Silsesquioxane dendrimers as catalysts: a bite-sized molecular dynamics study

A method of calculating the bite (P-M-P) angle for dendritic ligands is reported. Diphenylphosphine terminated dendritic ligands were modified with either a single rhodium or a rhodium complex [HRh(CO)(2)] and molecular dynamics techniques used to run simulations to determine the dynamic bite angle (beta(d)) as a time averaged property. The effects of changing the composition of the dendritic branches is investigated and comparison with experimental hydroformylation data reveals that the dendrimer with the highest linear: branched ratio also has a dynamic bite angle closest to the theoretical ideal value of 120 degrees .     

Nanosized molecular propellers by cyclodehydrogenation of polyphenylene dendrimers

In a polymer analogous approach, large dendritic oligophenylenes containing benzene and tetraphenylmethane cores are transformed via oxidative cyclodehydrogenation to novel propeller-shaped molecules with large polycyclic aromatic hydrocarbon units as "blades". Structure analysis is performed by a combination of MALDI-TOF mass spectrometry, UV/vis, fluorescence, and Raman spectroscopy using solid-state sample preparation methods. These methods are also utilized to determine the degree of the cyclodehydrogenation reaction.     

The structure of phosphine-functionalised silsesquioxane-based dendrimers: a molecular dynamics study

Molecular dynamics modelling has been used to simulate the structures of phopshine-functionalised, silsesquioxane-based dendrimers whose excellent catalytic properties have been previously demonstrated. The effect of changing the chemical composition of the dendrimer branches is simulated. The results indicate that adding a methylene unit to a branch increases the overall size of the dendrimer but replacing a methylene unit with an oxygen atom decreases the size of the dendrimer. The size and shape of the dendrimers have also been simulated on changing the temperature and polarity of the solvent. The distribution of phosphine groups on the exterior has also been modelled and this suggests that all are available for bonding to catalytic metals in all the compounds.     

Internal structure of dendrimers in the melt under shear: a molecular dynamics study

The molecular structure of fluids composed of dendrimers of different generations is studied using nonequilibrium molecular dynamics (NEMD). NEMD results for dendrimer melts undergoing planar Couette flow are reported and analyzed with particular attention paid to the shear-induced changes in the internal structure of dendrimers. The radii of gyration, pair distribution functions and the fractal dimensionality of the dendrimers are determined at different strain rates. The location of the terminal groups is analyzed and found to be uniformly distributed throughout the space occupied by the molecules. The fractal dimension as a function of strain rate displays crossover behavior analogous to the Newtonian/non-Newtonian transition of shear viscosity.     

Adsorption of charged dendrimers: a Brownian dynamics study

The adsorption of isolated charged dendrimers onto oppositely charged flat surfaces is studied in this work using Brownian dynamics simulations. The dendrimer is modeled as a freely jointed bead-rod chain in which excluded-volume interactions are modeled by a repulsive Lennard-Jones potential and bead-bead and bead-surface electrostatic interactions are described by screened Coulombic potentials. Adsorption behavior is studied as a function of inverse screening length, dendrimer generation, and dendrimer charge distribution. Adsorbed dendrimers adopt a disclike conformation in which they flatten in the direction normal to the surface and expand in the direction parallel to the surface. As the inverse screening length increases, the dendrimer expands in the normal direction and contracts in the parallel direction, adopting a conformation that is more stretched in the normal direction. When the inverse screening length becomes sufficiently large, the dendrimer desorbs and adopts a spherelike conformation. Bead density profiles show that adsorbed dendrimers form a two-layer structure, with one layer corresponding to adsorbed beads and a second, less dense layer corresponding to beads one rod length away from the surface. They also reveal how the distribution of monomers within the dendrimer and near the surface can be tailored by changing various problem parameters. The results presented here are expected to be helpful in providing qualitative guidance for dendrimer design in various applications.     

