Complete maps of molecular-loop conformational spaces

This paper presents a numerical method to compute all possible conformations of distance-constrained molecular loops, i.e., loops where some interatomic distances are held fixed, while others can vary. The method is general (it can be applied to single or multiple intermingled loops of arbitrary topology) and complete (it isolates all solutions, even if they form positive-dimensional sets). Generality is achieved by reducing the problem to finding all embeddings of a set of points constrained by pairwise distances, which can be formulated as computing the roots of a system of Cayley-Menger determinants. Completeness is achieved by expressing these determinants in Bernstein form and using a numerical algorithm that exploits such form to bound all root locations at any desired precision. The method is readily parallelizable, and the current implementation can be run on single- or multiprocessor machines. Experiments are included that show the method's performance on rigid loops, mobile loops, and multiloop molecules. In all cases, complete maps including all possible conformations are obtained, thus allowing an exhaustive analysis and visualization of all pseudo-rotation paths between different conformations satisfying loop closure.     

Interactions of 4-chlorophenol with TiO2 polycrystalline surfaces: a study of environmental interfaces by NEXAFS, XPS, and UPS

Despite a significant body of literature on the photocatalytic decomposition of 4-chlorophenol by TiO2 at liquid/solid and gas/solid interfaces, a fundamental understanding of the interaction of 4-chlorophenol with TiO2 is lacking. We present the first study of this interaction under well-defined UHV conditions by means of NEXAFS, time-dependent XPS, and UPS. XPS data show that the molecule adsorbs with the carbon framework intact and no scission of the C-Cl bond. The NEXAFS results indicate a coverage-dependent tilted geometry for the adsorbed molecule that is attached to the surface via a phenolate link. In contrast, because of the absence of an OH functionality, 1,2,4-trichlorobenzene lies flat. The adsorption of 4-chlorophenol is accompanied by a decrease in the TiO2 work function pointing to adsorbate --> substrate charge transfer. Interestingly, the UPS data suggest that 4-chlorophenol adsorption leads to the photosensitization of TiO2, thus providing a basis for understanding recent results on the visible light photocatalytic activity of TiO2 for 4-chlorophenol decomposition. It is also found that the molecule is stable against thermal decomposition at temperatures of up to approximately 473 K, which is well above the temperature range used for photocatalytic decomposition studies.     

Diffusion in tight confinement: a lattice-gas cellular automaton approach. II. Transport properties

In this second paper the authors study the transport properties of the lattice-gas cellular automaton presented in Paper I [J. Chem. Phys. 126, 194709 (2007)] to model adsorption and dynamics of particles in a lattice of confining cells. Their work shows how a surprisingly simple parallel rule applied to a static network of cells joined by links set in space and time can generate a wide range of dynamical behaviors. In their model the cells are the elementary constituent objects of the network. They are a portion of space structured in sites which are energetically different. Each cell can accommodate a given maximum number of particles, and each pair of neighboring cells can exchange at most one particle at a time. The predictions of the model are in qualitative agreement with both experimental observations and molecular dynamics simulation results.     

Superfluid to Mott-insulator transition in Bose-Hubbard models

We study the superfluid-insulator transition in Bose-Hubbard models in one-, two-, and three-dimensional cubic lattices by means of a recently proposed variational wave function. In one dimension, the variational results agree with the expected Berezinskii-Kosterlitz-Thouless scenario of the interaction-driven Mott transition. In two and three dimensions, we find evidence that, across the transition, most of the spectral weight is concentrated at high energies, suggestive of preformed Mott-Hubbard sidebands. This result is compatible with the experimental data by Stoferle et al. [Phys. Rev. Lett. 92, 130403 (2004)].     

Preparation of a set of 4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-4-ones as potential Hsp90 ligands

A synthetic route for the preparation of 4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-4-ones characterized by a decorated benzyl moiety at different positions of the five-membered ring has been developed, and some compounds have been tested as Hsp90 ligands. One of them displayed IC₅₀ = 50 μM representing an interesting starting point for further investigations.     

Heterogeneous Photocatalytic Recycling of FeX2/FeX3 for Efficient Halogenation of C−H Bonds Using NaX

Environmental-friendly halogenation of C−H bonds using abundant, non-toxic halogen salts is in high demand in various chemical industries, yet the efficiency and selectivity of laboratory available protocols are far behind the conventional photolytic halogenation process which uses hazardous halogen sources. Here we report an FeX₂ (X=Br, Cl) coupled semiconductor system for efficient, selective, and continuous photocatalytic halogenation using NaX as halogen source under mild conditions. Herein, FeX₂ catalyzes the reduction of molecular oxygen and the consumption of generated oxygen radicals, thus boosting the generation of halogen radicals and elemental halogen for direct halogenation and indirect halogenation via the formation of FeX₃. Recycling of FeX₂ and FeX₃ during the photocatalytic process enables the halogenation of a wide range of hydrocarbons in a continuous flow, rendering it a promising method for applications.     

