Fracture behaviors of pre-cracked monolayer molybdenum disulfide: A molecular dynamics study

• Qi-lin Xiong,
• Zhen-huan Li and
• Xiao-geng Tian

Beilstein J. Nanotechnol. 2016, 7, 1411–1420, doi:10.3762/bjnano.7.132

• the defect-free MoS2 sheets have been investigated by many researchers using different methods. Cooper et al. calculated the nonlinear elastic response of two-dimensional MoS2 with first-principles density functional theory (DFT) method [8]. Castellanos-Gomez et al. [9] performed bending test

• of monolayer MoS2 is 270 ± 100 GPa and breaking occurs at an effective strain between 6 and 11% with the average breaking strength of 23 GPa. Additionally, compared with the first-principles DFT and experimental approaches, MDS method has advantages in the computational cost and catching details [11

Preparation of alginate–chitosan–cyclodextrin micro- and nanoparticles loaded with anti-tuberculosis compounds

• Albert Ivancic,
• Fliur Macaev,
• Fatma Aksakal,
• Veaceslav Boldescu,
• Serghei Pogrebnoi and
• Gheorghe Duca

Beilstein J. Nanotechnol. 2016, 7, 1208–1218, doi:10.3762/bjnano.7.112

• density distribution. It has been detected that alginate–chitosan–cyclodextrin microparticulate systems loaded with INH and ISN are as effective as pure INH applied in higher dosages. Keywords: chitosan; β-cyclodextrin; density functional theory (DFT); isoconazole; isoniazid; molecular docking

• candidates for the development of novel antitubercular agents [28]. In this study, docking of isoconazole into the active site of InhA was carried out to predict the binding affinity and non-covalent interactions between them. Density functional theory (DFT) based calculations were also performed for the

• DFT at the B3LYP/6-31G (d,p) level of theory. The 3D structure of isoconazole and the InhA binding site was taken from the docking calculations. The electron density distribution on the frontier orbitals formed by the active-site residues of InhA with isoconazole is shown in Figure 13. As seen in

Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy

• Michael Klocke and
• Dietrich E. Wolf

Beilstein J. Nanotechnol. 2016, 7, 708–720, doi:10.3762/bjnano.7.63

• these models use ab initio molecular dynamics or DFT methods [2][18][19], which represent the material properties most reliably. Their computational demand is very high, though, so that the force between tip and sample surface is usually calculated for a quasistatic tip. Molecular dynamics (MD

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

• thermopower) at zero temperature. Furthermore, examples are presented that demonstrate that treating parts of electrodes adjacent to the embedded molecule and the remaining semi-infinite electrodes at different levels of theory (which is exactly what most NEGF-DFT approaches do) is a procedure that yields

• particularly true in (chemisorption) cases where the anchoring groups form covalent bonds to the electrodes. Within current approaches to molecular charge transport, mostly based on nonequilibrium Keldysh Green’s functions (NEGF) combined with density functional theory (DFT), the molecular device is

• computationally much more expensive approaches beyond NEGF-DFT treatments), as computation times can be radically reduced; see section “WBL-based schemes and realistic calculations” for more details. The restriction expressed by Equation 26 is imposed by the difference of the Fermi distributions, which are step

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

Current-induced runaway vibrations in dehydrogenated graphene nanoribbons

• Rasmus Bjerregaard Christensen,
• Jing-Tao Lü,
• Per Hedegård and
• Mads Brandbyge

Beilstein J. Nanotechnol. 2016, 7, 68–74, doi:10.3762/bjnano.7.8

• how armchair nanoribbons can serve as a possible testbed for probing the current-induced forces. Keywords: current-induced forces; density functional theory (NEGF-DFT); graphene; molecular electronics; Introduction The electronic and transport properties of graphene has been the focus of intense

• Calculation We have calculated the electronic and phononic structure of the graphene nanoribbon from density function theory (DFT) using the SIESTA/TranSIESTA codes [25][26]. The generalized gradient approximation is used for the exchange–correlation functional, and a single-ζ polarized basis set is used for

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

• central gold atom. On the Au20 cluster, only the 10 gold binding sites on the top layer were studied (labeled a–j in Figure 1c). Density functional theory (DFT) methodology. Calculations were performed using the generalized gradient approximation-based Perdew–Burke–Ernzerhof (PBE) functional [71] with and

• on Au as emphasized in the previous section, it was deemed necessary to incorporate dispersive corrections in the DFT formalism we employed. However, uncorrected DFT also includes some dispersion. To understand the actual impact of the correction on the observed adsorption behavior, a series of