Toward nanoamphiphiles: efficient synthesis of desymmetrized polyphenylene dendrimers

A new synthetic approach for the desymmetrization of polyphenylene dendrimers (PPDs) is described. Tetrakis(4-ethynylphenyl)methane undergoes facile Diels-Alder cycloaddition with substoichiometric quantities of tetraphenylcyclopentadienones bearing one polar functional group. A single ethynyl group is thereby converted to a rigid, selectively functionalized polyphenylene moiety, which serves as a focal point for further transformations or interfacial anchoring. This is the key feature for the design of desymmetrized monodisperse macromolecules with a spherical shape. The remaining unreacted ethynyl groups provide a trifold core for the stepwise elaboration of first- and second-generation polyphenylene dendrons, which may, in turn, bear specific numbers of different peripheral functional groups at their terminae. Moreover, the resulting macromolecules exhibit the characteristic shape-persistence and monodispersity of PPDs. This approach is an important achievement in nanosciences, especially for tailoring new nanoamphiphiles. It is also of synthetic importance, as it enables the separation of two regioisomeric polyphenylene dendrimers for the first time.     

Fluorescence quenching mechanism of a polyphenylene polyelectrolyte with other macromolecules: cytochrome c and dendrimers

This study investigates the fluorescence quenching of a polyphenyl based polyelectrolyte by positively charged macromolecules (proteins and dendrimers). This work shows that the fluorescence quenching of the dendrimer materials does not involve energy transfer or electron transfer but is correlated to the overall charge on the dendrimer and its size. The quenching is hypothesized to result from conformational changes that occur upon binding the polyelectrolyte to the protein or dendrimer. This mechanism is qualitatively different from that invoked for small-molecule analytes.     

Synthesis and optical properties of polyphenylene dendrimers based on perylenes

A series of polyphenylene-dendronized perylenes have been synthesized, and their physical and mesoscopic properties have been investigated. The attached polyphenylene dendrons have significant effects on the physical properties of the perylenes. They increase the solubility of perylenes in common organic solvents, suppress significantly the aggregation of the perylene core, and lead to red-shifted absorption and emission. The polyphenylene dendrons give rise to a strong absorption band in the UV region and exhibit efficient intramolecular energy transfer to the perylene moiety. The functionalization of perylenes with polyphenylene dendrons allows the preparation of films by spin-coating.     

Synthesis and circular dichroism of the optically active dendrimers with the planar chiral ferrocene core

The (S)- and (R)-enantiomers of new planar chiral enantiomerically enriched Frechet-type dendrimers with the 1,2-disubstituted ferrocene core were synthesized from one (S)-enantiomeric precursor. The synthesized compounds were characterized by the circular dichroism spectra.     

Spreading dynamics of chain-like monolayers: a molecular dynamics study

Using large-scale molecular dynamics simulations, we have shown previously that the spreading dynamics of sessile drops on solid surfaces can be described in detail using the molecular-kinetic theory of dynamic wetting. Here we present our first steps in extending this approach to investigate the spreading dynamics of Langmuir-Blodgett monolayers. We make use of a monolayer model originally developed by Karaborni and Toxvaerd, but somewhat simplified to facilitate large-scale simulations. Our preliminary results are in good agreement with recent experimental observations and also support a molecular-kinetic interpretation in which the driving force for spreading is the lateral pressure in the monolayer. Away from equilibrium, initial spreading rates are constant and logarithmically dependent on pressure. However, near equilibrium, spreading is pseudo-diffusive and follows the square root of time. In both regimes the controlling factor is the equilibrium frequency of molecular displacements within the monolayer.     

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Theta temperature: a Brownian dynamics study

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Theta conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.     

Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations

We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five third-generation peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles. A more detailed analysis is then performed using dissimilarity measures, principal coordinate analysis, and free energy landscapes, with the aim of identifying groups of similar conformations. The results point to a high conformational flexibility of these molecules, with no clear "folded state", although two markedly distinct behaviors were found: one of the dendrimers displayed mostly compact conformations clustered into distinct basins (rough landscape), while the remaining dendrimers displayed mainly noncompact conformations with no significant clustering (downhill landscape). This study brings new insight into the conformational behavior of peptide dendrimers and may provide better routes for their functional design. In particular, we propose a yet unsynthesized peptide dendrimer that might exhibit enhanced ability to coordinate aquocobalamin.     

