The vast majority of power/energy generation in our global economy is based on the chemical element carbon, specifically fossil carbon (coal) and hydrocarbon (oil and gas) fuels. Such an economy is not sustainable in the medium- to long-term for two fundamental reasons; first, there exists only a finite amount of fossil fuel, and, second, the carbon dioxide released during the combustion of fossil fuels induces anthropogenic climate change with costly and potentially disastrous consequences. Current energy technologies cannot support both a reduction in carbon dioxide emissions and an ever-expanding global economy. It is now recognized that hydrogen may be one of the leading contenders as a potential solution for a sustainable alternative to fossil fuels, especially for transport and for heat and power generation and energy storage. However, any transition from a carbon-based (fossil fuel) energy system to a hydrogen-based economy involves significant scientific, technological and socio-economic barriers. Our aim is to illustrate the “hydrogen nexus” as a possible connection or link from today's carbon economy to a sustainable energy future centred on hydrogen.

The local structure of the low-temperature ordered phase of the negative thermal expansion (NTE) material ${\mathrm{ZrW}}_2{\mathrm{O}}_8$ has been investigated by reverse Monte Carlo (RMC) modeling of neutron total scattering data. We obtain, for the first time, quantitative measurements of the extent to which the ${\mathrm{WO}}_4$ and ${\mathrm{ZrO}}_6$ polyhedra move as rigid units, and we show that these values are consistent with the predictions of rigid unit mode theory. We suggest that rigid unit modes are associated with the NTE. Our results do not support a recent interpretation of x-ray-absorption fine structure spectroscopy data in terms of a larger rigid structural component involving the Zr-O-W linkage.

We describe a new computational method, FRODA (framework rigidity optimized dynamic algorithm), for exploring the internal mobility of proteins. The rigid regions in the protein are first determined, and then replaced by ghost templates which are used to guide the movements of the atoms in the protein. Using random moves, the available conformational phase space of a 100 residue protein can be well explored in approximately 10-100 min of computer time using a single processor. All of the covalent, hydrophobic and hydrogen bond constraints are maintained, and van der Waals overlaps are avoided, throughout the simulation. We illustrate the results of a FRODA simulation on barnase, and show that good agreement is obtained with nuclear magnetic resonance experiments. We additionally show how FRODA can be used to find a pathway from one conformation to another. This directed dynamics is illustrated with the protein dihydrofolate reductase.

The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered on MolMovDB. In particular, we further developed the Morph Server to produce improved interpolations between two submitted structures. We added support for multiple chains to the original adiabatic mapping interpolation, allowing the analysis of subunit motions. We also added the option of using FRODA interpolation, which allows for more complex pathways, potentially overcoming steric barriers. We added an interface to a hinge prediction service, which acts on single structures and predicts likely residue points for flexibility. We developed tools to relate such points of flexibility in a structure to particular key residue positions, i.e. active sites or highly conserved positions. Lastly, we began relating our motion classification scheme to function using descriptions from the Gene Ontology Consortium.