Multiscale modelling of biomolecular corona formation on metallic surfaces

• Parinaz Mosaddeghi Amini,
• Ian Rouse,
• Julia Subbotina and
• Vladimir Lobaskin

Beilstein J. Nanotechnol. 2024, 15, 215–229, doi:10.3762/bjnano.15.21

• orientations of each protein treated as different potential adsorbates to allow for a more physically realistic model of corona formation for anisotropic proteins. In brief, a standard kinetic Monte Carlo routine is used to advance the simulation from one event, collision of an incoming adsorbate with the NP

• place otherwise. We parameterize this model using adsorption and desorption rate constants extracted from UnitedAtom results as described previously [16][45]. In brief, each potential adsorbate (e.g., a small molecule or a particular orientation of a protein) is projected onto the surface of the NP and

• a convex hull procedure used to estimate the area of the NP occupied by that adsorbate, Ai. The adsorbate is then assigned an effective radius Ri such that a sphere projected onto the NP would produce the same radius [16]. The per-site adsorption rates are calculated using kinetic theory for the

Two-dimensional molecular networks at the solid/liquid interface and the role of alkyl chains in their building blocks

• Suyi Liu,
• Yasuo Norikane and
• Yoshihiro Kikkawa

Beilstein J. Nanotechnol. 2023, 14, 872–892, doi:10.3762/bjnano.14.72

• alkyl chains contribute to the adsorption onto HOPG, in some cases, the number of adsorbed alkyl chains in 2D molecular networks is small compared to the number of alkyl chains originally present in the adsorbate molecule. This phenomenon has been explained by the dangling of alkyl chains toward the

The role of sulfonate groups and hydrogen bonding in the proton conductivity of two coordination networks

• Ali Javed,
• Felix Steinke,
• Stephan Wöhlbrandt,
• Hana Bunzen,
• Norbert Stock and
• Michael Tiemann

Beilstein J. Nanotechnol. 2022, 13, 437–443, doi:10.3762/bjnano.13.36

• maximum in the region from 103 to 104 Hz remains. The phase angle for the Pb-MOF sample shows only one maximum (at ca. 102 Hz) both before and after activation. We conclude that the second conductance mode in the non-activated Mg-CP material may be caused by interparticle water adsorbate layers that are

• successfully and irreversibly removed by activation. These findings are quite helpful, as they allow us to conversely conclude that the remaining mode of proton conductance is probably not caused by such adsorbate layers, but more likely occurs within the crystalline material, as will be elaborated in more

• with our above assumption that this additional conduction occurs within interparticle water adsorbate layers; these liquid-like layers may facilitate molecular diffusion to some extent. To explain the differences in proton conductivity between the (activated) Mg-CP and Pb-MOF materials, the respective

Low-energy electron interaction and focused electron beam-induced deposition of molybdenum hexacarbonyl (Mo(CO)₆)

• Po-Yuan Shih,
• Maicol Cipriani,
• Christian Felix Hermanns,
• Jens Oster,
• Klaus Edinger,
• Armin Gölzhäuser and
• Oddur Ingólfsson

Beilstein J. Nanotechnol. 2022, 13, 182–191, doi:10.3762/bjnano.13.13

• rapidly with increased electron dose and was already insignificant above 1 × 1017 e−/cm2. An XPS analysis of the remaining deposit revealed an average loss of two CO groups from the W(CO)6 adsorbate at about 7 × 1016 e−/cm2, but above that dose the dominating pathway becomes electron-induced CO

A comprehensive review on electrospun nanohybrid membranes for wastewater treatment

• Senuri Kumarage,
• Imalka Munaweera and
• Nilwala Kottegoda

Beilstein J. Nanotechnol. 2022, 13, 137–159, doi:10.3762/bjnano.13.10

• . Adsorption membranes decontaminate wastewater by adsorbing the impurities via chemisorption or physisorption. Polymeric membranes have functional groups that can interact with the solutes. In chemisorption, an irreversible chemical bond is formed between the adsorbate and the adsorbent, whereas in

• physisorption, only a reversible physical bond due to electrostatic interactions or intermolecular interactions forms between adsorbate and the adsorbent. An ideal adsorption membrane should exhibit both high adsorption capacity and a high adsorption rate. ENH membranes have been widely used as adsorption

