Temperature dependence of the dynamics and interfacial width in nanoconfined polymers via atomistic simulations.

We present a detailed computational study on the temperature effect of the dynamics and the interfacial width of unentangled cis-1,4 polybutadiene linear chains confined between strongly attractive alumina layers via long, several µs, atomistic molecular dynamics simulations for a wide range of temperatures (143-473 K). We examine the spatial gradient of the translational segmental dynamics and of an effective local glass temperature (TgL). The latter is found to be much higher than the bulk Tg for the adsorbed layer. It gradually reduces to the bulk Tg at about 2 nm away from the substrate. For distant regions (more than ≈1.2nm), a bulk-like behavior is observed; relaxation times follow a typical Vogel-Fulcher-Tammann dependence for temperatures higher than Tg and an Arrhenius dependence for temperatures below the bulk Tg. On the contrary, the polymer chains at the vicinity of the substrate follow piecewise Arrhenius processes. For temperatures below about the adsorbed layer's TgL, the translational dynamics follows a bulk-like (same activation energy) Arrhenius process. At higher temperatures, there is a low activation energy Arrhenius process, caused by high interfacial friction forces. Finally, we compute the interfacial width, based on both structural and dynamical definitions, as a function of temperature. The absolute value of the interfacial width depends on the actual definition, but, regardless, the qualitative behavior is consistent. The interfacial width peaks around the bulk Tg and contracts for lower and higher temperatures. At bulk Tg, the estimated length of the interfacial width, computed via the various definitions, ranges between 1.0 and 2.7 nm.

Structural Studies of Monounsaturated and ω-3 Polyunsaturated Free Fatty Acids in Solution with the Combined Use οf NMR and DFT Calculations-Comparison with the Liquid State.

Molecular structures, in chloroform and DMSO solution, of the free fatty acids (FFAs) caproleic acid, oleic acid, α-linolenic acid, eicosapentanoic acid (EPA) and docosahexaenoic acid (DHA) are reported with the combined use of NMR and DFT calculations. Variable temperature and concentration chemical shifts of the COOH protons, transient 1D NOE experiments and DFT calculations demonstrate the major contribution of low molecular weight aggregates of dimerized fatty acids through intermolecular hydrogen bond interactions of the carboxylic groups, with parallel and antiparallel interdigitated structures even at the low concentration of 20 mM in CDCl3. For the dimeric DHA, a structural model of an intermolecular hydrogen bond through carboxylic groups and an intermolecular hydrogen bond between the carboxylic group of one molecule and the ω-3 double bond of a second molecule is shown to play a role. In DMSO-d6 solution, NMR and DFT studies show that the carboxylic groups form strong intermolecular hydrogen bond interactions with a single discrete solvation molecule of DMSO. These solvation species form parallel and antiparallel interdigitated structures of low molecular weight, as in chloroform solution. This structural motif, therefore, is an intrinsic property of the FFAs, which is not strongly affected by the length and degree of unsaturation of the chain and the hydrogen bond ability of the solvent.

Effect of confinement on the dynamics of 1-propanol and other monohydroxy alcohols.

We report the effect of confinement on the dynamics of three monohydroxy alcohols (1-propanol, 2-ethyl-1-hexanol, and 4-methyl-3-heptanol) differing in their chemical structure and, consequently, in the dielectric strength of the "Debye" process. Density functional theory calculations in bulk 1-propanol identified both linear and ring-like associations composed of up to five repeat units. The simulation results revealed that the ring structures, with a low dipole moment (∼2 D), are energetically preferred over the linear assemblies with a dipole moment of 2.18 D per repeat unit. Under confinement in nanoporous alumina (in templates with pore diameters ranging from 400 to 20 nm), all dynamic processes were found to speed up irrespective of the molecular architecture. The characteristic freezing temperatures of the α and the Debye-like processes followed the pore size dependence: Ta,D=Ta,D bulk-A/d1/2, where d is the pore diameter. The characteristic "freezing" temperatures for the Debye-like (the slow process for confined 1-propanol is non-Debye) and the α-processes decrease, respectively, by 6.5 and 13 K in confined 1-propanol, by 9.5 and 19 K in confined 2-ethyl-1-hexanol, and by 9 and 23 K in confined 4-methyl-3-heptanol within the same 25 nm pores. In 2-ethyl-1-hexanol, confinement reduced the number of linearly associated repeats from approximately heptamers in the bulk to dimers within 25 pores. In addition, the slower process in bulk 2-ethyl-1-hexanol and 4-methyl-3-heptanol, where the signal is dominated by ring-like supramolecular assemblies, is clearly non-Debye. The results suggest that the effect of confinement is dominant in the latter assemblies.

