Stereochemistry of nucleic acids and their constituents. XXVI. The crystal and molecular structure of a 1: 1 adduct of ethanol and 3′-deoxy-3′-(dihydroxyphosphinylmethyl)adenosine, an analog of adenosine 3′-monophosphate

Sidney Hecht, M. Sundaralingam

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Abstract

The structure of 3′-deoxy-3′-(dihydroxyphosphinylmethyl)adenosine a synthetic analog of adenosine 3′-phosphate, has been determined using 1417 reflections measured on a diffractometer. The compound crystallized in the space group P212121 with four molecules of the analog and four molecules of ethanol in a unit cell having a = 5.592, b = 20.287,and c = 15.198Å dcalcd = 1.507gcm-3and dodsd = 1.503 g cm-3. The observed and calculated densities are consistent with the presence of four molecules of ethanol per unit cell, which was subsequently confirmed by X-ray analysis. The molecule is in the anti conformation with respect to the glycosyl torsion angle, having χ = 28.1°. The conformation about the C(4′)-C(5′) bond is gauche-gauche, where O(1′)-C(4′)-C(5′)-O(5′) = -69.0° and C(3′)-C(4′)-C(5′)-O(5′) = 49.2°. The conformation of the sugar ring is 3T2, the torsion angles about the ring bonds being O(1′)-C(1′) = 8.9°,C(1′)-C(2′) = -29.5°,C(2′)-C(3′) = 37.4°,C(3′)-C(4′) = - 33.1°, C(4′)-O(1′) = 15.4°. These conformational parameters are similar to those found in adenosine 3′-phosphate dihydrate. The molecule is a zwitterion N(1) of the base being protonated by an adjacent phosphonate hydrogen. The same phosphonate group is also hydrogen bonded to N(6) of the base. Similarly, the second hydrogen on N(6) and the site N(7) are involved in a hydrogen-bonded pair to a symmetry related phosphonate group. The base-phosphonate (or phosphate) hydrogen bonding is a characteristic feature of the crystal chemistry of adenine and cytidine nucleotides. The alcohol of solvation is hydrogen bonded to an adjacent ribose O(5′) atom. The remaining potential hydrogen bonding sites are also involved in hydrogen bonding.

Original languageEnglish (US)
Pages (from-to)4314-4319
Number of pages6
JournalJournal of the American Chemical Society
Volume94
Issue number12
StatePublished - 1972
Externally publishedYes

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Stereochemistry
Nucleic acids
Adenosine Monophosphate
Molecular Structure
Organophosphonates
Adenosine
Nucleic Acids
Molecular structure
Hydrogen
Ethanol
Crystal structure
Hydrogen Bonding
Molecules
Conformations
Hydrogen bonds
Phosphates
Torsional stress
Crystal chemistry
Cytidine
Ribose

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

@article{22f5e0cc0b2745b7969e7023973972ca,
title = "Stereochemistry of nucleic acids and their constituents. XXVI. The crystal and molecular structure of a 1: 1 adduct of ethanol and 3′-deoxy-3′-(dihydroxyphosphinylmethyl)adenosine, an analog of adenosine 3′-monophosphate",
abstract = "The structure of 3′-deoxy-3′-(dihydroxyphosphinylmethyl)adenosine a synthetic analog of adenosine 3′-phosphate, has been determined using 1417 reflections measured on a diffractometer. The compound crystallized in the space group P212121 with four molecules of the analog and four molecules of ethanol in a unit cell having a = 5.592, b = 20.287,and c = 15.198{\AA} dcalcd = 1.507gcm-3and dodsd = 1.503 g cm-3. The observed and calculated densities are consistent with the presence of four molecules of ethanol per unit cell, which was subsequently confirmed by X-ray analysis. The molecule is in the anti conformation with respect to the glycosyl torsion angle, having χ = 28.1°. The conformation about the C(4′)-C(5′) bond is gauche-gauche, where O(1′)-C(4′)-C(5′)-O(5′) = -69.0° and C(3′)-C(4′)-C(5′)-O(5′) = 49.2°. The conformation of the sugar ring is 3T2, the torsion angles about the ring bonds being O(1′)-C(1′) = 8.9°,C(1′)-C(2′) = -29.5°,C(2′)-C(3′) = 37.4°,C(3′)-C(4′) = - 33.1°, C(4′)-O(1′) = 15.4°. These conformational parameters are similar to those found in adenosine 3′-phosphate dihydrate. The molecule is a zwitterion N(1) of the base being protonated by an adjacent phosphonate hydrogen. The same phosphonate group is also hydrogen bonded to N(6) of the base. Similarly, the second hydrogen on N(6) and the site N(7) are involved in a hydrogen-bonded pair to a symmetry related phosphonate group. The base-phosphonate (or phosphate) hydrogen bonding is a characteristic feature of the crystal chemistry of adenine and cytidine nucleotides. The alcohol of solvation is hydrogen bonded to an adjacent ribose O(5′) atom. The remaining potential hydrogen bonding sites are also involved in hydrogen bonding.",
author = "Sidney Hecht and M. Sundaralingam",
year = "1972",
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T1 - Stereochemistry of nucleic acids and their constituents. XXVI. The crystal and molecular structure of a 1