Two dynamic modes to streamline challenging atomic force microscopy measurements

• Alexei G. Temiryazev,
• Andrey V. Krayev and
• Marina P. Temiryazeva

Beilstein J. Nanotechnol. 2021, 12, 1226–1236, doi:10.3762/bjnano.12.90

• [36], the lamellar structure was observed even when it was covered with a disordered adsorbate layer. The precise choice of the scanning parameters makes it possible to detect the presence of a lamellar structure with a period of 4–5 nm even with relatively blunt probes, for which a frequency curve

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF₃)₄

• Alexey Prosvetov,
• Alexey V. Verkhovtsev,
• Gennady Sushko and
• Andrey V. Solov’yov

Beilstein J. Nanotechnol. 2021, 12, 1151–1172, doi:10.3762/bjnano.12.86

• , morphology, size, and metal content of the deposited Pt-containing material are quantitatively analyzed as functions of electron fluence and adsorbate concentration. Computational Methodology Computer simulations of the FEBID process of Pt(PF3)4 have been performed by means of the MBN Explorer software

Molecular assemblies on surfaces: towards physical and electronic decoupling of organic molecules

• Sabine Maier and
• Meike Stöhr

Beilstein J. Nanotechnol. 2021, 12, 950–956, doi:10.3762/bjnano.12.71

• ][30][31][32]. Additional concepts to weaken adsorbate–surface interactions involve the post-deposition intercalation of atomic species such as iodine [33]. For semiconductors, for example, bare silicon or germanium, electronic decoupling of molecules can be achieved by either the growth of ultrathin

Modification of a SERS-active Ag surface to promote adsorption of charged analytes: effect of Cu²⁺ ions

• Bahdan V. Ranishenka,
• Andrei Yu. Panarin,
• Irina A. Chelnokova,
• Sergei N. Terekhov,
• Peter Mojzes and
• Vadim V. Shmanai

Beilstein J. Nanotechnol. 2021, 12, 902–912, doi:10.3762/bjnano.12.67

• introduces new states in the electronic structure of the metal–adsorbate complex leading to an increase in the Raman scattering cross section of the analyte [17]. Consequently, the CE mechanism should be accompanied by a change of spectral properties of the analyte, which was not observed in this study. Thus

Electromigration-induced formation of percolating adsorbate islands during condensation from the gaseous phase: a computational study

• Alina V. Dvornichenko,
• Vasyl O. Kharchenko and
• Dmitrii O. Kharchenko

Beilstein J. Nanotechnol. 2021, 12, 694–703, doi:10.3762/bjnano.12.55

• computational study of a change in the morphology of a growing thin film during condensation caused by electromigration effects. It will be shown, that separated circular adsorbate islands, realized in an isotropic system, become elongated in the direction of the applied electrical field. We discuss the

• dependence of the critical value of the strength of the applied electrical field, responsible for the formation of percolating adsorbate islands, on main control parameters. This study provides insight into details of electromigration effects during the self-organization of adatoms into percolating adsorbate

• islands during condensation from the gaseous phase. We will show that the elongated morphology of adsorbate islands remains stable if the electric field is turned off. Keywords: adsorptive systems; electromigration; numerical simulations; pattern formation; thin films; Introduction The processes of

Determining amplitude and tilt of a lateral force microscopy sensor

• Oliver Gretz,
• Alfred J. Weymouth,
• Thomas Holzmann,
• Korbinian Pürckhauer and
• Franz J. Giessibl

Beilstein J. Nanotechnol. 2021, 12, 517–524, doi:10.3762/bjnano.12.42

• experimental setup is to study an isolated surface feature, for instance, a defect or an adsorbate, on a flat terrace. In case of “normal” AFM, where the tip oscillates perpendicular to the surface, long-range forces including electrostatic and van der Waals forces contribute to the measured Δf signal, which

• molecular adsorbate [11][12]. Moreover, other methods, including the use of a long tip on a qPlus sensor that oscillates laterally at a higher flexural mode are also possible [13]. In LFM or normal AFM, the recorded frequency shift Δf is related to the force gradient kts in the direction of the tip

• = 100 meV, σ = 500 pm and λ = 50 pm. We first calculated the z-dependence of ⟨kts⟩ for a tip with no tilt oscillating vertically above the center of the adsorbate. For θ, as defined in Figure 1a, being 90°, the calculated values of ⟨kts⟩ are shown in Figure 2a (red dashed curve). We also calculated ⟨kts

