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

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