Is phenyl a good migrating group in the rearrangement of organoborates generated from sulfur ylides?

Calculations show that the unexpected low phenyl migratory aptitude observed in reactions of mixed alkyl-aryl boranes with benzylic sulfur ylides can be attributed to (1) a conformational issue, (2) the reduction of the usual neighbouring effect of the phenyl in the transition state by the benzylic nature of the migrating terminus, (3) steric hindrance suffered by the larger phenyl group migrating to the hindered migrating terminus and this despite (4) the increase in the barrier to alkyl migration by the presence of a 'non-migrating' phenyl on the boron atom.     

Is gluconate a good model for isosaccharinate in uranyl(VI) chemistry? A DFT study

The geometries, relative energies and spectroscopic properties of a range of α-isosaccharinate complexes of uranyl(VI) are studied computationally using ground state and time-dependent density functional theory. The effect of pH is accommodated by varying the number of water and hydroxide ligands accompanying isosaccharinate in the equatorial plane of the uranyl unit. For 1 : 1 complexes, the calculated uranyl ν(asym) stretching frequency decreases as pH increases, in agreement with previous experimental data. Three different isosaccharinate chelating modes are studied. Their relative energies are found to be pH dependent, although the energetic differences between them are not sufficient to exclude the possibility of multiple speciation. At higher pH, the uranyl-ligand interactions are dominated more by the equatorial OH(-) than by the organic ligands. Calculated electronic excitation energies support experiment in finding the lowest energy transitions to be ligand → metal charge transfer. (13)C NMR chemical shifts are calculated for the coordinated isosaccharinate in the high pH mimics, and show good agreement with experimental data, supporting the experimental conclusion that the five-membered chelate ring is favoured at high pH. The effect of increasing the isosaccharinate concentration is modelled by calculating 1 : 2 and 1 : 3 uranyl : α-isosaccharinate complexes. Comparison of the results of the present study with those from our closely related investigation of uranyl(VI)-D-gluconate complexes (Dalton Transactions 40 (2011) 11248) reveals strong similarities in structure, bonding, coordination geometry and electronic excitations, but also differences in ΔG for key ligand replacement reactions, suggesting that caution should be exercised when using gluconate as a thermodynamic model for isosaccharinate in uranyl(vi) chemistry.     

Is fifth-order MBPT enough?

Fifth- and higher-order MBPT results are reported for a series of examples, BH, Be₂, HF and H₂O, for which higher-order perturbation theory might be important. MBPT(5) differs from MBPT(4) by as much as 4.3 mh, and by constructing the size-extensive [2,1] Padé approximant, which is possible with E⁽⁵⁾, one can get exceptional agreement with the full CI results. Variational perturbation results are also reported.     

High-resolution continuum source graphite furnace atomic absorption spectrometry: Is it as good as it sounds? A critical review

The recent arrival of high-resolution continuum source atomic absorption spectrometry represents a potential revolution in this field, in particular for direct analysis of complex samples. This review tries to illustrate the main advantages of this technology, paying particular attention to the development of direct solid sampling methods. Three solid sampling applications will be discussed, each one of them highlighting one of the main advantages of this technique. The review also intends to clarify some misconceptions on the true potential of the instrumentation that is currently commercially available, such as its performance for multielemental analysis.     

Are 1,5-disubstituted semibullvalenes that have C2v equilibrium geometries necessarily bishomoaromatic?

Unrestricted density functional theory (UB3LYP), CASSCF, and CASPT2 calculations have been employed to compute the relative energies of the C(s) and C(2v) geometries of several 1,5-disubstituted semibullvalenes. Substitution at these positions with R = F, -CH(2)-, or -O- affords semibullvalenes that are predicted to have C(2v) equilibrium geometries. Calculated singlet-triplet energy splittings and the energies of isodesmic reactions are used to assess the amount of bishomoaromatic character at these geometries. The results of these calculations show that employing strain to destabilize the C(s) geometries of semibullvalenes can lead to a significant decrease in the amount of bishomoaromatic stabilization of the C(2v) geometries, due to reduced through-space interaction between the two allyl groups. However, the C(2v) equilibrium geometries of the 1,5-disubstituted semibullvalenes with R = F and -RR- = -O- do benefit from stabilizing through-bond interactions between the two allyl groups. These interactions involve mixing of the bisallyl HOMO with the low-lying C-F or C-O sigma orbital combinations of the same symmetry. In contrast, for -RR- = -CH(2)-, through-bond interactions destabilize the bisallyl HOMO and are predicted to make the ground state of this semibullvalene a triplet.     

Is the Chandler Period Stable?

