Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.     

Binding H2, N2, H-, and BH3 to transition-metal sulfur sites: synthesis and properties of [RuL(PR3)(N2Me2S2)] Complexes (L=eta2-H2, H-, BH3; R=Cy, iPr)

The reactions of [Ru(N₂)(PR₃)(‘N₂Me₂S₂’)] [‘N₂Me₂S₂’=1,2‐ethanediamine‐N,N′‐dimethyl‐N,N′‐bis(2‐benzenethiolate)(2?)] [ 1 a (R=iPr), 1 b (R=Cy)] and [μ‐N₂{Ru(N₂)(PiPr₃)(‘N₂Me₂S₂’)}₂] ( 1 c ) with H₂, NaBH₄, and NBu₄BH₄, intended to reduce the N₂ ligands, led to substitution of N₂ and formation of the new complexes [Ru(H₂)(PR₃)(‘N₂Me₂S₂’)] [ 2 a (R=iPr), 2 b (R=Cy)], [Ru(BH₃)(PR₃)(‘N₂Me₂S₂’)] [ 3 a (R=iPr), 3 b (R=Cy)], and [Ru(H)(PR₃)(‘N₂Me₂S₂’)]^? [ 4 a (R=iPr), 4 b (R=Cy)]. The BH₃ and hydride complexes 3 a , 3 b , 4 a , and 4 b were obtained subsequently by rational synthesis from 1 a or 1 b and BH₃?THF or LiBEt₃H. The primary step in all reactions probably is the dissociation of N₂ from the N₂ complexes to give coordinatively unsaturated [Ru(PR₃)(‘N₂Me₂S₂’)] fragments that add H₂, BH₄^?, BH₃, or H^?. All complexes were completely characterized by elemental analysis and common spectroscopic methods. The molecular structures of [Ru(H₂)(PR₃)(‘N₂Me₂S₂’)] [ 2 a (R=iPr), 2 b (R=Cy)], [Ru(BH₃)(PiPr₃)(‘N₂Me₂S₂’)] ( 3 a ), [Li(THF)₂][Ru(H)(PiPr₃)(‘N₂Me₂S₂’)] ([Li(THF)₂]‐ 4 a ), and NBu₄[Ru(H)(PCy₃)(‘N₂Me₂S₂’)] (NBu₄‐ 4 b ) were determined by X‐ray crystal structure analysis. Measurements of the NMR relaxation time T₁ corroborated the η² bonding mode of the H₂ ligands in 2 a (T₁=35 ms) and 2 b (T₁=21 ms). The H,D coupling constants of the analogous HD complexes HD‐ 2 a (¹J(H,D)=26.0 Hz) and HD‐ 2 b (¹J(H,D)=25.9 Hz) enabled calculation of the H? D distances, which agreed with the values found by X‐ray crystal structure analysis ( 2 a : 92 pm (X‐ray) versus 98 pm (calculated), 2 b : 99 versus 98 pm). The BH₃ entities in 3 a and 3 b bind to one thiolate donor of the [Ru(PR₃)(‘N₂Me₂S₂’)] fragment and through a B‐H‐Ru bond to the Ru center. The hydride complex anions 4 a and 4 b are extremely Brønsted basic and are instantanously protonated to give the η²‐H₂ complexes 2 a and 2 b .     

Solubility of (UO2)3(PO4)2?4H2O in H+-Na+-OH?-H2PO?4-HPO2?4-PO3?4-H2O and Its Comparison to the Analogous PuO2 +2 System

The objectives of this study were to address uncertainties in the solubility product of (UO₂)₃(PO₄)₂⋅4H₂O(c) and in the phosphate complexes of U(VI), and more importantly to develop needed thermodynamic data for the Pu(VI)-phosphate system in order to ascertain the extent to which U(VI) and Pu(VI) behave in an analogous fashion. Thus studies were conducted on (UO₂)₃(PO₄)₂⋅4H₂O(c) and (PuO₂)₃(PO₄)₂⋅4H₂O(am) solubilities for long-equilibration periods (up to 870 days) in a wide range of pH values (2.5 to 10.5) at fixed phosphate concentrations of 0.001 and 0.01 M, and in a range of phosphate concentrations (0.0001–1.0 M) at fixed pH values of about 3.5. A combination of techniques (XRD, DTA/TG, XAS, and thermodynamic analyses) was used to characterize the reaction products. The U(VI)-phosphate data for the most part agree closely with thermodynamic data presented in Guillaumont et al.,⁽¹⁾ although we cannot verify the existence of several U(VI) hydrolyses and phosphate species and we find the reported value for formation constant of UO₂PO⁻₄ is in error by more than two orders of magnitude. A comprehensive thermodynamic model for (PuO₂)₃(PO₄)₂⋅4H₂O(am) solubility in the H⁺-Na⁺-OH⁻-Cl⁻-H₂PO⁻₄-HPO²⁻₄-PO³⁻₄-H₂O system, previously unavailable, is presented and the data shows that the U(VI)-phosphate system is an excellent analog for the Pu(VI)-phosphate system.     

