CoCl_2·6H_2O or LaCl_3·7H_2O Catalyzed Biginelli Reaction. One-Pot Synthesis of 3,4-Dihydropyrimidin-2(1 H)-ones

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On-line coupling of capillary isoelectric focusing with transient isotachophoresis-zone electrophoresis: a two-dimensional separation system for proteomics

A microdialysis junction is employed as the interface for on-line coupling of capillary isoelectric focusing with transient isotachophoresis-zone electrophoresis in a two-dimensional separation system. Capillary isoelectric focusing not only provides high-resolution separation of tryptic peptides based on their differences in isoelectric point, but also potentially allows the analysis of low-abundance proteins with a typical concentration factor of 50-100 times. Carrier ampholytes, employed for the creation of a pH gradient during focusing, are further utilized as the leading electrolyte in the second separation dimension, transient isotachophoresis-zone electrophoresis. Many peptides which have the same isoelectric point would most likely have different charge-to-mass ratios, and thus different electrophoretic mobilities in zone electrophoresis. Two-dimensional separation of proteolytic peptides is demonstrated using standard proteins, including cytochrome c, ribonuclease A, and carbonic anhydrase II. The maximum peak capacity is estimated to be around approximately 1600 and can be significantly increased by simply increasing the capillary column length and manipulating the range of pH gradient in isoelectric focusing. In addition to enhanced separation efficiency and resolution, this two-dimensional electrokinetic separation system permits sensitive and comprehensive analysis of peptide fragments, especially when integrated with electrospray ionization mass spectrometry for peptide/protein identification.     

Synthesis and Structure of MnCl2(HDpyF) (HDpyF = N,N′‐di(2‐pyridyl)formamidine): New Crystallographic Disorder and Bonding Mode of the HDpyF Ligand

The reaction of N,N′‐di(2‐pyridyl)formamidine (HDpyF) with MnCl₂‐4H₂O afforded the complex MnCl₂(HDpyF), which was characterized by X‐ray crystallography. The HDpyF ligand chelates to the Mn(II) center through the first and the third nitrogen atoms to form a six‐membered ring, leaving the second and the fourth nitrogen atoms uncoordinated. The HDpyF ligand is crystallographically disordered such that two different molecules can be solved. The neutral HDpyF ligand adopts the new s‐cis‐syn‐s‐trans conformation.     

Neue Kupferkomplexe mit Phosphaalkenliganden. Molekülstruktur von [Cu{P(Mes*)C(NMe2)2}2]BF4 (Mes* = 2,4,6‐tBu3C6H2)

New Copper Complexes Containing Phosphaalkene Ligands. Molecular Structure of [Cu{P(Mes*)C(NMe₂)₂}₂]BF₄ (Mes* = 2,4,6‐tBu₃C₆H₂) Reaction of equimolar amounts of the inversely polarized phosphaalkene tBuP=C(NMe₂)₂ ( 1a ) and copper(I) bromide or copper(I) iodide, respectively, affords complexes [Cu₃X₃{μ‐P(tBu)C(NMe₂)₂}₃] ( 2 ) (X =Br) and ( 3 ) (X = I) as the formal result of the cyclotrimerization of a 1:1‐adduct. Treatment of 1a with [Cu(L)Cl] (L = PiPr₃; SbiPr₃) leads to the formation of compounds [CuCl(L){P(tBu)C(NMe₂)₂}] ( 4a ) (L = PiPr₃) and ( 4b ) (L = SbiPr₃), respectively. Reaction of [(MeCN)₄Cu]BF₄ with two equivalents of PhP=C(NMe₂)₂ ( 1b ) yields complex [Cu{P(Ph)C(NMe₂)₂}₂]BF₄ ( 5b ). Similarly, compounds [Cu{P(Aryl)C(NMe₂)₂}₂]BF₄ ( 5c (Aryl = Mes and 5d (Aryl = Mes*)) are obtained from ArylP=C(NMe₂)₂ ( 1c : Aryl = Mes; 1d : Mes*) and [(MeCN)₄Cu]BF₄ in the presence of SbiPr₃. Complexes 2 , 3 , 4a , 4b , and 5b‐5d are characterized by means of elemental analyses and spectroscopy (¹H‐, ¹³C{¹H}‐, ³¹P{¹H}‐NMR). The molecular structure of 5d is determined by X‐ray diffraction analysis.     

A zwitterion of 1,5‐bis­(2‐hydroxy­benzamido)‐3‐aza­pentane: a two‐dimensional hydrogen‐bonding network involving dimers

The title compound, 2‐{N‐[2‐(2‐hydroxy­benzamido)ethyl­ammonio­ethyl]amino­carbon­yl}phenolate, C₁₈H₂₁N₃O₄, crystallizes in a zwitterionic form as a result of inter­molecular proton transfer and possesses a negatively charged phenolate group and a protonated amino group. The 2‐hydroxy­benzamide and 2‐(amino­carbonyl)­phenolate moieties attached to the two ends of the C—C—N—C—C backbone adopt a cis conformation in relation to this backbone. All N‐ and O‐bound H atoms are involved in hydrogen‐bond formation; the zwitterions are first linked into head‐to‐tail dimers, which are further organized into a two‐dimensional network parallel to the crystallographic bc plane.     

Dynamic behavior of DNA base pairs containing 8-oxoguanine

The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.     

