On the Karplus relation for 3J(POCC) of nucleotides

The original Karplus parameters for analysing ³J(POCC) magnitudes of nucleotides in terms of conformational properties of the O? C bond were taken from results for 3′,5′-nucleotides and applied to 3′→ 5′-oligonucleotides; the parameters were later modified to take account of ‘largey’ magnitudes of ³J(POCC) observed in 2′ → 5′-oligonucleotides. In this work the origin of this discrepancy is explained in terms of substituent electronegativity effects at C-1′, and quantified using the ¹³C NMR results of 2′,3′-cyclic mononucleotides. A new set of Karplus parameters suitable for analysing ³J(POCC) magnitudes in 3′- and 5′-nucleotides and 3′ → 5′-oligonucleotides is determined from ¹³C NMR measurements on 3′-nucleotides and available results for 3′,5′-cyclic mononucleotides. A method of dealing with J(P, C-1′) coupling in 2′-nucleotides, 2′,3′-cyclic nucleotides and 2′ → 5′-oligonucleotides using the same Karplus relationship is suggested.     

Potentiometric differentiated titration of the components of nucleic acids and their derivatives. VII. Acidimetric determination of some N-acyl-2′-deoxyribonucleosides and their 5′-tritylated derivatives

The conditions have been investigated for the potentiometric titration of N-acyl-2′-deoxyribonucleotides and of trityl carbinol derivatives and their two-component mixtures with a nitromethane solution of perchloric acid. The influence of water, acetone, chloroform, and acetic acid on the conditions for the acidimetric analysis of tri-p-methyltrityl carbinol, p-monomethoxytrityl carbinol, and di-p-methoxy trityl carbinol in nitromethane have been shown. Procedures have been developed for the quantitative determination of N⁶-benzoyl-5′-di-p-methoxytrityl-2′-deoxyriboadenosine, the 5′-tri-p-methyltrityl and 5′-p-monomethoxytrityl derivatives of N⁴-benzoyl-2′-deoxyribocytidine, of N⁶-benzoyl-2′-deoxyriboadenosine, and of N²-isobutyryl-2′-deoxyriboguanosine by differentiated potentiometric titration. For the determination of the 5′-di-p-methoxy derivatives of N⁴-benzoyl-2′-deoxyribocytidine and of N⁶-benozyl-2′-deoxyriboadenosine a procedure is proposed which includes the use of two parallel titrations. Methods have been developed for the use of milligram amounts of substance.     

Conductometric study of complexation reaction of 4′-nitrobenzo-15-crown-5 with Mn+2, Co+2, Y+3, and ZrO+2 cations in acetonitrile,methanol and their binary solvent solutions

The complexation reactions of Mn²⁺, Co²⁺, Y³⁺, and ZrO²⁺ cations with the macrocyclic ligand, 4′-nitrobenz-15-crown-5 (4′-NB15C5), in acetonitrile (AN), methanol and AN-MeOH binary mixtures have been studied at various temperatures using the conductometric method. The conductance data stand for the Me : L stoichiometric ratio 1 : 1. Values of the formation constants of the complexes were accumulated by plotting molar conductivity curves using the computer program, GENPLOT. The order of stability of the metal-ion complexes in pure AN at 15°C was found to be: (4′-NB15C5 · ZrO)²⁺ > (4′-NB15C5 · Mn)²⁺ ≈ (4′-NB15C5 · Co)²⁺ > (4′-NB15C5 · Y)³⁺. In the case of AN-MeOH binary solvent solutions with 50 and 75 mole percent of AN at the same temperature, the sequence of stability of the complexes was the following: (4′-NB15C5 · Mn)²⁺ > (4′-NB15C5 · ZrO)²⁺ ≈ (4′-NB15C5 · Co)²⁺ 〉 (4′-NB15C5 · Y)³⁺, and (4′-NB15C5 · Mn)²⁺ > (4′-NB15C5 · Y)³⁺ ≈ (4′-NB15C5 · Co)²⁺ > (4′-NB15C5 · ZrO)²⁺, respectively. The complexes formed are entropy stabilized in all cases.     