Hexasubstituted Benzenes with Ultrastrong Dipole Moments.

Hexasubstituted benzenes have been synthesized with the highest known dipole moments, as determined by dielectric spectroscopy and DFT methods. Based on the preparation of 4,5-diamino-3,6-dibromophthalonitrile, combined with a novel method to synthesize dihydrobenzimidazoles, these benzene derivatives have dipole moments in excess of 10 debye. Such dipole moments are desirable in ferroelectrics, nonlinear optics, and in organic photovoltaics. Structure determination was achieved through single-crystal X-ray crystallography, and the optical properties were determined by UV/Vis absorption and fluorescence spectroscopy.

How to evict HP1 from H3: Using a complex salt bridge.

In an effort to unravel the unknown "binary switch" mechanisms underlying the "histone code" hypothesis of gene silencing and activation, we study the dynamics of Heterochromatin Protein 1 (HP1). We find in the literature that when HP1 is bound to tri-methylated Lysine9 (K9me3) of histone-H3 through an aromatic cage consisting of two tyrosines and one tryptophan, it is evicted upon phosphorylation of Serine10 (S10phos) during mitosis. In this work, the kick-off intermolecular interaction of the eviction process is proposed and described in detail on the basis of quantum mechanical calculations: specifically, an electrostatic interaction competes with the cation-π interaction and draws away K9me3 from the aromatic cage. An arginine, abundant in the histonic environment, can form an intermolecular "complex salt bridge" with S10phos and dislodge HP1. The study attempts to reveal the role of phosphorylation of Ser10 on the H3 tail in atomic detail.

Structural role of RKS motifs in chromatin interactions: a molecular dynamics study of HP1 bound to a variably modified histone tail.

The current understanding of epigenetic signaling assigns a central role to post-translational modifications that occur in the histone tails. In this context, it has been proposed that methylation of K9 and phosphorylation of S10 in the tail of histone H3 represent a binary switch that controls its reversible association to heterochromatin protein 1 (HP1). To test this hypothesis, we performed a comprehensive molecular dynamics study in which we analyzed a crystallographically defined complex that involves the HP1 chromodomain and an H3 tail peptide. Microsecond-long simulations show that the binding of the trimethylated K9 H3 peptide in the aromatic cage of HP1 is only slightly affected by S10 phosphorylation, because the modified K9 and S10 do not interact directly with one another. Instead, the phosphate group of S10 seems to form a persistent intramolecular salt bridge with R8, an interaction that can provoke a major structural change and alter the hydrogen-bonding regime in the H3-HP1 complex. These observations suggest that interactions between adjacent methyl-lysine and phosphoserine side chains do not by themselves provide a binary switch in the H3-HP1 system, but arginine-phosphoserine interactions, which occur in both histones and nonhistone proteins in the context of a conserved RKS motif, are likely to serve a key regulatory function.

Polarity Matters: Dielectric Relaxation in All-cis-Multifluorinated Cycloalkanes.

The polarity of all-cis-multifluorinated cyclohexanes can be fine-tuned by the number and relative orientation of fluoro substituents, giving rise to a series of compounds with strong dipole moments. Simulations provided the energetics, the dipole moments, and the respective molecular polarizabilities, while dielectric spectroscopy gave information on the dielectric permittivities and the molecular dynamics. In special cases, dipole moments in excess of 6 D and dielectric permittivities of over 300 were obtained by simulation and experiment. Melting temperatures within a given family of multifluorinated cyclohexanes were found to scale with the molecular volume. The less-symmetric all-cis-octafluorotetrahydronaphthalene did not readily crystallize, permitting an investigation of the molecular dynamics in an energetically unfavorable yet rigid and facially polarized isomer. The resulting dynamics above the glass temperature conform to the structural α-relaxation and to the celebrated Johari-Goldstein ß-relaxation.

Progressive Phosphorylation Modulates the Self-Association of a Variably Modified Histone H3 Peptide.

