Marc R Knecht

University of Miami, كورال غيبلز، فلوريدا, Florida, United States

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Publications (64)363.04 Total impact

  • Dennis B. Pacardo, Marc R. Knecht
    ChemInform 06/2015; 46(25):no-no. DOI:10.1002/chin.201525279
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    ABSTRACT: We report a synthetic approach to form octahedral Cu2O microcrystals with a tunable edge length and demonstrate their use as catalysts for the photodegradation of aromatic organic compounds. In this particular study, the effects of the Cu2+ and reductant concentrations and stoichiometric ratios were carefully examined to identify their roles in controlling the final material composition and size under sustainable reaction conditions. Varying the ratio and concentrations of Cu2+ and reductant added during the synthesis determined the final morphology and composition of the structures. Octahedral particles were prepared at selected ratios of Cu2+:glucose that demonstrated a range of photocatalytic reactivity. The results indicate that material composition, surface area, and substrate charge effects play important roles in controlling the overall reaction rate. Additionally, analysis of the post-reacted materials revealed photocorrosion was inhibited and that surface etching had preferentially occurred at the particle edges during the reaction, suggesting that the reaction predominately occurred at these interfaces. Such results advance the understanding of how size and composition affect the surface interface and catalytic functionality of materials.
    ACS Applied Materials & Interfaces 05/2015; 7(24). DOI:10.1021/acsami.5b04282 · 5.90 Impact Factor
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    ABSTRACT: Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information correlating peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach was used to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then elucidated by identification of the catalytic active sites at the atomic level. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through the rational tailoring of peptide sequences.
    ACS Nano 04/2015; 9(5). DOI:10.1021/acsnano.5b00168 · 12.03 Impact Factor
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    ABSTRACT: The use of peptides as capping ligands for materials synthesis has been widely explored. The ambient conditions of bio-inspired syntheses using molecules such as peptides represent an attractive route for controlling the morphology and activity of nanomaterials. Although various reductants can be used in such syntheses, no comprehensive comparison of the same bio-based ligand with different reductants has been reported. In this contribution, peptides AuBP1, AuBP2 and Pd4 are used in the synthesis of Au nanoparticles. The reductant strength is varied by using three different reducing agents: NaBH4, hydrazine, and ascorbic acid. These changes in reductant produce significant morphological differences in the final particles. The weakest reductant, ascorbic acid, yields large, globular nanoparticles with rough surfaces, while the strongest reductant, NaBH4, yields small, spherical and smooth nanomaterials. Studies of 4-nitrophenol reduction using the Au nanoparticles as catalysts reveal a decrease in activation energy for the large, globular, rough materials relative to the small, spherical, smooth materials. These studies demonstrate that modifying the reductant is a simple way to control the activity of peptide-capped nanoparticles.
    ACS Applied Materials & Interfaces 04/2015; 7(16). DOI:10.1021/acsami.5b01461 · 5.90 Impact Factor
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    ABSTRACT: Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins ( SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 01/2015; 12(1):193-204. DOI:10.1109/TCBB.2014.2321158 · 1.54 Impact Factor
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    ABSTRACT: Controllable 3D assembly of multicomponent inorganic nanomaterials by precisely positioning two or more types of nanoparticles to modulate their interactions and achieve multifunctionality remains a major challenge. The diverse chemical and structural features of biomolecules can generate the compositionally specific organic/inorganic interactions needed to create such assemblies. Toward this aim, we studied the materials-specific binding of peptides selected based upon affinity for Ag (AgBP1 and AgBP2) and Au (AuBP1 and AuBP2) surfaces, combining experimental binding measurements, advanced molecular simulation, and nanomaterial synthesis. This reveals, for the first time, different modes of binding on the chemically similar Au and Ag surfaces. Molecular simulations showed flatter configurations on Au and a greater variety of 3D adsorbed conformations on Ag, reflecting primarily enthalpically driven binding on Au and entropically driven binding on Ag. This may arise from differences in the interfacial solvent structure. On Au, direct interaction of peptide residues with the metal surface is dominant, while on Ag, solvent-mediated interactions are more important. Experimentally, AgBP1 is found to be selective for Ag over Au, while the other sequences have strong and comparable affinities for both surfaces, despite differences in binding modes. Finally, we show for the first time the impact of these differences on peptide mediated synthesis of nanoparticles, leading to significant variation in particle morphology, size, and aggregation state. Because the degree of contact with the metal surface affects the peptides ability to cap the nanoparticles and thereby control growth and aggregation, the peptides with the least direct contact (AgBP1 and AgBP2 on Ag) produced relatively polydispersed and aggregated nanoparticles. Overall, we show that thermodynamically different binding modes at metallic interfaces can enable selective binding on very similar inorganic surfaces and can provide control over nanoparticle nucleation and growth. This supports the promise of bionanocombinatoric approaches that rely upon materials recognition.
