Abstract: The interpretation of nuclear magnetic resonance (NMR) parameters is essential to understanding experimental observations at the molecular and supramolecular levels and to designing new and more efficient molecular probes. In many aromatic natural compounds, unusual (13)C NMR chemical shifts have been reported for out-of-plane methoxy groups bonded to the aromatic ring (~62 ppm as compared to the typical value of ~56 ppm for an aromatic methoxy group). Here, we analyzed this phenomenon for a series of aromatic natural compounds using Density Functional Theory (DFT) calculations. First, we checked the methodology used to optimize the structure and calculate the NMR chemical shifts in aromatic compounds. The conformational effects of the methoxy group on the (13)C NMR chemical shift then were interpreted by the Natural Bond Orbital (NBO) and Natural Chemical Shift (NCS) approaches, and by excitation analysis of the chemical shifts, breaking down the total nuclear shielding tensor into the contributions from the different occupied orbitals and their magnetic interactions with virtual orbitals. We discovered that the atypical (13)C NMR chemical shifts observed are not directly related to a different conjugation of the lone pair of electrons of the methoxy oxygen with the aromatic ring, as has been suggested. Our analysis indicates that rotation of the methoxy group induces changes in the virtual molecular orbital space, which, in turn, correlate with the predominant part of the contribution of the paramagnetic deshielding connected with the magnetic interactions of the BD(CMet-H)→BD*(CMet-OMet) orbitals, resulting in the experimentally observed deshielding of the (13)C NMR resonance of the out-of-plane methoxy group.
Abstract: Determination of nucleic acid (NA) structure with NMR spectroscopy is limited by the lack of restraints on conformation of NA phosphate. In this work, the (31)P chemical shielding tensor, the Γ(P,C5'H5'1) and Γ(P,C5'H5'2) cross-correlated relaxation rates, and the (2)J(P,C3'), (2)J(P,C5'), and (3)J(P,C4') coupling constants were calculated in dependence on NA backbone torsion angles ζ and α. While the orientation of the (31)P chemical shielding tensor was almost independent of the NA phosphate conformation, the principal tensor components varied by up to ~40 ppm. This variation and the dependence of the phosphate geometry on torsion angles ζ and α had only a minor influence on the calculated Γ(P,C5'H5'1) and Γ(P,C5'H5'2) cross-correlated relaxation rates, and therefore, the so-called rigid tensor approximation was here validated. For the first time, the (2)J(P,C) spin-spin coupling constants were correlated with the conformation of NA phosphate. Although each of the two J-couplings was significantly modulated by both torsions ζ and α, the (2)J(P,C3') coupling could be structurally assigned to torsion ζ and the (2)J(P,C5') coupling to torsion α. We propose qualitative rules for their structural interpretation as loose restraints on torsion angles ζ and α. The (3)J(P,C4') coupling assigned to torsion angle β was found dependent also on torsions ζ and α, implying that the uncertainty in determination of β with standard Karplus curves could be as large as ~25°. The calculations provided a unified picture of NMR parameters applicable for the determination of NA phosphate conformation.
Abstract: The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.
Abstract: Among rare gases, xenon features an unusually broad nuclear magnetic resonance (NMR) chemical shift range in its compounds and as a non-bonded Xe atom introduced into different environments. In this work we show that (129)Xe NMR chemical shifts in the recently prepared, matrix-isolated xenon compounds appear in new, so far unexplored (129)Xe chemical shift ranges. State-of-the-art theoretical predictions of NMR chemical shifts in compounds of general formula HXeY (Y = H, F, Cl, Br, I, -CN, -NC, -CCH, -CCCCH, -CCCN, -CCXeH, -OXeH, -OH, -SH) as well as in the recently prepared ClXeCN and ClXeNC species are reported. The bonding situation of Xe in the studied compounds is rather different from the previously characterized cases as Xe appears in the electronic state corresponding to a situation with a low formal oxidation state, between I and II in these compounds. Accordingly, the predicted (129)Xe chemical shifts occur in new NMR ranges for this nucleus: ca. 500-1000 ppm (wrt Xe gas) for HXeY species and ca. 1100-1600 ppm for ClXeCN and ClXeNC. These new ranges fall between those corresponding to the weakly-bonded Xe(0) atom in guest-host systems (δ < 300 ppm) and in the hitherto characterized Xe molecules (δ > 2000 ppm). The importance of relativistic effects is discussed. Relativistic effects only slightly modulate the (129)Xe chemical shift that is obtained already at the nonrelativistic CCSD(T) level. In contrast, spin-orbit-induced shielding effects on the (1)H chemical shifts of the H1 atom directly bonded to the Xe center largely overwhelm the nonrelativistic deshielding effects. This leads to an overall negative (1)H chemical shift in the range between -5 and -25 ppm (wrt CH(4)). Thus, the relativistic effects induced by the heavy Xe atom appear considerably more important for the chemical shift of the neighbouring, light hydrogen atom than that of the Xe nucleus itself. The predicted NMR parameters facilitate an unambiguous experimental identification of these novel compounds.