N,N-Dialkylierte N′-Ferrocenoylthioharnstoffe und Ferrocen-1,1′-dicarbonsäure-di-N,N-dialkyl-thioureide als Liganden für Übergangsmetalle: Darstellung,pH-potentiometrische,röntgenkristallstrukturanalytische und EPR-Einkristalluntersuchungen

N,N-Dialkyl-N′-ferrocenoylthioureas and Ferrocene-1,1′ -dicarbonic-acid-di-N,N-dialkylthioureides as Ligands for Transition Metals: Synthesis, Acid-Dissociation Constants, X-Ray Structure Determination, and EPR-Single Crystal Investigation Reaction of ferrocenoylisothiocyanate or ferrocene-1,1′ -dicarbonic acid -diisothiocyanate with secondary amines gives N,N-dialkyl-N′ -ferrocenoylthioureas or the respective ferrocene-1,1′-dicarbonic acid-di-N,N-dialkyl-thioureides. The former yield neutral complexes with transition metal ions (Ni²⁺, Cu²⁺, Co³⁺, Pt²⁺, Fe³⁺). The acid dissociation constants of the ligands were determined. The EPR spectra of a bis-(N,N-diⁿbutyl-N′-ferrocenoylthioureato)copper(II) single crystal are discussed. The X-ray structure determination of ferrocene-1,1′-dicarbonic acid-di-N,N-diethyl-thioureide and its different behaviour against Ni²⁺ and Cu²⁺ is presented.     

Five-membered 2,3-dioxo heterocycles: XCII. Reaction of 3-aroyl-1H-pyrrolo[2,1-c][1,4]benzoxazine-1,2,4-triones with ethyl (2Z)-(3,3-dimethyl-8-oxo-2-azaspiro[4.5]deca-6,9-dien-1-ylidene)ethanoate. Synthesis of bridged analogs of pyrrolizidine alkaloids

3-Aroyl-1H-pyrrolo[2,1-c][1,4]benzoxazine-1,2,4-triones reacted with ethyl (2Z)-(3,3-dimethyl-8-oxo-2-azaspiro[4.5]deca-6,9-dien-1-ylidene)acetate to give ethyl 6′-aryl-2′-(2-hydroxyphenyl)-11′,11′-dimethyl-3′,4,4′,13′-tetraoxospiro[2,5-cyclohexadiene-1,9′-(7′-oxa-2′,12′-diazatetracyclo[6.5.1.0^1,5.0^8,12]tetradec-5′-ene)]-14′-carboxylates whose structure was confirmed by X-ray analysis. The products may be regarded as bridged analogs of pyrrolizidine alkaloids, 7′-oxa-2′,12′-diazatetracyclo[6.5.1.01,5.08,12]tetradecanes.     

Polymer‐based fluorescence sensors incorporating chiral binaphthyl and benzo[2,1,3]thiadiazole moieties for Hg2+ detection

Three chiral polymers P‐1 , P‐2 , and P‐3 could be obtained by the polymerization of (R)‐6,6′‐dibutyl‐3,3′‐diiodo‐2, 2′‐binaphthol (R‐M‐1) , (R)‐6,6′‐dibutyl‐3,3′‐diiodo‐2,2′‐bisoctoxy‐1,1′‐binaphthyl ( R‐M‐2 ), and (R)‐6,6′‐dibutyl‐3,3′‐diiodo‐2,2′‐bis (diethylaminoethoxy)‐1,1′‐binaphthyl ( R‐M‐3 ) with 4,7‐diethynyl‐benzo[2,1,3]‐thiadiazole ( M‐1) via Pd‐catalyzed Sonogashira reaction, respectively. P‐1 , P‐2 , and P‐3 can show pale red, blue–green, and orange fluorescence. The responsive optical properties of these polymers on various metal ions were investigated by fluorescence spectra. Compared with other cations, such as Co²⁺, Ni²⁺, Ag⁺, Cd²⁺, Cu²⁺, and Zn²⁺, Hg²⁺ can exhibit the most pronounced fluorescence response of these polymers. P‐1 and P‐2 show obvious fluorescence quenching effect upon addition of Hg²⁺, on the contrary, P‐3 shows fluorescence enhancement. Three polymer‐based fluorescent sensors also show excellent fluorescence response for Hg²⁺ detection without interference from other metal ions. The results indicate that these kinds of tunable chiral polybinaphthyls can be used as fluorescence sensors for Hg²⁺ detection. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 997–1006, 2010     