    Chemistry of Materials 09/2014; 26(17):4960-4969. DOI:10.1021/cm501529u · 8.54 Impact Factor
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    ABSTRACT: Carbon carbon (C-C) coupling reactions are ubiquitously used for the generation of advanced chemical species; however, this reactivity remains inefficient and energy intensive. Transitioning such systems toward more sustainable and green conditions would be ideal where Pd nanoparticles represent unique catalysts to achieve this goal. In this contribution, we demonstrate the use of peptide-capped Pd nanoparticles as catalysts for driving Suzuki C-C coupling, focusing specifically on the effects of the transmetalation step in controlling the reactivity. These materials achieved C-C bond formation in water at room temperature using low Pd loadings. Coupling across a variety of mono- and disubstituted substrates was studied, where the reactivity was dependent upon the halogen moiety. Furthermore, studies of the reaction conditions revealed a strong sensitivity to the base identity, suggesting that competing transmetalation pathways and reaction equilibrium effects lead to variations in Suzuki coupling yields. Based on these results, and in comparison to the Stille coupling reactivity of the same materials, it is suggested that the transmetalation step is important in controlling the overall C-C coupling process. This evidence is significant for nanocatalysts to optimize reactivity under sustainable conditions.
    The Journal of Physical Chemistry C 08/2014; 118(32):18543-18553. DOI:10.1021/jp504371q · 4.84 Impact Factor
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    ABSTRACT: Peptide-driven nanomaterials synthesis and assembly has become a significant research thrust due to the capability to generate a range of multifunctional materials with high spatial precision and tunable properties. Despite the extensive amount of available literature, the majority of studies report the use of free peptides to drive synthesis and assembly. Such strategies are not an entirely accurate representation of nature, as many materials binding peptides found in biological systems are sterically constrained to a larger biological motif. Herein we report the synthesis of catalytic Pd nanomaterials using constrained peptides covalently attached to the surface of small, water-soluble dendrimers. Using the R5 peptide conjugated to polyamidoamine dendrimer as a bioconjugate, Pd nanomaterials were generated that displayed altered morphologies compared to nanomaterials templated with free R5. It was discovered that the peptide surface density on the dendrimer affected the resulting nanoscale morphology. Furthermore, the catalytic activities of Pd materials templated with R5/dendrimer are higher as compared to the R5-templated Pd materials for the hydrogenation of allyl alcohol, with an average increase in turnover frequency of ∼1500 mol product (mol Pd × h)−1. Small angle X-ray scattering analysis and dynamic light scattering indicate that Pd derived from R5/dendrimer templates remained less aggregated in solution and displayed more available reactive Pd surface area. Such morphological changes in solution are attributed to the constrained peptide binding motifs, which altered the Pd morphology and subsequent properties. Moreover, the results of this study suggest that constrained materials binding peptide systems can be employed as a means to alter morphology and improve resulting properties.
    Chemistry of Materials 07/2014; 26(14):4082-4091. DOI:10.1021/cm5007444 · 8.54 Impact Factor
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    ABSTRACT: Adsorption of small biomolecules onto the surface of nanoparticles offers a novel route to the generation of nanoparticle assemblies with predictable architectures. Previously, ligand exchange experiments on citrate-capped gold nanoparticles with the amino acid arginine were reported to support linear nanoparticle assemblies. Here, we use a combination of atomistic modelling with experimental characterization to explore aspects of the assembly hypothesis for these systems. Using molecular simulation, we probe the structural and energetic characteristics of arginine overlayers on the Au(111) surface under aqueous conditions, at both low and high coverage regimes. In the low density regime, the arginines lie flat on the surface. At constant composition, these overlayers are found to be lower in energy than the densely-packed films, although the latter case appears kinetically stable when arginine is adsorbed via the zwitterion group, exposing the charged guanidinium group to the solvent. Our findings suggest that zwitterion-zwitterion hydrogen-bonding at the gold surface, and minimization of the electrostatic repulsion between adjacent guanidinium groups, play key roles in determining arginine overlayer stability at the aqueous gold interface. Ligand-exchange experiments of citrate-capped gold nanoparticles with arginine derivatives agmatine and N-methyl-L-arginine reveal that modification at the guanidinium group significantly diminishes the propensity for linear assembly of the nanoparticles.
