Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters

Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.     

Adsorption of organic substances on broken clay surfaces: a quantum chemical study

Hydrogen-bonded interactions between local defect structures on broken clay surfaces modeled as molecular clusters and the organic molecules acetic acid, acetate, and N-methylacetamide (NMA) have been investigated. Density functional theory and polarized basis sets have been used for the computation of optimized interaction complexes and formation energies. The activity of the defect structures has been characterized as physical or chemical in terms of the strength of the hydrogen bonds formed. Chemical defects lead to significantly enhanced interactions with stronger hydrogen bonds and larger elongation of OH bonds in comparison to the physical defects. The type of interaction with the defect structure significantly influences the planarity of the model peptide bond in NMA. Both cases, enhancement of the planarity by increase of the CN double bond character and strong deviations from planarity, are observed.     

A thermal and structural study on Lanthanum Hexacyanocobaltate(III) pentahydrate,La[Co(CN)6]·5H2O. Part III

On dehydration of La[Co(CN)₆]·5H₂O, the color of the complex, changes from white to pale blue at around 230°C. Heating the pale blue specimen, the color changes to deep blue at around 290°C. This deep blue specimen is easily rehydrated to a pink one. As reported previously, in the pale blue specimen, Co³⁺ ions are situated in the center of the D_4h crystal field formed by six CN^- ions. The deep blue specimen is due to the presence of [Co(CN)₄]^2- ions in which Co²⁺ was situated in a T_d coordination field formed by four CN^- ions and the Co-C bond length is 1.67 Ĺ. The pink species corresponded to trans-[Co(CN)₄(H₂O)₂]^2- and the bond lengths of Co-C and Co-O are 1.89 and 1.85 Ĺ, respectively. The Raman spectra of the complex observed at 25°C displays two bands at 2157 and 2176 cm^-1 associated with the vibration of C-N bond, and the band of 2157 cm^-1 was split into two bands, 2150 and 2156 cm^-1, at around 100°C. When the complex was heated to around 230°C, three new bands were observed at 2103, 2116 and 2141 cm-1. The bands of 2103 and 2116 cm^-1 were assigned to the stretching vibration of C=N bonding to Co²⁺. The band of 2141 cm^-1 was assigned to the stretching vibration of the inverted CN^- as follows: Co-C=N-La→Co-N=C-La. The activation energy for the inversion of CN^- was estimated as 67 kJ mol^-1. This revised version was published online in August 2006 with corrections to the Cover Date.     

Beiträge zur Chemie der Alkylverbindungen von Übergangsmetallen. 59. Cyclopentadienyl-2-(dimethylaminomethyl)ferrocenyl-Verbindungen elektronenarmer 3 d-Elemente

Contributions to the Chemistry of Transition Metal Alkyl Compounds. 59. Cyclopentadienyl-2-(dimethylaminomethyl)ferrocenyl Compounds of Early 3 d-Elements Compounds of the type (C₅H₅)₂M(FcN) (M = Sc ( 1 ), Ti ( 2 ), V ( 3 ), Cr ( 4 ); FcN = 2-dimethylaminomethyl)ferrocenyl group), and (C₅H₅)M(FcN)₂ (M = Ti ( 5 ), Cr ( 6 ) were synthesized and investigated. A detailled characterization with respect to the existence of chelate structures was realized by the uv-vis, ¹H-n.m.r. spectroscopic measurements and determination of magnetic moments.     

Diborane (4) derivatives via coupling of amine monobromocyanoboranes: Study of the bromination of amine cyanoborane and molecular structures of the amine dibromocyanoboranes

