Peptide models XVI. The identification of selected HCO—L—SER—NH2 conformers via a systematic grid search using ab initio potential energy surfaces

Multidimensional conformational analysis (MDCA) predicted the existence of nine stable backbone conformations (α_L, α_D, β_L, γ_L, γ_D, δ_L, δ_D, ϵ_L, and ϵ_D) on the 2D-Ramachandran map, E = E(ϕ, ψ), for a single amino acid diamide (HCONH-CHR-CONH₂). The potential energy hypersurfaces (E = E[ϕ, ψ, χ₁, χ₂]) of For-L-Ser-NH₂ associated with the α_L-, bgr;_L-, γ_L-, δ_L-, and ϵ_L-type stable backbone orientations are investigated in this article. An appropriate number of side-chain rotamers is associated with each of the backbone conformers. In the case of serine, where R = −CH₂OH, the two sidechain torsional angles (χ₁, χ₂) should lead to 3 * 3 = 9 different sidechain orientations according to MDCA. For certain backbone structures, some of the sidechain conformations were nonexistent. © 1996 by John Wiley & Sons, Inc.     

Dilactone Formation by Chromic Anhydride Oxidation of the Germacranolide Stizolicin

The sidechain of the germacranolide stizolicin was oxidized by CrO₃ in Py to form a lactone. The structure of the product was established as 4,5α-epoxy-7α,5,6,8β(H)-germacr-1(10),11(13)-dien-8α (3′-oxo-2′,5′-dihydrofuran-3′-carboxylyl)-12,6-olide using spectral data.__________Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 117–118, March–April, 2005.     

The C–HCl2Cu(II) synthon in the structural direction and assembly of supramolecular complexes with the 3,3′-bis(2-benzimidazolyl)-2,2′-dipyridine ligand and its N-substituted derivatives

Three new Cu(II) supramolecular complexes [Cu(L₁)Cl₂]·2DMF (1), [Cu(L₂)Cl₂] (2) and [Cu(L₃)Cl₂]·DMF (3) (L₁ = 3,3′-bis(2-benzimidazolyl)-2,2′-dipyridine, L₂ = 3,3′- bis(N-ethyl-2-benzimidazolyl)-2,2′-dipyridine and L₃ = 3,3′-bis(N-benzyl-2-benzimidazolyl)-2,2′-dipyridine) have been prepared and characterized by elemental analysis, IR spectra and single crystal X-ray diffraction. X-ray structural analysis of L₁, L₂·3.5H₂O and L₃·H₂O indicates that all three ligands adopt the trans conformation with the two benzimidazole fragments located on opposite sides of the dipyridyl backbone. While in complexes 1–3, all the ligands display the cis conformation and behave as bidentate chelating reagents to coordinate with Cu(II). The inorganic chloride ions always act as a reliable hydrogen bonded acceptor in these structures, and the resulting C–HCl₂Cu supramolecular synthons play a significant role in the formation and stabilization of the structures. Moreover, additional non-covalent interactions, such as C–Hπ, are also identified to extend the discrete (0-D) or low-dimensional (1-D) motifs into high-dimensional architectures.     

Synthesis of some new N,N′-diarylsubstituted methylene-bis-dihydro-2H-1,3-benzoxazines

The synthesis of a new series of six-membered N,N′-diarylsubstituted methylene-bis-dihydro-2H-1,3-benzoxazines （5a-e） was achieved in excellent yields by Mannich-type condensation of N,N′-diarylsubstituted methylene-bis-o-hydroxybenzyl amines （4a- e） with formaldehyde in chloroform at reflux. These amines （4a-e） were obtained by the reduction of N, Nr-diarylsubstituted methylene-bis-o-hydroxybenzyl imines （3a-e） with NaBH4, which inturn were obtained by the condensation of methylene-bissalicylaldehyde （2） with various substituted arylamines.     

