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

• 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

• model. Keywords: core-level spectroscopy; DFT; germanene; STM; Introduction The properties of two-dimensional (2D) materials are currently subjected to intense experimental and theoretical studies. The research is focused on many important properties predicted by theory for various conceivable 2D

• 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

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

• , and suppress the nanoribbon–substrate interaction. The proposed structural model reproduces well all the experimental findings. Keywords: density functional theory (DFT); scanning tunneling microscopy (STM); silicene; Si nanoribbons; Introduction The discovery of the exotic nature of graphene [1][2

• 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

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

• , Izmir, Turkey ICTP-ECAR Eurasian Center for Advanced Research, Izmir Institute of Technology, 35430, Izmir, Turkey 10.3762/bjnano.8.182 Abstract By performing density functional theory (DFT)-based calculations, the performance of α-silicene as oxidation-resistant coating on Ag(111) surface is

• ]. Kirkland et al. investigated the electrochemical response of graphene-coated metal surfaces and found that graphene causes reduction in the corrosion rate [8]. In addition, Topsakal et al. showed that graphene is a suitable coating material to protect surfaces from oxidation by performing DFT-based

Non-intuitive clustering of 9,10-phenanthrenequinone on Au(111)

• Ryan D. Brown,
• Rebecca C. Quardokus,
• Natalie A. Wasio,
• Jacob P. Petersen,
• Angela M. Silski,
• Steven A. Corcelli and
• S. Alex Kandel

Beilstein J. Nanotechnol. 2017, 8, 1801–1807, doi:10.3762/bjnano.8.181

• noted, and used a mechanically-cut Pt/Ir tip. All calculations were performed using the Q-Chem software package. Structures were optimized with density functional theory (DFT) utilizing the B3LYP functional [38][39]. The 6-311++G(3df,3pd) basis set was employed with a Lebedev quadrature containing 100

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

• Li are presented in the section “Results and Discussion”. Lastly, we conclude our results in section “Conclusion”. Results and Discussion Computational methodology The present calculations were performed using density functional theory (DFT) and the projector-augmented wave (PAW) method, as

• calculations. The van der Waals (vdW) correction to the GGA functional was included by using the DFT-D2 method of Grimme [50]. To properly simulate the structures, a 3×3-reconstructed hydrogenated silicene phase was placed on top of a 4×4 supercell of a two-layer Ag(111) surface. A 3×3×1 Γ-centered k-point

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

• SiNR nanojunctions. Since the dI/dV spectrum essentially reflects the electronic density of states (DOS), we interpret the peak by comparing the dI/dV spectrum with the DOS spectra calculated for freestanding SiNR. The DFT studies have demonstrated that the geometric and electronic structures of SiNR

• H atoms, the honeycomb structure is unstable and vulnerable to the structural reconstruction at the edges. The DOS spectrum depends on the reconstructed structure. In the DFT study of Cahangirov et al. [29], the edge undergoes a reconstruction in which two deformed 6-membered rings are alternatively

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

• with the graphene surface was studied using the DFT code AIMPRO [57][58][59] by fitting the charge density to plane waves with an energy cutoff of 300 Ha. Relativistic pseudopotentials generated by Hartwigsen, Goedecker and Hutter [60] were used. Correspondingly, 38, 44, and 28 independent Gaussian

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

• in the core-level region, and polarization-dependent studies have often been carried out to study the molecular orientation on substrates. In addition to our experiments we performed calculations within the density functional theory (DFT) framework. We used a recent version of the NRLMOL all-electron

• DFT code [51][52], which uses large Gaussian-orbital basis sets for the representation of the electronic wavefunctions [53]. Unless noted otherwise we used the PBE functional [54] within the general gradient approximation (GGA) was used for all calculations. We semi-empirically included dispersion

• correction according to the Grimme DFT-D3 method [55] in all of our calculations. KxMnPc: formation of stable phases with MnPc anions The formation of compounds with composition KxMnPc was achieved by evaporation of potassium from so-called K dispensers (SAES Getters, S.P.A, Italy) onto MnPc thin films under

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

• carboxylato bridges within the N3Ni(μ-SR)2(μ1,3-O2CR)NiN3 core, we utilized a breakdown approach in which the carboxylate group was virtually removed to obtain the hypothetical [Ni2(L)]2+ dication, which was subjected to broken symmetry DFT density functional theory calculations. The details of these

