Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking

• Kendra Ramirez-Acosta,
• Ivan A. Rosales-Fuerte,
• J. Eduardo Perez-Sanchez,
• Alfredo Nuñez-Rivera,
• Josue Juarez and
• Ruben D. Cadena-Nava

Beilstein J. Nanotechnol. 2022, 13, 699–711, doi:10.3762/bjnano.13.62

• included in region III are characterized by a high fraction of random-coil secondary structures with binding energies between −5.7 and −6.3 kcal/mol. Additionally, the final surface area (Af) of peptides docked to the RBD increased, indicated by positive values of ∆A = Af − A0, where Af and A0 are the

• of binding energy. However, this computational tool gives comparably low binding energies of peptide–protein docking due to the molecular size, high flexibility, and complexing conformation of the peptide ligand, in addition to the simplification of the analysis of ADV (the electrostatic and

• similar to previous reports in which short peptides were docked to RBD [14]. However, the binding energy reported in the present research contrasts with several studies that reported higher binding energies between the theoretical peptides and RBD [62][63], probably due to the software used in the

Nanoarchitectonics of the cathode to improve the reversibility of Li–O₂ batteries

• Hien Thi Thu Pham,
• Jonghyeok Yun,
• So Yeun Kim,
• Sang A Han,
• Jung Ho Kim,
• Jong-Won Lee and
• Min-Sik Park

Beilstein J. Nanotechnol. 2022, 13, 689–698, doi:10.3762/bjnano.13.61

• (Figure 4a), strong signals were observed at binding energies of 778.9 and 794 eV, corresponding to the Co 2p3/2 and Co 2p1/2 orbitals of metallic Co, respectively, regardless of the Zn/Co ratio. In contrast, the signal of Zn was only detected in the Zn 2p spectrum of the Zn4Co1–C/CNT composite (Figure 4b

Investigation of a memory effect in a Au/(Ti–Cu)Ox-gradient thin film/TiAlV structure

• Damian Wojcieszak,
• Jarosław Domaradzki,
• Michał Mazur,
• Tomasz Kotwica and
• Danuta Kaczmarek

Beilstein J. Nanotechnol. 2022, 13, 265–273, doi:10.3762/bjnano.13.21

• 284.8 eV. Ultraviolet photoelectron spectroscopy (UPS) was performed using a non-monochromatic He I line (21.22 eV) excitation source with a step size of 0.025 eV. A bias voltage of −5 V was applied to the thin film sample during UPS measurements to obtain a clear secondary electron cutoff. The binding

• energies of the spectra were referred to the Fermi level (EF) determined from a cleaned reference Au sample. Measurement results were analyzed with the aid of CasaXPS software. In the case of XPS and UPS measurements, the results were averaged over a certain surface area, that is, the beam diameter was

Impact of device design on the electronic and optoelectronic properties of integrated Ru-terpyridine complexes

• Max Mennicken,
• Sophia Katharina Peter,
• Corinna Kaulen,
• Ulrich Simon and
• Silvia Karthäuser

Beilstein J. Nanotechnol. 2022, 13, 219–229, doi:10.3762/bjnano.13.16

• , and Au 4f were recorded. Data analysis was conducted using CasaXPS (Casa Software, Ltd.) after subtraction of a Shirley background. The binding energies (BE) were calibrated to give the signal for metallic gold Au 4f7/2 at 84.0 eV. Scanning electron microscopy (SEM) was performed with a Hitachi SU8000

• dark current, ΔIL_D; inset: on/off ratio. Red bars indicate one standard deviation. (b) Half-life of current decline after the peak induced by switching the light source “on” or “off”. Binding energies (in eV) of C 1s, Ru 3d5/2, and O 1s core levels given for the consecutive wire growth steps shown in

