Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field.

We present a mesoscale model of aqueous polyacrylamide in the infinitely dilute concentration regime, by combining an extant coarse-grained (CG) force-field, MARTINI, and the Iterative Boltzmann Inversion protocol (IBI). MARTINI force-field was used to retain the thermodynamics of solvation of the polymer in water, whereas the structural properties and intrapolymer interactions were optimized by IBI. Atomistic molecular dynamics simulations of polymer in water were performed to benchmark the mesoscale simulations. Our results from the CG model show excellent agreement in structure with the atomistic system. We also studied the dynamical behavior of our CG system by computing the shear viscosity and compared it with the standard IBI model. The viscosity trends of our model were similar to the atomistic system, whereas the standard IBI model was highly dissimilar as expected. In summary, our hybrid CG model sufficiently mimics an infinitely dilute system, and is superior to both MARTINI and IBI in representing the structure and thermodynamics of the atomistic system, respectively. Our hybrid coarse-graining strategy promises applicability in large-scale simulations of polymeric/biological systems where the structure needs to be replicated accurately while preserving the thermodynamics of a smoother surrounding.

Coarse-Grained Simulations of Polymer-Grafted Nanoparticles: Structural Stability and Interfacial Behavior.

In the tertiary oil recovery method known as "polymer flooding", the viscosity of the injected water is increased by dissolving partially hydrolyzed polyacrylamide so as to lower the mobility ratio and raise the vertical and areal sweep efficiencies. However, its drawbacks include the degradation of the polymer in the reservoir due to (1) shear while passing through chokes, perforations, and pore throats, (2) morphological changes induced by divalent ions, and (3) complete hydrolysis of the polymer at high temperatures. These factors adversely affect the viscosity of the polymer flood. Past experimental research showed that polymer-grafted nanoparticles (PNPs) could achieve the same viscosity enhancement at lower quantities than traditional linear polymers. The PNPs have the putative advantage of greater stability when confronted with the aforementioned reservoir conditions. In this work, we use dissipative particle dynamics (DPD) to simulate the oil-PNP-water system at the mesoscale and estimate its sensitivity to brine in ways that could serve as guidelines to experiments. We study the effect of salinity on the structure of linear and branched polyelectrolytes before extending the DPD model to PNPs at the oil-water interface. To this end, we parameterize the interactions of the polymer with the oil and water phases, and broadly map out solvent conditions that change the graft's morphology and affect the interfacial behavior of the grafted particle. We find that the equilibrium location of the grafted nanoparticle in an oil-brine system depends on its grafting density and the salinity.

Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes.

Understanding molecular recognition is of fundamental importance in applications such as therapeutics, chemical catalysis and sensor design. The most common recognition motifs involve biological macromolecules such as antibodies and aptamers. The key to biorecognition consists of a unique three-dimensional structure formed by a folded and constrained bioheteropolymer that creates a binding pocket, or an interface, able to recognize a specific molecule. Here, we show that synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymer-nanotube recognition complexes for riboflavin, L-thyroxine and oestradiol. In each case, the recognition was predicted using a two-dimensional thermodynamic model of surface interactions in which the dissociation constants can be tuned by perturbing the chemical structure of the heteropolymer. Moreover, these complexes can be used as new types of spatiotemporal sensors based on modulation of the carbon nanotube photoemission in the near-infrared, as we show by tracking riboflavin diffusion in murine macrophages.

Effect of bidispersity in grafted chain length on grafted chain conformations and potential of mean force between polymer grafted nanoparticles in a homopolymer matrix.

