Ab initio study of adsorption and diffusion of lithium on transition metal dichalcogenide monolayers

• Xiaoli Sun and
• Zhiguo Wang

Beilstein J. Nanotechnol. 2017, 8, 2711–2718, doi:10.3762/bjnano.8.270

• . Simulation Details All the spin-polarized DFT calculations were performed with SIESTA code [62], in which norm-conserving pseudopotentials and a Perdew–Burcke–Ernzerhof functional was used to describe the electron–ion interaction and electron exchange correlation, respectively. Numerical atomic orbits were

Inelastic electron tunneling spectroscopy of difurylethene-based photochromic single-molecule junctions

• Youngsang Kim,
• Safa G. Bahoosh,
• Dmytro Sysoiev,
• Thomas Huhn,
• Fabian Pauly and
• Elke Scheer

Beilstein J. Nanotechnol. 2017, 8, 2606–2614, doi:10.3762/bjnano.8.261

• positions in our DFT-based procedure. In pure DFT calculations, i.e., without the corrections of the DFT+Σ method, we find that the HOMO level of the closed form is positioned right at the Fermi energy, as typically the case for large conjugated molecules, while for the open form the HOMO resonance is

• visibility. The inset shows the corresponding conductance histograms after subtracting the exponential backgrounds indicated by green dashed lines in the main panel. (a) The geometric structure used in the DFT calculations is displayed for the open and closed forms of Au-C5F-ThM-Au junctions. (b) The

Adsorption of iron tetraphenylporphyrin on (111) surfaces of coinage metals: a density functional theory study

• Hao Tang,
• Nathalie Tarrat,
• Véronique Langlais and
• Yongfeng Wang

Beilstein J. Nanotechnol. 2017, 8, 2484–2491, doi:10.3762/bjnano.8.248

• The adsorption of the iron tetraphenylporphyrin (FeTPP) molecule in its deckchair conformation was investigated on Au(111), Ag(111) and Cu(111) surfaces by performing spin-polarized density functional theory (DFT) calculations taking into account both van der Waals (vdW) interaction and on-site

• junction, the line shape of zero-bias resonance of the adsorbed FeTPP molecule reversibly varies by adjusting the tip to surface distance, i.e., by mechanically squeezing the molecule. Density functional theory (DFT) calculations reveal that the spin state of the Fe centre undergoes a switch from S = 2 to

• strong enough to modify the ligand-field environment of Fe. This result reveals that an external permanent element such as a STM tip or an additional molecule is needed to use FeTPP or similar molecules as model system for molecular spin switches. Method and Computational Details Spin-polarized DFT

Au₅₅, a stable glassy cluster: results of ab initio calculations

• Dieter Vollath,
• David Holec and
• Franz Dieter Fischer

Beilstein J. Nanotechnol. 2017, 8, 2221–2229, doi:10.3762/bjnano.8.222

• bulk n·εbulk. This approach was introduced by Medasani et al. [30] to calculate the surface energy of silver clusters using DFT calculations. In their study, the surface energy γ was defined as The quantity a represents the surface area of the cluster. At the first view, this approach seems logical and

Comprehensive investigation of the electronic excitation of W(CO)₆ by photoabsorption and theoretical analysis in the energy region from 3.9 to 10.8 eV

• Mónica Mendes,
• Khrystyna Regeta,
• Filipe Ferreira da Silva,
• Nykola C. Jones,
• Søren Vrønning Hoffmann,
• Gustavo García,
• Chantal Daniel and
• Paulo Limão-Vieira

Beilstein J. Nanotechnol. 2017, 8, 2208–2218, doi:10.3762/bjnano.8.220

• of relevance to estimate neutral dissociation cross sections of W(CO)6, a precursor molecule in focused electron beam induced deposition (FEBID) processes, from electron scattering measurements. Keywords: cross sections; density functional theory (DFT) calculations; focused electron beam induced

• -dependent density functional theory (TDDFT) calculations [15], and electron momentum spectroscopy calculations [16] have been carried out. Other relevant studies include DFT calculations on the structure of W(CO)6 and its behaviour in infrared spectroscopy [17], as well as Raman [18] and infrared [18][19

Ester formation at the liquid–solid interface

• Nguyen T. N. Ha,
• Thiruvancheril G. Gopakumar,
• Nguyen D. C. Yen,
• Carola Mende,
• Lars Smykalla,
• Maik Schlesinger,
• Roy Buschbeck,
• Tobias Rüffer,
• Heinrich Lang,
• Michael Mehring and
• Michael Hietschold