Protein phosphorylation is a key regulatory mechanism in eukaryotic cells. In the intrinsically disordered histone tails, phosphorylation is often a part of combinatorial post-translational modifications and an integral part of the "histone code" that regulates gene expression. Here, we study the association between two histone H3 tail peptides modified to different degrees, using fully atomistic molecular dynamics simulations. Assuming that the initial conformations are either α-helical or fully extended, we compare the propensity of the two peptides to associate with one another when both are unmodified, one modified and the other unmodified, or both modified. The simulations lead to the identification of distinct inter- and intramolecular interactions in the peptide dimer, highlighting a prominent role of a fine-tuned phosphorylation rheostat in peptide association. Progressive phosphorylation appears to modulate peptide charge, inducing strong and specific intermolecular interactions between the monomers, which do not result in the formation of amorphous or ordered aggregates, as documented by experimental evidence derived from Circular Dichroism and NMR spectroscopy. However, upon complete saturation of positive charges by phosphate groups, this effect is reversed: intramolecular interactions prevail and dimerization of zero-charge peptides is markedly reduced. These findings underscore the role of phosphorylation thresholds in the dynamics of intrinsically disordered proteins. Phosphorylation rheostats might account for the divergent effects of histone modifications on the modulation of chromatin structure.

Nanometer Confinement Induces Nematic Order in 1-Dodecanol.

The phase state and molecular dynamics of 1-dodecanol are studied in the bulk and under nanometer confinement within self-ordered nanoporous alumina templates. A rotator phase in the bulk is absent under confinement. A nematic liquid crystalline phase is formed instead in pores with diameters from 400 down to 25 nm. Results are based on the changes in temperature-dependence of dielectric permittivity and X-ray diffraction. The phase diagram under confinement is explored, and the limits of the nematic-to-isotropic and crystalline-to-nematic phase transitions are identified. The phase diagram allows for a direct transition from the liquid to the low-temperature crystalline phase in pores with a diameter below 20 nm. Furthermore, we report on the dielectric fingerprint of the rotator phase and the molecular dynamics in bulk 1-dodecanol.

Eutectic liquid crystal mixture E7 in nanoporous alumina. Effects of confinement on the thermal and concentration fluctuations.

The eutectic mixture of liquid crystals E7 is studied in confinement by means of thermal and dielectric measurements. The uniform 1-D confinement provided by self-ordered nanoporous alumina leads to a decrease in the nematic to isotropic transition temperature due to interaction with the pore surface, e.g. surface anchoring. The prevalence of certain dynamic modes of relaxation is found to depend on the surface properties of the confining pores. The dynamics (i.e., relaxation times) were found to accelerate with increasing confinement, resulting in a decreasing glass temperature, independent of surface treatment. From the pre- and meta-transitional dependence of the dielectric permittivity on temperature we are able to deduce a weakening effect of confinement on the nematic to isotropic (N/I) transition which allows the determination of a critical pore diameter (in the range from 11 nm to 23 nm) below which the transition becomes continuous. Comparison of the N/I transition of E7 to those of its constituent liquid crystals reveals a significantly weaker transition occurring over a widened temperature range. This suggest the importance of concentration fluctuations in rounding first order phase transitions that are triggered by the different length scales and ranges of nematic stability in E7. The results have an impact beyond the present case and for several soft materials (e.g. oligomers used as OLEDs, polymers, colloids) as it demonstrates the importance of concentration fluctuations in addition to thermal fluctuation on the strength of phase transitions.

Multiple Segmental Processes in Polymers with cis and trans Stereoregular Configurations.

Altering the stereochemistry of a single double bond in the side group of a polymer resulted in systems with unprecedented local dynamics. These include (i) the appearance of three segmental processes in the cis-polymers all with Vogel-Fulcher-Tammann (VFT) temperature dependence, (ii) the low steepness index associated with fragility, m, and (iii) the lowest pressure coefficient of Tg, dTg/dP, ever reported for polymers. We show that it is the inability of the cis-polymer to pack the side groups efficiently that controls the dynamics. Furthermore, the trans-polymers have the ability to crystallize. The wealth of dynamics reflects the cis/trans stereochemistry and the presence of different dipoles at specific positions sampling both the side group and backbone dynamics.

8OCB and 8CB Liquid Crystals Confined in Nanoporous Alumina: Effect of Confinement on the Structure and Dynamics.

