Single-molecule force spectroscopy with an atomic force microscope has been widely used to study inter- and intramolecular interactions. To obtain data consistent with single molecular events, a well-defined method is critical to limit the number of molecules at the apex of an AFM probe to one or to a few. In this paper, we demonstrate an easy method for single-molecule probe modification by us...

We here give information for a deeper understanding of single molecule force spectroscopy (SMFS) data through the example of the blood protein von Willebrand factor (VWF). It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD) loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently...

Scanning probe microscopy can be used to probe the internal atomic structure of flat organic molecules. This technique requires an unreactive tip and has, until now, been demonstrated only at liquid helium and liquid nitrogen temperatures. We demonstrate intramolecular and intermolecular force contrast at room temperature on PTCDA molecules adsorbed on a Ag/Si(111)-(√[3]×√[3]) surface. The osci...

Bacteriorhodopsin is a model system for membrane proteins. This seven transmembrane helical protein isembedded within a membrane structure called purple membrane. Its structural stability against mechanical stress was recentlyinvestigated by atomic force microscopy experiments, in which single proteins were extracted from the purple membrane. Here,we study this process by all-atom m...

We investigated two important unresolved issues on excited state intramolecular proton transfer (ESIPT) reactions, i.e., their driving force and the charge state of the transferred species by means of quantum chemical topology. We related changes in the aromaticity of a molecule after electron excitation to reaction dynamics in an excited state. Additionally, we found that the conveyed particle...

We performed studies of fluctuating charge, fluctuating dipole, and combined models for substituted benzenes and concluded that dipoles are necessary to avoid errors in important cases. Force fields incorporating fluctuating dipoles for alanine, serine, and phenylalanine were developed that accurately reproduce both relative conformational energies and cooperative many-body energies as given by...

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined with atomic resolution, adsorption height differences with a precision of 3 pm, and tilts of the molecular plane within 0.2°. The method was applied to five π-conjugated molecules, including three...

The misfolding of α-synuclein (αS) to a cross-β-sheet amyloid structure is associated with pathological conditions in Parkinson's and other neurodegenerative diseases. Using pulse electron paramagnetic resonance spectroscopy combined with a cross-labeling strategy involving four double mutants, we were able to determine the intramolecular distance between the extremal β-strands. The distance of...

What do we mean when we talk about Supramolecular Chemistry? The easiest way to describe supramolecular chemistry is to consider the concept of “chemistry beyond the molecule”—We can think of supramolecular chemistry as more than the sum of the parts. In other words the way molecules interact and come together generates new and exciting properties that surpass those of the molecule. The very co...

Changes in the elastic properties of single deoxyribonucleic acid (DNA) molecules in the presence of different DNA-binding agents are identified using atomic force microscope single molecule force spectroscopy. We investigated the binding of poly(dG-dC) dsDNA with the minor groove binder distamycin A, two supposed major groove binders, an alpha-helical and a 3(10)-helical peptide, the intercala...