Synthesis and acid–base properties of (1H-benzimidazol-2-yl-methyl)phosphonate (Bimp<sup>2−</sup>). Evidence for intramolecular hydrogen-bond formation in aqueous solution between (N-1)H and the phosphonate group

Sánchez-Moreno, María José; Gómez‐Coca, Raquel B.; Fernández‐Botello, Alfonso; Ochocki, Justyn; Kotyński, Andrzej; Griesser, Rolf; Sigel, Helmut

doi:10.1039/b301281f

Cited by 21 publications

(27 citation statements)

References 87 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The two uridine units are shown in their dominating anti conformation. [21,22] 2005 Wiley [47,48] that the same difference also holds for the release of the primary phosphate proton, a value for H 2 (pUpU) À could be estimated based on the data for H 2 (UMP), that is, pK H H 2 ðpUpUÞ = 0.7+0.3 = 1.0. The increased basicity of the terminal phosphate group of pUpU 3À compared to that of UMP 2À is clearly a charge effect, and is in accordance with the observations made for UDP 3À and UTP 4À .…”

Section: Resultsmentioning

confidence: 99%

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Knobloch

Suliga

Okruszek

et al. 2005

Chemistry A European J

View full text Add to dashboard Cite

It is well known that Mg2+ and other divalent metal ions bind to the phosphate groups of nucleic acids. Subtle differences in the coordination properties of these metal ions to RNA, especially to ribozymes, determine whether they either promote or inhibit catalytic activity. The ability of metal ions to coordinate simultaneously with two neighboring phosphate groups is important for ribozyme structure and activity. However, such an interaction has not yet been quantified. Here, we have performed potentiometric pH titrations to determine the acidity constants of the protonated dinucleotide H2(pUpU)-, as well as the binding properties of pUpU3- towards Mg2+, Mn2+, Cd2+, Zn2+, and Pb2+. Whereas Mg2+, Mn2+, and Cd2+ only bind to the more basic 5'-terminal phosphate group, Pb2+, and to a certain extent also Zn2+, show a remarkably enhanced stability of the [M(pUpU)]- complex. This can be attributed to the formation of a macrochelate by bridging the two phosphate groups within this dinucleotide by these metal ions. Such a macrochelate is also possible in an oligonucleotide, because the basic structural units are the same, despite the difference in charge. The formation degrees of the macrochelated species of [Zn(pUpU)]- and [Pb(pUpU)]- amount to around 25 and 90 %, respectively. These findings are important in the context of ribozyme and DNAzyme catalysis, and explain, for example, why the leadzyme could be selected in the first place, and why this artificial ribozyme is inhibited by other divalent metal ions, such as Mg2+.

show abstract

Section: Resultsmentioning

confidence: 99%

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Knobloch

Suliga

Okruszek

et al. 2005

Chemistry A European J

View full text Add to dashboard Cite

show abstract

“…Potentiometric pH titrations: The instrumentation, including the desk computers, was the same as described previously. [24,46,54] All equilibrium constants were calculated by curve-fitting procedures with a Newton-Gauss nonlinear least-squares program. …”

Section: Methodsmentioning

confidence: 99%

“…+ was determined by titrating 50 mL of aqueous 3.6 mm HNO 3 (25 8C; I = 0.5 m, NaNO 3 ) in the presence and absence of 1.0 mm adenosine under N 2 with 1.8 mL of 0.1 m NaOH and by using the differences in NaOH consumption between such pairs of titrations for the calculations. The acidity constant was calculated (curve fitting) as described [46,54] within the pH range corresponding to about 10-99 % neutralization for the equilibrium HA C H T U N G T R E N N U N G (Ado) + /Ado. The final result is the average of 30 independent pairs of titrations.…”

Section: Wwwchemeurjorgmentioning

confidence: 99%

Understanding the Acid–Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7

Kapinos

Operschall

Larsen

et al. 2011

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H(3) (Ado)(3+) , and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H(+) and (N7)H(+). However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, pK(H)(H(3))((Ado)) = -4.02 and pK(H)(H(2))((Ado)) = -1.53; the third one was re-measured as pK(H)(H)((Ado)) = 3.64 ± 0.02 (25 °C; I=0.5 M, NaNO(3)), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H(+) site; this constant has now been determined in an unequivocal manner, and that of the (N3)H(+) site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H(+) site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order pk(N7-N1)(N7(Ado)N1·H)) = 3.63 ± 0.02 > pk(N7-N1)(H·N7(Ado)N1) = 2.15 ± 0.15 > pk(N3-N1,N7)(H·N3(Ado)N1,N7) =1.5 ± 0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above-mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)(+) , in aqueous solution; the results are 96.1, 3.2, and 0.7% for N7(Ado)N1·H(+), (+)H·N7(Ado)N1, and (+)H·N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)(+) exists to the largest part as N7(Ado)N1·H(+) having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion-binding properties; these aspects are briefly discussed.