The problem on the Chandler period is an unsolved one. Several authors suggested a hypothesis that the Chandler wobble is only one free period which slightly changes in time and is amplitude-dependent. In this paper, we shall examine the hypothesis more rigorous than that which has been carried yet. A new deconvolution method for Fourier transform is suggested. Using this method, the polar motion data since 1900 are analysed and the varying process of the Chandlerian period and amplitude are given. The analytical results show that the Chandler period is not stable and is indeed amplitude-dependent. The probable explanation for this phenomenon is that it might be caused by non-equilibrium response of the ocean.     

Is solar UV frying fish?

A personal selection of 39 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as the first natural polyarsenic organic natural product, arsenicin A, from the sponge Echinochalina bargibanti.     

Is 2-cyclopropylpropene really gauche?

Infrared spectra of gaseous and solid 2-cyclopropylpropene (2-CPP, c-C3H5C (CH3)CH2) have been recorded from 3500 to 40 cm-1, and Raman spectra (3200-150 cm-1) of the liquid as well as mid-infrared spectra of 2-CPP in liquid krypton solution (from -105 to -150 degrees C) were also obtained. Ab initio calculations, with basis sets up to 6-311+G(2df, 2pd), were carried out for this molecule, using the restricted Hartree-Fock (RHF) approach, with full electron correlation by the perturbation method to second order (MP2(full)) and density functional theory (DFT) by the B3LYP method. The combination of the experimental and computational results (particularly with the higher basis sets) unequivocally identifies the more stable conformer of 2-CPP as the trans form, with the gauche rotamer higher in energy, but also stable. The cis structure of this compound is not observed experimentally, and is predicted by the computational approaches to be a transition state. By studying the temperature variation of two well-resolved sets of conformational doublets of 2-CPP dissolved in liquid krypton, an average enthalpy difference between conformers of 182+/-18 cm-1 (2.18+/-0.22 kJ mol-1) has been determined, with the trans conformation lower in energy in the fluid states, and the sole conformer present in the polycrystalline solid phase. This enthalpy difference corresponds to an ambient temperature conformational equilibrium in the fluid phases of 2-cyclopropylpropene containing approximately 55+/-2% of the more stable trans rotameric form. A complete vibrational assignment for the trans conformer of 2-CPP is given, and many of the bands of the gauche rotamer have also been assigned. Structural parameters, dipole moments, and rotational constants for this molecule have been calculated at the MP2(full)/6-311+G(d,p) level, and these results--as well as the results from the experimental studies--are compared to similar quantities in related compounds.     

Is Water Templating Nanoporous Materials?

(H(2)O)(17), a cluster with pentagonal water arrangements, squeezed in the sodalite cage of the crystal structure MIL-74 (Zn(6)Al(12)P(24)O(96).[N(CH(2)CH(2)NH(3))(3)](8).(H(2)O)(34)), has its oxygen atoms well located by X-ray powder diffraction. Positioning of hydrogen atoms has been performed by a dynamic partial atomic charges and hardnesses analysis calculation, in which partial charges are recalculated for each hydrogen sub-network modification. Hydrogen atoms are therefore positioned by energy minimization. A quantitative estimation of the hydrogen bonds energy for each H-bond and for the network in the MIL-74 nanoporous compound has been obtained. This result allows a discussion of the effect of imprinting the nanoporous structure onto water or alternatively the templating effect of the cluster onto the inorganic framework.     

Is GVB-CI superior to CASSCF?

Presently the most reliable approach for the study of reaction pathways where chemical bonds are broken and formed is to carry out CASSCF calculations followed by corresponding multireference perturbation or CI treatments. The latter step generally relaxes the “antibonding character” of the CASSCF results. In this study we demonstrate that similar results can be well approximated by using a less optimized MCSCF method and not performing the multireference perturbation or CI step at all. This is accomplished by performing a complete CI calculation within the active orbital space of the generalized valence bond perfect pairing (GVB-PP) model. The local bond/antibond character of the orbital space of the GVB-PP method also allows development of a fast, but robust, Bethe–Goldstone algorithm, which reconstructs the CI energy to an accuracy of a few tenths of a millihartree for most types of bond breaking cases found in chemical reactions. This algorithm executes at a speed proportional to N where N_p is the number of localized electron pairs in the active space. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 999–1008, 1999     

Is the Cassie-Baxter formula relevant?

The utility of the Cassie-Baxter formula to predict the apparent contact angle of a drop on rough hydrophobic surfaces has been questioned recently. To resolve this issue, experimental and numerical data for advancing and receding contact angles are reported. In all cases considered it is seen that contact angles follow the overall trend of the Cassie-Baxter formula, except for the advancing front on pillar type roughness. It is shown that deviations from the Cassie-Baxter angle have a one-to-one correlation with microscopic distortions of the contact line with respect to its configuration in the Cassie-Baxter state.     

