Browsing by Author "Yildirim, T."

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Open Access
Adsorption and dissociation of hydrogen molecules on bare and functionalized carbon nanotubes
(American Physical Society, 2005) Dag, S.; Ozturk, Y.; Çıracı, Salim; Yildirim, T.
Interaction between hydrogen molecules and bare as well as functionalized single-wall carbon nanotubes (SWNT) is investigated using first-principles plane wave method. It is found that the binding energy of the H2 physisorbed on the outer surface of the bare SWNT is very weak, and cannot be enhanced significantly either by increasing the curvature of the surface through radial deformation, or by the coadsorption of a Li atom that makes the semiconducting tube metallic. Although the bonding is strengthened upon adsorption directly to the Li atom, its nature continues to be physisorption. However, the character of the bonding changes dramatically when SWNT is functionalized by the adsorption of a Pt atom. A single H2 is chemisorbed to the Pt atom on the SWNT either dissociatively or molecularly. The dissociative adsorption is favorable energetically and is followed by the weakening of the Pt-SWNT bond. Out of two adsorbed H2, the first one can be adsorbed dissociatively and the second one is chemisorbed molecularly. The nature of bonding is a very weak physisorption for the third adsorbed H2. Palladium also promotes the chemisorption of H2 with relatively smaller binding energy. Present results reveal the important effect of transition metal atom adsorbed on SWNT and these results advance our understanding of the molecular and dissociative adsorption of hydrogen for efficient hydrogen storage.
Open Access
Effects of hydrogen adsorption on single-wall carbon nanotubes: metallic hydrogen decoration
(American Physical Society, 2002) Gülseren, O.; Yildirim, T.; Çıracı, Salim
We show that the electronic and atomic structure of carbon nanotubes undergo dramatic changes with hydrogen chemisorption from first principle calculations. Upon uniform exohydrogenation at half coverage, the cross sections of zigzag nanotubes become literally square or rectangular, and they are metallic with very high density of states at the Fermi level, while other isomers can be insulating. For both zigzag and armchair nanotubes, hydrogenation of each carbon atom from inside and outside alternatively yield the most stable isomer with a very weak curvature dependence and a large band gap.
Open Access
Electronic structure of the contact between carbon nanotube and metal electrodes
(American Institute of Physics, 2003) Dag, S.; Gülseren, O.; Çıracı, Salim; Yildirim, T.
Our first-principles study of the contact between a semiconducting single-walled carbon nanotube ~s-SWNT! and metal electrodes shows that the electronic structure and potential depend strongly on the type of metal. The s-SWNT is weakly side-bonded to the gold surface with minute charge rearrangement and remains semiconducting. A finite potential barrier forms at the contact region. In contrast, the molybdenum surface forms strong bonds, resulting in significant charge transfer and metallicity at the contact. The radial deformation of the tube lowers the potential barrier at the contact and increases the state density at the Fermi level.
Open Access
Exohydrogenated single-wall carbon nanotubes
(American Physical Society, 2001) Yildirim, T.; Gülseren, O.; Çıracı, Salim
An extensive first-principles study of fully exohydrogenated zigzag (n,0) and armchair (n,n) single-wall carbon nanotubes (CnHn), polyhedral molecules including cubane, dodecahedrane, and C60H60 points to crucial differences in the electronic and atomic structures relevant to hydrogen storage and device applications. CnHn’s are estimated to be stable up to the radius of a ~8,8! nanotube, with binding energies proportional to 1/R. Attaching a single hydrogen to any nanotube is always exothermic. Hydrogenation of zigzag nanotubes is found to be more likely than armchair nanotubes with similar radius. Our findings may have important implications for selective functionalization and finding a way of separating similar radius nanotubes from each other.
Open Access
First-principles investigation of structural and electronic properties of solid cubane and its doped derivatives
(American Physical Society, 2000) Yildirim, T.; Çıracı, Salim; Kılıç, Ç.; Buldum, A.