Abstract: A range of purine derivatives modified at position 6 of the basic purine skeleton exhibit a variety of biological activities. Several derivatives are used or tested nowadays for pharmacological treatments. The present work aims to analyze the effects of substituents on the electron distribution in the purine core as reflected by NMR chemical shifts. We collected a comprehensive set of experimental NMR data for a variety of 6-substituted purines (-NH(2), -NHMe, -NMe(2), -OMe, -Me, -CCH, and -CN) and determined the molecular and crystal structures of three derivatives (-NHMe, -CCH, and -CN) by X-ray diffraction. The density-functional methods calibrated in our recent study (Phys. Chem. Chem. Phys., 2010, 12, 5126) have been employed to enable understanding of the substituent-induced changes in the NMR chemical shifts of the atoms in the purine skeleton. Analyses of the nuclear shielding using localized molecular orbitals (LMOs), specifically the natural LMOs (NLMOs) and Pipek-Mezey LMOs, were used to break down the values of the isotropic (13)C and (15)N NMR chemical shifts and the chemical shift tensors into the contributions of the individual LMOs. The experimental and calculated trends in the chemical shift of the N-3 atom correlate nicely with the Hammett constants (σ(para)) and the calculated natural charges on N-3, whereas the contributions of the LMOs to the N-1 and C-6 chemical shifts are found to be more complex.
Abstract: Metal atoms with a closed-shell electronic structure and positive charge as for example the Au(I), Pt(II), Ag(I), Tl(I) or Hg(II) atoms do not in some compounds repel each other due to the so-called metallophilic attraction (P. Pyykkö, Chem. Rev., 1997, 97, 597-636). Here we highlight the role of the Hg(II)Hg(II) metallophilic attraction between the consecutive metal-mediated mismatched base pairs of nucleic acids. Usually, the base stacking dominates the non-covalent interactions between steps of native nucleic acids. In the presence of metal-mediated base pairs these non-covalent interactions are enriched by the metal-base interactions and the metallophilic attraction. The two interactions arising due to the metal linkage of the mismatches were found in this study to have a stabilizing effect on nucleic acid structure. The calculated data are consistent with recent experimental observations. The stabilization due to the metallophilic attraction seems to be a generally important concept for the nucleic acids containing heavy metals with short contacts.
Abstract: The He-3 chemical shifts were calculated for He-n@C-84 (n = 1, 2) fullerenes to obtain characteristic NMR patterns for distinguishing their isomers in a mixture. The density functional methods were calibrated on experimental data. Accuracy within 1 ppm could be reached without further fitting of individual shifts. Such precision allows for a semi-quantitative assignment of He-3 NMR spectra. Additional criteria in the identification are discussed, such as the relative energies of the isomers, positions of the satellite di-helium peaks, and the differential 3He shifts in the fullerenes reduced to anions. Endohedral 3He shifts are predicted for so far experimentally unknown He@C-84 and He@(6-)(84) isomers. (C) 2010 Elsevier B.V. All rights reserved.
Abstract: The compounds I-IV derived from alpha-D-cyclodextrin moiety by bridging and/or interconnecting with various patterns of disulfide bonds were chosen as models for the spectroscopic study of conformation of the disulfide bridge. The energy gap between the disulfide and cyclodextrin's electronic transitions allows us to investigate absorption and electronic circular dichroism spectra without disturbing spectral overlaps with amides or aromatic amino acids in peptides or proteins. Raman optical activity (ROA) spectra were measured and the bands due to S-S and C-S stretching motion identified. Comparison with the quantum mechanical calculations of simple models indicates that sense of disulfide twist follows sign of the measured S-S ROA band. Chirality 22:E47-E55, 2010. (c) 2010 Wiley-Liss, Inc.
Notes: Sp. Iss. SI xD;674VV xD;Times Cited:0 xD;Cited References Count:40
Abstract: The formation and structure of the potassium complex with valinomycin in solution were studied by means of Raman and Raman optical activity (ROA) spectroscopy. The complexation caused significant spectral changes, particularly in the region 1200-1400 cm(-1). The experimental spectra were interpreted using first principles computations. A complete computational conformational search combined with the spectral analysis revealed the arrangement of the isopropyl side chains in the complex. From a total of 6579 unique conformers two predominant ones were confirmed in the solution by ROA. A third one was predicted theoretically, but its population in the experiment could be estimated only roughly. The most populated conformer does not exhibit C-3 symmetry, and is different from that present in the crystal and the NMR-derived structure. Molecular dynamics techniques were used to estimate the molecular flexibility and its effect on the spectra. Density functional computations and Cartesian coordinate transfer (CCT) techniques provided the ROA and Raman spectral shapes and intensities well comparable with the experiment. The polar solvent (methanol) environment modeled with a polarizable continuum model (PCM) leads to rather minor changes in the conformer populations and vibrational properties as compared to vacuum computations, due to the hydrophobic character of the complex. Additional computational experiments suggest that the vibrational interactions determining the ROA spectra are quite local, which contributes to the good spatial resolution of the method. A reduction of the noise in the experimental spectra as well as increased precision of the simulations is desirable for the further exploration of the potential of the ROA spectroscopy for biomolecular studies in the future.