Effects of electronic coupling and electrostatic potential on charge transport in carbon-based molecular electronic junctions

• Richard L. McCreery

Beilstein J. Nanotechnol. 2016, 7, 32–46, doi:10.3762/bjnano.7.4

• “compression” of tunneling barriers predicted to range over 2.4 eV based on the free molecule energy levels to an observed range of 1.3 ± 0.2 eV in carbon-based MJs [31][34]. The current report describes the application of density functional theory (DFT) to carbon-based MJs, in order to investigate which

• experimental results where possible. Experimental Common DFT procedures were used, in part to maximize availability to potential users. Gaussian09 version 9.5 (revision D.01 Windows 64 bit) and Gaussview 5.0.9 software packages were used for all calculations and visualization of molecular structures and

• of Gaussian09 for Windows. Orbital visualization with Gaussview used the default isovalue of 0.02, which is commonly used to represent the majority of the electron density. Predictions of charge transfer within model molecules used the Mulliken charges calculated during the DFT analysis. There is

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

• large-area OPE3 junctions [29] and theoretical predictions [30][31]. We would like to stress that, although we attributed each peak to a single vibrational mode, in the experiments, the peaks may originate from multiple modes that are located closely together, as can be seen in the DFT spectrum. The

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

Negative differential electrical resistance of a rotational organic nanomotor

• Hatef Sadeghi,
• Sara Sangtarash,
• Qusiy Al-Galiby,
• Rachel Sparks,
• Steven Bailey and
• Colin J. Lambert

Beilstein J. Nanotechnol. 2015, 6, 2332–2337, doi:10.3762/bjnano.6.240

• molecule. We use the SIESTA [42] implementation of the density functional theory (DFT) with a van der Waals density functional [43][44] and extended and corrected double-zeta-polarised basis sets of the pseudoatomic orbitals. The geometries were optimised by relaxing the atomic forces to less than 20 meV/Å

• molecule against the rotation angle of the rotor with respect to the backbone. The DFT-calculated energy profile yields an energy barrier to rotation of about 800 meV. Figure 2 shows the energy landscape as a function of rotation angle for four magnitudes of electric field between 1.0 and 3.5 V/nm. Figure

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

• splitting of the sigma resonances measured along the two in-plane molecular axes. Keywords: aluminum; density functional theory (DFT); near-edge X-ray absorption fine structure (NEXAFS); pentacene; X-ray photoelectron spectroscopy (XPS); Introduction Pentacene has been studied extensively as it is a

• experimental investigations, while the previous ab initio theoretical studies [13][14] on this system were missing long-range van der Waals (vdW) corrections. Simeoni and Picozzi reported a numerical investigation of pentacene on Al(001) by density functional theory (DFT) with the local density approximation

• evaluate by DFT the screening charges of the adsorbed system and relate them to the deformation of pentacene. Comparison of the results with those obtained for the undistorted non-physical adsorption at top (T) site allows for a better understanding of the system properties. The contributions to XPS and

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

Selective porous gates made from colloidal silica nanoparticles

• Roberto Nisticò,
• Paola Avetta,
• Paola Calza,
• Debora Fabbri,
• Giuliana Magnacca and
• Dominique Scalarone

Beilstein J. Nanotechnol. 2015, 6, 2105–2112, doi:10.3762/bjnano.6.215

• materials (see inset in Figure 3A). The N2 gas-volumetric isotherm shown in Figure 3A is of the IV type, with a small hysteresis loop of H2 type (from IUPAC classification) in the relative pressure range 0.9–1, next to the condensation limit. The BET surface area is of ca. 260 m2 g−1 and the DFT pore size

• for secondary electrons collection and EDS probe for elemental analyses. N2 adsorption-desorption experiments were carried out by means of ASAP 2020 instrument (Micromeritics) in order to determine specific surface area (BET model) [44] and porosity (DFT method) [27][45] of samples. The density

• functional theory (DFT) model for slit pores with low regularization was applied on the adsorption branch of the isotherm in order to examine simultaneously both micro- and mesoporosity of samples. The analyses were performed on powdery samples (ca. 100 mg) outgassed for several hours at 300 °C in vacuo

Controlled switching of single-molecule junctions by mechanical motion of a phenyl ring

• Yuya Kitaguchi,
• Satoru Habuka,
• Hiroshi Okuyama,
• Shinichiro Hatta,
• Tetsuya Aruga,
• Thomas Frederiksen,
• Magnus Paulsson and
• Hiromu Ueba