• 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

• the long-wavelength modes to density-functional results is included. Keywords: graphene; molybdenum disulfide; phonon; silicene; two-dimensional materials; Introduction Phonon spectra in two-dimensional (2D) nanomaterials have almost exclusively been computed using density-functional theory (DFT

• ]. 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

Two-dimensional silicon and carbon monochalcogenides with the structure of phosphorene

• Dario Rocca,
• Ali Abboud,
• Ganapathy Vaitheeswaran and
• Sébastien Lebègue

Beilstein J. Nanotechnol. 2017, 8, 1338–1344, doi:10.3762/bjnano.8.135

• of 1.0 eV was found for the HSE gap, which does not significantly differ from the PBE estimate. As shown in Table 1 the DFT values we found are in good agreement with the results in the literature [35][39]. As previously noted [39], the top of the valence band is slightly shifted from Γ and

Hierarchically structured nanoporous carbon tubes for high pressure carbon dioxide adsorption

• Julia Patzsch,
• Deepu J. Babu and
• Jörg J. Schneider

Beilstein J. Nanotechnol. 2017, 8, 1135–1144, doi:10.3762/bjnano.8.115

• linearized isotherm equation between P/P0 0.035 and 0.2 and the pore size was calculated by density functional theory (DFT) for slit pores. The scanning electron microscopy (SEM) micrographs were obtained using a Philips XL 30 FEG (20 kV) instrument equipped with an EDX (energy dispersive X-ray) detector

• isotherm of carbon tubes (4) (Figure 6a) resembles a type-IVa isotherm [45], however, with a high microporous content. These micropores are responsible for the observed steep increase in the adsorption at very low relative pressure (Figure 6b). The pore width distribution calculated by the DFT method

• (DFT, slit pore model) for carbon tubes (4) which are carbonized at 950 °C (black/triangles), 1300 °C (red/diamonds) and 1600 °C (blue/circles). TEM images of a SiC tube wall with interconnected, crystalline SiC particles (a) and the corresponding SAED pattern (b). Individual SiC crystallites are shown

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

• vacancies. This provides a pathway for the formation of fullerene-based nanostructures on Au at room temperature. Keywords: Au–C bonds; density functional theory (DFT); fullerenes; scanning tunneling microscopy (STM); sputtering; Introduction In single-molecule electronics, the active element in an

• atoms and molecules can be manipulated. In parallel, the use of atomistic simulations, mainly based on density functional theory (DFT), has allowed for a detailed understanding of the basic mechanisms that determine the electronic and nanoscale transport properties [1]. For spintronics, small organic

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

• , 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

• 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

The role of 2D/3D spin-polarization interactions in hybrid copper hydroxide acetate: new insights from first-principles molecular dynamics

• Ziyad Chaker,
• Guido Ori,
• Mauro Boero and
• Carlo Massobrio

Beilstein J. Nanotechnol. 2017, 8, 857–860, doi:10.3762/bjnano.8.86

• theory (DFT) have been useful to complement the missing structural information on the atomic positions obtained experimentally [5]. We also provided an exploratory insight into CuOHAc bonding and magnetic properties changes in response to an applied external pressure [6][7]. Recently, Banerjee et al. [8

• dynamics (FPMD) approach in the framework of Kohn–Sham density functional theory (DFT) with a generalized gradient approximation according to Becke [11] for the exchange energy and according to Lee, Yang and Parr [12] (BLYP) for the correlation functional. The valence electrons are treated explicitly

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

• matrix eigenvalues were found to be positive, so we are confident that these structures correspond to the minima on the DFT ground state potential energy surface. Conclusion In conclusion, it can be stated that sorption interactions between fullerenes and halogenated dibenzo-p-dioxin congeners – based on

• and fullerene structure was also examined. Calculations on the M06-2X DFT level were performed at this stage for a 2.5–5 Å distance between the PXDD molecule and C60 [52]. Supporting Information File 1 provides further details. A M06-2X DFT functional developed by Truhlar’s group is a hybrid DFT

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

• atom type inside molecules and the KCl surface using a genetic algorithm method. A detailed discussion of this potential-fitting method can be found in prior publications [25][43]. Briefly, a fitting dataset composed of 240 configurations was generated using density functional theory (DFT). These

