Structural development and energy dissipation in simulated silicon apices

• Samuel Paul Jarvis,
• Lev Kantorovich and
• Philip Moriarty

Beilstein J. Nanotechnol. 2013, 4, 941–948, doi:10.3762/bjnano.4.106

• stability of silicon tip apices by using density functional theory (DFT) calculations. We find that some tip structures - modelled as small, simple clusters - show variations in stability during manipulation dependent on their orientation with respect to the sample surface. Moreover, we observe that

• , more recently, submolecular investigations of planar molecules [11][12], have been revealed. In covalent systems in particular, density functional theory (DFT) calculations have been extremely successful in explaining the fundamental interactions that underpin NC-AFM experiments [2][3][13][14][15][16

• single rotational degree of freedom, the difference in tip–surface interactions can be as significant as for a completely different tip structure. Simulation details Our investigation is performed with ab initio density functional theory (DFT) simulations carried out by using the SIESTA code [41], which

Adsorption of the ionic liquid [BMP][TFSA] on Au(111) and Ag(111): substrate effects on the structure formation investigated by STM

• Benedikt Uhl,
• Florian Buchner,
• Dorothea Alwast,
• Nadja Wagner and
• R. Jürgen Behm

Beilstein J. Nanotechnol. 2013, 4, 903–918, doi:10.3762/bjnano.4.102

• comparable adsorption behavior. This is supported also by the results of density functional theory (DFT) calculations discussed below. These results can be compared with findings reported for other IL adsorption systems. For 1,3-dimethylimidazolium-[TFSA] ([MMIM][TFSA]) and 1-octyl-3-methylimidazolium-[TFSA

• ) [30][31], utilizing a combination of infrared reflection absorption spectroscopy (IRAS) and density functional theory (DFT) calculations. [OMIM][TFSA], which differs from [MMIM][TFSA] only by its longer alkyl chain, showed a coverage dependent adsorption geometry on Au(111): at coverages below 0.6 ML

• it was not possible to unambiguously identify the adsorbed IL species, specifically the adsorbed cations and anions in these images. This is possible by combination with dispersion corrected density functional theory (DFT-D) calculations, performed recently for adsorption of individual [BMP][TFSA

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

• Pavel V. Komarov,
• Pavel G. Khalatur and
• Alexei R. Khokhlov

Beilstein J. Nanotechnol. 2013, 4, 567–587, doi:10.3762/bjnano.4.65

• -conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to

• " recently developed by Kühne et al. [86]. This hybrid quantum mechanical simulation scheme combines Born–Oppenheimer quantum molecular dynamics (BOMD) [84] and Car–Parrinello molecular dynamics (CPMD) [87] within Kohn–Sham electron density functional theory (DFT) [88]. As in the original CPMD, the

Magnetic anisotropy of graphene quantum dots decorated with a ruthenium adatom

• Igor Beljakov,
• Velimir Meded,
• Franz Symalla,
• Karin Fink,
• Sam Shallcross and
• Wolfgang Wenzel

Beilstein J. Nanotechnol. 2013, 4, 441–445, doi:10.3762/bjnano.4.51

• stability of the Ru adatom on the hollow site, surrounded by less preferable positions over the C–C bridge and atop a C-atom, was reported for infinite graphene [15]. The graphene flake is considered fixed, as it would be on a substrate. Within our work we used density functional theory (DFT) [19] with the

Antiferromagnetic coupling of TbPc₂ molecules to ultrathin Ni and Co films

• David Klar,
• Svetlana Klyatskaya,
• Andrea Candini,
• Bernhard Krumme,
• Kurt Kummer,
• Philippe Ohresser,
• Valdis Corradini,
• Valentina de Renzi,
• Roberto Biagi,
• Loic Joly,
• Jean-Paul Kappler,
• Umberto del Pennino,
• Marco Affronte,
• Heiko Wende and
• Mario Ruben

Beilstein J. Nanotechnol. 2013, 4, 320–324, doi:10.3762/bjnano.4.36

• XMCD study together with comparison to ab initio calculations, e.g., by utilizing density functional theory (DFT). Magnetic coupling on a Co substrate The important difference between the Co and the Ni substrate is the orientation of the magnetic easy axis that is parallel to the surface for the 10 ML

Electronic and transport properties of kinked graphene

• Jesper Toft Rasmussen,
• Tue Gunst,
• Peter Bøggild,
• Antti-Pekka Jauho and
• Mads Brandbyge

Beilstein J. Nanotechnol. 2013, 4, 103–110, doi:10.3762/bjnano.4.12

• bending, of a graphene sheet is known to increase the chemical reactivity presenting an opportunity for templated chemical functionalisation. Using first-principles calculations based on density functional theory (DFT), we investigate the reaction barrier reduction for the adsorption of atomic hydrogen at

• are based on density functional theory (DFT) using the SIESTA [27] code, and the PBE-GGA exchange-correlation [28] functional. We employ periodic boundary conditions (PBC) in the direction along the bend with a cell-width of four carbon dimers, and 10 Monkhorst–Pack k-points. We use a mesh cut-off of

