Rare Events Sampling Methods for Quantum and Classical Ab Initio Molecular Dynamics.

We provide an approach to sample rare events during classical ab initio molecular dynamics and quantum wavepacket dynamics. For classical AIMD, a set of fictitious degrees of freedom are introduced that may harmonically interact with the electronic and nuclear degrees of freedom to steer the dynamics in a conservative fashion toward energetically forbidden regions. A similar approach when introduced for quantum wavepacket dynamics has the effect of biasing the trajectory of the wavepacket centroid toward the regions of the potential surface that are difficult to sample.

On the Possibility That Bond Strain Is the Mechanism of RING E3 Activation in the E2-Catalyzed Ubiquitination Reaction.

Ubiquitination is a type of post-translational modification wherein the small protein ubiquitin (Ub) is covalently bound to a lysine on a target protein. Ubiquitination can signal for several regulatory pathways including protein degradation. Ubiquitination occurs by a series of reactions catalyzed by three types of enzymes: ubiquitin activating enzymes, E1; ubiquitin conjugating enzymes, E2; and ubiquitin ligases, E3.

A conserved asparagine in a ubiquitin-conjugating enzyme positions the substrate for nucleophilic attack.

The mechanism used by the ubiquitin-conjugating enzyme, Ubc13, to catalyze ubiquitination is probed with three computational techniques: Born-Oppenheimer molecular dynamics, single point quantum mechanics/molecular mechanics energies, and classical molecular dynamics. These simulations support a long-held hypothesis and show that Ubc13-catalyzed ubiquitination uses a stepwise, nucleophilic attack mechanism. Furthermore, they show that the first step-the formation of a tetrahedral, zwitterionic intermediate-is rate limiting.

Far-Infrared Synchrotron Spectroscopy and Quantum Chemical Calculations of the Potentially Important Interstellar Molecule, 2-Chloroethanol.

The high brightness of the Australian synchrotron allowed for detailed spectra to be collected at high resolution (0.00096 cm) in the vicinity of the a/ b/ c-type ν band of 2-chloroethanol, which involves O-H torsional motion about the C-O bond. A rovibrational analysis was performed for both chlorine isotopologues in the ν fundamental (centered at ∼344 cm) which involved the assignment of 7153 lines ( J ≤ 90, K ≤ 41).