The electronic and structural properties of molecular and solid cubane have been studied by first-principles, self-consistent field total energy calculations. Calculated molecular properties such as equilibrium geometry and electronic and vibrational spectra are found to be in good agreement with experimental data. Structural parameters and the energetics of both the low-temperature, orientationally ordered and high-temperature, orientationally disordered or plastic phases of solid cubane are determined. The valence band of solid cubane is derived from the molecular states; the energy gap between the lowest unoccupied and highest occupied molecular orbital bands is rather large due to the saturated carbon atoms. The effect of alkali-metal-atom doping on the electronic energy bands is investigated. It is found that the metallic band of doped cubane is derived from the undoped solid cubane’s lowest conduction band with a significant contribution from the alkali-metal atom.
Open Access
A First-principles Study of the Structure and Dynamics of C8H8, Si8H8, and Ge8H8 Molecules
(American Chemical Society, 2000) Kiliç, Ç.; Yildirim, T.; Mehrez, H.; Çıracı, Salim
We present a first-principles study to elucidate the nature of the bonding, stability, energetics, and dynamics of individual X8H8 molecules (X = C, Si, Ge). The results obtained from both "local basis" and "pseudopotential" ab initio methods are in good agreement with the experimental data that exists for cubane (C8H8). The trends among these molecules are reminiscent of those prevailing in the bulk solids of C, Si, and Ge. High-temperature dynamics and fragmentation of X8H8 were studied by the quantum molecular dynamics method which shows that at high temperatures cubane is transformed to the 8-fold ring structure of cyclooctotetraene.
Open Access
Formation of quantum structures on a single nanotube by modulating hydrogen adsorption
(American Physical Society, 2003) Gülseren, O.; Yildirim, T.; Çıracı, Salim
Using first-principles density functional calculations we showed that quantum structures can be generated on a single carbon nanotube by modulating the adsorption of hydrogen atoms. The band gap of the hydrogen-free zone of the tube widens in the adjacent hydrogen covered zone. The sudden variation of the band gap leads to band offsets at the conduction- and valence-band edges. At the end, the band gap of the whole system is modulated along the axis of the tube, which generates quantum wells or quantum dots. Specific electronic states are confined in these quantum wells. The type and radius of the nanotube and the extent and sequence of hydrogen-free and hydrogen-covered zones can provide several options to design a desired optoelectronic nanodevice.
Open Access
Functionalization of carbon-based nanostructures with light transition-metal atoms for hydrogen storage
(American Physical Society, 2008) Durgun, Engin; Çıracı, Salim; Yildirim, T.
In a recent letter, the unusual hydrogen storage capacity of Ti decorated carbon nanotubes has been revealed. The present paper extends this study further to investigate the hydrogen uptake by light transition-metal atoms decorating various carbon-based nanostructures in different types of geometry and dimensionality, such as carbon linear chain, graphene, and nanotubes. Using first-principles plane-wave method we show that not only outer but also inner surface of a large carbon nanotube can be utilized to bind more transition-metal atoms and hence to increase the storage capacity. We also found that scandium and vanadium atoms adsorbed on a carbon nanotube can bind up to five hydrogen molecules. Similarly, light transition-metal atoms can be adsorbed on both sides of graphene and each adsorbate can hold up to four hydrogen molecules yielding again a high-storage capacity. Interestingly, our results suggest that graphene can be considered as a potential high-capacity H2 storage medium. We also performed transition state analysis on the possible dimerization of Ti atoms adsorbed on the graphene and single-wall carbon nanotube.