Nanostructure-directed chemical sensing: The IHSAB principle and the dynamics of acid/base-interface interaction

• James L. Gole and
• William Laminack

Beilstein J. Nanotechnol. 2013, 4, 20–31, doi:10.3762/bjnano.4.3

• ionic (hard acid/base) or covalent (soft acid/base) interactions. As an extrapolation of the HSAB concept developed by Pearson [14][15] and later correlated within the context of density functional theory (DFT) by Pearson [15][16][17][18], Parr, and others [19][20][21], the IHSAB model is somewhat

Structural and electronic properties of oligo- and polythiophenes modified by substituents

• Simon P. Rittmeyer and
• Axel Groß

Beilstein J. Nanotechnol. 2012, 3, 909–919, doi:10.3762/bjnano.3.101

• oligothiophenes of varying size have been considered based on density functional theory (DFT), and the properties of polythiophenes have been derived by using scaling relations [21]. Here, we focus on the modification of the electronic properties of oligo- and polythiophenes by substituents based on periodic DFT

Spontaneous dissociation of Co₂(CO)₈ and autocatalytic growth of Co on SiO₂: A combined experimental and theoretical investigation

• Kaliappan Muthukumar,
• Harald O. Jeschke,
• Roser Valentí,
• Evgeniya Begun,
• Johannes Schwenk,
• Fabrizio Porrati and
• Michael Huth

Beilstein J. Nanotechnol. 2012, 3, 546–555, doi:10.3762/bjnano.3.63

• irradiation of selected areas). To our knowledge, no systematic theoretical studies with in-depth DFT calculations on Co2(CO)8 adsorbed on different SiO2 surfaces are available. Therefore, we extent the study using density functional theory (DFT) calculations on slabs representing the various SiO2 surface

• flushed with dry nitrogen and evacuated again for image acquisition. Computational details We performed spin-polarized density functional theory (DFT) calculations within the generalized gradient approximation in the parametrization of Perdew, Burke and Ernzerhof (PBE) [35][36]. Corrections for long-range

Distribution of functional groups in periodic mesoporous organosilica materials studied by small-angle neutron scattering with in situ adsorption of nitrogen

• Monir Sharifi,
• Dirk Wallacher and
• Michael Wark

Beilstein J. Nanotechnol. 2012, 3, 428–437, doi:10.3762/bjnano.3.49

• 24 h. The Brunauer–Emmett–Teller (BET) method was used to determine the specific surface area. The pore volumes and pore diameters were calculated according to density functional theory (DFT) [34]. In order to determine the density of pure and SO3H-functionalized benzene-PMO materials the Archimedean

Models of the interaction of metal tips with insulating surfaces

• Thomas Trevethan,
• Matthew Watkins and
• Alexander L. Shluger

Beilstein J. Nanotechnol. 2012, 3, 329–335, doi:10.3762/bjnano.3.37

• contaminated by the surface [7]. Plane-wave density-functional-theory (DFT) calculations employing a periodic metallic-tip model demonstrated that the Cr tip apex interacts most strongly with anions (Cl−) in the surface, and that these ions correspond to protrusions in the image. Thus these experiments and the

Transmission eigenvalue distributions in highly conductive molecular junctions

• Justin P. Bergfield,
• Joshua D. Barr and
• Charles A. Stafford

Beilstein J. Nanotechnol. 2012, 3, 40–51, doi:10.3762/bjnano.3.5

• either single-particle or many-body methods, and which depends critically on accurate descriptions of the molecular energy levels and the lead–molecule coupling. In effective single-particle theories, including current implementations of density functional theory (DFT), it is often necessary [7][8][9][10

• based, e.g., on density-functional theory (DFT). However, this is not the case. Although the isolated-resonance approximation can also be derived within DFT, in practice, it is necessary to use an “extended molecule” to account for charge transfer between molecule and electrodes. Analyzing transport in

Direct monitoring of opto-mechanical switching of self-assembled monolayer films containing the azobenzene group

• Einat Tirosh,
• Enrico Benassi,
• Silvio Pipolo,
• Marcel Mayor,
• Michal Valášek,
• Veronica Frydman,
• Stefano Corni and
• Sidney R. Cohen

Beilstein J. Nanotechnol. 2011, 2, 834–844, doi:10.3762/bjnano.2.93

• : These vibrational frequencies, reduced masses and normal modes were obtained by ab initio QM calculations. A full geometry optimization of the electronic ground state of 1-DA, 2-DA, and 3-DA, both trans- and cis-isomers, was obtained in the vacuum phase at the level of density functional theory (DFT) by

Current-induced dynamics in carbon atomic contacts

• Jing-Tao Lü,
• Tue Gunst,
• Per Hedegård and
• Mads Brandbyge

Beilstein J. Nanotechnol. 2011, 2, 814–823, doi:10.3762/bjnano.2.90

• intensive Raman signals in unpassivated chains between graphene-like pieces [41]. The calculation was performed by using the SIESTA density-functional theory (DFT) method [42], which has been extended to study elastic [33] and inelastic [34] transport in molecular conductors. We used similar parameters as