Chemical vapor deposition of germanium-rich CrGe_x nanowires

• Vladislav Dřínek,
• Stanislav Tiagulskyi,
• Roman Yatskiv,
• Jan Grym,
• Radek Fajgar,
• Věra Jandová,
• Martin Koštejn and
• Jaroslav Kupčík

Beilstein J. Nanotechnol. 2021, 12, 1365–1371, doi:10.3762/bjnano.12.100

• multiplet peaks at higher binding energies associated with elemental Cr/germanide (CrGex) and multiplet splitting of the Cr(III) oxide species [13], respectively (Figure 4b). We were not able to separate elemental Cr and CrGex subpeaks as the XPS shift of a metal (chromium)/germanium in metal (chromium

Prediction of Co and Ru nanocluster morphology on 2D MoS₂ from interaction energies

• Cara-Lena Nies and
• Michael Nolan

Beilstein J. Nanotechnol. 2021, 12, 704–724, doi:10.3762/bjnano.12.56

• . The binding energies for the set of adsorption structures calculated using Equation 1 are shown in Table 1. Metal–substrate interaction energies calculated from Equation 2 are shown in Table 2, metal–metal interaction energies calculated from Equation 3 are shown in Table 3, and addition energies

• species are shown in Figure 1 and below in Figure 3, Figure 5, and Figure 7, while the geometries for Run species are shown below in Figure 2, Figure 4, Figure 6, and Figure 8. The energies shown in these figures are the binding energies computed using Equation 1. Structures are referred to and labelled

• (Figure 7G,H,K) is the most favourable geometry with a binding energy of −6.33 eV/atom, with a linear adsorption mode at site atop_Mo (Figure 7B) and a 3D tetrahedral configuration at site hollow (Figure 7L) showing binding energies of −6.10 and −6.05 eV, respectively. Generally, the 3D rectangle

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

• 100 (X-ray photoelectron diffraction) or 150 (monochromatized X-ray photoelectron spectroscopy) hemispherical analyzers (SPECS), and a four-grid LEED optics (SpectaLEED, Omicron, Germany). The PES binding energy scale is calibrated to reproduce the binding energies of Cu 2p3/2 (932.6 eV), Ag 3d5/2

• interface components were found. The small shift of the Ti 2p spectra in Figure 2a after deposition of CoPc to lower binding energies is also observed in the corresponding O 1s and Sr 3d spectra (Figure S2 and Figure S3, Supporting Information File 1) and might be assigned to an adsorbate-induced band

• spectra to 0.2–0.3 eV higher binding energies with respect to the 6.9 nm film in Figure 3. Many reasons, including charge transfer and a different screening of the photohole due to a different environment, may cause such shifts. The shift to higher binding energy at the substrate interface is rather

The role of gold atom concentration in the formation of Cu–Au nanoparticles from the gas phase

• Yuri Ya. Gafner,
• Svetlana L. Gafner,
• Darya A. Ryzkova and
• Andrey V. Nomoev

Beilstein J. Nanotechnol. 2021, 12, 72–81, doi:10.3762/bjnano.12.6

• displacement of Au atoms into the surface layer. Moreover, the rate of segregation increased with temperature, which was experimentally confirmed [24]. This effect is a direct consequence of the different binding energies of gold and copper atoms (i.e., with these nanoparticle sizes, the binding energy of

Free and partially encapsulated manganese ferrite nanoparticles in multiwall carbon nanotubes

• Saja Al-Khabouri,
• Salim Al-Harthi,
• Toru Maekawa,
• Mohamed E. Elzain,
• Ashraf Al-Hinai,
• Ahmed D. Al-Rawas,
• Abbsher M. Gismelseed,
• Ali A. Yousif and
• Myo Tay Zar Myint

Beilstein J. Nanotechnol. 2020, 11, 1891–1904, doi:10.3762/bjnano.11.170

• ], whereas the Fe2+ 2p3/2 peak is reported to be associated with a satellite peak at 6.0 eV above the main peak [24]. Multiple peaks at binding energies of 710.3 and 712.2 eV are reported for Fe3+ 2p3/2 components [23]. Therefore, the presence of only Fe3+ could be justified. The Mn 2p3/2 core level emission