Synthesis of 3′,5′‐Cyclic Phosphate and Thiophosphate Esters of 2′‐C‐Methyl Ribonucleosides

2′‐C‐Methylnucleosides are known to exhibit antiviral activity against Hepatitis C virus. Since the inhibitory activity depends on their intracellular conversion to 5′‐triphosphates, dosing as appropriately protected 5′‐phosphates or 5′‐phosphorothioates appears attractive. For this purpose, four potential pro‐drugs of 2′‐C‐methylguanosine, i.e., 3′,5′‐cyclic phosphorothioate of 2′‐C‐methylguanosine and 2′‐C,O⁶‐dimethylguanosine, 1 and 2 , respectively, the S‐[(pivaloyloxy)methyl] ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphorothioate and the O‐methyl ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphate, 3 and 4 , respectively, have been prepared.     

Ab initio determination of the diabatic multicrossing pattern in the (HeH2)+ molecular ion

A method is presented for obtaining quantitative information on the diabatic multicrossing pattern that involves the core-excited state (1a′, 2a′²)²A′ and the (1a′²r)²A′,²A″ Rydberg series of the (HeH₂)⁺ triatomic ion, “Quasi-diabatic“ single-configuration state functions are built from judiciously generated MOs (balanced SCF treatment of 1a′ and 2a′ and IVO scheme for the excited MO). Using O'Malley's projection operator technique, the configuration states that describe different characteristics are grouped into subspaces where CI calculations are performed. The salient features of the potential energy surfaces for various geometries are discussed.     

Analysis of anomalous vibrational and rotational distributions in the CN(B2Σ+) state produced in the reaction of Ar(3P0,2) metastables with BrCN

The CN(B²Σ⁺ - X²Σ⁺) tail band emission system for μ′ = 11–20 resulting from the energy transfer reaction Ar(³P_0,2) + BrCN in a flowing afterglow apparatus was measured. The vibrational and rotational distributions were determined as a function of argon pressure. Numerous perturbed rotational lines were observed; analysis of the dependences of these lines on argon pressure, with the aid of experimental information already published, led to the following assignments as to the origins of the perturbations: For μ′ = 11, N′ = 20 and μ′ = 13, N′ = 9, the perturbing state is a ⁴Σ⁺; for μ′ = 12, N′ = 10 and 14, μ′ = 14, N′ = 7 and 10, and μ′ = 17, N′ ≈ 17–19 the perturbing state is A ²Π_i. The perturbed rotational line, μ′ = 11, N′ = 20, is found to be the primary source of intensity in the μ′ =11 vibrational band, but in all other cases the perturbed rotational lines do not significantly aid in the populating of the vibrational state. The anomalously high vibrational populations found in the tail band emission system (μ′ = 12, 14, 17 and 18), as well as the significantly high rotational excitations observed in the μ′ = 12–20 vibrational bands, apparently arise directly from the reaction intermediate.     