T2 - 1 adduct of ethanol and 3′-deoxy-3′-(dihydroxyphosphinylmethyl)adenosine, an analog of adenosine 3′-monophosphate

AU - Hecht, Sidney

AU - Sundaralingam, M.

PY - 1972

Y1 - 1972

N2 - The structure of 3′-deoxy-3′-(dihydroxyphosphinylmethyl)adenosine a synthetic analog of adenosine 3′-phosphate, has been determined using 1417 reflections measured on a diffractometer. The compound crystallized in the space group P212121 with four molecules of the analog and four molecules of ethanol in a unit cell having a = 5.592, b = 20.287,and c = 15.198Å dcalcd = 1.507gcm-3and dodsd = 1.503 g cm-3. The observed and calculated densities are consistent with the presence of four molecules of ethanol per unit cell, which was subsequently confirmed by X-ray analysis. The molecule is in the anti conformation with respect to the glycosyl torsion angle, having χ = 28.1°. The conformation about the C(4′)-C(5′) bond is gauche-gauche, where O(1′)-C(4′)-C(5′)-O(5′) = -69.0° and C(3′)-C(4′)-C(5′)-O(5′) = 49.2°. The conformation of the sugar ring is 3T2, the torsion angles about the ring bonds being O(1′)-C(1′) = 8.9°,C(1′)-C(2′) = -29.5°,C(2′)-C(3′) = 37.4°,C(3′)-C(4′) = - 33.1°, C(4′)-O(1′) = 15.4°. These conformational parameters are similar to those found in adenosine 3′-phosphate dihydrate. The molecule is a zwitterion N(1) of the base being protonated by an adjacent phosphonate hydrogen. The same phosphonate group is also hydrogen bonded to N(6) of the base. Similarly, the second hydrogen on N(6) and the site N(7) are involved in a hydrogen-bonded pair to a symmetry related phosphonate group. The base-phosphonate (or phosphate) hydrogen bonding is a characteristic feature of the crystal chemistry of adenine and cytidine nucleotides. The alcohol of solvation is hydrogen bonded to an adjacent ribose O(5′) atom. The remaining potential hydrogen bonding sites are also involved in hydrogen bonding.

AB - The structure of 3′-deoxy-3′-(dihydroxyphosphinylmethyl)adenosine a synthetic analog of adenosine 3′-phosphate, has been determined using 1417 reflections measured on a diffractometer. The compound crystallized in the space group P212121 with four molecules of the analog and four molecules of ethanol in a unit cell having a = 5.592, b = 20.287,and c = 15.198Å dcalcd = 1.507gcm-3and dodsd = 1.503 g cm-3. The observed and calculated densities are consistent with the presence of four molecules of ethanol per unit cell, which was subsequently confirmed by X-ray analysis. The molecule is in the anti conformation with respect to the glycosyl torsion angle, having χ = 28.1°. The conformation about the C(4′)-C(5′) bond is gauche-gauche, where O(1′)-C(4′)-C(5′)-O(5′) = -69.0° and C(3′)-C(4′)-C(5′)-O(5′) = 49.2°. The conformation of the sugar ring is 3T2, the torsion angles about the ring bonds being O(1′)-C(1′) = 8.9°,C(1′)-C(2′) = -29.5°,C(2′)-C(3′) = 37.4°,C(3′)-C(4′) = - 33.1°, C(4′)-O(1′) = 15.4°. These conformational parameters are similar to those found in adenosine 3′-phosphate dihydrate. The molecule is a zwitterion N(1) of the base being protonated by an adjacent phosphonate hydrogen. The same phosphonate group is also hydrogen bonded to N(6) of the base. Similarly, the second hydrogen on N(6) and the site N(7) are involved in a hydrogen-bonded pair to a symmetry related phosphonate group. The base-phosphonate (or phosphate) hydrogen bonding is a characteristic feature of the crystal chemistry of adenine and cytidine nucleotides. The alcohol of solvation is hydrogen bonded to an adjacent ribose O(5′) atom. The remaining potential hydrogen bonding sites are also involved in hydrogen bonding.

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