Size Effect on the Raman Spectra and Electronic Structure of the Glycine-alanine Oligopeptide Chains

A theoretical study on oligopeptide chains of glycine-alanine by density functional theory(DFT) is given in this paper. Raman spectra of the oligopeptide chains are examined. The geometric structures, frontier orbital, energy gap, atomic charge distribution, density of states and chemical activity of the side chain are studied at the B3LYP/6-31G(d) level. Results show that, with the number of residues increasing, vibrations of typical functional groups present Raman frequency shift, and the energy gap is gradually reduced. The HOMO and LUMO focus on the amino and carboxyl at the ends of oligopeptides. It is helpful for oligopeptides to self-assemble into chains. In addition, different residues(glycine or alanine) at the ends of chains result in the even-odd effect of orbital energy in the growth process. The size effects of physical and chemical properties only exist when the oligopeptides are shorter, and the phenomenon disappeared as the chain continues to grow.     

Synthesis, solid-state structures, and aggregation motifs of phosphines and phosphine oxides bearing one 2-pyridone ring

Three phosphines and their corresponding oxides bearing one 2-pyridone ring and two benzene rings were synthesized. Their single-crystal X-ray analyses exhibited three kinds of molecular aggregation: bimolecular aggregates, chiral one-dimensional structures, and achiral one-dimensional structures. In the bimolecular aggregate of (2-oxo-1, 2-dihydro-x-pyridyl)diphenylphosphines (x = 3: 2a and 6: 2c), cyclic dimers that are derived from two 2-pyridone rings are observed. In contrast, (2-oxo-1,2-dihydro-5-pyridyl)diphenylphosphine (2b) molecules form a chiral one-dimensional chain via intermolecular hydrogen bonding. In the case of phosphine oxides, their oxygen always acts as a hydrogen acceptor of the hydrogen bonding. Thus, (2-oxo-1,2-dihydro-x-pyridyl)diphenylphosphine oxides (x = 3: 3a and 5: 3b) form hydrogen bonds intermolecularly between the oxygen atom on the phosphoryl group and the hydrogen atom on nitrogen to construct a chiral or an achiral one-dimensional chain. Interestingly, (2-oxo-1,2-dihydro-6-pyridyl)diphenylphosphine oxide (3c) exists as a 2-hydroxypyridine form (enol form) in a crystalline state, and intermolecular hydrogen bonds between the phosphoryl oxygen and the hydroxy proton construct an achiral one-dimensional chain.     

Influence of structural features on the self‐assembly of short ionic oligopeptides

We investigated the self‐aggregation of 12 short ionic oligopeptides constituted by 4–7 amino acid residues to establish useful structure–property relationships that might be exploited in the biomedical field by using the concept of molecular Lego. We show that the critical aggregation concentration (CAC) of tetrapeptides decreases with increasing hydrophobicity of neutral residues. Additionally, the dependence of the CAC of isomeric oligopeptides on the distribution of amino acid residues confirms the high tendency to self‐organization of molecules with alternating ionic and neutral residues. Indeed, atomic force microscopy (AFM) images recorded on oligopeptide solutions above the CAC show the presence of either fibrillar or spherical aggregates depending on oligopeptide structure and concentration, steric hindrance, solution pH, and time. The potential of the investigated oligopeptides in tissue engineering applications is supported by their in vitro cytocompatibility. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 889–897, 2010     

A Self-Assembled Unit Comprising 12 Squaraine Dyes Built Up from Two Star-Shaped Hexasquarainyl-Benzene Molecules

We describe the aggregate formation and optical properties of a star-shaped hexaarylbenzene with six squaraine chromophores (=hexasquarainyl benzene). Comprehensive concentration-dependence studies in acetone/CHCl₃ mixtures reveal a strong propensity to form discrete dimeric aggregates with a high binding constant in excess of 10⁶ m ⁻¹. In this context, a large hypsochromic shift of almost 2700 cm⁻¹ was found in the absorption spectrum, indicating H-type exciton coupling. The aggregate band is characterised by a very small band width of only 560 cm⁻¹, probably caused by exchange narrowing. Both experimental and computational methods were used to elucidate the supramolecular aggregate structure, which is assumed to consist of two stacked hexasquarainyl benzene monomers.     

