Coordination or local environments have been used to describe, analyze, and understand crystal structures for more than a century. Here, we present a new tool called ChemEnv, which can identify coordination environments in a fast and robust manner. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen package and the software can as well be used through a web app available on http://crystaltoolkit.org through the Materials Project.

Coordination or local environments (e.g., tetrahedra and octahedra) are powerful descriptors of the crystalline structure of materials. These structural descriptors are essential to the understanding of crystal chemistry and the design of new materials. However, extensive statistics on the occurrence of local environment are not available even on common chemistries such as oxides. Here, we present the first large-scale statistical analysis of the coordination environments of cations in oxides using a large set of experimentally observed compounds (about 8000). Using a newly developed method, we provide the distribution of local environment for each cation in oxides. We discuss our results highlighting previously known trends and unexpected coordination environments, as well as compounds presenting very rare coordinations. Our work complements the know-how of the solid state chemist with a statistically sound analysis and paves the way for further data mining efforts linking, for instance, coordination environments to materials properties.

CeO2-xnanorods are functional mimics of natural haloperoxidases. They catalyze the oxidative bromination of phenol red to bromophenol blue and of natural signaling molecules involved in bacterial quorum sensing. Laboratory and field tests with paint formulations containing 2 wt% of CeO2-x nanorods show a reduction in biofouling comparable to Cu2O, the most typical biocidal pigment.

In their perspective ‘‘Computational studies on organic reactivity in ionic liquids’’ Chiappe and Pomelli have written a short paragraph excluding COSMO-RS as a potential method for estimating reaction thermodynamics in ionic liquids. They write: ‘‘COSMO-RS, a model based on a simplified version of the polarizable continuum model, which is strongly parameterized, has been used to estimate the thermodynamics of a solvent. However, this model is unable to give a precise physical description of the system and the parameterization set does not include reaction barriers; therefore, COSMO-RS is not suitable for reactivity studies.’’ Since the authors reference just one out of many application papers by COSMO-RS users and do not give conclusive reasoning for their statement, we feel the necessity to comment on the usability of COSMO-RS for estimating reaction thermodynamics and kinetics in ionic liquid media. As a matter of fact, COSMO-RS is based on the Conductorlike Screening Model (COSMO), and COSMO is – although developed independently – a simpler and thus numerically more efficient continuum solvation model than the polarizable continuum model. Nevertheless it must be pointed out that there is no proof in the literature that the conceptual simplifications of COSMO have any negative influence on the quality of results. Instead, it turned out to be more accurate with respect to the outlying charge problem, and for that reason the COSMO boundary condition has even been integrated into the polarizable continuum model as C-PCM. COSMO-RS is a combination of COSMO – used in its limit of the perfect conductor – and a statistical thermodynamics of pair-wise interacting surface segments, where the surface interactions are quantified based on the COSMO polarization charge densities. By that COSMO-RS treats solutes and solvents on the same quantum chemical footing, and introduces the concepts of mixtures and temperature dependence in a natural, thermodynamically consistent way. As a result it does not require any chemistry dependent parameters for the solvents, which in almost all other solvation models require special parameterization. Altogether COSMO-RS thus has less adjustable parameters than most other solvation models. If the authors want to claim the opposite, they shall clearly demonstrate this claim. Quite surely COSMO-RS overall has by far less adjustable parameters than the specially adapted IL-force fields required for the QM/MM, recommended as the method of choice in this perspective. COSMO-RS has been proven in a large number of application papers to be well applicable to study solvation thermodynamics in ionic liquids, even though initially completely parameterized on neutral compounds and solvents. A GoogleScholar search for ‘‘Ionic Liquids’’ in combination with ‘‘COSMO-RS’’ yields 874 hits as of Nov. 29, 2012. On the other hand, COSMO-RS has been proven to be applicable to study reaction thermodynamics and reaction kinetics in solution. Very recently, various authors have reported the application of COSMO-RS to the study of chemical absorption of CO2 in ionic liquids. The trends predicted for the thermodynamic properties of different ILs using COSMO-RS, such as CO2 solubility, reaction enthalpy, and solvent reversal temperature, were verified by experimental data. These results suggest that COSMO-RS can be successfully used to predict reaction thermodynamics in systems involving ILs, providing a useful computational tool for the development of new CO2 absorbents. To our knowledge, COSMO-RS applications to estimate reaction a COSMOlogic GmbH&CoKG, Burscheider Str. 515, 51381 Leverkusen, Germany. E-mail: klamt@cosmologic.de; Tel: +49 2171 731681 b Institute of Physical and Theoretical Chemistry, University of Regensburg, Germany c Polymer Physics and Analytics, BASF SE, 67056 Ludwigshafen, Germany d Sección de Ingenierı́a Quı́mica (Departamento de Quı́mica Fı́sica Aplicada), Universidad Autónoma de Madrid, 28049 Madrid, Spain Received 22nd January 2013, Accepted 26th April 2013

The utility of a thiophene anchor unit as an alternative for thiols in the immobilisation of ruthenium and osmium complexes on gold and platinum is examined with special attention focused on the relative contributions of physi- and chemisorption of the complexes and the chemical stability of the thiophene anchoring unit. The redox and spectroscopic properties of the ruthenium(II) and osmium(II) complexes are described in solution and the effect of surface immobilisation examined through a combined electrochemical and surface-enhanced Raman spectroscopic study. A key finding is that although the thiophene unit is involved in surface anchoring it also undergoes chemical reactions with the gold surface as demonstrated by Raman spectroscopy.