Interface interaction of transition metal phthalocyanines with strontium titanate (100)

• Reimer Karstens,
• Thomas Chassé and
• Heiko Peisert

Beilstein J. Nanotechnol. 2021, 12, 485–496, doi:10.3762/bjnano.12.39

• be driven by the ionization potential difference between substrate and adsorbate. In addition, fluorination may affect significantly the adsorption geometry on surfaces as well as the single-crystal structure and arrangement in thin films [34][35][36][37]. Furthermore, local chemical interactions

• might become possible between particular atoms of substrate and adsorbate. For example, for many CoPc and CoPcF16 interfaces to noble metals, the interfacial interaction is governed by a local interaction between the Co 3dz2 orbital and states of the metal substrate [38][39][40]. Thus, the selected

• resublimed before usage. The materials were evaporated from temperature-controlled crucibles. The nominal layer thickness was estimated from substrate- and adsorbate-related XPS intensity ratios using photoemission cross sections from Yeh and Lindau [41]. A nominal monolayer of lying molecules corresponds to

The influence of an interfacial hBN layer on the fluorescence of an organic molecule

• Christine Brülke,
• Oliver Bauer and
• Moritz M. Sokolowski

Beilstein J. Nanotechnol. 2020, 11, 1663–1684, doi:10.3762/bjnano.11.149

Detecting stable adsorbates of (1S)-camphor on Cu(111) with Bayesian optimization

• Jari Järvi,
• Patrick Rinke and
• Milica Todorović

Beilstein J. Nanotechnol. 2020, 11, 1577–1589, doi:10.3762/bjnano.11.140

• Bayesian Optimization Structure Search (BOSS) method as an efficient solution for identifying the structure of non-planar adsorbates. We apply BOSS with density-functional theory simulations to detect the stable adsorbate structures of (1S)-camphor on the Cu(111) surface. We identify the optimal structure

• been applied in detecting molecular conformers [25] and adsorbate structures [26][27], in identifying stable molecular compounds [28], and in discovering materials with low thermal hysteresis [29] or thermal conductivity [30]. Typically, previous studies have employed customized material-specific

• detect the stable adsorbate structures of camphor on Cu(111). With BOSS, we build a surrogate model of the PES of adsorption and data-mine this PES to identify the stable structures in its minima. We converge the model for a reliable detection of all the PES minima, not only the global energy minimum. We

Controlling the electronic and physical coupling on dielectric thin films

• Philipp Hurdax,
• Michael Hollerer,
• Larissa Egger,
• Georg Koller,
• Xiaosheng Yang,
• Anja Haags,
• Serguei Soubatch,
• Frank Stefan Tautz,
• Mathias Richter,
• Alexander Gottwald,
• Peter Puschnig,
• Martin Sterrer and
• Michael G. Ramsey

Beilstein J. Nanotechnol. 2020, 11, 1492–1503, doi:10.3762/bjnano.11.132

• of such decoupling layers may effectively change the electron donating properties of the substrate, for example, by lowering its work function and thus enhancing the charging of the molecular adsorbate layer through electron tunneling. Here, an experimental study of the charging of para-sexiphenyl

• layer is not a sufficient condition for decoupling. Although it reduces wave function overlap with the substrate, it can in fact promote charge transfer via tunneling. The determining factor is the energy level alignment of the frontier orbitals of the adsorbate relative to the Fermi level (EF) of the

• that systematic thickness-dependent studies of charge transfer to 6P could not be performed. On dielectric interlayers, a simple measurement of the work function before and after the adsorbate overlayer growth is perhaps the most telling result with regard to electronic and physical coupling. If there

Impact of fluorination on interface energetics and growth of pentacene on Ag(111)

• Qi Wang,
• Meng-Ting Chen,
• Antoni Franco-Cañellas,
• Bin Shen,
• Thomas Geiger,
• Holger F. Bettinger,
• Frank Schreiber,
• Ingo Salzmann,
• Alexander Gerlach and
• Steffen Duhm

Beilstein J. Nanotechnol. 2020, 11, 1361–1370, doi:10.3762/bjnano.11.120

• adsorbate [9][10][11]. However, at such interfaces, vertical adsorption heights [12][13], interface dipoles (vacuum level shifts) [9][14] and consequently the energy level alignment [15][16][17] are affected by fluorination. Furthermore, fluorination can change the molecular multilayer growth [18][19][20