• peak is localized at 641.2 eV, with components at 641.0, 642.4, and 644.6 eV. The observed binding energies are reported for the Mn2+ 2p3/2 peak [24] and multiplet constituents [23] (Figure 8d). Hence, it could be inferred that manganese is present in the Mn2+ state. Three photoemission peaks

Unravelling the interfacial interaction in mesoporous SiO₂@nickel phyllosilicate/TiO₂ core–shell nanostructures for photocatalytic activity

• Bridget K. Mutuma,
• Xiluva Mathebula,
• Isaac Nongwe,
• Bonakele P. Mtolo,
• Boitumelo J. Matsoso,
• Rudolph Erasmus,
• Zikhona Tetana and
• Neil J. Coville

Beilstein J. Nanotechnol. 2020, 11, 1834–1846, doi:10.3762/bjnano.11.165

• 2p3/2 binding energies for 1:1 phyllosilicates compared to that of 2:1 phyllosilicates [59][60]. Moreover, no peak originating from NiO (which has a lower binding energy at Ni 2p3/2 levels of less than 855 eV) was observed. This was confirmed by the appearance of the satellite splitting peaks with a

• separation between the Ni 2p3/2 primary line and the satellite of less than 6 eV, which is smaller than that of nickel oxides [60][61]. The data for the mSiO2@NiPS/TiO2 suggest a decrease in binding energies (Ni 2p1/2 at 872.6 eV and Ni 2p3/2 at 853 eV), possibly indicative of an interaction with TiO2 and

• ) [60][62][63][64]. This illustrates that the samples were comprised of silicate and composites of nickel phyllosilicate with SiO2. The lower binding energies of the Si 2p peak in mSiO2@NiPS/TiO2 indicate a possible interaction between the silicates and TiO2 [65]. The O 1s spectrum was deconvoluted into

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

• identification of the underlying orbitals very difficult. The UPS features of DBP on h-BN/Ni(111), on the other hand, are much sharper and shifted to higher binding energies. The reduction of the line width can be explained by an increase of the structural order, which was already discussed in the last section

• , as well as by a decrease in hybridization. Probable reasons for the shift of the molecular orbitals to higher binding energies are the work function change as well as the less efficient photo hole screening compared to DBP on bare Ni(111). The adsorption of DBP molecules on the bare Ni(111) surface

• the binding energies (BE) of the N 1s, C 1s and B 1s core levels for DBP on bare Ni(111) (approx. 1.0 MLE) as well as h-BN on Ni(111) and DBP on h-BN/Ni(111) (less ordered (approx. 1.0 MLE) and highly ordered (approx. 1.6 MLE)). The uncertainty of the numerical fitting procedure is given in

Excitonic and electronic transitions in Me–Sb₂Se₃ structures

• Nicolae N. Syrbu,
• Victor V. Zalamai,
• Ivan G. Stamov and
• Stepan I. Beril

Beilstein J. Nanotechnol. 2020, 11, 1045–1053, doi:10.3762/bjnano.11.89

• single crystals was carried out by our group [24]. Since Sb2S3 and Sb2Se3 have a similar band structure, the four excitonic states (A, B, C and D) were also obtained for the Sb2S3 single crystals. Based in our previous work [24], the exciton binding energies, valence band parameters, valence band

Epitaxial growth and superconducting properties of thin-film PdFe/VN and VN/PdFe bilayers on MgO(001) substrates

• Wael M. Mohammed,
• Igor V. Yanilkin,
• Amir I. Gumarov,
• Airat G. Kiiamov,
• Roman V. Yusupov and
• Lenar R. Tagirov

