A quantum mechanical Hamiltonian for unhindered macromolecular chains: consistency with Gaussian models

A model for an open unhindered three-dimensional macromolecular chain, based upon quantum mechanics and proposed in previous works, is studied in order to investigate its physical properties and consistency. The chain is formed by N particles interacting through harmonic-like vibrational potentials in the high-frequency limit (in which all successive bond lengths become fixed). This formulation leads to a specific Hamiltonian for the chain: it constitutes an improvement in comparison with standard Gaussian models, which do not. The classical partition function Z_c resulting from the quantum formulation is represented through an integral, which exhibits explicitly rotational invariance in the integrand and provides the basis for further approximations for large N. Approximate formulae are obtained for correlations between pairs of bond vectors, the distribution function for the end-to-end vector, distribution functions for individual bond vectors, “rubber eleasticity” (when stretching forces act) and the structure factor for small wave vector. In all cases, the results which have arisen from the quantum mechanical formulation coincide with those obtained for the standard Gaussian chain. This agreement appears to confirm the physical consistency of the quantum Hamiltonian characterizing the model.     

RI-MP2: first derivatives and global consistency

The evaluation of RI-MP2 first derivatives with respect to nuclear coordinates or with respect to an external electric field is described. The prefix RI indicates the use of an approximate resolution of identity in the Hilbert space of interacting charge distributions (Coulomb metric), i.e., the use of an auxiliary basis set to approximate charge distributions. The RI technique is applied to first derivatives of the MP2 correlation energy expression while the (restricted) Hartree-Fock reference is treated in the usual way. Computational savings by a factor of 10 over conventional approaches are demonstrated in an application to porphyrin. It is shown that the RI approximation to MP2 derivatives does not entail any significant loss in accuracy. Finally, the relative energetic stabilities of a representative sample of closed-shell molecules built from first and second row elements have been investigated by the RI-MP2 approach, and thus it is tested whether such properties that refer to potential energy hypersurfaces in a more global way can be described with similar consistency to the more locally defined derivatives. Received: 17 December 1996 / Accepted: 27 March 1997     

Multiconfiguration perturbation theory: size consistency at second order

A modified version of a previously elaborated multiconfiguration perturbation theory (MCPT) [Rolik et al. J. Chem. Phys. 119, 1922 (2003)] is presented. In the modified formulation size consistency is ensured at second order in energy, by omitting projectors from the zero order Hamiltonian operator. This MCPT formulation is abbreviated as SC2-MCPT (size consistent at second order). To ensure proper separability, we also require that energy denominators are constructed as differences of some one-particle energies. A similar choice for energy denominators also renders the well-known multireference Moller-Plesset (MRMP) energy size consistent at second order. The same thing applies to the related multireference perturbation theory by Witek, Nakano, and Hirao.     

When bigger is better: intermolecular hydrofunctionalizations of activated alkenes catalyzed by heteroleptic alkaline Earth complexes

New alkaline-earth amido complexes catalyze the regioselective intermolecular hydroamination (see scheme; Ae=alkaline earth) and hydrophosphination of styrene and isoprene with unprecedented activities. The catalytic performances increased linearly with the size of the metal.     

Azadibenzophospholes: functional building blocks with pronounced electron-acceptor character

A series of azadibenzophospholes with varying location of the nitrogen center has been synthesized and comprehensively characterized. In the context of the study, suitably brominated phenylpyridine precursors were accessed via Suzuki-Miyaura cross-coupling for the first time. Despite being nonfluorescent, X-ray crystallographic studies of two azadibenzophosphole oxides revealed planar conjugated scaffolds with high degree of π-conjugation. The P-oxidized species were found to show desirable reversible reduction features that support promising electron-accepting properties of the materials. The presence of the nitrogen as well as phosphorus centers within the scaffold allowed for further functionalization with transition metals, as well as methyl groups that result in altered absorption and redox features for the materials. Subsequent bromination of the scaffold selectively occurred at the exocyclic P-phenyl group, as confirmed via X-ray crystallography. This halogenation allowed for further modification of the system via catalytic cross-coupling with pyridine.     

Biotechnology and polymer chemistry: a growing relationship

DuPont is using biotechnology to make chemical compounds and materials, especially polymers and polymer intermediates ‐ demonstrating that biotechnology can lead to more effective and productive manufacturing processes for traditional chemical businesses as well as pharmaceuticals, agricultural products, and new products for improved nutrition and health.     

Density functional theory: Approximating quasiparticle density functional

A constructive approach for deriving the approximating quasiparticle energy density functional is proposed. As a matter of fact, the proposed approach is the direct development of the Kohn–Sham quasiparticle concept and the Levy–Valone approach. The approach presented takes into account a pseudopotential character of the exchange-correlation part of the density functional and results in a system of functional equations to obtain ground-state energies of many-electron systems.     

