To what question is the clamped-nuclei electronic potential the answer?

An examination is made of how the nuclear motion Hamiltonian arises from a consideration of solutions to the eigenvalue problem for the full Coulomb Hamiltonian and the role played by the usual clamped-nuclei electronic Hamiltonian in the construction of such solutions.     

SCC-DFTB: what is the proper degree of self-consistency?

The approximate SCC-DFTB method (Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, Th.; Suhai, S.; Seifert, G. Phys. Rev. B 1998, 58, 7260) is derived from DFT by a second-order expansion of the total energy expression. In this article, basic approximations and assumptions underlying the DFTB method are discussed in detail, and further extensions to include third-order terms are proposed. Further, the SCC-DFTB and semiempirical NDDO formalisms are compared to elucidate similarities and differences.     

Natural and biotech-derived therapeutic proteins: what is the future?

A myriad of novel proteins and ligands of unknown function will be generated by the Human Genomic Project. Due to differences in post-translational processing, proteins produced by recombinant DNA technology may not possess proper biological activity. One way to find their function is to search for their natural counterparts. Proteins are produced in the tissues, and many of them are secreted into plasma and excreted into urine. There is a virtually "unlimited" array of human proteins in our plasma and urine, many of them in a fully active form. They include small molecules like steroids, peptides, and large glycoproteins like human menopausal gonadotropin. A library of plasma and urinary proteins could be developed to serve as a reference for the novel proteins generated by the functional genomic projects.     

"Oscillating" metallocene catalysts: what stops the oscillation?

The 150 MHz (13)C NMR microstructural analysis of polypropylene samples produced with two representative "oscillating" metallocene catalysts of largely different steric hindrance, namely [(2-(3,5-di-tert-butyl-4-methoxyphenyl)indenyl)(2)ZrP](+) and [(2-phenylindenyl)(2)ZrP](+) (P = polymeryl), and the implications on the origin of the stereocontrol are presented and discussed in detail. The original mechanistic proposal of an "oscillation" between a rac-like (isotactic-selective) and a meso-like (nonstereoselective) conformation cannot explain the observed polymer configuration. The isotactic-stereoblock nature of the polymers obtained with the former catalyst proves unambiguously that the active cation "oscillates" between the two enantiomorphous rac-like conformations at an average frequency that, even at high propene concentration, is only slightly lower than that of monomer insertion. The less-hindered [(2-phenylindenyl)(2)ZrP](+) gives instead a largely stereoirregular polypropylene, which is the logical consequence of a faster ligand rotation; however, depending on the use conditions (in particular, on the nature of the cocatalyst and the polarity of the solvent), the polymerization products may also contain appreciable amounts of a fairly isotactic fraction. The peculiar microstructure of this fraction, with isotactic blocks of the same relative configuration spanned by very short atactic ones, rules out the possibility that the latter are due to an active species in meso-like conformation and points rather to a conformationally "locked" rac-like species with restricted ring mobility. The hypothesis of a stereorigidity induced by the proximity to a counteranion, which would play the role of the interannular bridge in the rac-bis(indenyl) ansa-metallocenes, was tested by computer modeling on a [rac-(2-phenylindenyl)(2)ZrMe(C(3)H(6))][B(C(6)F(5))(4)] ion couple and found viable.     

Elongated dihydrogen complexes: what remains of the H-H bond?

Of the several hundred examples of transition metal dihydrogen complexes that have been reported to date, the vast majority have H-H distances of less than 1.0 Angstrom. A small number of complexes have been reported with distances in the range of 1.1 to 1.5 Angstrom. These complexes have been termed elongated dihydrogen complexes. In this review, experimental methods for structure determination of such complexes are summarized, along with computational approaches which have proven useful in understanding the structures of these molecules.     

Structure and reactivity of the polarised liquid–liquid interface: what we know and what we do not

Charge transfer phenomena at the interface between two immiscible electrolyte solutions (ITIES) are electrochemical reactions taking place in soft media. Owing to their liquid nature, the ITIES shows a large panel of electrochemical reactions including electron transfer reactions, ion transfer reactions, coupled electron–ion transfer reactions or biomimetic redox reactions. Nevertheless, the mechanisms by which these reactions proceed are yet to be fully understood. The goal of this short review is to summarise the work accomplished over the past decades towards the elucidation of the structure and reactivity at the ITIES, highlighting the main questions still to be answered.     

Protein microarrays and multiplexed sandwich immunoassays: what beats the beads?

