Molecular size scaling in families of protein native folds

The mean size of the most compact native states of globular proteins, independent of folding type, follows the scaling law of collapsed polymers R _g ~ n ^1/3, relating the radius of gyration R _g to the number of protein residues, n. Until now, this behaviour has only been observed within a small subset of unrelated single-domain proteins with n < 300. Here, we employ the SCOP database of protein folds to study systematically the scaling behaviour of well-defined families of domains that share structural and functional characteristics. In the particular case of helical proteins, we identify the folding types that can be associated with scaling laws corresponding to compact behaviour (e.g., the cytochrome-C monodomains) and noncompact behaviour (e.g., the immunoglobulin/albumin-binding and spectrin-repeat domains). Our results quantify the size variations within some folding families, as well as reveal that some distinct folds represent structures with equivalent compactness.     

Trends in shift rules in carbon-13 nuclear magnetic resonance spectroscopy and computer-aided shift prediction

A major problem in the use of ¹³C-NMR spectroscopy for structure identification is to estimate the ¹³C shifts of compounds known or suspected to be present in the spectrum. The substituent chemical shifts of different functional groups were studied and new, detailed empirical rules are reported. Trends in these shift parameters are noted. It appears that for functional groups containing more than one nucleus, the observed shift parameters (x=α, β, γ, δ shifts) can be approximated by the shift parameters of the component nuclei (x_comp) in the functional group, i.e., x_obs ≈ x_comp. The detailed shift behavior and shift additivity rules were computerized. The resulting program (CSPEC) has many user friendly features, e.g., ease of input, modification of structure, storage and retrieval of known shifts, and rapid computation.     

Emulsifier-free emulsion polymerization of tetrafluoroethylene by radiation. II. Effects of reaction conditions on polymer particle size and number

The size, distribution, and number of PTFE particles formed by radiation-induced emulsifier-free polymerization were measured by electron microscope and automatic particle analyzer (centrifugation method). From the electron micrographs we found that the particles are formed within 5 min. The change in the number of polymer particles (n_p) with reaction time (t) depends on the relative concentration of growing polymer chains to stabilizing species produced by the radiolysis of water and monomer; that is, it was governed by TFE pressure/dose rate ratio and classified into three cases: case I, dn_p/dt = 0 (e.g., at 3 × 10⁴ rad/hr and 20 kg/cm²); case II, dn_p/dt < 0 (e.g., at dose rate below 1.9 × 10⁴ rad/hr and 20 kg/cm²); case III, dn_p/dt > 0 (e.g., at 3 × 10⁴ rad/hr and 2 kg/cm²). The polymer molecular weight above 10⁶ is almost independent of the particle size. The polymerization loci are mainly on the surface of polymer particles dispersed in the aqueous phase in cases I and II except in the initial stage. In case III new particles are formed successively during polymerization. Therefore the polymerization loci are mainly in the aqueous phase. Especially in case I, we concluded that after the generation of particles the propagation proceeds mainly on the surface of polymer particles like the core shell model proposed by Granico and Williams.     

Complexes of Co(II), Ni(II), and Cu(II) chlorides and bromides with tetrazol-1-yl-tris(hydroxymethyl)methane: Synthesis and structure

The reactions of Co(II), Ni(II), and Cu(II) chlorides and bromides and their metallic powders with tetrazol-1-yl-tris(hydroxymethyl)methane (L) afforded new complexes ML₂Hal₂ · mH₂O(M = Co(II) or Ni(II), Hal = Cl⁻; M = Cu(II), Hal = Cl⁻ or Br⁻, m = 0; and M = Co(II) or Ni(II), Hal = Br⁻, m = 2), MLnCl₂ (M = Co(II) or Ni(II), n = 2 or 4; M = Cu(II), n = 2), and MLnBr₂ · mH₂O (M = Ni(II), n = 2, m = 2; M = Cu(II), n = 2, m = 0). The compositions and structures of the synthesized complexes were determined by elemental analysis, IR spectroscopy (50–4000 cm⁻¹), and X-ray diffraction analysis. The introduction of a bulky substituent into position 1 of the tetrazole cycle was shown to exert almost no effect on the coordination mode but affected the composition and structure of the complexes.     

