Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA

Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.     

The Surface Analysis Working Group at the Consultative Committee for Amount of Substance,Metrology in Chemistry and Biology: A successful initiative by Martin Seah

Dr Martin Seah, NPL, was the initiator, founder, and first chairman of the Surface Analysis Working Group (SAWG) at the Consultative Committee for Amount of Substance, Metrology in Chemistry and Biology (CCQM) at the Bureau International des Poids et Mesures (BIPM), the international organization established by the Metre Convention. This tribute letter summarizes his achievements during his chairmanship and his long-running impact on the successful work of the group after his retirement.     

Metallorganische Verbindungen mit N-substituierten 3-Hydroxy-2-methyl-4-pyridon-Liganden: quadratisch-planare Rhodium(I)-, Iridium(I)- und Palladium(II)-Komplexe

Organometallic Compounds with N -substituted 3-Hydroxy-2-methyl-4-pyridone Ligands: square planar Rhodium(I), Iridium(I), and Palladium(II) Complexes Reactions of [(OC)₂MCl]₂ (M = Rh, Ir) or [(cod)RhCl]₂ with the anions of N-Aryl or N-Alkyl substituted 3-hydroxy-2-methyl-4-pyridones (O–O′) yield complexes of the general formula [L₂M(O–O′)]. Compounds of this type are also available from reactions of [(OC)₂Rh(acac)] with the corresponding neutral ligands. Substitution of one carbonyl-ligand of the N-phenyl complex [(OC)₂Rh(C₁₂H₁₀NO₂)] ( 2 ) with cyclooctene affords [(OC)(C₈H₁₄)Rh(C₁₂H₁₀NO₂)] ( 8 ). The palladium complexes [(R₃P)Pd(O–O′)Cl] (R = Et, Bu), [(C₆H₄CH₂NMe₂) · Pd(O–O′)] and [(Et₃P)₂Pd(O–O′)]BF₄ ( 9 – 12 ) were synthesized from [(R₃P)PdCl₂]₂, [(C₆H₄CH₂NMe₂)PdCl]₂ or [(Et₃P)PdCl₂]. The structures of the N-methyl compounds [(OC)₂Rh(C₇H₈NO₂)] ( 1 ) and [(Ph₃P)Pd(C₇H₈NO₂)Cl] ( 9 ) were determined by single crystal X-ray diffraction.     

Electronic determinants of photoacidity in cyanonaphthols

We present semiempirical AM1 calculations for the ground and excited state of 2-naphthol and some of its cyano derivatives in the gas phase. Following photoexcitation, the Mulliken electron density on the oxygen diminishes slightly for the acid and more conspicuously for the anionic conjugated base. This agrees with the measured solvatochromic parameters for 2-naphthol. In both electronic states, we find a nice correlation with the measured pK values in water. The electronic charge distribution on the distal ring of the anion agrees with the experimental acidity order in both S(0) and S(1). Upon excitation, it increases predominantly in positions 3, 5, and 8. The ring system of the anion assumes an alternate quinoidal structure in the ground state of the anion, which becomes more symmetric in the relaxed excited state. This suggests that the enhanced aromatic character of a 4n electron system in the excited state allows for better delocalization of the oxygen charge within the ring.     

Complex series [Ru(tpy)(dpk)(X)]n+ (tpy = 2,2':6',2''-terpyridine; dpk = 2,2'-dipyridyl ketone; X = Cl-, CH3CN, NO2(-), NO+, NO*, NO-): substitution and electron transfer, structure, and spectroscopy

The complex framework [Ru(tpy)(dpk)]2+ has been used to study the generation and reactivity of the nitrosyl complex [Ru(tpy)(dpk)(NO)]3+ ([4]3+). Stepwise conversion of the chloro complex [Ru(tpy)(dpk)(Cl)]+ ([1]+) via [Ru(tpy)(dpk)(CH3CN)]2+ ([2]2+) and the nitro compound [Ru(tpy)(dpk)(NO2)]+ ([3]+) yielded [4]3+; all four complexes were structurally characterized as perchlorates. Electrochemical oxidation and reduction was investigated as a function of the monodentate ligand as was the IR and UV-vis spectroscopic response (absorption/emission). The kinetics of the conversion [4]3+/[3]+ in aqueous environment were also studied. Two-step reduction of [4]3+ was monitored via EPR, UV-vis, and IR (nu(NO), nu(CO)) spectroelectrochemistry to confirm the {RuNO}7 configuration of [4]2+ and to exhibit a relatively intense band at 505 nm for [4]+, attributed to a ligand-to-ligand transition originating from bound NO-.     