    ACS Applied Materials & Interfaces 06/2014; 6(13). DOI:10.1021/am502119g · 5.90 Impact Factor
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    ABSTRACT: Biomimetic nanotechnologies that use peptides to guide the growth and assembly of nanostructures offer new avenues for the creation of functional nanomaterials and manipulation of their physicochemical properties. However, the impacts of peptide sequence and binding motif upon the surface characteristics and physicochemical properties of nanoparticles remain poorly understood. The configurations of the biomolecules are expected to be extremely important for directing the synthesis and achieving desired material functionality, and these binding motifs will vary with the peptide sequence. Here, we have prepared a series of Au nanoparticles capped with a variety of materials-directing peptides with known affinity for metal surfaces. These nanomaterials were characterized by UV-vis and circular dichroism spectroscopies, transmission electron microscopy, and ζ-potential measurement. Then their catalytic activity for 4-nitrophenol reduction was analyzed. The results indicate that substantially different Au-peptide interfaces are generated using different peptide sequences, even when these sequences have similar binding affinity. This is consistent with recent work showing that Au-peptide binding affinity can have varying entropic and enthalpic contributions, with enthalpically- and entropically-driven binders exhibiting quite different ensembles of configurations on the Au surface. The catalytic activity, as reflected by the measured activation energy, did not correlate with the particle size or with the binding affinity of the peptides, suggesting that the reactivity of these materials is governed by the more subtle details of the conformation of the bound peptide and on the nanoparticle surface reconstruction as dictated by the peptide structure. Such variations in both nanoparticle surface reconstruction and peptide configuration could potentially be used to program specific functionality into the peptide-capped nanomaterials.
    Nanoscale 02/2014; 6(6). DOI:10.1039/c3nr06201e · 6.74 Impact Factor
  • Dennis B. Pacardo, Eric Ardman, Marc R. Knecht
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    ABSTRACT: Advancing catalytic processes toward sustainable conditions is necessary to maintain current production levels in light of dwindling natural resources. Nanomaterial-based catalysts have been suggested as a possible route to achieve this goal; however, the effects of particle structure on the reaction remain unclear. Furthermore, for each reaction, different substrates are likely to be used that vary the molecular size, functional group composition, and reactive moiety site that could significantly alter the reactivity of nanomaterial-based catalysts. In this contribution, we have studied the effects of the molecular substrate structure on the reactivity of peptide-templated Pd nanomaterials with selectable morphologies. In this regard, spherical, ribbon-like, and networked metallic nanomaterials were studied that demonstrated significant degrees of reactivity of olefin hydrogenation using the substrates that varied the molecular size and reactive group position. The results demonstrated that substrate isomerization, rather than molecular structure, plays a significant role in attenuating the reactivity of the materials. Furthermore, the Pd structures demonstrated the ability to drive multistep reactivity for the complete hydrogenation of substrates with multiple reactive groups. Such results advance the structure/function relationship of nanocatalysis that could be important in addressing future sustainability goals.
    The Journal of Physical Chemistry C 01/2014; 118(5):2518–2527. DOI:10.1021/jp410255g · 4.84 Impact Factor
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    ABSTRACT: Transitioning energy-intensive and environmentally intensive processes toward sustainable conditions is necessary in light of the current global condition. To this end, photocatalytic processes represent new approaches for H2 generation; however, their application toward tandem catalytic reactivity remains challenging. Here, we demonstrate that metal oxide materials decorated with noble metal nanoparticles advance visible light photocatalytic activity toward new reactions not typically driven by light. For this, Pd nanoparticles were deposited onto Cu2O cubes to generate a composite structure. Once characterized, their hydrodehalogenation activity was studied via the reductive dechlorination of polychlorinated biphenyls. To this end, tandem catalytic reactivity was observed with H2 generation via H2O reduction at the Cu2O surface, followed by dehalogenation at the Pd using the in situ generated H2. Such results present methods to achieve sustainable catalytic technologies by advancing photocatalytic approaches toward new reaction systems.
