Synthesis and characterization of a [3-15N]-labeled cis-syn thymine dimer-containing DNA duplex

Cis-syn thymine dimers are the major photoproducts of DNA and are the principal cause of mutations induced by sunlight. To better understand the nature of base pairing with cis-syn thymine dimers, we have synthesized a decamer oligodeoxynucleotide (ODN) containing a cis-syn thymine dimer labeled at the N3 of both T's with 15N by two efficient routes from [3-15N]-thymidine phosphoramidite. In the postsynthetic irradiation route, an ODN containing an adjacent pair of [3-15N]-labeled T's was irradiated and the cis-syn dimer-containing ODN isolated by HPLC. In the mixed building block route, a mixture of cis-syn and trans-syn dimer-containing ODNs was synthesized from a mixture of [3-15N]-labeled thymine dimer phosphoramidites after which the cis-syn dimer-containing ODN was isolated by HPLC. The N3-nitrogen and imino proton signals of an (15)N-labeled thymine dimer-containing decamer duplex were assigned by 2D 1H-15N heterocorrelated HSQC NMR spectroscopy, and the 15N-1H coupling constant was found to be 1.8 Hz greater for the 5'-T than for the 3'-T. The larger coupling constant is indicative of weaker H-bonding that is consistent with the more distorted nature of the 5'-base pair found in solution state NMR and crystallographic structures.     

Use of 13C as an indirect tag in 15N specifically labeled nucleosides. Syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues

We have previously reported the use of a 13C tag at the C2 of 15N-multilabeled purine nucleosides to distinguish the adjacent-labeled 15N atoms from those in an untagged nucleoside. We now introduce the use of an indirect tag at the C8 of 15N7-labeled purine nucleosides. This tag allows unambiguous differentiation between a pair of 15N7-labeled purines in which only one is 13C8 labeled. Although the very small C8-N7 coupling (<1 Hz) precludes its direct detection in 1D 15N spectra, 2D 1H-15N NMR experiments display the large C8-H8 coupling (>200 Hz) because H8 is coupled to both N7 and C8. The 13C8 atom is introduced by means of a ring closure of the exocyclic amino groups of a pyrimidinone using [13C]sodium ethyl xanthate. Here, we present methods for the syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues.     

Complete 1H, 13C and 15N NMR assignment of tirapazamine and related 1,2,4-benzotriazine N-oxides

1H, 13C and 15N NMR measurements (1D and 2D including 1H--15N gs-HMBC) have been carried out on 3-amino-1, 2,4-benzotriazine and a series of N-oxides and complete assignments established. N-Oxidation at any position resulted in large upfield shifts of the corresponding N-1 and N-2 resonances and downfield shifts for N-4 with the exception of the 3-amino-1,2,4-benzotriazine 1-oxide in which a small upfield shift of N-4 was observed. Density functional GIAO calculations of the 15N and 13C chemical shifts [B3LYP/6-31G(d)//B3LYP/6-311+G(2d,p)] gave good agreement with experimental values confirming the assignments. The combination of 13C and 15N NMR provides an unambiguous method for assigning the 1H and 13C resonances of N-oxides of 1,2,4-benzotriazines.     

Evidence for the production of N4 via the N2 A3Sigma(u)+ + N2 A3Sigma(u)+ energy pooling reaction

We report mass spectrometric evidence supporting our proposed mechanistic pathway for the production of N4 through the energy pooling reaction N2 A3Sigma(u)+ + N2 A3Sigma(u)+. N2 A3Sigma(u)+ is generated from the quenching of resonantly excited xenon in a mixture of xenon, 15N2, and 14N2 that is illuminated with xenon resonant lamps (147 nm). Mass spectra are periodically taken of the mixture. Over time, we observe significant isotopic scrambling of the 15N2 and 14N2, generating 15N14N in concentrations approaching 10% (approximately 2 Torr) of the initial 15N2 concentration. Though we do not observe the direct formation of N4, the isotopic ratios indicate that an excited complex (15N2(14)N2) exists long enough so that scrambling of the nitrogen atoms can occur, offering a possible route to the formation of tetrahedral nitrogen (1Td N4).     