Towards quantitative accuracy in first-principles transport calculations: The GW method applied to alkane/gold junctions

• Mikkel Strange and
• Kristian S. Thygesen

Beilstein J. Nanotechnol. 2011, 2, 746–754, doi:10.3762/bjnano.2.82

• length dependence: Gn = Gc exp(−βn). The main difference from standard density functional theory (DFT) calculations is a significant reduction of the contact conductance, Gc, due to an improved alignment of the molecular energy levels with the metal Fermi energy. The molecular orbitals involved in the

• junction geometry, a quantitatively accurate description of electron transport from first principles remains a formidable task. Numerous studies based on density functional theory (DFT) have shown a significant overestimation of conductance relative to experimental values [3][4][5][6][7][8][9][10][11][12

Distinction of nucleobases – a tip-enhanced Raman approach

• Regina Treffer,
• Xiumei Lin,
• Elena Bailo,
• Tanja Deckert-Gaudig and
• Volker Deckert

Beilstein J. Nanotechnol. 2011, 2, 628–637, doi:10.3762/bjnano.2.66

• atoms: The pyrimidine N1 and N3, the imidazole N7 and the N10 of the exocyclic NH2 group. N9 is the binding site to the ribose and therefore cannot bind to the metal nanoparticle. Density functional theory (DFT) calculations show changes in Raman band intensities and positions for the four respective

Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces

• David M. Benoit,
• Bruno Madebene,
• Inga Ulusoy,
• Luis Mancera,
• Yohann Scribano and
• Sergey Chulkov

Beilstein J. Nanotechnol. 2011, 2, 427–447, doi:10.3762/bjnano.2.48

• calculated from a PES constructed with periodic density functional theory (DFT), and an assessment of DFT for the description of properties of small neutral gold clusters is given. We conclude this paper with an outlook on future work in the field of theoretical descriptions of vibrational spectra of

• structures methods or performance of the implemented algorithms. This capability is a necessity for the investigation of large systems as the many packages that implement efficient density functional theory (DFT) are still in development and change on a regular basis. Scalability of the vibrational approach

Charge transfer through single molecule contacts: How reliable are rate descriptions?

• Denis Kast,
• L. Kecke and
• J. Ankerhold

Beilstein J. Nanotechnol. 2011, 2, 416–426, doi:10.3762/bjnano.2.47

• experimental data. For this purpose, basically two strategies have been followed. One is based on ab initio schemes that have been successfully employed for isolated molecular structures, such as, e.g., density functional theory (DFT). Combining DFT with nonequilibrium Green’s functions (NEGF) allows us to

Simulation of bonding effects in HRTEM images of light element materials

• Simon Kurasch,
• Jannik C. Meyer,
• Daniela Künzel,
• Axel Groß and
• Ute Kaiser

Beilstein J. Nanotechnol. 2011, 2, 394–404, doi:10.3762/bjnano.2.45

• Theoretical Chemistry, University of Ulm, 89069 Ulm, Germany 10.3762/bjnano.2.45 Abstract The accuracy of multislice high-resolution transmission electron microscopy (HRTEM) simulation can be improved by calculating the scattering potential using density functional theory (DFT) [1][2]. This approach accounts

Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction

• Jan Kučera and
• Axel Groß

Beilstein J. Nanotechnol. 2011, 2, 384–393, doi:10.3762/bjnano.2.44

• molecules, periodic density functional theory (DFT) calculations of the bare Au/ATP/Pd junction, assuming a () structure of the ATP molecules, were able to reproduce the experimentally observed downshift of the Pd DOS reasonably well [2][12] under the assumption that the amino groups of the ATP molecules

Synthesis of LiNbO₃ nanoparticles in a mesoporous matrix

• Anett Grigas and
• Stefan Kaskel

Beilstein J. Nanotechnol. 2011, 2, 28–33, doi:10.3762/bjnano.2.3

• specific surface area was calculated from the BET (Brunauer–Emmet–Teller) equation (p/p0 = 0.05–0.20). The pore volume was determined at relative pressure of p/p0 = 0.95. The pore size distribution was estimated from the desorption branch of the isotherm using Density Functional Theory (DFT). Chemical

On the reticular construction concept of covalent organic frameworks

• Binit Lukose,
• Agnieszka Kuc,
• Johannes Frenzel and
• Thomas Heine

Beilstein J. Nanotechnol. 2010, 1, 60–70, doi:10.3762/bjnano.1.8

• total energy in the Density-Functional Theory (DFT) with respect to charge density fluctuations. This can be considered as a non-orthogonal tight-binding method parameterized from DFT, which does not require large amounts of empirical parameters, however, maintains all the qualities of DFT. The main

• -DFT calculations, they are typically in the correct range within the DFTB method. For validation of our method, we have calculated some of the structures using Density Functional Theory (DFT) as implemented in ADF code [25][26]. Periodic boundary conditions were used to represent frameworks of the

• concept of reticular chemistry is investigated to explore the applicability of the formation of Covalent Organic Frameworks (COFs) from their defined individual building blocks. Thus, we have designed, optimized and investigated a set of reported and hypothetical 2D COFs using Density Functional Theory