A variety of oxidation products of antioxidants based on N,N′-substituted p-phenylenediamines

Electrochemical and spectroscopic (EPR, UV–Vis, IR) studies of the aromatic secondary amines N,N′-diphenyl-1,4-phenylenediamine (DPPD), N-phenyl-N′-isopropyl-p-phenylene diamine (IPPD), N-phenyl-N′-(α-methylbenzyl)-p-phenylenediamine (SPPD) and N-phenyl-N′-(1,3-dimethyl-butyl)-p-phenylenediamine (6PPD), which represent the most important group of antioxidants used in the rubber industry, are presented. During oxidation, all the compounds show reversible redox couples in acetonitrile/0.1 M TBABF₄. The first oxidation potential depends substantially on the R substituent at the –N′H– moiety. Very similar UV–VIS spectra of monocation radicals and dications for all the compounds were observed by applying anodic oxidation as well as oxidation by tert-butyl hydroperoxide both in air and in inert atmosphere. The samples with N′-bonded aliphatic carbon in the molecule (e.g. IPPD) heated in air undergo consecutive chemical reactions leading to the formation of –N′C– group. By the use of RO₂ radicals only very low concentration of nitroxide radicals was obtained. Very high concentration of nitroxide radicals was achieved using 3-chloroperbenzoic acid. In the oxidation of investigated aromatic secondary amines with powder PbO₂ no EPR spectra were observed and UV–Vis and IR studies indicate the rapid formation of the final dehydrogenated oxidation product.     

Fluorocarbohydrates Part XXV. Synthesis and structure of 2-deoxy-2-fluorolactose and related compounds

Experimental details describing the addition of CF₃OF to hexa- -accetyl- -lactal (I) are presented. Four fluorinated disaccharides: trifluoromethyl 3,6-di- -acetyl-2-fluoro-4- -(2′,3′,4′,6′-tetra- -acetyl-β-D-galactopyranosyl)-β- -mannopyrinoside (V), trifluoromethyl 3,6-di- -acetyl-2-deoxy-2-fluoro-4- -(2′,3′,4′,6′-tetra- -acetyl-β-D-galactopyranosyl)-α- -glucopyranoside (VI), 3,6-di- -acetyl-2-deoxy-2-fluoro-4- -(2′,3′,4′,6′-tetra- -acetyl-β- -galactopyranosyl)-β- -mannopyranosyl fluoride (VII), and 3,6-di- -acetyl-2-deoxy-2-fluoro-4- -(2′,3′,4′,6′-tetra- -acetyl-β-D-galactopyranosyl)-α- -glucopyranosyl fluoride (VIII) were isolated from the product mixture. The profound changes in both the rate and the major products of the addition, compared to those reported for related monosaccharide glycals, are discussed in relation to the steric influence exerted by the presence of the non-reducing (galactoside-B) ring of the disacchride glycals. The configuration and the confirmation of the fluorinated portion of the adducts were assigned on the basis of ¹⁹F.m.r. spectroscopic parameters and the structural     

Micellization behavior of [C16-12-C16], 2Br gemini surfactant in binary aqueous-solvent mixtures

The micellization behavior of bis cationic gemini surfactant, N,N′-dihexadecyl-N,N,N′,N′-tetramethyl-1,12-dodecanediammonium dibromide [C₁₆H₃₃N⁺(CH₃)₂-(CH₂)₁₂-N⁺(CH₃)₂C₁₆H₃₃, 2Br⁻] has been studied in binary aqueous mixtures of dimethyl sulfoxide, methanol, 1,4-dioxane, glycerol and ethylene glycol by conductivity and surface tension measurements at 300 K. The critical micellar concentration, degree of micelle ionization (α), surface excess concentration (Г_max), minimum surface area per molecule of surfactant (A_min), Gibbs free energy of micellization (ΔG_m°), the surface pressure at cmc (π_cmc), and the Gibbs energy of adsorption (ΔG_ad°) of the gemini surfactant have also been determined. The cmc, α, A_min increases where as (ΔG_m°), Г_max, and π_cmc decreases with increasing volume percentage of the solvents in the solvent–water binary mixture. The interfacial properties of the gemini surfactant, solute–solute, solvent–solute interactions and the effectiveness of a surface-active molecule in binary solvent systems have been discussed.     