Synthesis of poly(ethylene‐co‐vinyl alcohol)‐g‐polystyrene graft copolymer and their applications for ordered porous film and compatibilizer

A series of new functional poly(ethylene‐co‐vinyl alcohol)‐g‐polystyrene graft copolymers (EVAL‐g‐PS) with controlled molecular weight (M_n = 38,000–94,000 g mol^?1) and molecular weight distribution (M_w/M_n = 2.31–3.49) were synthesized via a grafting from methodology. The molecular structure and component of EVAL‐g‐PS graft copolymers were confirmed by the analysis of their ¹H NMR spectra and GPC curves. The porous films of such copolymers were fabricated via a static breath‐figure (BF) process. The influencing factors on the morphology of such porous films, such as solvent, temperature, polymer concentration, and molecular weight of polymer were investigated. Ordered porous film and better regularity was fabricated through a static BF process using EVAL‐g‐PS solution in CHCl₃. Scanning electron microscopy observation reveals that the EVAL‐g‐PS graft copolymer is an efficient compatibilizer for the blend system of low‐density polyethylene/polystyrene. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 516–524     

Room‐Temperature Amination of Deactivated Aniline and Aryl Halide Partners with Carbonate Base Using a Pd‐PEPPSI‐IPentCl‐ o‐Picoline Catalyst

Current state‐of‐the‐art protocols for the coupling of unreactive amines (e.g., electron‐poor anilines) with deactivated oxidative‐addition partners (e.g., electron‐rich and/or hindered aryl chlorides) involve strong heating (usually >100 °C) and/or tert‐butoxide base, and even then not all couplings are successful. The aggressive base tert‐butoxide reacts with and in many instances destroys the typical functional groups that are necessary for the function of most organic molecules, such as carbonyl groups, esters, nitriles, amides, alcohols, and amines. The new catalyst described herein, Pd‐PEPPSI‐IPent^Cl‐o‐picoline, is able to aminate profoundly deactivated coupling partners when using only carbonate base at room temperature.     

Design,Synthesis, and Properties of Substituted Polyacetylenes

This article reviews recent topics on the polymerization of substituted acetylenes, focusing on the synthesis of poly(diphenylacetylenes) and the living polymerization of phenylacetylenes. Diphenylacetylene (DPA) polymerizes with TaCl_s-n-Bu₄Sn to give a polymer which is thermally very stable but insoluble in any solvents. DPAs with various groups (e.g.,p-Me₃Si,m-Me₃Ge, p-t-Bu,and_p-PhO) polymerize similarly. These polymers are soluble and their M¯_w's reach 1 × 10⁶ to 3 × 10⁶. Some of them are more gas-permeable than poly(dimethylsiloxane). Several acetylenes (e.g., ClC -n-C₆H₁₃ and HCUC-t-Bu) have been found to undergo living polymerization with MoOCl₄-n-Bu₄Sn-EtOH. Whereas phenylacetylene (PA) does not polymerize in a living fashion, ortho-substituents in PA more or less suppress termination and chain transfer. PAs with bulky ortho groups (e.g., CF₃ and Me₃Ge) especially undergo virtually ideal living polymerization.     

Cobalt(II), nickel(II) and copper(II) complexes of 5-(2-carboxyphenylazo)-2-thiohydantoin

A new series of hexacoordinate cobalt(II), nickel(II) and copper(II) complexes of 5-(2-carboxyphenylazo)-2-thiohydantoin HL having formulae [LM(OAc)(H₂O)₂] · nH₂O (M = Co^II, Cu^II and Ni^II), [LMCl(H₂O)₂] · nH₂O (M = Co^II and Ni^II), [LCuCl(H₂O)]₂ · 2H₂O, [LCu(H₂O)₃](ClO₄) and [LCu(HSO₄)(H₂O)₂] were isolated and characterized by elemental analyses, molar conductivities and magnetic susceptibilities, and by i.r., electronic and e.s.r. spectral measurements, as well as by thermal (t.g. and d.t.g.) analyses. The i.r. spectra indicate that the ligand HL behaves as a monobasic tridentate towards the three divalent metal ions via an azo-N, carboxylate-O and thiohydantoin-O atom. The magnetic moments and electronic spectral data suggest an octahedral geometry for Co^II complexes, distorted octahedral geometry for both Ni^II and Cu^II complexes with a dimeric structure for [LCuCl(H₂O)]₂ · 2H₂O through bridged chloro ligands. The X-band e.s.r. spectra reveal an axial symmetry for the copper(II) complexes with unsymmetrical M_s = ± 1 signal and G-parameter less than four for the dimeric [LCuCl(H₂O)]₂ · 2H₂O. The thermogravimetry (t.g. and d.t.g.) of some complexes were studied; the order and kinetic parameters of their thermal degradation were determined by applying Coats–Redfern method and discussed.     