Synthesis and applications of [1-(15)N]-labeled 4,6-dimethyl-4H-[1,2,5]oxadiazolo[3,4-d]pyrimidine-5,7-dione 1-oxide as a useful tool for mechanistic investigations

[1-(15)N]-Labeled 4,6-dimethyl-4H-[1,2,5]oxadiazolo[3,4-d]pyrimidine-5,7-dione 1-oxide (1-(15)N1) was easily prepared by nitration of commercially available 6-amino-1,3-dimethyl-1H-pyrimidine-2,4-dione using 15N-enriched nitric acid followed by an intramolecular oxidative cyclization with iodosylbenzene diacetate under mild conditions. On the basis of the experimental results using 1-(15)N1, the formation of 8-phenyltheophylline (3), the 1,3-dimethylalloxazines (4: n = 0, 1), and 1,3,7,9-tetramethyl-1H,9H-pyrimido[5,4-g]pteridine-2,4,6,8-tetraone++ + (5) in the thermal reaction of the N-oxide 1 with benzylamine, aniline, or piperidine, and the generation of NO or NO-related species in the reaction with N-acetylcysteamine were reasonably explained by considering the initial attack of the employed nucleophiles on the 3a-position of 1.     

Reactions of N,N'-Dimethyl-N,N'-bis(trimethylsilyl)methylphosphonic Diamide with Chloral and Chloromethyldimethylchlorosilane

N,N'-Dimethyl-N,N'-bis(trimethylsilyl)methylphosphonic diamide reacts with chloral to form 1,2,3-trimethyl-4,4-dichloro-5-trimethylsiloxy-1,3,2-diazaphospholidine 2-oxide and with chloromethyldi- methylchlorosilane to form 1,2,3,4,4-pentamethyl-1,3-diaza-2-phospha-4-silacyclopentane 2-oxide.     

A FLUOROGENIC ACTINOMETER FOR NUCLEIC ACID PHOTOCHEMISTRY UTILIZING 1-DEAZAPURINE N(3)-OXIDES

A convenient and very sensitive actinometery system for UV radiation with wavelengths in the range250–310 nm is described, which is based on the fluorogenic photorearrangement of 1-deazapurine N(3)-oxide. The product, 1-deazapruin-2-one, can be estimated fluoremetrically in the presence of the N-oxide of 1-deazapurine and 1-methyl-1-deazapurine fail in the range 0.13-0.15 and do not vary significantly with wavelength. There is potential for using 1-deazupurine N(3)-oxides as UV-photoactivable fluorophores.     

Optimized synthesis of [3-N]-labeled uridine phosphoramidites

A short and high-yielding synthetic route to [3-¹⁵N]-labeled uridine phosphoramidite 1 (26% overall yield from uridine) has been developed. This will enable automated synthesis of isotopically labeled RNA strands and facilitate their use in structural studies.     

Computation of aromatic C3N4 networks and synthesis of the molecular precursor N(C3N3)3Cl6

The successful synthesis and structural characterization of molecules that represent segments of extended solids is a valuable strategy for learning metric and stereochemical characteristics of those solids. This approach has been useful in cases in which the solids are particularly difficult to crystallize and thus their atomic connectivity and overall structures become difficult to deduce with X-ray diffraction techniques. One such class of materials is the covalently linked C(x)N(y) extended solids, where molecular analogues remain largely absent. In particular, structures of C(3)N(4) solids are controversial. This report illustrates the utility of a simple molecule, N(C(3)N(3))(3)Cl(6), in answering the question of whether triazine based C(3)N(4) phases are layered or instead they adopt 3D structures. Here, we present density functional calculations that clearly demonstrate the lower stability of graphitic C(3)N(4) relative to 3D analogues.     

