Formation of dinitrophenoxide ion from 2,4- and 2,6-dinitrochlorobenzene (2,4- and 2,6-DNCB) and OH − (OD − ) in 70:30 and 80:20 (v/v) DMSO−H 2 O (D 2 O) is accompanied by extensive 1 H NMR line broadening of unreacted substrate and exchange of arene hydrogen with D 2 O, which is quantitative at the 3-position of 2,4-DNCB. Unproductive Meisenheimer complexes are detected spectrophotometrically in the course of reaction. For reaction of 2,4-DNCB, the Meisenheimer 3-complex is formed first and then the more stable 5-complex can be detected and characterized by NMR spectrometry. There is no hydrogen exchange of Meisenheimer complexes or dinitrophenoxide ions and their 1 H NMR signals are not broadened. These results do not fit the classical mechanism of single-step nucleophilic addition, but they, and the kinetic results, are fitted by a reaction scheme involving single-electron transfer from OH − to give a charge-transfer complex of OH • and a radical anion which collapses to give Meisenheimer complexes and aryl oxide ion

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Complexes of Co(III)bis(phenanthroline) with β-d-mannosamine and α-d-galactosamine can be isolated as the triiodide salts. The complex with d-mannosamine has the Δ-configuration at Co(III). Complexation with d-galactoamine gives the Δ- in excess over the Λ- complex, and the Δ-complex can be isolated chromatographically. Complexation involves cis-1-OH and 2-NH2 groups, eq, ax respectively with β-mannosamine and ax, eq respectively, with α-galactosamine, as with α-glucosamine, based on 1H NMR spectra. Galactosamine complexes in aqueous solution decompose to the free sugar, but the mannosamine complex is much more stable.

Peroxymonosulfate ion, HSO−5, as Oxone, readily converts phosphorus(V) esters of thiols into the phosphorus(V) and sulfonic acids. The esters were Ph2PO·SC6H4R(p) with R=MeO (1a), Me (1b), H (1c), Cl (1d) and NO2 (1e), (EtO)2PO · SPh (2), Ph2OI · SEt (3) and PhPO(OEt)SEt (4). Reactions are first order in each reactant and second-order rate constants, k2, for 1a–e fit the Hammett equation with ρ=−0.46. The rate constants increase markedly with increasing water content of H2O–MeCN, the activation enthalpies are low and the entropies are negative. Despite the low value of −ρ, these esters are much less reactive than thiol ethers, but the rate constants of reactions of these compounds and acyl thiols qualitatively follow the ionization potentials of the ethers and the esters. © 1997 John Wiley & Sons, Ltd.

A novel polyazacyclophane hexa-amine (1) has been designed, synthesized and characterized by X-ray crystallography, 1H NMR and fluorescence spectroscopy. 1 has the structural shape and disposition of charges complementary to the major groove of B-DNA. Acid dissociation constants for the protonated 1 were pKa1(D) = 4.8 and pKa2(D) = 8.5. Equilibrium constants for the binding of 1 to ctDNA and T4 DNA were 1.2 × 105 and 1.8 × 106, respectively.

The central pyrrole of a site-selective DNA minor groove binding tripyrrole peptide 1 has been attached to a branched decaaza decabutylamine via a -(CH2)3-NHCO-(CH2)3- linker to provide the decaaza-microgonotropen (8). The decaaza decabutylamine moiety of 8 was designed to have a much greater affinity to the phosphodiester linkages of the backbone of DNA. Employing Hoechst 33258 (Ht) as a fluorescent titrant, the equilibrium constants for the binding of 8 to the hexadecameric duplex d(GGCGCA3T3GGCGG)/d(CCGCCA3T3GCGCC) and to calf thymus DNA were determined. The log of the product of equilibrium constants (log K1.1K1.2) for 1:1 and 1:2 complexes formation at A3T3 is 17 (35°C). Results of studies of the inhibition of the binding of several proteins to target DNA are discussed. Binding of the E2F1 transcription factor to its DNA target is 50% inhibited at ∼2 nM concentration of 8.

D-beta-Mannosamine reacts with cobalt(III) bis-phenanthroline to form a single 1:1 complex with the Delta configuration. at Co(III) which can be isolated as the stable tri-iodide salt.