    Journal of the American Chemical Society 01/2014; 136(1):32-5. DOI:10.1021/ja410465s · 11.44 Impact Factor
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    ABSTRACT: Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomolecules and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomolecules and inorganic nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, molecular-level understanding of biomolecule-inorganic nanoparticle interactions. Here, we introduce an integrated method for building this understanding using experimental measurements and advanced molecular simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quantitatively demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in our laboratories to a range of inorganic nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.
    ACS Nano 10/2013; 7(11). DOI:10.1021/nn404427y · 12.03 Impact Factor
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    ABSTRACT: With the rapid development of bionanotechnology, there has been a growing interest recently in identifying the affinity classes of the inorganic materials binding peptide sequences. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on our new amino acid transition matrix, and then the probability of test sequences belonging to a specific affinity class is calculated through solving an objective function. In addition, the objective function is solved through iterative propagation of probability estimates among sequences and sequence clusters. Experimental results on a real inorganic material binding sequence dataset show that the proposed framework is highly effective on identifying the affinity classes of inorganic material binding sequences.
    Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics; 09/2013
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    ABSTRACT: Diverse classes of metallic nanostructures have been explored recently for a variety of applications, including energy efficient catalytic transformations. The morphology, size, and local chemical environment of the catalytic nanomaterials can have dramatic effects on their reactivity. Herein, we demonstrate a peptide-template-based approach for the synthesis of Pd and Pt nanostructures of varying morphologies under ambient conditions. In this report, we examine the effect of the metal/peptide ratio over an expansive range to demonstrate the stepwise production of materials ranging from nanospheres to nanoparticle networks for the Pd structures. Interestingly, when the metallic composition was changed to Pt, only spherical materials were generated, indicating that the metallic composition of the nanostructures plays a key role in the final morphology. The hydrogenation of allyl alcohol was then employed as a model reaction to examine the catalytic reactivity of these metallic nanomaterials. Under environmentally benign reaction conditions, high turnover frequency values were observed for the metallic Pd and Pt nanocatalysts that was independent of the material morphology. Given their high degree of reactivity and facile synthetic preparation, these materials could prove to be versatile and efficient catalysts for a variety of industrially and environmentally important reactions.
    The Journal of Physical Chemistry C 08/2013; 117(35):18053–18062. DOI:10.1021/jp403796h · 4.84 Impact Factor
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    ABSTRACT: Au nanomaterials are well-known for their optical properties, where Au nanorods have demonstrated unique capabilities because of their readily tunable size and shape. Unfortunately, functionalization of the material surface is challenging because of their lack of stability after only a few purification cycles. Here, we demonstrate that enhanced Au-nanorod stability can be achieved by purifying the materials using dilute cetyltrimethylammonium bromide (CTAB) wash solutions. To this end, purifying the materials in such a manner shifts the passivant on/off equilibrium to maintain surfactant adsorption to the metal surface, leading to enhanced stability. Interestingly, from this study, a bimodal distribution of Au nanorods was evident, where one species was prone to bulk aggregation, whereas the second population remained stable in solution. This likely arose from defects within the CTAB bilayer at the nanorod surface, resulting in selective material aggregation. For this, those structures with high numbers of defects aggregated, whereas nanorods with a more pristine bilayer remained stable. Coating of the Au nanorods using polyelectrolytes was also explored for enhanced stability, where the composition of the anionic polymer played an important role in controlling materials stability. Taken together, these results demonstrate that the stability of Au nanorods can be directly tuned by the solvent-exposed surface structure, which could be manipulated to allow for the extensive material functionalization that is required for the generation of nanoplatforms with multiple applications.
    ACS Applied Materials & Interfaces 08/2013; 5(16). DOI:10.1021/am401997q · 5.90 Impact Factor
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    ABSTRACT: Peptide-based methods represent new approaches to selectively produce nanostructures with potentially important functionality. Unfortunately, biocombinatorial methods can only select peptides with target affinity and not for the properties of the final material. In this work, we present evidence to demonstrate that materials-directing peptides can be controllably modified to substantially enhance particle functionality without significantly altering nanostructural morphology. To this end, modification of selected residues to vary the site-specific binding strength and biological recognition can be employed to increase the catalytic efficiency of peptide-capped Pd nanoparticles. These results represent a step toward the de novo design of materials-directing peptides that control nanoparticle structure/function relationships.