Probing platinum azido complexes by 14N and 15N NMR spectroscopy

Metal azido complexes are of general interest due to their high energetic properties, and platinum azido complexes in particular because of their potential as photoactivatable anticancer prodrugs. However, azido ligands are difficult to probe by NMR spectroscopy due to the quadrupolar nature of (14)N and the lack of scalar (1)H coupling to enhance the sensitivity of the less abundant (15)N by using polarisation transfer. In this work, we report (14)N and (15)N NMR spectroscopic studies of cis,trans,cis-[Pt(N(3))(2)(OH)(2)(NH(3))] (1) and trans,trans,trans-[Pt(N(3))(2)(OH)(2)(X)(Y)], where X=Y=NH(3) (2); X=NH(3), Y=py (3) (py=pyridine); X=Y=py (4); and selected Pt(II) precursors. These studies provide the first (15)N NMR data for azido groups in coordination complexes. We discuss one- and three-bond J((15)N,(195)Pt) couplings for azido and am(m)ine ligands. The (14)N(α) (coordinated azido nitrogen) signal in the Pt(IV) azido complexes is extremely broad (W(1/2)≈2124 Hz for 4) in comparison to other metal azido complexes, attributable to a highly asymmetrical electric field gradient at the (14)N(α) atom. Through the use of anti-ringing pulse sequences, the (14)N NMR spectra, which show resolution of the broad (14)N(α) peak, were obtained rapidly (e.g., 1.5 h for 10 mM 4). The linewidths of the (14)N(α) signals correlate with the viscosity of the solvent. For (15) N-enriched samples, it is possible to detect azido (15)N resonances directly, which will allow photoreactions to be followed by 1D (15)N NMR spectroscopy. The T(1) relaxation times for 3 and 4 were in the range 5.7-120 s for (15)N, and 0.9-11.3 ms for (14)N. Analysis of the (1)J((15)N,(195)Pt) coupling constants suggests that an azido ligand has a moderately strong trans influence in octahedral Pt(IV) complexes, within the series 2-pic相似文献   

Synthesis of 15N-enriched pseudouridine derivatives

[reaction: see text]. A procedure for the chemical synthesis of [3-15N]-labeled pseudouridine and a methylated derivative was developed. A suitably protected pseudouridine precursor was nitrated at N3 followed by treatment with 15NH4Cl to afford the 15N-labeled product in six steps with a 20% yield. This methodology will allow for the production of RNAs with [3-15N]pseudouridine and [3-15N-methyl]pseudouridine at specific locations.     

Vibrational spectra and structure of 4-amino-1H-quinazolin-2-one 3-oxide

On the basis of a study of the vibrational spectra in the solid state of the product of the reaction of 2-cyanophenyl isocyanate with hydroxylamine and its isotopic analogs (¹⁵N O and ¹⁵NH₂) it was demonstrated that the compound obtained has the 4-amino-1H-quinazolin-2-one 3-oxide structure.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 968–972, July, 1981.     

Crystal structures of two polymorphs of Ca3[Al2N4

Green transparent single crystals of alpha-Ca3[Al2N4] (monoclinic, P2(1)/c, No. 14, a = 957.2(3) pm, b = 580.2(3) pm, c = 956.3(5) pm, beta = 111.62(3) degrees; Z = 4) were obtained from reactions of mixtures of the representative metals with nitrogen above temperatures of 1000 degrees C. beta-Ca3[Al2N4] (monoclinic, C2/c, No. 15, a = 1060.6(2) pm, b = 826.0(2) pm, c = 551.7(1) pm, beta = 92.1(1) degrees; Z = 4) was formed as a byproduct of a reaction of calcium with alumina under nitrogen at T = 930 degrees C in form of colorless crystals. The crystal structures of the two polymorphs contain edge- and corner-sharing AlN4 tetrahedra, leading to different layered anionic partial structures: infinity 2[AlN2/2N2/3)2(AlNN2/2N1/3)6/3(12-)] in the alpha-phase and infinity 2[Al2N2N4/2(6-)] in the beta-polymorph.     

First structural characterization of neutral, base-stabilized group 15-pentaazides: single crystal X-ray structures of dmap-As(N3)5 and dmap-Sb(N3)5

Two neutral group 15-pentaazides dmap-As(N(3))(5) (1) and dmap-Sb(N(3))(5) (2) were synthesized and structurally characterized for the first time (dmap = 4-dimethylaminopyridine). Base-stabilization was confirmed to be very suitable for the kinetic stabilization of highly explosive covalent main group polyazides.     