Short strand DNA oligomers (A5G3A5, GA4G3A4G, G2A3G3A3G2, and G2A2G5A2G2) and the guanidinium (g) linked thymidyl nucleoside d(Tg)4-T-azido associate as triplexes. The melting temperatures, Tm, the association and dissociation kinetic and thermodynamic parameters and activation energies for the triplexes were determined by UV thermal analysis. The hypochromic shift and Tm for triplex formation increases with increase in concentration and decreases with the number of mismatches. The melting temperatures are between 35 and 55 degrees C in the range of ionic strength of 0.06-0.24 and decrease with increase in ionic strength at 100 deg/(ionic strength unit). The melting and cooling curves exhibit hysteresis behavior in the temperature range 5-95 degrees C at 0.2 deg/min thermal rate. From these curves, the rate constants and the energies of activation for association (k(on), E(on)) and dissociation (k(off), E(off)) processes were obtained. The second-order rate constants, k(on), for the triplex formation at 288 K are between 10 and 500 M(-2) s(-1). Values of k(on) increase with the decrease in the ionic strength. The first order rate constants for the dissociation, k(off), at 288 K are between 10(-6) and 40 x 10(-6) s(-1) and increase with increase in ionic strength. The energies of activation for the association and dissociation processes are in the range -22 to -9 kcal/mol and 8 to 29 kcal/mol, respectively. At 6.3 x 10(-5) M/base and at the physiological ionic strength (0.15-0.30) and below, the triplex structures formed with d(Tg)4-T-azido and A5G3A5 and GA4G3A4G have well-defined Tm values. The melting curves with G2A3G3A3G2 and G2A2G5A2G2 are very shallow with small hypochromic shifts denoting negligible binding at physiological ionic strength. Therefore, with the increase in the G content (mismatched base pairs) at a certain concentration (e.g., 6.3 x 10(-5) M/base), discrimination (change in fidelity) occurs in the formation and strength of binding of d(Tg)4-T-azido to d(pAn pGm) oligomers. The standard molar enthalpies for triplex formation have in general larger negative values at low ionic strength than at high ionic strength, indicating that at lower mu values the formation of triplexes of d(Tg)4-T-azido with d(pAn pGm) are more favorable. The values of deltaH(standard)(288) calculated from the activation parameters are between -17 and -49 kcal/mol, and the values of deltaG(standard)(288) are between -7.5 and -11.8 kcal/mol for A5G3A5, GA4G3A4G, G2A3G3A3G2, and G2A2G5A2G2, respectively. There is a linear relationship in the enthalpy-entropy compensation for the triplex melting thermodynamics.

Acid dissociation constants of α- and β-d-glucos-, mannos-, and galactos-ammonium ions have been determined from 1H NMR chemical shifts of the individual anomers in D2O. Values of pKa(D) for the α- and β-ammonium ions are, respectively: glucosamine, 8.12 and 7.87, mannosamine, 7.78 and 8.50, galactosamine, 8.49 and 8.02. The differences are ascribed largely to differences in the hydration requirements of ammonium and amino groups in the axial and equatorial positions and hydration at upper and lower faces of the sugars. Acid dissociation constants of the 1-hydroxyl group of nonionic d-glucosamine and d-glucose are higher for the β than the α anomer.

Hydroxamic acids and their anions exhibit geometrical isomerism due to amide-like resonance and an increase in the C-N bond order which can be monitored by H-1-NMR spectroscopy. N-Phenylpropiono- and dodecanohydroxamic acids, la and 2a, respectively, exist as E-isomers in DMSO-d(6) and CD3OD but la is an E-Z mixture in D2O. The corresponding hydroxamate ions, Ib and 2b, also exist as E-isomers in DMSO-d(6), but Z-isomers form on addition of D2O and Z-2b is dominant with chi(D2O) greater than or equal to 0.9. In CD3OD E- and Z-isomers coexist, but Z-2b becomes dominant on addition of D(2)0. The E:Z ratio of Ih is very similar in cetyltrimethylammonium bromide (CTABr) and in D2O, but only Z-2b is detected in cationic CTABr micelles and in anionic, zwitterionic, and nonionic micelles. Formation of Z-2b in micelles and water-rich mixed solvents is favored by hydrophobic interactions between phenyl and n-alkyl groups, despite the proximity of anionoid oxygens. In micelles of sodium dodecyl sulfate the N-phenyl residue of 2b is in a more aqueous region of the micelle-water interface than in micelles of the other surfactants.