Protein microarray technology allows the simultaneous determination of a large variety of parameters from a minute amount of sample within a single experiment. Assay systems based on this technology are currently applied for the identification, quantitation and functional analysis of proteins. Protein microarray technology is of major interest for proteomic research in basic and applied biology as well as for diagnostic applications. Miniaturized and parallelized assay systems have reached adequate sensitivity and hence have the potential to replace singleplex analysis systems. However, robustness and automation needs to be demonstrated before this technology will finally prove suitable for high-throughput applications. Miniaturized and parallelized sandwich immunoassays are the most advanced assays formats among the different protein microarray applications. Multiplexed sandwich immunoassays can be used for the identification of biomarkers and the validation of potential target molecules. In this review an overview will be given on the current stage of protein microarray technology with a special focus on miniaturized multiplexed sandwich immunoassays.     

Metal-based antitumour drugs in the post-genomic era: what comes next?

In our Dalton Transactions Perspective article entitled, 'Metal-based antitumour drugs in the post genomic era', (Dalton Trans., 2006, 1929-1933) we discussed metal-based drugs in light of past decades of research. We concluded that the post-genomic era would dictate a change in the direction of the field with knowledge of the genome increasingly allowing protein targets to be identified and not simply assuming that DNA is the only relevant target of metal-based drugs. Since our article was published new insights into the mode of action of metal-based drugs have emerged making some older findings increasingly relevant to current drug design. In this article we discuss these developments in terms of what we believe should be the future direction for the field.     

Fracture of polymer interfaces: what are the relevant length scales?

While it is tempting to relate directly the molecular structure of an interface (between glassy or between semi‐cristalline polymers) with its fracture toughness, these two parameters are simply the two end‐points of a complex network which needs to be understood in order to control the mechanical strength of the interface. The important mechanisms occur at three different length scales: the molecular scale (stress‐transfer across the interface), the microscopic scale (plastic deformation at the crack tip) and the macroscopic scale (loading geometry and elastic constants of the polymers). The couplings existing between these length scales in glassy polymer interfaces are reviewed in this paper in light of the latest experimental studies.     

Nickel-mediated hydrogenolysis of C-O bonds of aryl ethers: what is the source of the hydrogen?

Mechanistic studies of the hydrogenolysis of aryl ethers by nickel were undertaken with (diphosphine)aryl methyl ethers. A Ni(0) complex containing Ni-arene interactions adjacent to the aryl-O bond was isolated. Heating led to aryl-O bond activation and generation of a nickel aryl methoxide complex. Formal β-H elimination from this species produced a nickel aryl hydride which can undergo reductive elimination in the presence of formaldehyde to generate a carbon monoxide adduct of Ni(0). The reported complexes map out a plausible mechanism of aryl ether hydrogenolysis catalyzed by nickel. Investigations of a previously reported catalytic system using isotopically labeled substrates are consistent with the mechanism proposed in the stoichiometric system, involving β-H elimination from a nickel alkoxide rather than cleavage of the Ni-O bond by H(2).     

To what extent is the magnitude of the Cole-Cole α of the β-dielectric dispersion of cell suspensions explicable in terms of the cell size distribution?

The Cole-Cole α is a number that is often used to describe the divergence of a measured dielectric dispersion from the ideal dispersion exhibited by a Debye type of dielectric relaxation, and is widely assumed to be related to a distribution of the relaxation times in the system involved. The magnitude and relaxation time of the β-dielectric dispersion due to the charging of the plasma membrane capacitance of cell suspensions depend, inter alia, on the cell radius. An investigation was carried out to determine whether there might therefore be a relationship between the Cole-Cole α of the β-dispersion of yeast cell suspensions and the distribution of cell sizes. Changes in the Cole-Cole α during the batch culture of baker's yeast were recorded, showing an increase in the Cole-Cole α during the exponential phase (more than 0.3) relative to those of the lag phase (about 0.28) and the stationary phase (about 0.2). Although the cell size distribution, measured by flow cytometry, also showed an increase in breadth during the exponential phase, this was not strictly related to the changes in the Cole-Cole α observed. Further, the Cole-Cole α calculated from the measured cell size distribution was significantly smaller than that obtained experimentally. Simulations in which the internal conductivity or membrane capacitance per unit area of individual cells were allowed to vary substantially did not account for the “excessive” Cole-Cole α. Thus the magnitude of the Cole-Cole α of the β-dispersion of yeast cells cannot be ascribed simply to the charging of a static membrane capacitance in cells of differing sizes and/or internal conductivities.     