Biosynthesis of tetronate antibiotics: A growing family of natural products with broad biological activities

Tetronate antibiotics, a growing family of natural products featuring a characteristic tetronic acid moiety, are of importance and of particular interest for their typical structures, especially the spirotetronate structure, and corresponding versatile biological activities. Considerable efforts have persistently performed since the first tetronate was isolated, to elucidate the biosynthesis of natural tetronate products, by isotope-labeled feeding experiments, genetical characterization of biosynthetic gene clusters, and biochemical reconstitution of key enzymatic catalyzed reactions. Accordingly, the biosynthesis of spirotetronates has been gradually determined, including biosynthesis of a polyketide-derived backbone for spirotetronate aglycone, incorporation of a glycerol-derived three-carbon unit into tetronic acid moiety, formation of mature aglycone via Diels-Alder-like reaction, and decorations of aglycone with various deoxysugar moieties. In this paper, the biosynthetic investigations of natural tetronates are well documented and a common biosynthetic route for this group of natural products is summarized accordingly.     

On the optimal partitioning of data with K-means,growing K-means,neural gas,and growing neural gas

In this paper, the performance of new clustering methods such as Neural Gas (NG) and Growing Neural Gas (GNG) is compared with the K-means method for real and simulated data sets. Moreover, a new algorithm called growing K-means, GK, is introduced as the alternative to Neural Gas and Growing Neural Gas. It has small input requirements and is conceptually very simple. The GK leads to nearly optimal values of the cost function, and, contrary to K-means, it is independent of the initial data set partition. The incremental property of GK additionally helps to estimate the number of "natural" clusters in data, i.e., the well-separated groups of objects in the data space.     

Improved hybrid functional for solids: the HSEsol functional

We introduce the hybrid functional HSEsol. It is based on PBEsol, a revised Perdew-Burke-Ernzerhof functional, designed to yield accurate equilibrium properties for solids and their surfaces. We present lattice constants, bulk moduli, atomization energies, heats of formation, and band gaps for extended systems, as well as atomization energies for the molecular G2-1 test set. Compared to HSE, significant improvements are found for lattice constants and atomization energies of solids, but atomization energies of molecules are slightly worse than for HSE. Additionally, we present zero-point anharmonic expansion corrections to the lattice constants and bulk moduli, evaluated from ab initio phonon calculations.     

Kinetic stabilization of growing gold clusters by passivation with thiolates

Small gold clusters (<1 nm), protected by monolayers of glutathione, N-(2-mercaptopropionyl)glycine, or mercaptosuccinic acid, were prepared by reducing the corresponding Au(I)-thiolate polymers and were fractionated by size using polyacrylamide gel electrophoresis (PAGE). Mass analysis of the fractionated clusters revealed that their core sizes varied with the molecular structures of the thiolates. This finding indicates that the reduction of the Au(I)-thiolate polymers yields small clusters whose growth is kinetically hindered by passivation with thiolates. Optical spectra of the clusters with identical compositions exhibited different profiles depending on the thiolate molecular structures. This observation implies that deformation of the underlying gold cores is induced by interligand interactions.     

Carbohydrate analysis by high-performance anion-exchange chromatography with pulsed amperometric detection: the potential is still growing

This article reviews recent advances of carbohydrate analysis by high-performance anion-exchange chromatography with pulsed amperometric detection. Starting from the paper of Dennis C. Johnson [1] in which the great analytical promise of such a technique was anticipated, a multitude of exciting new research possibilities have recently emerged. The great attractiveness of high-performance anion-exchange chromatography is largely due to its compatibility with such a sensitive, selective and reliable detection method as pulsed amperometry. This very good match between liquid chromatography and electrochemical detection has allowed the determination of carbohydrates in a variety of complex matrices, for instance, foods, beverages, diary and biotechnological products, vegetal tissues, and also in the area of clinical diagnostics. For this reason, the introduction of HPAEC-PAD into regulated methods is becoming increasingly accepted. A comprehensive collection of applications to carbohydrates and samples of interest is given, with special focus on the separation of closely related sugar compounds using dilute alkaline eluents. Advances in pulsed potential waveforms are also discussed, and a comparison with other liquid chromatographic methods addressed. 2-keto-3-deoxy-D-glycero-D-galactonononic acid; KDO, 2-keto-3-deoxyoctulosonic acid; FOS, fructooligosaccharides; GF5, GF6, and GF7, oligofructans: Hib, Haemophilus influenzae type b; FAB, fast atom bombardment; ESI, electrospray ionization; MALDI-TOF, matrix assisted laser desorption ionization-time of flight.     