The effect of oxygen substitution is studied in two homologous compounds of n-cyanobiphenyls with n = 8 in the bulk and under confinement within self-ordered nanoporous alumina (AAO). Oxygen substitution in 8OCB increases the dipole moment and stabilizes the crystalline, smectic, and nematic phases to higher temperatures relative to 8CB. Within their smectic- A (SmA) phase both 8CB and 8OCB behave as weak viscoelastic solids with low shear moduli reflecting the underlying supramolecular defect structure. Dielectric spectroscopy assisted by DFT calculations identified strong dipolar associations within the isotropic phases characterized by a Kirkwood-Fröhlich interaction parameter, g ∼ 0.36. Dielectric spectroscopy further identified a slow process (∼ kHz) of low dielectric strength. The proximity of this process to the rheology time scale suggests as common origin a cooperative relaxation of the defect structure. Confinement alters the phase diagram by stabilizing certain crystalline phases and by reducing the N-I transition temperature in agreement with surface tension effects. However, the N-I transition seems to retain its first order character. Surface treatment with n-decyltrichlorosilane results in destabilization of the SmA phase at the expense of the N phase. This is consistent with a picture of surface anchored LC molecules at the pore walls that stabilize the nematic phase.

Dicyanobenzothiadiazole Derivatives Possessing Switchable Dielectric Permittivities.

Benzothiadiazoles are important electron acceptors and are frequently employed as electron-deficient components of donor-acceptor polymers. We report the effect of nitrile functionalities on the reactivity, steric hindrance, optoelectronic properties, and dielectric permittivity in dicyanobenzothioadiazole (DCNBT). Dielectric spectroscopy in the bulk and in solution assisted by DFT-calculations revealed that these molecules can be engineered to engender maximum values of the dipole moment and of dielectric permittivity due to the strong electron-withdrawing effect of the nitrile groups. The self-assembly in the bulk was investigated by X-ray scattering performed on single crystals, fibers (2D-WAXS), and thin films (GiWAXS). Combining these results, we found a switching of dielectric permittivity of the 4,7-alkylthienyl-substituted dicyanobenzothiadiazole at the transition from the liquid crystalline to the isotropic phase with values capable of competing with the best known rodlike liquid crystals.

Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action.

There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens.

NMR Studies of Hetero-Association of Caffeine with di-O-Caffeoylquinic Acid Isomers in Aqueous Solution.

Caffeine hetero-association with 3,5-di-O-caffeoylquinic acid, 3,4-di-O-caffeoylquinic acid and 4,5-di-O-caffeoylquinic acid in aqueous solution has been investigated by one-dimensional (1D) and two-dimensional (2D) high resolution 1H and 13C NMR spectroscopy. Self-association of the di-O-caffeoylquinic acid isomers has been studied as well. Caffeine-di-O-caffeoylquinic acid isomers association constants were measured. The value of the association constant of the caffeine-di-O-caffeoylquinic acid complexes is compatible with previous studies and within the typical range of reported association constants for other caffeine-polyphenols complexes. Structural features of the three different complexes have also been investigated by NMR spectroscopy combined with quantum chemical calculations, and the complex conformation is discussed. Our results show that stacking interactions drive the formation of the complexes and that multiple equilibria are present in the interaction of caffeine with 3,4-di-O-caffeoylquinic acid and 4,5-di-O-caffeoylquinic acid while the complex with 3,5-di-O-caffeoylquinic acid seems to be better defined.

Developing predictive rules for coordination geometry from visible circular dichroism of copper(II) and nickel(II) ions in histidine and amide main-chain complexes.

Circular dichroism (CD) spectroscopy in the visible region (vis-CD) is a powerful technique to study metal-protein interactions. It can resolve individual d-d electronic transitions as separate bands and is particularly sensitive to the chiral environment of the transition metals. Modern quantum chemical methods enable CD spectra calculations from which, along with direct comparison with the experimental CD data, the conformations and the stereochemistry of the metal-protein complexes can be assigned. However, a clear understanding of the observed spectra and the molecular configuration is largely lacking. In this study, we compare the experimental and computed vis-CD spectra of Cu(2+)-loaded model peptides in square-planar complexes. We find that the spectra can readily discriminate the coordination pattern of Cu(2+) bound exclusively to main-chain amides from that involving both main-chain amides and a side-chain (i.e. histidine side-chain). Based on the results, we develop a set of empirical rules that relates the appearance of particular vis-CD spectral features to the conformation of the complex. These rules can be used to gain insight into coordination geometries of other Cu(2+)- or Ni(2+)-protein complexes.