Where to bind in buckybowls? The dilemma of a metal ion

An exhaustive computational study at the M05-2X/cc-pVDZ level which explores the binding possibilities of cations (Li(+), Na(+), K(+) and Cu(+)) to the concave and convex sides of the hub and rim rings of prototypical buckybowls, sumanene (C(21)H(12)) and corannulene (C(20)H(10)), has been carried out. Five distinct minima on the potential energy surface of sumanene and four on the potential energy surface of corannulene were identified. The complex where the metal ion binds to the convex side of the 6-membered rim ring is adjudged as the most stable complex for both the bowls considered. The cation-π interaction energies of buckybowls are compared with model systems such as benzene, cyclopentadiene, indene and coronene. Energy decomposition analysis has also been performed to delineate the contribution from various components contributing to the cation-π binding strength.     

The possibility of semiconductor–metal transition in a spherical quantum dot

We observe an abrupt change in diamagnetic susceptibility at critical donor concentration for an $\text{ Al }_\mathrm{x}\text{ Ga }_\mathrm{1-x}\text{ As/GaAs }$ Al x Ga 1 ? x As/GaAs quantum dot system in the effective mass approximation indicating a possible semiconductor metal transition. The effect of confining potential and the laser intensity on the abrupt change in diamagnetic susceptibility has also been studied. The effect of nonparabolicity of the conduction band has been included in our calculations. Results are presented and discussed.     

Metallophosphoranes: The hidden face of transition metal–phosphine complexes

Reactions in which metallophosphoranes, of general formula L_nMPR₄, have been implicated as intermediates or possible transition states are reviewed. Such species can be accessed via nucleophilic attack on metal–phosphine complexes, with the source of nucleophile being either external or internal in the form of an anionic co-ligand. The reverse process, transfer of a group from a {PR₄} ligand to a metal, has also been observed with the formation of a metal phosphine. Thus metallophosphoranes have been postulated to play a role in isomerization processes and novel M–X/P–R exchange reactions. Metallophosphoranes have also been implicated in unusual ‘phosphine-assisted C–F bond activation’ reactions. Recent computational studies on these processes are discussed.     

How deeply are core electrons perturbed when valence electrons are spin polarized? The case study of transition metal compounds

The ferromagnetic and antiferromagnetic wave functions of the KMnF₃ perovskite have been evaluated quantum-mechanically by using an all electron approach and, for comparison, pseudopotentials on the transition metal and the fluorine ions. It is shown that the different number of α and β electrons in the d shell of Mn perturbs the inner shells, with shifts between the α and β eigenvalues that can be as large as 6 eV for the 3s level, and is far from negligible also for the 2s and 2p states. The valence electrons of F are polarized by the majority spin electrons of Mn, and in turn, spin polarize their 1s electrons. When a pseudopotential is used, such a spin polarization of the core functions of Mn and F can obviously not take place. The importance of such a spin polarization can be appreciated by comparing (i) the spin density at the Mn and F nuclear position, and then the Fermi contact constant, a crucial quantity for the hyperfine coupling, and (ii) the ferromagnetic–antiferromagnetic energy difference, when obtained with an all electron or a pseudopotential scheme, and exploring how the latter varies with pressure. This difference is as large as 50% of the all electron datum, and is mainly due to the rigid treatment of the F ion core. The effect of five different functionals on the core spin polarization is documented.     

