There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum.

Abstract. PySpline is a modern computer program for processing raw averaged XAS and EXAFS data using an intuitive approach which allows the user to see the immediate effect of various processing parameters on the resulting k-and Rspace data. The Python scripting language and Qt and Qwt widget libraries were chosen to meet the design requirement that it be cross-platform (i.e. versions for Windows, Mac OS X, and Linux). PySpline supports polynomial pre-and post-edge background subtraction, splining of the EXAFS region with a multi-segment polynomial spline, and Fast Fourier Transform (FFT) of the resulting k 3 -weighted EXAFS data.

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Sulfur K-edge x-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of a series of Mo tris(dithiolene) complexes, [Mo(mdt)

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 ortho to the phenol hydroxyl group and tert-butyl groups in the 4,6-positions for stability (HOAr-NH2, HOAr-Py, and HOAr-CH2Py, 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-tBu3C6H2OH, a phenol without a pendent base and tert-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 kCPET values with those from prior thermal stopped-flow kinetic studies gives datasets for the oxidations of HOAr-NH2 and of HOAr-CH2Py that span over 107 in kCPET and nearly 0.9 eV in driving force (ΔGo′). Plots of log(kCPET) vs. ΔGo′ define a single Marcus parabola in each case, each including both excited state anthracenes and ground state aminium radical cations. These two datasets are thus well described by semi-classical Marcus theory, providing a strong validation of the use of this theory for MS-CPET. The parabolas give λCPET ≅ 1.15–1.2 eV and Hab ≅ 20–30 cm−1. These experiments represent the most direct measurements of Hab 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 non-adiabatic. The non-adiabatic character slows the reactions by a factor of ~45. Results for the oxidation of HOAr-Py, in which the phenol and base are conjugated, and for oxidation of 2,4,6-tBu3C6H2OH, 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.

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two Mo bis-dithiolene complexes, [Mo(OSi)(bdt) 2 ] 1− and [MoO(OSi)(bdt) 2 ] 1− where OSi = [OSiPh 2 t Bu] 1− and bdt = benzene-1,2-dithiolate(2−), that model the Mo(IV) and Mo(VI)=O states of the DMSO reductase family of molybdenum enzymes. These results show that the Mo(IV) complex undergoes metalbased oxidation unlike the Mo(IV) tris-dithiolene complexes, indicating that the dithiolene ligands are behaving innocently. Experimentally-validated calculations have been extended to model the oxo-transfer reaction coordinate using dimethylsulfoxide (DMSO) as a substrate. The reaction proceeds through a transition state (TS1) to an intermediate with DMSO weakly bound, followed by a subsequent transition state (TS2) which is the largest barrier of the reaction. The factors that control the energies of these transition states, the nature of the oxo transfer process, and the role of the dithiolene ligand are discussed.

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 wavefunctions 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 wavefunctions, 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 perturbations dramatically affect the nature of the proton PESs and wavefunctions. 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 1 vs. the CH2-pyridyl 2, but the computed factor of 5 is smaller than the experimental 102. The amine derivative is calculated to react similarly to 1, 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.

BackgroundThe 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.ResultsThis 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.ConclusionsWe 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.