Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.Peer Reviewe

Release of cclib version 1.4

This is an archive of the source code for cclib version 1.4, orginally released on github (https://github.com/cclib/cclib/releases/tag/v1.4)

Structural, electronic, and thermochemical preference for multi-PCET reactivity of ruthenium(II)-amine and ruthenium(IV)-amido complexes

The multiredox reactivity of bioinorganic cofactors is often coupled to proton transfers. Here we investigate the structural, thermochemical, and electronic structure of ruthenium-amino/amido complexes with multi- proton-coupled electron transfer reactivity. The bis(amino)ruthenium(II) and bis(amido)ruthenium(IV) complexes [RuII(bpy)(en*)2]2+ (RuII-H0 ) and [RuIV(bpy)(en*-H2)2]2+ (RuIV-H2 ) interconvert reversibly with the transfer of 2e-/2H+ (bpy = 2,2'-bipyridine, en* = 2,3-diamino-2,3-dimethylbutane). X-ray structures allow correlations between the structural and electronic parameters, and the thermochemical data of the 2e-/2H+ multi-square grid scheme. Redox potentials, acidity constants and DFT calculations reveal potential intermediates implicated in 2e-/2H+ reactivity with organic reagents in non-protic solvents, which shows a strong inverted redox potential favouring 2e-/2H+ transfer. This is suggested to be an attractive system for potential one-step (concerted) transfer of 2e-and 2H+ due to the small changes of the pseudo-octahedral geometries and the absence of charge change, indicating a relatively small overall reorganization energy.Fil: Cattaneo, Mauricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Química del Noroeste. Universidad Nacional de Tucumán. Facultad de Bioquímica, Química y Farmacia. Instituto de Química del Noroeste; ArgentinaFil: Parada, Giovanny A.. University of Yale; Estados Unidos. College of New Jersey; Estados UnidosFil: Tenderholt, Adam L.. University of Washington; Estados UnidosFil: Kaminsky, Werner. University of Washington; Estados UnidosFil: Mayer, James M.. University of Yale; Estados Unido

Probing Quantum and Dynamic Effects in Concerted Proton–Electron Transfer Reactions of Phenol–Base Compounds

The oxidation of three phenols, which contain an intramolecular hydrogen bond to a pendent pyridine or amine group, has been shown, in a previous experimental study, to undergo concerted proton−electron transfer (CPET). In this reaction, the electron is transferred to an outer-sphere oxidant, and the proton is transferred from the oxygen to nitrogen atom. In the present study, this reaction is studied computationally using a version of Hammes-Schiffer’s multistate continuum theory where CPET is formulated as a transmission frequency between neutral and cation vibrational-electronic states. The neutral and cation proton vibrational wave functions are computed from one-dimensional potential energy surfaces (PESs) for the transferring proton in a fixed heavy atom framework. The overlap integrals for these neutral/cation wave functions, considering several initial (i.e., neutral) and final (i.e., cation) vibrational states, are used to evaluate the relative rates of oxidation. The analysis is extended to heavy atom configurations with various proton donor–acceptor (i.e., O–N) distances to assess the importance of heavy atom “gating”. Such changes in <i>d</i>_ON dramatically affect the nature of the proton PESs and wave functions. Surprisingly, the most reactive configurations have similar donor–acceptor distances despite the large (∼0.2 Å) differences in the optimized structures. These theoretical results qualitatively reproduce the experimental faster reactivity of the reaction of the pyridyl derivative <b>1</b> versus the CH₂–pyridyl <b>2</b>, but the computed factor of 5 is smaller than the experimental 10². The amine derivative is calculated to react similarly to <b>1</b>, which does not agree with the experiments, likely due to some of the simplifying assumptions made in applying the theory. The computed kinetic isotope effects (KIEs) and their temperature dependence are in agreement with experimental results

Sulfur K-Edge X-ray Absorption Spectroscopy and Density Functional Theory Calculations on Monooxo MoIV and Bisoxo MoVI Bis-dithiolenes: Insights into the Mechanism of Oxo Transfer in Sulfite Oxidase and Its Relation to the Mechanism of DMSO Reductase

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two complexes [MoIVO(bdt)2]2– and [MoVIO2(bdt)2]2– (bdt = benzene-1,2-dithiolate(2−)) that relate to the reduced and oxidized forms of sulfite oxidase (SO). These are compared with those of previously studied dimethyl sulfoxide reductase (DMSOr) models. DFT calculations supported by the data are extended to evaluate the reaction coordinate for oxo transfer to a phosphite ester substrate. Three possible transition states are found with the one at lowest energy, stabilized by a P–S interaction, in good agreement with experimental kinetics data. Comparison of both oxo transfer reactions shows that in DMSOr, where the oxo is transferred from the substrate to the metal ion, the oxo transfer induces electron transfer, while in SO, where the oxo transfer is from the metal site to the substrate, the electron transfer initiates oxo transfer. This difference in reactivity is related to the difference in frontier molecular orbitals (FMO) of the metal–oxo and substrate–oxo bonds. Finally, these experimentally related calculations are extended to oxo transfer by sulfite oxidase. The presence of only one dithiolene at the enzyme active site selectively activates the equatorial oxo for transfer, and allows facile structural reorganization during turnover