Application of Dipotassium Glycoxides–Activated 18-Crown-6 for the Synthesis of Poly(propylene oxide) with Increased Molar Mass

Mono- and dipotassium salts of dipropylene glycol were applied for the polymerization of propylene oxide in mild conditions, i.e., tetrahydrofuran solution at ambient temperature. The structure of polymers was investigated by use of ¹³C NMR and MALDI-TOF techniques. The structure depends strongly on the kind of initiator and additives that are used such as coronand 18-crown-6 and dipropylene glycol. The lowest unsaturation, represented by allyloxy starting groups, has the polymer obtained by use of monopotassium salt without the ligand. The highest unsaturation degree is for the polymer synthesized in the presence of dipotassium salt–activated 18-crown-6. This polymer, obtained at high initial monomer concentration and low initial concentration of initiator, consists of two fractions, i.e., a low molar mass fraction (M_n = 9400) containing mainly macromolecules with alkoxide starting and end groups and a much higher molar mass fraction (M_n = 29500 g/mol) containing macromolecules with allyloxy starting groups and alkoxide or hydroxyl end groups. Addition of free glycol to this system decreases the molar mass of polymers. Similar results were obtained by use of dipotassium salts of other glycols. The mechanisms of the studied processes are discussed.     

Coefficients of molecular packing and intrinsic birefringence of aromatic polyimides estimated using refractive indices and molecular polarizabilities

Molecular structure dependences of the coefficients of molecular packing (K_p) and the intrinsic birefringence (Δn⁰) were investigated for aromatic polyimides (PIs) using a method based on the modified Lorentz–Lorenz equation and the Vuks equation. This method needs only average refractive indices and polarizability tensors ( ) for PI repeating units. αˆ was calculated using the density functional theory at the B3LYP/6-31+G(d) theory level that was confirmed as optimal for PI repeating units. Because bent or kinked structures in main chain hinder the ordering of polymer chains, K_p decreases in cases that ether linkages are introduced in the main chain and that kinked-structured dianhydrides are used. Introduction of side groups, trifluoromethyl ( CF₃) groups in particular, also causes decreases in K_p. On the other hand, the estimated values of Δn⁰ are proportional to the calculated anisotropy in αˆ (Δα/V_vdw), thus Δn⁰ can be well predicted by computation. The values of Δα/V_vdw are decreased not only by bent structures in the main chain (e.g., ether linkage), presence of side groups, but also by large fractions of imide rings in the polymer structures. The estimated values of Δn⁰ range from 0.338 to 0.470, which are much larger than the reported ones for optically transparent conventional polymers. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2354–2366, 2004     

Spectral,magnetic studies and molecular orbital calculations for (4,5-dimethyl-3-pyrazolyl)aldazine copper(II) complexes

Summary A new series of copper(II) complexes derived from (4,5-dimethyl-3-pyrazolyl) aldazine (DMPA), formulated as: (a) [LCuX₂]·nEtOH; (b) [LCu(H₂O)](ClO₄)₂; and (c) [LCuX]BF₄·nH₂O, where n = 1/2 or 1, X = Cl or Br and L = DMPA, have been synthesized. The formulations are based on elemental analyses and molar conductivity data. I.r., u.v.-vis., e.s.r. and magnetic data reveal that the complexes are trigonal bipyramidal, tetrahedral and stacked square-planar structures for (a), (b) and (c), respectively. The trigonal bipyramidal structure for class (a) compounds is confirmed using the atom superposition and electron delocalization-molecular orbital calculations, which agree with the experimental electronic spectral data. Variable temperature magnetic susceptibility data shows a ferromagnetic interaction within copper(II) complexes of class (c).     