Beilstein J. Nanotechnol. 2020, 11, 807–813, doi:10.3762/bjnano.11.65

• ). Figure 3a,b shows the XPS spectra of the as-deposited VN/Pd0.92Fe0.08 thin film heterostructure. The binding energies of the Fe 2p1/2, Fe 2p3/2, and Pd 3d3/2 and Pd 3d5/2 states are 721.0, 707.7, and 340.2 and 335.0 eV, respectively, which agrees well with literature data [33][36]. Figure 3c,d shows the

• XPS spectra of the VN thin film on MgO. The binding energies of the V 2p1/2, V 2p3/2 and N 1s states are 521.1, 513.6 and 397.4 eV, respectively, which are very close to that given in the literature for crystalline VN [37][38]. The presence of a characteristic satellite at a binding energy of ca. 515

• an accuracy of ±0.5%. Neither impurities nor surface contaminations were detected (compare with [40]). All recorded high-resolution XPS spectra of VN and Pd1−xFex films were calibrated to the binding energies of crystalline VN at 513.6 eV and of metallic Pd at 335.0 eV [33][37], respectively

Nickel nanoparticles supported on a covalent triazine framework as electrocatalyst for oxygen evolution reaction and oxygen reduction reactions

• Secil Öztürk,
• Yu-Xuan Xiao,
• Dennis Dietrich,
• Beatriz Giesen,
• Juri Barthel,
• Jie Ying,
• Xiao-Yu Yang and
• Christoph Janiak

Beilstein J. Nanotechnol. 2020, 11, 770–781, doi:10.3762/bjnano.11.62

• -OOH* formation steps, whereas the ORR activity is limited by the S-OH* and O2 reduction steps. In this regard, ORR and OER catalysts need to have different binding energies for intermediates for optimum activity. In addition to this, metal species undergo oxidation at the high positive potentials

Silver-decorated gel-shell nanobeads: physicochemical characterization and evaluation of antibacterial properties

• Marta Bartel,
• Katarzyna Markowska,
• Marcin Strawski,
• Krystyna Wolska and
• Maciej Mazur

Beilstein J. Nanotechnol. 2020, 11, 620–630, doi:10.3762/bjnano.11.49

• the spectra suggests another spin–orbit pair with binding energies at 368.8 and 374.8 eV. This indicates the presence of some other form of silver, e.g., Ag bonded to organic molecules [32] or non-reduced silver ions [33] embedded in the gel layer. The content of this form of silver is ca. 37.1% (w/w

Soybean-derived blue photoluminescent carbon dots

• Shanshan Wang,
• Wei Sun,
• Dong-sheng Yang and
• Fuqian Yang

Beilstein J. Nanotechnol. 2020, 11, 606–619, doi:10.3762/bjnano.11.48

• measurement shown in Figure 7. This result confirms again the important role of nitrogen in the PL response of the soybean-derived CDs. Figure 8b–f shows the deconvoluted high-resolution spectra of O 1s, N 1s and C 1s in the soybean-derived CDs. The binding energies of O 1s are 532, 533, and 533 eV for the

• HTC-CDs, annealed-CDs and LA-CDs-10%, respectively, which are deconvoluted to C–O and C=O bonds. For the HTC-CDs, the binding energies of N 1s determined from the deconvoluted high-resolution spectrum of N 1s are 398.1, 399.3, 401.5, and 402.1 eV, which are assigned to pyridinic, amine, pyrrolic and

• graphitic nitrogen, respectively [49][50]. For the LA-CDs-10%, the binding energies of the corresponding N 1s are 398.7, 399.6, 401.0 and 402.1 eV, respectively. Thus, both of the HTC-CDs and the LA-CDs-10% likely possess the same types of surface-functional groups but with different fractions. The

Evolution of Ag nanostructures created from thin films: UV–vis absorption and its theoretical predictions

• Robert Kozioł,
• Marcin Łapiński,
• Paweł Syty,
• Damian Koszelow,
• Wojciech Sadowski,
• Józef E. Sienkiewicz and
• Barbara Kościelska