Encapsulation of metal cations by the PhePhe ligand: a cation-π ion cage

Structures and binding thermochemistry are investigated for protonated PhePhe and for complexes of PhePhe with the alkaline-earth ions Ba(2+) and Ca(2+), the alkali-metal ions Li(+), Na(+), K(+), and Cs(+), and the transition-metal ion Ag(+). The two neighboring aromatic side chains open the possibility of a novel encapsulation motif of the metal ion in a double cation-π configuration, which is found to be realized for the alkaline-earth complexes and, in a variant form, for the Ag(+) complex. Experimentally, complexes are formed by electrospray ionization, trapped in an FT-ICR mass spectrometer, and characterized by infrared multiple photon dissociation (IRMPD) spectroscopy using the free electron laser FELIX. Interpretation is assisted by thermochemical and IR spectral calculations using density functional theory (DFT). The IRMPD spectrum of protonated PhePhe is reproduced with good fidelity by the calculated spectrum of the most stable conformation, although the additional presence of the secondmost stable conformation is not excluded. All metal-ion complexes have charge-solvated binding modes, with zwitterion (salt bridge) forms being much less stable. The amide oxygen always coordinates to the metal ion, as well as at least one phenyl ring (cation-π interaction). At least one additional chelation site is always occupied, which may be either the amino nitrogen or the carboxy carbonyl oxygen. The alkaline-earth complexes prefer a highly compact caged structure with both phenyl rings providing cation-π stabilization in a "sandwich" configuration (OORR chelation). The alkali-metal complexes prefer open-cage structures with only one cation-π interaction, except perhaps Cs(+). The Ag(+) complex shows a unique preference for the closed-cage amino-bound NORR structure. Ligand-driven perturbations of normal-mode frequencies are generally found to correlate linearly with metal-ion binding energy.     

Theoretical study of the syn- and anti-conformers of 2,2ʹ-bifuran derivatives: rotational barrier and solvent effect

The optimised molecular structures, vibrational wavenumbers and corresponding vibrational assignments of the syn- and anti-conformers of 2,2?-bifuran and its nitro, fluoro, methyl and hydroxyl derivatives were obtained using density functional theory. The starting structures with C₂ symmetry of all the ground state structures were considered and the transition state arising from syn-anti isomerisation was also modelled. All structures were fully optimised, and the geometries, dipole moments, charge, thermodynamic properties, and energies are reported. The calculated vibrational wavenumbers were assigned to the various fundamental modes of vibrations. The integral Equation Formalism Polarisation Continuum Model (IEF-PCM) was used to calculate the optimised geometry and the vibrational wavenumbers for all the compounds in different solvents. The results indicate that in the gas phase, the syn-conformer is more stable while in solution phases the conformational preference depends on the polarity of the solvent.     

Origin of activation barriers in the dimerization of neutral radicals: a "nonperfect synchronization" effect?

Dimerizations of delocalized neutral radicals may be endowed with quite significant activation barriers. The origin of these barriers is discussed in terms of a model that emphasizes the role of localization of the unpaired radical upon bond formation. Several examples are given in which the model is compared with the results of quantum chemical calculations including the coupling of allyl radicals and of benzyl radicals at various possible carbon sites. The dimerization behavior of radicals in the NADH family is also examined. The connection between the reasons that underlay the existence of the activation barrier and the principle of "nonperfect synchronization" is discussed. The dimerization of conjugated radicals indeed offers a precious example that can be used to decipher the reasons behind these behaviors, being devoid of the ambiguities arising from the simultaneous involvement of ionic and covalent states, significant solvent reorganization, and the contribution of extensive proton tunneling, in the mostly discussed case of proton transfer at carbon.     

Properties of glass-forming metallic liquids: when is there a hard-sphere-like behaviour?

Chathoth and coworkers (Phys. Rev. Lett. 101, 037801 (2008)) have reported examples of multicomponent glass-forming metallic liquids in which the packing fraction appears to be a dominant parameter. Here, we first summarise, for 15 pure liquid metals, properties of the Ornstein–Zernike direct correlation function c(r) which provide a necessary, though not sufficient, condition for hard-sphere-like (HS) liquid behaviour. Returning to multicomponent melts, NiNb and NiNbSn systems have been studied by Chathoth and coworkers. Pure Ni, according to c(r) data near melting, satisfies the necessary condition for HS behaviour, while Sn certainly does not. But the Sn concentration is low in the metallic glass-forming liquid NiNbSn investigated by Chathoth and coworkers. Suitable experimental diffraction data to obtain c(r) in pure liquid Nb seems not to be available presently. Finally, a brief discussion is given of atomic transport in supercooled multicomponent metallic liquids, the status of the Stokes–Einstein relation being one focus.     

