Showing papers by "Bobby G. Sumpter published in 2007"

Unique chemical reactivity of a graphene nanoribbon's zigzag edge.

Abstract: The zigzag edge of a graphene nanoribbon possesses a unique electronic state that is near the Fermi level and localized at the edge carbon atoms. The authors investigate the chemical reactivity of these zigzag edge sites by examining their reaction energetics with common radicals from first principles. A "partial radical" concept for the edge carbon atoms is introduced to characterize their chemical reactivity, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules. In addition, the uniqueness of the zigzag-edged graphene nanoribbon is further demonstrated by comparing it with other forms of sp2 carbons, including a graphene sheet, nanotubes, and an armchair-edged graphene nanoribbon.

The unique chemical reactivity of a graphene nanoribbon's zigzag edge

Abstract: The zigzag edge of a graphene nanoribbon possesses a unique electronic state that is near the Fermi level and localized at the edge carbon atoms. We investigate the chemical reactivity of these zigzag edge sites by examining their reaction energetics with common radicals from first principles. A "partial radical" concept for the edge carbon atoms is introduced to characterize their chemical reactivity, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules. In addition, the uniqueness of the zigzag-edged graphene nanoribbon is further demonstrated by comparing it with other forms of sp2 carbons, including a graphene sheet, nanotubes, and an armchair-edged graphene nanoribbon.

Nitrogen-Mediated Carbon Nanotube Growth: Diameter Reduction, Metallicity, Bundle Dispersability, and Bamboo-like Structure Formation

Abstract: Carbon nanotube growth in the presence of nitrogen has been the subject of much experimental scrutiny, sparking intense debate about the role of nitrogen in the formation of diverse structural features, including shortened length, reduced diameters, and bamboo-like multilayered nanotubules. In this paper, the origin of these features is elucidated using a combination of experimental and theoretical techniques, showing that N acts as a surfactant during growth. N doping enhances the formation of smaller diameter tubes. It can also promote tube closure which includes a relatively large amount of N atoms into the tube lattice, leading to bamboo-like structures. Our findings demonstrate that the mechanism is independent of the tube chirality and suggest a simple procedure for controlling the growth of bamboo-like nanotube morphologies.

First principles study of magnetism in nanographenes.

Abstract: Magnetism in nanographenes [also known as polycyclic aromatic hydrocarbons (PAHs)] is studied with first principles density functional calculations. We find that an antiferromagnetic (AFM) phase appears as the PAH reaches a certain size. This AFM phase in PAHs has the same origin as the one in infinitely long zigzag-edged graphene nanoribbons, namely, from the localized electronic state at the zigzag edge. The smallest PAH still having an AFM ground state is identified. With increased length of the zigzag edge, PAHs approach an infinitely long ribbon in terms of (1) the energetic ordering and difference among the AFM, ferromagnetic, and nonmagnetic phases and (2) the average local magnetic moment at the zigzag edges. These PAHs serve as ideal targets for chemical synthesis of nanographenes that possess magnetic properties. Moreover, our calculations support the interpretation that experimentally observed magnetism in activated carbon fibers originates from the zigzag edges of the nanographenes.

Structure and stability of small boron and boron oxide clusters.

Abstract: To rationally design and explore a potential energy source based on the highly exothermic oxidation of boron, density functional theory (DFT) was used to characterize small boron clusters with 0−3 oxygen atoms and a total of up to ten atoms. The structures, vibrational frequencies, and stabilities were calculated for each of these clusters. A quantum molecular dynamics procedure was used to locate the global minimum for each species, which proved to be crucial given the unintuitive structure of many of the most stable isomers. Additionally, due to the plane-wave, periodic DFT code used in this study a straightforward comparison of these clusters to the bulk boron and B2O3 structures was possible despite the great structural and energetic differences between the two forms. Through evaluation of previous computational and experimental work, the relevant low-energy structures of all but one of the pure boron clusters can be assigned with great certainty. Nearly all of the boron oxide clusters are described h...

