Intuitive human interface to a scanning tunnelling microscope: observation of parity oscillations for a single atomic chain

• Sumit Tewari,
• Jacob Bakermans,
• Christian Wagner,
• Federica Galli and
• Jan M. van Ruitenbeek

Beilstein J. Nanotechnol. 2019, 10, 337–348, doi:10.3762/bjnano.10.33

• give rise to interatomic forces) and take the forces as coming from parameterised equations that only depend on the interatomic distances. This is typically called a force-field simulation. A more accurate method would be obtained by using ab initio calculations that take into account both the nuclear

• and the electronic degrees of freedom. But these ab initio calculations are computationally very expensive and thus are not suitable for our purpose. The simulation we discuss in this article is only made for metallic systems, so in this case all the atoms involved are Au atoms. Here a semi-empirical

Silicene, germanene and other group IV 2D materials

• Patrick Vogt

Beilstein J. Nanotechnol. 2018, 9, 2665–2667, doi:10.3762/bjnano.9.248

• 2D layer properties, for example, via chemical functionalization or external fields. This could be efficiently utilized in a transistor, where the electronic band gap can then be tuned by the electric field applied perpendicular to the lattice plane. As an example, ab initio calculations have shown

Improved catalytic combustion of methane using CuO nanobelts with predominantly (001) surfaces

• Qingquan Kong,
• Yichun Yin,
• Bing Xue,
• Yonggang Jin,
• Wei Feng,
• Zhi-Gang Chen,
• Shi Su and
• Chenghua Sun

Beilstein J. Nanotechnol. 2018, 9, 2526–2532, doi:10.3762/bjnano.9.235

• approximation (GGA) [29] together with the functional by Perdew, Burke, and Ernzerhof [30], which was embedded in the Vienna Ab-Initio Simulation Package [31]. The calculation was carried out with a kinetic cutoff energy of 380 eV, with the use of the projector augmented wave (PAW) method. The k-space was

Surface energy of nanoparticles – influence of particle size and structure

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

Beilstein J. Nanotechnol. 2018, 9, 2265–2276, doi:10.3762/bjnano.9.211

• particle size. Different approaches, such as classical thermodynamics calculations, molecular dynamics simulations, and ab initio calculations, exist to predict this quantity. Generally, considerations based on classical thermodynamics lead to the prediction of decreasing values of the surface energy with

• be expected by the formation of a disordered or quasi-liquid layer at the surface. The atomistic approach, based either on molecular dynamics simulations or ab initio calculations, generally leads to values with an opposite tendency. However, it is shown that this result is based on an insufficient

• particle size is found. The main conclusion of this work is that surface energy values for the equivalent bulk materials should be used if detailed data for nanoparticles are not available. Keywords: ab initio calculations; classical thermodynamics; molecular dynamics simulation; surface energy; surface

Recent highlights in nanoscale and mesoscale friction

• Andrea Vanossi,
• Dirk Dietzel,
• Andre Schirmeisen,
• Ernst Meyer,
• Rémy Pawlak,
• Thilo Glatzel,
• Marcin Kisiel,
• Shigeki Kawai and
• Nicola Manini

Beilstein J. Nanotechnol. 2018, 9, 1995–2014, doi:10.3762/bjnano.9.190

• , only small particles adhere to the sublinear superlubric scaling law, while larger particles show a linear scaling between friction and area, equivalent to a constant shear stress [100]. This can be explained by an enhanced interaction between the Sb atoms and the substrate, as was found by ab initio

• interface [50][51]. Moreover, recent studies have highlighted that structural lubricity can also be observed for nanoparticle systems under ambient conditions. More specifically, a sublinear dependence of friction on the area was found both for gold [47] (Figure 2) and platinum particles [48] on HOPG. Ab

• initio simulations additionally elucidated how interface contamination is prevented by sufficiently large energy barriers and how absolute friction values are compatible with the atomic interactions upon application of the scaling laws. A recent study has pointed out that mechanical cleaning of

The inhibition effect of water on the purification of natural gas with nanoporous graphene membranes