Liquid dewetting of ultrathin polystyrene films: Is there a molecular architecture effect?

We have used a liquid dewetting method to investigate the glass transition temperature T_g of high molecular weight linear, long branched 3-arm star, and short branched 8-arm star polystyrene (PS) in the form of ultrathin films. The results of these dewetting experiments are consistent with prior studies of dewetting of linear PS films and show that, independent of molecular architecture, the glass transition temperature T_g reductions with decreasing film thickness, while important below about 20 nm, are weaker than those observed for linear PS supported on a rigid substrate and as well as those observed in freely standing films. The lack of a strong molecular architecture effect on the T_g-reductions is consistent with the T_g reductions for the dewetting from a liquid substrate reflects changes in segmental dynamics upon confinement rather than chain effects. This contrasts with changes, including increases seen in dewetting from a rigid substrate, for different molecular architectures reported in the literature.     

Statistics of single molecule SERS signals: is there a Poisson distribution of intensities?

This paper is aimed at clarifying the statistics of single molecule (SM) surface enhanced Raman scattering (SERS) signals. The argument of the possible existence of a Poisson distribution in the statistics of intensities in SM-SERS has been used many times in the last decade as a proof of single molecule detection. We show theoretically and experimentally that the conditions under which a Poisson distribution would be present are so unlikely to exist in a real system that there is no other option but to attribute the claims to poor statistical sampling. We believe the argument based on Poisson statistics should be dropped as a proof of single molecule detection in SERS.     

Electronic structure of high-valent transition metal corrolazine complexes. The young and innocent?

This is a first quantum chemical study of corrolazine complexes. DFT calculations suggest that despite their extremely contracted central cavities, compared with porphyrins, a variety of corrolazine complexes may be expected to exist as stable compounds. The calculations also indicate that corrolazine complexes may be regarded as strongly electron-deficient analogues of corrole complexes. Thus, the calculated valence ionization potentials of P(V) and Cu(III) corrolazine derivatives are dramatically higher than those of analogous corrole derivatives. In addition, DFT calculations on Fe(IV) and Mn(IV) corrole and corrolazine derivatives suggest that compared with the often noninnocent corrole ligands, corrolazines are electronically more innocent and stabilize "purer" high-valent states of transition metal ions.     

The lysosome/endosome membrane: a barrier to polymer‐based drug delivery?

Drug delivery by means of polymer conjugates that are internalized into cells by endocytosis is now a viable therapeutic approach. Successful deployment of this model depends upon release of the free drug within the endosome/lysosome compartments and its efflux into the cytoplasm. The latter process involves the drug crossing the endosome/lysosome membrane, which is known to be impermeable to all large and many small molecules and which is equipped with numerous substrate‐specific transporters that allow metabolites across. Passive diffusion is the only viable mechanism for most xenobiotics to cross the endosome/lysosome membrane. Studies are reported on the permeability of the rat liver lysosome membrane. These demonstrate that permeance of molecules correlates inversely with their hydrogen‐bonding capacity, a function that can be calculated from inspection of structural formulae. It is deduced that drug molecules containing cationic and/or anionic functional groups, or numerous hydrogen‐bonding moieties such as hydroxy, ether or carbonyl, will cross the lysosome membrane unacceptably slowly, but that many drugs will cross at a satisfactory rate. This conclusion is supported by the rather meagre data available on membrane permeability of lysosomes in situ within cells. Systematic experimental studies on the endosome membrane are lacking, but there is every reason to suppose that its permeability is similar to that of the lysosome membrane.     

Electronic properties of 3d transition metal dihalide monolayers predicted by DFT methods: Is there a pattern or are the results random?

