Semilocal density functionals predict that the stable adsorption site of carbon monoxide ͑CO͒ on Pt͑111͒ is the hollow fcc site, in disagreement with experimental studies which indicate that CO adsorbs on the top site at low coverage. This site preference depends on a subtle balance between the interaction of the lowest unoccupied molecular orbital ͑LUMO͒ and highest occupied molecular orbital ͑HOMO͒ with the metal substrate. Local and semilocal functionals seem to overestimate the interaction of the LUMO with the metal substrate, in turn favoring the wrong site. It is argued that this error is related to the ''gap'' problem of present density functionals and might be cured by functionals that increase the HOMO-LUMO separation.Adsorption of carbon monoxide on metal surfaces is a prototypical system in surface science, with studies dating back at least 30 years. The Pt͑111͒ substrate has recently attracted attention, as present density functionals seem to predict the wrong stable adsorption site. 1 Experiments indicate that CO adsorbs on the top site on the Pt ͑111͒ substrate at low coverage. The most important experimental data are the high CO stretch frequency (2100 cm Ϫ1 ) observed for CO on Pt͑111͒ at low coverage, 2,3 and diffuse low-energy electron diffraction data. 4 Furthermore, in a recent scanning tunneling microscopy study of CO on a Pt-Co surface alloy, CO molecules were observed exclusively on top of Pt atoms. 5 The theoretical studies, however, yield a different result. A recent investigation applying large clusters and local orbitals indicates that the hollow site is preferred over the top site for sufficiently large clusters and semilocal density functionals. 6 Another comprehensive study applying slabs and three different plane wave based approaches showed as well that CO prefers the hollow site. 1 Two of the density functional codes were based on ultrasoft pseudopotentials and the projector augmented-wave ͑PAW͒ method, whereas the third one used the linearized augmented plane-wave method ͑LAPW͒. All three programs have been applied to a vast number of adsorption problems before, are mature and highly reliable ͑at least within the boundaries established by DFT͒, and, additionally, the authors of the aforementioned study have done careful tests to obtain technically converged results. The conjecture is clear and not particularly ''friendly'': the present local and semilocal density functionals predict the wrong adsorption site for CO on Pt͑111͒, and they do so by at least 100 meV. A point worthwhile mentioning is that-although all codes agreed on the hollow site to be more stable-the energy difference between the hollow and top site varied by almost 100 meV between the three plane wave codes, even though identical density functionals were used.These results are a serious challenge for the prospects and future of density functional based calculations. If computational ab initio modeling wants to be predictive, this deficiency has to be addressed. As a first step, it is vital to understand why presen...

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Spectroelectrochemical experiments and density functional theory (DFT) based calculations are combined to elucidate the nature of the species adsorbed when a perchloric acid solution saturated with carbon dioxide is in contact with well-defined electrode surfaces. Previous results reported for the Pt(111) electrode are revised and completed with new data for a palladium monolayer deposited on the Pt(111) electrode. From the DFT calculations and from the potential and pH dependent behavior of the main adsorbate vibrational bands, it is suggested that, for potentials below 0.65 V, bicarbonate species are adsorbed at the Pt(111) electrode surface in a short-bridge bidentate configuration. At higher potentials, the adsorbate adlayer is completed by the formation of adsorbed carbonate also in a short-bridge configuration. The ratio between the surface coverages of adsorbed bicarbonate and carbonate depends on both the electrode potential and the solution pH. Adsorbed bicarbonate prevails at the palladium monolayer irrespective of the electrode potential. This behavior, together with a concomitant lower adsorbate coverage, can be related to the competitive adsorption of hydroxylated species.

A combined in situ spectroelectrochemical and theoretical study of CO adsorbed on clean and palladium-covered Pt(111) single-crystal electrodes is presented. The in situ spectra of CO adsorbed on the Pt(111) and Pd supported on Pt(111) single-crystal electrodes show different bands corresponding to the C−O stretching mode that are assigned with the help of density functional cluster model calculations. For the palladium-covered Pt(111) electrode with a palladium coverage close to the monolayer, the resulting spectra can be interpreted by using a pure Pd cluster model only. A shift to higher vibrational frequencies is observed which increases with increasing CO coverage. This shift can be interpreted as a change in the adsorption site because of coverage effects in agreement with UHV results at 300 K. The present study shows that the combined use of spectroelectrochemical and first principles calculations is a promising and powerful tool for the interpretation of complex electrochemical interfaces.

Summary Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health (GA4GH) project we developed RNAget, an API for secure access to genomic quantification data in matrix form. RNAget provides for slicing matrices to extract desired subsets of data and is applicable to all expression matrix-format data, including RNA-seq and microarrays. Further, it generalizes to quantification matrices of other sequence-based genomics such as ATAC-seq and ChIP-seq. Availability and Implementation https://ga4gh-rnaseq.github.io/schema/docs/index.html Supplementary information Supplementary data are available at Bioinformatics online.