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。     

Geometries,vibrational frequencies,and electron affinities of X2Cl (X=C,Si,Ge) clusters

Ab initio quantum chemical calculations have been performed on X₂Cl^? and X₂Cl (X = C, Si, Ge) clusters. The geometrical structures, vibrational frequencies, electronic properties and dissociation energies are investigated at the Hartree–Fock (HF), Møller–Plesset second‐ and fourth‐order (MP2, MP4), CCSD(T) level with the 6‐311+G(d) basis set. The X₂Cl (X = C, Si, Ge) and X₂Cl^? (X = Si, Ge) take a bent shape obtained at the ground state, while C₂Cl^? has a linear structure. The impact on internal electron transfer between the X₂Cl and the corresponding anional clusters is studied. The three different types of electron affinities (EAs) at the CCSD(T) are reported. The most reliable adiabatic electronic affinities, obtained at the CCSD(T)/cc‐pvqz level of theory, are predicted to be 3.30, 2.62, and 1.98 eV for C₂Cl, Si₂Cl, and Ge₂Cl, respectively. The calculated EAs of C₂Cl and Ge₂Cl are in good agreement with theoretical results reported. The correlation effects and basis sets effects on the geometrical structures and dissociation energies are discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Coulombic Basis for Relative Hydrogen-Bonding Basicities and Conformational Energies of Tertiary Amine Oxides and Phosphine Oxides

The structures, energies, and natural atomic charges of 2-dimethylaminophenol oxide, 2-Me₂N-(O)C₆H₄OH, and 2-dimethylphosphinylphenol, 2-Me₂P(O)C₆H₄OH, in three different conformations were computed at the ab initio MP2/6-31G* level. Computed natural charges indicate distributions of electron density in amine oxides and phosphine oxides that are quite different from what is normally assumed on the basis of the formal charges in the usual representations of these compounds. The charges on nitrogen and phosphorus in these compounds are typically computed to be approximately zero on nitrogen and +2 on phosphorus, and the oxygen is considerably more negative in the phosphine oxide than in the amino oxide. Electronegativity differences thus play a larger role and formal charges a smaller one in determining atomic charges in these compounds than is generally believed. Despite the more negative oxygen in phosphine oxides, amine oxides are computed to be considerably more basic when participating in hydrogen bonding. Calculations treating the computed natural charges on these six conformations as point charges for classical approximations of the coulombic energies support the idea that the quantum mechanically computed relative energies are largely determined by coulombic interactions.     

Theoretical study of endohedral metallofullerenes: Sc3−nLanN@C80 (n=0–3)

To provide theoretical insight into the structures and properties of Sc₃N@C₈₀, which has been isolated in high yield and purity as a new stable endohedral metallofullerene, density functional calculations are carried out for the Sc_3?nLa_nN@C₈₀ (n=0–3) series. Because of electron transfer from Sc₃N to C₈₀, the electronic structure of Sc₃N@C₈₀ is formally described as (Sc₃N)⁶⁺C$_{80}^{6-}$. The encapsulated Sc₃N cluster takes a planar structure with long Sc–Sc distances and is highly stabilized inside the I_h cage of C₈₀, which rotates rapidly. As the number of La atoms increases, the Sc_3?nLa_nN cluster is forced to maintain a pyramidal structure in Sc_3?nLa_nN@C₈₀. In addition, the C₈₀ cage takes an open‐shell electronic structure due to an increase in the number of electrons transferring from Sc_3?nLa_nN. These make the endohedral structure less stable and more reactive. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1353–1358, 2001     

Phenylmercury(II) derivatives of tetraorganodichalcogenoimidodiphosphorus acids. Crystal and molecular structure of [PhHg{(OPR2)(SPPh2)N}]2 (R=Me, Ph)

The reactions between PhHgCl or PhHgAc and M[(XPR₂)(YPR′₂)N] (M=Na, K; X, Y=O, S; R, R′=Me, Ph, OEt), in 1:1 molar ratio, have been investigated. PhHg[(XPR₂)(YPR′₂)N] derivatives were isolated as microcrystalline powders and were characterised using IR and NMR (¹H, ¹³C and ³¹P) spectroscopy and mass spectrometry. The molecular structure of PhHg[(OPR₂)(SPPh₂)N] [R=Me (1), Ph (2)] was investigated by X-ray diffraction. In the monomeric unit, PhHg[(OPR₂)(SPPh₂)N], the mercury atom forms the primary bonds with the carbon of the phenyl group and the sulfur atom of the phosphorus ligand [Hg(1)-S(1) 2.405(1) Å for 1, 2.398(2) Å for 2]. These primary bonds are significantly deviated from the expected linear arrangement [C(1)-Hg(1)-S(1) 166.4(2)° for 1, 165.0(2)° for 2]. Both compounds exhibit dimeric associations in the crystal through S,O-bridging organophosphorus ligands [Hg(1)-O(1) 2.556(4) Å for 1, 2.588(4) Å for 2], thus resulting in a distorted T-shaped arrangement of the CHgSO coordination core.. The formation of a 12-membered Hg₂O₂S₂P₄N₂ ring with different conformation in 1 and 2, respectively, results in different additional chalcogen atoms being in the proximity of the metal atom. Weak transannular Hg?O [2.753(4) Å] are also established in 1, leading to a tricyclic ladder structure with a planar central Hg₂O₂ ring.     

Tractability frontiers in probabilistic team semantics and existential second-order logic over the reals

Probabilistic team semantics is a framework for logical analysis of probabilistic dependencies. Our focus is on the axiomatizability, complexity, and expressivity of probabilistic inclusion logic and its extensions. We identify a natural fragment of existential second-order logic with additive real arithmetic that captures exactly the expressivity of probabilistic inclusion logic. We furthermore relate these formalisms to linear programming, and doing so obtain PTIME data complexity for the logics. Moreover, on finite structures, we show that the full existential second-order logic with additive real arithmetic can only express NP properties. Lastly, we present a sound and complete axiomatization for probabilistic inclusion logic at the atomic level.