Isomerisierung bei der Komplexbildung von 3-Acetyl-tetramsäure: Struktur und magnetische Eigenschaften des CuII- und NiII-Komplexes von 2,7-Bis(1′, 5′, 5′-trimethylpyrrolidin-2′, 4′-dion-3′ -yl)-3, 6-diazaocta-2, 6-dien

Isomerization at the Complexation of 3-Acetyltetramic Acid: Structure and Magnetic Properties of the Cu^II- and Ni^II-Complex of 2,7-Bis (1′, 5′, 5′ -trimethylpyrrolidin-2′,4′ -dion-3′ -yl)-3,6-diazaocta-2,6-dien 2,7-Bis(1′, 5′, 5′ -trimethylpyrrolidin-2′, 4′ -dion-3′ -yl)-3,6-diazaoctadien formes Cu^II and Ni^II complexes with different constitutions (because of the Z/E isomerization). Results of X-ray analysis of N,N′ -ethylenbis(1′, 5′, 5′ -trimethylpyrrolidin-2′, 4′ -dion-3′ -acetiminato)nickel(II) 1 respectively -copper(II) 2 shows, that the complexing agent in 1 occurs in the E-form, whereas the ligand of the Cu^II complex forms the Z-form. Magnetic susceptibility and shift effects of the ¹³C-NMR signals point to a weak paramagnetism of the Ni^II complex. ESR-spectra are obtained from 2 only. Furthermore, the Cu^II complex reduces the relaxation times T₁ and T₂ of ¹H and ¹⁷O nuclei spins from water. From the temperature dependence of the shortening of the relaxation times an activation energy is calculated which describes the reorientation of the copper complex in the “water matrix”.     

Cyclopropanation of 2-arylmethylidenemalononitriles,alkyl 3-aryl-2-cyanoprop-2-enoates,and N-substituted 3-aryl-2-cyanoprop-2-enamides with bromine-containing zinc enolates

Zinc enolates derived from 2,2-dibromoindan-1-one and 2,2-dibromo-1,2,3,4-tetrahydronaphthalen-1-one reacted with 2-arylmethylidenemalononitriles, alkyl 3-aryl-2-cyanoprop-2-enoates, and N-substituted 3-aryl-2-cyanoprop-2-enamides to give, respectively, 3-aryl-1′-oxo-1′,3′-dihydrospiro[cyclopropane-1,2′-indene]-2-2-dicarbonitriles, 3-aryl-1′-oxo-3′,4′-dihydro-1′H-spiro[cyclopropane-1,2′-naphthalene]-2,2-dicarbonitriles, alkyl 3-aryl-2-cyano-1′-oxo-1′,3′-dihydrospiro[cyclopropane-1,2′-indene]-2-carboxylates, alkyl 3-aryl-2-cyano-1′-oxo-3′,4′-dihydro-1′H-spiro[cyclopropane-1,2′-naphthalene]-2-carboxylates, and N-substituted 3-aryl-2-cyanol-1′-oxo-3′,4′-dihydro-1′H-spiro[cyclopropane-1,2′-naphthalene]-2-carboxamides as a single diastereoisomer. The stereoconfiguration of the products was determined by ¹H and ¹³C NMR spectroscopy.     

SCHWEFELDIIMIDE MIT SILYL-, GERMYL-, STANNYL- UND PHOSPHINYL-HETEROSUBSTITUENTEN. SYNTHESE UND NMR-SPEKTROSKOPISCHE CHARAKTERISIERUNG

Abstract

Reactions of the salts K₂SN₂ and K[(NSN)R] (R = ′Bu, SiMe₃ and P′Bu₂) with organoelement chlorides R′R′ěl have been used to prepare four series of model sulfur diimides: R′R″E(NSN)ER″R′, ′Bu(NSN)ER″R′, Me₃Si(NSN)E″R′ and ^tBu₂P(NSN)ER″R′, respectively (E = C, Si, Ge, Sn; R′ and R″ = alkyl or aryl group). All compounds have been characterized by ′H and ¹³C NMR and—if possible—by ³¹P, ²⁹Si and ¹¹⁹Sn NMR spectroscopy. The configuration (Z or E) of the substituents R and E″R′ has been assigned in several cases using ^tBu(NSN)^tBu (1) as a reference. The E,Z assignment of ¹H, ¹³C and ¹⁵N nuclei in 1 is based on selectively ¹H-decoupled refocused INEPT ¹⁵N NMR and two-dimensional (2D) ¹³C/¹H heteronuclear shift correlations. The sulfur diimides under study are in general fluxional in solution.     

