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O- and S-heterocyclic carbenes (OHCs, SHCs) are shown experimentally and computationally to be stronger pi acceptors than NHCs and lack, of course, substituents at the heteroatoms. These different electronic and steric characteristics make OHCs and SHCs interesting ligands for coordination chemistry. Convenient synthetic routes are presented to access their iridium(I), iridium(III), and coinage-metal(I) (Cu, Ag, Au) complexes in good yields by means of dissociation of olefins, deprotonation of precursor salts, and transmetalation from a silver carbene complex Molecular structures and detailed bonding analyses of these complexes are presented.

ispartof: Acs Catalysis vol:11 issue:21 pages:13603-13648 status: published

openaire: EC/H2020/824143/EU//MAX CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Some examples of atropoisomeric pseudorotaxanes in which the isomerism arises by the different conformations adopted by the wheel are reported here. Upon threading hexahexyloxycalix[6]arene 1 with ammonium axles 2+ or 3+, bearing biphenyl or trifluoromethylbenzyl moieties, respectively, two atropoisomeric pseudorotaxanes were formed in which the calix[6]-wheel 1 adopts the 1,2,3-alternate and cone conformations. The interconversion between them cannot be obtained by simple rotation around the ArCH2Ar bonds of the calixarene wheel, which is blocked by the presence of the axle inside its cavity. Therefore, it can only be obtained through a mechanism of de-threading/re-threading of the axle. In all the examined cases, the 1,2,3-alternate and cone atropoisomers are, respectively, the kinetic and the thermodynamic ones.

The characteristic cross-beta-sheet-rich amyloid fibril formation by intrinsically disordered alpha-synudein proteins is one of the pathological hallmarks of Parkinson's disease. Although unstructured in solution, the presence of auto inhibitory long-range contacts in monomeric form prevents protein aggregation. Out of the various factors that affect the rate of amyloid formation, familial mutations play an important role in a-synuclein aggregation. Even though these mutations are believed to form an aggregation-prone intermediate by perturbing these contacts, the correlation between perturbation and rate of fibril formation is not very straightforward. A combination of solution and solid-state NMR in conjunction with other biophysical methods has been used to identify the underlying mechanism behind the anomaly in the rate of aggregation for the novel mutants H50Q (fast aggregating) and G51D (slow aggregating). Perturbation of long-range contacts at the mutation sites and C-termini in all of the six familial mutants of a-synudein during the diseased condition (acidic pH) was observed. These contacts get rearranged at physiological pH resulting in the shielding of mutation sites. Additional contacts at the mutation site in a slow aggregating mutant could be the reason for slower aggregation. Indeed, these contacts provide more rigidity to the monomeric G51D. Nonetheless, these mutations did not alter the overall secondary structure. The differential pattern of the long-range contacts at the monomeric level resulted in the perturbation of the fibrillar-core region, which was evident in the solid-state NMR spectra. Our results provide valuable insights in understanding the effect of long-range contacts on the aggregation of a-synuclein and its mutants.

The halogenation of the C-H bond by metal-oxo-peroxo species and the decarbonylation of aldehydes by metal-peroxo species are performed routinely in biological systems. However, metal-mediated decarbonylative halogenation is unknown in nature. In this work, we have shown that widely available V2O5 and VO(acac)(2) (acac=acetylacetonate) can catalyze decarbonylative halogenation through the generation of an inter-mediate vanadium-oxo-peroxo species, which was characterized by using V-51 NMR, UV/Vis, and resonance Raman spectroscopy. Further detection of formic acid from the reaction mixture confirmed the biomimetic aspects of decarbonylative halogenation. A detailed experimental and DFT study indicated a concerted mechanism for this decarbonylative halogenation performed under simple and mild reaction conditions.

In this brief review, synthesis, structural and reactivity aspects of heavier organochalcogen (RS+n, RSe+n, RTe+n;n = 1-3) cations have been described. The orgaosulfenium ions (RS+) and related sulfur cations have been already reported in detail and, therefore, will not be discussed here. Structurally characterised organochalcogen cations of heavier chalcogens (Se, Te) will be the main focus of the review and only a few relevant examples, which are not structurally characterized, will be discussed for comparison purposes. The collection of chalcogen cations enlisted here shall benefit the readers who are interested in isolating and utilizing the organochalcogen cations for particular applications.

A completely unsymmetrical porous organic cage was synthesized from a C2v symmetrical building block that was identified by a computational screen. The cage was formed through a 12-fold imine condensation of a tritopic C2v symmetric trialdehyde with a di-topic C2 symmetric diamine in a [4+6] reaction. The cage was rigid and microporous, as predicted by the simulations, with an apparent Brunauer-Emmett-Teller surface area of 578 m2 g-1. The reduced symmetry of the tritopic building block relative to its topicity meant there were 36 possible structural isomers of the cage. Experimental characterization suggests a single isomer with 12 unique imine environments, but techniques such as NMR could not conclusively identify the isomer. Computational structural and electronic analysis of the possible isomers was used to identify the most likely candidates, and hence to construct a 3-dimensional model of the amorphous solid. The rational design of unsymmetrical cages using building blocks with reduced symmetry offers new possibilities in controlling the degree of crystallinity, porosity, and solubility, of self-assembled materials.

Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins., The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.

Aromatic properties of two recently synthesized dithienothiophene-bridged (DTT) [34]octaphyrins have been investigated by calculating magnetically induced current densities and vertical excitation energies. These intriguing molecules have been proposed to be the first synthesized neutral bicycloaromatic compounds. The triplet state of their dications was even suggested to be Baird-type bicycloaromatic rendering them very interesting as a new prototype of molecules possessing simultaneously the two rare types of aromaticity. Here, we investigate computationally the aromatic properties of the neutral as well as the singly and doubly charged DTT-bridged [34]octaphyrins. Our study provides unambiguous information about changes in the aromatic properties of the DTT-bridged [34]octaphyrins upon oxidation. The calculations identify two independent diatropic ring currents in the neutral DTT-bridged [34]octaphyrins, showing that they are indeed bicycloaromatic. The current-density flow of the two independent ring currents of the bicycloaromatic compounds are visualized and individual aromatic pathways are quantified by performing numerical integration. The calculations show that two independent diatropic ring currents can indeed be sustained by molecules consisting of two aromatic rings that share a common set of π electrons. The current density calculations on the singly charged DTT-bridged [34]octaphyrins show that they are weakly antiaromatic, which does not agree with the suggested aromatic character deduced from spectroscopical studies. The triplet state of the two DTT-bridged [34]octaphyrin cations with very similar molecular structures have unexpectedly different aromatic character. One of them is Baird-type bicycloaromatic, whereas the triplet state of the other dication has one aromatic and one nonaromatic ring, which could not be resolved from available spectroscopical data. Calculations of excitation energies reveal that a simple model cannot be employed for interpreting the electronic excitation spectra of the present molecules, because more than 20 excited states contribute to the spectra above 2.5 eV (500 nm) showing the importance of computations. The present work illustrates how detailed information about molecular aromaticity can nowadays be obtained by scrutinizing calculated current densities.

Access to chiral calix[4]arenes can unlock novel supramolecular architectures for enantioselective catalysis and molecular recognition. However, accessibility to these structures has been significantly hindered so far. We report herein the synthesis and characterization of di- and trifunctionalized cone-calix[4]arenes featuring a lactone moiety spanning the distal positions at the upper rim. The lactones force the whole skeleton to assume pinched-cone conformations. The ring-closure is favored by the high conformational flexibility of the calixarene scaffold. The new lactones are remarkably stable in the solid state, while a quick hydrolysis to restore the parent carboxylic acids occurs in solution under acidic/basic conditions. Slow aminolyses of lactones 2-3 yield inherently chiral products featuring three different functionalities at the upper rim, at room temperature. The subsequent ring-closing/opening methodology presented here highlights the versatility of these lactones as powerful synthons for the preparation of a variety of threefold upper rim functionalized, inherently chiral calix[4]arenes fixed in the cone structure.

Magnetically induced current densities and ring-current pathways have been calculated at density functional theory (DFT) and second-order Moller-Plesset perturbation theory (MP2) levels of theory for a set of expanded porphyrins consisting of five or six pyrrolic rings. The studied molecules are sapphyrin, cyclo [6]pyrrole, rubyrin, orangarin, rosarin, and amethyrin. Different functionals have been employed to assess the functional dependence of the ring-current strength susceptibility. Vertical singlet and triplet excitation energies have been calculated at the second-order approximate coupled cluster (CC2), expanded multiconfigurational quasi-degenerate perturbation theory (XMC-DPT2), and time-dependent density functional theory levels. The lowest electronic transition of the antiaromatic molecules was found to be pure magnetic transitions providing an explanation for the large paratropic contribution to the total current density. Rate constants for different nonradiative deactivation channels of the lowest excited states have been calculated yielding lifetimes and quantum yields of the lowest excited singlet and triplet states. The calculations show that the spin-orbit interaction between the lowest singlet (S-0) and triplet (T-1) states of the antiaromatic molecules is strong, whereas for the aromatic molecule the spin-orbit coupling vanishes. The experimentally detected fluorescence from S-2 to S-0 of amethyrin has been explained. The study shows that there are correlations between the aromatic character and optical properties of the investigated expanded porphyrins.

Nuclear magnetic shieldings have been calculated at the density functional theory (DFT) level for stacks of benzene, hexadehydro[12]annulene, dodecadehydro[18]annulene, and hexabenzocoronene. The magnetic shieldings due to the ring currents in the adjacent molecules have been estimated by calculating nucleus independent molecular shieldings for the monomer in the atomic positions of neighbor molecules. The calculations show that the independent shielding model works reasonably well for the H-1 NMR shieldings of benzene and hexadehydro[12]annulene, whereas for the larger molecules and for the C-13 NMR shieldings the interaction between the molecules leads to shielding effects that are at least of the same size as the ring current contributions from the adjacent molecules. A better agreement is obtained when the nearest neighbors are also considered at full quantum mechanical (QM) level. The calculations suggest that the nearest solvent molecules must be included in the quantum mechanical system, at least when estimating solvent shifts at the molecular mechanics (MM) level. Current density calculations show that the stacking does not significantly affect the ring current strengths of the individual molecules, whereas the shape of the ring current for a single molecule differs from that of the stacked molecules.

