The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica-exchange of the chemical potential significantly reduces the variance of the GCMC data. This improvement comes at a negligible increase in computational expense when simulations comprise of runs at different chemical potentials. Replica-exchange GCMC is also found to substantially increase the precision of water binding free energies as calculated with grand canonical integration, which has allowed us to address a missing standard state correction.

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The structure and bonding of guanine-Cu and uracil-Cu (neutral, anionic, and cationic) are discussed on the basis of the calculated structures and energies. The interaction of the metal atom with guanine and uracil has been analyzed using the B3LYP density-functional approach. The removal of one electron from the neutral complexes produces the stabilization of one of the isomers, while the addition of one electron leads to a system where the metal atom is weakly bounded to guanine or uracil, according to the metal-bases bond distance that is long (2.29-2.90). For guanine-Cu and uracil-Cu, the vertical ionization energy of the anion is close to the dissociation energy of one hydrogen atom from guanine-Cu or uracil-Cu. In these cases, it could be possible to produce the detachment of one electron from the anion and also the removal of one hydrogen atom. This is important since the photoelectron spectroscopy of atomic or mixed-atomic cluster anions has proven to be a very effective tool in the study of small systems. For the analysis of copper atoms with DNA bases such as guanine and uracil, it is expected that the photoelectron spectra of the anion-bases complexes strongly resemble the spectrum of Cu(-1), just shifted to higher electron binding energies due to the product stabilization. Hopefully, this information will be useful for the experimental groups.

Predictions on the photoelectron spectra of deprotonated cytosine anions (cytosinate, Cye(-)) have been made with ab initio electron propagator methods. Two imino-oxo forms are most stable, but four other isomers have energies within 10 kcal/mol. The first vertical electron detachment energies (VEDEs) for the three most stable Cye(-) isomers are approximately 3.4 eV. Imino-oxy VEDEs are about 0.3 eV smaller. For each anion, the lowest VEDE corresponds to a pi Dyson orbital. The order of higher final states is changed when relaxation and correlation effects are considered. Considerable mixing between lone-pair and bonding lobes occurs in the sigma Dyson orbitals.

/npsi/ctrl?action=rtdoc&an=12327971&lang=en http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=12327971&lang=fr READ THESE TERMS AND CONDITIONS CAREFULLY BEFORE USING THIS WEBSITE.http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/jsp/nparc_cp.jsp?lang=en Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions? Contact the NRC Publications Archive team atPublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. For the publisher's version, please access the DOI link below./ Pour consulter la version de l'éditeur, utilisez le lien DOI ci-dessous.http://doi.org/10.1021/jp0506944The Journal of Physical Chemistry A, 109, 32, pp. 7046-7056, 2005-07- Sciences, National Research Council of Canada, 100 Sussex DriVe, Ottawa, Ontario, Canada K1A 0R6 ReceiVed: February 8, 2005; In Final Form: May 13, 2005 Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb 8 and Nb 10 , for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb 10 , yielding either Nb n C 2 H 2 or Nb n C 2 . Over the range Nb-Nb 6 , the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C 2 H 4 ,C 2 H 2 ,o rC 2 . With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb n cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calcu...