Beilstein J. Nanotechnol. 2017, 8, 2139–2150, doi:10.3762/bjnano.8.213

• temperature for 10 min and then the substrate was cooled down to room temperature for STM imaging. DFT calculations were carried out using the grid-based projector augmented wave method (GPAW) [37]. The PBE exchange-correlation functional [38] and the LCAO mode [37] with the standard double-zeta-polarized

Electronic structure, transport, and collective effects in molecular layered systems

• Torsten Hahn,
• Tim Ludwig,
• Carsten Timm and
• Jens Kortus

Beilstein J. Nanotechnol. 2017, 8, 2094–2105, doi:10.3762/bjnano.8.209

• approach. In the second part we present our approach to combine DFT calculations and the master equation approach to quantum transport. Finally we present results of this new approach to describe tunnelling effects in monolayers. DFT-NEGF transport theory The ground-state electronic structure of the

• the I–V characteristics of our model devices. For the transport calculations, the electronic structure is obtained by DFT calculations using the common approach of constructing a model device for which the molecule of interest together with additional electrode atoms (scattering region, see below

• density of states as obtained from the DFT calculations. While the electronic structure of CoPc and F16CoPc is qualitative similar after surface contact, the manganese center in the F16CoPc/MnPc yields a larger local magnetic moment and more strongly occupied metal 3d states close to the Fermi level. Both

Intercalation of Si between MoS₂ layers

• Rik van Bremen,
• Qirong Yao,
• Soumya Banerjee,
• Deniz Cakir,
• Nuri Oncel and
• Harold J. W. Zandvliet

Beilstein J. Nanotechnol. 2017, 8, 1952–1960, doi:10.3762/bjnano.8.196

• found a similar height variation using density functional theory (DFT) calculations of the intercalation of a single silicon layer in between two MoS2 layers. These calculations are discussed after the presentation of the experimental results. It is immediately obvious from Figure 1f that the transition

Coexistence of strongly buckled germanene phases on Al(111)

• Weimin Wang and
• Roger I. G. Uhrberg

Beilstein J. Nanotechnol. 2017, 8, 1946–1951, doi:10.3762/bjnano.8.195

• images show hexagonal patterns in contrast to the honeycomb pattern reported in [13]. Our experimental data in combination with DFT calculations lead to a new model that can explain the experimental observations in terms of buckled germanene. Results and Discussion Figure 1a shows a LEED pattern, which

• -ordered hexagonal structures with (3×3) and (√7×√7) periodicities with respect to Al (1×1). Our DFT calculations show that the Ge layer relaxes to a hexagonal structure when two Ge atoms are positioned above threefold hollow sites on Al(111). The experimental and theoretical findings are consistent with a

• using an Omicron variable temperature STM in the UHV system at Linköping University. All STM images were measured in constant current mode with a tunneling current of 200 pA. First-principles density functional theory (DFT) calculations were used to investigate the atomic structure of the Ge layer on

Structural model of silicene-like nanoribbons on a Pb-reconstructed Si(111) surface

• Agnieszka Stępniak-Dybala and
• Mariusz Krawiec

Beilstein J. Nanotechnol. 2017, 8, 1836–1843, doi:10.3762/bjnano.8.185

• into the physics and chemistry of silicene/substrate systems density functional theory (DFT) calculations have usually been required. In all these cases silicene was reported to be formed in 2D domains with a corrugated hexagonal structure. Nevertheless, not all experiments, most notably on Ag(111

• ), support the scenario of silicene formation, mainly due to a problem with electronic properties. Therefore there is still a significant amount of skepticism about this issue. In many cases density functional theory (DFT) calculations were required to get more detailed information on what structures have

• DFT calculations proposed a hexagonal structure of the Si NRs. However, recent theoretical and experimental studies [42][43][44] have found this structure to be incorrect, and opt for the so-called “pentamer” model, in which Si atoms are arranged into chains composed of pentagonal rings running along

Transport characteristics of a silicene nanoribbon on Ag(110)

• Ryoichi Hiraoka,
• Chun-Liang Lin,
• Kotaro Nakamura,
• Ryo Nagao,
• Maki Kawai,
• Ryuichi Arafune and
• Noriaki Takagi