• calculations were performed using the CP2K code [47], the PBE GGA density functional [48], the MOLOPT basis set [49], and semi-empirical long-range dispersion corrections [50]. Since vdW interactions are poorly described in DFT, we assessed the accuracy of the semi-empirical corrections against higher-accuracy

• was 1024 elements and they were evolved for 1000 generations. In order to avoid over-fitting of the potential, high-energy configurations obtained from ab initio DFT were included in the dataset. In each generation 5% of the population was randomly mutated in order to reduce artificial convergence

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

• also occurs with β-CD. The geometry of the γ-CD·aescin complex is characterised by the inclusion of the triterpene segment of aescin into the host cavity. Keywords: aescin; cyclodextrin inclusion; DFT; 1H NMR; ROESY; Introduction Aescin is the main component of the crystalline saponins obtained from

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

Nanoscale isoindigo-carriers: self-assembly and tunable properties

• Tatiana N. Pashirova,
• Andrei V. Bogdanov,
• Lenar I. Musin,
• Julia K. Voronina,
• Irek R. Nizameev,
• Marsil K. Kadirov,
• Vladimir F. Mironov,
• Lucia Ya. Zakharova,
• Shamil K. Latypov and
• Oleg G. Sinyashin

Beilstein J. Nanotechnol. 2017, 8, 313–324, doi:10.3762/bjnano.8.34

• 15N NMR spectra (conversion factor to NH3: −380.2 ppm). The quantum chemical calculations The quantum chemical calculations were performed using Gaussian 03 software package [83]. Full geometry optimizations were carried out within the framework of DFT (B3LYP) method using 6-31G(d) basis sets

Colorimetric gas detection by the varying thickness of a thin film of ultrasmall PTSA-coated TiO₂ nanoparticles on a Si substrate

• Urmas Joost,
• Andris Šutka,
• Meeri Visnapuu,
• Aile Tamm,
• Meeri Lembinen,
• Mikk Antsov,
• Kathriin Utt,
• Krisjanis Smits,
• Ergo Nõmmiste and
• Vambola Kisand

Beilstein J. Nanotechnol. 2017, 8, 229–236, doi:10.3762/bjnano.8.25

• -electron DFT code implemented in the projector augmented-wave (PAW) [16]. The ground-state energy was calculated with the geometry obtained from Gaussian 09 calculations using PBE functionals and a grid spacing of h = 0.16 Å. For C, O, S and N atoms core electrons were excited one by one to obtain the

• in the gas phase was first optimized with Gaussian 09 [22] using the density functional theory (DFT)-based exchange and correlation functional Perdew–Burke–Ernzerhof (PBE) [23][24], and cc-pvtz basis sets [25][26][27][28]. The optimized geometry was then used to calculate the XPS spectra. These were

Tunable plasmons in regular planar arrays of graphene nanoribbons with armchair and zigzag-shaped edges

• Cristian Vacacela Gomez,
• Michele Pisarra,
• Mario Gravina and
• Antonello Sindona

Beilstein J. Nanotechnol. 2017, 8, 172–182, doi:10.3762/bjnano.8.18

• , width and chirality of each GNR, or the in-plane distance between contiguous GNRs. Our study is carried out using time-dependent (TD) density functional theory (DFT), within the random phase approximation (RPA). The computations are performed at room temperature (T = 300 K), including both intrinsic and

• arrays'). Results and Discussion Theoretical framework Our TDDFT approach is divided into two steps. First, the (ground-state) electronic properties of the different GNRs (and graphene) are obtained by DFT. Second, the basic equation of linear-response theory in the RPA is employed, with a corrected

• electron–electron interaction, to calculate the dielectric properties, and hence the plasmon structure, of the systems. DFT method Density-functional calculations are performed using the plane-wave (PW) basis-set [32], i.e., the normalized space functions , which depend on the wave-vectors k of the first

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

• behaviour and a good quality of ohmic palladium–graphene contacts. Keeping in mind the strong sensitivity of graphene to analytes we propose the possibility to use the graphene/SiC Schottky diode as a sensing platform for the recognition of toxic heavy metals. Using density functional theory (DFT

• 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