Mass spectrometry and hydrogen/deuterium exchange measurements of alcohol-induced structural changes in cellular retinol-binding protein type I

To bind and release its ligand, cellular retinol-binding protein type I (CRBP) needs to undergo conformational and dynamic changes to connect the inner, solvent-shielded cavity, where retinol is found to bind, and the outside medium. Retinol dissociation in vitro is favoured by water/alcohol mixtures whose moderately low dielectric constants mimic a property characteristic of the membrane microenvironment where this process occurs in vivo. Apo- and holo-CRBP, in either water/methanol or water/trifluoroethanol (TFE) mixtures, were analyzed at equilibrium by electrospray ionization with orthogonal quadrupole time-of-flight mass spectrometry (ESI-Q-TOFMS) to identify the alcohol-induced species. The questions were asked whether the presence of alcohols affects protein dynamics, as reflected by hydrogen/deuterium (H/D) exchange monitored by continuous-labelling experiments, and to which extent retinol dissociation influences the process. With increasing methanol, at pH near neutrality, apo-CRBP exhibits a progressively more compact conformation, resulting in reduced H/D exchange with respect to the native protein in water. Retinol dissociation from the holo-protein did not promote hydrogen replacement. Similarly, in the presence of the low TFE concentration sufficient to cause retinol dissociation, the hydrogen exchange of the resulting apo-protein was not exalted. However, in contrast with the alkanol, higher TFE concentrations induced a transition of apo-CRBP to a new alpha-helix conformation capable of exchanging all available hydrogen atoms.     

Interface engineering of synthetic pores: towards hypersensitive biosensors

Hydrophilic anchoring is introduced as a promising strategy to constructively control the various interactions of synthetic pore sensors with the surrounding biphasic environment. Artificial rigid-rod beta barrels are selected as classical synthetic multifunctional pores and random-coil tetralysines are attached as hydrophilic anchors. The synthesis of this advanced pore is accomplished in 32 steps from commercially available starting materials. With regard to pore activity as such, the key impact of hydrophilic anchoring is a change from a Hill coefficient n<1 to n=4. This change confirms successful suppression of the competing self-assembly with precipitation from the aqueous phase as the origin of the accomplished increase in pore activity. The hydrophilic anchors do not interfere with the blockage of the synthetic pore sensors by anionic analytes. In the case of stoichiometric binding of blockers (K(D)=EC(50) of the pore; EC(50)=concentration needed to observe 50 % pore activity), however, the increase in pore activity achieved by hydrophilic anchoring results in improved pore blockage under high dilution conditions. Controls confirm that this increase does not occur with analytes that do not exhibit stoichiometric binding (K(D)>EC(50)). These results not only reveal stoichiometric binding as the expected origin of the sensitivity limit of synthetic pore sensors, they also provide promising solutions for this problem. The combination of hydrophilic anchoring with targeted pore formation emerges as a particularly promising strategy to further reduce effective pore concentrations. The scope and limitations of this approach are exemplified with pertinent analyte pairs that are essential for the sensing of sucrose, lactose, acetate, and glutamate with synthetic pores in samples from the supermarket.     

A Modular Tubular Flow System with Replaceable Photocatalyst Membranes for Scalable Coupling and Hydrogenation

Heterogeneous photocatalysis is effective for the selective synthesis of value-added chemicals at lab-scale, yet falls short of requirements for mass production (low cost and user friendliness). Here we report the design and fabrication of a modular tubular flow system embedded with replaceable photocatalyst membranes for scalable photocatalytic C−C, C−N homocoupling and hydrogenation reactions, which can be operated in either circular and continuous flow mode with high performance. The photocatalyst membranes almost fully occupy the volume of the reactor, thus enabling optimal absorption of the incident light. Additionally, the porous structured photocatalyst membranes facilitate the mass transfer of the reactants to efficiently use the active sites, resulting in 0^th-order reaction kinetics and a high space-time yield compared to the batch reaction system at practical application levels and prolonged reaction times.     

Kinetic and Product Study of the S-oxidation vs HAT Chemoselectivity in Reactions Promoted by Nonheme Iron(IV)-oxo Complex/NHPI Mediator System

The chemoselectivity between S-oxidation and hydrogen atom transfer (HAT) from C−H bonds has been investigated in the oxidations of a series of aryl sulfides, alkyl aromatic compounds and benzylic alcohols promoted by the iron(IV)-oxo complex [(N4Py)Fe^IV(O)]²⁺ (N4Py: N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)-methylamine) either alone or in the presence of the N-hydroxyphthalimide (NHPI) mediator via kinetic and product studies. Kinetic analyses indicate a generally higher reactivity of [(N4Py)Fe^IV(O)]²⁺ for S-oxidation process while HAT is favored in the reactions promoted by phthalimide-N-oxyl radical (PINO) deriving from NHPI oxidation. Product analysis in intermolecular competitive oxidations confirms the kinetic results with sulfoxides obtained as major products in the oxidation promoted by [(N4Py)Fe^IV(O)]²⁺. Conversely, when NHPI is employed as a mediator, significant differences in terms of chemoselectivity are observed, and HAT-derived products are obtained in higher yields which translate into an inversion of selectivity in the case of the substrates containing activated C−H bonds like diphenylmethane, triphenylmethane and benzylic alcohols. A similar change of chemoselectivity is also observed in the oxidation of aromatic substrates containing both a sulfur atom and α to OH benzylic C−H bonds, with the sulfoxide product more abundant in the absence of NHPI and carbonyl products prevailing with the [(N4Py)Fe^IV(O)]²⁺/NHPI system.