Self-organizing bioinspired oligothiophene–oligopeptide hybrids

• Alexey K. Shaytan,
• Eva-Kathrin Schillinger,
• Elena Mena-Osteritz,
• Sylvia Schmid,
• Pavel G. Khalatur,
• Peter Bäuerle and
• Alexei R. Khokhlov

Beilstein J. Nanotechnol. 2011, 2, 525–544, doi:10.3762/bjnano.2.57

• –peptide conjugates and to gain more insight into the structure and dynamical behavior of the aggregates at finite temperatures, a theoretical methodology based on classical mechanical force fields and molecular dynamics simulations was developed [23]. Although molecular models based on classical mechanics

Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces

• David M. Benoit,
• Bruno Madebene,
• Inga Ulusoy,
• Luis Mancera,
• Yohann Scribano and
• Sergey Chulkov

Beilstein J. Nanotechnol. 2011, 2, 427–447, doi:10.3762/bjnano.2.48

• the prediction of vibrational frequencies. From a theoretical point of view, the accuracy of the data obtained from high resolution spectra provides an ideal opportunity to validate the interaction models used to describe the observed molecule, be they empirical force fields or quantum chemical

• conformationally flexible molecules. Due to its conceptual simplicity and the ready availability of reliable empirical force fields (or forces computed ab initio), molecular dynamics is currently the most popular method for determining anharmonic frequencies of large systems (see [7] for an overview of some

Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

• Michael Roos,
• Benedikt Uhl,
• Daniela Künzel,
• Harry E. Hoster,
• Axel Groß and
• R. Jürgen Behm

Beilstein J. Nanotechnol. 2011, 2, 365–373, doi:10.3762/bjnano.2.42

• of a “hill” site from that of a “valley” position. Table 1 and Table 2 show the differences between these sites for different force fields. Clearly, the calculated binding energies strongly depend on the force field used, as found before in force field calculations addressing 3,3'-BTP adsorption on

• calculated adsorption energy for both the hill and the valley position and the resulting corrugation of the adsorption potential ΔE for PTCDA molecules on graphene/Ru(0001) for different force fields. Dependent on the applied force field, the resulting ΔE ranges from −0.435 to −0.690 eV. To rationalize the

• placed on top of the two different adsorption sites (“hill” and “valley”) and four different force fields were used to optimize the adsorption geometry of the adsorbate (Compass [40], CVFF [41], Dreiding [42], and UFF [43] as implemented in the Accelrys Materials Studio program package). Note that the