Beilstein J. Nanotechnol. 2017, 8, 1699–1704, doi:10.3762/bjnano.8.170

• of ≈1.5 nm width with the zigzag edges. Very recently, pentagonal chain models were proposed for SiNR on Ag(110) [27][28]. In this model, Si atoms constitute a five-membered ring to form a 1D chain. Density functional theory (DFT) calculations have demonstrated that freestanding honeycomb SiNR

Effect of the fluorination technique on the surface-fluorination patterning of double-walled carbon nanotubes

• Lyubov G. Bulusheva,
• Yuliya V. Fedoseeva,
• Emmanuel Flahaut,
• Jérémy Rio,
• Christopher P. Ewels,
• Victor O. Koroteev,
• Gregory Van Lier,
• Denis V. Vyalikh and
• Alexander V. Okotrub

Beilstein J. Nanotechnol. 2017, 8, 1688–1698, doi:10.3762/bjnano.8.169

• ]. There is little known in the literature concerning the mechanism of BrF3 fluorination, so we performed a series of DFT calculations to clarify this point. Importantly, we find that a decomposition of BrF3 over pristine graphene to give BrF2 and surface-bound F is endothermic (+0.25 eV) with a reaction

Charge transfer from and to manganese phthalocyanine: bulk materials and interfaces

• Florian Rückerl,
• Daniel Waas,
• Bernd Büchner,
• Martin Knupfer,
• Dietrich R. T. Zahn,
• Francisc Haidu,
• Torsten Hahn and
• Jens Kortus

Beilstein J. Nanotechnol. 2017, 8, 1601–1615, doi:10.3762/bjnano.8.160

• energy. Results of the DFT calculations for the MnPc/F4TCNQ dimer model systems: a) The SOMO of MnPc and the LUMO of F4TCNQ hybridize and charge is transferred into the newly formed bonding hybrid state. b) Comparison of the eigenvalues of the Kohn–Sham orbitals as obtained from the calculations for a

• . The appearance of a structure of low binding energy for the thin F16CoPc layer clearly indicates a reduction of the Co center in this molecule (adapted from [31]). Results of the DFT calculations for the MnPc/F16CoPc model systems: a) The hybrid state is formed by the Mn 3dxz and the Co states. b

Deposition of exchange-coupled dinickel complexes on gold substrates utilizing ambidentate mercapto-carboxylato ligands

• Martin Börner,
• Laura Blömer,
• Marcus Kischel,
• Peter Richter,
• Georgeta Salvan,
• Dietrich R. T. Zahn,
• Pablo F. Siles,
• Maria E. N. Fuentes,
• Carlos C. B. Bufon,
• Daniel Grimm,
• Oliver G. Schmidt,
• Daniel Breite,
• Bernd Abel and
• Berthold Kersting

Beilstein J. Nanotechnol. 2017, 8, 1375–1387, doi:10.3762/bjnano.8.139

• susceptibility measurements (for 7 and 8) and (broken symmetry) density functional theory (DFT) calculations. An S = 2 ground state is demonstrated by temperature-dependent susceptibility and magnetization measurements, achieved by ferromagnetic coupling between the spins of the Ni(II) ions in 7 (J = +22.3 cm−1

• accessible voids) of ≈1000 Å3 attributed to MeCN or EtOH solvate molecules. Only the structure of the complex cation could be identified. Computational details DFT calculations were carried out utilizing density functional theory (DFT). Perdew, Burke and Ernzerhof’s PBE0 hybrid functional [69][70] and

Comprehensive Raman study of epitaxial silicene-related phases on Ag(111)

• Dmytro Solonenko,
• Ovidiu D. Gordan,
• Guy Le Lay,
• Dietrich R. T. Zahn and
• Patrick Vogt

Beilstein J. Nanotechnol. 2017, 8, 1357–1365, doi:10.3762/bjnano.8.137

• explicitly considered in the modeling of this structure and of its properties in DFT calculations. Proposed structural models that are entirely based on the ordered parts of this structure are genuinely bound to fail in the correct description of the “” structure. Discussion Based on the in situ Raman

3D continuum phonon model for group-IV 2D materials

• Morten Willatzen,
• Lok C. Lew Yan Voon,
• Appala Naidu Gandi and
• Udo Schwingenschlögl

Beilstein J. Nanotechnol. 2017, 8, 1345–1356, doi:10.3762/bjnano.8.136

• ]. In addition to obtaining a spectrum, it is often also useful to be able to predict and/or interpret properties of the spectrum based upon either microscopic or symmetric arguments. An excellent example is the prediction of a Dirac cone for silicene on the basis of symmetry [7] when DFT calculations