Open Access
Half-metallic properties of atomic chains of carbon-transition-metal compounds
(American Physical Society, 2005) Dag, S.; Tongay, S.; Yildirim, T.; Durgun, Engin; Senger, R. T.; Fong, C. Y.; Çıracı, Salim
We found that magnetic ground state of one-dimensional atomic chains of carbon-transition-metal compounds exhibit half-metallic properties. They are semiconductors for one spin direction, but show metallic properties for the opposite direction. The spins are fully polarized at the Fermi level and net magnetic moment per unit cell is an integer multiple of Bohr magneton. The spin-dependent electronic structure can be engineered by changing the number of carbon atoms and type of transition metal atoms. These chains, which are stable even at high temperatures and some of which keep their spin-dependent electronic properties even under moderate axial strain, hold the promise of potential applications in nanospintronics.
Open Access
Hydrogen absorption properties of metal-ethylene complexes
(American Physical Society, 2007) Zhou. W.; Yildirim, T.; Durgun, Engin; Çıracı, Salim
Recently, we have predicted that a single ethylene molecule can form stable complexes with light transition metals (TMs) such as Ti and the resulting TMn -ethylene complex can absorb up to ∼12 and 14 wt % hydrogen for n=1 and 2, respectively. Here we extend this study to include a large number of other metals and different isomeric structures. We obtained interesting results for light metals such as Li. The ethylene molecule is able to complex with two Li atoms with a binding energy of 0.7 eV Li which then binds up to two H2 molecules per Li with a binding energy of 0.24 eV H2 and absorption capacity of 16 wt %, a record high value reported so far. The stability of the proposed metal-ethylene complexes was tested by extensive calculations such as normal-mode analysis, finite temperature first-principles molecular-dynamics (MD) simulations, and reaction path calculations. The phonon and MD simulations indicate that the proposed structures are stable up to 500 K. The reaction path calculations indicate about 1 eV activation barrier for the TM2 -ethylene complex to transform into a possible lower energy configuration where the ethylene molecule is dissociated. Importantly, no matter which isometric configuration the TM2 -ethylene complex possesses, the TM atoms are able to bind multiple hydrogen molecules with suitable binding energy for room-temperature storage. These results suggest that co-deposition of ethylene with a suitable precursor of TM or Li into nanopores of light-weight host materials may be a very promising route to discovering new materials with high-capacity hydrogen absorption properties.
Open Access
Hydrogen storage capacity of titanium met-cars
(IOP Publishing Ltd., 2006) Akman, N.; Durgun, Engin; Yildirim, T.; Çıracı, Salim
The adsorption of hydrogen molecules on the titanium metallocarbohedryne (met-car) cluster has been investigated by using the first-principles plane wave method. We have found that, while a single Ti atom at the corner can bind up to three hydrogen molecules, a single Ti atom on the surface of the cluster can bind only one hydrogen molecule. Accordingly, a Ti8C12 met-car can bind up to 16H2 molecules and hence can be considered as a high-capacity hydrogen storage medium. Strong interaction between two met-car clusters leading to the dimer formation can affect H2 storage capacity slightly. Increasing the storage capacity by directly inserting H 2 into the met-car or by functionalizing it with an Na atom have been explored. It is found that the insertion of neither an H2 molecule nor an Na atom could further promote the H2 storage capacity of a Ti8C12 cluster. We have also tested the stability of the H2-adsorbed Ti8C12 met-car with ab initio molecular dynamics calculations which have been carried out at room temperature.
Open Access
Metal nanoring and tube formation on carbon nanotubes
(American Physical Society, 2002) Bagci, V. M. K.; Gülseren, O.; Yildirim, T.; Gedik, Z.; Ciracil, S.
The structural and electronic properties of aluminum-covered single-wall carbon nanotubes (SWNT's) are studied from first principles for a large number of coverages. Aluminum-aluminum interaction, that is stronger than aluminum-tube interaction, prevents uniform metal coverage, and hence gives rise to the clustering. However, a stable aluminum ring and aluminum nanotube with well defined patterns can also form around the semiconducting SWNT's and lead to metallization. The persistent current in the Al nanoring is discussed to show that a high magnetic field can be induced at the center of SWNT.