H-Bond in methanol: a molecular dynamics study

A set of molecular dynamics (MD) simulations of methanol-d₄ at three temperatures in the liquid range (200, 250 and 300K) have been carried out. The equations of motion of 256 molecules interacting through a potential model due to Haughney et al. [J. Phys. Chem., 91 (1987) 4934] were solved using the velocity version of the Verlet algorithm. This rather large number of molecules was required for studying the behaviour of the system at momentum transfers as low as 0.25 Å⁻¹. It was found that the system experiences long period fluctuations, and therefore very long MD runs (of the order of 100 ps) are necessary in order to obtain accurate statistical averages. Computed static properties are in good agreement with those reported by Haughney et al. and the neutron weighted g(r) and the static structure factor compare favourably with available neutron diffraction data. The study of time-dependent properties through centre-of-mass autocorrelation functions (VACF, F_s(Q,t) and F(Q,t)) and their memory functions reveals features unknown in simple liquids and very similar to those found in liquid water. A close agreement between centre-of-mass single-particle autocorrelation functions and the translational part of QENS data is also observed. The dynamic structure factor for the centres of mass show distinctive side peaks in the same region of the (Q,ω) plane where recently collective excitations have been studied using coherent neutron scattering thus establishing the presence of propagating short wavelength modes. fa]Presented at the International Symposium on Hydrogen Bond Physics held at Il Ciocco, Barga, Italy, 11–14 September 1990.     

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.     

Host-guest complexes between an aromatic molecular tweezer and symmetric and unsymmetric dendrimers with a 4,4'-bipyridinium core

We have investigated the spectroscopic and electrochemical behavior of symmetric and unsymmetric first-, second-, and third-generation dendrimers comprising an electron-acceptor 4,4'-bipyridinium core (viologen type) and electron-donor 1,3-dimethyleneoxybenzene (Fréchet-type) dendrons. The quite strong fluorescence of the symmetrically and unsymmetrically disubstituted 1,3-dimethyleneoxybenzene units of the dendrons is completely quenched as a result of donor-acceptor interactions that are also evidenced by a low-energy tail in the absorption spectrum. In dichloromethane solution, the 4,4'-bipyridinium cores of the investigated dendrimers are hosted by a molecular tweezer comprising a naphthalene and four benzene components bridged by four methylene units. Host-guest formation causes the quenching of the tweezer fluorescence. The association constants, as measured from fluorescence and (1)H NMR titration plots, (i) are of the order of 10(4) M(-1), (ii) decrease on increasing dendrimer generation, and (iii) are slightly larger for the unsymmetric than for the symmetric dendrimer of the same generation. The analysis of the complexation-induced shifts of the temperature-dependent (1)H NMR signals of the host and guest protons confirms that the bipyridinium core is positioned inside the tweezer cavity and allows the conclusions that (i) shuttling of the tweezer from one to the other pyridinium ring is fast (DeltaG < 10 kcal/mol), (ii) in the case of the unsymmetric dendrimers, the less substituted pyridinium ring is preferentially complexed in apolar solvents, and (iii) complexation of the 4,4'-bipyridinium core proceeds by clipping for the symmetric dendrimers and by threading in the case of unsymmetric ones. Host-guest formation causes a displacement of the first reduction wave of the 4,4'-bipyridinium unit toward more negative potential values, whereas the second reduction wave is unaffected. These results show that the host-guest complexes between the tweezer and the dendrimers are stabilized by electron donor-acceptor interactions and can be reversibly assembled/disassembled by electrochemical stimulation.     