Many technically relevant chemical processes in the condensed phase involve as elementary reactive steps the formation of ions from neutral species or, as the opposite, recombination of ions. Such reactions that generate or annihilate charge defy the standard gas phase quantum chemical treatment, and also continuum solvation models are only partially able to account for the right amount of stabilization in solution. In this work, for such types of reaction, a solvation treatment involving the COSMO‐RS method is assessed, which leads to improved results, i.e., errors of only around 10 kJ/mol for both protic and aprotic solvents. The examples discussed here comprise protolysis reactions and organo halide heterolysis, for both of which a comparison with reliable experimental data is possible. It is observed that for protolysis, the quality of results does not strongly depend on the quantum chemical method used for energy calculation. In contrast, in the case of heterolytic carbon‐chlorine bond cleavage, clearly better results are obtained for higher correlated (coupled cluster) methods or the density functional M06‐2X, which is well known for its accuracy if applied to organic chemistry. This hints at least that the right answer is obtained for the right reason and not due to a compensation of errors from gas phase thermodynamics with those from the solvation treatment. Problems encountered with certain critical solvents or upon decomposing Gibbs free energies into heats or entropies of reaction are found to relate mostly to the parameterization of the H‐bonding term within COSMO‐RS. © 2012 Wiley Periodicals, Inc.

We present the software package M O V I P AC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. M O V I P AC unites the latest versions of the programs S NF and A KIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, M O V I P AC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 ( S )‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 3 10 ‐helical analogs. © 2012 Wiley Periodicals, Inc.

In this work, we investigate the mechanism of the ammonia-dinitrogen exchange reaction, which is the decisive step to close the catalytic cycle of Schrock's dinitrogen reduction sequence under ambient conditions. We identify several viable pathways for the approach of dinitrogen to the five-coordinate molybdenum center of the ammonia complex by means of first-principles molecular-dynamics simulations. These exploratory simulations are then complemented by rigorous quantum-chemical structure optimizations. Our calculations have been performed for the full Schrock catalyst without simplifying the large chelate ligand, and are hence not affected by model assumptions. We show that the reaction obeys an addition-elimination mechanism via a stable six-coordinate intermediate. This intermediate has been fully characterized by stationary quantum-chemical methods. The predicted infrared spectrum of this species features an N[triple bond]N stretching vibration, which is well separated in frequency from all other N[triple bond]N stretching vibrations of N(2)-binding complexes involved in the Schrock cycle. Depending on the life time of this intermediate in the reaction liquor, the production of this intermediate might even be monitored by the absorption of the N[triple bond]N stretching vibration.

Catalytic dinitrogen reduction with the Schrock complex is still hampered by low turn-over numbers that are likely to result from a degradation of the chelate ligand. In this work, we investigate modifications of the original HIPTN(3)N ligand applied by Schrock and co-workers in catalytic reduction of dinitrogen with density functional methods. We focus on ligands that are substituted in the para position of the central phenyl ring of the terphenyl moieties and on a ligand where the bridging nitrogen is exchanged by phosphorus. In addition, results for tris(pyrrolyl-alpha-methyl)amine, tris(pyrrolyl-alpha-ethyl)amine, and tris[2-(3-xylyl-imidazol-2-ylidene)ethyl]amine are reported. For this study, we take into account the full ligands without approximating them by model systems. Reaction energies for the various derivatives of HIPTN(3)N are found to be similar to those of the unchanged parent system. However, the most promising results for catalysis are obtained for the [{tris[2-(3-xylyl-imidazol-2-ylidene)ethyl]amine}Mo](N(2)) complex. Feasibility of the exchange of NH(3) by N(2) is found to be the pivotal question whether a complex can become a potential catalyst or not. A structure-reactivity relationship is derived which allows for the convenient estimation of the reaction energy for the NH(3)/N(2) exchange reaction solely from the wavenumber of the N[triple bond]N stretching vibration. This relationship may guide experiments as soon as a dinitrogen Mo complex is formed.