• the photon energy, which allowed to determine the coherent position (PH) and the coherent fraction (fH) of the adsorbate atoms [66][69]. The former gave the adsorption distance in terms of the lattice spacing of the silver substrate: dH = d0(n + PH) (typical precision < 0.05 Å), with n being an

• integer. The coherent fraction 0 ≤ fH ≤ 1 describes the degree of vertical order of the adsorbate atoms, with fH = 0 for a completely disordered system and fH = 1 for all probed adsorbate atoms having the same adsorption distance. XSW measurements were performed for two (sub)monolayer coverages of F4PEN

Hybridization vs decoupling: influence of an h-BN interlayer on the physical properties of a lander-type molecule on Ni(111)

• Maximilian Schaal,
• Takumi Aihara,
• Marco Gruenewald,
• Felix Otto,
• Jari Domke,
• Roman Forker,
• Hiroyuki Yoshida and
• Torsten Fritz

Beilstein J. Nanotechnol. 2020, 11, 1168–1177, doi:10.3762/bjnano.11.101

• corresponding epitaxy matrix as well as the lattice parameters are summarized in Table 1. We used the projection method proposed by Forker et al. to identify possible coincidences of the adsorbate and the substrate lattice [35]. We find more than one possible coincidence within the error margin of the epitaxy

• ordered DBP on h-BN/Ni(111), suitable coincidences with the lowest substrate orders are the on-line coincidences (1, 2), (−1, −2), (−2, 1), and (2, −1). A comparison with reported lateral structures of DBP on Ag(111) [34] and Au(111) [33] shows very similar adsorbate lattice parameters except for the unit

• by the LT-STM measurement shown in Figure 3b. We superimposed the STM image by the contours of the two molecules in the unit cell as well as the adsorbate lattice as determined by LEED. A DBP molecule is characterized by four bright protrusions, which correspond to the phenyl substituents oriented

Scanning tunneling microscopy and spectroscopy of rubrene on clean and graphene-covered metal surfaces

• Karl Rothe,
• Alexander Mehler,
• Nicolas Néel and
• Jörg Kröger

Beilstein J. Nanotechnol. 2020, 11, 1157–1167, doi:10.3762/bjnano.11.100

• monatomically thin buffer layers (BLs) on metal surfaces, i.e., as intermediate films that efficiently reduce the hybridization of an adsorbate with the metallic substrate. The minimization of the adsorbate–substrate coupling is motivated by the desire to preserve genuine properties of the free atom or molecule

• resonances on surfaces are desirable because they increase the residence time of injected charge at the adsorbate, which is favorable for, e.g., energy conversion processes or the observation of vibronic progression [1]. Structural aspects of adsorption on the prominent two-dimensional materials graphene [2

• adjacent molecules. A finite adsorbate–substrate interaction is reflected by the presence of a molecular superstructure that matches the period of the Au(111) reconstruction. However, the HOMO resonance width has decreased by a factor of three compared to its width on Pt(111). Even vibronic progression due

Adsorption behavior of tin phthalocyanine onto the (110) face of rutile TiO₂

• Lukasz Bodek,
• Mads Engelund,
• Aleksandra Cebrat and
• Bartosz Such

Beilstein J. Nanotechnol. 2020, 11, 821–828, doi:10.3762/bjnano.11.67

• molecular adsorbate and the substrate, as was presented for CuTPP on rutile (110) [33]. The charge state of a CuTPP molecule depends on the particular localization of hydroxy groups under the molecule. For Sn-down Pc molecules, the relaxation brings the macrocycle closer to the surface, which increases long

Adsorptive removal of bulky dye molecules from water with mesoporous polyaniline-derived carbon

• Hyung Jun An,
• Jong Min Park,
• Nazmul Abedin Khan and
• Sung Hwa Jhung

Beilstein J. Nanotechnol. 2020, 11, 597–605, doi:10.3762/bjnano.11.47

• adsorption time and the type of adsorbate or dye. In order to determine the maximum adsorption capacity of KOH-900 and AC for AR1, adsorption isotherms were obtained from adsorption for 6 h with a wide range of AR1 concentrations. The adsorption isotherms and Langmuir plots are illustrated in Figure 6a and

• bonding [57][58][59], were applied to interpret various adsorption events. In order to understand the plausible mechanism, especially in aqueous phase, adsorption over a wide range of pH conditions is very effective [60] since both the adsorbate and adsorbent can be changed in terms of charge or

