Stoichiometric compounds of magnesium dichloride with ethanol for the supported Ziegler-Natta catalysis: first recognition and multidimensional MAS NMR study

Ethanol associates easily with MgCl(2) to form adducts of complex architecture, but until now available characterization methods have failed to identify the pure stoichiometric compounds and their structures. To remedy this, we set about applying homonuclear and heteronuclear 2D correlated solid-state NMR spectroscopy to identify the pure compounds and the ethanol-to-magnesium coordination pattern. High spinning speed and Lee-Goldburg sequences were able to reduce the hydrogen spin-diffusion and homonuclear coupling in the crystalline solid, thus achieving high resolution also in the hydrogen domain. On this basis, the pure adducts, of interest as catalyst supports for Ziegler-Natta polymerization, were isolated for the first time. Magnesium coordination sites with given numbers of ligands and their multiplicity in the crystal cells were determined in the new-found stoichiometric complexes. Variable temperature and 2D carbon-carbon exchange NMR, as well as relaxation times in the fast motion regime, revealed the disordering phenomena generated by ethanol dynamics in the crystal. Decoding the intriguing polymorphism of the precursors permits to trace the genealogy of tailored MgCl(2) titanate granules, active as highly productive catalysts for the stereospecific polymerization of olefins.     

A strategy for the NMR characterization of type II copper(II) proteins: the case of the copper trafficking protein CopC from Pseudomonas Syringae

CopC from Pseudomonas syringae was found to be a protein capable of binding both Cu(I) and Cu(II) at two different sites. The solution structure of the apo protein is available, and structural information has been obtained on the Cu(I) bound form. We attempt here to set the limits for the determination of the solution structure of a Cu(II) protein, such as the Cu(II) bound form of CopC, in which the Cu(II) ion takes a type II coordination. The electron relaxation time is estimated from NMRD measurements to be 3 ns which leads to a correlation time for the nuclear spin-electron spin dipolar interaction of 2 ns. This information allowed us to tailor the NMR experiments and to fully exploit purely heteronuclear spectroscopy to assign as many signals as possible. In this way, 37 (13)C and 11 (15)N signals that completely escape detection with conventional approaches were assigned. Paramagnetic based structural constraints were obtained by measuring paramagnetic longitudinal relaxation enhancements (rho(para)) which allowed us to precisely locate the copper ion within the protein frame. Pseudocontact shifts (pcs's) were also used as constraints for 83 (1)H and 18 (13)C nuclei. With them, together with other standard structural constraints, a structure is obtained (and submitted to PDB) where information is only missing in a sphere with a 6 A radius from the copper ion. If we borrow information from EXAFS data, which show evidence of two copper coordinated histidines, then His 1 and His 91 are unambiguously identified as copper ligands. EXAFS data indicate two more light donor atoms (O/N) which could be from Asp 27 and Glu 89, whereas the NMRD data indicate the presence of a semicoordinated water molecule at 2.8 A (Cu-O distance) roughly orthogonal to the plane identified by the other four ligands. This represents the most extensively characterized structure of a type II Cu(II) protein obtained employing the most advanced NMR methods and with the aid of EXAFS data. The knowledge of the location of the Cu(II) in the protein is important for the copper transfer mechanism.     

The conductor of one-dimensional gorenstein rings in their blowing-up

Let (A,M) be a local, one-dimensional, Cohen-Macaulay ring of multiplicity e=e(A)>1 and Hilbert function H(A). Let I=Ann_A (B/A) be the conductor of A in its blowing up B. Northcott and Matlis have proved that if the embedding dimension emdim A of A is 2 then I=M^e−1 [3; Corollary 13.8]. If emdim A>2 little is know about I. In [6] and [7] I is computed when the associated graded ring G(A) is reduced (in this case B in the integral closure of A). In this paper we compute I when A is Gorenstein. There are in general upper and lower bounds for I in terms of a power of M and we start discussing when these bounds are attained. In particular we show that in the extremal situation I=M^e−1 one has emdimA=2 (thus inverting the result of Northcott and Matlis). Then we consider the case of Gorenstein rings. We prove that if G(A) in Gorenstein then I=M^ϑ where ϑ=Min{n‖H(n)=e}. If more generally A is Gorenstein then I⊂M² or emdim A=e(A)=2. When A is the local ring of a curve at a singular point p we get, as a consequence of this last result a proof of the following conjecture of Catanese which has interesting geometric applications [1]: if the conductor J of A in its normalization is not contained in M² then p is a node.     

A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists

Summary In the absence of a 3D structure of the target biomolecule, to propose the 3D requirements for a small molecule to exhibit a particular bioactivity, one must supply both a bioactive conformation and a superposition rule for every active compound. Our strategy identifies both simultaneously. We first generate and optimize all low-energy conformations by any suitable method. For each conformation we then use ALAD-DIN to calculate the location of points to be considered as part of the superposition. These points include atoms in the molecule and projections from the molecule to hydrogen-bond donors and acceptors or charged groups in the binding site. These positions and the relative energy of each conformation are the input to our new program DISCO. It uses a clique-detection method to find superpositions that contain a least one conformation of each molecule and user-specified numbers of point types and chirality. DISCO is fast; for example, it takes about 1 min CPU to propose pharmacophores from 21 conformations of seven molecules. We typically run DISCO several times to compare alternative pharmacophore maps. For D₂ dopamine agonists DISCO shows that the newer 2-aminothiazoles fit the traditional pharmacophore. Using site points correctly identifies the bioactive enantiomers of indoles to compare with catechols whereas using only ligand points leads to selecting the inactive enantiomer for the pharmacophore map. In addition, DISCO reproduces pharmacophore maps of benzodiazepines in the literature and proposes subtle improvements. Our experience suggests that clique-detection methods will find many applications in computational chemistry and computer-assisted molecular design.     