The first examples of diborane (4) compounds derived from amine cyanoboranes are described. A series of monobromo derivatives of amine cyanoboranes (A:BHBrCN), and dibromo derivatives (A:BBr₂CN), 1-7, were prepared. Lithiation of the monobromo derivative of trimethylamine cyanoborane, using n-BuLi, did not produce the C-lithiated intermediate Li⁺ [CH₂NMe₂BHBrCN]⁻, but instead the B-lithiated intermediate Li⁺ [Me₃NBHCN]⁻, was obtained. This intermediate, when allowed to react for 16 h, coupled with the un-lithiated trimethylamine monobromocyanoborane (Me₃NBHBrCN) and resulted in diborane (4) derivative formation as the 2LiBr complex. The same result was obtained when one equiv of the trimethylamine monobromocyanoborane was added to the reaction mixture 1 h after lithiation. Following the same procedure, novel diborane (4) derivatives of amine cyanoboranes were successfully obtained, 8-11, as their 2LiBr complexes from the monobromo derivatives of the corresponding amine cyanoboranes. Molecular structures of the trimethylamine dibromocyanoborane, 6, and the triethylamine dibromocyanoborane, 7, were determined using X-ray crystallography.     

Determining the chromophore in the amylopectin–iodine complex by theoretical and experimental studies

A partial hydrolysis of amylose followed by the addition of iodine provides a spectrum almost identical to that of the amylopectin–iodine (API) complex suggesting the involvement of smaller “amylose-like” units in the API complex. Our theoretical studies on different polyiodine and polyiodide species suggest that a nearly linear I₄ unit stabilized within the cavity of a small “amylose-like” helix is responsible for the characteristic API spectrum. Since there are 2.75 anhydroglucose residues (AGU) for every iodine atom in the amylose–iodine (AI) complex and a structural similarity exists between the API and the AI (amylose–iodine) complexes, we identify (C₆H₁₀O₅)₁₁I₄ to be the chromophore in the API complex. © 1994 John Wiley & Sons, Inc.     

Structural Consequences of S → Se Substitution in some Symmetrical [M(S2CNR2)3] Complexes

The consequences of replacement of the symmetrically chelate ligands in [M(E₂CNR₂)₃] (E = S, Se) complexes of potential 32 symmetry by analogous mixed S,Se unsymmetrical chelates are explored for both small (M = Co) and large (M = In) metal atoms, and R = primary (Et) and secondary (ⁱPr) alkyl substituents by way of low‐temperature single crystal X‐ray studies of [(Co(SSeCNEt₂)₃] ([Co(Se₂CNEt₂)₃] also determined as datum), and [In(SSeCNR₂)₃], R = Et, ⁱPr. The structure of [(ⁱPr₂N·CS·Se)₂] is also recorded.     

Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

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Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

Electrochemical Synthesis and Characterization of Nickel(II) Complexes with N‐2‐Pyridyl‐sulfonamide Ligands

Heteroleptic nickel(II) complexes [NiL₂L′] of a series of monoanionic and potentially bidentate N‐2‐pyridyl‐sulfonamide ligands [HL] and 2,2′‐bipyridine or 1,10‐Phenanthroline (L′) have been prepared by electrochemical oxidation of a nickel anode in an acetonitrile solution of the ligands. The complexes have been characterized by microanalysis, IR and electronic spectroscopy, magnetic measurements and LSI mass spectrometry. The crystal structure of [Ni(Ms6mepy)₂(bipy)] has been determined by x‐ray diffraction and shows the metal in an octahedral NiN₆ environment. Octahedral structures are also proposed for the other complexes with the N‐2‐pyridyl‐sulfonamide ligands acting as N,N′ or N, O bidentate systems, depending on the position of the methyl substituent on the pyridine ring.     

C_(59)F_(2n)HN(n=1,2)异构体的结构与稳定性的理论研究

分别用MNDO和AM1两种半经验方法,对C59F2nHN (n = 1, 2) 的异构体进行几何构型全优化,结合频率分析及HF/6-31G单点能计算,确定了各异构体的基态结构及其相对稳定性。计算结果表明,C59HN的F加成物的立体选择性规律与C60的不同,最稳定异构体不是1-2加成物。C59F2HN的最稳定异构体是1-4加成的6, 18-或12, 15-异构体; C59F4HN的最稳定异构体是1-4,1-4加成的6, 18; 12, 15-异构体,其能量远小于其它各异构体的能量。N原子取代碳笼骨架C原子后,改变了碳笼F加成物的立体选择性规律。