Synthesis and antimalarial effects of 5,6-dichloro-2-[(4-||4-(diethylamino)-i-methylbutyl] amino||-6-methyl-2-pyrirnidinyl)amino] benzimidazole and related benzimidazoles and lH-imidazo[4,5-b] pyridines

A group of fifty-five 2-[(4-11[(dialkylamino)alkyI]amino11-6-methyl-2-pyrimidinyl)amino]-benzimidazoles (VII) was synthesized in 3-88% yield by the condensation of the requisite 2-[(2-benzimidazolyl)amino]-4-chloro-6-methylpyrimidine (VI) with the appropriate polyamine in ethanol-hydrochloric acid or neat with excess amine containing potassium iodide. The 2-[(2-benzimidazolyl)amino]-6-methyl-4-pyrirnidinol precursors (V), obtained in 11-51% yield by cyclization of 2-(cyanoamino)-4-hydroxy-6-methylpyrimidine with a suitably substituted o-phenylenediamine, were chlorinated with phosphorus oxychloride to give the intermediate 2-[(2-benzimidazolyl)amino]-4-chloro-6-rnethylpyrimidines (VI) (27-99%). Oxidation of 5,6-dichloro-2-[(4-11[4-(diethylamino)-l-methylbutyl] amino 11-6-methyl-2-pyrimidinyl) amino ]benzimidazole ( 29 ) with m-chloroperbenzoic acid gave the distal N⁴'-oxide ( 31 ) (19%). Fusion of 2,3-uiaminopyridine with 2-(cyanoamino)-4-hydroxy-6-methylpyrimidine provided 2-[(4-hydroxy-6-tnethyl-2-pyrimidinyl)amino]-lH-imitlazo[4,5-b]pyrimidine (VIII) (30%), which upon chlori-nation with phosphorus oxychloride (63%) followed by amination with i N, N-diethylethylene-diamine afforded 2-(4-11[2-(diethylamino)ethyl] amino 11-6-methyl-2-pyrimidinyl)-lH-imidazo [4,5-b]pyridine (X) (8%). Thirty-eight of the novel 2-[(4-amino-6-methyl-2-pyrimidinyl)amino]-benzimidazoles possessed “curative” activity against Plasmodium berghei at single subcutaneous doses ranging from 20.640 mg./kg. Orally, thirty-one compounds exhibited suppressive activity against P. berghei comparable with or superior to the reference drugs 1-(p-chlorophenyl)-3-(4-11[2-(diethylarnino)ethyl]amino 11-6-methyl-2-pyrimidinyl)guanidine (I) and quinine hydrochloride, while twelve of them were 5 to 28 times as potent as I and quinine hydrochloride. Eight compounds also displayed strong suppressive activity against P. gallinaceum in chicks. 5,6-Dichloro-2-[(4-112-(diethylamino)ethyl]amino11-6-methyl-2-pyrimidinyl] benzimidazole (18) showed marked activity against a cycloguanil-resistant line of P. berghei, and the most promising member of the series, namely 5,6-dichloro-2-[(4-11[4-(diethylamino)-l-methylbutyl]amino11-6-methyl-2-pyrimidinyl)amino]benzimidazole ( 29 ) (Q = 28), was designated for preclinical toxico-logical studies and clinical trial. Structure-activity relationships are discussed.     