Beilstein J. Nanotechnol. 2015, 6, 2088–2095, doi:10.3762/bjnano.6.213

• and can successfully lift up the molecules. The computational approach was detailed in [12]. Briefly, we used Kohn–Sham density functional theory (DFT) implemented in VASP [15][16] to obtain the atomic structure and total energy using the optPBE-vdW [17] exchange-correlation functional. Electron

• transport was computed with the DFT-based codes TranSIESTA [18][19] and Inelastica [20] using GGA-PBE [21] for the junctions connected to semi-infinite electrodes. The voltage-induced atomic forces were computed as the difference in the Hellman–Feynman force on each atom between the finite sample voltage

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

Metal hydrides: an innovative and challenging conversion reaction anode for lithium-ion batteries

• Luc Aymard,
• Yassine Oumellal and
• Jean-Pierre Bonnet

Beilstein J. Nanotechnol. 2015, 6, 1821–1839, doi:10.3762/bjnano.6.186

• search for the existence of new stable hydrides in the Mg–Li–H system was also addressed by several groups through density functional theory approach (DFT) [74][75]. Ternary hydrides in the system Li–Mg–H, such as Li2MgH4 and LiMgH3, are insulators dominated by ionic bonds. Their preparation from Li, Mg

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

• density-functional theory (DFT) approaches. In addition, using DFT-based molecular dynamics, the manipulation of nanostructures by SPM tools and the changes made to the system by the characterization tools, e.g., the production of defects under electron irradiation and their evolution over time, can be

• 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

Simple and efficient way of speeding up transmission calculations with k-point sampling

• Jesper Toft Falkenberg and
• Mads Brandbyge

Beilstein J. Nanotechnol. 2015, 6, 1603–1608, doi:10.3762/bjnano.6.164

• -processing; shortest-path; Introduction Calculations of electronic conductance based on first principle methods such as density functional theory (DFT) provide a valuable tool in order to gain insights into electronic transport in nano-conductors and comparison to experiments without employing fitting

• parameters. This is for example the case in the field of single-molecular devices [1]. Popular methods are based on DFT in combination with the non-equilibrium Green’s function approach (DFT-NEGF), see, e.g., [2][3][4], or scattering wave-function approaches [5]. The electrodes in such calculations are

• scheme and conclude in section Conclusion. Results and Discussion Description of the method The use of computationally “expensive” first principles DFT-NEGF calculations for determining the transmission through nano-structured systems is limited by the amount of time one can afford to spend on the k-grid

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

• of such conductance-time breaking traces. Theoretical calculations. Electronic ground state properties are calculated using density functional theory (DFT) as implemented in the ADF package [38][39], using the GGA-PBE functional [40], and the triple-ζ plus polarization (TZP) basis set. The zeroth

• of the two outer gold layers. Every ten steps (40 pm) we calculate the transmission through the molecular junction using non-equilibrium Green’s function (NEGF) formalism by connecting the outer gold layer to wide-band limit electrodes. To account for well-known problems in the DFT eigenvalues we

• include DFT + Σ corrections [41]. Results and Discussion Figure 3a shows examples of conductance-distance breaking traces recorded in presence of molecules 1–4 and plotted on a semi-logarithmic scale for the conductance. The traces show step-like features for conductance values above 1G0, where the

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

Electron and heat transport in porphyrin-based single-molecule transistors with electro-burnt graphene electrodes

• Hatef Sadeghi,
• Sara Sangtarash and
• Colin J. Lambert

Beilstein J. Nanotechnol. 2015, 6, 1413–1420, doi:10.3762/bjnano.6.146

• interactions. The central porphyrin is also connected to two side groups, which stabilize the molecule within the junction. We first use density functional theory (DFT) to study the electronic structure of the PM. To characterize the gas phase molecule, the isolated PM shown in Figure 1a is relaxed to reach

• the ground state energy (see Computational Methods). We carried out a spin-polarized calculation since the d orbitals of the Zn atom could be filled to different degrees. It is well-known that Kohn–Sham DFT eigenvalues usually underestimate the HOMO–LUMO gap and DFT typically does not predict their

• yields Eg = 3.84 eV. The Kohn–Sham DFT eigenvalues predict and using the generalised gradient approximation/Perdew–Burke–Ernzerhof exchange-correlation functional (GGA/PBE), which results in a Kohn–Sham DFT gap of for the gas phase molecule. Figure 2 shows the iso-surfaces of the HOMO−1, HOMO, LUMO and