One of the most debilitating diseases Malaria, in its different forms, is caused by protozoan of Plasmodium species. Deadliest among these forms is the "cerebral malaria" which is afflicted upon by Plasmodium falciparum. Plasmodium adopts numerous strategies including various post-translational modifications (PTMs) to infect and survive in the human host. These PTMs have proven their critical requirement in the Plasmodium biology. Recently, sumoylation has been characterized as one of the important PTMs and many of its putative substrates have been identified in Plasmodium. Sumoylation is the covalent attachment of SUMO protein to the substrate protein, which is mediated by an enzyme cascade involving activating (E1), conjugating (E2), and ligating enzymes (E3). Here, we report resonance assignment for H-1, C-13 and N-15 of Plasmodium falciparum SUMO (Pf-SUMO) protein determined by various 2D and 3D heteronuclear NMR experiments along with predicted secondary structures.

Hybrid materials, with co-networks of organic and inorganic components, are increasing in popularity due to their tailorable degradation rates and mechanical properties. To increase mechanical stability, particularly in water, covalent bonding must occur between the components. This can be introduced using crosslinking agents such as 3-glycidoxypropyl trimethoxysilane (GPTMS). Attachment of GPTMS to polymers in aqueous conditions is hypothesized to occur by opening of the epoxide ring by nucleophiles on the polymer chain. Despite side reactions that occur between the epoxide ring of GPTMS and water, a range of NMR techniques showed that the carboxylic acid group of poly(γ-glutamic acid) reacted with GPTMS. This result was used to identify the amino acids in gelatin that reacted most rapidly with the GPTMS epoxide ring, confirming that covalent bonding occurred in gelatin–silica hybrid materials.

The periplasmic binding protein (PBP) FepB plays a key role in transporting the catecholate siderophore ferric enterobactin from the outer to the inner membrane in Gram-negative bacteria. The solution structures of the 34-kDa apo- and holo-FepB from Escherichia coli, solved by NMR, represent the first solution structures determined for the type III class of PBPs. Unlike type I and II PBPs, which undergo large "Venus flytrap" conformational changes upon ligand binding, both forms of FepB maintain similar overall folds; however, binding of the ligand is accompanied by significant loop movements. Reverse methyl cross-saturation experiments corroborated chemical shift perturbation results and uniquely defined the binding pocket for gallium enterobactin (GaEnt). NMR relaxation experiments indicated that a flexible loop (residues 225-250) adopted a more rigid and extended conformation upon ligand binding, which positioned residues for optimal interactions with the ligand and the cytoplasmic membrane ABC transporter (FepCD), respectively. In conclusion, this work highlights the pivotal role that structural dynamics plays in ligand binding and transporter interactions in type III PBPs.

Cyclophilin catalyzes the ubiquitous process "peptidyl-prolyl cis-trans isomerization," which plays a key role in protein folding, regulation, and function. Here, we present a detailed characterization of the unfolding of yeast mitochondria' cyclophilin (CPR3) induced by urea. It is seen that CPR3 unfolding is reversible and proceeds via two intermediates, I1 and 12. The II state has native-like secondary structure and shows strong anilind-8-naphthalenesulphonate binding due to increased exposure of the solvent-accessible cluster of non-polar groups. Thus, it has some features of a molten globule. The 12 state is more unfolded, but it retains some residual secondary structure, and shows weak anilino-8-naphthalenesulphonate binding. Chemical shift perturbation analysis by H-1-N-15 heteronuclear single quantum coherence spectra reveals disruption of the tertiary contacts among the regions close to the active site in the first step of unfolding, i.e., the N-11 transition. Both of the intermediates, 11 and 12, showed a propensity to self-associate under stirring conditions, but their kinetic profiles are different; the native protein did not show any such tendency under the same conditions. All these observations could have significant implications for the function of the protein.

The General AMBER Force Field (GAFF) has been extended to describe a series of selenium and tellurium diphenyl dichalcogenides. These compounds, besides being eco-friendly catalysts for numerous oxidations in organic chemistry, display peroxidase activity, i.e., can reduce hydrogen peroxide and harmful organic hydroperoxides to water/alcohols and as such are very promising antioxidant drugs. The novel GAFF parameters are tested in MD simulations in different solvents and the (77)Se NMR chemical shift of diphenyl diselenide is computed using structures extracted from MD snapshots and found in nice agreement with the measured value in CDCl3. The whole computational protocol is described in detail and integrated with in-house code to allow easy derivation of the force field parameters for analogous compounds as well as for Se/Te organocompounds in general.

The stereochemistry of all four stereoisomers of brivaracetam was determined using vibrational circular dichroism (VCD) spectroscopy. By comparing experimentally obtained VCD spectra and computationally simulated ones, the absolute configurations can be confidently assigned without prior knowledge of their relative stereochemistry. Neither the corrected mean absolute errors analysis of the nuclear magnetic resonance (NMR) data, nor the matching of experimental and calculated infrared spectra allowed the diastereoisomers to be distinguished. VCD spectroscopy itself suffices to establish the absolute configurations of all diastereoisomers. The relative stereochemistry could also be statistically confirmed by matching experimental and computed NMR spectra using the CP3 algorithm. The combination of VCD and NMR is recommended for molecules bearing more than one chiral center, as the relative configurations obtained from NMR serve as an independent check for those established with VCD. Analysis of the calculated VCD spectra reveals that the localized NH2 scissoring mode at around 1600 cm(-1) is characteristic for intramolecular hydrogen bonding, while the orientation of the ethyl group is reflected by the delocalized modes between 1150 and 1050 cm(-1). Chirality 28:215-225, 2016. (c) 2016 Wiley Periodicals, Inc.