Racemic beta-sheets as templates for the generation of homochiral (isotactic) peptides from aqueous solutions of (RS)-valine or -leucine N-carboxy- anhydrides: relevance to biochirogenesis

As part of our program on biochirogenesis of homochiral peptides from racemic precursors, we report the feasibility of obtaining peptides with homochiral sequences composed of up to 25 residues of the same handedness in the polymerization of racemic valine or leucine N-carboxyanhydrides in aqueous solutions, as initiated by amines. The composition of the oligopeptides was determined by MALDI-TOF mass spectrometry, and the sequences of some of the heterochiral diastereoisomers were studied by MALDI-TOF MS/MS performed on samples in which the S enantiomers of the monomer were tagged with deuterium atoms. The process comprises several steps: 1) a Markov mechanism of asymmetric induction in the early stages of the polymerization yields libraries of racemic oligopeptides enriched with isotactic diastereoisomers, together with oligopeptide sequences containing enantiomeric blocks of homochiral residues; 2) the short peptides self-assemble into racemic colloidal architectures that serve as regio-enantioselective templates in the ensuing process of chain elongation; 3) homochiral residues of the amino acids located at the periphery of these colloidal aggregates exert efficient enantioselection, which results in the formation of long isotactic oligopeptides. The final diastereoisomeric distribution of the peptides depends upon the composition of the templates, which is determined by the concentration of the initiator. The racemic mixtures of isotactic peptides can be desymmetrized by using enantiopure methyl esters of alpha-amino acids as initiators.     

Mass Spectrometry Study of Multiply Negatively Charged, Gas-Phase NaAOT Micelles: How Does Charge State Affect Micellar Structure and Encapsulation?

We report the formation and characterization of multiply negatively charged sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, by electrospray ionization of methanol/water solution of NaAOT followed by detection using a guided-ion-beam tandem mass spectrometer. Singly and doubly charged aggregates dominate the mass spectra with the compositions of [Na_n-zAOT_n]^z– (n?=?1–18 and z?=?1–2). Solvation by water was detected only for small aggregates [Na_n-1AOT_nH₂O]^– of n?=?3–9. Incorporation of glycine and tryptophan into [Na_n-zAOT_n]^z– aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Na_n-zAOT_n]^z– of n?≥?7, and at most two glycine molecules could be hosted in that of n?≥?13. In contrast to glycine, up to four tryptophan molecules could be accommodated within single aggregates of n?≥?6. However, deprotonation of tryptophan significantly decrease its affinity towards aggregates. Collision-induced dissociation (CID) was carried out for mass-selected aggregate ions, including measurements of product ion mass spectra for both empty and amino acid-containing aggregates. CID results provide a probe for aggregate structures, surfactant-solute interactions, and incorporation sites of amino acids. The present data was compared with mass spectrometry results of positively charged [Na_n+zAOT_n]^z+ aggregates. Contrary to their positive analogues, which form reverse micelles, negatively charged aggregates may adopt a direct micelle-like structure with AOT polar heads exposed and amino acids being adsorbed near the micellar outer surface.      

Some Cyclic Oligopeptide with S2n Symmetry

Some cyclic oligopeptides formed by an equal number of alternating D- and L-amino-acid residues have been synthesized by using the hydrochloride of the open-chain peptide acid as precursor and the mixed-anhydride condensation method. The cyclic oligopeptides (tetra-, hexa-, and octavaline, hexaleucine, and hexaphenylalanine) form very stable H-bonded structures (IR-amide band at 3270–3290 cm^?1) which are insoluble in common organic solvents. In CF₃COOH/CDCI₃ (25°), they yield ¹H-NMR spectra snowing the expected equivalency of the various amino-acid residues.     