Co(III) complexes of Me-salpn and Me-salbn and the ring size effect on the coordination modes and electrochemical properties: The crystal structures of trans-[Co(Me-salpn)(py)2]PF6 and cis-α-[Co(Me-salbn)(4-Mepy)2]BPh4 · 4-Mepy

The synthesis and characterization of a series of cobalt(III) complexes of the general type [Co(N₂O₂)(L₂)]⁺ are described. The N₂O₂ Schiff base ligands used are Me-salpn (H₂Me-salpn = N,N′-bis(methylsalicylidene)-1,3-propylenediamine) (1–3) and Me-salbn (H₂Me-salbn = N,N′-bis(methylsalicylidene)-1,4-butylenediamine) (4–5). The two ancillary ligands L include: pyridine (py) 1, 3-metheylpyridine (3-Mepy) 2, 1-methylimidazole (1-MeIm) 3, 4-methylpyridine (4-Mepy) 4 and pyridine (py) 5. These complexes have been characterized by elemental analyses, IR, UV–Vis, and ¹H NMR spectroscopy. The crystal structures of trans-[Co^III(Me-salpn)(py)₂]PF₆, 1, and cis-α-[Co^III(Me-salbn)(4-Mepy)₂]BPh₄ · 4-Mepy, 4, have been determined by X-ray diffraction. Examination of the solution and crystalline structures revealed that the outer coordination sphere of the complexes exerts a noticeable influence on the inner coordination sphere of the Co(III) ion. The electrochemical reduction of these complexes at a glassy carbon electrode in acetonitrile solution indicates that the first reduction process corresponding to Co^III–Co^II is electrochemically irreversible, which is accompanied by the dissociation of the axial (R-py)–cobalt bonds. It has also been observed that the Co(III) state is stabilized with increasing the flexibility of the ligand environment.     

Crystallographic and theoretical study of phenyl 2,3,4,6-tetra-O-acetyl-1-thio-α-D-mannopyranoside

The thiomannoside is a key intermediate in the synthesis of polymannosaccharide. But its crystallographic study has not been reported. X-ray crystal structure analysis shows that the crystal of phenyl 2,3,4,6-tetra-O-acetyl-1-thio-α-D-mannopyranoside is in orthorhombic system, has P2₁2₁2₁ space group. Its unit cell dimensions are a=9.1731(11), b=11.574(2), and c=21.199(3) Å, α=β=γ=90.00°, Z=4, V=2250.6(6) ų, D_c=1.300 g/cm³. The crystallographic study reveals that the thiomannoside is an α-anomer. Most interestingly, the structure provides an evidence of existing C–HO and C–HS intramolecular and intermolecular hydrogen bonds.     

Terminal group effects on the fluorescence spectra of Eu(III) nitrate complexes with a family of amide-based 1,10-phenanthroline derivatives

Four ligands 1,10-phenanthroline-5,6-bis(N,N-dibenzyl-1′-oxopropylamide) (L^a) 1,10-phenanthroline-5,6-bis(N-methyl-N-benzyl-1′-oxopropylamide) (L^b) 1,10-phenanthroline-5,6-bis(N-benzyl-1′-oxopropylamide) (L^c) and 1,10-phenanthroline-5,6-bis(N,N-diethyl-1′-oxopropylamide) (L^d), and their lanthanide(III) (La and Eu) complexes were synthesized. The complexes were characterized by elemental analysis, IR, fluorescence spectroscopy and conductivity. The lanthanide atoms are coordinated by O atoms from C=O, Ar–O –C and N atoms from phen With the difference of the ligands, the fluorescent intensities of the Eu(III) complexes vary regularly in the THF solution. Some factors that influence the fluorescent intensity were discussed.     

