Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

Dynamik linearer Molekülanionen in den Hydrogensulfiden von Natrium,Kalium und Rubidium: Differential-Scanning-Kalorimetrie,Röntgen- und Neutronenbeugung

Dynamical Behaviour of Linear Molecular Anions in the Hydrogensulfides of Sodium, Potassium and Rubidium: Differential Scanning Calorimetry, X-ray and Neutron Diffraction Hydrogensulfides of the alkali metals M ? Na, K, Rb were prepared in autoclaves by the reaction of the corresponding metals with H₂S and D₂S, respectively, in the temperature range from 50°C to 150°C. Differential scanning calorimetry, X-ray and neutron diffraction methods reveal that both, the HS^?-and DS^?-compounds occur in three crystalline modifications with HT ? high-, MT ? medium- and LT ? low-temperature form: The temperatures and enthalpies for the changes of modifications of the H- and D-compounds are given and the atomic arrangements revealed mainly by neutron diffraction data are discussed, in relation to, for example, size of cations.     

Photochemical synthesis of a palladium dichloromethyl complex, {(hexyl)HC(N-methyl-imidazol-2-yl)2}Pd(CHCl2)Cl.: X-ray molecular structures of {(hexyl)HC(N-methylimidazolyl-2-yl)2}Pd(X)Cl, X=Cl, and CHCl2

The reaction of (hexyl)HC(mim)₂ (1, mim=N-methyl-imidazol-2-yl) with (cod)PdMeCl in C₆H₆ yields {(hexyl)HC(mim)₂}Pd(Me)Cl (3). The photochemical reaction of 3 with CH₂Cl₂ at 23 °C in ambient room light yields {(hexyl)HC(mim)₂}Pd(CHCl₂)Cl (4). It is proposed that this reaction proceeds by homolytic scission of the PdMe bond of 3.     

Neue neutrale und kationische Mono‐Aziridin‐Komplexe des Typs [CpMn(CO)2Az], [CpCr(NO)2Az]+ und [(Ph3P)(CO)4ReAz]+ über CO‐, Hydrid‐ und Chlorid‐Abspaltungsreaktionen

Novel Neutral and Cationic Mono‐Aziridine Complexes of the Type [CpMn(CO)₂Az], [CpCr(NO)₂Az]⁺, and [(Ph₃P)(CO)₄ReAz]⁺ via CO‐, Hydride‐, and Chloride‐Elimination Reactions The monoaziridine complexes 1 — 5 are obtained by three differently induced substitution reactions. The photolytically induced CO substitution reaction of [CpMn(CO)₃] with 2, 2‐dimethylaziridine leads to the neutral N‐coordinate aziridine complex [Cp(CO)₂Mn{$\overline{N(H)CMe₂C}$ H₂}] ( 1 ). The protonation of [(Ph₃P)(CO)₄ReH] with CF₃SO₃H and consecutive treatment with 2, 2‐dimethylaziridine or 2‐ethylaziridine gives the salt‐like aziridine complexes [(Ph₃P)(CO)₄Re{$\overline{N(H)CMe₂C}$ H₂}](CF₃SO₃) ( 2 ) or [(Ph₃P)(CO)₄Re{ H₂}](CF₃SO₃) ( 3 ) by hydride elimination reactions. The like‐wise salt‐like complexes [Cp(NO)₂Cr{$\overline{N(H)CMe₂C}$ H₂}](BF₄) ( 4 ) and [Cp(NO)₂Cr{ H₂}](CF₃SO₃) ( 5 ) are synthesized from [CpCr(NO)₂Cl] by chloride elimination with AgX (X = BF₄, CF₃SO₃) in the presence of 2, 2‐dimethylaziridine or 2‐ethylaziridine, respectively. As a result of X‐ray structure analyses, the metal atoms are trigonal pyramidally ( 1, 4, 5 ) or octahedrally ( 2, 3 , cis‐position) configurated; the intact three‐membered rings coordinate through the distorted tetrahedrally configurated N atoms. All compounds 1‐5 are stable with respect to the directed thermal alkene elimination to give the corresponding nitrene complexes; the IR, ¹H‐ and ¹³C{¹H}‐NMR, and MS spectra are reported and discussed.     

SinH/SinH-(n=3～8)的结构和电子亲合能的研究

选用四种不同的密度泛函理论方法(B3LYP，B3P86，BLYP，BP86)，在全电子的双ξ加极化加弥散函数基组(DZP )下，对SinH／SinH^-(n=3～8)体系进行研究，获得它们的基态结构和电子亲合能。预测Si3H／Si3H^-,Si4H／Si4H^-,Si5H／Si5H^-,Si6H／Si6H^-，Si7H／Si7H^-和Si8H／Si8H^-的基态结构分别为C2v(^2B2)／C2v(1^A1)氢桥结构，Cs(^2A’)／C(^1A’)，C2v(^2B2)／C2v(^1A1)，C2v(^2B2或^2B1)／C4v(^1A1)，C5v(^2A1)／C5v(^1A1)和C5(^2A‘‘)／C3v(^1A1)。在电子亲合能方面，B3LYP方法预测的电子亲合能是最可靠的，预测Si3H，Si4H，Si5H，Si6H，Si7H和Si8H的电子亲合能分别为2．56，2．59，2．84，2．86，3．19和3．14eV。     

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.