Competing magnetic interactions in a dinuclear Ni(II) complex: Antiferromagnetic O-H center dot center dot center dot O moiety and ferromagnetic N-3(-) ligand

Synthesis, structural characteristics, magnetic studies and DFT calculations in Ni(II) dinuclear complexes containing two bridging N-3(-) and an O-(HO)-O-... linkage reveal the existence of ferromagnetic interactions between Ni(II) centers via N-3(-) ligands and antiferromagnetic interactions through the H-bonded moiety. The overall magnetic behavior of the system depends on the delicate balance between these two competing interactions.

Temporal associations in fig-wasp-ant interactions: diel and phenological patterns

In a complex multitrophic plant-animal interaction system in which there are direct and indirect interactions between species, comprehending the dynamics of these multiple partners is very important for an understanding of how the system is structured. We investigated the plant Ficus racemosa L. (Moraceae) and its community of obligatory mutualistic and parasitic fig wasps (Hymenoptera: Chalcidoidea) that develop within the fig inflorescence or syconium, as well as their interaction with opportunistic ants. We focused on temporal resource partitioning among members of the fig wasp community over the development cycle of the fig syconia during which wasp oviposition and development occur and we studied the activity rhythm of the ants associated with this community. We found that the seven members of the wasp community partitioned their oviposition across fig syconium development phenology and showed interspecific variation in activity across the day-night cycle. The wasps presented a distinct sequence in their arrival at fig syconia for oviposition, with the parasitoid wasps following the galling wasps. Although fig wasps are known to be largely diurnal, we documented night oviposition in several fig wasp species for the first time. Ant activity on the fig syconia was correlated with wasp activity and was dependent on whether the ants were predatory or trophobiont-tending species; only numbers of predatory ants increased during peak arrivals of the wasps.

Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C–H⋯F and C–H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C–H⋯F and C–H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O–H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4, 5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule. (C) 2012 Elsevier B.V. All rights reserved.

New 4-(2-(4-alkoxyphenyl)-6-methoxypyridin-4-yl) benzonitriles: synthesis, liquid crystalline behavior and photo physical properties

A new series of luminescent 4-(2-(4-alkoxyphenyl)-6-methoxypyridin-4-yl) benzonitriles containing three ring systems, viz. methoxy pyridine, benzonitrile and alkoxy benzene with variable alkoxy chain length, with bent-core structures were synthesized as potential mesogens and characterized by spectral techniques. Their liquid crystalline behavior was investigated by polarizing optical microscopy (POM), differential scanning calorimetry (DSC) and variable temperature powder X-ray diffraction (PXRD) measurements. The study reveals that compounds with shorter chain lengths i.e. m = 4] exclusively exhibit the nematic phase while compounds with longer chain lengths i.e. m = 6-14 (only even)] show predominantly the orthorhombic columnar phase. Single crystal X-ray analysis of 4-(2-(4-butyloxy/octyloxyphenyl)-6-methoxypyridin-4-yl) benzonitriles reveals that they possess slightly non-planar unsymmetrical bent structures and their molecular packing consists of nonconventional H-bond interactions; it also explains the observed liquid crystalline phase. An optical study indicates that the title compounds are good blue emitting materials showing absorption and emission bands in the range 335-345 nm and 415-460 nm, respectively. An electrochemical study of 4-(2-(4-octyloxyphenyl)-6-methoxypyridin-4-yl) benzonitrile shows a band gap of 1.89 eV with HOMO and LUMO energy levels of -5.06 and -3.17 eV, respectively. Also, density functional theory (DFT) calculations confirm its optimized geometry, electronic absorption and frontier molecular orbital distributions.