Abstract: A prototypical study of NMR chemical shifts in biologically relevant heteroaromatic compounds containing a heavy halogen atom is presented for two isomers of halogen-substituted purines. Complete sets of H-1-, C-13-and N-15-NMR chemical shifts are determined experimentally in solution. Experimental results are complemented by quantum-chemical calculations that provide understanding of the trends in the chemical shifts for the studied compounds and which show how different physical effects influence the NMR parameters. Chemical shifts for isolated molecules are calculated using density-functional theory methods, the role of solvent effects is studied using polarised continuum models, and relativistic corrections are calculated using the leading-order Breit-Pauli perturbation theory. Calculated values are compared with the experimental data and the effects of structure, solvent and relativity are discussed. Overall, we observe a good agreement of theory and experiment. We find out that relativistic effects cannot be neglected even in the chlorine species when aiming at high precision and a good agreement with the experimental data. Relativity plays a crucial role in the bromine and iodine species. Solvent effects are of smaller importance for 13 C shifts but are shown to be substantial for particular N-15 shifts. The test of method performance shows that the BLYP and B3LYP functionals provide the most reliable computational results after inclusion of the solvent and relativistic effects while BHandHLYP may-depending on atom in question-slightly improve but mostly deteriorate the data. Ab initio Hartree-Fock suffers from triplet instability in the Breit-Pauli relativistic part while MP2 provides no clear improvement over DFT in the nonrelativistic region. This work represents the first full application of the Breit-Pauli perturbation theory to an organic chemistry problem.
Abstract: An attempt is made to express the interaction energy in an endohedral A@B system starting from a one-center (r(<))(l)/(r(>))(l+1) expansion. Electrostatic, induction, and dispersion contributions are obtained from Rayleigh-Schrodinger perturbation theory. New electric polarizabilities with r(-l-1) radial integrals are calculated for l = 0, 1 and 2 for the outer system B. For a 'breakable' B, they can be related to the usual London formula. The new polarizabilities are used to successfully estimate the Born-type charge solvation energy and to roughly estimate the lowest-order, l = 1 dispersion term. The latter, London-type expression is now also derived from a Casimir-Polder-type argument. It is applied on A = He-Xe, Zn-Hg, and several molecules with B = C-60 and the results are compared against MP2 and SCS-MP2 supramolecular calculations. The l = 2 dispersion terms are smaller than the l = 1 ones.
Abstract: The recently observed nonintuitive pH dependence of methylene H-1 chemical shifts in cobalt(Ill) polyamine complexes upon deprotonation of coordinated aqua or (poly)alcohol coligands (J. Am. Chem. Soc. 2004, 126, 6728) was attributed to differential spin-orbit effects on the H-1 shifts transmitted over three bonds from the cobalt low-spin d(6) center. These remarkably large spin-orbit effects due to the comparably light Co center have now been examined closely by comparative computations for homologous Rh and Ir complexes, as well as by NMR titrations for a Rh complex. While larger spin-orbit effects (proportional to Z(2)) would have been expected for the heavier metal centers, the characteristic H-1 deshieldings upon deprotonation of [Rh(tren)(OH2)(2)](3+) [tren = tris(2-aminoethyl)-amine] turn out to be smaller than for the Co homologous Co complex. Systematic computational studies ranging from smaller models to the full complexes confirm these results and extend them to the Ir homologues. Closer analysis indicates that the spin-orbit shift contributions do not follow the expected 22 behavior but are modulated dramatically by increasing energy denominators in the perturbation expressions. This is related to the increasing ligand-field splitting from 3d to 4d to 5d system, leading to almost identical differential spin-orbit shifts for the Co and Rh complexes and to only moderately larger effects for the Ir complex (by a factor of about two). Moreover, the differential nonspin-orbit deprotonation shifts cancel the spin-orbit induced contributions largely in the Rh complex, leading to the experimentally observed inverted behavior. The full multidentate polyamine complexes studied experimentally exhibit different three- and four-bond Fermi-contact pathways for transmission of the spin-orbit H-1 shifts. The novel four-bond pathways have different conformational dependencies than the Karplus-like three-bond pathways established previously. Both types of contributions are of similar magnitude. The H-1 NMR deprotonation shift patterns of [Ir(tren)(OH2)(2)](3+) have been predicted computationally.
