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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.

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.

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 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.

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.

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

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

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.