Fluorine prefers hydrogen bonds over halogen bonds! Insights from crystal structures of some halofluorobenzenes

Crystal structures of a series of isomers of chlorofluorobenzene, bromofluorobenzene and iodofluorobenzene, all of which are liquids under ambient conditions, are determined by a technique of in situ cryocrystallography. These simple dihalo substituted benzenes provide clear insights into subtle interplay of packing interactions preferred by fluorine and heavier halogens for example, C-H center dot center dot center dot X hydrogen bonds vs. X center dot center dot center dot X halogen bonds (X=F, Cl, Br, I). The interaction patterns noted here are purely characteristic of halogens, having not been influenced by other stronger interactions. Variability of principal supramolecular synthons among the isomers highlights the importance of molecular shape and relative position of interacting atoms while preserving the basic intermolecular bonds. Mutually exclusive occurrence of homo (I center dot center dot center dot I) and hetero (I center dot center dot center dot F) halogen bonds in polymorphs of 4-iodofluorobenzene questions the robustness and reliability of these interactions.

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

Rich data bearing on the structural and evolutionary principles of protein protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial `driver' mutations in oncogenesis. They also provide the foundation toward the design of protein protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. (C) 2014 Elsevier Ltd. All rights reserved.

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-pi and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to beta-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

Suspensions of polymer-grafted nanoparticles with added polymers-Structure and effective pair-interactions

We present the results of combined experimental and theoretical (molecular dynamics simulations and integral equation theory) studies of the structure and effective interactions of suspensions of polymer grafted nanoparticles (PGNPs) in the presence of linear polymers. Due to the absence of systematic experimental and theoretical studies of PGNPs, it is widely believed that the structure and effective interactions in such binary mixtures would be very similar to those of an analogous soft colloidal material-star polymers. In our study, polystyrene-grafted gold nanoparticles with functionality f = 70 were mixed with linear polystyrene (PS) of two different molecular weights for obtaining two PGNP: PS size ratios, xi = 0.14 and 2.76 (where, xi = M-g/M-m, M-g and M-m being the molecular weights of grafting and matrix polymers, respectively). The experimental structure factor of PGNPs could be modeled with an effective potential (Model-X), which has been found to be widely applicable for star polymers. Similarly, the structure factor of the blends with xi = 0.14 could be modeled reasonably well, while the structure of blends with xi = 2.76 could not be captured, especially for high density of added polymers. A model (Model-Y) for effective interactions between PGNPs in a melt of matrix polymers also failed to provide good agreement with the experimental data for samples with xi = 2.76 and high density of added polymers. We tentatively attribute this anomaly in modeling the structure factor of blends with xi = 2.76 to the questionable assumption of Model-X in describing the added polymers as star polymers with functionality 2, which gets manifested in both polymer-polymer and polymer-PGNP interactions especially at higher fractions of added polymers. The failure of Model-Y may be due to the neglect of possible many-body interactions among PGNPs mediated by matrix polymers when the fraction of added polymers is high. These observations point to the need for a new framework to understand not only the structural behavior of PGNPs but also possibly their dynamics and thermo-mechanical properties as well. (C) 2015 AIP Publishing LLC.

Nanoparticle induced miscibility in LCST polymer blends: critically assessing the enthalpic and entropic effects