A Novel Dinuclear Nickel(II) Complex with Three Bridges of Cl–, OAc– and (‐OCH2CH2O‐) Group of N,N, N′, N′‐Tetrakis(2‐benzimidazolyl methyl‐1, 4‐di‐ethylene amino) Glycol Ether

The novel dinuclear Ni²⁺ complex [Ni₂(μ‐Cl)(μ‐OAc) (EGTB)]·Cl·ClO₄·2CH₃OH, where EGTB is N, N, N′, N′‐tetrakis (2‐benzimidazolyl methyl‐1, 4‐di‐ethylene amino)glycol ether, crystallizes in the orthorhombic space group Pnma with a = 15.272(2), b = 14.768(2), c = 22.486(3) Å, V = 5071.4(12) ų, Z = 4, D_calc = 1.414 g cm^?3, and is bridged by triply bridging agents of a chloride ion, an acetate and an intra‐ligand (‐OCH₂CH₂O‐) group. The nickel coordination geometry is that of a slightly distorted octahedron with a NiN₃O₂Cl arrangement of the ligand donor atoms. The Ni–Cl distance is 2.361(2) Å, and two Ni–O distances are 1.996(5) and 2.279(6) Å. The three Ni–N distances are 2.033(7), 2.060(6), and 2.166(6) Å with the Ni–N bond trans to an ether oxygen the shortest, the Ni–N bond trans to an acetate oxygen the middle and the Ni–N bond trans to Cl the longest.     

Preparation and Properties of Nickel and Iron Oxides obtained by Calcination of Layered Double Hydroxides

A constant pH precipitation method has been applied to obtain solids with Ni/Fe molar ratios of 2/1, 3/2, 1/1, 2/3, and 1/2. In all cases, a phase with the hydrotalcite‐like structure is obtained, containing Ni^II and Fe^III in the brucite‐like layers and carbonate in the interlayer, and, for samples with a Ni/Fe molar ratio lower than 2/1, amorphous hydrated iron oxides, undetected by X‐ray diffraction, are also formed. The solids have been characterized by element chemical analysis, powder X‐ray diffraction, differential thermal analysis, thermogravimetric and differential thermogravimetric analysis, FT‐IR spectroscopy, temperature‐programmed reduction and assessment of specific surface area by nitrogen adsorption at ?196 °C. In all cases reduction leads to zero‐valent state for the metals, reduced nickel particles probably favouring reduction of Fe^III species; the specific surface area increases with the iron content, probably due to the amorphous nature of the hydrated iron oxides formed. Calcination at 1200 °C in air leads to well crystallized solids, formed by NiFe₂O₄ spinel and, additionally, rocksalt‐type NiO for Ni/Fe ratios larger than 1/2. In this way, solids with tailored compositions of these two phases can be prepared.     

Study of the first nucleation steps of thin films by XPS inelastic peak shape analysis

The initial steps in the formation of thin films have been investigated by analysis of the peak shape (both inelastic background and elastic contributions) of X‐ray photoelectron spectra. Surface coverage and averaged height of the deposited particles have been estimated for several overlayers (nanometre range) after successive deposition cycles. This study has permitted the assessment of the type of nucleation and growth mechanisms of the films. The experiments have been carried out in situ in the preparation chamber of an XPS spectrometer. To check the performance of the method, several materials (i.e. cerium oxide, vanadium oxide and cadmium sulfide) have been deposited on different substrates using a variety of preparation procedures (i.e. thermal evaporation, ion beam assisted deposition and plasma enhanced chemical vapour deposition). It is shown that the first deposited nuclei of the films are usually formed by three‐dimensional particles whose heights and degree of surface coverage depend on the chemical characteristics of the growing thin film and substrate materials, as well as the deposition procedure. It is concluded that XPS peak shape analysis can be satisfactorily used as a general method to characterize morphologically the first nanometric moieties that nucleate a thin film. Copyright © 2006 John Wiley & Sons, Ltd.     

Proteomic analysis of apoptosis initiation induced by all-trans retinoic acid in human acute promyelocytic leukemia cells

The irreversible destiny of apoptosis in its early stage might play a critical role in the apoptosis of human acute promyelocytic leukemia (APL) cell line induced by all-trans retinoic acid (ATRA). To characterize protein alterations during the apoptosis-initiation phase and to understand the metabolic status at that time, we investigated the protein profiles in the apoptosis-initiation phase of APL cell line HL-60 by proteomic analysis. ATRA-withdrawal was conducted to demonstrate that there was committed initiation phase of apoptosis triggered by 10(-6) M ATRA at day 3. Only after that time point, ATRA-treated cells irreversibly went to apoptosis. Also at that time point, the positive regulators of apoptosis such as STAT3 increased at protein level, whereas negative regulators (Bcl-2 and p-STAT3) decreased. In addition, caspase-3 also increased after that time. Furthermore, comparative proteomic analysis was utilized to examine the protein expression profiles during the initiation stage of apoptosis. Our results showed 12 upregulated and 7 downregulated proteins experiencing twofold alteration, including key regulators of signal transduction such as G-proteins and nucleic receptors, proteins related with metabolism, oxidation and reduction, proteins associated with the nucleus and cytoskeleton-related proteins. Some of them could be positive modulators to trigger apoptosis, whereas others could contribute to intracellular defense against apoptosis induced by exogenous triggers. The results above suggest that there is a subtle balance between apoptosis and the intracellular defense against apoptosis. Once the balance is disturbed, cells would irreversibly initiate to undergo the execution of apoptosis.