Open Access
Molecular and dissociative adsorption of multiple hydrogen molecules on transition metal decorated C60
(American Physical Society, 2005) Yildirim, T.; Íñiguez, J.; Çıracı, Salim
Recently we have predicted [Phys. Rev. Lett. 94, 175501 (2005)] that Ti-decorated carbon nanotubes can adsorb up to 8 wt.% hydrogen at ambient conditions. Here we show that a similar phenomenon occurs in light transition-metal decorated C60. While Sc and Ti prefer the hexagon (H) sites with a binding energy of 2.1eV, V and Cr prefer double-bond (D) sites with binding energies of 1.3 and 0.8eV, respectively. Heavier metals such as Mn, Fe, and Co do not bond on C60. Once the metals are adsorbed on C60, each can bind up to four hydrogen molecules with an average binding energy of 0.3-0.5eV H2. At high metal coverage, we show that a C60 can accommodate six D-site and eight H-site metals, which can adsorb up to 56 H2 molecules, corresponding to 7.5wt.%.
Open Access
Oxygenation of carbon nanotubes: Atomic structure, energetics, and electronic structure
(American Physical Society, 2003) Dag, S.; Gülseren, O.; Yildirim, T.; Çıracı, Salim
This paper presents an extensive and systematic analysis of the oxygenation of semiconducting and metallic single-wall carbon nanotubes by using the first principles pseudopotential plane wave method. Our study involves the physisorption of oxygen molecules, chemisorption of oxygen atoms and formation of an oxide, and deals with the equilibrium binding geometry and corresponding electronic energy structure. The binding energies of an oxygen molecule physisorbed at different sites are determined by calculating short and long range interactions. The triplet state of the physisorbed oxygen molecule is energetically favorable, whereas the nonmagnetic (spin paired) state yields a relatively stronger binding energy. An oxygen atom is adsorbed on top of the carbon-carbon bond. The zigzag bonds of the nanotubes are weakened and eventually are replaced by a carbon-oxygen-carbon bridge bond. Chemisorption of atomic oxygen and physisorption of an oxygen molecule modify the electronic energy structure of the bare tube in different ways. For a different coverage and pattern, self-consistent field electronic energy structure calculations using the optimized physisorption geometry corresponding to the triplet ground state result in a small energy gap between unoccupied oxygen levels and the top of the valence band of the semiconducting carbon nanotube. These results invalidate the hole doping of the semiconducting carbon nanotube upon the physisorption of oxygen.
Open Access
Pentagonal nanowires: a first-principles study of the atomic and electronic structure
(American Physical Society, 2002) Sen, P.; Gülseren, O.; Yildirim, T.; Batra, I. P.; Çıracı, Salim
We performed an extensive first-principles study of nanowires in various pentagonal structures by using pseudopotential plane wave method within the density functional theory. Our results show that nanowires of different types of elements, such as alkali, simple, transition, and noble metals and inert gas atoms, have a stable structure made from staggered pentagons with a linear chain perpendicular to the planes of the pentagons and passing through their centers. This structure exhibits bond angles close to those in the icosahedral structure. However, silicon is found to be energetically more favorable in the eclipsed pentagonal structure. These quasi-one-dimensional pentagonal nanowires have higher cohesive energies than many other one-dimensional structures and hence may be realized experimentally. The effects of magnetic state are examined by spin-polarized calculations. The origin of the stability is discussed by examining optimized structural parameters, charge density and electronic band structure, and by using analysis based on the empirical Lennard-Jones-type interaction. Electronic band structure of pentagonal wires of different elements are discussed and their effects on quantum ballistic conductance are mentioned. It is found that the pentagonal wire of silicon exhibits metallic band structure.
Open Access
Pressure-induced interlinking of carbon nanotubes
(American Physical Society, 2000) Yildirim, T.; Gülseren, O.; Kiliç, Ç.; Çıracı, Salim
We predict new forms of carbon consisting of one- and two-dimensional networks of interlinked single-wall carbon nanotubes, some of which are energetically more stable than van der Waals packing of the nanotubes on a hexagonal lattice. These interlinked nanotubes are further transformed with higher applied external pressures to more dense and complicated stable structures, in which curvature-induced carbon sp3 rehybridizations are formed. We also discuss the energetics of the bond formation between nanotubes and the electronic properties of these predicted novel structures.