Abstract: We report density functional theory (DFT) studies on the endohedral scandium carbide fullerene Sc3C2@C-80 and its monoanion [Sc3C2@C-80](-). The system consisting of a Sc3C2 moiety inside the I-h C-80 fullerene has been studied by using first principles molecular dynamics simulations at the DFT level. On the picosecond time scale, the triangle defined by the scandium atoms is seen to jump between orientations along the equatorial six-membered ring belt of the cage. The confined carbide unit, in turn, is engaged in a flipping motion through the Sc-3 plane. In contrast to the equilibrium geometry optimisations using large basis sets that predict a trigonal bipyramidal structure, a planar Sc3C2-moiety is preferred during the finite-temperature simulation. In the molecular dynamics picture, Sc3C2@C-80 is best described as an equilibrium between the two static minimum structures. Calculations of the vibrational frequencies show that the earlier predicted C-2 and C-2v symmetric isomers are in fact saddle points, with one imaginary normal mode frequency that is related to the flipping motion of the confined carbon dimer. Reoptimisation revealed two new minimum energy structures where the C-2 unit is tilted with respect to its orientation in the earlier suggested higher-symmetry structures. The nature of the bonding in the static structures of the two isomers of Sc3C2@C-80 has been investigated using the electron localisation function and natural population analysis. Some increased electron pair localisation is detected on the six-membered rings closest to the Sc atoms. C-13 nuclear magnetic resonance (NMR) chemical shifts have been calculated for the closed-shell monoanion of Sc3C2@C-80. The C-13 shifts were also calculated for Sc2C2@C-84, for further comparison to experimentally measured spectra. The confined carbon atoms are strongly deshielded in these metallofullerenes, implying an incorrect earlier interpretation of the experimental C-13 NMR spectrum of Sc2C2@C-84. The neutral Sc3C2@C-80 system with one unpaired electron is further characterised by calculating the hyperfine coupling constants, the g tensor, as well as paramagnetic NMR (pNMR) C-13 shifts for both static isomers. The chemical shifts of the con. ned carbon atoms and the hyperfine coupling constants of all the con. ned atoms are strongly dependent on the conformation of the Sc3C2 moiety. Consequently, dynamical effects are expected to be important in the modelling of the magnetic properties of endohedral scandium carbide fullerenes. The two low-lying isomers have rather different pNMR C-13 shifts, implying the potential of this method in structural assignment.
Abstract: We calculate the Xe-129 chemical shift in endohedral Xe@C-60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe center dot center dot center dot C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption Xe-129 chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the Xe-129 shift. Solvent effects evaluated with a polarized continuum model are found to be very small.
Abstract: We perform a computational mapping study of a family of new inorganic species, based on idea of donor-acceptor type bonding between N+ and a ligand L with a terminal electron lone pair. The nitrogen ion is seen as being in an atomic D-1 state, with empty 2p acceptor orbitals [I.S.K. Kerkines., A. Papakondylis, A. Mavridis, J. Phys. Chem. A, 2002, 106, 4435]. We consider a series of small ligands, such as PN, CCH-, CCCN-, NH2-, and others. Chemical bonding analysis confirms the suggested bonding picture as characteristic for experimentally known N-5(+) and N(CO)(2)(+) as well as for most of the predicted species. A number of these new compounds is found to be thermodynamically stable with respect to the existing N-5(+) or N(CN)(2)(-). They are candidates for new synthetic targets. (C) 2008 Elsevier B.V. All rights reserved.
Abstract: The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate, i.e. the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work.
Abstract: We present constant-pressure Monte Carlo simulations of nuclear magnetic resonance (NMR) spectral parameters, nuclear magnetic shielding relative to the free atom as well as nuclear quadrupole coupling, for atomic xenon dissolved in a model thermotropic liquid crystal. The solvent is described by Gay-Berne (GB) molecules with parametrization kappa=4.4, kappa(')=20.0, and mu=nu=1. The reduced pressure of P-star=2.0 is used. Previous simulations of a pure GB system with this parametrization have shown that upon lowering the temperature, the model exhibits isotropic, nematic, smectic-A, and smectic-B/molecular crystal phases. We introduce spherical xenon solutes and adjust the energy and length scales of the GB-Xe interaction to those of the GB-GB interaction. This is done through first principles quantum chemical calculations carried out for a dimer of model mesogens as well as the mesogen-xenon complex. We preparametrize quantum chemically the Xe nuclear shielding and quadrupole coupling tensors when interacting with the model mesogen, and use the parametrization in a pairwise additive fashion in the analysis of the simulation. We present the temperature evolution of Xe-129/131 shielding and Xe-131 quadrupole coupling in the different phases of the GB model. From the simulations, separate isotropic and anisotropic contributions to the experimentally available total shielding can be obtained. At the experimentally relevant concentration, the presence of the xenon atoms does not significantly affect the phase behavior as compared to the pure GB model. The simulations reproduce many of the characteristic experimental features of Xe NMR in real thermotropic LCs: Discontinuity in the value or trends of the shielding and quadrupole coupling at the nematic-isotropic and smectic-A-nematic phase transitions, nonlinear shift evolution in the nematic phase reflecting the behavior of the orientational order parameter, and decreasing shift in the smectic-A phase. The last observation is due to the preference of the xenon solutes to occupy the interlayer space where the density of the medium is reduced as compared to the layers. There are systematic deviations, however, in the magnitude of the shielding and its discontinuities, as well as the distribution of the solutes in the translationally ordered smectic-A phase, between the simulation and experiment. These deficiencies are believed to result from the lack of flexibility of the GB model.
