexes, is observed in the solid state.