Fragmentation and erosion of two-dimensional aggregates in shear flow

We consider single two-dimensional aggregates containing glass particles trapped at a water/oil or water/air interface. Two modes for aggregate break-up are observed: break-up by fragmentation into a few parts and break-up by erosion of single particles. We have studied the critical shear rate for these modes as a function of the aggregate size. Two different particle sizes were used. The smaller particles, with a radius of 65 microm, form aggregates that break up predominantly by erosion at a shear rate between 0.5 and 0.7 s(-1). This value hardly depends on the size of the aggregates. The larger particles, with a radius of 115 microm, form aggregates that break by erosion or by fragmentation. In both modes, the critical shear rate again depends only weakly on the size of the aggregates and ranges between 1.6 and 2.2 s(-1). Also the structural changes inside the aggregate before break-up were studied. The aggregate behavior at the water/air and water/oil interfaces is quite similar. The critical shear rate for break up was also modeled. The model shows in both modes a weak dependence of the critical shear rate on the aggregate size, which is consistent with the experimental observations. The kinetics of the erosion process was also modeled and compared with the experimentally obtained time dependence of the aggregate size. The differences in the large and small particle systems can be attributed to the occurrence of friction forces between the particles, which one expects to be much larger for the large particle system, due to the stronger two-particle interaction.     

Preparation of a novel aggregate like sugar-ball micelle composed of poly(methylglutamate) and poly(ethyleneglycol) modified by lactose and its molecular recognition by lectin

We report the preparation and characteristics of a novel micellar aggregate of an amphiphilic diblock copolymer, poly(methylglutamate) (PMG)-poly(ethyleneglycol) (PEG), whose terminus was modified by lactose lactone (LA). Due to the terminal LA moiety, this aggregate could be specifically recognized by RCA120 lectin. PMG-PEG-LA was synthesized by polymerizing the N-carboxy anhydride of L-glutamic acid gamma-methyl ester with H2N-PEG-LA as a polymerization initiator. By applying a fluorescence method using pyrene as a probe molecule, we found that PMG-PEG-LA could form the aggregate in aqueous solution. Fluorescence measurements showed that the critical aggregation concentration (C.A.C.) was 1.1 x 10(-5) M. The average diameter of the aggregate was 220 nm at 25 degrees C, as determined by the dynamic light scattering method. Circular dichroism measurements for the aggregate solution showed that the PMG residue took an alpha-helical structure, and that they associated to constitute the hydrophobic core of the aggregate. By adding RCA120 lectin to the aggregate solution, the turbidity of the solution increased rapidly, due to association of the aggregates. This implies that the aggregate could be recognized by lectin, and also suggests that sugar residues locate at the surface of the aggregates. From these findings, we concluded that the PMG-PEG-LA molecules form an aggregate like a "sugar ball" micelle, whose surface is covered by the sugar moieties. Application of the present aggregate system as a drug carrier is briefly discussed.     

Evidence of Shear Rate Dependence on Restructuring and Breakup of Latex Aggregates

Small-angle static light scattering has been used to probe the evolution of aggregate size and structure in the shear-induced aggregation of latex particles. The size of aggregates obtained from the particle-sizing instrument (Coulter LS230) was compared with the size of those obtained with another approach utilizing the Guinier equation on the scattering data. Comparison of the two methods for studying the effects of mixing on the evolution of the aggregate size with time revealed similar trends. The aggregate structures were quantified in terms of their fractal dimensions on the grounds of the validity of Rayleigh-Gans-Debye scattering theory for the fractal aggregates. Analysis of the scattering patterns of aggregates verified that restructuring of the aggregates occurred as the aggregates were exposed to certain shear environments, resulting in a scale-dependent structure that could not be quantified by a fractal dimension. The effect of restructuring on aggregate size was particularly noticeable when the aggregates were exposed to average shear rates of 40 to 80 s(-1), whereas no significant restructuring occurred at lower shear rates. At 100 s(-1), the fragmentation of aggregates appeared to be more significant than aggregate compac-tion. Copyright 2001 Academic Press.     

Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors

Many false positives in early drug discovery owe to nonspecific inhibition by colloid-like aggregates of organic molecules. Despite their prevalence, little is known about aggregate concentration, structure, or dynamic equilibrium; the binding mechanism, stoichiometry with, and affinity for enzymes remain uncertain. To investigate the elementary question of concentration, we counted aggregate particles using flow cytometry. For seven aggregate-forming molecules, aggregates were not observed until the concentration of monomer crossed a threshold, indicating a "critical aggregation concentration" (CAC). Above the CAC, aggregate count increased linearly with added organic material, while the particles dispersed when diluted below the CAC. The concentration of monomeric organic molecule is constant above the CAC, as is the size of the aggregate particles. For two compounds that form large aggregates, nicardipine and miconazole, we measured particle numbers directly by flow cytometry, determining that the aggregate concentration just above the CAC ranged from 5 to 30 fM. By correlating inhibition of an enzyme with aggregate count for these two drugs, we determined that the stoichiometry of binding is about 10,000 enzyme molecules per aggregate particle. Using measured volumes for nicardipine and miconazole aggregate particles (2.1 x 10(11) and 4.7 x 10(10) A(3), respectively), computed monomer volumes, and the observation that past the CAC all additional monomer forms aggregate particles, we find that aggregates are densely packed particles. Finally, given their size and enzyme stoichiometry, all sequestered enzyme can be comfortably accommodated on the surface of the aggregate.     

A simple model for polysoaps' thread-like aggregates

The equilibrium polymerization, a model for one-dimensional reversible aggregates is used under conditions of theta and bad solvent to describe thread-like aggregates of polysoaps. In two dimensions, the aggregate size distribution decreases always more slowly than an exponential distribution and the dependence of the mean aggregate size L on the density φ and end-cap energy E of the polysoap cylindrical micelle is of the form L[φexp(E/KT)]^δ with δ<1/2. On the other hand, in three dimensions in the bad solvent regime, the dependence of L on φ becomes exponential explaining the high φ dependence of the viscosity in experimental results.     

Experimental research and DPD simulation on the interaction between an ethoxy-modified trisiloxane and F127

The interactions between surfactants and polymers are widely investigated due to favorable changes on properties in their mixtures. Silicone surfactants and pluronic copolymers, both having low toxicity, are used in the detergent, cosmetics, medical, and pharmaceutical fields. Their mixture may gain better performance in their further applications. Therefore, we investigated the interaction between an ethoxy-modified trisiloxane (a silicone surfactant named Ag-64) and a block polyether F127 in this paper. From aggregation behavior of Ag-64 and F127, the formation mechanism and conformation of the aggregates were proposed based on experiments and dissipative particle dynamics (DPD) simulation. The surface activity and aggregation behavior of Ag-64 are affected by F127 in aqueous solutions. As the amounts of added Ag-64 increase, two types of aggregates (Ag-64/F127 aggregate with F127 as skeleton and the “pearl- necklace” aggregate in which Ag-64 micelles are strung along F127 chain) form successively. At higher polymer concentration, F127 twists together to form a coil/cluster aggregate with Ag-64. The results of DPD simulation approve that two main factors, the hydrophobic association and twist of F127 coil, contribute to the formation of different aggregates of Ag-64 and F127.     

Supramolecular aggregates constructed from gold nanoparticles and l-try-CD polypseudorotaxanes as captors for fullerenes

A series of cyclodextrin-based polypseudorotaxanes (PPRs) were constructed by threading native beta-cyclodextrin or l-tryptophan-modified beta-cyclodextrin onto the amino-terminated PPG chains of different lengths. Subsequently, these PPRs were further assembled to form netlike supramolecular aggregates through the linkage of gold nanoparticles, and the resulting water-soluble Au-PPR aggregates were comprehensively characterized by FT-IR, UV, NMR, fluorescence spectroscopy, powder X-ray diffraction patterning, TG-DTA, and transmission electron microscopy. The results showed that the size and sedimentation rate of the Au-PPR aggregates were mainly dependent on the lengths of the PPG chains. Significantly, the Au-PPR aggregate 8, involving many l-tryptophan residues, showed not only a satisfactory water solubility but also a good capturing ability for fullerenes in aqueous solution. The 8-fullerene conjugate thus formed exhibited a good DNA cleavage ability under light irradiation.     

