Space Group Research

The figure below shows the SFG spectrum for the water/vapor interface calculated using Time Correlation Function (TCF) methods.  By comparing this spectrum to the inset experimental spectrum (by Shen, et al.), we can see that TCF theory is capable of accurately reproducing the shape and polarization dependence of the signal.

Here, we have identified species that give rise to spectral peaks for the water/vapor interface.  The water molecule shown in blue is a free O-H mode at 3694 cm^-1, green represents a wagging motion at 858 cm^-1, black highlights a translation parallel to the interface at 197 cm^-1, and yellow is a translation perpendicular to the interface at 46 cm^-1.

Molecularly detailed information can be obtained for other interfaces using similar methods, as is shown below for the water/CCL₄ interface.

Hydrogen Storage in Charged Metal-Organic Frameworks

Additional areas of active study include Monte Carlo simulations of metal-organic framework materials (MOFs) in order to model hydrogen sorption.   In particular, we are interested in materials that exhibit large molecular hydrogen uptake capacity, and understanding the physical characteristics that lead to enhanced hydrogen uptake. 

Here we can see the structure of a MOF, and on the right, its corresponding hydrogen density isosurface calculated from simulation.  Below are hydrogen dipole isosurfaces at 0.18 D (left) and 0.33 D (right).
For additional visualization, use the following links to view 3-D animations of MOF structures and isosurfaces in MPEG format. A rotating MOF with isosurface shown A stationary MOF with scanning isosurface A rotating MOF with fading isosurface

Volume Determination of Globular Proteins

Using molecular dynamics methods, we are interested in studying the molecular volumes of various proteins, in order to link specific events to the thermodynamic observables that experimentalists measure.  Shown below is a periodic cell containing myoglobin solvated with 10,796 water molecules, in comparison with a system containing only the bulk water.  The difference in volume between each cell under NPT dynamics results in the apparent molecular volume of the myoglobin.  Click here to see a rotating 3-D animation of the myoglobin system dynamics!

The comparison below shows the alignment between the X-ray crystal structure of myoglobin versus the equilibrium structure due to solvation in the NPT ensemble.  While the root mean squared deviation between the two configurations was 2.34 Å, the region near the GLY80 shows a difference of 6.0 Å.