Synthesis,spectroscopic, magnetic and biological activity studies of copper(II) complexes of an antipyrine Schiff base

The Schiff base, 4-(2-pyrrolylmethylideneamino)antipyrine (HPAP), (1), and its copper(II) complexes were synthesized and characterized by elemental analysis and by physical and spectral methods such as i.r., u.v.–vis., ¹H-n.m.r., ¹³C-n.m.r. and e.s.r. as well as by molar conductance and magnetic moment determinations. Both the bis-ligand, [(HPAP)₂Cu]X₂ (4, 5), [(PAP)₂Cu] (6), and the dimer, [(PAP)Cu]₂X₂ (2, 3), complexes were isolated. In these complexes, the Schiff base acts as a bidentate or tridentate neutral or monobasic ligand. Interaction of the isolated [(PAP)Cu]₂Cl₂ (2), with strong coordinating organic bases was studied and the resultant adducts, [(PAP)CuLs]Cl; Ls = pyridine (7), -picoline (8), -picoline (9), -picoline (10) or n-propylamine (11), were isolated and characterized. Biological activity screening was studied and an activity correlation coefficients matrix was constructed for HPAP and the copper(II) complexes against gram-positive, gram-negative and fungi species. The copper content, structure of the complex as well as the degree of exposure of the metal center control the biological activity of the isolated complexes.     

Copper(II) and cadmium(II) complexes of 2-benzylthio-4-formyl-1-p-methoxyphenylimidazole: crystal structure,spectral properties and thermal behaviour

Summary The coordinative capacity of 2-benzylthio-4-formyl-1-p-methoxyphenylimidazole (ALME) with several transition metal ions has been investigated and has led to only copper(II) and cadmium(II) complexes of general formula [M^IICl₂(ALME)₂]·nH₂O. These compounds were studied by spectral (i.r., u.v.-vis. n.i.r. and e.p.r.) and thermal methods (t.g., d.t.g. and d.s.c.) as well as magnetic susceptibility measurements.The crystal structure of the copper complex has been solved, although a full refinement of the structure has not been possible as very few measured reflections were observed. The structure consists of discrete [CuCl₂-(ALME)₂] units in which Cu(II) ion is 4 + 2 Cl₂N₂O₂ surrounded [Cu{ie481-01}Cl(1), 2.28(1) Å; Cu{ie481-02}Cl(2), 2.29(1) Å; Cu{ie481-03}N, 2.00(2) Å; Cu{ie481-04}O, 2.71(2) Å]. The ALME ligand acts as bidentate chelator through the N(3) imidazolic atom and the oxygen of the formyl group, the Cu{ie481-05}O interaction being very weak. Water molecules have not been localized.     

Reactivities of d<Superscript>0</Superscript> transition metal complexes toward oxygen: Synthetic and mechanistic studies

Transition metals such as Fe in porphyrin complexes are known to bind or react with O₂, and such reactions are critical to many biological functions and catalytic oxidation using O₂. The transition metals in these reactions often contain valence d electrons, and oxidation of metals is an important step. In recent years, reactions of O₂ with d⁰ transition metal complexes such as Hf(NR₂)₄ (R = alkyl) have been used to make metal oxide thin films as insulating gate materials in new microelectronic devices. This feature article discusses our recent studies of such reactions and the formation of TiO₂ thin films. In contrast to the reactions of many d ⁿ complexes where metals are often oxidized, reactions of d⁰ complexes such as Hf(NMe₂)₄ and Ta(NMe₂)₄(SiR₃) with O₂ usually lead to the oxidation of ligands, forming, e.g., -ONMe₂ and -OSiR₃ from -NMe₂ and -SiR₃ ligands, respectively. Mechanistic and theoretical studies of these reactions have revealed pathways in the formation of the metal oxide thin films as microelectronic materials.     

