Surface-site reactivity in small-molecule adsorption: A theoretical study of thiol binding on multi-coordinated gold clusters

• Elvis C. M. Ting,
• Tatiana Popa and
• Irina Paci

Beilstein J. Nanotechnol. 2016, 7, 53–61, doi:10.3762/bjnano.7.6

• initial (user input) configuration. This limitation can be particularly problematic in cases where there is an overwhelming contributor to the potential energy surface such as in the case of molecule–surface interactions [70]. An elegant workaround is to use thermal energy as provided by an ab initio

Calculations of helium separation via uniform pores of stanene-based membranes

• Guoping Gao,
• Yan Jiao,
• Yalong Jiao,
• Fengxian Ma,
• Liangzhi Kou and
• Aijun Du

Beilstein J. Nanotechnol. 2015, 6, 2470–2476, doi:10.3762/bjnano.6.256

• . Most interestingly, the 2D Sn-based materials can be further strain-engineered to achieve improved He separation performance by taking both diffusion and selectivity into account. Computational Method Density functional theory (DFT) calculations were carried out using the Vienna ab initio simulation

Vibration-mediated Kondo transport in molecular junctions: conductance evolution during mechanical stretching

• David Rakhmilevitch and
• Oren Tal

Beilstein J. Nanotechnol. 2015, 6, 2417–2422, doi:10.3762/bjnano.6.249

• ascribed to metal–molecule bond rupture. This process can also lead to lower Kondo transport by reducing the coupling of the relevant molecular orbitals to at least one of the electrodes [12]. Former ab initio calculations found a good coupling between a certain vibration mode that shows non-monotonic

Negative differential electrical resistance of a rotational organic nanomotor

• Hatef Sadeghi,
• Sara Sangtarash,
• Qusiy Al-Galiby,
• Rachel Sparks,
• Steven Bailey and
• Colin J. Lambert

Beilstein J. Nanotechnol. 2015, 6, 2332–2337, doi:10.3762/bjnano.6.240

• pendant moiety anchored to an organic backbone between two C60 fullerenes, which in turn are connected to gold electrodes. Ab initio density functional calculations are used to demonstrate that an electric field induces rotation of the pendant group, leading to a nonlinear current–voltage relation. The

Core-level spectra and molecular deformation in adsorption: V-shaped pentacene on Al(001)

• Anu Baby,
• He Lin,
• Gian Paolo Brivio,
• Luca Floreano and
• Guido Fratesi

Beilstein J. Nanotechnol. 2015, 6, 2242–2251, doi:10.3762/bjnano.6.230

• experimental investigations, while the previous ab initio theoretical studies [13][14] on this system were missing long-range van der Waals (vdW) corrections. Simeoni and Picozzi reported a numerical investigation of pentacene on Al(001) by density functional theory (DFT) with the local density approximation

Large-voltage behavior of charge transport characteristics in nanosystems with weak electron–vibration coupling

• Tomáš Novotný and
• Wolfgang Belzig

Beilstein J. Nanotechnol. 2015, 6, 1853–1859, doi:10.3762/bjnano.6.188

• IETS signals usually proceeds via combination of ab initio structural density functional theory (DFT) calculations determining the parameters of an effective electron–vibrational Hamiltonian with the non-equilibrium Green’s functions (NEGF) evaluation of the IETS features [10]. It had turned out that

• expressions are well known in the literature [10][12][19][25] and can/have been applied to cases with multiple electronic levels, finite temperatures, and/or external damping (whose magnitude can be even assessed from ab-initio calculations [33]). In particular, all the relevant quantities for the multilevel

Simple and efficient way of speeding up transmission calculations with k-point sampling

• Jesper Toft Falkenberg and
• Mads Brandbyge

Beilstein J. Nanotechnol. 2015, 6, 1603–1608, doi:10.3762/bjnano.6.164

• electrostatic gating etc. Our interpolation scheme can easily be implemented in already existing code. We provide a sample MatLAB code (Supporting Information File 1) that can read and interpolate data obtained from TranSiesta and TBTrans [2], which are built on-top of the ab initio software package Siesta [17

Alternative types of molecule-decorated atomic chains in Au–CO–Au single-molecule junctions

• Zoltán Balogh,
• Péter Makk and
• András Halbritter

Beilstein J. Nanotechnol. 2015, 6, 1369–1376, doi:10.3762/bjnano.6.141

• to the ab initio simulations in [29][30]. The conductance of the second molecular peak (M2) coincides with the calculated conductance of a bridge-like molecular configuration (0.6–0.7G0), where the CO molecule sits between two neighboring Au chain atoms in a perpendicular direction with respect to

Can molecular projected density of states (PDOS) be systematically used in electronic conductance analysis?