Notes: Part 1 xD;151XL xD;Times Cited:3 xD;Cited References Count:57
Abstract: A London-type formula is derived for endohedral systems. It involves the static dipole polarisability, alpha(1)(A) of the inner system, A, and a new type of dipole polarisability, alpha(-2)(B) with an r(-2) radial operator, for the outer system, B. The new formula has no explicit dependence on the radius, R, of B. The predicted interaction energies are compared against MP2 supermolecular calculations for A@C-60, A=He-Xe, Zn, Cd, Hg, and CH4.
Abstract: We calibrate the methodology for the calculation of nuclear magnetic resonance (NMR) properties in novel organo-xenon compounds. The available state-of-the-art quantum-chemical approaches are combined and applied to the HXeCCH molecule as the model system. The studied properties are Xe-129, H-1, and C-13 chemical shifts and shielding anisotropies, as well as Xe-131 and H-2 nuclear quadrupole coupling constants. The aim is to obtain, as accurately as currently possible, converged results with respect to the basis set, electron correlation, and relativistic effects, including the coupling of relativity and correlation. This is done, on one hand, by nonrelativistic correlated ab initio calculations up to the CCSD(T) level and, on the other hand, for chemical shifts and shielding anisotropies by the leading-order relativistic Breit-Pauli perturbation theory (BPPT) with correlated ab initio and density-functional theory (DFT) reference states. BPPT at the uncorrelated Hartree-Fock level as well as the corresponding fully relativistic Dirac-Hartree-Fock method are found to be inapplicable due to a dramatic overestimation of relativistic effects, implying the influence of triplet instability in this multiply bonded system. In contrast, the fully relativistic second-order Moller-Plesset perturbation theory method can be applied for the quadrupole coupling, which is a ground-state electric property. The performance of DFT with various exchange-correlation functionals is found to be inadequate for the nonrelativistic shifts and shielding anisotropies as compared to the CCSD(T) results. The relativistic BPPT corrections to these quantities can, however, be reasonably predicted by DFT, due to the improved triplet excitation spectrum as compared to the Hartree-Fock method, as well as error cancellation within the five main BPPT contributions. We establish three computationally feasible models with characteristic error margins for future calculations of larger organo-xenon compounds to guide forthcoming experimental NMR efforts. The predicted Xe-129 chemical shift in HXeCCH is in a novel range for this nucleus, between weakly bonded or solvated atomic xenon and xenon in the hitherto characterized molecules. (c) 2007 American Institute of Physics.
Abstract: The title systems, including EThE', are treated at DFT level using a B3LYP functional and small-core quasirelativistic pseudopotentials. Most of the studied systems are bent, like their isoelectronic ThO2, analogue, except for some anionic systems containing Ir. The bond lengths vary considerably and can lie above or below the sum of triple-bond covalent radii. Among the studied systems, the iridium-containing species show the strongest back-donation to Th. The bonding can be simply understood and could theoretically go up to a '24-electron principle' limit at the actinide. (c) 2006 Elsevier B.V. All rights reserved.
Abstract: We report density functional calculations of He-3 nuclear magnetic resonance chemical shifts in a series of experimentally known endohedral helium fullerenes, He-n@C-m(q) (n = 1, 2; m = 60, 70, 76, 78; q = 0, 6-), including for the first time anionic and di-helium species. Despite the lack of dispersion in the density functional model, the results are in promising agreement with experiment. Density functional theory performs better than Hartree-Fock for the anionic systems. In the di-helium species confined in the small C-60 cage, besides the atomic displacements from the center position, the direct He-He interactions contribute to the He-3 shift.
Abstract: The solid-state structure and NMR parameters of the heavier carbene analogue [Pb{Ph2PC(H)Py}-{N(SiMe3)(2)}] (1), obtained in the reaction of the phosphane Ph2P(CH2Py) with [Pb{N(SiMe3)(2)}(2)] are discussed.
Abstract: The relationship between structure and bonding in actinide 6d(0)5f(0) MX6q complexes (M = Th, Pa, U, Np; X = H, F; q = -2,-1, 0, +1) has been studied, based on density functional calculations with accurate relativistic actinide pseudopotentials. The detailed comparison of these prototype systems with their 5d(0) transition metal analogues (M = Hf, Ta, W, Re) reveals in detail how the 5f orbitals modify the structural preferences of the actinide complexes relative to the transition metal systems. Natural bond orbital analyses on the hydride complexes indicate that 5f orbital involvement in sigma-bonding favors classical structures based on the octahedron, while d orbital contributions to sigma-bonding favor symmetry lowering. The respective roles of f and d orbitals are reversed in the case of pi-bonding, as shown for the fluoride complexes.