Research announcement on gaierkirfs method for a class of integra equations of the first kind

Let X and Y be locally convex spaces with K a closed convex cone in X Necessary and sufficient conditions are given for the image AK to be closed in Ywhen A:X→Y is a continuous linear map. This result is used to generalize a theorem of Abrams to infinite dimensional spaces and also to give sufficient conditions for the Hurwicz version of the Farkas lemma for locally convex spaces to hold.     

Modeling loop backbone flexibility in receptor‐ligand docking simulations

The relevance of receptor conformational change during ligand binding is well documented for many pharmaceutically relevant receptors, but is still not fully accounted for in in silico docking methods. While there has been significant progress in treatment of receptor side chain flexibility sampling of backbone flexibility remains challenging because the conformational space expands dramatically and the scoring function must balance protein–protein and protein–ligand contributions. Here, we investigate an efficient multistage backbone reconstruction algorithm for large loop regions in the receptor and demonstrate that treatment of backbone receptor flexibility significantly improves binding mode prediction starting from apo structures and in cross docking simulations. For three different kinase receptors in which large flexible loops reconstruct upon ligand binding, we demonstrate that treatment of backbone flexibility results in accurate models of the complexes in simulations starting from the apo structure. At the example of the DFG‐motif in the p38 kinase, we also show how loop reconstruction can be used to model allosteric binding. Our approach thus paves the way to treat the complex process of receptor reconstruction upon ligand binding in docking simulations and may help to design new ligands with high specificity by exploitation of allosteric mechanisms. © 2012 Wiley Periodicals, Inc.     

Structural, magnetic, high-frequency and high-field EPR investigation of double-stranded heterometallic [{Ni(en)2}2(micro-NCS)4Cd(NCS)2](n).nCH3CN polymer self-assembled from cadmium oxide, nickel thiocyanate and ethylenediamine

A novel heterometallic 1D coordination polymer [{Ni(en)2}2(micro-NCS)4Cd(NCS)2](n) x nCH3CN (en = ethylenediamine) has been prepared using the self-assembly process in a one-pot reaction of cadmium oxide, nickel and ammonium thiocyanates with an acetonitrile solution of ethylenediamine. The complex consists of an uncommon cis-Cd(SCN)4(NCS)2(4-) fragment and a rare combination of cis-Ni(en)2(2+) and trans-Ni(en)2(2+) building blocks linked by micro(1,3)-NCS bridges into a double-stranded zigzag chain structure. Each chain is comprised of [Ni2Cd2(micro-NCS-N,S)4)] macrocycles with chair-like and rectangular-like shapes arrayed alternately. The shortest intrachain CdCd separations are 9.535(1) and 10.868(2) A, while the nearest NiNi distances are 5.418(1) and 6.612(2) A. A network of weak N-HS hydrogen bonds, involving the terminal NCS ligands and NH2-groups of en, links the infinite chains and results in the formation of an extended supramolecular three-dimensional framework. Variable-temperature (1.8-300 K) magnetic susceptibilities show a slight change of the micro(B) value at low temperature, indicative of weak antiferromagnetic interactions (J = 1.55 cm-1) between magnetic canters. High-field, high-frequency (100-400 GHz) EPR spectra were simulated using S = 1 ground state for separate Ni2+ ions with the spin Hamiltonian parameters g = 2.165, D = 0.45 cm-1 and E = 0.03 cm(-1). According to DFT calculations, the D and E parameters are -0.35 cm(-1) and 0.049 cm-1 for the cis arrangement of Ni2+ and 0.58 cm(-1) and 0.012 cm(-1) for trans.