Conjugated dendrimers with triazine peripheries and a distyrylanthracene core

We describe the synthesis and luminescence characterization of conjugated dendrimers with triazine peripheries and a distyrylanthracene core that are suitable for electroluminescence applications. The dendrimers consist of dendritic triazine wedges with high electron affinity, stilbene branches, and a distyrylanthracene core as an emitting moiety. The dendrimers have lowest unoccupied molecular orbital values of about ?2.7 eV. Photoluminescence studies have indicated that a cascade energy transfer occurs from the triazine wedges to the stilbene bridges and finally to the distyrylanthracene core. Thus, the emission wavelength is determined by the distyrylanthracene core unit. The energy‐transfer efficiency of the distyrylanthracene‐cored dendrimers is about 47 and 20% for the first and second generations, respectively. A preliminary electroluminescence property investigation has also been conducted. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5855–5862, 2006     

Microstructure of neat alcohols: a molecular dynamics study

Neat methanol and tert-butanol are studied by molecular dynamics with the focus on the microstructure of these two alcohols. The site-site radial distribution functions, the corresponding structure factors, and an effective local one-body density function are shown to be the appropriate statistical quantities that point in a complementary manner towards the same microstructure for any given liquid. Methanol is found to be a weakly associated liquid forming various chainlike patterns (open and closed) while tert-butanol is almost entirely associated and forms micellelike primary pattern. The presence of stable local microheterogeneity within homogeneous disordered phase appears as a striking feature of these liquids. The absence of any such apparent clustering in water--a stronger hydrogen bonding liquid--through the same two statistical quantities is analyzed.     

Multichromophoric polyphenylene dendrimers: toward brilliant light emitters with an increased number of fluorophores

Two routes for the introduction of highly fluorescent peryleneimide chromophores into the scaffolding of polyphenylene dendrimers via iterative Diels-Alder cycloadditions are presented. The key intermediates for the divergent dendrimer buildup were two cyclopentadienone branching units carrying two peryleneimides and two masked terminal alkynes. The difference between the two reagents is the mode of incorporation of the chromophores. In the first case, the chromophores were attached to the alpha-position of the tetraphenylcyclopentadienones. In the second case, peryleneimides are used as a "spacer" in the beta-position of the cyclopentadienones giving rise to dendrimers with extended molecular diameters (up to 12 nm) and 24 chromophores within their scaffold. Absorption and emission characteristics of the new multichromophoric nanoparticles were investigated and compared to those of the parent dyes. Additionally, an asymmetrically substituted first-generation dendrimer with six perylene diimide chromophores and one ester functionality is reported. The ester serves as a potential anchor group, and this nanoemitter paves the way to a multichromophoric fluorescence label. All dendrimers have good solubility in common organic solvents, high fluorescence quantum yields, and defined distances between the chromophores, making them attractive candidates for single-molecule spectroscopy.     

Synthesis and characterization of a novel tantalum chalcogen-rich molecular cluster with square planar metal core

Black single crystals of Ta(4)Se(9)I(8) are obtained in a high yield by heating Ta, Se, and I(2) at 300 degrees C in 1:2.2:1.0 molar ratio. In the structure, the tantalum atoms form a square, with four Se(2) ligands bridging the Ta-Ta edges and one capping the square. Each Ta atom has two terminal iodine atoms. The compound is diamagnetic and has only two electrons for metal-metal bonding.     

Force-induced insulin dimer dissociation: a molecular dynamics study

Understanding the forces and dynamics of insulin dissociation is critical for devising formulations for the treatment of insulin-dependent diabetes. In earlier work, we applied AFM-based force spectroscopy to covalently tethered and oriented insulin monomers to assess the effect of molecular orientation on insulin-insulin binding forces. We report here on steered molecular dynamics simulations of the insulin dissociation force spectroscopy experiment. Consistent with our experiments, our simulation results suggest that insulin dimer dissociation occurs near the limit of extensibility of the B-chain. We have also found that the forced dissociation of the insulin dimer is a rate-dependent process, involving significant conformational changes to the monomer(s). The insulin dimer dissociation pathway also depends on the relative strength of the inter-monomer interactions across the antiparallel beta-sheet interface and the intra-monomer interactions of residues A1 and A30 with the insulin B-chain. Our simulation results strongly support the design of bioactive insulin analogues that involves altering hydrogen bonding and hydrophobic interactions across the beta-sheet dimer interface.