The macrocyclic ligand [13]aneN(4) (L1, 1,4,7,10-tetra-azacyclotridecane) was reacted with Zn(II) perchlorate and CO2 in an alkaline methanol solution. It was found that, by means of subtle changes in reaction conditions, two types of complexes can be obtained: (a) the mu(3) carbonate complex 1, {[Zn(L1)](3)(mu(3)-CO3)}(ClO4)(4), rhombohedral crystals, space group R3c, with pentacoordinate zinc in a trigonal bipyramidal enviroment, and (b) an unprecedenced dimeric Zn(II) carbamate structure, 2, [Zn(L2)](2)(ClO4)(2), monoclinic crystals, space group P2(1)/n. The ligand L2 (4-carboxyl-1,4,7,10-tetra-azacyclotridecane) is a carbamate derivative of L1, obtained by transformation of a hydrogen atom of one of the NH moieties into carbamate by means of CO2 uptake. In compound 2, the distorted tetrahedral Zn(II) coordinates to the carbamate moiety in a monodentate manner. Most notably, carbamate formation can occur upon reaction of CO2 with the [ZnL1](2+) complex, which implicates that a Zn-N linkage is cleaved upon attack of CO2. Since complexes of tetra-azamacrocycles and Zn(II) are routinely applied for enzyme model studies, this finding implies that the Zn-azamacrocycle moiety generally should no longer be considered to play always only an innocent role in reactions. Rather, its reactivity has to be taken into account in respective investigations. In the presence of water, 2 is transformed readily into carbonate 1. Both compounds have been additionally characterized by solid-state NMR and infrared spectroscopy. A thorough comparison of 1 with related azamacrocycle ligated zinc(II) carbonates as well as a discussion of plausible reaction paths for the formation of 2 are given. Furthermore, the infrared absorptions of the carbamate moiety have been assigned by calculating the vibrational modes of the carbamate complex using DFT methods and the vibrational spectroscopy calculation program package SNF.

In this work, we investigate with density functional methods mechanistic details of catalytic dinitrogen reduction mediated by Schrock's molybdenum complex under ambient conditions. We explicitly take into account the full HIPTN 3N ligand without approximating it by model systems. Our data show that replacement of the bulky HIPT substituent by smaller groups leads to deviations in energy of up to 100 kJ mol (-1). Alternatives to the Chatt-like mechanism are also investigated. It turns out that for the generation of the first molecule of ammonia, protonation of the ligand plays a crucial role. With an increasing number of hydrogens on the terminal nitrogen atom, the reduction becomes more difficult. The energetically most feasible step is the generation of the first molecule of ammonia, while the preceding transfer of the second electron and proton is the most difficult one. Reaction energies are not only reported for decamethyl chromocene as in previous studies but also for a series of other metallocenes. Furthermore, results are provided in a way to allow for a convenient estimation of the thermochemical boundary conditions of catalysis with an arbitrary combination of acid and reductant. We demonstrate that the [Mo](NNH 3) (+) complex easily loses ammonia even in the absence of a reductant. For some complexes, spin states with higher multiplicity are the ground state instead of those with lower spin multiplicity.

Carbonic anhydrase (CA) is known to react with carbonyl sulfide, an atmospheric trace gas, whereby H(2)S is formed. It has been shown that, in the course of this reaction, the active catalyst, the His(3)ZnOH structural motif, is converted to its hydrosulfide form: His(3)ZnOH+COS-->His(3)ZnSH+CO(2). In this study, we elucidate the mechanism of reactivation of carbonic anhydrase (CA) from its hydrosulfide analogue by using density functional calculations, a model reaction and in vivo experimental investigation. The desulfuration occurs according to the overall equation His(3)ZnSH+H(2)O right harpoon over left harpoon His(3)ZnOH+H(2)S. The initial step is a protonation equilibrium at the zinc-bound hydrosulfide. The hydrogen sulfide ligand thus formed is then replaced by a water molecule, which is subsequently deprotonated to yield the reactivated catalytic centre of CA. Such a mechanism is thought to enable a plant cell to expel H(2)S or rapidly metabolise it to cysteine via the cysteine synthase complex. The proposed mechanism of desulfuration of the hydrosulfide analogue of CA can thus be regarded as the missing link between COS consumption of plants and their sulfur metabolism.

Chiral examples of phosphazene bases 2a-c were synthesized by treatment of (S)-2-(dialkylaminomethyl)pyrrolidine 1a-c, derived from 5-oxo-(S)-proline, with phosphorus pentachloride and subsequent addition of gaseous ammonia. The phosphazenes 2a-c were isolated as HBF4 salts in high yields and fully characterized by H-1, C-11 and P-31 NMR spectroscopy, various 1D and 2D NTAR experiments and mass spectrometry (EI). The molecular structure and the absolute configuration of the salts 2a-c center dot HBF4 were determined by Xray analysis. DFT calculations indicate that 2a is more basic than the Schwesinger base P-1 by approximately nine pK(a) units. ((c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006).

The chemcompounds.dtx package allows for a simple consecutive num- bering of chemical compounds. Optionally, it is possible to supply a custom name for each compound. By default the compounds are numbered following the order of their appearance in the text.