Biomedical subjects

Bobby G Sumpter

Publications and source records attributed to Bobby G Sumpter.

9 recordsLinked to original sources

PubMed2006

How do aryl groups attach to a graphene sheet?

How aryl groups attach to a graphene sheet is an experimentally unanswered question. Using first principles density functional theory methods, we shed light on this problem. For the basal plane, isolated phenyl groups are predicted to be weakly bonded to the graphene sheet, even though a new single C-C bond is formed between the phenyl group and the basal plane by converting a sp2-carbon in the graphene sheet to sp3. However, the interaction can be strengthened significantly with two phenyl groups attached to the para positions of the same six-membered ring to form a pair on the basal plane. The strongest bonding is found at the graphene edges. A 1,2-addition pair is predicted to be most stable for the armchair edge, whereas the zigzag edge possesses a unique localized state near the Fermi level that shows a high affinity for the phenyl group.

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PubMed2006

Olefin adsorption on silica-supported silver salts--a DFT study.

Recent experiments have shown that silver salts supported on mesoporous silicas display excellent adsorption selectivities of ethylene over ethane and propylene over propane. Employing the techniques of density functional theory, we have investigated the fundamental bases of this separation process by examining silver salts dispersed on model silica surfaces. Our model system includes Ag+ cations, their counteranions, silica supports, and surface silanols. Both adsorption geometries and energetics of ethylene and propylene were explored. Our results indicate that the nature of the Ag-olefin interaction is predominantly hybridization between Ag d and olefin pi states, which is supported by analyses of electron density difference plots and density of states. The counteranions, such as NO3- were found to interact strongly with surface silanols through multiple hydrogen bonds but have limited effect on the adsorption energy of olefins on the Ag+ cations. The current work supports recent experiments, which indicate that Ag-salt/silica may be a very promising adsorbent for olefin/paraffin separation.

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PubMed2006

Structure and bonding between an aryl group and metal surfaces.

Modifying solid surfaces with aryl groups has many potential applications. Using first principles density functional theory methods, we investigated the trend of the structure and bonding of the phenyl group (C6H5, the simplest aryl group) on selected transition metals across the periodic table. We found that the bond between C6H5 and metal surfaces is chemical in nature. Decreasing bond strength is found from left to right, concurrent with a switching of the preferred orientation for C6H5 from the flat-lying configuration to the upright configuration. This switching is attributed to the increasing of d-electrons; that is, early transition metals, lacking d-electrons, favor the carbon-metal pi-bond and therefore the flat-lying configuration, while late transition metals rich in d-electrons prefer the carbon-metal sigma-bond and thus the upright fashion. C6H5 is also found to undergo beta-dehydrogenation on early transition metals. This work invites further theoretical and experimental research on the aryl-solid interface.

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PubMed2006

Size-expanded yDNA bases: an ab initio study.

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.

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PubMed2005

Size-expanded DNA bases: an ab initio study of their structural and electronic properties.

The size-expanded DNA bases, xA, xC, xG, and xT, are benzo-homologue forms of the natural DNA bases; i.e., their structure can be seen as the fusion of a natural base and a benzene ring. Recently, a variety of DNAs, known as xDNAs, have been synthesized in which size-expanded and natural bases are paired. In this paper we use second-order Møller-Plesset perturbation theory and density functional theory to investigate the structural and electronic properties of xA, xC, xG, and xT and their natural counterparts. We find that whereas natural and size-expanded bases have both nonplanar amino groups the latter have also nonplanar aromatic rings. When density functional theory is used to investigate the electronic properties of size-expanded and natural bases, it is found that the HOMO-LUMO gap of the size-expanded bases is smaller than that of the natural bases. Also, xG should be easier to oxidize than G.

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PubMed2005

Electronic structure and properties of isoreticular metal-organic frameworks: the case of M-IRMOF1 (M = Zn, Cd, Be, Mg, and Ca).

We investigate the possibility of tailoring the electronic properties of isoreticular metal-organic materials by replacing the metal atom in the metal-organic cluster and by doping. The electronic structure of M-IRMOF1, where IRMOF1 stands for isoreticular metal-organic framework 1 and M = Be, Mg, Ca, Zn, and Cd, was examined using density-functional theory. The results show that these materials have similar band gaps (ca. 3.5 eV) and a conduction band that is split into two bands, the lower of which has a width that varies with metal substitution. This variation prompted us to investigate whether doping with Al or Li could be used to tailor the electronic properties of the Zn-IRMOF1 and Be-IRMOF1 materials. It is shown that replacing one metal atom with Al can effectively be used to create IRMOFs with different metallic properties. On the other hand, adding Li produces structural changes that render this approach less suitable.

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PubMed2005

Amphoteric doping of carbon nanotubes by encapsulation of organic molecules: electronic properties and quantum conductance.

In order to investigate and optimize the electronic transport processes 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 quantum conductance. Our approach is based on an original scheme where quantum chemistry calculations on finite systems are recast to infinite, non-periodic (i.e., open) systems, therefore mimicking actual working devices. Results from these calculations clearly suggest that the electronic structure of a carbon nanotube can be easily manipulated by encapsulating appropriate organic molecules. Charge transfer processes induced by encapsulated organic molecules lead to efficient n- and p-type doping of the carbon nanotube. Even though a molecule can induce p and n doping, it is shown to have a minor effect on the transport properties of the nanotube as compared to a pristine tube. This type of doping therefore preserves the intrinsic properties of the pristine tube as a ballistic conductor. In addition, the efficient process of charge transfer between the organic molecules and the nanotube is shown to substantially reduce the susceptibility of the pi electrons of the nanotube to modification by oxygen while maintaining stable doping (i.e., no dedoping) at room temperature.

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PubMed2005

Computational study of the structure, dynamics, and photophysical properties of conjugated polymers and oligomers under nanoscale confinement.

Computational simulations were used to investigate the dynamics and resulting structures of several para-phenylenevinylene (PPV) based polymers and oligomers (PPV, 2-methoxy-5-(2'-ethyl-hexyloxy)-p-phenylenevinylene --> MEH-PPV and 2,5,2',5'-tetrahexyloxy-7,8'-dicyano-p-phenylenevinylene --> CN-PPV). The results show how the morphology and structure are controlled to a large extent by the nature of the solute-solvent interactions in the initial solution-phase preparation. Secondary structural organization is induced by using the solution-phase structures to generate solvent-free single molecule nanoparticles. Isolation of these single molecule nanostructures from microdroplets of dilute solution results in the formation of electrostatically oriented nanostructures at a glass surface. Our structural modeling suggests that these oriented nanostructures consist of folded PPV conjugated segments with folds occurring at tetrahedral defects (sp3 C-C bonds) within the polymer chain. This picture is supported by detailed experimental fluorescence and scanning probe microscopy studies. We also present results from a fully quantum theoretical treatment of these systems which support the general conclusion of structure-mediated photophysical properties.

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PubMed2004

Photon antibunching from oriented semiconducting polymer nanostructures.

Fluorescence intensity correlation measurements reveal that z-oriented nanostructures from single chains of a cyano-substituted polyphenylene vinylene (CN-PPV) polymer act as single-quantum emitters. Photon antibunching is observed for the first time on individual polymer nanostructures with a modulation depth exceeding 90%, providing definitive proof that radiative recombination of molecular excitons occurs at a single localized site within the folded polymer chain.

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