Synthesis and characterization of complexes of lanthanide nitrates with N,N′-dinaphthyl-N,N′-diphenyl-3,6-dioxaoctanediamide

Solid complexes of lighter lanthanide nitrates with N,N′-dinaphthyl-N,N′-diphenyl-3,6-dioxaoctanediamide (DDD), Ln(NO₃)₃(DDD) (Ln = La---Nd, Sm) have been prepared in non-aqueous media. These complexes have been characterized by elemental analysis, conductivity measurements, IR spectra, electronic spectra and TG-DTA techniques. In all the complexes, DDD and NO₃⁻ are coordinated to the lanthanide ions as tetradentate and bidentate ligands, respectively. The differences in the IR and electronic spectra between these complexes and lanthanide nitrate complexes with N,N,N′,N′-tetraphenyl-3,6-dioxaoctanediamide (TDD) are discussed.     

Isotachophoretic determination of stability constants of Ho and Y complexes with diethylenetriaminepentaacetic acid and 1,4,7,10-tetraazadodecane-N,N′,N″,N-tetraacetic acid

The method of capillary isotachophoresis with conductivity detection was applied for the determination of the physico-chemical characteristics (conditional stability constants log β′) of holmium and yttrium complexes with DTPA (diethylenetriaminepentaacetic acid) and DOTA (1,4,7,10-tetraazadodecane-N,N′,N″,N-tetraacetic acid). The log β′ determination is based on the linear relation between the stability constants of lanthanide–DTPA (lanthanide–DOTA) complexes and the reduction of the zone of the complex owing to the bleeding phenomena (liberating free metal ion). The stability constants calculated using this relationship are comparable with the literary data obtained by other methods for both holmium (log β′_Ho–DTPA=21.9, log β′_Ho–DOTA=24.5) and yttrium complexes (log β′_Y–DTPA=21.2, log β′_Y–DOTA=24.4). Capillary isotachophoresis was applied for the determination of the optimum composition of the reaction mixture (metal:ligand ratio) as well.     

Structure of the CuCl2 adduct of trans-chloro-1,4-bis(p-methoxyphenyl)-1,4-diaza-3-methylbutadien-2-yl-bis(triphenylphosphine) -palladium(II)

An X-ray structure analysis of binuclear complex [CuCl₂{RN---C(Me)C(R′)---NR}] (R = p-C₆H₄OMe; R′ = trans-PdCl(PPh₃)₂) has shown that the Pd---C σ-bonded 1,4-diaza-3-methylbutadien-2-yl-group acts as σ,σ-N,N chelating ligand witha tetragonally distorted tetrahedral geometry around the copper atom. No exchange of ancillary ligands has occured between the two metallic centers of the molecule, which are 4.75 » apart from each other.     

Theoretical study of the stereodynamics of the reactions O(D) + H2, D2 and HD

Calculations of the dynamics of the reactions O(¹D) + H₂ → OH + H, O(¹D) + HD → OH + D, O(¹D) + HD → OD + H and O(¹D) + D₂ → OD + D have been performed using the quasi-classical trajectory (QCT) method with symplectic integration. The theoretical calculations were carried out on the ground state 1A′ potential energy surfaces (PES) by Dobbyn and Knowles. The distributions of the dihedral angle P(_r), the angle between k and j′, P(θ_r), and the product vibrational state are presented. The results show that the intermediate geometrical structures and lifetimes of the reactive collisions play a vital role in these reactions.     

Heterometallic clusters arising from cubic Ni3M′O4 (M′=K and Na) entity: Solvothermal synthesis with/without the assistance of microwave

Solvothermal reaction assisted with microwave leads to the formation of two unique heterometallic cubic clusters [Ni₃M′(L)₃(OH)(CH₃CN)₃]₂·CH₃CN (M′=K for 1 and M′=Na for 2, where L is an anion of 2-[(2-hydroxy-3-methoxy-benzylidene)-amino]-ethanesulfonate) with higher efficiency, yields and purity than those without it. The 6-metallacrown-3 [Ni₃(OH)(L)₃]⁻ groups exhibit interesting ion trapping and self-assembly of size-different Na⁺ and K⁺ through form recognition and coordination activity in 1 and 2. The magnetic studies for 1 and 2 suggest that the {Ni₃M′O₄} (M′=K and Na) cores both display dominant ferromagnetic interactions from the nature of the binding modes of μ₃-O (oxidophenyl) and μ₃-OH.     