Photochemical properties of carotenoids: what can we get from the VB model?

Photo-isomerization and anti-oxidation of carotenoids have been studied for many years be-cause of their diverse roles in photobiology, photochemistry and photomedicine[1—6]. The experi-mental works revealed that the changes in the geometry between S0 (the ground state) and T1 (the first triplet state) states are very important for the two processes. Meanwhile, theoretical studies have also been carried out to investigate these processes. The polyenes have usually been used as the models for…     

Paradigms and paradoxes: what are the 54 electron affinities of O2?

Only one electron affinity of oxygen, 43(1) kJ mol⁻¹ is generally cited since the molecular orbital theory anion bond order [3/4] gives an electron affinity, 14 kJ mol⁻¹. However, electron correlation rules predict 27 bonding and 27 antibonding spin orbital coupling states. The relative bond orders (RBOs), 12/13 to [1/4] and the 13 valence electrons of superoxide are used to calculate electron affinities 103 to −243 kJ mol⁻¹ consistent with experimental and theoretical values. These are used to construct 54 ionic Morse potentials.     

Planar or nonplanar: what is the structure of urea in aqueous solution?

A combined quantum chemical statistical mechanical method has been used to study the solvation of urea in water, with emphasis on the structure of urea. The model system consists of three parts: a Hartree-Fock quantum chemical core, 99 water molecules described with a polarizable force-field, and a dielectric continuum. A free-energy profile along the transition of urea from planar to a nonplanar structure is calculated. This mode in aqueous solution is found to be floppy. That is, the structure of urea in water is not well-defined because the planar to nonplanar transition requires an energy of the order of the thermal energy at room temperature. We discuss the implications of this finding for simulation studies of urea in polar environments like water and proteins.     

Prediction of the phase structure in polymer blends: what is needed for success?

Rules for prediction of the phase structure in immiscible polymer blends from the knowledge of their composition, component properties and the flow field in a mixing or processing device are discussed. The reliability of qualitative prediction of the dependence of phase structure on system parameters is used as a criterion of plausibility of the rules. No general reliable rule for prediction of the phase structure type (continuity of phases) is available in the literature. Dependence of the droplet break‐up frequency on its size, contribution of simultaneous collisions of three or more droplets to coalescence and the effect of complex flow field on coalescence must be better described for a reliable qualitative prediction of the dependence of the droplet size on the system parameters.     

An independently addressable microbiosensor array: what are the limits of sensing element density?

A microdisc sensor array, prepared by thin film technology, has been used as a model for miniaturized multi-functional biosensors. It consists of a series of wells, 20 microns in diameter, possessing a 1000 A Pt layer at the bottom that serves as the indicating electrode. The depth of the wells ranged from 2.3-24 microns, depending on the photoresist employed and the spinning speed used to coat the electrode interconnect grid. Ten such wells were arranged in a circular array within an area of radius 130 microns. The center to center distance between any two of the discs ranged from 30 to 155 microns. Each disc is connected by a conductive film line to corresponding pads on the side of the sensor chip. A cylinder placed on top of the chip array formed the electrochemical cell into which a common reference and counter electrode were placed. The reference electrode was operated at ground potential. Prior to the evaluation of enzyme sensors, an assessment of "chemical cross-talk", the perturbation of sensor response resulting from the overlap of proximal diffusion layers, was made using Fe(CN)6(4-). The preliminary conclusion is that the sensing elements probably must be separated by about 100 microns in order to avoid interference from adjacent sensors. A technique was developed for the precision delivery of enzyme and cross-linking agent to the 2.3 microns cavity, having a capacity of 4 pL. This procedure makes possible the preparation of sensor arrays capable of detecting different analytes by employing different enzymes. The sensors gave reasonably rapid (2-4 s) response with linearity (up to about 10 mM. However, the sensors in the center of the array clearly showed the effects of depletion of substrates by the surrounding sensors.     

Investigation of the mechanisms of the action of chemical modifiers for electrothermal atomic absorption spectrometry: what for and how?

Modern trends in the research of the action of chemical modifiers for electrothermal atomic absorption spectrometry (ETAAS) are discussed critically. The most prolific approach is that of investigation of processes occurring during the drying and pyrolysis stages with wide application of data from different fields of chemistry and physics.     

What is an element? What is the periodic table? And what does quantum mechanics contribute to the question?