Abstract: Quantum chemical calculations have been carried out to understand better solvent effects on the isotropic muon and proton hyperfine coupling constants in the C(6)H(6)Mu center dot radical. Both polarizable continuum solvent models and explicit inclusion of water molecules into supermolecular complexes were used. Changes in the hyperfine couplings of in- plane hydrogen atoms are very small and difficult to discuss, partly due to relatively large experimental error bars. In contrast, the out- of- plane proton and muon hyperfine couplings exhibit more pronounced changes. These are partly due to structural changes of the radical and partly due to direct electronic polarization effects. Polarizable continuum solvent models agree well with experimental changes for benzene but overshoot the enhancement of the hyperfine couplings for water. Explicit inclusion of water molecules reduces this overestimated spin density increase and thereby tends to bring theory and experiment into closer agreement. The enhancement of the spin density on the out- of- plane hydrogen or muon atoms by the solvent environment is mainly due to an increased polarization of the singly occupied MO towards this side.
Abstract: The F-19 NMR nuclear shieldings of fluoride ligands in uranium complexes UFnCl6-n (n = 1-6) have been studied quantum chemically, using different exchange-correlation functionals and a relativistic small-core pseudopotential on uranium. In contrast to a recent study [G. Schreckenbach, S.W. Wolff, T. Ziegler, J. Phys. Chem. A 104 (2000) 8244] we find that pseudopotential methods are well suited for calculations of ligand chemical shifts in actinide compounds, provided that a sufficiently small core-size definition is used. With modern relativistic small-core pseudopotentials and gradient-corrected density functionals we obtain results of the same accuracy as were found with all-electron density functional ZORA or Pauli calculations. The unusually large dependence of the shifts on the exchange-correlation functional is discussed in the context of the description of sigma- and pi-bonding, and also with respect to the accuracy of the optimized structures. (C) 2004 Elsevier B.V. All rights reserved.
Abstract: While the thermochemical stability of gas-phase HgF4 against F-2 elimination was predicted by accurate quantum chemical calculations more than a decade ago, experimental verification of "truly transition-metal" mercury(IV) chemistry is still lacking. This work uses detailed density functional calculations to explore alternative species that might provide access to condensed-phase Hg-IV chemistry. The structures and thermochemical stabilities of complexes (HgX4)-X-IV and (HgF2X2)-F-IV (X- = AlF4-, Al2F7-, AsF6-, SbF6-, As2F11-, Sb2F11-, OSeF5-, OTeF5-) have been assessed and are compared with each other, with smaller gas-phase HgX4 complexes, and with known related noble gas compounds. Most species eliminate F-2 exothermically, with energies ranging from only about -60 kJ mol(-1) to appreciable -180 kJ mol(-1). The lower stability of these species compared to gas-phase HgF4 is due to relatively high coordination numbers of six in the resulting Hg-II complexes that stabilize the elimination products. Complexes with AsF6 ligands appear more promising than their SbF6 analogues, due to differential aggregation effects in the Hg-II and Hg-IV states. HgF2X2 complexes with X- = OSeF5- or OTeF5- exhibit endothermic fluorine elimination and relatively weak interactions in the Hg-II products. However, elimination of the peroxidic (OEF5)(2) coupling products of these ligands provides an alternative exothermic elimination pathway with energies between -120 and -130 kJ mol(-1). While all of the complexes investigated here thus have one exothermic decomposition channel, there is indirect evidence that the reactions should exhibit nonnegligible activation barriers. A number of possible synthetic pathways towards the most interesting condensed-phase Hg-IV target complexes are proposed.
Abstract: The pH-dependent H-1 NMR characteristics of a series of Co-III-(polyamin)-aqua and Co-III-(polyamin)-(polyalcohol) complexes, [Co(tach)(ino-kappa(3)-O-1,O-3,O-5)](3+) (1(3+)), [Co(tach)(ino-K-3-O-1,O-2,O-6)](3+) (2(3+)), [Co(tach)(taci-kappa-N-1-kappa(2)-O-2,O-6)](3+) (3(3+)), [Co(ditame)(H2O)](3+) (4(3+)), and [Co(tren)(H2O)(2)](3+) (5(3+)), were studied in D2O by means of titration experiments (tach = all-cis-cyclohexane-1,3,5-triamine, ino = cis-inositol, taci = 1,3,5-triamino-1,3,5-trideoxy-cis-inositol, tren = tris(2-aminoethyl)amine, ditame = 2,2,6,6-tetrakis(aminomethyl)-4-aza-heptane). A characteristic shift was observed for H(-C) hydrogen atoms in the a-position of a coordinated amino group upon deprotonation of a coordinated oxygen donor. For a cis-H-C-N-Co-O-H arrangement, deprotonation of the oxygen donor resulted in an additional shielding (shift to lower frequency) of the H(-C) proton, whereas for a trans-H-C-N-Co-O-H arrangement, deprotonation resulted in a deshielding (shift to higher frequency). The effect appears to be of rather general nature: it is observed for primary (1(3+) -5(3+)), Secondary (4(3+)), and tertiary (5(3+)) amino groups, and for the deprotonation of an alcohol (1(3+)-3(3+)) or a water (4(3+), 5(3+)) ligand. Spin-orbit-corrected density functional calculations show that the high-frequency deprotonation shift for the trans-position is largely caused by a differential cobalt-centered spin-orbit effect on the hydrogen nuclear shielding. This effect is conformation dependent due to a Karplus-type behavior of the spin-orbit-induced Fermi-contact shift and thus only significant for an approximately antiperiplanar H-C-N-Co arrangement. The differential spin-orbit contribution to the deprotonation shift in the trans-position arises from the much larger spin-orbit shift for the protonated than for the deprotonated state. This is in turn due to a trans-effect of the deprotonated (hydroxo or alkoxo) ligand, which weakens the trans Co-N bond and thereby interrupts the Fermi-contact mechanism for transfer of the spin-orbit-induced spin polarization to the hydrogen nucleus in question. The unexpectedly large long-range spin-orbit effects found here for 3d metal complexes are traced back to small energy denominators in the perturbation theoretical expressions of the spin-orbit shifts.