The use of copolymer and polymer blends widened the possibility of creating materials with multilayered architectures. Hierarchical polymer systems with a wide array of micro and nanostructures are generated by thermally induced phase separation (TIPS) in partially miscible polymer blends. Various parameters like the interaction between the polymers, concentration, solvent/non-solvent ratio, and quenching temperature have to be optimized to obtain these micro/nanophase structures. Alternatively, the addition of nanoparticles is another strategy to design materials with desired hetero-phase structures. The dynamics of the polymer nanocomposite depends on the statistical ordering of polymers around the nanoparticle, which is dependent on the shape of the nanoparticle. The entropic loss due to deformation of polymer chains, like the repulsive interactions due to coiling and the attractive interactions in the case of swelling has been highlighted in this perspective article. The dissipative particle dynamics has been discussed and is correlated with the molecular dynamics simulation in the case of polymer blends. The Cahn Hillard Cook model on variedly shaped immobile fillers has shown difference in the propagation of the composition wave. The nanoparticle shape has a contributing effect on the polymer particle interaction, which can change the miscibility window in the case of these phase separating polymer blends. Quantitative information on the effect of spherical particles on the demixing temperature is well established and further modified to explain the percolation of rod shaped particles in the polymer blends. These models correlate well with the experimental observations in context to the dynamics induced by the nanoparticle in the demixing behavior of the polymer blend. The miscibility of the LCST polymer blend depends on the enthalpic factors like the specific interaction between the components, and the solubility product and the entropic losses occurring due to the formation of any favorable interactions. Hence, it is essential to assess the entropic and enthalpic interactions induced by the nanoparticles independently. The addition of nanoparticles creates heterogeneity in the polymer phase it is localized. This can be observed as an alteration in the relaxation behavior of the polymer. This changes the demixing behavior and the interaction parameter between the polymers. The compositional changes induced due to the incorporation of nanoparticles are also attributed as a reason for the altered demixing temperature. The particle shape anisotropy causes a direction dependent depletion, which changes the phase behavior of the blend. The polymer-grafted nanoparticles with varying grafting density show tremendous variation in the miscibility of the blend. The stretching of the polymer chains grafted on the nanoparticles causes an entropy penalty in the polymer blend. A comparative study on the different shaped particles is not available up to date for understanding these aspects. Hence, we have juxtaposed the various computational studies on nanoparticle dynamics, the shape effect of NPs on homopolymers and also the cases of various polymer blends without nanoparticles to sketch a complete picture on the effect of various particles on the miscibility of LCST blends.

Functional evaluation of noncovalent interactions in neuroreceptors and progress toward the expansion of unnatural amino acid methodology

This dissertation primarily describes chemical-scale studies of G protein-coupled receptors and Cys-loop ligand-gated ion channels to better understand ligand binding interactions and the mechanism of channel activation using recently published crystal structures as a guide. These studies employ the use of unnatural amino acid mutagenesis and electrophysiology to measure subtle changes in receptor function.

In chapter 2, the role of a conserved aromatic microdomain predicted in the D3 dopamine receptor is probed in the closely related D2 and D4 dopamine receptors. This domain was found to act as a structural unit near the ligand binding site that is important for receptor function. The domain consists of several functionally important noncovalent interactions including hydrogen bond, aromatic-aromatic, and sulfur-π interactions that show strong couplings by mutant cycle analysis. We also assign an alternate interpretation for the linear fluorination plot observed at W6.48, a residue previously thought to participate in a cation-π interaction with dopamine.

Chapter 3 outlines attempts to incorporate chemically synthesized and in vitro acylated unnatural amino acids into mammalian cells. While our attempts were not successful, method optimizations and data for nonsense suppression with an in vivo acylated tRNA are included. This chapter is aimed to aid future researchers attempting unnatural amino acid mutagenesis in mammalian cells.

Chapter 4 identifies a cation-π interaction between glutamate and a tyrosine residue on loop C in the GluClβ receptor. Using the recently published crystal structure of the homologous GluClα receptor, other ligand-binding and protein-protein interactions are probed to determine the similarity between this invertebrate receptor and other more distantly related vertebrate Cys-loop receptors. We find that many of the interactions previously observed are conserved in the GluCl receptors, however care must be taken when extrapolating structural data.

Chapter 5 examines inherent properties of the GluClα receptor that are responsible for the observed glutamate insensitivity of the receptor. Chimera synthesis and mutagenesis reveal the C-terminal portion of the M4 helix and the C-terminus as contributing to formation of the decoupled state, where ligand binding is incapable of triggering channel gating. Receptor mutagenesis was unable to identify single residue mismatches or impaired protein-protein interactions within this domain. We conclude that M4 helix structure and/or membrane dynamics are likely the cause of ligand insensitivity in this receptor and that the M4 helix has an role important in the activation process.