Synthesis and characterization of biodegradable poly(L-aspartic acid-co-PEG)

The melt polycondensation reaction of the prepolymer prepared from N-(benzyloxycarbonyl)-L -aspartic acid anhydride (N-CBz-L -aspartic acid anhydride) and low molecular weight poly(ethylene glycol) (PEG) using titanium isopropoxide (TIP) as a catalyst produced the new biodegradable poly(L -aspartic acid-co-PEG). This new copolymer had pendant amine functional groups along the polymer backbone chain. The optimal reaction conditions for the preparation of the prepolymer were obtained by using a 0.12 mol % of p-toluenesulfonic acid with PEG 200 for 48 h. The weight-average molecular weight of the prepolymer increased from 1,290 to 31,700 upon melt polycondensation for 6 h at 130°C under vacuum using 0.5 wt % TIP as a catalyst. The synthesized monomer, prepolymer, and copolymer were characterized by FTIR, ¹H- and ¹³C-NMR, and UV spectrophotometers. Thermal properties of the prepolymer and the protected copolymer were measured by DSC. The glass transition temperature (T_g) of the prepolymer shifted to a significantly higher temperature with increasing molecular weight via melt polycondensation reaction, and no melting temperature was observed. The in vitro hydrolytic degradation of these poly(L -aspartic acid-co-PEG) was measured in terms of molecular weight loss at different times and pHs at 37°C. This pH-dependent molecular weight loss was due to a simple hydrolysis of the backbone ester linkages and was characterized by more rapid rates of hydrolysis at an alkaline pH. These new biodegradable poly(L -aspartic acid-co-PEG)s may have potential applications in the biomedical field. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 2949–2959, 1998     

X-ray Crystal and Ab Initio Structures of 3′,5′-di-O-Acetyl-N(4)-Hydroxy-2′-Deoxycytidine and Its 5-Fluoro Analogue: Models of the N(4)-OH-dCMP and N(4)-OH-FdCMP Molecules Interacting with Thymidylate Synthase

The crystal and molecular structures of the 3′,5′-di-O-acetyl-N(4)-hydroxy-2′-deoxycytidine molecule and its 5-fluoro congener have been determined by X-ray single crystal diffraction. The 3′,5′-di-O-acetyl-N(4)-hydroxy-5-fluoro-2′-deoxycytidine molecule crystallizes in the space group C2 with the following unit cell parameters: a = 21.72 Å, b = 8.72 Å, c = 8.61 Å, and β = 90.42^∘. 3′,5′-di-O-acetyl-N(4)-hydroxy-2′-deoxycytidine also belongs to the monoclinic space group C2 and the unit cell parameters are: a = 39.54 Å, b = 8.72 Å, c = 22.89 Å, and β = 95.26^∘. The non-fluorine analogue demonstrates a rare example of crystal structure with five symmetry-independent molecules in the unit cell. All the molecules in both crystal structures have the sugar residue anti oriented with respect to the base, as well as have the N(4)-OH residue in cis conformation relatively to the N(3)-nitrogen atom. In addition to the molecular geometries from X-ray experiment, the optimized molecular geometries have been obtained with the use of theoretical ab initio calculations at the RHF/6-31G(d) level. The corresponding geometric parameters in the molecules of 3′,5′-di-O-acetyl-N(4)-hydroxy-2′-deoxycytidine and its 5-fluoro congener have been compared. The differences including the C(5)=C(6) bond shortening and C(4)—C(5)—C(6) angle widening in the fluorine analogue are discussed in this paper in relation to the molecular mechanism of enzyme, thymidylate synthase, inhibition by N(4)-hydroxy-2′-deoxycytidine monophosphate and its 5-fluoro congener.     