Hydroxide-promoted redox reactions in water of α-Phenyl-4-nitro-benzenemethanol, α-(p-Nitrophenyl)-4-pyridinemethanol,and α-(p-Nitrophenyl)-4-Pyridinemethanol N-Oxide steric inhibition of resonance

α-Phenyl-4-nitrobenzenemethanol ( 3 ) reacted with 1 M sodium hydroxide to yield 4, 4′-dibenzoyl-azoybenzene ( 5 ) (51%), 4-hydroxy-4′-benzoylazobenzene ( 6 ) and benzoic acid (12% each), and smaller amounts of 4-aminobenzophenone and 4-nitrobenzophenone. Both α-phenyl-2-nitrobenzenemethanol ( 9 ) and 3, 5-dimethyl-4-nitrobenzenemethanol ( 10a ) did not react with 1 M sodium hydroxide, presumably due to steric hindrance. α-(p-Nitrophenyl)-4-pyridinemethanol ( 14 ) and its N-oxide 11 with 1 M sodium hydroxide yielded 4,4′-diaroylazoxybenzenes 15a and 12a , respectively, 4,4′-diaroylazobenzenes 15b and 12b , respectively, as well as 4-hydroxy-4′-aroylazobenzenes 16 and 13 , respectively. The relative reaction rates were 11 > 14 > 3 . Studies with 11 showed that the nitro group is involved in the redox reaction in preference to the N-oxide group.     

Iodide, azide, and cyanide complexes of (N,C), (N,N), and (N,O) metallacycles of tetra- and pentavalent uranium

In contrast to the neutral macrocycle [UN*(2)(N,C)] (1) [N* = N(SiMe(3))(3); N,C = CH(2)SiMe(2)N(SiMe(3))] which was quite inert toward I(2), the anionic bismetallacycle [NaUN*(N,C)(2)] (2) was readily transformed into the enlarged monometallacycle [UN*(N,N)I] (4) [N,N = (Me(3)Si)NSiMe(2)CH(2)CH(2)SiMe(2)N(SiMe(3))] resulting from C-C coupling of the two CH(2) groups, and [NaUN*(N,O)(2)] (3) [N,O = OC(═CH(2))SiMe(2)N(SiMe(3))], which is devoid of any U-C bond, was oxidized into the U(V) bismetallacycle [Na{UN*(N,O)(2)}(2)(μ-I)] (5). Sodium amalgam reduction of 4 gave the U(III) compound [UN*(N,N)] (6). Addition of MN(3) or MCN to the (N,C), (N,N), and (N,O) metallacycles 1, 4, and 5 led to the formation of the anionic azide or cyanide derivatives M[UN*(2)(N,C)(N(3))] [M = Na, 7a or Na(15-crown-5), 7b], M[UN*(2)(N,C)(CN)] [M = NEt(4), 8a or Na(15-crown-5), 8b or K(18-crown-6), 8c], M[UN*(N,N)(N(3))(2)] [M = Na, 9a or Na(THF)(4), 9b], [NEt(4)][UN*(N,N)(CN)(2)] (10), M[UN*(N,O)(2)(N(3))] [M = Na, 11a or Na(15-crown-5), 11b], M[UN*(N,O)(2)(CN)] [M = NEt(4), 12a or Na(15-crown-5), 12b]. In the presence of excess iodine in THF, the cyanide 12a was converted back into the iodide 5, while the azide 11a was transformed into the neutral U(V) complex [U(N{SiMe(3)}SiMe(2)C{CHI}O)(2)I(THF)] (13). The X-ray crystal structures of 4, 7b, 8a-c, 9b, 10, 12b, and 13 were determined.     

First Synthesis of 3-Mercapto-2(1H)-pyridinone, a Simple Disubstituted Pyridine Useful for Synthesis of the 4-Azaphenoxathiine Ring System and Its Novel Diazaphenoxathiine Analogs: 1,6-Diazaphenoxathiine and 2,6-Diazaphenoxathiine(1)

3-Mercapto-2(1H)-pyridinone (1) can be synthesized in three simple high-yielding steps from readily available 2-tert-butylthiazolo[4,5-b]pyridine (2). Its disodium salt condenses with o-chloronitrobenzene, 2-chloro-3-nitropyridine, and 3-chloro-4-nitropyridine 1-oxide to give respectively 4-azaphenoxathiine (10), 1,6-diazaphenoxathiine (12), and 2,6-diazaphenoxathiine 2-oxide (14) which reduces to 2,6-diazaphenoxathiine (15). The structures of these previously unreported azaphenoxathiine systems were confirmed by assignment of their respective (13)C NMR spectra.     