An advanced structural characterization of templated meso-macroporous carbon monoliths by small- and wide-angle scattering techniques

• Felix M. Badaczewski,
• Marc O. Loeh,
• Torben Pfaff,
• Dirk Wallacher,
• Daniel Clemens and
• Bernd M. Smarsly

Beilstein J. Nanotechnol. 2020, 11, 310–322, doi:10.3762/bjnano.11.23

• adsorbates such as nitrogen, argon, krypton or carbon monoxide. We chose p-xylene as an adsorbate for vapour sorption to address the sorption at room temperature. To obtain a detailed view of the nanopore space, which exhibits micro-, meso- and macropores, but with an upper limit of ca. 100 nm, small-angle

Antimony deposition onto Au(111) and insertion of Mg

• Lingxing Zan,
• Da Xing,
• Abdelaziz Ali Abd-El-Latif and
• Helmut Baltruschat

Beilstein J. Nanotechnol. 2019, 10, 2541–2552, doi:10.3762/bjnano.10.245

• ]. Unfortunately, the resolution between the rows is not sufficient to estimate a second (incommensurate) lattice vector of the adsorbate. We therefore only show a model for the arrangement of the atoms in the direction of the rows in Figure 6 (vector ). Bulk deposition of Sb on Au(111) A freshly prepared Au(111

The role of Ag⁺, Ca²⁺, Pb²⁺ and Al³⁺ adions in the SERS turn-on effect of anionic analytes

• Stefania D. Iancu,
• Andrei Stefancu,
• Vlad Moisoiu,
• Loredana F. Leopold and
• Nicolae Leopold

Beilstein J. Nanotechnol. 2019, 10, 2338–2345, doi:10.3762/bjnano.10.224

• adsorption sites specific for the anionic analytes. The turn-on of the SERS effect is explained in the context of the chemical mechanism of SERS. The adions form SERS-active sites on the silver surface enabling a charge transfer between the adsorbate and the silver surface. High-intensity SERS spectra of

• adsorbate and the metal nanosurface, the coupling to the silver surface being mediated by adsorbed atoms (adatoms) such as Ag+, Cl−, I−, Br− [3][4][5][6]. In this context, several reports explain the SERS enhancement by the formation of stable surface complexes of atomic scale roughness. For example, a Ag

•  2B). Comparing the Raman spectrum of salicylic acid in aqueous solution (0.1 M) with the SERS spectrum reveals that several bands shift to lower wave numbers due to the interaction of the adsorbate with the silver surface (Supporting Information File 1, Figure S3B). For example, the C=C stretching

Pulsed laser synthesis of highly active Ag–Rh and Ag–Pt antenna–reactor-type plasmonic catalysts

• Kenneth A. Kane and
• Massimo F. Bertino

Beilstein J. Nanotechnol. 2019, 10, 1958–1963, doi:10.3762/bjnano.10.192

• return to ground-state potential energy with additional vibrational energy. The process does not require charge extraction from the metal. Rather, it leads to an electronic excitation in the adsorbate–metal complex, forming transient adsorbate ions. The adsorbate ions can survive on metal surfaces tens

• of femtoseconds before relaxation, which is sufficient for chemical transformation or additional vibrational energy to be transferred to the adsorbate, leading to reaction [14]. There are two mechanisms that can lead to the electronic excitation in the adsorbate–metal complex. The first is the

• unpopulated adsorbate states. The second mechanism is the direct transfer of energy, or the direct excitation of charge carriers from the metal to unpopulated adsorbate states within the metal–reactant complex [15]. Light energy, localized at the surface of a plasmonic NP, can be transferred to a neighboring

The impact of crystal size and temperature on the adsorption-induced flexibility of the Zr-based metal–organic framework DUT-98

• Simon Krause,
• Volodymyr Bon,
• Hongchu Du,
• Rafal E. Dunin-Borkowski,
• Ulrich Stoeck,
• Irena Senkovska and
• Stefan Kaskel

Beilstein J. Nanotechnol. 2019, 10, 1737–1744, doi:10.3762/bjnano.10.169

• , known to be a rather weakly interacting adsorbate, cannot initiate a structural contraction in downsized crystals of DUT-98. The contraction mechanism in DUT-98(1) was previously shown to depend on pore shrinkage along a reorganization of water molecules within the structure close to the Zr cluster [23