Side radical influence on the nonlinear optical properties and thermal stability of poled polymer films

Films of polyetherketone doped with the chromophores Disperse Red 1 (DR1) and Disperse Red 13 (DR13) were prepared by spin-coating method. By the in situ Second-harmonic Generation (SHG) signal intensity measurement, the optimal poling temperatures were obtained. For the investigated polyetherketone polymer doped with DR1 (DR1/PEK-c) and polyetherketone polymer doped with DR13 (DR13/PEK-c) films, the optimal poling temperatures were 150degreesC and 140degreesC, respectively. Under the optimal poling conditions, the high second-order nonlinear optical coefficient chi(33)((2)) = 11.02 pm/V has been obtained for the DR1/PEK-c; and for DR13/PEK-c at the same conditions the coefficient is 17.9 pm/V. The SHG signal intensity DR1/PEK-c could maintain more than 80% of its initial value when the temperature was under 100degreesC, and the SHG signal intensity of the DR13/PEK-c could maintain more than 80% of its initial value when the temperature was under 135degreesC. (C) 2002 Kluwer Academic Publishers.

A simple computational model for predicting .pi.-facial selectivity in reductions of sterically unbiased ketones. Relative importance of electrostatic and orbital interactions

Various factore controlling the preferred facial selectivity in the reductions of a number of sterically unbiased ketones have been evaluated using a semiempirical MO procedure. MNDO optimized geometries do not reveal any significant ground-state distortions which can be correlated with the observed face selectivities. Electrostatic effecta due to an approaching reagent were modeled by placing a test negative charge at a fixed distance from the carbonyl carbon on each of the two faces. A second series of calculations was carried out using the hydride ion as a test nucleophile. The latter calculations effectively include orbital interactions involving the u and u* orbitals of the newly formed bond in the reaction. The computed energy differences with the charge model are generally much larger compared to those with the hydride ion. However, both models lead to predictions which are qualitatively consistent with the experimentally determined facial preferences for most of the systems. Thus, electrostatic interactions between the nucleophile and the substrate seem to effectively determine the face selectivities in these molecules. However, there are a few exceptions in which orbital interactions are found to contribute significantly and occasionally reverse the preference dictated by electrostatic effecta. The remarkable succew of the hydride model calculations, in spite of retaining the unperturbed geometries of the substrates, points to the unimportance of torsional effeds and orbital distortions associated with the pyramidalized carbonyl unit in the transition state in most of the substrates considered. Additional experimental results are reported which provide useful calibration for the present computational approach.

Electrostatic and Hydrophobic Interactions Involved in CNT Biofunctionalization with Short ss-DNA

This work is aimed at studying the adsorption mechanism of short chain 20-mer pyrimidinic homoss-DNA (oligodeoxyribonucleotide, ODN: polyC(20) and polyT(20)) onto CNT by reflectometry. To analyze the experimental data, the effective-medium theory using the Bruggemann approximation represents a Suitable optical model to account for the surface properties (roughness, thickness, and optical constants) and the size of the adsorbate. Systematic information about the involved interactions is obtained by changing the physicochemical properties of the system. Hydrophobic and electrostatic interactions are evaluated by comparing the adsorption oil hydrophobic CNT and oil hydrophilic silica and by Modulating the ionic Strength With and without Mg(2+). The ODN adsorption process oil CNT is driven by hydrophobic interactions only when the electrostatic repulsion is Suppressed. The adsorption mode results in ODN molecules in a side-on orientation with the bases (nonpolar region) toward the surface. This unfavorable orientation is partially reverse by adding Mg(2+). On the other hand, the adsorption oil silica is dominated by the strong repulsive electrostatic interaction that is screened at high ionic strength or mediated by Mg(2+). The cation-mediated process induces the interaction of the phosphate backbone (polar region) with the surface, leaving the bases free for hybridization. Although the general adsorption behavior of the pyrimidine bases is the same, polyC(20) presents higher affinity for the CNT Surface due to its acid-base properties.