Complementary short-strand DNA homooligomers and guanidinium-linked homonucleosides associate and form triplexes in solution, The melting temperatures, T-m the association and dissociation kinetic and thermodynamic parameters, and activation energies were determined by UV thermal analysis for the triplexes of short strand DNA homooligomers {d(pA)(5)-d(pA)(12-18)} and poly(dA) with the guanidinium-linked nucleoside d(Tg)(4)-T-azido {DNG(5)}. The melting and cooling curves exhibit hysteresis behavior in the temperature range of 5-95 degrees C at 0.2 deg/min thermal rate, From these curves the rate constants and the energies of activation for association (k(on), E(on)) and dissociation (k(off), E(off)) processes were obtained, The T-m decreases with the ionic strength and increases slightly with increase in concentration of the monomers, A greater increase in the T-m results from an increase in the length of the DNA strand d(pA)(x). En the case of d(pA)(5) and d(pA)(6), triplexes are formed, with T-m = 34 and 39 degrees C, respectively, only above 0.063 mM/(adenine base) concentration when ionic strength is 0.08. The rate constants k(on) and k(off) at a reference temperature (258 K) are dependent on the DNA strand length and also decrease and increase respectively with the ionic strength. The energies of activation for the association and dissociation processes are in the range of -10 to -50 and 17 to 44 kcal/mol, respectively. The equilibrium for the formation of the triplexes {(d(Tg)(4)-T-azido)(2) . d(pA)(x), x = 5-10)} is favored by several orders of magnitude when compared to the triplexes of DNA. The standard molar enthalpies for tripler formation have larger negative values at low ionic strength than at high ionic strength indicating that at lower mu values the formation of triplexes of d(Tg)(4)-T-azido with d(pA)(x) is more favored. The values of Delta H degrees(288) calculated from the activation parameters are between -30 and -60 kcal/(mol base) and the Values of Delta G degrees(288) are between -8 and -13 kcal/(mol base) for short-strand DNA. There is a linear relationship in the enthalpy-entropy compensation for the triplex-melting thermodynamics.

The central pyrrole of a site-selective DNA minor groove binding tripyrrole peptide (1) has been attached to N-protected pentaazapentacosanoic acid (17) via a -(CH2)3-NHCO-(CH2)3- linker to provide 19, subsequent deprotection provided the pentaaza microgonotropen 4. The polyamine moiety of 4 reaches out of the minor groove and binds to the phosphate backbone of DNA. We find when employing Hoechst 33258 (Ht) as a fluorescent titrant to follow binding of 4 to the hexadecameric duplex d(GGCGCAAATTTGGCGG)/(CCGCCAAATTTGCGCC) and by 1H NMR titration of d(CGCAAATTTGCG)2 with 4 that the latter forms both 1:1 and 2:1 dsDNA complexes. Certain aspects of the structure of 4:d(CGCAAATTTGCG)2 complex derived via 1H NMR are discussed. The electrophoretic mobilities of phi X-174 DNA digested with HaeIII endonuclease restriction fragments complexed to 4 shows that the latter brings about a greater conformational change in the DNA fragments than observed previously with other microgonotropens.

Examination of H-1 chemical shifts of a complex of D-glucosamine with bisphenanthroline cobalt (III) shows that the dominant Delta-complex is formed from alpha-D-glucosamine. A molecular mechanics simulation of the structure of this complex indicates that the sugar residue is not markedly perturbed by complexation of Co(III) at the 1-alkoxide and 2-amino groups. The circular dichroism spectrum of the complex formed in solution agrees with that of the isolated material.

The structure and conformation of 2-triphenylphosphoranylidenesuccinic acid derivatives have been studied by 1H, 13C and 31P NMR spectroscopy, in various solvents and at variable temperatures. In 2-triphenylphosphoranylidenesuccinic anhydride (1) the conformation is constrained but in the corresponding monoethyl (2) and the diethyl (3) esters there is an anticlinal relationship between the phosphorus and hydrogens on C-3 and signals of Z and E isomers were observed with the diethyl ester 3 in solvent-dependent ratios based on 1H, 13C and 31P resonances. Similar results were obtained with the diethyl ester of the 3-methyl derivative 4. Protonation (deuteronation) of 2 and 3 changes their conformation and P–H couplings. The NMR evidence on conformations of the phosphoranylidenesuccinic acid esters is consistent with T1 relaxation times and results of molecular modelling.