• Krzysztof Nieszporek,
• Tomasz Pańczyk and
• Jolanta Nieszporek

Beilstein J. Nanotechnol. 2018, 9, 1906–1916, doi:10.3762/bjnano.9.182

• interesting review on carbon- and nitrogen-based materials [10]. Hauser and Schwerdtfeger [11] studied theoretically the ability of functionalized graphene nanopores to separate methane from air. Recently, Guerrero-Avilés and Orellana performed ab initio MD simulations to study the interactions between

Improving the catalytic activity for hydrogen evolution of monolayered SnSe_2(1−x)S_2x by mechanical strain

• Sha Dong and
• Zhiguo Wang

Beilstein J. Nanotechnol. 2018, 9, 1820–1827, doi:10.3762/bjnano.9.173

• implemented in the Vienna ab initio simulation package (VASP) [60][61] within the framework of the projector augmented wave method [62]. Electron exchange–correlation was described with the generalized gradient approximation (GGA) within the Perdew–Burke–Ernzerhof (PBE) functional [63]. An energy cutoff of

Free-radical gases on two-dimensional transition-metal disulfides (XS₂, X = Mo/W): robust half-metallicity for efficient nitrogen oxide sensors

• Chunmei Zhang,
• Yalong Jiao,
• Fengxian Ma,
• Sri Kasi Matta,
• Steven Bottle and
• Aijun Du

Beilstein J. Nanotechnol. 2018, 9, 1641–1646, doi:10.3762/bjnano.9.156

• NO, NO2 adsorbed on monolayer XS2 (X = Mo, W) are performed using DFT within generalized gradient approximation (GGA) of the Perdew–Burke–Ernzerhof (PBE) functional, as implemented in the Vienna ab initio simulation package (VASP) [34][35][36]. To study 2D systems under the periodic boundary

• meV and 3 Å, suggesting that water is physically adsorbed on the surface of the WS2 nanosheet. Monolayer MoS2 [38] and multilayer MoS2 field effect transistors [17] for sensing NO at room temperature have been fabricated experimentally. In this work, the ab initio molecular dynamics simulations at

Computational exploration of two-dimensional silicon diarsenide and germanium arsenide for photovoltaic applications

• Sri Kasi Matta,
• Chunmei Zhang,
• Yalong Jiao,
• Anthony O'Mullane and
• Aijun Du

Beilstein J. Nanotechnol. 2018, 9, 1247–1253, doi:10.3762/bjnano.9.116

• . Computational Details Density functional theory (DFT) using plane wave Vienna ab initio simulation package (VASP) code is used for first-principle calculations for this study [11][12]. The geometry optimisation is done with generalized gradient approximation in the Perdew–Burke–Ernzerhof form (GGA-PBE) exchange

An implementation of spin–orbit coupling for band structure calculations with Gaussian basis sets: Two-dimensional topological crystals of Sb and Bi

• Sahar Pakdel,
• Mahdi Pourfath and
• J. J. Palacios

Beilstein J. Nanotechnol. 2018, 9, 1015–1023, doi:10.3762/bjnano.9.94

• categories: those making use of plane-waves and those using localized orbitals. Arguably, the most reliable implementations of SOC can be found in the code FLEUR [11] and also in codes such as Vienna Ab initio Simulation Package [12] (VASP) or QuantumEspresso [13][14] (QE), all of them employing plane-waves

Electro-optical interfacial effects on a graphene/π-conjugated organic semiconductor hybrid system

• Karolline A. S. Araujo,
• Luiz A. Cury,
• Matheus J. S. Matos,
• Thales F. D. Fernandes,
• Luiz G. Cançado and
• Bernardo R. A. Neves

Beilstein J. Nanotechnol. 2018, 9, 963–974, doi:10.3762/bjnano.9.90

• probe microscopy, optical spectroscopy (photoluminescence and Raman) and ab initio calculations. The graphene/RA interaction induces the formation of a well-organized π-conjugated self-assembled monolayer (SAM) at the interface. Such structural organization leads to the high optical emission efficiency