Absence of triazirine intermediates in the photolytic formation of azides from mesoionic 3-substituted 1,2,3,4-oxatriazolylio-5-oxides : Isotope labelling experiments

Irradiation of 3-phenyl-1,2,3,4-oxatriazolylio-5-oxide (1) leads to formation of CO₂, N₂O, phenyl azide and phenyl isocyanate. The two latter compounds are observed only in low yields because of secondary photolytic reactions. Photolysis in CCl₄ or Cl₂CCCl₂ of 2-¹⁵N labelled (1) leads almost exclusively to the formation of 3-¹⁵H labelled phenyl azide identified by IR spectroscopy on comparison with authentic 1-¹⁵N, 2-¹⁵N and 3-¹⁵N labelled phenyl azides, respectively. These results show that phenyl azide is formed photolytically from (1) via phenyl migration and not via “antiaromatic”, phenyl triazirine (2).     

Synthesis of 1D {Cu6(mu3-SC3H6N2)4(mu-SC3H6N2)2(mu-I)2I4}n and 3D {Cu2(mu-SC3H6N2)2(mu-SCN)2}n polymers with 1,3-imidazolidine-2-thione: bond isomerism in polymers

The reaction of copper(I) iodide with 1, 3-imidazolidine-2-thione (SC3H6N2) in a 1:2 molar ratio (M/L) has formed unusual 1D polymers, {Cu6(mu3-SC3H6N2)4(mu-SC3H6N2)2(mu-I)2I4}n (1) and {Cu6(mu3-SC3H6N2)2(mu-SC3H6N2)4(mu-I)4I2}n (1a). A similar reaction with copper(I) bromide has formed a polymer {Cu6(mu3-SC3H6N2)2(mu-SC3H6N2)4(mu-Br)4Br2}n (3a), similar to 1a, along with a dimer, {Cu2(mu-SC3H6N2)2(eta1-SC3H6N2)2Br2} (3). Copper(I) chloride behaved differently, and only an unsymmetrical dimer, {Cu2(mu-SC3H6N2)(eta1-SC3H6N2)3Cl2} (4), was formed. Finally, reactions of copper(I) thiocyanate in 1:1 or 1:2 molar ratios yielded a 3D polymer, {Cu2(mu-SC3H6N2)2(mu-SCN)2}n (2). Crystal data: 1, C9H18Cu3I3N6S3, triclinic, P, a = 9.6646(11) A, b = 10.5520(13) A, c = 12.6177(15) A, alpha = 107.239(2) degrees , beta = 99.844(2) degrees , gamma = 113.682(2) degrees , V = 1061.8(2) A(3), Z = 2, R = 0.0333; 2, C(4)H(6)CuN(3)S(2), monoclinic, P2(1)/c, a = 7.864(3) A, b = 14.328(6) A, c = 6.737(2) A, beta = 100.07(3) degrees , V = 747.4(5), Z = 4, R = 0.0363; 3, C12H24Br2Cu2N8S4, monoclinic, C2/c, a = 19.420(7) A, b = 7.686(3) A, c = 16.706(6) A, beta = 115.844(6) degrees , V = 2244.1(14) A(3), Z = 4, R = 0.0228; 4, C12H24Cl2Cu2N8S4, monoclinic, P2(1)/c, a = 7.4500(6) A, b = 18.4965(15) A, c = 16.2131(14) A, beta = 95.036(2) degrees , V = 2225.5(3) A(3), Z = 4, R = 0.0392. The 3D polymer 2 exhibits 20-membered metallacyclic rings in its structure, while synthesis of linear polymers, 1 and 1a, represents an unusual example of I (1a)-S (1) bond isomerism.     

Catalytic two-electron reductions of N2O and N3- by myoglobin in surfactant films

Myoglobin (Mb), in films of dimethyldidodecylammonium bromide (ddab) on graphite electrodes, is used as a catalyst to mediate the electrochemical reduction of nitrous oxide (N2O) as well as the isoelectronic ion azide (N3-) in aqueous solutions. The electrocatalytic reductions are characterized by a rate-dependent irreversibility in cyclic voltammograms of Mb/ddab in the presence of the substrates. Bulk electrolysis shows that the reduction of 15N15NO by Mb/ddab yields 15N15N as shown by GC/MS. The catalytic reduction of azide results in almost quantitative formation of ammonia. These electrocatalytic processes are rationalized as two-electron reductions, with the catalyst cycling between the Fe(I) and Fe(III) states of Mb. To our knowledge, this is the first characterization of N2O reduction by an Fe porphyrin or heme protein.