Carbohydrate analysis by high-performance anion-exchange chromatography with pulsed amperometric detection: The potential is still growing

This article reviews recent advances of carbohydrate analysis by high-performance anion-exchange chromatography with pulsed amperometric detection. Starting from the paper of Dennis C. Johnson [1] in which the great analytical promise of such a technique was anticipated, a multitude of exciting new research possibilities have recently emerged. The great attractiveness of high-performance anion-exchange chromatography is largely due to its compatibility with such a sensitive, selective and reliable detection method as pulsed amperometry. This very good match between liquid chromatography and electrochemical detection has allowed the determination of carbohydrates in a variety of complex matrices, for instance, foods, beverages, diary and biotechnological products, vegetal tissues, and also in the area of clinical diagnostics. For this reason, the introduction of HPAEC-PAD into regulated methods is becoming increasingly accepted. A comprehensive collection of applications to carbohydrates and samples of interest is given, with special focus on the separation of closely related sugar compounds using dilute alkaline eluents. Advances in pulsed potential waveforms are also discussed, and a comparison with other liquid chromatographic methods addressed.     

Porphyrazines with tosylamine functional groups

Metal-free (3b) and metallo-porphyrazines (3a, 3c, 3d) (M  Mg, Ni and Co) carrying eight functional tosylaminoethylthia-groups on peripheral positions have been synthesised for the first time from cyclotetramerization of 1,2-bis(2-tosylaminoethylthia)maleonitrile (2) in the presence of magnesium propoxide; the metal-free derivative 3b was obtained by treatment of 3a with trifluoroacetic acid and it was further converted into Co(II) (3c) and Ni(II) (3d) derivatives by using acetate salts of corresponding metal ions. The reactivity of tosylamino-groups was verified by its alkylation to yield octakis[(tosyl)(hexyl)amino- ethylthia]porphyrazinatomagnesium(II) (4a).The new compounds were characterised by elemental analysis, IR, NMR and UV-vis spectra.     

Ethylene-styrene copolymerization with constrained geometry catalysts: a density functional study

A density functional theory (DFT) study of the ethylene-styrene copolymerization process with titanium-based constrained geometry catalyst (CGC) is presented. To establish the difference between simplified CGC or real CGC models, i.e., considering all ligands of the catalyst, we have performed calculations for ethylene and styrene insertions in both models. Thus, we have used two different DFT functional, BP86 and B3L YP along with two basis set, LANL 2DZ (without polarization functions) and DZVP (including polarization functions). We have noted certain differences between theoretical results published by other authors and our theoretical and experimental data.     

Small fullerenes with BN belts: a density functional theory investigation

Density functional calculations have been carried out on a series of BCN hybrid fullerenes with certain substitution patterns in comparison with their parent compounds Cn (n = 30, 32, 36, 38, 40, 44, 48, 50, 52). The substitutional structures, energy gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, ionization potentials, electron affinities, as well as molecular electrostatic potentials have been systematically investigated. The following important points of BCN hybrid fullerenes are stressed: The present studied fullerenes, comprising tubular "belt" and polar "cap", could be divided into three types of structure; each has different indexes of tubular structure and terminal caps. The properties of BCN hybrid fullerenes depend on the type of "tubular belt + polar cap" structures, especially, the HOMO and LUMO characters and MEPs of BCN fullerene are strongly governed by their structure types.     

All-electron time-dependent density functional theory with finite elements: time-propagation approach

We present an all-electron method for time-dependent density functional theory which employs hierarchical nonuniform finite-element bases and the time-propagation approach. The method is capable of treating linear and nonlinear response of valence and core electrons to an external field. We also introduce (i) a preconditioner for the propagation equation, (ii) a stable way to implement absorbing boundary conditions, and (iii) a new kind of absorbing boundary condition inspired by perfectly matched layers.     

Aggregation-induced chemical reactions: acid dissociation in growing water clusters

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.     

Improved consistency in 2D gel electrophoresis: Sheep plasma as a test case

Two‐dimensional (2D) gel electrophoresis is a well‐proven proteomic technique; however, sample‐specific optimisation can often be necessary in order to get consistent quantitation. In particular, plasma samples are often smeared on 2D gels making spot matching difficult. A variety of different sample preparation and 2D methods were tested by using sheep plasma, and it was found that lowering sample pH prior to precipitation, using a long voltage gradient for isoelectric focusing and the inclusion of carrier ampholytes in the electrode wicks, improved both the quality and consistency of spot resolution. Analysis of the internal standards from two different DIGE experiments, one with conventional methodology and one with the improved method, showed that along with substantially improving the number of spots resolved, the average CV (coefficient of variation) of matched standards was lower with the new method. 428 matched spots were found using the improved method compared to 208 matched spots using conventional methodology. For the 174 spots that were matched between the two DIGE experiments, the average CV's of spot volumes were also significantly lower, at 0.20 for the new method compared to 0.24 for the conventional method (p < 0.001).