show abstract

“…[7] Instead of HCl, HBr may also be used. [7][8][9] Trifluoroacetic acid-catalyzed hydrolysis of phosphinates was also reported. [10] It is also possible to carry out hydrolyses under basic conditions using aqueous NaOH or KOH.…”

Section: Introductionmentioning

confidence: 97%

“…Occasionally, dioxane was also used as a cosolvent or as the sole solvent . Instead of HCl, HBr may also be used . Trifluoroacetic acid‐catalyzed hydrolysis of phosphinates was also reported .…”

Section: Introductionmentioning

confidence: 99%

A study on the acidic hydrolysis of cyclic phosphinates: 1‐Alkoxy‐3‐phospholene 1‐oxides, 1‐ethoxy‐3‐methylphospholane 1‐oxide, and 1‐ethoxy‐3‐methyl‐1,2,3,4,5,6‐hexahydrophosphinine 1‐oxide

Keglevich

Rádai

Harsági

et al. 2017

Heteroatom Chemistry

View full text Add to dashboard Cite

The hydrochloric acid‐catalyzed hydrolysis of phosphinates was studied on 1‐alkoxy‐3‐phospholene 1‐oxides, 1‐ethoxy‐3‐methylphospholane 1‐oxide, and 1‐ethoxy‐3‐methyl‐1,2,3,4,5,6‐hexahydrophosphinine 1‐oxide as the model compounds. Under the conditions applied, the isomerization of the 3‐phospholene moiety to the 2‐phospholene ring also occurred leading to mixtures of the corresponding 1‐hydroxy‐3‐phospholene oxide and 1‐hydroxy‐2‐phospholene oxide. According to our optimized method, using 3 equivalents (0.5 mL) of concentrated hydrochloric acid in 1 mL of water per ca. 2 mmol of the substrate at reflux, the completion required 3‐10 hour. The hydrolyses were characterized by pseudo‐first‐order rate constants and the isomerizations by rate constants. The application of p‐toluenesulfonic acid under microwave irradiation at 140°C in the hydrolysis of 1‐alkoxy‐3‐methyl‐3‐phospholene oxides associated with reaction times of 1‐3 hour. The reactivity order of the 5‐ and 6‐ring phosphinates in hydrolysis was set up.

show abstract

Synthesis and acid–base properties of (1H-benzimidazol-2-yl-methyl)phosphonate (Bimp²⁻). Evidence for intramolecular hydrogen-bond formation in aqueous solution between (N-1)H and the phosphonate group

Cited by 21 publications

References 87 publications

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Understanding the Acid–Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7

A study on the acidic hydrolysis of cyclic phosphinates: 1‐Alkoxy‐3‐phospholene 1‐oxides, 1‐ethoxy‐3‐methylphospholane 1‐oxide, and 1‐ethoxy‐3‐methyl‐1,2,3,4,5,6‐hexahydrophosphinine 1‐oxide

Contact Info

Product

Resources

About

Synthesis and acid–base properties of (1H-benzimidazol-2-yl-methyl)phosphonate (Bimp2−). Evidence for intramolecular hydrogen-bond formation in aqueous solution between (N-1)H and the phosphonate group

Cited by 21 publications

References 87 publications

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU3−)

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU3−)

Understanding the Acid–Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7

A study on the acidic hydrolysis of cyclic phosphinates: 1‐Alkoxy‐3‐phospholene 1‐oxides, 1‐ethoxy‐3‐methylphospholane 1‐oxide, and 1‐ethoxy‐3‐methyl‐1,2,3,4,5,6‐hexahydrophosphinine 1‐oxide

Contact Info

Product

Resources

About

Synthesis and acid–base properties of (1H-benzimidazol-2-yl-methyl)phosphonate (Bimp²⁻). Evidence for intramolecular hydrogen-bond formation in aqueous solution between (N-1)H and the phosphonate group

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)

Acid–Base and Metal‐Ion Binding Properties of the RNA Dinucleotide Uridylyl‐(5′→3′)‐[5′]uridylate (pUpU³⁻)