In efforts to produce polymeric materials with tailored physical properties, significant interest has grown around the ability to control the spatial organization of nanoparticles in polymer nanocomposites. One way to achieve controlled particle arrangement is by grafting the nanoparticle surface with polymers that are compatible with the matrix, thus manipulating the interfacial interactions between the nanoparticles and the polymer matrix. Previous work has shown that the molecular weight of the grafted polymer, both at high grafting density and low grafting density, plays a key role in dictating the effective inter-particle interactions in a polymer matrix. At high grafting density nanoparticles disperse (aggregate) if the graft molecular weight is higher (lower) than the matrix molecular weight. At low grafting density the longer grafts can better shield the nanoparticle surface from direct particle-particle contacts than the shorter grafts and lead to the dispersion of the grafted particles in the matrix. Despite the importance of graft molecular weight, and evidence of non-trivial effects of polydispersity of chains grafted on flat surfaces, most theoretical work on polymer grafted nanoparticles has only focused on monodisperse grafted chains. In this paper, we focus on how bidispersity in grafted chain lengths affects the grafted chain conformations and inter-particle interactions in an implicit solvent and in a dense homopolymer polymer matrix. We first present the effects of bidispersity on grafted chain conformations in a single polymer grafted particle using purely Monte Carlo (MC) simulations. This is followed by calculations of the potential of mean force (PMF) between two grafted particles in a polymer matrix using a self-consistent Polymer Reference Interaction Site Model theory-Monte Carlo simulation approach. Monte Carlo simulations of a single polymer grafted particle in an implicit solvent show that in the bidisperse polymer grafted particles with an equal number of short and long grafts at low to medium grafting density, the short grafts are in a more coiled up conformation (lower radius of gyration) than their monodisperse counterparts to provide a larger free volume to the longer grafts so they can gain conformational entropy. The longer grafts do not show much difference in conformation from their monodisperse counterparts at low grafting density, but at medium grafting density the longer grafts exhibit less stretched conformations (lower radius of gyration) as compared to their monodisperse counterparts. In the presence of an explicit homopolymer matrix, the longer grafts are more compressed by the matrix homopolymer chains than the short grafts. We observe that the potential of mean force between bidisperse grafted particles has features of the PMF of monodisperse grafted particles with short grafts and monodisperse grafted particles with long grafts. The value of the PMF at contact is governed by the short grafts and values at large inter-particle distances are governed by the longer grafts. Further comparison of the PMF for bidisperse and monodisperse polymer grafted particles in a homopolymer matrix at varying parameters shows that the effects of matrix chain length, matrix packing fraction, grafting density, and particle curvature on the PMF between bidisperse polymer grafted particles are similar to those seen between monodisperse polymer grafted particles.

Peptide secondary structure modulates single-walled carbon nanotube fluorescence as a chaperone sensor for nitroaromatics.

A class of peptides from the bombolitin family, not previously identified for nitroaromatic recognition, allows near-infrared fluorescent single-walled carbon nanotubes to transduce specific changes in their conformation. In response to the binding of specific nitroaromatic species, such peptide-nanotube complexes form a virtual "chaperone sensor," which reports modulation of the peptide secondary structure via changes in single-walled carbon nanotubes, near-infrared photoluminescence. A split-channel microscope constructed to image quantized spectral wavelength shifts in real time, in response to nitroaromatic adsorption, results in the first single-nanotube imaging of solvatochromic events. The described indirect detection mechanism, as well as an additional exciton quenching-based optical nitroaromatic detection method, illustrate that functionalization of the carbon nanotube surface can result in completely unique sites for recognition, resolvable at the single-molecule level.

Single molecule detection of nitric oxide enabled by d(AT)15 DNA adsorbed to near infrared fluorescent single-walled carbon nanotubes.

We report the selective detection of single nitric oxide (NO) molecules using a specific DNA sequence of d(AT)(15) oligonucleotides, adsorbed to an array of near-infrared fluorescent semiconducting single-walled carbon nanotubes (AT(15)-SWNT). While SWNT suspended with eight other variant DNA sequences show fluorescence quenching or enhancement from analytes such as dopamine, NADH, L-ascorbic acid, and riboflavin, d(AT)(15) imparts SWNT with a distinct selectivity toward NO. In contrast, the electrostatically neutral polyvinyl alcohol enables no response to nitric oxide, but exhibits fluorescent enhancement to other molecules in the tested library. For AT(15)-SWNT, a stepwise fluorescence decrease is observed when the nanotubes are exposed to NO, reporting the dynamics of single-molecule NO adsorption via SWNT exciton quenching. We describe these quenching traces using a birth-and-death Markov model, and the maximum likelihood estimator of adsorption and desorption rates of NO is derived. Applying the method to simulated traces indicates that the resulting error in the estimated rate constants is less than 5% under our experimental conditions, allowing for calibration using a series of NO concentrations. As expected, the adsorption rate is found to be linearly proportional to NO concentration, and the intrinsic single-site NO adsorption rate constant is 0.001 s(-1) µM NO(-1). The ability to detect nitric oxide quantitatively at the single-molecule level may find applications in new cellular assays for the study of nitric oxide carcinogenesis and chemical signaling, as well as medical diagnostics for inflammation.

A kinetic Monte Carlo analysis for the production of singularly tethered carbon nanotubes.