A systematic characterization of the competing kosmotropic and chaotropic effects of a series of divalent salts on the aqueous H-bonding structure by means of first-principles molecular dynamics simulations is presented. The structural properties are quantified by means of experimental and computed (HNMR)-H-1 chemical shifts, whereby the local environments of cations and anions can be discriminated. Complementary to the well-established structural features, a dynamical aspect is added to the concept of kosmotropes and chaotropes. The H-bond dynamics, quantified in terms of the H-bonding autocorrelation functions, shows a good correlation with the structural kosmotropic and chaotropic modifications, which are commonly referred to as the Hofmeister series. The considerably enhanced (reduced) fluctuations of the H-bonding network in the hydration shells around the anions (cations) are a complementary dynamical dimension to the concept of kosmotropic/chaotropic behavior of solvated ions.

Much attention has been paid to the role of vortices in the magnetic response properties of superconductors, but less so for molecular systems. Here we present a theoretical analysis on nanographenes subject to a strong homogeneous magnetic field. The analysis is based on the simple Huckel-London model, for which we derive the topological definition of vorticity. The results are confirmed by a more elaborate model that includes nonnearest neighbor interaction, the explicit presence of nuclei and all terms due to the magnetic field. We find that due to frontier orbital intersections, large changes in magnetic dipole moments occur. Orbital energy minima and maxima can be related to change of vortex patterns with flux. ispartof: Journal of Physical Chemistry B vol:110 issue:39 pages:19340-19351 ispartof: location:United States status: published

MBF1 (multi-protein bridging factor 1) is a protein containing a conserved HTH (helix–turn–helix) domain in both eukaryotes and archaea. Eukaryotic MBF1 has been reported to function as a transcriptional co-activator that physically bridges transcription regulators with the core transcription initiation machinery of RNA polymerase II. In addition, MBF1 has been found to be associated with polyadenylated mRNA in yeast as well as in mammalian cells. aMBF1 (archaeal MBF1) is very well conserved among most archaeal lineages; however, its function has so far remained elusive. To address this, we have conducted a molecular characterization of this aMBF1. Affinity purification of interacting proteins indicates that aMBF1 binds to ribosomal subunits. On sucrose density gradients, aMBF1 co-fractionates with free 30S ribosomal subunits as well as with 70S ribosomes engaged in translation. Binding of aMBF1 to ribosomes does not inhibit translation. Using NMR spectroscopy, we show that aMBF1 contains a long intrinsically disordered linker connecting the predicted N-terminal zinc-ribbon domain with the C-terminal HTH domain. The HTH domain, which is conserved in all archaeal and eukaryotic MBF1 homologues, is directly involved in the association of aMBF1 with ribosomes. The disordered linker of the ribosome-bound aMBF1 provides the N-terminal domain with high flexibility in the aMBF1–ribosome complex. Overall, our findings suggest a role for aMBF1 in the archaeal translation process.

International audience; The ability of (95)Mo solid-state nuclear magnetic resonance (SSNMR) spectroscopy to probe the atomic and electronic structures of inorganic molybdenum cluster materials has been demonstrated for the first time. Six cluster compounds were studied: MoBr(2), Cs(2)Mo(6)Br(14), (Bu(4)N)(2)Mo(6)Br(14), each containing the octahedral Mo(6)Br(14)(2-) cluster unit, and MoS(2)Cl(3), Mo(3)S(7)Cl(4), and MoSCl that contain metallic dimers, trimers, and tetramers, respectively. To overcome inherent difficulties due to the low sensitivity of (95)Mo SSNMR, both high-magnetic-field spectrometers and the quadrupolar Carr-Purcell Meiboom-Gill sensitivity enhancement pulse sequence under magic-angle-spinning conditions, combined with a hyperbolic-secant pulse were used. Experimental measurements as well as characterization of the (95)Mo electric field gradient and chemical shift tensors have been performed with the help of quantum-chemical calculations under periodic boundary conditions using the projector augmented-wave and the gauge-including projector augmented-wave methods, respectively. A large (95)Mo chemical shift range is measured, ∼3150 ppm, and the isotropic chemical shift of the Mo atoms is clearly correlated to their formal oxidation degree in the various clusters. Furthermore, a direct relation is evidenced between the molybdenum quadrupolar coupling constant and the bond lengths with its surrounding ligands. Our results demonstrate the efficiency of the combined use of quantum-chemical calculations and (95)Mo SSNMR experiments to study inorganic molybdenum cluster compounds.