Solid-State Combustion of Metallic Nanoparticles: New Possibilities for an Alternative Energy Carrier

Abstract: As an alternative to conventional methods of conveying and delivering energy in mobile applications or to remote locations, we have examined the combustion of nanostructured metal particles assembled into metal clusters. Clusters containing iron nanoparticles (~50 nm in diameter) were found to combust entirely in the solid state due to the high surface-to-volume ratio typical of nanoparticles. Optical temperature measurements indicated that combustion was rapid (~500 msec), and occurred at relatively low peak combustion temperatures (1000-1200 K). Combustion produces a mixture of Fe(III) oxides. Xray diffraction and gravimetric analysis indicated that combustion was nearly complete (93-95% oxidation). Oxide nanoparticles could be readily reduced at temperatures between 673 and 773 K using hydrogen at 1 atmosphere pressure, and then passivated by the growth of a thin oxide layer. The nanostructuring of the particles is retained throughout the combustion-regeneration cycle. Modeling of the combustion process is in good agreement with observed combustion characteristics.

Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA.

Abstract: M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G−Zn−C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G−Zn−C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the ...

Selective tuning of the electronic properties of coaxial nanocables through exohedral doping.

Abstract: The electronic properties of exohedrally doped double-walled carbon nanotubes (DWNTs) have been investigated using density functional theory and resonance Raman spectroscopy (RRS) measurements. First-principles calculations elucidate the effects of exohedral doping on the M@S and S@M systems, where a metallic (M) tube is either inside or outside a semiconducting (S) one. The results demonstrate that metallic nanotubes are extremely sensitive to doping even when they are inner tubes, in sharp contrast to semiconducting nanotubes, which are not affected by doping when the outer shell is a metallic nanotube (screening effects). The theoretical predictions are in agreement with RRS data on Br2- and H2SO4-doped DWNTs. These results pave the way to novel nanoscale electronics via exohedral doping.

Electronic structure of xDNA.

Abstract: xDNA is an artificial duplex made of natural and benzo-homologated bases. The latter can be seen as a fusion between benzene and a natural base. We have used two different ab initio techniques, one based on B3LYP and a Gaussian expansion of the wave functions, and the other on GGA and plane-waves, to investigate the electronic properties of an xDNA duplex and a natural one with an analogous sequence. The calculations were performed in dry conditions, i.e., H atoms were used to neutralize the charge. It is found that the HOMO-LUMO gap of xDNA is about 0.5 eV smaller than that of B-DNA, independent of the technique used. The pi-pi* gap of xDNA is 1.3 or 1.0 eV smaller than that of B-DNA, depending on whether one uses B3LYP/6-31G or GGA/plane-waves, respectively. An analysis of how saturation changes the electronic properties of the nucleotide pairs that make up these duplexes suggests that different saturation schemes significantly affect the HOMO-LUMO gap value of xDNA and B-DNA. The same is not true for the pi-pi* gap. That xDNA has a smaller pi-pi* gap than B-DNA suggests that xDNA could be a plausible candidate for molecular-wire applications.

Nonvolatile memory elements based on the intercalation of organic molecules inside carbon nanotubes.

Abstract: We propose a novel class of nonvolatile memory elements based on the modification of the transport properties of a conducting carbon nanotube by the presence of an encapsulated molecule. The guest molecule has two stable orientational positions relative to the nanotube that correspond to conducting and nonconducting states. The mechanism, governed by a local gating effect of the molecule on the electronic properties of the nanotube host, is studied using density functional theory. The mechanisms of reversible reading and writing of information are illustrated with a F4TCNQ molecule encapsulated inside a metallic carbon nanotube. Our results suggest that this new type of nonvolatile memory element is robust, fatiguefree, and can operate at room temperature. The concept of information as organized knowledge can be formally described, but dealing with practical information in the real world is generally related to a physical medium [1]. Operations on information such as processing, modification, and storage take place through processes based on intrinsic properties of matter, and from that point of view, it is the intricate interplay between information and physical mechanisms that constitutes the fundamental ground for information technology. Electronic switches can be considered as the fundamental basis for information processing and storage. In an electronic switch, the flow of electrons is modified by changing the state of the switching device, via a controlled writing mechanism, while the current flow through the device is used as a reading mechanism. Information is stored in the state of the switch, which can be modified either mechanically or electrically using the same or additional electrodes.

Use of drug discovery tools in rational organometallic catalyst design.