• monolayers across the graphene surface (Figure 1c, Figure 2b,d). Besides molecular structural configuration, the charge transfer within the graphene/RA hybrid has also been estimated via ab initio calculations. The results indicate that electrons are transferred from graphene to RA molecules, resulting in p

• estimated via Raman scattering experiment is of order of 1013 cm−2, consistent with the value predicted from ab initio calculations. Conclusion Organic semiconductor dyes and 2D materials are classes of materials which have enormous potential applications by themselves. The possibility of creating hybrid

Dynamics and fragmentation mechanism of (C₅H₄CH₃)Pt(CH₃)₃ on SiO₂ surfaces

• Kaliappan Muthukumar,
• Harald O. Jeschke and
• Roser Valentí

Beilstein J. Nanotechnol. 2018, 9, 711–720, doi:10.3762/bjnano.9.66

• substrates, (C5H4CH3)Pt(CH3)3 precursor molecules, and the combined substrate/precursor molecule system were performed using the projector augmented wave (PAW) method [15][16] as implemented in the Vienna ab initio simulation package (VASP-5.2.11) [17][18][19]. The generalized gradient approximation in the

Gas-sensing behaviour of ZnO/diamond nanostructures

• Marina Davydova,
• Alexandr Laposa,
• Jiri Smarhak,
• Alexander Kromka,
• Neda Neykova,
• Josef Nahlik,
• Jiri Kroutil,
• Jan Drahokoupil and
• Jan Voves

Beilstein J. Nanotechnol. 2018, 9, 22–29, doi:10.3762/bjnano.9.4

• , the peaks presented at 44.8° and 52.3° are assigned to the (111) and (002) diffraction peaks of Au in the interdigitated electrodes. Simulation of interaction between gas molecules and hybrid ZnO NRs/NCD sensor structure In order to better understand the gas sensor measurements, ab initio simulations

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

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

• calculations were performed using a slightly modified version of the Vienna ab initio simulation package VASP [27][28][29][30]. Projector-augmented wave (PAW) pseudo-potential [31][32], as well as the exchange–correlation functional proposed by Perdew–Burke–Ernzerhof (PBE) in the framework of the generalized

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

• theoretically. However, up to now, the results of these studies are still inconsistent. Consequently, we have carried out the present ab initio study of the Au55 cluster, using up-to-date computational concepts, in order to clarify these issues. Our calculations have confirmed the experimental result that the

• are only sparse experimental results. The Au55 cluster is an exception, since this cluster, consisting of a magic number of atoms, is very stable. Consequently, some experimental data are available for comparison with predictions obtained by ab initio calculations. There are a few “magic” numbers

• means of molecular dynamics or ab initio modeling. These studies resulted in puzzling and often contradictory conclusions regarding the nanoparticle structure: crystalline vs non-crystalline, icosahedral vs cuboctahedral or even unspecific shapes. Doye and Wales [16] described their resulting Au55

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

• -adsorbed W(CO)6 molecules have shown contaminations by C and O due to incomplete ligand desorption yielding tungsten oxide and an enhanced degree of tungsten oxidation from the presence of co-adsorbed water. These contaminations are then incorporated into the carbonaceous matrix. Recently, we note ab

• initio molecular dynamics simulations of focused electron beam induced deposition (FEBID) precursor molecules adsorbed on fully and partially hydroxylated SiO2 surfaces [24]. Electron-induced reactions in FEBID processes are initiated by low-energy secondary electrons rather than the high-energy primary

Adsorbate-driven cooling of carbene-based molecular junctions

• Giuseppe Foti and
• Héctor Vázquez

Beilstein J. Nanotechnol. 2017, 8, 2060–2068, doi:10.3762/bjnano.8.206

• notation for the parameter J. This value of J falls in the range of previous ab initio calculations [37][40] and ensures at the same time a relatively low effective temperature [40] of the junction even at high bias (1.2 V). A stronger damping parameter would dominate over the electronic contributions

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

• DFT as implemented in the Vienna ab initio simulation package (VASP) [37]. The exchange–correlation interactions are treated using the generalized gradient approximation (GGA) within the Perdew–Burke–Ernzerhof (PBE) formulation [38]. The plane waves are expanded with an energy cut of 400 eV. Since the