Zwitterionic micelles of N -tetradecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (SB3-14) inhibit oxidations of 3-chloroethyl phenyl sulfide (PhSCH2CH2Cl) and 1-methoxy-4(methylthio)benzene (ArSMe) by peroxymonosulfate ion (HSO-5) and the periodate ion oxidation of ArSMe, but there are slow residual reactions of micellar-bound substrates. Measurements of the critical micelle concentration and conductance of solutions of NaIO4 and SB3-14 show that IO-4 binds to sulfobetaine micelles and changes in the 1 H chemical shifts of SB3-14 confirm this assumption. The estimated second order rate constants for reaction of IO-4 and ArSMe are similar in SB3-14 and cationic micelles but lower than that in water by a factor of ca. 103. These low rate constants are due to charge-charge interactions in the transition states of reactions at micellar surfaces. Similar results were observed with HSO-5. These rate constants at surfaces of zwitterionic and cationic micelles are much lower than at surfaces of anionic micelles.

d-Fructose and 1,10-phenanthroline form complexes with Co(III). Configurations about Co(III) are assigned from the CD and ORD spectra of the separated Λ and Δ diastereomers, and Λ strongly predominates in the mixture. Most of the 1H NMR signals of the complexes are shifted strongly upfield, relative to those of d-fructose, due to shielding by aromatic residues, and the effect is especially strong for hydrogens at positions 1 and 6. Signals of the fructose residue are assigned for the Λ diastereomer and coupling constants estimated, but only some of the signals can be assigned for the Δ diastereomer. The marked changes in chemical shifts on formation of the complexes from fructose are rationalized in terms of predicted conformations based on molecular-mechanics calculations with MM2 parameters, which predict the higher stability of the Λ over the Δ diastereomer, and also complexation at positions 2 and 3.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrolysis of a Phosphate Diester by Simultaneous Carboxylate and Carboxyl Group Participation in a Rigid System with Kinetically Unfavorable Rotamers Frozen OutThomas C. Bruice, Andrei Blasko, Ramesh D. Arasasingham, Jang-Seob Kim, and Mark E. PetyakCite this: J. Am. Chem. Soc. 1995, 117, 12, 3639–3640Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://doi.org/10.1021/ja00117a044Request reuse permissionsArticle Views73Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (777 KB) Get e-Alertsclose Get e-Alerts

The energies of rotamer conformations of bis(2-carboxyphenyl) phosphate (2), where one o-carboxy group is ionized and the other is not, have been determined by semiempirical (SAM1, AM1/SM2.1) calculations in order to approximate the probability of the presence of conformations in which the o-CO2- is in position to act as a nucleophile toward phosphorus and the o-CO2H function can hydrogen bond to prostereogenic oxygens of the -(PO2-)(conformer B) or leaving phenoxide oxygen (conformer A). With simulated water phase, conformer B appears to be at the global energy minima and conformer A is somewhat less stable. The kinetics and the mechanism of hydrolysis of bis(2-carboxyphenyl) phosphate (2) have been elucidated by use of H-1 and P-31 NMR spectroscopy in acetonitrile/water 95:5 and D2O at pD up to 5.0 (39 degrees C). The hydrolysis of 2 is initiated by nucleophilic attack of the o-CO2- upon phosphate phosphorus resulting in the elimination of salicylic acid to provide salicyloyl cyclic phosphate (3) with a rate constant of 1-5 x 10(-3) s(-1) and 3 converts to salicyl monophosphate with rate constants varying between 1 and 5 x 10(-4) s(-1). The rapidity of the formation of 3 from 2 suggests the importance of both o-CO2- and o-CO2H participation {a subject of the following manuscript}.

Fractionation factors, phi(M), of interfacial water at surfaces of cationic and zwitterionic surfactants were determined from the dependence of the H-1 chemical shift of water on the isotopic composition of the solvent (H2O plus D2O). Values of phi(M) are greater than unity, showing that interfacial water is more structured than bulk water, whose fractionation factor = 1, by definition. The structuring increases with increasing bulk of the headgroup, but is unaffected by the length of the cationic surfactant hydrophobic tail. The effect of zwitterionic sulfobetaine surfactants on the structure of their water of hydration is less than that of cationic surfactants that have otherwise similar headgroups. Values of phi(M) for cationic micelles are: cetyldimethylphenylammonium chloride, 1.08; cetylpyridinium chloride, 1.06; and dodecyltrimethylammonium bromide, 1.06. Values of phi(M) for sulfobetaine micelles are: 3-N-tetradecyl-N,N-di-n-butylammonio-1-propane sulfonate, 1.07, and 3-N-tetradecyl-N,N-diethylammonio-1-propane sulfonate, 1.03.