Neutron diffraction study of the β′ and γ phases of LiFeO2

The β, β′, γ and α phases of LiFeO₂, synthesized as powders, were annealed at different temperatures and characterized by X-ray measurements. The β′ and γ modifications were also studied by time-of-flight neutron diffraction (ISIS Facility, UK). The structure of the β′ phase was refined in the monoclinic C2/c space group (a=8.566(1), b=11.574(2), c=5.1970(5) Å, β=146.064(5)°) to wR_p=0.071–0.080 (data from four counter banks). Fe and Li atoms are ordered over two of the four independent sites, and partially disordered over the other two. The ordered Li has a distorted tetrahedral coordination. The γ structure was refined at RT (a=4.047(1), c=8.746(2) Å) and at 570 °C (a=4.082(3), c=8.822(6) Å) in the I4₁/amd symmetry, showing full order with Li in octahedral coordination at RT, and in a split-atom configuration at high temperature. On annealing, the β′ polymorph was found to transform to γ at 550 °C, thus suggesting that it is a metastable phase. Electrostatics is discussed as the driving force for the α→β′→γ ordering process of LiFeO₂.     

Reactions of bis(isopropylxanthato)nickel(II) with nitrogen-donor ligands—II

New complexes of bivalent nickel with isopropylxanthates and nitrogen-donor ligands of composition [Ni(Prⁱxa)₂(L)], [Ni(Prⁱxa)₂(L¹)₂], [Ni(L²)₂](Prⁱxa)₂, and [Ni(L³)₃] (Prⁱxa)₂ have been synthesized, where Prⁱxa = i-C₃H₇OCS₂⁻, L = 1,2-diaminopropane (1,2-pn), N,N,N′,N′=tetramethylethylenediamine (tmen) or 4,4′-bipyridine (4,4′-bipy), L¹ = pyridine (py), L² = diethylenetriamine (dien) and L³ = ethylenediamine (en), 1,2-diaminopropane or 1,10-phenanthroline (phen). The compounds have been characterized by elemental analysis, IR and UV-vis spectroscopy, magnetochemical measurements, molar conductivity and thermal analysis. The compounds containing the complex cation have been one-electron irreversibly oxidized using cyclic voltammetry. The crystal and molecular structures of [Ni(Prⁱxa)₂(tmen)] and [Ni(phen)₃](Prⁱxa)₂ have been elucidated.     

New results in the ammonolysis of hexafluoro-cyclo-triphosphazene: Crystal structure of P3N3F5–NH–P3N3F4NH2

The reaction of hexafluoro-cyclo-triphosphazene P₃N₃F₆ with ammonia in acetonitrile has been studied. New compounds, (2-imino-2,4,4,6,6-pentafluoro-2λ⁵,4λ⁵,6λ⁵-cyclo-triphosphaza-1,3,5-trienyl)-2-amino-4,4,6,6-tetrafluoro-2λ⁵,4λ⁵,6λ⁵-cyclo-triphosphaza-1,3,5-triene, P₃N₃F₅–NH–P₃N₃F₄NH₂ (2) and cis and trans isomers of non-gem-2,4-diamino-2,4,6,6-tetrafluoro-2λ⁵,4λ⁵,6λ⁵-cyclo-triphosphaza-1,3,5-triene, P₃N₃F₄(NH₂)₂ (4, 5)_, were detected by GC/MS, and ³¹P NMR spectroscopy in reaction mixtures. X-ray diffraction analysis of P₃N₃F₅–NH–P₃N₃F₄NH₂ (2) revealed two conformational polymorphs, 2A and 2B, the latter being built up of two different conformers that were further denoted as 2B_a (the same as the single conformer in 2A) and 2B_b. The compound 2 was characterized by spectroscopic methods and its 2D potential energy surface (PES) was described by density functional theory computations depending on two dihedral angles. The calculated PES spans over 30 kJ/mol in energy including 8 local minima and all first and second order saddle points. The occurrence of the two experimentally observed conformers 2B_a and 2B_b seems to be governed by crystal packing effects.