A quench-precipitated sample of highly syndiotactic polypropylene (s-PP) (with 86% fully syndiotactic pentads), which shows an X-ray spectrum near that calculated for an ideal orthorhombic C-centered structural model of packing as proposed by Corradini et al. (with chains in a helical (TTGG) n conformation), has been analyzed by high-resolution solid-state 13 C-NMR spectroscopy. The 13 C-NMR CP MAS spectra of this sample, in addition to the resonances already reported in the literature for s-PP (in the B-centered structure), exhibit additional peaks in the regions of the methyl (at 18.9 and 22.4 ppm) and methylene (at 44.9 ppm) groups. It is established that these additional resonances belong indeed to nuclei in well-defined conformational environments fixed in rigid structures placed at the interface of the crystallites and within the strained or disordered area of the crystallites themselves. In particular, the peak at 44.9 ppm in assigned to CH 2 carbon atoms in a TX.YG conformational environment, whereas the resonance at 18.9 ppm is assigned to CH 3 in trans-planar portions of the chain (γ-gauche effect). This indicates local disorder in the C-centered crystalline s-PP sample, due to the presence of conformationally disordered chains. Models of s-PP chains comprising defective but energetically feasible portions of chains in a trans-planar conformation (disturbing the (TTGG) n dominating conformation) are imagined as packed according to a C-pseudocentered structure. In order to keep the methyl groups in a crystalline register and the chains well interdigitated, the defects should be clustered on planes which cross 3D ordered portions in the crystals. The chemical shifts of the carbon atoms in the regions comprising the defect for model chains have been calculated on an ab initio level through the IGLO method, and the results are compared with the experiments. The calculations provide a good explanation of the peculiarities of the experimental 13 C-NMR spectra of the s-PP sample under study. Thus, detailed information on chain defects can be obtained by combining X-ray scattering, solid-state NMR, and computer simulations.

Mild thermolysis of tantalaborane [(Cp*Ta) 2B 5H 11], 1 (Cp* = ? 5-C 5Me 5) in presence of halogen sources affords the open cage clusters [(Cp*TaX) 2B 5H 11], 2-4 (2: X = Cl, 3: X = Br, and 4: X = I) in good yields. In contrast, the tetraborohydride cluster, [(Cp*Ta) 2B 4H 9(?-BH 4)], 5, under the same reaction conditions forms the B-H substituted cluster [(Cp*Ta) 2B 4H 8I(?-BH 4)], 6. All the new metallaboranes have been characterized by mass spectrometry, 1H, 11B, 13C NMR spectroscopy, and elemental analysis, and the structural types were established by crystallographic analysis of clusters 3, 4, and 6. Density functional theory (DFT) calculations at the BP86/TZ2P ZORA level reveal geometries in agreement with the structure determinations, large gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) in accord with their stabilities. B3LYP-computed 11B chemical shifts accurately reflect the experimentally measured shifts. Clusters 2-4 can be viewed as 7-sep 7-vertex oblatoarachno M 2B 5 clusters which can be generated from a 7-sep 9-vertex oblatocloso M 2B 7 cluster by removal of two equatorial boron atoms. Cluster 6 can be considered as an electron-deficient 6-sep 6-vertex oblatoarachno M 2B 4 cluster derived from an 8-vertex oblatocloso hexagonal bipyramidal cluster, in which BH 4 - anion is weakly bonded in a bidentate mode. � 2012 American Chemical Society.

The shaping of a calix(7)ar- ene macrocycle into cone-like structure 3, through exhaustive alkylation of doubly bridged calix(7)arene derivative 2 with bulky groups, has been investi- gated. Conformational details about the structure adopted by calix(7)arene derivative 3 in solution have been ob- tained by using chemical shift surface maps, as previously reported by our group. Thus, chemical shift contour plots indicated that 3 adopted a cone- shaped structure in solution analogous to that adopted by the known p-tert-bu- tylcalix(7)arene heptacarboxylic acid derivative 4. Interestingly, the X-ray structure of derivative 3 showed a high degree of similarity to the theoretical structure, which confirmed the validity of the contour plots method. The pre- organized calix(7)arene host 3 showed interesting recognition abilities toward both organic and alkali cations. In fact, an unprecedented endo-cavity com- plexation of linear and branched alkyl ammonium cations with a larger cal- ix(7)arene host was evidenced. A com- parable affinity for branched tBuNH3 + and linear nBuNH3 + guests was ob