Nanoparticles that possess a single covalent tether to either another particle or a surface play an increasingly important role in nanotechnology, serving as a foundation for aggregation-based plasmonic sensors, chemically assembled framework structures, and scanning probe tips. Using a theoretical approach, we explore the reaction conditions necessary to maximize singular tethering for several cases of homogeneously dispersed nanoparticles, with a particular focus on single-walled carbon nanotubes. In the limit of particles of monodisperse size and equal site reactivity, the number of tethers versus the reaction conversion is statistically described by the well-known binomial distribution, with a variance that is minimal for the single tether case. However, solutions of nanoparticles often deviate from this ideal, and reaction events can introduce steric hindrance to neighboring sites or alter particle electronic properties, both of which can influence local reactivity. In order to study these cases we use the electron transfer reactions of single-walled carbon nanotubes. We find that the distribution in the number of monofunctional tubes, as a function of conversion, is largely dependent on the distribution of nanotube rate constants, and therefore tube chiralities, in the initial solution. As a contemporary example, we examine the implications of this result on the metallic-semiconductor separation of carbon nanotubes using electron transfer chemistry.

Effect of monomer sequences on conformations of copolymers grafted on spherical nanoparticles: a Monte Carlo simulation study.

Functionalizing nanoparticles with organic ligands, such as oligomers, polymers, DNA, and proteins, is an attractive way to manipulate the interfacial interactions between the nanoparticles and the medium the particles are placed in, and thus control the nanoparticle assembly. In this paper we have conducted a Monte Carlo simulation study on copolymer grafted spherical nanoparticles to show the tremendous potential of using monomer sequence on the copolymers to tune the grafted chain conformation, and thus the effective interactions between copolymer grafted nanoparticles. We have studied AB copolymers with alternating, multiblock, or diblock sequences, where either A monomers or B monomers have monomer-monomer attractive interactions. Our focus has been to show the nontrivial effect of monomer sequence on the conformations of the grafted copolymers at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We observe that the monomer sequence, particle diameter, and grafting density dictate whether (a) the grafted chains aggregate to bring attractive monomers from multiple grafted chains together (interchain and intrachain monomer aggregation) if the enthalpy gained by doing so offsets the entropic loss caused by stretching of chains, or (b) each grafted chain folds onto itself to bring its attractive monomers together (only intrachain monomer aggregation) if the entropic loss from interchain aggregation cannot be overcome by the enthalpic gain. For six copolymers of chain length N=24 grafted on a spherical particle of diameter D=4, interchain and intrachain monomer aggregation occurs, and the radius of gyration varies nonmonotonically with increasing blockiness of the monomer sequence. At larger particle diameters the grafted chains transition to purely intrachain monomer aggregation. The radius of gyration varies monotonically with monomer sequence for intrachain monomer aggregation because as the sequence becomes blockier (like monomers are grouped together), the copolymer chain has to fold less compactly to maximize the enthalpically favorable contacts while maintaining high conformational entropy. The radius of gyration of alternating and diblock copolymers scales with chain length N through a power law (1/2) = alphaN(nu) with the prefactor alpha and scaling exponent nu, varying with monomer sequence and monomer-monomer attraction strength.

Chemically driven carbon-nanotube-guided thermopower waves.

Theoretical calculations predict that by coupling an exothermic chemical reaction with a nanotube or nanowire possessing a high axial thermal conductivity, a self-propagating reactive wave can be driven along its length. Herein, such waves are realized using a 7-nm cyclotrimethylene trinitramine annular shell around a multiwalled carbon nanotube and are amplified by more than 10(4) times the bulk value, propagating faster than 2 m s(-1), with an effective thermal conductivity of 1.28+/-0.2 kW m(-1) K(-1) at 2,860 K. This wave produces a concomitant electrical pulse of disproportionately high specific power, as large as 7 kW kg(-1), which we identify as a thermopower wave. Thermally excited carriers flow in the direction of the propagating reaction with a specific power that scales inversely with system size. The reaction also evolves an anisotropic pressure wave of high total impulse per mass (300 N s kg(-1)). Such waves of high power density may find uses as unique energy sources.

Dynamics of surfactant-suspended single-walled carbon nanotubes in a centrifugal field.

