Terahertz (THz) absorption spectra of the similarly structured amino acids L-serine and L-cysteine in the solid phase at 77 and 298 K are reported and compared to isolated molecule and solid-state infrared vibrational spectral calculations using empirical force field and density functional theory. These comparisons suggest that many higher frequency internal modes can readily be assigned but lo...

Using the atomic force microscope (AFM) in situ during the crystallization of the protein apoferritin, we show that for this system the kink density along the steps is an equilibrium property that, multiplied by the frequency of molecular attachment, fully determines the propagation of growth steps. The intermolecular bond energy is 3.2k(B)T. Point defects are nonequilibrial and are caused by i...

Measured single-photon zero-kinetic-energy pulsed field ionization ~ZEKE-PFI! photoelectron spectra of the sodium–water complex are presented and compared with the results of rotationally resolved ab initio calculations. The very nonatomiclike behavior of the photoionization of this Na~H2O! complex is essential in accounting for several significant features in these spectra. Agreement between t...

We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between intermolecular and intramolecular interactions, and the promotion or disruption of secondary structure brought on by the proximity of the two molecules. In particular, we de...

Detonation processes probed with atomistic details have remained elusive due to highly complex reactions in heterogeneous shock structures. Here, we provide atomistic details of the initial reaction pathways during shock-induced decomposition of 2,4,6-triamino-1,3,5-trinitrobenzene (TATB) crystal using large reactive molecular dynamics simulations based on reactive force fields. Simulation resu...

The effects of adsorption on the graphite(0001) surface on the nonplanar distortions of nickel(II)octaethylporphyrin were studied by molecular mechanics (MM) approach. Using the Consistent Force Field (CFF) program with previously developed parameters for metalloporphyrins and supplemented to treat intermolecular interactions geometry optimizations were carried out for 43 conformations of 28 di...

Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loo...

Force spectroscopy measurement of rupture forces of bound molecules becomes an important physicochemical tool in characterizing intermolecular interactions. Atomic force microscopy (AFM) measurements are among the most common approaches in implementation of this technique. Kinetic information about the molecular bond under study is usually extracted assuming that the detected rupture force come...

The direct quantification of weak intermolecular binding interactions is very important for many applications in biology and medicine. Techniques that can be used to investigate such interactions under a controlled environment, while varying different parameters such as loading rate, pulling direction, rupture event measurements, and the use of different functionalized probes, are still lacking...