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

• 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

Spin relaxation in antiferromagnetic Fe–Fe dimers slowed down by anisotropic Dy^III ions

• Valeriu Mereacre,
• Frederik Klöwer,
• Yanhua Lan,
• Rodolphe Clérac,
• Juliusz A. Wolny,
• Volker Schünemann,
• Christopher E. Anson and
• Annie K. Powell

Beilstein J. Nanotechnol. 2013, 4, 807–814, doi:10.3762/bjnano.4.92

• unpredictable behaviour and the strong dependence of magnetic anisotropy and orientation of the easy axis of the magnetization of the DyIII ion on very small changes in the ligand environment was predicted by ab-initio calculations [5]. But only recently, we have shown that such radical changes can also be seen

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

• . The force field has a significant effect on the results of any atomistic MD simulation. In this work, a class II (second-generation) polymer-consistent force field (PCFF) [65] was employed. PCFF is an ab-initio based force field in which the total potential energy of an atomistic system is represented

• redistribution and the change of coordinates of classical atoms, i.e., the Schrödinger and Newton equations are solved in combination at each time step. The approach consists in the determination of forces affecting atoms "on the fly" from electronic structure calculations based on the first (ab initio) quantum

• an ion conducting nanochannel (Model II), our main goal was to reveal the details of the structural and dynamic mechanism of charge transfer. The statistical analysis of the 120-ps trajectories obtained from ab initio MD simulations allows us to establish some general features of the mechanism

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

Size variation of infrared vibrational spectra from molecules to hydrogenated diamond nanocrystals: a density functional theory study

• Mudar A. Abdulsattar

Beilstein J. Nanotechnol. 2013, 4, 262–268, doi:10.3762/bjnano.4.28

• Mudar A. Abdulsattar Ministry of Science and Technology, Baghdad, Iraq; Tel. +964-7901335231 10.3762/bjnano.4.28 Abstract Infrared spectra of hydrogenated diamond nanocrystals of one nanometer length are calculated by ab initio methods. Positions of atoms are optimized via density functional

• appear shifted from their exact positions due to overlap with neighboring modes. Keywords: ab initio; diamond; infrared spectroscopy; nanocrystals; vibration; Introduction Diamond nanocrystals are a very important material theoretically and experimentally. This importance seems to originate from the

• systematic frequency error that results from ab initio calculations [10]. The previous estimation of this scale factor for PBE theory by using the 3-21G basis is 0.991 [14]. Note that different authors use different scale factors for the same basis at the same level of calculation [10][14][15]. The present

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

• addressed charged polythiophenes in order to model doped systems and to check whether the modified electronic properties can simply be regarded as effects resulting from band filling or band emptying. Methods Our calculations are based on the periodic DFT code implemented in the Vienna Ab initio Simulation

Towards atomic resolution in sodium titanate nanotubes using near-edge X-ray-absorption fine-structure spectromicroscopy combined with multichannel multiple-scattering calculations

• Carla Bittencourt,
• Peter Krüger,
• Maureen J. Lagos,
• Xiaoxing Ke,
• Gustaaf Van Tendeloo,
• Chris Ewels,
• Polona Umek and
• Peter Guttmann

Beilstein J. Nanotechnol. 2012, 3, 789–797, doi:10.3762/bjnano.3.88

• we now turn to the simulations. In Figure 5 the O K-edge spectra are compared with density functional calculations performed in the local density approximation with the Vienna ab initio package [43][44]. As for the Ti L23-edge, the structural model “H(1,3)” for H2TiO3 of [23] is used for the (Na,H

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

• calculated total energy differences ΔE for substrates, precursor molecules, and the complex of the substrate with adsorbed precursor molecules, as reported previously [9][33] using the projector augmented wave method [42][43] as implemented in the Vienna Ab-initio Simulation Package (VASP) [44][45][46]. In

An NC-AFM and KPFM study of the adsorption of a triphenylene derivative on KBr(001)

• Antoine Hinaut,
• Adeline Pujol,
• Florian Chaumeton,
• David Martrou,
• André Gourdon and
• Sébastien Gauthier

Beilstein J. Nanotechnol. 2012, 3, 221–229, doi:10.3762/bjnano.3.25

• field [36]. This force field is well adapted to the system that we consider here, because it has been parameterized by using condensed-phase properties in addition to ab initio and empirical data for isolated molecules [37][38]. It is well known from previous studies that the adsorption of organic

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

• utilize an effective-field theory of interacting π-electrons to accurately model the electrostatic influence of the leads, and we develop an ab initio tunneling model to describe the details of the lead–molecule bonding over an ensemble of junction geometries. We also develop a simple decomposition of