    Journal of the American Chemical Society 07/2013; 135(30). DOI:10.1021/ja402215t · 11.44 Impact Factor
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    ABSTRACT: Surfactant-stabilized metal nanoparticles have shown promise as catalysts although specific surface features and their influence on catalytic performance have not been well understood. We quantify the thermodynamic stability, the facet composition of the surface, and distinct atom types that affect rates of atom leaching for a series of twenty near-spherical Pd nanoparticles of 1.8 to 3.1 nm size using computational models. Cohesive energies indicate higher stability of certain particles that feature an approximate 60/20/20 ratio of {111}, {100}, and {110} facets while less stable particles exhibit widely variable facet composition. Unique patterns of atom types on the surface cause apparent differences in binding energies and changes in reactivity. Estimates of the relative rate of atom leaching as a function of particle size were obtained by the summation of Boltzmann-weighted binding energies over all surface atoms. Computed leaching rates are in good qualitative correlation with the measured catalytic activity of peptide-stabilized Pd nanoparticles of the same shape and size in Stille coupling reactions. The agreement supports rate-controlling contributions by atom leaching in the presence of reactive substrates. The computational approach provides a pathway to estimate the catalytic activity of metal nanostructures of engineered shape and size, and possible further refinements are described.
    Physical Chemistry Chemical Physics 03/2013; DOI:10.1039/c3cp00135k · 4.20 Impact Factor
  • Dennis B. Pacardo, Marc R. Knecht
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    ABSTRACT: Herein we systematically probed the atom-leaching mechanism of Pd nanoparticle-driven Stille coupling to further elucidate the fate of the highly active Pd0 atoms released in solution. In this regard, initial oxidative addition at the particle surface results in Pd atom abstraction for reactivity in solution. As a result, two reaction sites are present, the particle surface and pre-leached Pd atoms, thus different degrees of reactivity are possible. This effect was probed via aryl halide combinations that varied the halogen identity allowing for oxidative addition of two substrates simultaneously. The results demonstrate that the system was highly reactive for iodo-based compounds in the mixture at room temperature; however, reactivity at bromo-based substrates was only observed at slightly elevated temperatures of 40.0 °C. As such, substrate selectivity was evident from the catalytic materials that can be controlled based upon the aryl halide composition and reaction temperature. Furthermore, both intermolecular and intramolecular selectivity is possible, thus raising the degree of reaction complexity that can be achieved.
    02/2013; 3(3):745-753. DOI:10.1039/C2CY20636F
  • Manish Sethi, Marc R Knecht
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    ABSTRACT: Nanoparticles possess unique properties that are enhanced due to their small size and varied shapes. These properties can be directly manipulated by controlling the aggregation state, which can further be exploited for applications in bio/chemical sensing, plasmonics, and as supports for catalysts. While the advantages of controlled aggregates of nanomaterials are great, synthetic strategies to achieve such structures with precision over the final arrangement of the materials in three-dimensional space remain limited. We have shown that ligand exchange reactions on Au nanomaterials of various shapes using simple amino acids can induce the formation of linear aggregates of the materials. The assembly process is mediated by partial ligand exchange on the particle surface, followed by the surface segregation of the two ligands that produces an electric dipole across the nanomaterial from which alignment occurs in solution via dipole-dipole interactions. This linear-based assembly can be used to tune the optical properties of the materials and could represent new pathways to study the interactions between biological molecules and inorganic nanomaterials.
    Methods in molecular biology (Clifton, N.J.) 01/2013; 1026:149-61. DOI:10.1007/978-1-62703-468-5_12 · 1.29 Impact Factor

Publication Stats

1k Citations
363.04 Total Impact Points


  • 2011–2014
    • University of Miami
      • Department of Chemistry
      كورال غيبلز، فلوريدا, Florida, United States
  • 2008–2013
    • University of Kentucky
      • Department of Chemistry
      Lexington, KY, United States
  • 2006–2009
    • University of Texas at Austin
      • • Department of Chemistry and Biochemistry
      • • Center for Nano- and Molecular Science and Technology
      Austin, Texas, United States
    • Texas A&M University
      • Department of Chemistry
      College Station, Texas, United States
  • 2003–2006
    • Vanderbilt University
      • Department of Chemistry
      Nashville, MI, United States