Transport and retention of TiO2 rutile nanoparticles in saturated porous media under low-ionic-strength conditions: measurements and mechanisms

The mechanisms governing the transport and retention kinetics of titanium dioxide (TiO(2), rutile) nanoparticle (NP) aggregates were investigated in saturated porous media. Experiments were carried out under a range of well-controlled ionic strength (from DI water up to 1 mM) and ion valence (NaCl vs CaCl(2)) comparable to the low end of environmentally relevant solution chemistry conditions. Solution chemistry was found to have a marked effect on the electrokinetic properties of NP aggregates and the sand and on the resulting extent of NP aggregate transport and retention in the porous media. Comparable transport and retention patterns were observed for NP aggregates in both NaCl and CaCl(2) solutions but at much lower ionic strength with CaCl(2). Transport experimental results showed temporal and spatial variations of NP aggregate deposition in the column. Specifically, the breakthrough curves displayed a transition from blocking to ripening shapes, and the NP retention profiles exhibited a shift of the maximum NP retention segment from the end toward the entrance of the column gradually with increasing ionic strength. Additionally, the deposition rates of the NP aggregates in both KCl and CaCl(2) solutions increased with ionic strength, a trend consistent with traditional Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Upon close examination of the results, it was found that the characteristics of the obtained transport breakthrough curves closely followed the general trends predicted by the DLVO interaction-energy calculations. However, the obtained NP retention profiles were found to deviate severely from the theory. We propose that a NP aggregate reconformation through collision between NP aggregates and sand grains reduced the repulsive interaction energies of NP-NP and NP-sand surfaces, consequently accelerating NP deposition with transport distance and facilitating approaching NP deposition onto NPs that had already been deposited. It is further suggested that TiO(2) NP transport and retention are determined by the combined influence of NP aggregate reconformation associated with solution chemistry, travel distance, and DLVO interactions of the system.     

Simultaneous analysis of 13C‐glutathione as its dimeric form GSSG and its precursor [1‐13C]glycine using liquid chromatography/isotope ratio mass spectrometry

Determination of glutathione kinetics using stable isotopes requires accurate measurement of the tracers and tracees. Previously, the precursor and synthesized product were measured with two separate techniques, liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) and gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS). In order to reduce sample volume and minimize analytical effort we developed a method to simultaneously determine ¹³C‐glutathione as its dimeric form (GSSG) and its precursor [1‐¹³C]glycine in a small volume of erythrocytes in one single analysis. After having transformed ¹³C‐glutathione into its dimeric form GSSG, we determined both the intra‐erythrocytic concentrations and the ¹³C‐isotopic enrichment of GSSG and glycine in 150 µL of whole blood using liquid chromatography coupled to LC/IRMS. The results show that the concentration (range of µmol/mL) was reliably measured using cycloleucine as internal standard, i.e. with a precision better than 0.1 µmol/mL. The ¹³C‐isotopic enrichment of GSSG and glycine measured in the same run gave reliable values with excellent precision (standard deviation (sd) <0.3‰) and accuracy (measured between 0 and 5 APE). This novel method opens up a variety of kinetic studies with relatively low dose administration of tracers, reducing the total cost of the study design. In addition, only a minimal sample volume is required, enabling studies even in very small subjects, such as preterm infants. Copyright © 2009 John Wiley & Sons, Ltd.     

DNA melting in aggregates: impeded or facilitated?