This article considers two important traditions concerning the chemical elements. The first is the meaning of the term “element” including the distinctions between element as basic substance, as simple substance and as combined simple substance. In addition to briefly tracing the historical development of these distinctions, I make comments on the recent attempts to clarify the fundamental notion of element as basic substance for which I believe the term “element” is best reserved. This discussion has focused on the writings of Fritz Paneth which are here analyzed from a new perspective. The other tradition concerns the reduction of chemistry to quantum mechanics and an understanding of chemical elements through their microscopic components such as protons, neutrons and electrons. I claim that the use of electronic configurations has still not yet settled the question of the placement of several elements and discuss an alternative criterion based on maximizing triads of elements. I also point out another possible limitation to the reductive approach, namely the failure, up to now, to obtain a derivation of the Madelung rule. Mention is made of some recent similarity studies which could be used to clarify the nature of ‘elements’. Although it has been suggested that the notion of element as basic substance should be considered in terms of fundamental particles like protons and electrons, I resist this move and conclude that the quantum mechanical tradition has not had much impact on the question of what is an element which remains an essentially philosophical issue.     

Is the bound substrate in nitric oxide synthase protonated or neutral and what is the active oxidant that performs substrate hydroxylation?

We present here results of a series of density functional theory (DFT) studies on enzyme active site models of nitric oxide synthase (NOS) and address the key steps in the catalytic cycle whereby the substrate (L-arginine) is hydroxylated to N(omega)-hydroxo-arginine. It has been proposed that the mechanism follows a cytochrome P450-type catalytic cycle; however, our calculations find an alternative low energy pathway whereby the bound L-arginine substrate has two important functions in the catalytic cycle, namely first as a proton donor and later as the substrate in the reaction mechanism. Thus, the DFT studies show that the oxo-iron active species (compound I) cannot abstract a proton and neither a hydrogen atom from protonated L-arginine due to the strength of the N-H bonds of the substrate. However, the hydroxylation of neutral arginine by compound I and its one electron reduced form (compound II) requires much lower barriers and is highly exothermic. Detailed analysis of proton transfer mechanisms shows that the basicity of the dioxo dianion and the hydroperoxo-iron (compound 0) intermediates in the catalytic cycle are larger than that of arginine, which makes it likely that protonated arginine donates one of the two protons needed during the first catalytic cycle of NOS. Therefore, DFT predicts that in NOS enzymes arginine binds to the active site in its protonated form, but is deprotonated during the oxygen activation process in the catalytic cycle by either the dioxo dianion species or compound 0. As a result of the low ionization potential of neutral arginine, the actual hydroxylation reaction starts with an initial electron transfer from the substrate to compound I to create compound II followed by a concerted hydrogen abstraction/radical rebound from the substrate. These studies indicate that compound II is the actual oxidant in NOS enzymes that performs the hydroxylation reaction of arginine, which is in sharp contrast with the cytochromes P450 where compound II was shown to be a sluggish oxidant. This is the first example of an enzyme where compound II is able to participate in the reaction mechanism. Moreover, arginine hydroxylation by NOS enzymes is catalyzed in a significantly different way from the cytochromes P450 although the active sites of the two enzyme classes are very similar in structure. Detailed studies of environmental effects on the reaction mechanism show that environmental perturbations as appear in the protein have little effect and do not change the energies of the reaction. Finally, a valence bond curve crossing model has been set up to explain the obtained reaction mechanisms for the hydrogen abstraction processes in P450 and NOS enzymes.     

Nucleophilic or electrophilic phosphinidene complexes ML(n)=PH; what makes the difference?

Density functional studies, based on the local density approximation including nonlocal corrections for correlation and exchange self-consistently, have been carried out for the equilibrium structures of the phosphinidene transition metal complexes ML(n)=PH, with M = Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Fe, Ru, Os, Co, Rh, Ir and L = CO, PH(3), Cp. The chemical reactivity of the transition metal-stabilized phosphinidene P-R is influenced by its spectator ligands L. Ligands with strong sigma-donor capabilities on the metal increase the electron density on the phosphorus atom, raise the pi-orbital energy, and enhance its nucleophilicity. Spectator ligands with strong pi-acceptor capabilities lower the charge concentration on P and stabilize the pi-orbital, which results in a higher affinity for electron-rich species. The ML(n)=PH bond is investigated using a bond energy analysis in terms of electrostatic interaction, Pauli repulsion, and orbital interaction. A symmetry decomposition scheme affords a quantitative estimate of the sigma- and pi-bond strengths. It is shown that the investigated phosphinidenes are strong pi-acceptors and even stronger sigma-donors. The metal-phosphinidene interaction increases on going from the first to the second- and third-row transition metals.