• Tonatiuh Rangel,
• Gian-Marco Rignanese and
• Valerio Olevano

Beilstein J. Nanotechnol. 2015, 6, 1247–1259, doi:10.3762/bjnano.6.128

• establishment of ab initio approaches to quantum transport. The DFT-Landauer framework is one of the most popular. It has proven successful in calculating zero-bias conductances in good agreement with the experiment in some systems such as the hydrogen molecule between platinum wires [13]. In other systems

• model [18][19][20][21] or ab initio GW corrections [22][23], arising a yet-to-be solved controversy [24][25][26][27][28][29][30][31][32]. In addition to calculations and measurements, a physical interpretation of the conductance is needed. In the end, a complete picture of the mechanisms governing

• organized as follows: The first section introduces quantum transport ab initio theory, together with the definitions of all the relevant quantities and the two traditional methods to identify MOs and PDOS. In the second and third sections, we present the results for the BDA and BDT molecular junctions

Electronic interaction in composites of a conjugated polymer and carbon nanotubes: first-principles calculation and photophysical approaches

• Florian Massuyeau,
• Jany Wéry,
• Jean-Luc Duvail,
• Serge Lefrant,
• Abu Yaya,
• Chris Ewels and
• Eric Faulques

Beilstein J. Nanotechnol. 2015, 6, 1138–1144, doi:10.3762/bjnano.6.115

• mechanisms between conjugated polymers and carbon nanotubes blended at various concentrations is not yet established [14]. Poly(paraphenylene vinylene) (PPV) constitutes an excellent model system for ab initio calculations and photophysical experiments since it exhibits both highly efficient emission in the

Multiscale modeling of lithium ion batteries: thermal aspects

• Arnulf Latz and
• Jochen Zausch

Beilstein J. Nanotechnol. 2015, 6, 987–1007, doi:10.3762/bjnano.6.102

• special cases the averaged thermal behavior can be captured very well by porous electrode theory. Keywords: lithium ion batteries; multiscale modeling; heat transport; Introduction The main challenge for establishing an ab initio multiscale simulation approach for batteries or electrochemical storage

• usually concentrate on individual electronic processes without considering the interplay with the environment or competing electronic processes, which might be statistically and thus macroscopically much more significant [7]. In ab initio thermodynamics, DFT is combined with ideas from statistical

• upscaling procedure to ensure the consistency with pore-resolved theory. Where possible, we will point out the necessary input from ab initio atomistic scale theories. The microscopic as well as the cell-level theory are simulated for a virtual microstructure and its homogenized effective porous electrode

Carrier multiplication in silicon nanocrystals: ab initio results

• Ivan Marri,
• Marco Govoni and
• Stefano Ossicini

Beilstein J. Nanotechnol. 2015, 6, 343–352, doi:10.3762/bjnano.6.33

• approaches [21][24][25][26][27][28][29][30] although only recently was a full ab initio interpretation of CM proposed [31]. Recently, a relevant photocurrent enhancement arising from CM was observed in a PbSe-based, quantum dot (QD) solar cell [32], which proves the possibility of exploiting CM effects to

• “e” and “h” identify mechanisms ignited by relaxation of an electron and a hole, respectively. In Equation 1 and Equation 2, the rates are expressed as a function of the energy of the initial carrier, without considering the lattice vibration (a detailed ab initio calculation of phonon-assisted CM

• a realistic determination of high energy, excited carrier dynamics. It is thus evident that a detailed estimation of (Ei) requires an accurate description of the atomistic properties of the systems that, especially for nanostructures, can be obtained only through a parameter-free, ab initio

Multifunctional layered magnetic composites

• Maria Siglreitmeier,
• Baohu Wu,
• Tina Kollmann,
• Martin Neubauer,
• Gergely Nagy,
• Dietmar Schwahn,
• Vitaliy Pipich,
• Damien Faivre,
• Dirk Zahn,
• Andreas Fery and
• Helmut Cölfen