A hydrodynamic model is used to describe the motion of surfactant-suspended single-walled carbon nanotubes in a density gradient, while being subjected to a centrifugal field. The number of surfactant molecules adsorbed on each nanotube determines its effective density and, hence, its position in the gradient after centrifugation has been completed. Analysis of the spatial concentration distributions of CoMoCAT nanotubes suspended with 2 w/v% sodium cholate yielded 2.09, 2.14, and 2.08 surfactant molecules adsorbed per nanometer along the length of the (6,5), (7,5), and (8,7) nanotubes, respectively. The estimates are commensurate with experimental values reported in the literature and can be used to predict the fate of sodium cholate-suspended nanotubes in the separation process. Since the density of the surfactant-nanotube assembly is highly sensitive to the number of adsorbed molecules, a perturbation would cause it to be enriched at a different location in the gradient. The level of sensitivity is also reflected in the 95% confidence levels that are reported in this work.

Modelling the increase in anisotropic reaction rates in metal nanoparticle oxidation using carbon nanotubes as thermal conduits.

Nanostructured energetic materials are attracting attention for their faster reaction rates compared to materials with micron-scale particles. We numerically solve the coupled energy balances for a carbon nanotube with an annular coating of reactive metal, such that coupling to thermal transport in the nanotube accelerates reaction in the annulus. For the case of Zr metal, the nanotube increases the velocity of the reaction front in the direction of the nanotube length from 530 to 5100 mm s(-1). This offers a proof-of-concept for one-dimensional anisotropic energetic materials, which could find new applications in inorganic synthesis and novel propellants. Nanotube conductivity as well as the relative sizes of the Zr annulus and the nanotube limit enhancement of the reaction velocity to a maximum of a factor of ∼10. Interestingly, the interfacial heat conductance is not the most significant factor affecting the coupling, due to the large temperature differences (more than 1000 K) between the nanotube and the annulus at the reaction front and directional heat conduction in the nanotube. Although the enhancement is insufficient to change a Zr/nanotube composite from a deflagrating to a detonating material, using faster-reacting materials may enable nanotubes to effect this transition.

Controlling the electrophoretic mobility of single-walled carbon nanotubes: a comparison of theory and experiment.

The electrophoretic mobilities of single-walled carbon nanotubes (SWNTs) in agarose gels subjected to negatively charged covalent functionalization and noncovalent anionic surfactant adsorption are compared using a simplified hydrodynamic model. Net charges are calculated on the basis of estimated friction coefficients for cylindrical rodlike particles. The effects of functionalization with negatively charged 4-hydroxybenzene diazonium and anionic sodium cholate are quantified and compared with model predictions. The adsorption of Na+ counterions into the nonionic surfactant layer adsorbed on SWNTs (Triton-X-405) is shown to induce a positive charge and reverse the mobility under select conditions. This effect has not been identified or quantified for nanoparticle systems and may be important in the processing of these systems.

A structure-reactivity relationship for single walled carbon nanotubes reacting with 4-hydroxybenzene diazonium salt.

The first structure-reactivity relationship for electron-transfer reactions of single walled carbon nanotubes (SWNTs) has been derived and experimentally validated using 4-hydroxybenzene diazonium as a model electron acceptor. The model describes steady-state reaction data using an adsorption-controlled scheme, and electron transfer theories are used to explain the difference in reactivities between different nanotube chiralities. The formalism provides a mechanistic insight into electronically selective reactions. The influence of reagent concentration and external illumination (approximately 0.764 mW/cm2) on the reaction selectivity is described by the rate model, with quantitative descriptions of the changes in the UV-vis-nIR absorption spectra of nanotubes during reaction. Illumination was shown to decrease the selectivity of the reagent to metallic SWNTs over semiconducting SWNTs. We attribute this to the greater activity of the reagent in solution when exposed to light, resulting in greater extents of reaction for each SWNT and, hence, lower selectivity.

Estimation of the (n,m) concentration distribution of single-walled carbon nanotubes from photoabsorption spectra.

Deconvolution of the absorption spectrum of single-walled carbon nanotubes (SWNTs) into distinct (n,m) contributions is complicated because transition energies are closely spaced. The algorithm presented in this work attempts to simplify the problem by grouping nanotubes with similar transition energies and assigning weights to their spectral contributions. Voigt line shapes were used to fit absorption spectra of sodium dodecyl sulfate suspended HiPco SWNT and CoMoCat SWNT. Line widths for the metallic (93.42 meV) and two semiconducting regions (57.96 and 29.86 meV) were obtained from the absorption spectra of DNA-wrapped SWNT fractionated by ion-exchange chromatography. The method is used to describe the reaction kinetics of certain HiPco SWNTs upon reaction with 4-chlorobenzene diazonium and 4-hydroxybenzene diazonium salts. The code for deconvolution has been provided as open source in the Supporting Information for future modifications.