A comparison of performance of various analytical columns in pharmaceutical analysis: conventional C18 and high throughput C18 zorbax columns

New improved types of analytical columns Zorbax Eclipse XDB-C18 (75 mm x 4.6 mm i.d., 3.5 microm) and Zorbax Eclipse XDB-C18 (50 mm x 4.6 mm i.d., 1.8 microm) have been tested for determination of estradiol (active substance), methylparaben, propylparaben (preservatives) and estrone (degradation product) and compared with the conventional C18 columns (250 mm x 3.0 mm i.d., 5.0 microm). The Zorbax columns differ with their particle size, column length and ODS (octadecylsilica) type as well. Higher flow-rates (up to about 2.5 ml min(-1)) could be applied regardless to back-pressure. The analysis - previously done at 40 degrees C - could be performed even at ambient temperature. Analytical run was shortened to 3.5 min (from 12 min used for the conventional C18 column) with the same or better retention characteristics. System suitability data for all Zorbax columns show the advantages of these columns for the practical use in routine quality control of pharmaceuticals, particularly from the point of view of speed of analysis and solvent consumption.     

Binding N2, N2H2, N2H4, and NH3 to transition-metal sulfur sites: modeling potential intermediates of biological N2 fixation

In the quest for low-molecular-weight metal sulfur complexes that bind nitrogenase-relevant small molecules and can serve as model complexes for nitrogenase, compounds with the [Ru(PiPr(3))('N(2)Me(2)S(2)')] fragment were found ('N(2)Me(2)S(2)'(2-)=1,2-ethanediamine-N,N'-dimethyl-N,N'-bis(2-benzenethiolate)(2-)). This fragment enabled the synthesis of a first series of chiral metal sulfur complexes, [Ru(L)(PiPr(3))('N(2)Me(2)S(2)')] with L=N(2), N(2)H(2), N(2)H(4), and NH(3), that meet the biological constraint of forming under mild conditions. The reaction of [Ru(NCCH(3))(PiPr(3))('N(2)Me(2)S(2)')] (1) with NH(3) gave the ammonia complex [Ru(NH(3))(PiPr(3))('N(2)Me(2)S(2)')] (4), which readily exchanged NH(3) for N(2) to yield the mononuclear dinitrogen complex [Ru(N(2))(PiPr(3))('N(2)Me(2)S(2)')] (2) in almost quantitative yield. Complex 2, obtained by this new efficient synthesis, was the starting material for the synthesis of dinuclear (R,R)- and (S,S)-[micro-N(2)[Ru(PiPr(3))('N(2)Me(2)S(2)')](2)] ((R,R)-/(S,S)-3). (Both 2 and 3 have been reported previously.) The as-yet inexplicable behavior of complex 3 to form also the R,S isomer in solution has been revealed by DFT calculations and (2)D NMR spectroscopy studies. The reaction of 1 or 2 with anhydrous hydrazine yielded the hydrazine complex [Ru(N(2)H(4))(PiPr(3))('N(2)Me(2)S(2)')] (6), which is a highly reactive intermediate. Disproportionation of 6 resulted in the formation of mononuclear diazene complexes, the ammonia complex 4, and finally the dinuclear diazene complex [micro-N(2)H(2)[Ru(PiPr(3))('N(2)Me(2)S(2)')](2)] (5). Dinuclear complex 5 could also be obtained directly in an independent synthesis from 1 and N(2)H(2), which was generated in situ by acidolysis of K(2)N(2)(CO(2))(2). Treatment of 6 with CH(2)Cl(2), however, formed a chloromethylated diazene species [[Ru(PiPr(3))('N(2)Me(2)S(2)')]-micro-N(2)H(2)[Ru(Cl)('N(2)Me(2)S(2)CH(2)Cl')]] (9) ('N(2)Me(2)S(2)CH(2)Cl'(2-) =1,2-ethanediamine-N,N'-dimethyl-N-(2-benzenethiolate)(1-)-N'-(2-benzenechloromethylthioether)(1-)]. The molecular structures of 4, 5, and 9 were determined by X-ray crystal structure analysis, and the labile N(2)H(4) complex 6 was characterized by NMR spectroscopy.     