Abstract: A computational procedure is detailed where techniques common in the drug discovery process2D- and 3D-quantitative structure−activity relationships (QSAR)are applied to rationalize the catalytic activity of a synthetically flexible, Ti−NP ethylene polymerization catalyst system. Once models relating molecular properties to catalyst activity are built with the two QSAR approaches, two database mining approaches are used to select a small number of ligands from a larger database that are likely to produce catalysts with high activity when grafted onto the Ti−NP framework. The software employed throughout this work is freely available, is easy to use, and was applied in a “black box” approach to highlight areas where the drug discovery tools, designed to address organic molecules, have difficulty in addressing issues arising from the presence of a metal atom. In general, 3D-QSAR offers an efficient way to screen new potential ligands and separate those likely to lead to poor catalysts from those that are lik...

A toxicity evaluation and predictive system based on neural networks and wavelets.

Abstract: A computational approach has been developed for performing efficient and reasonably accurate toxicity evaluation and prediction. The approach is based on computational neural networks linked to modern computational chemistry and wavelet methods. In this paper, we present details of this approach and results demonstrating its accuracy and flexibility for predicting diverse biological endpoints including metabolic processes, mode of action, and hepato- and neurotoxicity. The approach also can be used for automatic processing of microarray data to predict modes of action.

Multi-intelligent system for toxicogenomic applications (mista)

Abstract: A system ( 100 ) and method ( 800 ) to predict toxicological effects of molecules is provided. The method can include obtaining ( 802 ) a three-dimensional (3-D) structure of a molecule from a database, transforming ( 804 ) the 3-D structure to a one-dimensional (1-D) geometrical representation using a combination of a molecular transform ( 114 ) and wavelet transform ( 115 ), computing a topology and electronic structure of the molecule via topological indices, and generating a feature vector ( 500 ) comprising the 1-D geometrical representation ( 510 ), and the topology and the electronic structure ( 520 ). The system can predict at least one among metabolic processes, modes of action, hepatotoxicity, and neurotoxicity.

Electronic Structure Investigation of Surface−Adsorbate and Adsorbate−Adsorbate Interactions in Multilayers of CH4 on MgO(100)

Abstract: The adsorption of methane on MgO(100) is examined using extensive first-principles DFT methods combined with inelastic neutron scattering. The results provide evidence that the structure of the first adsorbed methane layer is dominated by surface-adsorbate interactions, although adsorbate-adsorbate interactions still play a role. More specifically, the former selects for a structure wherein partially positive hydrogen atoms are oriented towards lattice oxygen sites, whereas the latter effect dictates that each methane molecule is rotated by 90 with respect to its neighbor. The structure of a second added layer is consistent with that predicted solely based on interadsorbate repulsion, although, as this structure is also favored by the electrostatic character of the surface, the roles of each effect can not be entirely evaluated independently. At the third layer, and presumably all higher layers, methane is structures so that the number of close H-H contacts is minimized. Quantum molecular dynamics simulations lend further support to the highly influential role of repulsive interadsorbate interactions in determining structure. Methane rotation at each layer is also studied.

A New Class of Supramolecular Wires

Abstract: We present an unconventional approach to the development of 1-D supramolecular wires based on the self-assembly of donor−σ−acceptor molecules. The concept is demonstrated using one class of these systems, 1-aza-adamantanetriones (AATs), that are well-characterized in terms of their solution/solid-state self-assembly and chemical manipulation. Our results show that accompanying spontaneous organization of the molecules into 1-D periodic arrays is delocalization of the frontier molecular orbitals through the saturated tricyclic cores of the monomers that span the entire system. The electronic band structure for the 1-D wire reveals significant dispersion and can be tuned from the insulating regime to the semiconducting regime by suitable chemical functionalization of the core. The theoretical understanding of this new class of supramolecular structures sets the stage for the tailored design of novel functional materials that are an alternative to those comprised of traditional π-conjugated systems.

Benzo-homologated nucleobases in a nanotube-electrode set-up for DNA sequencing

Abstract: Motivated by the possibility that the conductivity signatures of benzo-homologated DNA bases could be used to sequence DNA, we have investigated the conductivity properties of these bases when they are non-covalently sandwiched between two (5,5) nanotube electrodes. It is found that these bases conduct poorly, making it very difficult to distinguish them. An analysis of the changes in the conductivity of benzo-adenine as a function of the distance between the tips of the nanotubes revealed that, even though the conductance increases by four orders of magnitude when the electrodes are brought closer together, the net conductance remains rather small. These results suggest that benzo-homologated bases, despite having smaller HOMO-LUMO gaps than their natural counterparts, when non-covalently bound to the electrodes cannot be used to sequence DNA by means of conductivity measurements.