The molecular and electronic structures, stabilities, bonding features, and magnetoresponsive properties of three-membered [c-Ln(3)](+/0/-) (Ln = La, Ce, Pr, Nd, Gd, Lu) and heterocyclic six-membered [c-Ln(3)E(3)](q) (Ln = La, Ce, Pr, Nd, Gd, Lu; E = C, N; q = 0 or 1) rings have been investigated by means of electronic structure calculation methods at the DFT level. The [c-Ln(3)](+/0/-) clusters are predicted to be bound with respect to dissociation to their constituent atoms, the estimated binding energies ranging from 45.8 to 2056.4 kJ/mol. The [c-Ln(3)] rings capture easily a planar three-coordinated nitrogen atom at the center or above the center of the ring yielding the lanthanide nitride clusters [c-Ln(3)(mu(3)-N)] adopting a planar geometry, except [c-La(3)(mu(3)-N)] which exhibits pyramidal geometry. The [c-Ln(3)(mu(3)-N)] clusters are predicted to be bound, with respect to dissociation to N ((4)S) atom and [c-Ln(3)] clusters in their ground states, the binding energies ranging from 53.9 to 257.9 kcal/mol. The six-membered [c-Ln(3)E(3)](q) rings are predicted to be bound with respect to dissociation to LnE(q) monomers in their ground states with dissociation energies in the range of 173.8 to 318.0 kcal/mol. Calculation of the NICS(zz)-scan curves of the clusters predicted a "hermaphrodic" magnetic response of the [c-Ln(3)](+/0/-) and heterocyclic six-membered [c-Ln(3)E(3)](q) rings, manifested by the coexistence of successive diatropic (aromatic) and paratropic (antiaromatic) zones. The [c-La(3)](+/0/-) and [c-Lu(3)](-) are predicted to be weakly antiaromatic, the [c-Lu(3)](0/+), [c-Lu(3)C(3)](+), and [c-Lu(3)N(3)] double (sigma+pi) aromatic, and the [c-Gd(3)C(3)] and [c-Gd(3)N(3)](+) rings (sigma+delta)-aromatic systems. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 620-638, 2011 Journal of Computational Chemistry

Oxidative protein folding in the mitochondrial intermembrane space requires the transfer of a disulfide bond from MIA40 to the substrate. During this process MIA40 is reduced and regenerated to a functional state through the interaction with the flavin-dependent sulfhydryl oxidase ALR. Here we present the mechanistic basis of ALR–MIA40 interaction at atomic resolution by biochemical and structural analyses of the mitochondrial ALR isoform and its covalent mixed disulfide intermediate with MIA40. This ALR isoform contains a folded FAD-binding domain at the C-terminus and an unstructured, flexible N-terminal domain, weakly and transiently interacting one with the other. A specific region of the N-terminal domain guides the interaction with the MIA40 substrate binding cleft (mimicking the interaction of the substrate itself), without being involved in the import of ALR. The hydrophobicity-driven binding of this region ensures precise protein–protein recognition needed for an efficient electron transfer process.

This work is funded by the EPSRC A series of eight 1-halo-8-(alkylchalcogeno)naphthalene derivatives ( 1 – 8 ; halogen=Br, I; alkylchalcogen=SEt, SPh, SePh, TePh) containing a halogen and a chalcogen atom occupying the peri positions have been prepared and fully characterised by using X-ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Naphthalene distortion due to non-covalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X-ray data for 1 , 2 , 4 and 5 – 8 were compared. Molecular structures were analysed in terms of naphthalene ring torsions, peri-atom displacement, splay angle magnitude, X⋅⋅⋅E interactions, aromatic ring orientations and quasi-linear X⋅⋅⋅EC arrangements. A general increase in the X⋅⋅⋅E distance was observed for molecules that contain bulkier atoms at the peri positions. The I⋅⋅⋅S distance of 4 is comparable with the I⋅⋅⋅Te distance of 8 , and is ascribed to a stronger lone pair–lone pair repulsion due to the presence of an axial S(naphthyl) ring conformation. Density functional theory (B3LYP) calculations performed on 5 – 8 revealed Wiberg bond index values of 0.05–0.08, which indicate minor interactions taking place between the non-bonded atoms in these compounds. Postprint

The molecular structure of 1-selena-closo-dodecaborane(11), 1-SeB11H11, has been determined by the concerted use of quantum chemical calculations and gas-phase electron diffraction. The structure has C5v symmetry and is distorted from a regular icosahedron mainly through the expansion of the pentagon of boron atoms adjacent to selenium, with ra3,1(B-B) = 192.2(2) pm. The Se-B bond length is extremely well determined [ra3,1(Se-B) = 212.9(2) pm] and this is reflected by a pronounced peak in the radial-distribution curve. The accuracy of the experimental structure, as well as that calculated at the MP2/962(d) level, has been gauged by comparison of the 11B chemical shifts (calculated at two different gauge-including atomic orbitals (GIAO) levels) with experimental NMR values. The inclusion of electron correlation in the magnetic property calculations (GIAO-MP2) gave superior results to those carried out using GIAO-Hartree-Fock.

Detailed information about unfolded states is required to understand how proteins fold. Knowledge about folding intermediates formed subsequently is essential to get a grip on pathological aggregation phenomena. During folding of apoflavodoxin, which adopts the widely prevalent alpha-beta parallel topology, most molecules fold via an off-pathway folding intermediate with helical properties. To better understand why this species is formed, guanidine hydrochloride-unfolded apoflavodoxin is characterized at the residue level using heteronuclear NMR spectroscopy. In 6.0 M denaturant, the protein behaves as a random coil. In contrast, at 3.4 M denaturant, secondary shifts and (1)H-(15)N relaxation rates report four transiently ordered regions in unfolded apoflavodoxin. These regions have restricted flexibility on the (sub)nanosecond time scale. Secondary shifts show that three of these regions form alpha-helices, which are populated about 10% of the time, as confirmed by far-UV CD data. One region of unfolded apoflavodoxin adopts non-native structure. Of the alpha-helices observed, two are present in native apoflavodoxin as well. A substantial part of the third helix becomes beta-strand while forming native protein. Chemical shift changes due to amino acid residue replacement show that the latter alpha-helix has hydrophobic interactions with all other ordered regions in unfolded apoflavodoxin. Remarkably, these ordered segments dock non-natively, which causes strong competition with on-pathway folding. Thus, rather than directing productive folding, conformational preorganization in the unfolded state of an alpha-beta parallel-type protein promotes off-pathway species formation.