Beilstein J. Nanotechnol. 2020, 11, 494–507, doi:10.3762/bjnano.11.40

• of 4 mm was used for analyzing the emitted photoelectrons. The binding energies were corrected using the background C 1s line (285.0 eV). XPS spectra were analyzed with the Casa-XPS software using a Shirley background subtraction and Gaussian–Lorentzian curves as fitting algorithm. The theoretical

DFT calculations of the structure and stability of copper clusters on MoS₂

• Cara-Lena Nies and
• Michael Nolan

Beilstein J. Nanotechnol. 2020, 11, 391–406, doi:10.3762/bjnano.11.30

• monolayer is presented by Rawal et al. [25] to study the effect of defects in MoS2 on the catalytic activity of the supported nanoparticles. They observe that the magnitude of binding energy and charge transfer follows the trend Cu > Ag > Au. On the pristine surface the binding energies of the nanoparticles

• investigate how Cu begins to nucleate on a monolayer of MoS2, we start by adsorbing small Cun (n = 1–4) species on a MoS2 monolayer. All binding energies for the different structures calculated from Equation 1 are shown in Table 1. Binding energies calculated with Equation 2 are shown in Table 2 and addition

• and Figure 4, respectively. The binding energies shown in these images are the binding energies per atom from Equation 1. When a single Cu atom adsorbs at each of the three adsorption sites, Cu binds exothermically with adsorption energies of −0.81, −1.32 and −1.18 eV at sites 1, 2 and 3, respectively

Size effects of graphene nanoplatelets on the properties of high-density polyethylene nanocomposites: morphological, thermal, electrical, and mechanical characterization

• Tuba Evgin,
• Alpaslan Turgut,
• Georges Hamaoui,
• Zdenko Spitalsky,
• Nicolas Horny,
• Matej Micusik,
• Mihai Chirtoc,
• Mehmet Sarikanat and
• Maria Omastova

Beilstein J. Nanotechnol. 2020, 11, 167–179, doi:10.3762/bjnano.11.14

• (C 1s at ≈284.6 eV) and contained a small amount of oxygen (O 1s at ≈531–534 eV). The C 1s peak centered at ≈284.6 eV, with an asymmetry towards higher binding energies, which is characteristic for an sp2 carbon atom. The broad peak observed at ca. 291 eV (labeled ‘Pi–Pi*’ in Figure 2b) occurred due

Fabrication of Ag-modified hollow titania spheres via controlled silver diffusion in Ag–TiO₂ core–shell nanostructures

• Bartosz Bartosewicz,
• Malwina Liszewska,
• Bogusław Budner,
• Marta Michalska-Domańska,
• Krzysztof Kopczyński and
• Bartłomiej J. Jankiewicz

Beilstein J. Nanotechnol. 2020, 11, 141–146, doi:10.3762/bjnano.11.12

• ]. The peak associated with silver oxide appears at lower binding energies than the peak of metallic silver [26][27]. Due to the very small offset for different forms of silver oxide, only one peak located between 367.27 and 367.58 eV with a half-width of 1.03–1.07 eV was modeled in the spectra. The

Design and facile synthesis of defect-rich C-MoS₂/rGO nanosheets for enhanced lithium–sulfur battery performance

• Chengxiang Tian,
• Juwei Wu,
• Zheng Ma,
• Bo Li,
• Pengcheng Li,
• Xiaotao Zu and
• Xia Xiang

Beilstein J. Nanotechnol. 2019, 10, 2251–2260, doi:10.3762/bjnano.10.217

•  4c). The two peaks of pristine MoS2 at 228.9 and 232.1 eV in Figure 4d are assigned to binding energies of Mo 3d5/2 and 3d3/2 for Mo4+, respectively, corresponding to the 2H phase of MoS2[20]. The two peaks at 162.78 and 161.7 eV are attributed to the S 2p1/2 and S 2p3/2 orbital of divalent sulfide