Investigation of the nanoscale self-assembly of donor-σ-acceptor molecules

Abstract: Electronic structure calculations are used to explore the nature of the interactions that lead to the self-assembly of a new class of functionalized donor-sigma-acceptor molecules, 1-aza-adamantanetriones (AATs), and the consequences of molecular structure on the resulting supramolecular systems The results show how the self-assembly process originates from the saturated core of the molecules that underlies their shape, conformational preferences, and dipole-directed one-dimensional assembly The solvation properties of the monomers are explored and 1H NMR chemical shift values are determined and compared to experimental trends A theoretical understanding of this class of supramolecular structures coupled with their molecular-level tunability introduces the possibility to design novel functional materials for specific electronic and optoelectronic applications

Tuning the conductance of carbon nanotubes with encapsulated molecules

Abstract: It was recently shown that a molecule encapsulated inside a carbon nanotube can be used to devise a novel type of non-volatile memory element. At the heart of the mechanism for storing and reading information is the new concept of a molecular gate where the molecule acts as a passive gate that hinders the flow of electrons for a given position relative to the nanotube host. By systematically exploring the effects of encapsulation of an acceptor molecule in a series of carbon nanotubes, we show that the reliability of the memory mechanism is very sensitive to the interaction between the nanotube host and the molecule guest.

A Toxicity Evaluation and Predictive System Based on Neural Networks and Wavelets.

Abstract: A computational approach has been developed for performing efficient and reasonably accurate toxicity evaluation and prediction. The approach is based on computational neural networks linked to modern computational chemistry and wavelet methods. In this paper, we present details of this approach and results demonstrating its accuracy and flexibility for predicting diverse biological endpoints including metabolic processes, mode of action, and hepato- and neurotoxicity. The approach also can be used for automatic processing of microarray data to predict modes of action.

Structure and Stability of Small Boron and Boron Oxide Clusters

Abstract: To rationally design and explore a potential energy source based on the highly exothermic oxidation of boron, density functional theory (DFT) was used to characterize small boron clusters with 0−3 oxygen atoms and a total of up to ten atoms. The structures, vibrational frequencies, and stabilities were calculated for each of these clusters. A quantum molecular dynamics procedure was used to locate the global minimum for each species, which proved to be crucial given the unintuitive structure of many of the most stable isomers. Additionally, due to the plane-wave, periodic DFT code used in this study a straightforward comparison of these clusters to the bulk boron and B2O3 structures was possible despite the great structural and energetic differences between the two forms. Through evaluation of previous computational and experimental work, the relevant low-energy structures of all but one of the pure boron clusters can be assigned with great certainty. Nearly all of the boron oxide clusters are described h...

Optimizing the Electronic Properties of Carbon Nanotubes using Amphoteric Doping

Abstract: Present day semiconductor devices are rapidly approaching their physical limits, prompting an increasing number of researchers across multiple disciplines to attempt devising innovative ways for decreasing the size and increasing the performance of critical features in microelectronic circuits. One possible route is based on the idea of using molecules and molecular structures as functional electronic devices. Carbon nanotubes may provide one of the best materials for molecular electronic devices as they present a flexible and well structured architecture. However, practical realizations of new nanotube-based electronic devices hinge on a number of outstanding problems, such as the capability of achieving large-scale air-stable and controlled doping. Amphoteric doping by encapsulating suitable organic molecules inside of nanotubes may hold tremendous promise in this respect. In order to investigate and optimize the electronic transport properties in carbon nanotubes doped with organic molecules we have performed large-scale quantum electronic structure calculations coupled with a Green's function formulation for determining the conductance. By implementing this hybrid computational approach for examination of the electronic properties of molecular-based structures, an efficient and accurate procedure has been demonstrated for studying the effects of amphoteric doping of carbon nanotubes. With this method, a computational framework for the optimal design ofmore » nanotube based electronic devices is becoming routinely accessible. Results from our calculations suggest that the electronic structure of a carbon nanotube can be easily manipulated by encapsulating appropriate organic molecules leading to charge transfer processes that induce efficient n- and p-type doping of the carbon nanotube. Even though a molecule may cause n- or p-doping, we have found it to generally have minor effects on the transport properties of the nanotube as compared to a pristine tube.« less