Open Access
A recombinant PvpA protein-based diagnostic prototype for rapid screening of chicken mycoplasma gallisepticum infections
(Elsevier, 2008) Büyüktanir, O.; Yildirim, T.; Yakicier, C.; Genç, O.; Yurdusev, N.
Mycoplasma gallisepticum is the primary agent of chronic respiratory disease causing important economic losses in the poultry industry. Serological monitoring is essential to maintain mycoplasma-free breeder flocks and often complicated by the cross-reactions between different mycoplasma species. To overcome serological cross-reactions, a large fragment of the M. gallisepticum PvpA cytadhesin, species-specific surface-exposed protein, was produced in E. coli as a recombinant protein (rPvpA336) and used as a potential diagnostic antigen. The rPvpA336 protein possesses 336 mycoplasma-specific amino acids with relative molecular weight of 44 kDa. A deletion region of 37 amino acids was identified when compared to the wild-type PvpA protein. Immunoreactivity of the rPvpA336 protein has been demonstrated by Western blot analysis with M. gallisepticum-positive and -negative chicken sera. Furthermore, an enzymatic rapid immunofiltration assay (ERIFA) prototype based on the rPvpA336 protein has been developed and its species-specific detection capability has been demonstrated by using M. gallisepticum and/or M. synoviae-positive and -negative chicken sera. In addition to its species-specificity, the ERIFA prototype presents certain advantages such as rapidity, field-applicability and cost-effectiveness. Therefore, these advantages would make the prototype a species-specific rapid diagnostic tool of choice in the field and limited laboratory conditions for screening M. gallisepticum infections. © 2007 Elsevier B.V. All rights reserved.
Open Access
Reversible band-gap engineering in carbon nanotubes by radial deformation
(American Physical Society, 2002-03) Gülseren, O.; Yildirim, T.; Çıracı, Salim; Kılıç, Ç.
We present a systematic analysis of the effect of radial deformation on the atomic and electronic structure of zigzag and armchair single wall carbon nanotubes using the first-principle plane wave method. The nanotubes were deformed by applying a radial strain, which distorts the circular cross section to an elliptical one. The atomic structure of the nanotubes under this strain are fully optimized, and the electronic structure is calculated self-consistently to determine the response of individual bands to the radial deformation. The band gap of the insulating tube is closed and eventually an insulator-metal transition sets in by the radial strain which is in the elastic range. Using this property a multiple quantum well structure with tunable and reversible electronic structure is formed on an individual nanotube and its band lineup is determined from first principles. The elastic energy due to the radial deformation and elastic constants are calculated and compared with classical theories.
Open Access
Storytelling in the stories of Efrâsiyâb
(2005) Yildirim, T.
It is possible to find the traces of traditional storytelling in modern novels. In this study, the narrator's discourse in Ihsan Oktay Anar's Efrâsiyâb'in Hikâyeleri (The Stories of Afrasiab) is compared to the narrators that are found in folk stories. The storytelling in Anar's novel is examined within the development of the traditional story that sets the frame of the work.
Open Access
Systematic ab initio study of curvature effects in carbon nanotubes
(American Physical Society, 2002) Gülseren, O.; Yildirim, T.; Çıracı, Salim
We investigate curvature effects on geometric parameters, energetics, and electronic structure of zigzag nanotubes with fully optimized geometries from first-principle calculations. The calculated curvature energies, which are inversely proportional to the square of radius, are in good agreement with the classical elasticity theory. The variation of the band gap with radius is found to differ from simple rules based on the zone folded graphene bands. Large discrepancies between tight binding and first-principles calculations of the band gap values of small nanotubes are discussed in detail.