Abstract: While quantum chemical predictions have strongly suggested a decade ago the existence of mercury in its oxidation state +IV, no experimental evidence has been found yet. To enable the search for alternative targets and preparation routes by quantum chemical methods, the present work has validated density functional methods against accurate CCSD(T) results for structures, reaction energies and activation barriers for X-2-elimination, and atomization energies for three HgX4 systems (X = F, Cl, H). Hybrid functionals with ca. 20% Hartree-Fock exchange like B3LYP, B1LYP or MPW1PW91 have provided the best energetics, whereas local or gradient-corrected "pure" functionals overestimate, and the BHandHLYP hybrid functional underestimates the stability of the Hg-IV state. Basis sets are suggested that provide a reasonable compromise between accuracy and computational effort in calculations on larger systems.
Abstract: Relativistic small-core pseudopotential B3LYP and CCSD(T) calculations and frozen-core PW91-PW91 studies are reported for the series UF4X2 (X = H, F, Cl, CN, NC, NCO, OCN, NCS and SCN). The bonding in UF6 is analyzed and found to have some multiple-bond character, approaching at a theoretical limit a bond order of 1.5. In addition to these sigma and pi orbital interactions, the electrostatic attraction is important. Evidence for pi bonding in the other systems studied was also found. The triatomic pseudohalides as well as fluorine and chlorine are in this sense better ligands than cyanide. The -CN group is a sigma donor and pi acceptor, as uranium itself, and hence is unfit to bond to U(VI). The sigma-bonded UH6 is octahedral.
Abstract: High-energy nitrogen-rich pentazolides of groups 6 and 13-16 are studied theoretically. Many of them have experimentally known azide analogues. Our highest nitrogen-to-element ratio of 40:1 is achieved in the systems [M(N-5)(8)](2-) (M = Cr, Mo, W). The thermodynamic and kinetic stability of the studied systems grows with the negative charge on the system and is highest for tetra-pentazolides and hexa-pentazolides of B, Al, and Si. Systems such as B(N-5)(4)(-) or Si(N-5)(6)(2-) are examples of the most stable candidates for these new species. N(N-5)(2-) is a candidate for a new all-nitrogen system. Neutral and positive systems were less stable. Pentazole derivatives of "dinuclear" C2Hn and N2Hn systems were investigated and were found to be of comparable stability as their "mononuclear" analogues. Pentazole derivatives of benzene, the C6H6-n(N-5)(n) (n = 2, 3, 6) systems, have a similar stability as the experimentally known phenylpentazole. A borazine analogue, N3B3H3(N-5)(3) is predicted to be one of the most stable systems of this family.
Abstract: Mercury tetrahydride (D-4h) is calculated to have similar bond lengths and vibrational frequencies as the already known HgH2 and to lie energetically 200 kJ mol(-1) above HgH2 + H-2, in a local well, about 40 kJ mol(-1) below a transition state.
Abstract: The possibility of stabilizing the N-6 species as a planar hexagonal ring in M(eta(6)-N-6) (M = Ti, Zr, Hf, Th) systems was studied theoretically. The M(eta(6)-N-6) systems were found to have minima at C-60 geometry, which corresponds to an eta(6) complex of a metal with planar N-6 ring, They lie approximately 70-130 kcal/mol above the energy of a metal atom and three N-2 molecules and substantially below the energy of any naked N-6 isomer. The stabilization of the planar N-6 is attributed to the interaction of the ring pi system with the metal d and f orbitals. A five-fold bond is observed between the N-6 ring and a metal. At the ionic limit, the systems can be regarded as complexes of an M4+ cation and an N-6(4-) ligand. Further planar aromatic N-n(q) (n = 3-8) rings are briefly discussed. Of them, the pi-electron-rich anions could be a viable eta(n) ligands in transition metal complexes. (C) 2002 Elsevier Science B.V. All rights reserved.