Tandem mass spectrometry study of p38α kinase inhibitors and related substances

The p38 mitogen‐activated protein kinase α (p38α) is an important drug target widely investigated for therapy of chronic inflammatory diseases. Its inhibitors are rather lipophilic and as such not very favourable lead compounds in drug discovery. Therefore, we explored various approaches to access new chemical space, create diversity, and generate lead libraries with improved solubility and reduced lipophilicity, based on known p38α inhibitors, e.g., BIRB796 and TAK‐715. Compound modification strategies include incubation with human liver microsomes and bacterial cytochrome P450 mutants from Bacillus megaterium and treatment by electrochemical oxidation, H₂O₂, and intense light irradiation. The MS/MS fragmentation pathways of p38α inhibitors and their conversion products have been studied in an ion‐trap–time‐of‐flight MSⁿ instrument. Interpretation of accurate mass MSⁿ data for four sets of related compounds revealed unexpected and peculiar fragmentation pathways that are discussed in detail. Emphasis is put on the usefulness of HRMSⁿ‐based structure elucidation in a screening setting and on peculiarities of the fragmentation with regard to the analytes and the MS instrument. In one example, an intramolecular rearrangement reaction accompanied by the loss of a bulky group is observed. For BIRB796, the double‐charge precursor ion is used in MS², providing a wider range of fragment ions in our instrument. For TAK‐715, a number of related compounds could be produced in a large‐scale incubation with a Bacillus megaterium mutant, thus enabling comparison of the structure elucidation by ¹H NMR and MSⁿ. A surprisingly large number of homolytic cleavages are observed. Competition between two fragmentation pathways involving either the loss of CH₃^? or OH^? radicals was observed for SB203580 and its conversion products. Copyright © 2013 John Wiley & Sons, Ltd.     

Syntheses,characterization, and crystal structures of coordination polymers: {NH4 · [Ln(OVA)4]} n (Ln=Pr,Nd, Gd,and Ho; OVA=2-hydroxy-3-methoxybenzoate)

The title complexes {NH₄ · [Ln(OVA)₄]} _n (Ln = Pr, Nd, Gd, and Ho; OVA = 2-hydroxy-3-methoxybenzoate) were synthesized in water and characterized by FT-IR, elemental analysis, TGA, and X-ray single-crystal diffraction analysis. Two distinct structure types were isolated. Structure type I with formula {NH₄ · [Ln(OVA)₄]} _n (Ln = Pr, Nd, Gd) contains Ln–COO^? quadruply-bridged helical 1-D chains, with all carboxylates bridging. The structure type II with formula {NH₄ · [Ho(OVA)₄]} _n contains bridging and chelating carboxylates, resulting in Ho–COO^? double helical 1-D chains. The passage from type I to type II structure is ascribed to the lanthanide contraction. These 1-D chains are extended to 3-D supramolecular architecture by hydrogen bonds.     

Structure and stability for (AlN)n+ and (AlN)n+ (n=1–15) clusters

Using density functional theory (DFT) method with 6-31G* basis set, we have carried out the optimizing calculation of geometry, vibrational frequency and thermodynamical stability for (AlN) _n ⁺ and (AlN) _n ⁺ (n=1–15) clusters. Moreover, their ionic potential (IP) and electron affinity (EA) were discussed. The results show that the electrical charge condition of the cluster has a relatively great impact on the structure of the cluster and with the increase of n, this kind of impact is reduced gradually. There are no Al-Al and N-N bonds in the stable structure of (AlN) _n ⁺ or (AlN) _n ^-, and the Al-N bond is the sole bond type. The magic number regularity of (AlN) _n ⁺ and (AlN) _n ^- is consistent with that for (AlN) _n , indicating that the structure with even n such as 2, 4, 6, ... is more stable. In addition, (AlN₁₀ has the maximal ionization power (9.14 eV) and the minimal electron affinity energy (0.19 eV), which manifests that (AlN)₁₀ is more stable than other clusters.     

New P,N-Cyclic Ligands

Abstract

The anions of P,N-cyclic metaphosphimic acids (MPm^n-, n = =3, 4…) interact with cations as conformationally labile multidentate ligands. They belong to the cyclophosphazane class and can be obtained from chloroderivatives (NPCl₂)_n associated with a related class of P,N-compounds (cyclophosphazenes. Besides halogens, a great variety of organic radicals can act as substituents in the cyclophospnazenes. An additional introduction of donating atoms or groups in these radicals results in new multidentate ligands. Like the MPm^n- they demonstrate a cation binding ability. Thus P,N-cyclic ligands can contain endocyclic functional groups POO- which are inherent to common MPm^n- or various exo-cyclic groups, e.g. -COO^?, -PR₂O^?, -PROO^?, -NR₂etc., linked to the cycle via side chains. Furthermore, miscellaneous phosphazane-phosphazene structures as well as those with an additional heteroatom can be designed. We have obtained the first examples of P,N-cyclic chelantes of some structural types. These are bicycles based on MPm^n- cross-linked by organic bridges. Such ligands can take a sandwich configuration. Neutral and acido-ligands of cyclo-pendante type involving groups -COO^?, -PPh₂O and >O as well as a ligand with endocyclic sulfur have been obtained too. Selective or universal chelantes, extragents, coloured ligands and other reagents can be synthesized depending on a ligand structure design, the nature of organic fragments linked to the cycle and the type of functional groups.     