Beilstein J. Nanotechnol. 2015, 6, 134–148, doi:10.3762/bjnano.6.13

• (MPMS). For measurements, dried samples were introduced into gelatin capsules and magnetization loop measurements at 2 K and 293 K were performed. Simulation studies Molecular Simulation: as described in [34] a series of FeIII(OH)x(OH2)4−x and FeII(OH)y(OH2)6−y clusters were pre-modeled from ab-initio

Synthesis of boron nitride nanotubes and their applications

• Saban Kalay,
• Zehra Yilmaz,
• Ozlem Sen,
• Melis Emanet,
• Emine Kazanc and
• Mustafa Çulha

Beilstein J. Nanotechnol. 2015, 6, 84–102, doi:10.3762/bjnano.6.9

• positions in an ab initio theoretical study. The hydrogen molecules approached the SWBNNTs in perpendicular position to the surface, which slightly polarized and raised the binding energy of the molecules. On the other hand, the hydrogen atoms interacted with the nitrogen atoms more than the boron atoms [94

Influence of the supramolecular architecture on the magnetic properties of a Dy^III single-molecule magnet: an ab initio investigation

• Julie Jung,
• Olivier Cador,
• Kevin Bernot,
• Fabrice Pointillart,
• Javier Luzon and
• Boris Le Guennic

Beilstein J. Nanotechnol. 2014, 5, 2267–2274, doi:10.3762/bjnano.5.236

• transferable into single-molecule devices. Keywords: ab initio calculations; dysprosium; magnetic properties; single-molecule magnets; supramolecular effects; Introduction At the molecular level, single-molecule magnets (SMMs) can be seen as magnets in which the magnetic information relies on the magnetic

• -crystal magnetometry, low temperature luminescence, and wavefunction-based ab initio calculations, has demonstrated that subtle modification of the DyIII environment such as the rotation of the water molecule is enough to be the driving force of the easy-axis orientation in such a molecule [40

• SMM in which supramolecular effects impact the magnetic properties is investigated on the basis of single-crystal angular-resolved magnetometry and ab initio calculations. Results and Discussion We have focused our investigation on two DyIII-based complexes that were reported by some of us recently

Cathode lens spectromicroscopy: methodology and applications

• T. O. Menteş,
• G. Zamborlini,
• A. Sala and
• A. Locatelli

Beilstein J. Nanotechnol. 2014, 5, 1873–1886, doi:10.3762/bjnano.5.198

• recently demonstrated by an ab initio study that clarified the interpretation of LEEM-I(V) curves [42]. An important aspect is the integration of LEEM with low energy electron diffraction (LEED). Diffraction experiments permit a full characterization of the crystal structure and quality of graphene. For

• means of ab initio calculations, which could prove the very large corrugation of graphene in this system and establish a correlation between C 1s binding energy and C–substrate separation [44]. On the same system, μ-probe diffraction analyses were carried out in combination with dark-field imaging

Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

• Danny E. P. Vanpoucke,
• Jan W. Jaeken,
• Stijn De Baerdemacker,
• Kurt Lejaeghere and
• Veronique Van Speybroeck

Beilstein J. Nanotechnol. 2014, 5, 1738–1748, doi:10.3762/bjnano.5.184

• framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å3. The transition

• . In each of these cases, a fundamental understanding of the electronic and magnetic properties was obtained by means of high-quality ab initio methods. In this work, we present an ab initio investigation of the MIL-47(V) MOF [1] (cf. Figure 1a). The were three reasons to chose this particular MOF: (1

• Density functional theory calculations Density functional theory (DFT) calculations are performed within the projector augmented wave (PAW) method as implemented in the “Vienna ab initio Simulation Package” (VASP) while using the generalized gradient approximation (GGA) functional as constructed by Perdew

On the structure of grain/interphase boundaries and interfaces

• K. Anantha Padmanabhan and
• Herbert Gleiter

Beilstein J. Nanotechnol. 2014, 5, 1603–1615, doi:10.3762/bjnano.5.172

• densities for different materials. There are some works in which such computations based on ab initio methods, e.g., tight binding model, are described [17][18]. Similar ab initio calculations have also been undertaken for boron. It has been shown that the structural details of beta-rhombohedral boron, such