How does DNA melt in columnar aggregate relative to its melting in diluted solution? Is the melting temperature increased or decreased with the aggregate density? Have DNA-DNA interactions, predominantly of electrostatic nature, an effect on the character of the melting transition? In attempt to answer these questions, we have incorporated the theory of electrostatic interactions between DNA duplexes into the simplest model of DNA melting. The analysis shows that the effect of aggregate density is very different for aggregates built of homologous (or identical) DNA fragments relative to the case of DNA with random base pair sequences. The putative attraction between homologous DNA helices hampers their melting and increases the melting temperature and can even dramatically change the character of the transition. In the aggregate of nonhomologous DNAs, the pattern of electrostatic interactions is more complicated, and their effect could be opposite; in some cases we may even expect electrostatically induced melting. These findings define new directions for melting experiments in dense DNA assemblies.     

Fractal-like Aggregates: Relation between Morphology and Physical Properties

A number of modern technological applications require a detailed calculation of the physical properties of aggregated aerosol particles. For example, in probing soot aerosols by the method called laser-induced incandescence (LII), the soot clusters are suddenly heated by a short, powerful laser pulse and then cool down to the temperature of the carrier gas. LII sizing is based on rigorous calculation of the soot aggregate heat-up and cooling and involves prediction of laser light absorption and energy and mass transfer between aggregated particles and the ambient gas. This paper describes results of numerical simulations of the mass or energy transfer between the gas and fractal-like aggregates of N spherical particles in either the free-molecular or continuum regime, as well as the light scattering properties of random fractal-like aggregates, based on Rayleigh-Debye-Gans (RDG) theory. The aggregate geometries are generated numerically using specially developed algorithms allowing "tuning" of the fractal dimension and prefactor values. Our results are presented in the form of easily applicable scaling laws, with special attention paid to relations between the aggregate gyration radius and the effective radius describing various transport processes between the aggregates and the carrier gas. Copyright 2000 Academic Press.     

Aggregation behaviour of peptide-polymer conjugates containing linear peptide backbones and multiple polymer side chains prepared by nitroxide-mediated radical polymerization

A series of peptides with an alternating sequence of alkoxyamine conjugated lysine and glycine residues were synthesized by classical solution phase peptide coupling. The resulting peptides containing up to eight alkoxyamine moieties were used as initiators in nitroxide-mediated polymerization (NMP) to obtain peptide-polymer conjugates with well defined linear peptide backbones and a defined number of polymeric side chains. Polymerization of styrene and N-isopropylacrylamide (NIPAM) occurred in a highly controlled fashion. Molecular weight and polydispersity index (PDI) were determined by gel permeation chromatography (GPC). Aggregation behaviour of these hybrid materials was investigated by dynamic light scattering (DLS) and atomic force microscopy (AFM). Depending on composition, number and length of the polymer side chains, the conjugates aggregate to different topologies. Whereas peptide-polystyrene conjugates may aggregate to so called honeycomb structures, peptide-poly-N-isopropylacrylamide conjugates show differentiated aggregation behaviour.     

Complex Formation Equilibria and Molecular Structure of Divalent Metal Ions–Vitamin B3–Glycine Oligopeptides Systems

Complex formation of divalent transition metal ions (copper(II), cobalt(II) and nickel(II)), vitamin B3 (nicotinic acid) and glycine oligopeptides (glycine, glycylglycine, glycyl-l-phenylalanine, and glycylglycylglycine) were studied at 298 K in aqueous solutions using the pH-potentiometric technique. The copper Cu(II), cobalt Co(II), and nickel Ni(II) complexing capacity of vitamin B3 in the absence and in the presence of glycine peptides and their overall stability constants in aqueous solutions were obtained and explained by the HYPERQUAD 2008 program using the potentiometric data. From the protonation and complex formation constants, representative complex species distribution diagrams were obtained using HYSS 2009 software. The UV–Vis spectroscopic, cyclic voltammeteric and conductometric titration measurements were carried out to give qualitative information about the conformation of the complexes formed in these solutions and their stoichiometric ratios. The Gibbs energies and the molecular structures of the complexes were evaluated and predicted using Gaussian 09 software molecular modeling and density functional theory calculations.