• coordinate in the analysis to reveal the true phonon dispersions as observed experimentally and in DFT calculations. The general 3D elastic equations are given by the equation of motion [14] where Tik is the stress tensor, ρ is the mass density, and ui is the displacement. Equation 1 contains all the physics

• before, which led to a decoupling of the out-of-plane vibrations. The coupling is a consequence of the finite thickness of the sheet with no mirror symmetry imposed. Thus, our model is sufficiently general to apply to multilayers. Earlier DFT calculations [15] had argued that there is no coupling between

Stable Au–C bonds to the substrate for fullerene-based nanostructures

• Taras Chutora,
• Jesús Redondo,
• Bruno de la Torre,
• Martin Švec,
• Pavel Jelínek and
• Héctor Vázquez

Beilstein J. Nanotechnol. 2017, 8, 1073–1079, doi:10.3762/bjnano.8.109

• tunneling microscope. These features are stable at room temperature against diffusion on the surface. We carry out DFT calculations of fullerene molecules having one missing carbon atom to simulate the vacancies in the molecules resulting from the sputtering process. These modified fullerenes have an

Triptycene-terminated thiolate and selenolate monolayers on Au(111)

• Jinxuan Liu,
• Martin Kind,
• Björn Schüpbach,
• Daniel Käfer,
• Stefanie Winkler,
• Wenhua Zhang,
• Andreas Terfort and
• Christof Wöll

Beilstein J. Nanotechnol. 2017, 8, 892–905, doi:10.3762/bjnano.8.91

• spectra were acquired at a resolution of 2 cm−1. Calculation of IR spectra Theoretical values of the vibrational frequencies of the isolated molecules were obtained employing quantum-chemical density functional theory (DFT) calculations with the Gaussian 03 program package [54], using the B3LYP hybrid

• , while bands with TDMs (mostly) parallel to the surface will be attenuated or even completely extinguished. Thus, from comparison of relative band intensities in neat substance spectra to those in spectra of monolayers, information can be gained on the alignment of the molecules. With the help of DFT

• calculations, in the IR spectra of the triptycene-based molecules, two types of vibrational bands can be identified. The TDMs of the first type (designated || in Table 1) are parallel to the molecular main axis that passes through both aliphatic C atoms of the triptycene unit (compare Figure 1). The other type

Modeling adsorption of brominated, chlorinated and mixed bromo/chloro-dibenzo-p-dioxins on C₆₀ fullerene using Nano-QSPR

• Piotr Urbaszek,
• Agnieszka Gajewicz,
• Celina Sikorska,
• Maciej Haranczyk and
• Tomasz Puzyn

Beilstein J. Nanotechnol. 2017, 8, 752–761, doi:10.3762/bjnano.8.78

• also been studied [38]. There are also a few studies aimed at using in silico methods, such as semi-empirical or density functional theory (DFT) calculations, for exploring interactions on nanoparticle surfaces [39][40][41]. Our results provide new knowledge about: i) general sorption interaction

Calculating free energies of organic molecules on insulating substrates

• Julian Gaberle,
• David Z. Gao and
• Alexander L. Shluger

Beilstein J. Nanotechnol. 2017, 8, 667–674, doi:10.3762/bjnano.8.71

• . The atomic charges of atoms within the TCB and CDB molecules were assigned using Mulliken population analysis of the DFT dataset and classical charges of ±1 were used for KCl. The adsorption geometries obtained using this force field reproduced the results of vdW corrected DFT calculations well and

Association of aescin with β- and γ-cyclodextrins studied by DFT calculations and spectroscopic methods

• Ana I. Ramos,
• Pedro D. Vaz,
• Susana S. Braga and
• Artur M. S. Silva

Beilstein J. Nanotechnol. 2017, 8, 348–357, doi:10.3762/bjnano.8.37

• functional theory (DFT) calculations on the interaction of aescin Ib with CDs show that an inclusion can indeed occur and it is further demonstrated that the wider cavity of γ-CD is more adequate to accommodate this large guest. ROESY spectroscopy is consistent with the formation of a complex in which the

• triterpenic moiety of aescin is included into the cavity of γ-CD. The higher stability of this geometry was confirmed by DFT. Furthermore, DFT calculations were applied to determine the chemical shifts of the protons H3 and H5 of the CDs in the optimised structures of the inclusion complexes. The calculated