Crystal structures of thecis-anti photodimer of uracil

Irradiation of uracil in ice produces a small quantity of thecis-anti cyclobutyl type photodimer. The molecule contains a pseudo two-fold axis and a cyclobutyl ring which is puckered, with dihedral angles near 150°. Torsion angles about the C(5)-C(6) and C(5)-C(6) bonds are 21°. Each uracil residue has seven atoms which are coplanar to within 0-07 Å, while C(6) and C(6) are 0·38 Å and 0·35 Å out of the planes of their respective residues. Each molecule participates in eight NH...O bonds which range from 2·83 to 2·97 Å. The material crystallizes in the triclinic space group P¯1 with unit cell parametersa = 8·594 Å,b = 7·478 Å,c = 6·915 Å, = 96·9 °, = 95·4 ° and = 85·5 °. The structure was solved by means of the symbolic addition procedure for phase determination.National Academy of Science-National Research Council Postdoctoral Resident Research Associate.     

Dual Illumination Enhances Transformation of an Engineered Green‐to‐Red Photoconvertible Fluorescent Protein

The molecular mechanisms for the photoconversion of fluorescent proteins remain elusive owing to the challenges of monitoring chromophore structural dynamics during the light‐induced processes. We implemented time‐resolved electronic and stimulated Raman spectroscopies to reveal two hidden species of an engineered ancestral GFP‐like protein LEA, involving semi‐trapped protonated and trapped deprotonated chromophores en route to photoconversion in pH 7.9 buffer. A new dual‐illumination approach was examined, using 400 and 505 nm light simultaneously to achieve faster conversion and higher color contrast. Substitution of UV irradiation with visible light benefits bioimaging, while the spectral benchmark of a trapped chromophore with characteristic ring twisting and bridge‐H bending motions enables rational design of functional proteins. With the improved H‐bonding network and structural motions, the photoexcited chromophore could increase the photoswitching‐aided photoconversion while reducing trapped species.     

Monitoring the Interaction of α-Synuclein with Calcium Ions through Exclusively Heteronuclear Nuclear Magnetic Resonance Experiments

Many properties of intrinsically disordered proteins (IDPs), or protein regions (IDRs), are modulated by the nature of amino acid side chains as well as by local solvent exposure. We propose a set of exclusively heteronuclear NMR experiments to investigate these features in different experimental conditions that are relevant for physiological function. The proposed approach is generally applicable to many IDPs/IDRs whose assignment is available in the Biological Magnetic Resonance Bank (BMRB) to investigate how their properties are modulated by different, physiologically relevant conditions. The experiments, tested on α-synuclein, are then used to investigate how α-synuclein senses Ca²⁺ concentration jumps associated with the transmission of nerve signals. Novel modules in the primary sequence of α-synuclein optimized for calcium sensing in highly flexible, disordered protein segments are identified.     

Selective bond breaking in beta-D-ribose by gas-phase electron attachment around 8 eV

Electron attachment experiments are carried out on the beta-d-ribose molecule in the gas phase for the energy region around 8 eV, and clear fragmentation products are observed for different mass values. A computational analysis of the relevant dynamics is also carried out for the beta-d-ribose in both the furanosic and pyranosic form as gaseous targets around that energy range. The quantum scattering attributes obtained from the calculations reveal in both systems the presence of transient negative ions (TNIs). An analysis of the spatial features of the excess resonant electron, together with the computation and characterization of the target molecular normal modes, suggests possible break-up pathways of the initial, metastable molecular species.     

Pyrroloquinoxaline hydrazones as fluorescent probes for amyloid fibrils

Here we describe the identification and preliminary characterization of a new class of pyrrolo(imidazo)quinoxaline hydrazones as florescent probes for Aβ(1-42) fibrils. All the newly developed compounds were able to bind amyloid fibrils formed in vitro and some of them displayed an increase of their fluorescence upon binding. When tested on brain tissue preparations presenting Aβ deposits, the described hydrazones selectively stained amyloid structures and did not display aspecific binding. The hydrazones did not show antifibrillogenic activity and electron microscopy analysis revealed that they do not interfere with fibrils structure. The described pyrrolo(imidazo)quinoxalines could be useful for studying amyloid structures in vitro. Moreover, their experimentally proven ability to cross the blood-brain barrier in mouse opens the possibility of developing these compounds as potential amyloid imaging agents for in vivo applications.     

Oxidative coupling as a biomimetic approach to the synthesis of scytonemin

The first total synthesis of the dimeric alkaloid pigment scytonemin is described. The key transformations in its synthesis from 3-indole acetic acid are a Heck carbocyclization and a Suzuki-Miyaura cross-coupling, orchestrated in a stereospecific tandem fashion, followed by a biosynthetically inspired oxidative dimerization. The tandem sequence generates a tetracyclic (E)-3-(arylidene)-3,4-dihydrocyclopenta[b]indol-2(1H)-one that is subsequently dimerized into the unique homodimeric core structure of scytonemin.