Substrate and Metal Control of Barrier Heights for Oxo Transfer to Mo and W Bis-dithiolene Sites

Reaction coordinates for oxo transfer from the substrates Me₃NO, Me₂SO, and Me₃PO to the biologically relevant Mo­(IV) bis-dithiolene complex [Mo­(OMe)­(mdt)₂]⁻ where mdt = 1,2-dimethyl-ethene-1,2-dithiolate­(2-), and from Me₂SO to the analogous W­(IV) complex, have been calculated using density functional theory. In each case, the reaction first proceeds through a transition state (TS1) to an intermediate with substrate weakly bound, followed by a second transition state (TS2) around which breaking of the substrate X–O bond begins. By analyzing the energetic contributions to each barrier, it is shown that the nature of the substrate and metal determines which transition state controls the rate-determining step of the reaction

Release of cclib version 1.5

<p>This is an archive of the source code for cclib version 1.5, orginally released on github (https://github.com/cclib/cclib/releases/tag/v1.5).</p

Substrate and Metal Control of Barrier Heights for Oxo Transfer to Mo and W Bis-dithiolene Sites

Reaction coordinates for oxo transfer from the substrates Me₃NO, Me₂SO, and Me₃PO to the biologically relevant Mo­(IV) bis-dithiolene complex [Mo­(OMe)­(mdt)₂]⁻ where mdt = 1,2-dimethyl-ethene-1,2-dithiolate­(2-), and from Me₂SO to the analogous W­(IV) complex, have been calculated using density functional theory. In each case, the reaction first proceeds through a transition state (TS1) to an intermediate with substrate weakly bound, followed by a second transition state (TS2) around which breaking of the substrate X–O bond begins. By analyzing the energetic contributions to each barrier, it is shown that the nature of the substrate and metal determines which transition state controls the rate-determining step of the reaction

Multiple-Site Concerted Proton–Electron Transfer Reactions of Hydrogen-Bonded Phenols Are Nonadiabatic and Well Described by Semiclassical Marcus Theory

Photo-oxidations of hydrogen-bonded phenols using excited-state polyarenes are described to derive fundamental understanding of multiple-site concerted proton–electron transfer reactions (MS-CPET). Experiments have examined phenol bases having −CPh₂NH₂, −Py, and −CH₂Py groups <i>ortho</i> to the phenol hydroxyl group and <i>tert</i>-butyl groups in the 4,6-positions for stability (<b>HOAr-NH</b>_<b>2</b>, <b>HOAr-Py</b>, and <b>HOAr-CH</b>_<b>2</b><b>Py</b>, respectively; Py = pyridyl; Ph = phenyl). The photo-oxidations proceed by intramolecular proton transfer from the phenol to the pendent base concerted with electron transfer to the excited polyarene. For comparison, 2,4,6-^<i>t</i>Bu₃C₆H₂OH, a phenol without a pendent base and <i>tert</i>-butyl groups in the 2,4,6-positions, has also been examined. Many of these bimolecular reactions are fast, with rate constants near the diffusion limit. Combining the photochemical <i>k</i>_CPET values with those from prior thermal stopped-flow kinetic studies gives data sets for the oxidations of <b>HOAr-NH</b>_<b>2</b> and <b>HOAr-CH</b>_<b>2</b><b>Py</b> that span over 10⁷ in <i>k</i>_CPET and nearly 0.9 eV in driving force (Δ<i>G</i>^o′). Plots of log­(<i>k</i>_CPET) vs Δ<i>G</i>^o′, including both excited-state anthracenes and ground state aminium radical cations, define a single Marcus parabola in each case. These two data sets are thus well described by semiclassical Marcus theory, providing a strong validation of the use of this theory for MS-CPET. The parabolas give λ_CPET ≅ 1.15–1.2 eV and <i>H</i>_ab ≅ 20–30 cm^–1. These experiments represent the most direct measurements of <i>H</i>_ab for MS-CPET reactions to date. Although rate constants are available only up to the diffusion limit, the parabolas clearly peak well below the adiabatic limit of ca. 6 × 10¹² s^–1. Thus, this is a very clear demonstration that the reactions are nonadiabatic. The nonadiabatic character slows the reactions by a factor of ∼45. Results for the oxidation of <b>HOAr-Py</b>, in which the phenol and base are conjugated, and for oxidation of 2,4,6-^<i>t</i>Bu₃C₆H₂OH, which lacks a base, show that both have substantially lower λ and larger pre-exponential terms. The implications of these results for MS-CPET reactions are discussed