In vivo analysis of interactions between trans-acting factors and their target genes

The investigations presented in this thesis use various in vivo techniques to understand how trans-acting factors control gene expression. The first part addresses the transcriptional regulation of muscle creatine kinase (MCK). MCK expression is activated during the course of development and is found only in differentiated muscle. Several in vivo footprints are observed at the enhancer of this gene, but all of these interactions are limited to cell types that express MCK. This is interesting because two of the footprints appear to represent muscle specific use of general transcription factors, while the other two correspond to sites that can bind the myogenic regulator, MyoD1, in vitro. MyoD1 and these general factors are present in myoblasts, but can bind to the enhancer only in myocytes. This suggests that either the factors themselves are post-translationally modified (phosphorylation or protein:protein interactions), or the accessibility of the enhancer to the factors is limited (changes in chromatin structure). The in vivo footprinting study of MCK was performed with a new ligation mediated, single-sided PCR (polymerase chain reaction) technique that I have developed.

The second half of the thesis concerns the regulation of mouse metallothionein (MT). Metallothioneins are a family of highly conserved housekeeping genes whose expression can be induced by heavy metals, steroids, and other stresses. By adapting a primer extension method of genomic sequencing to in vivo footprinting, I've observed both metal inducible and noninducible interactions at the promoter of MT-I. From these results I've been able to limit the possible mechanisms by which metal responsive trans-acting factors induce transcription. These interpretations correlate with a second line of experiments involving the stable titration of positive acting factors necessary for induction of MT. I've amplified the promoter of MT to 10^2-10^3 copies per cell by fusing the 5' and 3' ends of the MT gene to the coding region of DHFR and selecting cells for methotrexate resistance. In these cells, there is a metal-specific titration effect, and although it acts at the level of transcription, it appears to be independent of direct DNA binding factors.

Interactions of thiamine monophosphate (TMP) with one- and two-dimensional polymeric halogenomercurate anions. Crystal structures of (TMP)(Hg2Br5)center dot 0.5H(2)O and (TMP)(2)(Hg3I8)

An investigation into the interactions between thiamine monophosphate (TMP) and anions has resulted in the preparation and X-ray characterization of the compounds (TMP)(Hg2Br5).0.5H(2)O (1) and (TMP)(2)(Hg3I8) (2). In each compound the TMP molecule exists as a monovalent cation in the usual F conformation. The halogenomercurate anions occur in two-dimensional (2-D) network in 1 or one-dimensional (1-D) chain in 2. In both 1 and 2, the structures consist of alternating cationic sheets of the hydrogen-bonded TMP molecules and anionic sheets of the polymeric halogenomercurate anions. The TMP molecule binds to the polymeric anions through the characteristic 'anion bridge I', C(2)-H..X...pyrimidinium (X = Br in 1 and 1 in 2), and electrostatic interactions between electropositive S(1) and halogen atoms. The 'anion bridge II' of the type N(4'1)-H...X...thiazolium (X = phosphate group) plays a role in stabilizing the molecular conformation. The biological implication of the host-guest-like complexation between TMP and polymeric anions is discussed.

Dissociative charge exchange and ionization of O-2 by fast H+ and O+ ions: Energetic ion interactions in Europa's oxygen atmosphere and neutral torus

Measurements of electron capture and ionization of O-2 molecules in collisions with H+ and O+ ions have been made over an energy range 10 - 100 keV. Cross sections for dissociative and nondissociative interactions have been separately determined using coincidence techniques. Nondissociative channels leading to O-2(+) product formation are shown to be dominant for both the H+ and the O+ projectiles in the capture collisions and only for the H+ projectiles in the ionization collisions. Dissociative channels are dominant for ionizing collisions involving O+ projectiles. The energy distributions of the O+ fragment products from collisions involving H+ and O+ have also been measured for the first time using time-of-flight methods, and the results are compared with those from other related studies. These measurements have been used to describe the interaction of the energetic ions trapped in Jupiter's magnetosphere with the very thin oxygen atmosphere of the icy satellite Europa. It is shown that the ionization of oxygen molecules is dominated by charge exchange plus ion impact ionization processes rather than photoionization. In addition, dissociation is predominately induced through excitation of electrons into high-lying repulsive energy states ( electronically) rather than arising from momentum transfer from knock-on collisions between colliding nuclei, which are the only processes included in current models. Future modeling will need to include both these processes.