Two New Lead(II) Coordination Polymers with (Substituted) Bipyridine and Auxiliary Nitrate Ligands

The reaction of lead(II) nitrate with 4,4′‐bipyridine (4,4′‐bpy) and 4,4′‐dimethyl‐2,2′‐bipyridine (4,4′‐dm‐2,2′‐bpy) or 5,5′‐dimethyl‐2,2′‐bipyridine (5,5′‐dm‐2,2′‐bpy) resulted in the fomation of single crystals of [Pb₂(4,4′‐bpy)(5,5′‐dm‐2,2′‐bpy)₂(NO₃)₄] ( 1 ) and [Pb₃(4,4′‐bpy)₂(4,4′‐dm‐2,2′‐bpy)₂(NO₃)₆] ( 2 ). The new compounds have been characterized by single‐crystal X‐ray diffraction structure analysis as well as through elemental analysis, IR, ¹H‐NMR and ¹³C‐NMR spectroscopy and their stability has been studied by thermal analysis. In the crystal structure of ( 1 ) formula‐like dimers are further connected to a 2‐D network through the auxiliary nitrate ligands. The crystal structure of ( 2 ) exhibits two crystallographically independent Pb^II central atoms (in a ratio of 1:2). With the aid of the 4,4′‐bpy and the nitrate ions, a 3‐D polymeric structure is achieved.     

Behaviour of 2,2′-bipyridyl towards methylethyl- and n-propyl-(n-butyl)-tin dichlorides in nitrobenzene

The conductivities of mixtures of 2,2′-bipyridyl with MeEtSnCl₂ or BuPrSnCl₂ in nitromethane are interpreted in terms of formation of (i) RR′SnCl₂ · bipy, (ii) [RR′SnClbipy]⁺ Cl^?, and (iii) (RR′SnCl₃)^?.     

Synthesis of 1-(3′-deoxy-β-D-glycero-pentofuran-2′-ulosyl)uracil by selective elimination reactions

For the synthesis of y 1-(3′-deoxy-β-D-glycero-pentofuran-2′-ulosyl)uracil (16), the precursor, 5′-O-benzoyl derivative (2),² was elaborated in a variety of ways. 1-(5′-O-Benzoyl-3′-O-tosyl-β-D- lyxofuranosyl)uracil (4)² was benzoylated to N³-benzoyl-1-(2′,5′-di-O-benzoyl-3′-O-tosyl-β-D- lyxofuranosyl)uracil (5), which directly yielded 2 on treatment with sodium benzoate. 1-(3′,5′-Di-O- benzoyl-2′-O-tosyl-β-D-lyxofuranosyl)uracil (8) and its 3′,5′-O-isopropylidene analog (10) resisted elimination reactions, thus proving absolute selectivity in the elimination of the derivatives of 1-β-D- lyxofuranosyl-uracil. Seeking a more economical path to 2, 1-(5′-O-benzoyl-β-D-lyxofuranosyl)uracil (11) was first benzoylated to give 2′,5′-di-O-benzoate (12), accompanied by 3′,5′-di- and 2′,3′,5′-tri-O- benzoate. Mesylation of the major product (12) gave 1-(2′,5′-di-O-benzoyl-3′-O-mesyl-β-D- lyxofuranosyl)uracil (15), which, on treatment with sodium benzoate, gave 2 in an highly improved yield. Basic hydrolysis on 2 gave compound 16.     