Freely available conformer generation methods: how good are they?

Conformer generation has important implications in cheminformatics, particularly in computational drug discovery where the quality of conformer generation software may affect the outcome of a virtual screening exercise. We examine the performance of four freely available small molecule conformer generation tools (Balloon, Confab, Frog2, and RDKit) alongside a commercial tool (MOE). The aim of this study is 3-fold: (i) to identify which tools most accurately reproduce experimentally determined structures; (ii) to examine the diversity of the generated conformational set; and (iii) to benchmark the computational time expended. These aspects were tested using a set of 708 drug-like molecules assembled from the OMEGA validation set and the Astex Diverse Set. These molecules have varying physicochemical properties and at least one known X-ray crystal structure. We found that RDKit and Confab are statistically better than other methods at generating low rmsd conformers to the known structure. RDKit is particularly suited for less flexible molecules while Confab, with its systematic approach, is able to generate conformers which are geometrically closer to the experimentally determined structure for molecules with a large number of rotatable bonds (≥10). In our tests RDKit also resulted as the second fastest method after Frog2. In order to enhance the performance of RDKit, we developed a postprocessing algorithm to build a diverse and representative set of conformers which also contains a close conformer to the known structure. Our analysis indicates that, with postprocessing, RDKit is a valid free alternative to commercial, proprietary software.     

Is the stereomutation of methane possible?

Large basis set ab initio calculations at correlated levels, including MP2, single reference, as well as multireference configuration interaction, carried out on the methane potential energy surface, have located and characterized a transition structure for stereomutation (one imaginary frequency). This structure is best described as a pyramidal complex between singlet methylene and a side-on hydrogen molecule with C_s symmetry. At the single reference CI level, it lies 105 kcal/mol above the methane T_d-ground state but is stable relative to dissociation into CH₂(¹A₁) and H₂ by 13 kcal/mol at 0 K (with harmonic zero point energy (ZPE) corrections for all structures). Dissociation of the transition state into triplet methylene and hydrogen also is endothermic (by 4 kcal/mol), but single bond rupture to give CH and H^. is 3 kcal/mol exothermic. Thus, it does not appear likely that methane can undergo stereomutation classically beneath the dissociation limit. Confirming earlier conclusions, side-on insertion of ¹A₁ CH₂ into H₂ in a perpendicular geometry occurs without activation energy. Planar (D_4h) methane (130.5 kcal/mol) has four imaginary frequencies. Two of these are degenerate and lead to equivalent planar C_2v structures with one three-center, two-electron bond and two two-electron bonds and two imaginary frequencies. The remaining imaginary frequencies of the D_4h form lead to tetrahedral (T_d) and pyramidal (C_4v) methane. The latter has three negative eigenvalues in the force-constant matrix; one of these leads to the T_d global minimum and the other to the C_s (parallel) stereomutation transition structure. Multireference CI calculations with a large atomic natural orbitals basis set produce similar results, with the electronic energy of the C_s stereomutation transition state 0.7 ± 0.5 kcal/mol higher than that of CH + H^. dissociation products, and a ZPE-corrected energy which is 5 ± 1 kcal/mol higher. Also considered are photochemical pathways for stereomutation and the possible effects of nuclear spin, inversion tunneling, and the parity-violating weak nuclear interaction on the possibility of an experimental detection of stereomutation in methane. © 1995 by John Wiley & Sons, Inc.     

Is osmium diboride an ultra-hard material?

We report first-principles calculations of ideal tensile and shear strength for the recently synthesized orthorhombic OsB2 that is a primary example of a new class of ultra-hard materials synthesized by combining small, light, and covalent elements with large, electron-rich transition metals. Our calculations show that the shear strength on the (001) plane is highly anisotropic with a low peak stress of 9.1 GPa in the (001)[010] shear direction but a much higher peak stress of 26.9 GPa in the (001)[100] direction. The strong resistance against (001)[100] shear deformation prevents the indenter from making a deep imprint, giving rise to a high Vickers hardness on the (001) plane, despite the weak shear strength in the (001)[010] shear direction. The calculated peak stress of 26.9 GPa in the (001)[100] shear direction agrees well with the 30 GPa Vickers hardness observed experimentally on the (001) plane in OsB2. However, the weak shear strength (9.1 GPa) in the (001)[010] shear direction severely limits its application as abrasives and cutting tools for ferrous metals as well as scratch-resistance coatings. Our results highlight the importance of understanding atomistic deformation modes under various loading conditions in designing new ultra-hard materials.     

Is Enantioselectivity Predictable in Asymmetric Catalysis?

S ee ing into the future : A range of computational methods have been applied to harmonize predicted ee values with experimental values. Novel ways of combining quantum mechanics and molecular mechanics feature prominently.