• in order to utilize its defect sites to catalyze the conversion of polysulfides and to improve the energy storage performance. The binding energies of Mo 3d5/2 and Mo 3d3/2 in C-MoS2/rGO composite shift to 228.6 and 231.8 eV, respectively (Figure 4d). Similarly, the binding energies of S 2p3/2 and S

• 2p1/2 in the C-MoS2/rGO composite shift to lower energies by about 0.2 eV relative to pristine MoS2. This can be attributed to the interactions of MoS2, amorphous carbon and rGO, which weakens the binding energy of Mo and S [39]. However, after annealing, the binding energies of Mo 3d5/2, Mo 3d3/2, S

Ultrathin Ni_1−xCo_xS₂ nanoflakes as high energy density electrode materials for asymmetric supercapacitors

• Xiaoxiang Wang,
• Teng Wang,
• Rusen Zhou,
• Lijuan Fan,
• Shengli Zhang,
• Feng Yu,
• Tuquabo Tesfamichael,
• Liwei Su and
• Hongxia Wang

Beilstein J. Nanotechnol. 2019, 10, 2207–2216, doi:10.3762/bjnano.10.213

• 2p1/2 and Ni 2p3/2 (Figure 2b) with binding energies of 855.9 eV and 873.3 eV are observed, respectively, with an energy gap of 17.4 eV. Two satellite (indicated as “Sat.”) peaks are also observed at 859.9 eV and 878.4 eV. Thus, the existence of Ni2+ is confirmed in the sulfurised resultants [30][31

Improved adsorption and degradation performance by S-doping of (001)-TiO₂

• Xiao-Yu Sun,
• Xian Zhang,
• Xiao Sun,
• Ni-Xian Qian,
• Min Wang and
• Yong-Qing Ma

Beilstein J. Nanotechnol. 2019, 10, 2116–2127, doi:10.3762/bjnano.10.206

• °C were measured, and Figure 4 representatively shows the results for 2-S1 and 2-S3. The chemical states of Ti, O and S, the corresponding binding energies (BE) and the CS ratios derived for 2-S0, 2-S0.5, 2-S1, 2-S2, 2-S3, 2-S4 and 2-S5 are listed in Table 3. For all samples synthesized at 250 °C

• dispersions, (e, f, g, h) DMPO–•O2− formed in methanol dispersion. The unit cell parameters a, c and the c/a value for S-doped (001)-TiO2 at 250 °C. Position of the FTIR absorption peaks and the corresponding vibrational modes. The chemical states (CSs) of Ti, O and S and the corresponding binding energies

Review of advanced sensor devices employing nanoarchitectonics concepts

• Katsuhiko Ariga,
• Tatsuyuki Makita,
• Masato Ito,
• Taizo Mori,
• Shun Watanabe and
• Jun Takeya

Beilstein J. Nanotechnol. 2019, 10, 2014–2030, doi:10.3762/bjnano.10.198

• binding energies that are controlled by external stimuli. This can also be regarded as the origination of molecular function control by external stimuli. It shares working principles with molecular machines which are usually operated by switching between several states [186][187][188]. Unlike these

Synthesis of nickel/gallium nanoalloys using a dual-source approach in 1-alkyl-3-methylimidazole ionic liquids

• Ilka Simon,
• Julius Hornung,
• Juri Barthel,
• Jörg Thomas,
• Maik Finze,
• Roland A. Fischer and
• Christoph Janiak

Beilstein J. Nanotechnol. 2019, 10, 1754–1767, doi:10.3762/bjnano.10.171

• Information File 1, Figure S6) indicates only one Ga species, but we note that the binding energies of the different Ga oxidation states are within 1 eV [50], which does not allow for an unequivocal assignment. The O 1s peaks at 531.30 eV and 531.18 eV clearly show only the presence of organic oxygen and no