Electrostatic potentials and polarization effects in proton-molecule interactions by means of multipoles from the quantum theory of atoms in molecules

Some atomic multipoles (charges, dipoles and quadrupoles) from the Quantum Theory of Atoms in Molecules (QTAIM) and CHELPG charges are used to investigate interactions between a proton and a molecule (F2, Cl2, BF, AlF, BeO, MgO, LiH, H2CO, NH3, PH3, BF3, and CO2). Calculations were done at the B3LYP/6-311G(3d,3p) level. The main aspect of this work is the investigation of polarization effects over electrostatic potentials and atomic multipoles along a medium to long range of interaction distances. Large electronic charge fluxes and polarization changes are induced by a proton mainly when this positive particle approaches the least electronegative atom of diatomic heteronuclear molecules. The search for simple equations to describe polarization on electrostatic potentials from QTAIM quantities resulted in linear relations with r-4 (r is the interaction distance) for many cases. Moreover, the contribution from atomic dipoles to these potentials is usually the most affected contribution by polarization what reinforces the need for these dipoles to a minimal description of purely electrostatic interactions. Finally, CHELPG charges provide a description of polarization effects on electrostatic potentials that is in disagreement with physical arguments for certain of these molecules. (c) 2012 Wiley Periodicals, Inc.

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

Fluorescence spectrometric study on the interactions of isoprocarb and sodium 2-isopropylphenate with bovine serum albumin

The binding interaction of the pesticide Isoprocarb and its degradation product, sodium 2-isopropylphenate, with bovine serum albumin (BSA) was studied by spectrofluorimetry under simulated physiological conditions. Both Isoprocarb and sodium 2-isopropylphenate quenched the intrinsic fluorescence of BSA. This quenching proceeded via a static mechanism. The thermodynamic parameters (ΔH°, ΔS° and ΔG°) obtained from the fluorescence data measured at two different temperatures showed that the binding of Isoprocarb to BSA involved hydrogen bonds and that of sodium 2-isopropylphenate to BSA involved hydrophobic and electrostatic interactions. Synchronous fluorescence spectroscopy of the interaction of BSA with either Isoprocarb or sodium 2-isopropylphenate showed that the molecular structure of the BSA was changed significantly, which is consistent with the known toxicity of the pesticide, i.e., the protein is denatured. The sodium 2-isopropylphenate, was estimated to be about 4–5 times more toxic than its parent, Isoprocarb. Synchronous fluorescence spectroscopy and the resolution of the three-way excitation–emission fluorescence spectra by the PARAFAC method extracted the relative concentration profiles of BSA, Isoprocab and sodium 2-isopropylphenate as a function of the added sodium 2-isopropylphenate. These profiles showed that the degradation product, sodium 2-isopropylphenate, displaced the pesticide in a competitive reaction with the BSA protein.

Bending and bundling of metal-free vertically aligned ZnO nanowires due to electrostatic interaction

Bending and bundling was observed from vertically aligned arrays of ZnO nanowires with flat (0001) top surfaces, which were synthesized using a vapor-phase method without metal catalysts. Sufficient evidence was found to exclude electron-beam bombardment during scanning electron microscopy as a cause for bending and bundling. We attribute the bending and bundling to electrostatic interactions due to charged (0001) polar surfaces, and also discussed the threshold surface charge densities for the bending and bundling based on a simple cantilever-bending model. Some growth features were indicative of the operation of electrostatic interactions during the growth.