• protons were also found, namely with H5, H7 and H15. This suggests that aescin is included into γ-CD by its triterpenic moiety, in a good match with the geometry calculated for the complex γ1 in the following section. Investigation of the CD·aescin inclusion modes by DFT calculations The geometry of

Tailoring bifunctional hybrid organic–inorganic nanoadsorbents by the choice of functional layer composition probed by adsorption of Cu²⁺ ions

• Veronika V. Tomina,
• Inna V. Melnyk,
• Yuriy L. Zub,
• Aivaras Kareiva,
• Miroslava Vaclavikova,
• Gulaim A. Seisenbaeva and
• Vadim G. Kessler

Beilstein J. Nanotechnol. 2017, 8, 334–347, doi:10.3762/bjnano.8.36

• of stabilization and the relation to the activity in adsorption of copper(II) cations has been more recently discussed in the works of Soler-Illia and co-workers [36][37]. Using DFT calculations it was demonstrated that the protonated amino groups are irreversibly transmitting a proton to the Si–O

Monolayer graphene/SiC Schottky barrier diodes with improved barrier height uniformity as a sensing platform for the detection of heavy metals

• Ivan Shtepliuk,
• Jens Eriksson,
• Volodymyr Khranovskyy,
• Tihomir Iakimov,
• Anita Lloyd Spetz and
• Rositsa Yakimova

Beilstein J. Nanotechnol. 2016, 7, 1800–1814, doi:10.3762/bjnano.7.173

• Schottky barrier diodes with improved barrier height uniformity, formed on uniform 1 ML graphene. Based on density functional theory (DFT) calculations and experimental findings we propose a strategy for development of a sensing platform for detection of the toxic heavy metals Cd, Hg and Pb. Experimental

• draw conclusions about the selectivity of the graphene-based sensors towards different heavy metals. DFT analysis and computational details An important step is to study the interaction between heavy metals and the graphene surface by DFT calculations. Furthermore, in order to establish the most

• the Becke3LYP level of density functional theory with a 6-31G basis set on carbon and a basis set of Stuttgart-Dresden SDD effective core potentials [53] on Cd, Hg and Pb atoms. DFT calculations of small graphene clusters and geometry optimization are performed using the default convergence criteria

First-principles study of the structure of water layers on flat and stepped Pb electrodes

• Xiaohang Lin,
• Ferdinand Evers and
• Axel Groß

Beilstein J. Nanotechnol. 2016, 7, 533–543, doi:10.3762/bjnano.7.47

• Xiaohang Lin Ferdinand Evers Axel Gross Institut für Theoretische Chemie, Universität Ulm, 89069 Ulm, Germany Institut für Theoretische Physik, Universität Regensburg, 93040 Regensburg, Germany 10.3762/bjnano.7.47 Abstract On the basis of perodic density functional theory (DFT) calculations, we

• , but rather becomes disordered [30][40]. In the present work, we have addressed structural and electronic properties of water layers on flat and stepped Pb surfaces using periodic density functional theory (DFT) calculations. We will show the consequences of the large lattice constant of Pb on the

• surfaces. Theoretical Methods Periodic DFT calculations have been performed employing the Vienna ab initio simulation package (VASP) [41][42] within the generalized gradient approximation (GGA) to describe the exchange–correlation effects, using the Perdew, Burke and Ernzerhof (PBE) exchange–correlation

Invariance of molecular charge transport upon changes of extended molecule size and several related issues

• Ioan Bâldea

Beilstein J. Nanotechnol. 2016, 7, 418–431, doi:10.3762/bjnano.7.37

• molecule, currents computed within the WBL and FBL would approach the values computed exactly. From this perspective, the results presented in Figure 5 are interesting. They show that even for extended molecules that are much larger than NEGF-DFT calculations can handle (given presently available computing

• under which conditions (i)–(iii) are usually listed in the context of realistic (DFT) calculations. The “extended” molecule should be taken large enough so that effects of the cluster to the (Kohn–Sham) potential outside the scattering region is screened. Outside the sufficiently large, extended

• functions in Equation 6) become ε-independent has a two-fold advantage. This scheme enables one to perform conventional DFT calculations for a finite, isolated, extended molecule (i.e., uncoupled to semi-infinite electrodes). In principle, this can be done with any common DFT package. The implementation is