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

Rigid multipodal platforms for metal surfaces

• Michal Valášek,
• Marcin Lindner and
• Marcel Mayor

Beilstein J. Nanotechnol. 2016, 7, 374–405, doi:10.3762/bjnano.7.34

• . Consequently, no further dilution of the molecules is required. The rod-like substituent is almost perpendicular to the plane determined by the three thiols and the head ferrocenyl group is 16 Å above the gold surface, as optimized by density functional theory (DFT) calculations. The extended analysis of the

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

• unsaturated, but also provided sufficient neighboring surface atoms available to interact dispersively to the molecular backbone. Experimental Configurational sampling. Zero-temperature DFT calculations suffer from an inability to broadly sample the configurational space, and are often trapped close to the

Probing the local environment of a single OPE3 molecule using inelastic tunneling electron spectroscopy

• Riccardo Frisenda,
• Mickael L. Perrin and
• Herre S. J. van der Zant

Beilstein J. Nanotechnol. 2015, 6, 2477–2484, doi:10.3762/bjnano.6.257

• electrodes when describing inelastic contributions to transport through single-molecule junctions. Keywords: current–voltage characteristics; DFT calculations; mechanically controllable break junction (MCBJ); molecule–electrode interaction; vibrational modes; Introduction Vibrational degrees of freedom in

• and performed density function theory (DFT) calculations of the OPE3 molecular junction. All calculations were optimized using a TZP Slater-type orbital local basis-set and the PBE GGA functional. We stretch the molecular junction starting from the configuration shown in the left panel of Figure 5a

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

• systematically investigated by DFT calculations. At room temperature, the pristine 2D Sn is impermeable for noble gases. To increase the diffusion rate of noble gases, two practical strategies were proposed: stretch and fluorination. With a high concentration of uniform pores, 2D Sn-based materials exhibited

Sub-monolayer film growth of a volatile lanthanide complex on metallic surfaces

• Hironari Isshiki,
• Jinjie Chen,
• Kevin Edelmann and
• Wulf Wulfhekel

Beilstein J. Nanotechnol. 2015, 6, 2412–2416, doi:10.3762/bjnano.6.248

• -dikenonate ligands (see Figure 1) and the total charge of the molecule is zero. Recent DFT calculations for Ln(thd)3 in gas phase show that the D3 symmetry structure corresponds to the minimum of the potential energy [14]. Though remarkable magnetic properties of Ln(thd)3 in bulk have not been reported, some

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

• NEXAFS associated with the energy splitting of the sigma resonances, is computed and explained in terms of modified C–C bond lengths. Computational Methods The DFT calculations of the pentacene/Al(001) system were carried out using the Quantum-ESPRESSO package [34]. We choose the GGA as proposed by

A single-source precursor route to anisotropic halogen-doped zinc oxide particles as a promising candidate for new transparent conducting oxide materials

• Daniela Lehr,
• Markus R. Wagner,
• Johanna Flock,
• Julian S. Reparaz,
• Clivia M. Sotomayor Torres,
• Alexander Klaiber,
• Thomas Dekorsy and
• Sebastian Polarz

Beilstein J. Nanotechnol. 2015, 6, 2161–2172, doi:10.3762/bjnano.6.222

• software TeraLyzer. The DFT calculations have been carried out using the def2-TZVP basis set for all atoms and B3LYP functional. Results and Discussion Precursor synthesis Alkylzinc–alkoxides with heterocubane structure [CH3ZnOR]4 are well known precursors for the synthesis of various ZnO materials [58][59

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

Atomic scale interface design and characterisation

• Carla Bittencourt,
• Chris Ewels and
• Arkady V. Krasheninnikov

Beilstein J. Nanotechnol. 2015, 6, 1708–1711, doi:10.3762/bjnano.6.174

• simulated. An impressive example of how STM experiments and DFT calculations together can unravel the atomic structure of the material is given in the article by J. A. Lawlor and M. S. Ferreira [26] focused on the identification of dopant impurities in graphene. Synergy effects of TEM and DFT are

Electrical properties and mechanical stability of anchoring groups for single-molecule electronics

• Riccardo Frisenda,
• Simge Tarkuç,
• Elena Galán,
• Mickael L. Perrin,
• Rienk Eelkema,
• Ferdinand C. Grozema and
• Herre S. J. van der Zant

Beilstein J. Nanotechnol. 2015, 6, 1558–1567, doi:10.3762/bjnano.6.159

• -breaking regime, giving rise to more variability in the probed conductance of the self-breaking experiment. To gain more insight in the different anchoring geometry and the observed variations in lifetimes and conductance values, we have performed DFT calculations by modelling the molecule of interest in

• characterization of a bare gold sample where no molecules were deposited, additional details about DFT calculations, the analysis of the fitting parameters of the I–V s of molecules 1–4. Acknowledgements This work was financially supported by the Dutch organization for Fundamental Research on Matter (FOM) and by

Possibilities and limitations of advanced transmission electron microscopy for carbon-based nanomaterials

• Xiaoxing Ke,
• Carla Bittencourt and
• Gustaaf Van Tendeloo

Beilstein J. Nanotechnol. 2015, 6, 1541–1557, doi:10.3762/bjnano.6.158

• binding energy through DFT calculations [67]. Similarly, the electron affinity and binding energy difference can influence the reactions inside the CNTs, although the interior of the CNTs is regarded as inert due to its concave surface [76][77]. Recent studies using AC-TEM at the atomic scale have

Enhanced fullerene–Au(111) coupling in (2√3 × 2√3)R30° superstructures with intermolecular interactions

• Michael Paßens,
• Rainer Waser and
• Silvia Karthäuser

Beilstein J. Nanotechnol. 2015, 6, 1421–1431, doi:10.3762/bjnano.6.147

• around Ubias = 0.5 V. This behavior is attributed to different electronic structures of bright and dim molecules [16][28] though it could not be confirmed by DFT calculations [29][30], which indicate only a minor charge transfer from the substrate to the molecule. The origin of the voltage-dependent

• ) surface. Thus, additional Pt–C covalent bonds form between C60 and Pt adatoms and further stabilize the reconstructed surface. In addition, new DFT calculations of C60 on Au(111) reveal [30] that the missing energy to thermodynamically allow for the vacancy–adatom formation is only 0.29 eV. This energy

• by DFT calculations [29][30]. For reference purposes we first probed the dI/dV spectra of a bright C60 molecule. A typical spectrum showing molecular resonances of bright C60 is displayed in Figure 6 (blue). It is in full agreement with dI/dV spectra reported in literature for bright C60 embedded in