Synthesis and characterization of lead(II) complexes with substituted 2,2′-bipyridines,trifluoroacetate, and furoyltrifluoroacetonate

Two substituted 2,2′-bipyridine lead(II) complexes, [Pb(5,5′-dm-2,2′-bpy)(tfac)₂] _n (1) (5,5′-dm-2,2′-bpy?=?5,5′-dimethyl-2,2′-bipyridine and tfac?=?trifluoroacetate) and [Pb₂(4,4′-dmo-2,2′-bpy)₂(ftfa)₄] (2) (4,4′-dmo-2,2′-bpy?=?4,4′-dimethoxy-2,2′-bipyridine and ftfa?=?furoyltrifluoroacetonate), have been synthesized and characterized by elemental analysis, IR, ¹H NMR, and ¹³C NMR spectroscopies, thermal behavior, and X-ray crystallography. Complexes 1 and 2 are 1D coordination polymer and dinuclear complex, respectively. The supramolecular features in these complexes are guided by weak directional intermolecular interactions.     

Mechanism of Formation of Ribonucleoside Cyclic 2′,3′-Phosphates in the Reaction of Appropriate 3′,5′-Phos-Phorothioates with Epoxides

Abstract

It has been recently demonstrated in our laboratory CD that ribonucleoside cyclic 3′,5′-phosphorothioates react with epoxides to give as a major product corresponding cyclic 5′,3′-phosphates, We now report the results OF our ste-reochemical studies OF this reaction. WE have Found that the diastereomerically pure (Sp) 3′.5′-CUFLPS when treated with styrene [¹⁰O]-oxide in ethanol gives the same isotopomer OF 2′,3′-[¹⁰O]cUMP as that obtained From the reaction of endo-2′.3′-cUMPS with styrene [¹⁰O]-oxide. This result strongly supports our previous assumption that reaction of 3′,5′-cNMPS with epoxides proceeds via 3′-oxathiaphosphorylated intermediate (L) which is Formed with inversion and decomposes to 2′,3′-cNMP with retention of configuration at phosphorus atom.     

Influence of methyl group position in bipyridine ligand on structure and luminescence of related zinc(II) nitrate complexes

Three new zinc(II) complexes of [Zn(6-mbipy)(η²-NO₃)₂] (1), [Zn(6,6′-dmbipy)(η²-NO₃)₂] (2) and [Zn(5,5′-dmbipy)(η²–NO₃)(H₂O)₂](NO₃).H₂O (3) were prepared from the reaction of 6-methyl-2,2′-bipyridine (6-mbipy), 6,6′-dimethyl-2,2′-bipyridine (6,6′-dmbipy) and 5,5′-dimethyl-2,2′-bipyridine (5,5′-dmbipy) with Zn(NO₃)₂·4H₂O in methanol, respectively. These three complexes were thoroughly characterized by elemental analysis, thermal gravimetric analysis, differential thermal analysis, infrared, UV–Vis, ¹H NMR and ¹³C{¹H} NMR spectroscopy, and their structures have all been determined by the single-crystal X-ray diffraction. The luminescence spectra of the title complexes show that the intensity of their emission bands is stronger than the bands for the free ligands.     

Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer

Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH₃)₂}₂(μ‐trans‐Pt(NH₃)₂{NH₂(CH₂)₆NH₂}₂)]⁴⁺ (BBR3464, 1 ), [{trans‐PtCl(NH₃)₂}₂(μ‐NH₂(CH₂)₆NH₂)]²⁺ (BBR3005, 2 ), [{trans‐PtCl(NH₃)₂}₂(μ‐H₂N(CH₂)₃NH₂(CH₂)₄)]³⁺ (BBR3571, 3 ) and [{trans‐PtCl(NH₃)₂}₂{μ‐H₂N(CH₂)₃‐N(COCF₃)(CH₂)₄}]²⁺ (BBR3571‐COCF₃, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [¹H, ¹⁵N] HSQC NMR spectroscopy studies of the reaction of [¹⁵N]‐ 1 with the sequence 5′‐d{TATACATGTATA}₂ allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)₂. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [¹⁵N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.