Synthesis and structural studies of new Mannich base ligands and their metal complexes

The new Mannich bases bis(1,4-diphenylthiosemicarbazide methyl) phosphinic acid H₃L¹ and bis(1,4-diphenylsemicarbazide methyl) phosphinic acid H₃L² were synthesised from the condensation of phosphinic acid, formaldehyde with 1,4-diphenyl thiosemicarbazide and 1,4-diphenylsemicarbazide, respectively. Monomeric complexes of these ligands, of general formulae K₂[Cr^III(L ⁿ )Cl₂], K₃[Mn^II(L ⁿ )Cl₂] and K[M(L ⁿ )] (M = Co(II), Ni(II), Cu(II), Zn(II) or Hg(II); n = 1, 2), are reported. The mode of bonding and overall geometry of the complexes were determined through physico-chemical and spectroscopic methods. These studies revealed octahedral geometries for the Cr(III), Mn(II) complexes, square planar for Co(II), Ni(II) and Cu(II) complexes and tetrahedral for the Zn(II) and Hg(II) complexes.     

Photophysical Analysis of 1,10‐Phenanthroline‐Embedded Porphyrin Analogues and Their Magnesium(II) Complexes

The synthesis, characterization, photophysical properties, and theoretical analysis of a series of tetraaza porphyrin analogues ( H? Pn : n=1–4) containing a dipyrrin subunit and an embedded 1,10‐phenanthroline subunit are described. The meso‐phenyl‐substituted derivative ( H? P1 ) interacts with a Mg²⁺ salt (e.g., MgCl₂, MgBr₂, MgI₂, Mg(ClO₄)₂, and Mg(OAc)₂) in MeCN solution, thereby giving rise to a cation‐dependent red‐shift in both the absorbance‐ and emission maxima. In this system, as well as in the other H? Pn porphyrin analogues used in this study, the four nitrogen atoms of the ligand interact with the bound magnesium cation to form Mg²⁺–dipyrrin–phenanthroline complexes of the general structure MgX? Pn (X=counteranion). Both single‐crystal X‐ray diffraction analysis of the corresponding zinc‐chloride derivative ( ZnCl? P1 ) and fluorescence spectroscopy of the Mg‐adducts that are formed from various metal salts provide support for the conclusion that, in complexes such as MgCl? P1 , a distorted square‐pyramidal geometry persists about the metal cation wherein a chloride anion acts as an axial counteranion. Several analogues ( H? Pn ) that contain electron‐donating and/or electron‐withdrawing dipyrrin moieties were prepared in an effort to understand the structure–property relationships and the photophysical attributes of these Mg–dipyrrin complexes. Analysis of various MgX? Pn (X=anion) systems revealed significant substitution effects on their chemical, electrochemical, and photophysical properties, as well as on the Mg²⁺‐cation affinities. The fluorescence properties of MgCl? Pn reflected the effect of donor‐excited photoinduced electron transfer (d‐PET) processes from the dipyrrin subunit (as a donor site) to the 1,10‐phenanthroline acceptor subunit. The proposed d‐PET process was analyzed by electron paramagnetic resonance (EPR) spectroscopy and by femtosecond transient absorption (TA) spectroscopy, as well as by theoretical DFT calculations. Taken together, these studies provide support for the suggestion that a radical species is produced as the result of an intramolecular charge‐transfer process, following photoexcitation. These photophysical effects, combined with a mixed dipyrrin–phenanthroline structure that is capable of effective Mg²⁺‐cation complexation, lead us to suggest that porphyrin‐inspired systems, such as H? Pn , have a role to play as magnesium‐cation sensors.