The molecular and electronic structures, stabilities, bonding features, and spectroscopic properties of prototypical ligand stabilized [cyclo-Ru-3(mu(2)-X)(3)](0,3+) (X = H, BH, CH2, NH2, OH, Cl, NH, CO, O, PH2, CF2, CCl2, CNH, N-3) isocycles have been thoroughly investigated by means of electronic structure calculation methods at the DFT level of theory. All [cyclo-Ru-3(mu(2)-X)(3)](0,3+) species, except [cyclo-Ru-3(mu(2)-H)(3)](3+), are predicted to be aromatic molecules. In contrast, the [cyclo-Ru-3(mu(2)-H)(3)](3+) species exhibits a high antiaromatic character, which would be responsible for the well-established peculiar reaction field of hydrido-bridged triruthenium core structures. The aromaticity/antiaromaticity of the model [cyclo-Ru-3(mu(2)-X)(3)](0,3+) isocycles was verified by an efficient and simple criterion in probing the aromaticity/antiaromaticity of a molecule, that of the nucleus-independent chemical shift, NICS(0), NICS(1), NICS(-1), NICSzz(1), and NICSzz(-1), along with the NICS scan profiles. The versatile chemical reactivity of the antiaromatic [cyclo-Ru-3(mu(2)-H)(3)](3+) molecule related to the activation of small molecules that leads to the breaking of various strong single and double bonds is thoroughly investigated by means of electronic structure computational techniques, and the mechanistic details for a representative activation process, that of the dehydrogenation of NH3, to form a triply bridging imido-group (mu(3)-NH) face-capping the Ru-3 ring are presented. Finally, the molecular and electronic structures, stabilities, and bonding features of a series of [cyclo-Ru-3(mu(2)-H)(3)(mu(3)-Nuc)](0,1,2+) (Nuc = BH, BCN, BOMe, C4-, CH3-, CMe3-, N3-, NH, N3-, NCO-, OCN-, NCS-, O2-, S2-, OH-, P3-, POH2-, Cl-, O2(2-), NCH, AlMe, GaMe, C6H6, and cyclo-C3H2Me) products formed upon reacting the archetype [cyclo-Ru-3(mu(2)-H)(3)](3+) molecule with the appropriate substrates are also comprehensibly analyzed. J Am Chem Soc

We report quantum chemistry investigations of the magnetic response of large polycyclic hydrocarbons to a high magnetic field. In strong fields the magnetisation vs. field of nanosize molecules becomes strongly non-monotonic. For nanographenes containing thousands of atoms this effect develops at ca. 10(1)-10(2) T. It is related to the motion of vortices in the frontier molecular orbitals and transformations of ring current patterns. The described phenomenon is general, in principle observable in all conjugated planar nanosize molecules. (c) 2006 Elsevier B.V. All rights reserved. ispartof: Chemical Physics Letters vol:428 issue:1 pages:119-124 status: published

We derive a multi-band formulation of the orbital magnetization in a normal periodic insulator (i.e., one in which the Chern invariant, or in 2d the Chern number, vanishes). Following the approach used recently to develop the single-band formalism [T. Thonhauser, D. Ceresoli, D. Vanderbilt, and R. Resta, Phys. Rev. Lett. {\bf 95}, 137205 (2005)], we work in the Wannier representation and find that the magnetization is comprised of two contributions, an obvious one associated with the internal circulation of bulk-like Wannier functions in the interior and an unexpected one arising from net currents carried by Wannier functions near the surface. Unlike the single-band case, where each of these contributions is separately gauge-invariant, in the multi-band formulation only the \emph{sum} of both terms is gauge-invariant. Our final expression for the orbital magnetization can be rewritten as a bulk property in terms of Bloch functions, making it simple to implement in modern code packages. The reciprocal-space expression is evaluated for 2d model systems and the results are verified by comparing to the magnetization computed for finite samples cut from the bulk. Finally, while our formal proof is limited to normal insulators, we also present a heuristic extension to Chern insulators (having nonzero Chern invariant) and to metals. The validity of this extension is again tested by comparing to the magnetization of finite samples cut from the bulk for 2d model systems. We find excellent agreement, thus providing strong empirical evidence in favor of the validity of the heuristic formula., 14 pages, 8 figures. Fixed a typo in appendix A