Ruthenium(II) complexes with ferrocene-modified arene ligands: synthesis and electrochemistry

A series of arene-ruthenium complexes of the general formula [RuCl₂{η⁶-C₆H₅(CH₂)₂R}L] with R=OH, CH₂OH, OC(O)Fc, CH₂OC(O)Fc (Fc=ferrocenyl) and L=PPh₃, (diphenylphosphino)ferrocene, or bridging 1,1^′-bis(diphenylphosphino)ferrocene, have been synthesized. Two synthetic pathways have been used for these ferrocene-modified arene-ruthenium complexes: (a) esterification of ferrocene carboxylic acid with 2-(cyclohexa-1,4-dienyl)ethanol, followed by condensation with RuCl₃ · nH₂O to afford [RuCl₂{η⁶-C₆H₅(CH₂)₂OC(O)Fc}]₂, and (b) esterification between ferrocene carboxylic acid and [RuCl₂{η⁶-C₆H₅(CH₂)₃OH}L] to give [RuCl₂{η⁶-C₆H₅(CH₂)₃OC(O)Fc}L]. All new compounds have been characterized by NMR and IR spectroscopy as well as by mass spectrometry. The single-crystal X-ray structure analysis of [RuCl₂{η⁶-C₆H₅(CH₂)₃OH}(PPh₃)] shows that the presence of a CH₂CH₂CH₂OH side-arm allows [RuCl₂{η⁶-C₆H₅(CH₂)₃OH}(PPh₃)] to form an intramolecular hydrogen bond with a chlorine atom. The electrochemical behavior of selected representative compounds has been studied. Complexes with ferrocenylated side arms display the expected cyclic voltammograms, two independent reversible one-electron waves of the Ru(II)/Ru(III) and Fe(II)/Fe(III) redox couples. Introduction of a ferrocenylphosphine onto the ruthenium is reflected by an additonal reversible, one-electron wave due to ferrocene/ferrocenium system which is, however, coupled with the Ru(II)/Ru(III) redox system.     

Capillary ion chromatography

This review summarizes progress in capillary ion chromatography. Theoretical aspects and practical limitations of packed and open tubular capillary columns are considered. Applications of packed and open tubular capillary IC are described. Emerging technologies such chip-scale IC and the use of monolithic columns are discussed.     

Utilization of cleavage of the [1]benzofuro[2,3‐e][1,2,4]triazine ring for the synthesis of oxygen,nitrogen and sulfur derivatives of [1,2,4]triazine

A series of 6‐azacytosines 4a‐4k and 5a‐5c were prepared by nucleophilic cleavage of furan ring of [1]benzofuro[2,3‐e][1,2,4]triazine derivative 1 . Some of them were used for the preparation of derivatives of [1,2,4]triazolo[4,3‐d][1,2,4]triazine ( 6a‐6d ) and tetrazolo[1,5‐d][1,2,4]triazine (7). The reaction of 1 with hydrogen sulfide afforded the corresponding 6‐(2‐hydroxyphenyl)‐2‐phenyl‐5‐thioxo‐4,5‐dihydro‐1,2,4‐tri‐azin‐3(2H)‐one ( 8 ), while with hydrogen selenide 6‐(2‐hydroxyphenyl)‐2‐phenyl‐4,5‐dihydro‐1,2,4‐triazin‐3(2H)‐one ( 9 ) was formed. The prepared compounds were tested for biological activity.     

Toward the development of new photolabile protecting groups that can rapidly release bioactive compounds upon photolysis with visible light

The synthesis and characterization of a new photolabile protecting group (caging group) for carboxylic acids, the 2-(dimethylamino)-5-nitrophenyl (DANP) group, is described. This compound has a major absorption band in the visible wavelength region with a maximum near 400 nm (epsilon400 = 9077 M(-1) cm(-1) at pH 7.4 and 21 degrees C). The caging group is attached through an ester linkage to the carboxyl functionality of beta-alanine, which activates the inhibitory glycine receptor in the mammalian central nervous system. Such caged compounds play an important role in transient kinetic investigations of fast cellular processes. Upon photolysis of DANP-caged beta-alanine, the caging group is released within 5 micros. Quantum yields of 0.03 and 0.002 were obtained in the UV region (308 and 360 nm) and the visible region (450 nm), respectively. Laser-pulse photolysis experiments, using 337 or 360 nm light, were performed with the caged compound equilibrated with HEK 293 cells transiently transfected with cDNA encoding the alpha1 homomeric, wild-type glycine receptor. The experiments demonstrated that neither DANP-caged beta-alanine nor its byproducts inhibit or activate the glycine receptors on the cell surface. Under physiological conditions, the DANP-caged beta-alanine is water-soluble and stable and can be used for transient kinetic measurements.