• estimates from ab initio methods such as density functional theory. Note, however, that the use of “improved” values of the parameters in our effective Hamiltonian is unlikely to improve agreement with the experimental data that we considered, precisely because we optimized the π-EFT predictions for these

• lead and molecule was described by using an “ab initio” model in which the tunneling matrix elements between all relevant lead tip wavefunctions and the molecule were included, producing multi-channel junctions naturally from a physically motivated ensemble over various contact geometries. Coulomb

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

• dynamics (MD) simulations of the SAM. In the QM approach, the stiffness of the SAM is first related to a molecular quantity, the weighted molecular force constant , through a simple model. Then, is obtained by rigorous ab initio calculations (details in Experimental section). The molecular

• : 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

An MCBJ case study: The influence of π-conjugation on the single-molecule conductance at a solid/liquid interface

• Wenjing Hong,
• Hennie Valkenier,
• Gábor Mészáros,
• David Zsolt Manrique,
• Artem Mishchenko,
• Alexander Putz,
• Pavel Moreno García,
• Colin J. Lambert,
• Jan C. Hummelen and
• Thomas Wandlowski

Beilstein J. Nanotechnol. 2011, 2, 699–713, doi:10.3762/bjnano.2.76

• and the Fermi levels of the leads, based on a comparison with ab initio transport calculations and the corresponding transmission curves [58]. For comparison with the conductance–distance measurements shown in Figure 4, we calculated the slopes of the linear parts (typically in the range between −0.30

• than that of AC. This trend demonstrates that the cross-conjugated motif of AQ indeed gives rise to a lower conductance as compared to the linear-conjugated AC, which is in agreement with ab initio transport calculations predicting a destructive quantum interference present in AQ, but which is absent

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

• conformationally flexible molecules. Due to its conceptual simplicity and the ready availability of reliable empirical force fields (or forces computed ab initio), molecular dynamics is currently the most popular method for determining anharmonic frequencies of large systems (see [7] for an overview of some

• process. This is due to the necessity to first construct a potential energy surface (PES), which is then used to compute the vibrational Hamiltonian. The PES can also be generated directly from ab initio programs (direct-VSCF), thus leading to a straightforward route from electronic structure theory to a

• initio techniques. Thus, in this method, the speed at which the PES can be computed is directly related to the number of mode–mode couplings taken into account and to the amount of computing power allocated to the ab initio calculation of each grid point. However, the latter constitutes one of the main

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

• molecular electronics in the last decade. However, a theoretical description of molecular contacts as the building blocks of future devices is challenging, as it has to combine the properties of Fermi liquids in the leads with charge and phonon degrees of freedom on the molecule. Outside of ab initio

• orders of magnitude less expensive than elaborate numerical simulations that, however, provide exact solutions as benchmarks. Adjustable parameters obtained, e.g., from ab initio calculations allow for the treatment of various realizations. Even though not as rigorously formulated as, e.g

• 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

• changes in the electronic state, such as electron energy loss spectroscopy [4] or scanning tunneling microscopy [5], make use of advanced simulation methods to model the specimen. In 1997, Gemming and Möbus performed ab-initio HRTEM simulations of ionic crystals and justified the use of conventional image

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

• for the stability in the water complex. Ab initio molecular dynamics simulations showed that at room temperature the hexagonal water bilayer structure on bulk metal surfaces becomes disordered [19], but it may persist on the Au/Mpy/Pd junction because of the higher stability of the H2O layer, which is

• thus can not explain the experimentally observed strong reduction of the DOS of the Pd layer in the junction at the Fermi energy. Experimental Self-consistent periodic DFT calculations were performed employing the Vienna ab initio simulation package (VASP) [33]. The exchange-correlation effects were

Structural and magnetic properties of ternary Fe_1–xMn_xPt nanoalloys from first principles

• Markus E. Gruner and
• Peter Entel

Beilstein J. Nanotechnol. 2011, 2, 162–172, doi:10.3762/bjnano.2.20

• alloy in one specific case by means of large scale ab initio total energy calculations in the framework of density functional theory. For representative system sizes in the range of a few nanometers, where the surface-to-volume ratio is balanced and competitive effects should be expected such

• % surface atoms characterized by a reduced coordination in the first neighbor shell and are thus predetermined to monitor the competition between surface and bulk contributions with changing valence electron number. Computational The calculations were carried out using the Vienna Ab-initio Simulation

• restriction was also made for the 4d and 5d elements. This has proven to be a reasonable compromise in a recent ab initio study of the lattice dynamics of ordered Fe rich alloys with Pt group elements [50]. For a few selected isomers, single-point calculations with an increased value Ecut = 335 eV were