Intermolecular Interactions of Noble-Gas-Containing Species

The importance of intermolecular interactions to chemistry, physics, and biology is difficult to overestimate. Without intermolecular forces, condensed phase matter could not form. The simplest way to categorize different types of intermolecular interactions is to describe them using van der Waals and hydrogen bonded (H-bonded) interactions. In the H-bond, the intermolecular interaction appears between a positively charged hydrogen atom and electronegative fragments and it originates from strong electrostatic interactions. H-bonding is important when considering the properties of condensed phase water and in many biological systems including the structure of DNA and proteins. Vibrational spectroscopy is a useful tool for studying complexes and the solvation of molecules. Vibrational frequency shift has been used to characterize complex formation. In an H-bonded system A∙∙∙H-X (A and X are acceptor and donor species, respectively), the vibrational frequency of the H-X stretching vibration usually decreases from its value in free H-X (red-shift). This frequency shift has been used as evidence for H-bond formation and the magnitude of the shift has been used as an indicator of the H-bonding strength. In contrast to this normal behavior are the blue-shifting H-bonds, in which the H-X vibrational frequency increases upon complex formation. In the last decade, there has been active discussion regarding these blue-shifting H-bonds. Noble-gases have been considered inert due to their limited reactivity with other elements. In the early 1930 s, Pauling predicted the stable noble-gas compounds XeF6 and KrF6. It was not until three decades later Neil Bartlett synthesized the first noble-gas compound, XePtF6, in 1962. A renaissance of noble-gas chemistry began in 1995 with the discovery of noble-gas hydride molecules at the University of Helsinki. The first hydrides were HXeCl, HXeBr, HXeI, HKrCl, and HXeH. These molecules have the general formula of HNgY, where H is a hydrogen atom, Ng is a noble-gas atom (Ar, Kr, or Xe), and Y is an electronegative fragment. At present, this class of molecules comprises 23 members including both inorganic and organic compounds. The first and only argon-containing neutral chemical compound HArF was synthesized in 2000 and its properties have since been investigated in a number of studies. A helium-containing chemical compound, HHeF, was predicted computationally, but its lifetime has been predicted to be severely limited by hydrogen tunneling. Helium and neon are the only elements in the periodic table that do not form neutral, ground state molecules. A noble-gas matrix is a useful medium in which to study unstable and reactive species including ions. A solvated proton forms a centrosymmetric NgHNg+ (Ng = Ar, Kr, and Xe) structure in a noble-gas matrix and this is probably the simplest example of a solvated proton. Interestingly, the hypothetical NeHNe+ cation is isoelectronic with the water-solvated proton H5O2+ (Zundel-ion). In addition to the NgHNg+ cations, the isoelectronic YHY- (Y = halogen atom or pseudohalogen fragment) anions have been studied with the matrix-isolation technique. These species have been known to exist in alkali metal salts (YHY)-M+ (M = alkali metal e.g. K or Na) for more than 80 years. Hydrated HF forms the FHF- structure in aqueous solutions, and these ions participate in several important chemical processes. In this thesis, studies of the intermolecular interactions of HNgY molecules and centrosymmetric ions with various species are presented. The HNgY complexes show unusual spectral features, e.g. large blue-shifts of the H-Ng stretching vibration upon complexation. It is suggested that the blue-shift is a normal effect for these molecules, and that originates from the enhanced (HNg)+Y- ion-pair character upon complexation. It is also found that the HNgY molecules are energetically stabilized in the complexed form, and this effect is computationally demonstrated for the HHeF molecule. The NgHNg+ and YHY- ions also show blue-shifts in their asymmetric stretching vibration upon complexation with nitrogen. Additionally, the matrix site structure and hindered rotation (libration) of the HNgY molecules were studied. The librational motion is a much-discussed solid state phenomenon, and the HNgY molecules embedded in noble-gas matrices are good model systems to study this effect. The formation mechanisms of the HNgY molecules and the decay mechanism of NgHNg+ cations are discussed. A new electron tunneling model for the decay of NgHNg+ absorptions in noble-gas matrices is proposed. Studies of the NgHNg+∙∙∙N2 complexes support this electron tunneling mechanism.

Free energy calculations of glycosaminoglycan - Protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.

