We present a simple phenomenological model to describe elastic responses of a collapsed single DNA molecule. The model is represented by the elastic theory for the wormlike chain combined with the order-parameter equation, which accounts for the intramolecular transition kinetics. Our continuum and discrete model reproduces the force plateaus and the stick-release patterns in the force-extensio...

The ability of force fields to reproduce relative conformational energies for seven molecules is probed. The correlation against LMP2/cc-pVTZ results for standard force field employing fixed partial charges deteriorates as the molecules become more polar. Inclusion of multipole moments and intramolecular polarization can improve the correlation, and both contributions are of similar importance....

Autosolvation is an important factor in stabilizing the architecture of medium complicated molecules. It is a kind of “supramolecular force” acting in intramolecular manner, consisting of orbital-orbital interactions between polar groups, separated by more than one covalent bonds within the same molecule. This effect facilitates also the development of chiral conformations. Two typical alkylcob...

Statistical thermodynamics provides a powerful theoretical framework for analyzing, understanding and predicting the conformational properties of biomolecules. The central quantity is the potential of mean force or effective energy as a function of conformation, which consists of the intramolecular energy and the solvation free energy. The intramolecular energy can be reasonably described by mo...

The reliability of four force fields developed for 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids are compared to an ab inito molecular dynamics simulation regarding structural properties. Except the hydrogen bond structure between the most acidic hydrogen atom of the imidazolium ring and the nitrogen atom of the anion as well as the intramolecular potential surface...

Intramolecular methyl–methyl coupling on Au (111) is explored as a new on-surface protocol for edge extension in graphene nanoribbons (GNRs). Characterized by high-resolution scanning tunneling microscopy, noncontact atomic force and Raman spectroscopy, the proven to indeed proceed at armchair edges of GNRs, forming six-membered rings with sp3- or sp2-hybridized carbons.

Here we review the applications of atomic force microscopy to the study of samples of biological origin. Emphasis is given to provide the reader with information on the broad range of different biophysical applications that, to date, such a technique can deal with. After recalling briefly the operating principles of an atomic force microscope, the broad field of bio-imaging applications is face...

We here report the synthesis and characterization of a complex polymeric architecture based on a block copolymer with a cylindrical brush block and a single-chain polymeric nanoparticle block folded due to strong intramolecular hydrogen-bonds. The self-assembly of these constructs on mica surfaces was studied with atomic force microscopy, corroborating the distinct presence of block copolymer a...