Noah+Johnson+-+Log

Chemistry Information Retrieval 2011 Log Noah Johnson

Crystallographic Databases

=Free=

Provides access to crystal structures of biological macromolecules, such as proteins, nucleic acids, and polysaccharides. http://www.wwpdb.org/
 * Worldwide Protein Databank**

Contains a wide variety of crystal structures, from organic and inorganic molecules to metals and alloys. It is maintained by Portland State University, and has built-in capabilities for viewing crystal structures through a Java applet. http://nanocrystallography.research.pdx.edu/
 * Open Access Crystallography**

Focused entirely on nucleic acids, this database has been run by Rutgers University since 1992. http://ndbserver.rutgers.edu/
 * Nucleic Acid Database**

Commercial
A large database of small organic and organometallic molecules. http://www.ccdc.cam.ac.uk/products/csd/
 * Cambridge Structural Database**

This is a nearly complete listing of inorganic crystal structures. It contains data from as early as 1913. http://www.fiz-karlsruhe.de/icsd_content.html
 * Inorganic Crystal Structure Database**

This database focuses on metals, alloys, and intermetallic compounds. http://www.tothcanada.com/databases.htm
 * CRYSTMET**

Noam Agmon "The Grotthuss mechanism" Chemical Physics Letters 244 (1995) 456-462

[|http://dx.doi.org/10.1016/0009-2614(95)00905-J]
 * [Full Marks JCB]**


 * Water has a high proton conductivity, and while the exact cause is unknown, it is thought to arise from a “hopping” mechanism between water molecules.
 * All models disagree with experimental data in some way, but they all contain pieces of the true mechanism, which might someday be confirmed by molecular simulations.
 * There are two ways to consider the role of water in proton transfer. One is that a proton jumps from a hydronium ion to a nearby water molecule, which is either freely rotating or induced to direct its lone pair toward the proton.
 * The other way is to consider the water as a large, hydrogen-bonded network, which the proton jumps through. The transfer can then be limited either by the proton movement alone or by the movement of water molecules to receive the moving proton; the former tends to be true in ice, while the latter is true in water.
 * These two methods are described in many textbooks, but both disagree with experimental data to some extent, as will be shown.
 * X-ray diffraction, Raman experiments, and molecular dynamics simulations all show that water doesn’t rotate freely, but is related to nearby water molecules by (temperature dependent) hydrogen bonding in tetrahedral symmetry.
 * However, proton conductivity does correlate with water rotation, as proton hopping times are on the same order of magnitude as water reorientation (1-2 ps). So, while water rotation is involved, it is not in the form of a free rotor.
 * The fact that water is somewhat structured does not mean that protons hop in a relay mechanism; it contradicts a large amount of experimental data.
 * Protons aren’t delocalized over large quantities of liquid water.
 * This would predict that protons are more mobile in more tightly structured water, however, protons move slower in ice than in water of the same temperature; it also increases with temperature, which has the property of weakening hydrogen bonds.
 * The hopping times obtained from NMR are explained by assuming transfers occur one water molecule at a time. This makes a much more reasonable guess at transfer in water.
 * Fluorescence measurements can also support this view, by quantitatively describing the proton movement through the water as occurring in a force field, which is true under a wide variety of conditions.
 * The rate limiting step is not proton movement in water clusters, as seen in a number of observations:
 * The deuterium isotope effect is very small, which would not be expected in a hopping mechanism between two water molecules.
 * Proton conductivity has a low activation energy, but theoretically, the activation energy of a hopping mechanism at equilibrium should be zero.
 * The breaking of water clusters is rate-limiting, but a sample of water can be thought of as one large cluster, so what does it mean to form bonds at the edges?
 * Proton movement is connected with the breaking of hydrogen bonds, and not their formation.
 * The NMR and protons have roughly the same activation energy, which also corresponds to hydrogen bond strength. This indicates water rotation.
 * The isotope effect can be explained by rotation of the water molecule rather than hopping of the proton.
 * No current explanation can account for all data, especially considering that hydronium ions only allow one acceptor for a hydrogen bond. This is more accurately described as one proton with three water molecules.
 * Hydrogen bonding in hydronium is stronger than in bulk water, meaning activation in this step would involve higher energies,
 * This has been largely ignored by most authors, even though it is a largely simplistic explanation. No explanation matches the breaking of this hydrogen bond.
 * Proton hopping mechanisms are also disallowed by this observation, due to breaking of hydrogen bonds.
 * While this has led some to claim the proton is between two water molecules, it cannot account for all, as three-molecule coordination is more stable.
 * There are therefore a number of conditions that must be met in any explanation:
 * The jump has to be incoherent
 * Protons must move faster than the solvent
 * The rate determining step must break a normal hydrogen bond
 * This disallows anything in the first solvation shell
 * The donor and acceptor waters must be identical
 * This is obvious
 * A three coordinated proton cleaves a bond in the second solvation shell as the rate-limiting step.
 * This broken water can then reorient.
 * Readjustment of the water molecule occurs on the femtosecond scale, to bring the water into proximity of the proton, which can then jump to a new water molecule.
 * This will most likely be proven by computation rather than experiment, and has been indicated by past simulations.
 * In summary, jumping of protons is driven by the cleavage of hydrogen bonds in the path of the proton, with the proton jumping forward to the "free" water.