Interactions of linear dicationic molecules with lipid A: structural requisites for optimal binding affinity

The structural determinants of the binding affinity of linear dicationic molecules toward lipid A have been examined with respect to the distance between the terminal cationic functions, the basicity, and the type of cationic moieties using a series of spermidine derivatives and pentamidine analogs by fluorescence spectroscopic methods, The presence of two terminal cationic groups corresponds to enhanced affinity, A distinct sigmoidal relationship between the intercationic distance and affinity was observed with a sharp increase at 11 Angstrom, levelling off at about 13 Angstrom. The basicity (pK) and nature of the cationic functions are poor correlates of binding potency, since molecules bearing primary amino, imidazolino, or guanido termini are equipotent, The interaction of pentamidine, a bisamidine drug, with lipid A, characterized in considerable detail employing the putative intermolecular excimerization of the drug, suggests a stoichiometry of 1:1 in the resultant complex, The binding is driven almost exclusively by electrostatic forces, and is dependent on the ionization states of both lipid A and the drug, Under conditions when lipid A is highly disaggregated, pentamidine binds specifically to bis-phosphoryl- but not to monophosphoryl-lipid A indicating that both phosphate groups of lipid A are necessary for electrostatic interactions by the terminal amidininium groups of the drug, Based on these data, a structural model is proposed for the pentamidine-lipid A complex, which may be of value in designing endotoxin antagonists from first principles.

Evaluation of solute-solvent interactions from solvent blue-shifts of n → π* transitions of C=O, C=S, NO2 and N=N groups: hydrogen bond energies of various donor-acceptor systems

Effects of non-polar, polar and proton-donating solvents on the n → π* transitions of C=O, C=S, NO2 and N=N groups have been investigated. The shifts of the absorption maxima in non-polar and polar solvents have been related to the electrostatic interactions between solute and solvent molecules, by employing the theory of McRAE. In solvents which can donate protons the solvent shifts are mainly determined by solute-solvent hydrogen bonding. Isobestic points have been found in the n → π* bonds of ethylenetrithio-carbonate in heptane-alcohol and heptane-chloroform solvent systems, indicating the existence of equilibria between the hydrogen bonded and the free species of the solute. Among the different proton-donating solvents studied water produces the largest blue-shifts. The blue-shifts in alcohols decrease in the order 2,2,2-trifluoroethanol, methanol, ethanol, isopropanol and t-butanol, the blue-shift in trifluoroethanol being nearly equal to that in water. This trend is exactly opposite to that for the self-association of alcohols. It is suggested that electron-withdrawing groups not merely decrease the extent of self-association of alcohols, but also increase the ability to donate hydrogen bonds. The approximate hydrogen-bond energies for several donor-acceptor systems have been estimated. In a series of aliphatio ketones and nitro compounds studied, the blue-shifts and consequently the hydrogen bond energies decrease with the decrease in the electron-withdrawing power of the alkyl groups. It is felt that electron-withdrawing groups render the chromophores better proton acceptors, and the alcohols better donors. A linear relationship between n → π* transition frequency and the infrared frequency of ethylenetrithiocarbonate has been found. It is concluded that stabilization of the electronic ground states of solute molecules by electrostatic and/or hydrogen-bond interactions determines the solvent shifts.

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

Unusual Salt-Induced Color Modulation through Aggregation-Induced Emission Switching of a Bis-cationic Phenylenedivinylene-Based pi Hydrogelator

The synthesis, hydrogelation, and aggregation-induced emission switching of the phenylenedivinylene bis-N-octyl pyridinium salt is described. Hydrogelation occurs as a consequence of pi-stacking, van der Waals, and electrostatic interactions that lead to a high gel melting temperature and significant mechanical properties at a very low weight percentage of the gelator. A morphology transition from fiber-to-coil-to-tube was observed depending on the concentration of the gelator. Variation in the added salt type, salt concentrations, or temperature profoundly influenced the order of aggregation of the gelator molecules in aqueous solution. Formation of a novel chromophore assembly in this way leads to an aggregation-induced switch of the emission colors. The emission color switches from sky blue to white to orange depending upon the extent of aggregation through mere addition of external inorganic salts. Remarkably, the salt effect on the assembly of such cationic phenylenedivinylenes in water follow the behavior predicted from the well-known Hofmeister effects. Mechanistic insights for these aggregation processes were obtained through the counterion exchange studies. The aggregation-induced emission switching that leads to a room-temperature white-light emission from a single chromophore in a single solvent (water) is highly promising for optoelectronic applications.