Abstract: The molecular structures, the nuclear magnetic shieldings, and the aromatic ring-current shieldings (ARCS) have been calculated for Al-4(2-), Al4Li-, and Al4Cu- at the Hartree-Fock (HF) level, the second-order Moller-Plesset (MP2) level, the coupled-cluster singles and doubles (CCSD) level, and the coupled-cluster singles and doubles level augmented by a perturbative correction for triple excitations (CCSD(T)). The ARCS calculations show that the square-shaped Al-4(2-) ring sustains a very large diatropic ring current in an external magnetic field. Because the induced ring current is one measure of the molecular aromaticity, the Al-4(2-) ring can be considered aromatic. Molecular structure optimizations on the group IIIA analogues show that B-4(2-), Ga-4(2-), In-4(2-), and Tl-4(2-) also exist and have D-4h symmetry. The ARCS calculations indicate that they are aromatic, too. New neutral Al-4(2-) analogues such as Si2B2, Si2Al2, and Si2Ga2 are proposed. The molecular structure and ARCS calculations on the neutral analogues yield planar ring structures with large diatropic ring-current susceptibilities.
Abstract: Fully relativistic, four-component Dirac-Fock calculations and quasirelativistic pseudopotential calculations at different ab initio levels are used to study the bonding trends among the naked, triatomic [OAnO](q+) groups or the oxyfluorides [AnO(n)F(m)](q) with f(0) configurations. The triatomic f(0) series is suggested to range from the bent ThO2 via the linear OPaO+ to at least NPO23+, a possible new gas-phase species. The neutral oxyfluoride molecules include, the experimentally unknown NpO2F3 and PuO2F4. The latter is a candidate for the so far unknown oxidation state Pu(VIII), which is found to lie considerably above Pu(VI), but to be locally stable. Their all-oxygen isoelectronic analogues are NpO53-, known in the solid state, and the unknown PuO64-. Further possible candidates for Pu(VIII) are PUO4(D-4h) and the cube-shaped PuF8(O-h). Isoelectronic UF82- is calculated to be D-4d, in agreement with experiment.
Abstract: Electron structures of polysilane, 1-methyl polysilane, 1,1-dimethyl polysilane, 1-phenyl polysilane, 1,1-diphenyl polysilane, and 1-methyl 1-phenyl polysilane in solid state were calculated using the cyclic cluster orbital method (CCO), based on a Hartree-Fock approach using a quasirelativistic INDO Hamiltonian applied to cyclic clusters. Effect of the redistribution of electron density on the silicon backbone chains after the substitution of hydrogen by methyl and phenyl groups has been investigated. Going from one- to three-dimensional models, significant changes appear in calculated electron distributions, as well as in the band structure topologies of the corresponding polymers. (C) 2001 John Wiley & Sons, Inc.
Abstract: In this paper, we present the theoretical study of the crystal and electron structure of an intercalated compound of graphite -the graphite monofluoride {CF}(n). The latter is widely used as a lubricant under extremely high temperatures and high vacuum, and as a successful cathodic depolarizer in batteries with high energy density. The layered structure of the graphite monofluoride has been confirmed, but statistical distributions of the individual layers are possible. This fact helps in understanding the problems linked to an experimental determination of the structure of this material. Small interlayer dissociation energies show that the bonding between the individual layers is mainly due to the weak interlayer electrostatic forces, which explains the excellent lubricant properties of this material. Band structure calculations reveal that, whereas some layer arrangements of the bulk material lead to insulating properties, others have a conductive character. This fact explains the weak overall conductive properties of synthetic graphite monofluoride, (C) 2000 Academic Press.
Abstract: The title compounds are used to determine, for the first time, the energy of the 'metallophilic' attraction between two Hg(ii) compounds. The dispersion and electrostatic multipole components to this attraction are analyzed. The present purely theoretical molecular data suggest a mercury(ii) van der Waals radius of 175(7) pm.
Abstract: The formally dodecavalent, octahedral (UO6)-O-XII is found to be a local energy minimum at Several theoretical levels, including quasirelativistic single-reference (HF, B3LYP, MP2 and CCSD(T)) and multireference CI approaches. The fully relativistic, single-configuration Dirac-Fock (DF) approach gives similar U-O bond lengths but has one imaginary frequency. In this hypothetical compound the largest formal oxidation state of uranium would be increased from +VI to +XII. (C) 2000 Elsevier Science B.V.
Abstract: The possibility of an attractive interaction between two closed-shell molecules containing In(I) or Tl(I) was studied using relativistic pseudopotentials and correlated ab initio methods ranging from MP2 to CCSD(T). The results for the simple test system (TlH)(2) qualitatively agree with earlier ones by Schwerdtfeger (Inorg. Chem., 1991, 30, 1660). The calculated dimerization energy is -20 kJ mol(-1). The results for the more realistic [M(eta(5)-Cp)](2) model (M=In, Tl; Cp=cyclopentadiene, C5H5) yield a weaker attraction of about - 12 and - 16 kJ mol(-1), respectively. The M-M secondary bond lengths are somewhat longer and the M-M-Cp angles more acute than in the dimers found in solids. This is attributed to the crystal effects. The calculated structures for [M(eta(5)-Cp)(2)](-) anions agree with experimental ones for the known M=Tl case. Predicted structures are given for the [M(eta(5)-Cp-2)](+) cations and for a hypothetical M(eta(5)-Cp)(3).