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

• functional of Perdew, Burke and Ernzerhof (PBE) and the projector augmented wave (PAW) method Vienna ab initio simulation package (VASP) code [16]. The energy cutoff of the plane-wave basis set was 465 eV, and the k-point mesh was (4×4×1) for both cases. All atoms were relaxed until the average force was

Spin-dependent transport and functional design in organic ferromagnetic devices

• Guichao Hu,
• Shijie Xie,
• Chuankui Wang and
• Carsten Timm

Beilstein J. Nanotechnol. 2017, 8, 1919–1931, doi:10.3762/bjnano.8.192

• ]. The above proposed prototype of a molecular spin diode has been supported by ab initio calculations. Zhu et al. [63] have studied a biradical (5-bromo-2,4-dimethoxy-1,3-phenylene)bis(N-tert-butylnitroxide) molecule connected to two gold electrodes. The molecule is magnetic and spatially asymmetric

• atoms, which will modify the spin states of both the molecules and the metal atoms close to the interface. Ab initio tools will be useful in determining the details. In spite of this, we hope that the works discussed in this contribution deepen our understanding of the electron transport through OFs

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

• around 400 K for 5 min. Density functional theory calculations were performed within the Perdew–Burke–Ernzerhof (PBE) [48] generalized gradient approximation (GGA) using projector-augmented-wave potentials, as implemented in the VASP (Vienna ab initio simulation package) [49][50]. The plane wave energy

α-Silicene as oxidation-resistant ultra-thin coating material

• Ali Kandemir,
• Fadil Iyikanat,
• Cihan Bacaksiz and
• Hasan Sahin

Beilstein J. Nanotechnol. 2017, 8, 1808–1814, doi:10.3762/bjnano.8.182

• silicene on top of Ag(111). First principles calculations were performed using the Vienna ab initio simulation package (VASP) [22][23], which is based on density functional theory. The projector-augmented wave (PAW) [24][25] formalism was used in the calculations. For the exchange–correlation energy, the

Adsorption and diffusion characteristics of lithium on hydrogenated α- and β-silicene

• Fadil Iyikanat,
• Ali Kandemir,
• Cihan Bacaksiz and
• Hasan Sahin

Beilstein J. Nanotechnol. 2017, 8, 1742–1748, doi:10.3762/bjnano.8.175

• , silicene exhibits a low-buckled structure. Although bulk silicon does not have a layered structure, syntheses of a 2D form of silicon via epitaxial growth on several metal substrates such as Ag(111) [5][20], Ir(111) [21], and ZrB2(0001) [22] were achieved. By performing ab initio calculations, Liu et al

• hydrogenated forms of α- and β-silicene phases on a Ag(111) surface using ab initio calculations within density functional theory. The paper is organized as follows: Computational methodology, hydrogenated structures of the silicene phases on Ag(111) surface, and the diffusion and adsorption characteristics of

• implemented in the “Vienna ab initio Simulation Package” (VASP) [47][48]. The exchange–correlation energy was described by the generalized gradient approximation (GGA) using the Perdew–Burke–Ernzerhof (PBE) functional [49]. A plane-wave basis set with kinetic energy cutoff of 500 eV was used for all the

A nanocomplex of C₆₀ fullerene with cisplatin: design, characterization and toxicity

• Svitlana Prylutska,
• Svitlana Politenkova,
• Kateryna Afanasieva,
• Volodymyr Korolovych,
• Kateryna Bogutska,
• Andriy Sivolob,
• Larysa Skivka,
• Maxim Evstigneev,
• Viktor Kostjukov,
• Yuriy Prylutskyy and
• Uwe Ritter

Beilstein J. Nanotechnol. 2017, 8, 1494–1501, doi:10.3762/bjnano.8.149

• complexation were investigated by calculating the energy-minimized spatial structure of their complex, shown in Figure 3. The initial location coordinates of Cis above the C60 fullerene surface were taken from the ab initio structure [39]. Then we performed the molecular dynamics simulation of this nanocomplex