We use periodic DFT calculations at LDA and PBE level to investigate 3d transition metal dihalide (TMDH) monolayers in H- and T-phase. By analyzing the phonon dispersion, we have obtained a rough overview which combinations may form stable structures. We have focused on identifying and explaining trends in the predicted electronic properties. Although their geometric structures are simple, the associated electronic and magnetic properties are not as easy to understand. At first glance, it seems that there is no clear trend, as even isovalence-electronic TMDH monolayers formed from the same metal but different halides can feature different magnetic moments. The identification of potential trends is further complicated by the fact that for a significant number of species, LDA results and PBE results predict different ground-state electronic structures. By rigorously analyzing the potential energy surfaces associated with different magnetic moments, we could show that the apparent inconsistencies can be easily understood as a result of the differences in the relative energy between electronic states of different magnetic moments. We further show that the trends in the band gaps can be easily rationalized by an electron counting rule based on simple symmetry arguments.     

DNA microarrays: is there a role for analytical chemistry?

DNA microarrays, or "DNA chips", represent a relatively new technology that is having a profound impact on biology and medicine, yet analytical research into this area is somewhat sparse. This article presents an overview of DNA microarrays and their application to gene expression analysis from the perspective of analytical chemistry, treating aspects of array platforms, measurement, image analysis, experimental design, normalization, and data analysis. Typical approaches are described and unresolved issues are discussed, with a view to identifying some of the contributions that might be made by analytical chemists.     

The heat capacities and standard entropies of corresponding potassium and ammonium ion species: is there a constant difference?

It is found that there is a nearly constant difference between the normalized values of the heat capacities and standard entropies of potassium and ammonium ion salts in the condensed phase, both solid salts and their aqueous solutions. Extension to the free gaseous ions remains moot.     

The Jahn-Teller effect: a case of incomplete theory for d4 complexes?

We present relativistic calculations at the four-component Dirac-DFT level for the geometries of the series of group 9 monoanionic hexafluorides MF(6)(-), M = Co, Rh, Ir. Highly correlated four-component relativistic CCSD(T) energies were also calculated for the optimized geometries. Spin-orbit coupling effects influence the geometrical preferences for molecular structures: relativistic calculations predict ground states with octahedral symmetries O(h)* for all hexafluorides in this study, while at the nonrelativistic limit, a structural deviation toward D(4h) ground state symmetries is predicted. Our findings suggest that relativistic effects have an important role in molecular structure preferences for the title hexafluorides.     

A universal approach for continuum solvent pK a calculations: are we there yet?

This paper reviews several pK _a calculation strategies that are commonly used in aqueous acidity predictions. Among those investigated were the direct or absolute method, the proton exchange scheme, and the hybrid cluster–continuum (Pliego and Riveros) and implicit–explicit (Kelly, Cramer and Truhlar) models. Additionally, these protocols are applied in the pK _a calculation of 55 neutral organic and inorganic acids in conjunction with various solvent models, including the CPCM-UAKS/UAHF, IPCM, SM6 and COSMO-RS, with a view to identifying a universal approach for accurate pK _a predictions. The results indicate that the direct method is unsuitable for general pK _a calculations, although moderately accurate results (MAD <3 units) are possible for certain classes of acids, depending on the choice of solvent model. The proton exchange scheme generally delivers good results (MAD <2 units), with CPCM-UAKS giving the best performance. Furthermore, the sensitivity of this approach to the choice of reference acid can be substantially lessened if the solvation energies for ionic species are calculated via the IPCM cluster–continuum approach. Reference-independent hybrid approaches that include explicit water molecules can potentially give reasonably accurate values (MAD generally ~2 units) depending on the solvent model and the number of explicit water molecules added.     

The effect of inclusion inβ-cyclodextrin on the chemistry of peroxides: Reactions of radicals withβ-cyclodextrin

Studies by electron paramagnetic resonance (EPR), differential scanning calorimetry, thermogravimetric analysis, HPLC and NMR showed that radicals produced by thermolysis and photolysis of benzoyl peroxide,t-butyl peroxide and cumene hydroperoxide included in-cyclodextrin (-CD), undergo significant reaction with the-CD. The formation of-CD radicals was observed by EPR. Products formed by addition of radicals to-CD were also observed. Such host:guest radical reactions explain the reported stabilization of peroxides, found with-CD inclusion, as being primarily due to the interruption of chain reactions by trapping of the chain carriers. A small increase in activation barrier for cleavage of the included peroxide in-CD was also observed.