• developed [27]. Enormous efforts that will involve ab initio methods and take into account interatomic (including electronic) interactions will be necessary to improve the situation. Lower limit: the concept of representative volume (with a focus on the region of disorder) It was pointed out [27] that a

• summarized in [53][54][55][56][57][60][61][62]. The shear modulus and the free volume present in the basic sliding unit, γ0, (composition, impurity/solute/dopant content dependent) can be determined by using ab initio calculations, in particular the tight binding model, which is computationally less

Double layer effects in a model of proton discharge on charged electrodes

• Johannes Wiebe and
• Eckhard Spohr

Beilstein J. Nanotechnol. 2014, 5, 973–982, doi:10.3762/bjnano.5.111

• proton motion is usually small so that proton tunneling is less important than in many other cases. However, there is evidence for quantum effects due to the delocalized nature of the protons, in particular from ab initio MD simulations [4][36][37]. Such calculations show that an adequate incorporation

Nanostructure sensitization of transition metal oxides for visible-light photocatalysis

• Hongjun Chen and
• Lianzhou Wang

Beilstein J. Nanotechnol. 2014, 5, 696–710, doi:10.3762/bjnano.5.82

• several experimental and theoretical researches. For instance, Du et al. used ab initio calculations to demonstrate that a graphene/titania interface in the ground electronic state forms a charge-transfer complex due to the large difference of work functions between graphene and TiO2 [99]. Most

Constant chemical potential approach for quantum chemical calculations in electrocatalysis

• Wolfgang B. Schneider and
• Alexander A. Auer

Beilstein J. Nanotechnol. 2014, 5, 668–676, doi:10.3762/bjnano.5.79

• the following sections. Furthermore, Bonnet et al. showed that it is possible to calculate the properties of a system for a given potential in the framework of ab-initio molecular dynamics [30]. In this work, we present an algorithm that allows to calculate the electronic structure for a given system

En route to controlled catalytic CVD synthesis of densely packed and vertically aligned nitrogen-doped carbon nanotube arrays

• Slawomir Boncel,
• Sebastian W. Pattinson,
• Valérie Geiser,
• Milo S. P. Shaffer and
• Krzysztof K. K. Koziol

Beilstein J. Nanotechnol. 2014, 5, 219–233, doi:10.3762/bjnano.5.24

• structure of the catalyst nanoparticles and/or of the nanotube themselves. Nevidomskyy et al. reported in their ab-initio studies that nitrogen incorporation into SWCNTs could cause the formation of covalent junctions between neighbouring tubes if the nitrogen atoms were opposed to each other [57

Change of the work function of platinum electrodes induced by halide adsorption

• Florian Gossenberger,
• Tanglaw Roman,
• Katrin Forster-Tonigold and
• Axel Groß

Beilstein J. Nanotechnol. 2014, 5, 152–161, doi:10.3762/bjnano.5.15

• functional theory (DFT) program Vienna Ab initio Simulation Package (VASP) was used. The exchange and correlation energy was calculated by using the generalized gradient approximation (GGA) with the PBE functional, developed by Perdew, Burke and Ernzerhof [23]. This functional is widely used, as it has been

Core level binding energies of functionalized and defective graphene

• Toma Susi,
• Markus Kaukonen,
• Paula Havu,
• Mathias P. Ljungberg,
• Paola Ayala and
• Esko I. Kauppinen

Beilstein J. Nanotechnol. 2014, 5, 121–132, doi:10.3762/bjnano.5.12

• large unit cells to avoid computational artifacts. In select cases, we compared the results to all-electron calculations using an ab initio molecular simulations (FHI-aims) code. We calculated the carbon and oxygen 1s core level binding energies for oxygen and hydrogen functionalities such as graphane

Influence of the adsorption geometry of PTCDA on Ag(111) on the tip–molecule forces in non-contact atomic force microscopy

• Gernot Langewisch,
• Jens Falter,
• André Schirmeisen and
• Harald Fuchs

Beilstein J. Nanotechnol. 2014, 5, 98–104, doi:10.3762/bjnano.5.9

• molecule A as well as for molecule B. Previous ab-initio simulations of PTCDA on Ag(111) predict a slight asymmetry of the end groups in the dissipation channel at small distances [17], but only for one molecular orientation. Therefore we speculate that this effect is related to an asymmetry of the tip