Properties of dianionic oxyphosphorane intermediates: Implication to the reaction profile for base-catalyzed RNA hydrolysis

Kazunari Taira (Corresponding Author), Tadafumi Uchimaru, Joey Storer, Ari Yliniemelä, Masami Uebayasi, Kazutoshi Tanabe

Research output: Contribution to journalArticleScientificpeer-review

38 Citations (Scopus)

Abstract

From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis (which also represents the base-catalyzed methanolysis of ethylene phosphate monoanion in reverse), a pentacoordinate dianionic intermediate 2a (Storer et al. J. Am. Chem. Soc. 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. However, the intermediate, which has a well depth on the order of k(B)T, is unlikely to be kinetically significant. The endocyclic P-O(2') bond is found to be much weaker than the exocyclic P-O(5') bond. In agreement with this finding, calculations on 2a at the 6-31+G* level abolishes TS1 and the pentacoordinate intermediate, leaving only TS2 as the sole transition state. Thus, for all the cases examined, the rate-limiting transition-state structure is TS2 which has an extended P-O(5') breaking bond. These results and the mode of cleavage of a simpler compound 3b are in accord with stereoelectronic predictions (see text for the definition). Moreover, solvation appears to stabilize the pentacoordinate intermediate. In the gas phase, the simplest oxyphosphorane 3b has the least tendency to form a pentacoordinate intermediate. However, 3b does form a pentacoordinate intermediate when it is solvated with six water molecules. These results support the hypothesis that phosphoryl-transfer reactions take place via pentacoordinate intermediates not only in acidic but also in basic media.
Original languageEnglish
Pages (from-to)3009 - 3017
Number of pages9
JournalJournal of Organic Chemistry
Volume58
Issue number11
DOIs
Publication statusPublished - 1993
MoE publication typeA1 Journal article-refereed

Fingerprint

Hydrolysis
RNA
Solvation
Gases
Phosphates
Molecules
Water
ethylene

Cite this

Taira, Kazunari ; Uchimaru, Tadafumi ; Storer, Joey ; Yliniemelä, Ari ; Uebayasi, Masami ; Tanabe, Kazutoshi. / Properties of dianionic oxyphosphorane intermediates : Implication to the reaction profile for base-catalyzed RNA hydrolysis. In: Journal of Organic Chemistry. 1993 ; Vol. 58, No. 11. pp. 3009 - 3017.
@article{6de843cc55534700a649130bef3dceb8,
title = "Properties of dianionic oxyphosphorane intermediates: Implication to the reaction profile for base-catalyzed RNA hydrolysis",
abstract = "From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis (which also represents the base-catalyzed methanolysis of ethylene phosphate monoanion in reverse), a pentacoordinate dianionic intermediate 2a (Storer et al. J. Am. Chem. Soc. 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. However, the intermediate, which has a well depth on the order of k(B)T, is unlikely to be kinetically significant. The endocyclic P-O(2') bond is found to be much weaker than the exocyclic P-O(5') bond. In agreement with this finding, calculations on 2a at the 6-31+G* level abolishes TS1 and the pentacoordinate intermediate, leaving only TS2 as the sole transition state. Thus, for all the cases examined, the rate-limiting transition-state structure is TS2 which has an extended P-O(5') breaking bond. These results and the mode of cleavage of a simpler compound 3b are in accord with stereoelectronic predictions (see text for the definition). Moreover, solvation appears to stabilize the pentacoordinate intermediate. In the gas phase, the simplest oxyphosphorane 3b has the least tendency to form a pentacoordinate intermediate. However, 3b does form a pentacoordinate intermediate when it is solvated with six water molecules. These results support the hypothesis that phosphoryl-transfer reactions take place via pentacoordinate intermediates not only in acidic but also in basic media.",
author = "Kazunari Taira and Tadafumi Uchimaru and Joey Storer and Ari Yliniemel{\"a} and Masami Uebayasi and Kazutoshi Tanabe",
year = "1993",
doi = "10.1021/jo00063a018",
language = "English",
volume = "58",
pages = "3009 -- 3017",
journal = "Journal of Organic Chemistry",
issn = "0022-3263",
publisher = "American Chemical Society ACS",
number = "11",

}

Properties of dianionic oxyphosphorane intermediates : Implication to the reaction profile for base-catalyzed RNA hydrolysis. / Taira, Kazunari (Corresponding Author); Uchimaru, Tadafumi; Storer, Joey; Yliniemelä, Ari; Uebayasi, Masami; Tanabe, Kazutoshi.

In: Journal of Organic Chemistry, Vol. 58, No. 11, 1993, p. 3009 - 3017.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Properties of dianionic oxyphosphorane intermediates

T2 - Implication to the reaction profile for base-catalyzed RNA hydrolysis

AU - Taira, Kazunari

AU - Uchimaru, Tadafumi

AU - Storer, Joey

AU - Yliniemelä, Ari

AU - Uebayasi, Masami

AU - Tanabe, Kazutoshi

PY - 1993

Y1 - 1993

N2 - From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis (which also represents the base-catalyzed methanolysis of ethylene phosphate monoanion in reverse), a pentacoordinate dianionic intermediate 2a (Storer et al. J. Am. Chem. Soc. 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. However, the intermediate, which has a well depth on the order of k(B)T, is unlikely to be kinetically significant. The endocyclic P-O(2') bond is found to be much weaker than the exocyclic P-O(5') bond. In agreement with this finding, calculations on 2a at the 6-31+G* level abolishes TS1 and the pentacoordinate intermediate, leaving only TS2 as the sole transition state. Thus, for all the cases examined, the rate-limiting transition-state structure is TS2 which has an extended P-O(5') breaking bond. These results and the mode of cleavage of a simpler compound 3b are in accord with stereoelectronic predictions (see text for the definition). Moreover, solvation appears to stabilize the pentacoordinate intermediate. In the gas phase, the simplest oxyphosphorane 3b has the least tendency to form a pentacoordinate intermediate. However, 3b does form a pentacoordinate intermediate when it is solvated with six water molecules. These results support the hypothesis that phosphoryl-transfer reactions take place via pentacoordinate intermediates not only in acidic but also in basic media.

AB - From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis (which also represents the base-catalyzed methanolysis of ethylene phosphate monoanion in reverse), a pentacoordinate dianionic intermediate 2a (Storer et al. J. Am. Chem. Soc. 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. However, the intermediate, which has a well depth on the order of k(B)T, is unlikely to be kinetically significant. The endocyclic P-O(2') bond is found to be much weaker than the exocyclic P-O(5') bond. In agreement with this finding, calculations on 2a at the 6-31+G* level abolishes TS1 and the pentacoordinate intermediate, leaving only TS2 as the sole transition state. Thus, for all the cases examined, the rate-limiting transition-state structure is TS2 which has an extended P-O(5') breaking bond. These results and the mode of cleavage of a simpler compound 3b are in accord with stereoelectronic predictions (see text for the definition). Moreover, solvation appears to stabilize the pentacoordinate intermediate. In the gas phase, the simplest oxyphosphorane 3b has the least tendency to form a pentacoordinate intermediate. However, 3b does form a pentacoordinate intermediate when it is solvated with six water molecules. These results support the hypothesis that phosphoryl-transfer reactions take place via pentacoordinate intermediates not only in acidic but also in basic media.

U2 - 10.1021/jo00063a018

DO - 10.1021/jo00063a018

M3 - Article

VL - 58

SP - 3009

EP - 3017

JO - Journal of Organic Chemistry

JF - Journal of Organic Chemistry

SN - 0022-3263

IS - 11

ER -