Predictions of the unpolarized vibrational absorption and vibrational circular dichroism (VCD) spectra of the chiral molecule 6,8-dioxabicyclo[3.2.1]octane (1) are reported. Harmonic force fields and atomic polar tensors are obtained using the density functional theory (DFT), MP2 and SCF methodologies, and the 3-21G and 6-31G* basis sets. Three functionals, LSDA, BLYP, and B3LYP, are used in DFT calculations. Atomic axial tensors are obtained using the Distribution Origin gauge; distributed atomic axial tensors are calculated using gauge-invariant atomic orbitals (GIAOs) at the SCF level of approximation. The quality of the predicted spectra is highly dependent on the methodology and the basis set is employed. Spectra calculated using 6-31G* MP2 and DFT/B3LYP force fields are very similar and in excellent agreement with experimental spectra. 6-31G* SCF, DFT/LSDA and DFT/BLYP calculations are in significantly worse agreement with experiment, as are 3-21G MP2 and DFT/B3LYP calculations. When both accuracy and computational effort are considered, at this time, predictions of vibrational absorption and VCD spectra of molecules comparable to 1 in size are optimally performed using 6-31G* or equivalent basis sets and (i) harmonic force fields and atomic polar tensors calculated via DFT and a hybrid density functional; (ii) Distributed Origin gauge atomic axial tensors; and (iii) SCF GIAO-based distributed atomic axial tensors.

Atomic axial tensors (AATs) calculated using gauge-invariant atomic orbitals (GIAOs) are more accurate than AATs calculated using field-independent atomic orbitals (FIAOs). Consequently, vibrational rotational strengths and vibrational circular dichroism (VCD) intensities are more accurately predicted using GIAO-based AATs. The increase in accuracy resulting from the use of GIAOs depends on the basis set size. We report calculations of the vibrational rotational strengths and VCD spectra of three chiral moIecules-trans-2,3-d(2)-oxirane, 4-methyl-2-oxetanone, and 6,8-dioxabicydo[3.2.1]octane-at the 6-31G'' basis set level. Harmonic force fields and atomic polar tensors are calculated via density functional theory using the B3LYP functional. Distributed AATs are calculated at the SCF level using both GIAOs and FIAOs. Comparison to experimental VCD spectra (and, in the case of trans-2,3-d(2)-oxirane, to calculations at the TZ2P basis set level) demonstrates the significantly greater accuracy of the calculations using GIAOs.

We present the first calculations of molecular magnetizabilities using London atomic orbitals at the multiconfigurational self-consistent field level. The natural connection is introduced to ensure a numerically stable evaluation of the magnetizability. Furthermore, the natural connection enables us to study the paramagnetic and diamagnetic contributions to the total magnetizability using London atomic orbitals. Large MCSCF calculations are presented for the isoelectronic series BEH(-), BH and CH+, for which correlation is known to be important. The geometry dependence of the magnetizability is investigated and shown to be small. It is demonstrated that BeH- is diamagnetic, contrary to the prediction of a recent study. Our calculated magnetizabilities for the three molecules are: (204-207) x 10(-30) J T-2 (BH), (313-318) x 10(-30) J T-2 (CH+), and (- 62 +/- 5) x 10(-30) J T-2 (BeH-).

The magnetizability of a large number of hydrocarbons-saturated, unsaturated, and aromatic-have been investigated by ab initio methods at the Hartree-Fock level. Gauge-origin independence and size extensivity are imposed by the use of London atomic orbitals (also known as gauge-invariant atomic orbitals). Using a standard basis set adapted for magnetizabilities, results close to the Hartree-Fock limit are obtained. Correlation has a moderate effect on the magnetizabilities. Using an overall scaling factor for the Hartree-Fock results, we obtain magnetizabilities within the experimental error bars for most of the molecules considered. The calculations suggest that the observed gas-phase magnetizabilities contain a calibration error.

We report a systematic investigation of the magnetizability of a series of small molecules. The use of London atomic orbitals ensures gauge invariance and a fast basis set convergence. Good agreement is obtained with experimental magnetizabilities, both isotropic and anisotropic. The calculations suggest a reinvestigation of some of the semi-experimental isotropic magnetizabilities. We have verified experimentally observed changes in the out-of-plane minus the average in-plane magnetizability anisotropy upon fluorine substitution in some planar molecules. Our results do not support the experimental changes observed for similar fluorine substitutions in linear molecules.

Ab initio calculations of Raman differential intensities are presented at the self-consistent field (SCF) level of theory. The electric dipole-electric dipole, electric dipole-magnetic dipole and electric dipole-electric quadrupole polarizability tensors are calculated at the frequency of the incident light, using SCF linear response theory. London atomic orbitals are employed, imposing gauge origin invariance on the calculations. Calculations have been carried out in the harmonic approximation for CFHDT and methyloxirane.

Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C6H6)(CO)(3), MnO3F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omega PBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters. Postprint

Proton MR spectra of the brain, especially those measured at short and intermediate echo times, contain signals from mobile macromolecules (MM). A description of the main MM is provided in this consensus paper. These broad peaks of MM underlie the narrower peaks of metabolites and often complicate their quantification but they also may have potential importance as biomarkers in specific diseases. Thus, separation of broad MM signals from low molecular weight metabolites enables accurate determination of metabolite concentrations and is of primary interest in many studies. Other studies attempt to understand the origin of the MM spectrum, to decompose it into individual spectral regions or peaks and to use the components of the MM spectrum as markers of various physiological or pathological conditions in biomedical research or clinical practice. The aim of this consensus paper is to provide an overview and some recommendations on how to handle the MM signals in different types of studies together with a list of open issues in the field, which are all summarized at the end of the paper.