Bioorganometallic chemistry. 27. Synthetic, x-ray crystallographic, and competitive binding studies in the reactions of nucleobases, nucleosides, and nucleotides with [Cp*Rh(H2O)3](OTf)2, as a function of pH, and the utilization of several Cp*Rh-DNA base complexes in host-guest chemistry

David P. Smith, Hong Chen, Seiji Ogo, Ana I. Elduque, Miriam Eisenstein, Marilyn M. Olmstead, Richard H. Fish

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Abstract

The reactions of the air- and water-stable tris(aqua) complex [Cp*Rh(H2O)3](OTf)2 (1; OTf = trifluoromethanesulfonate) with nucleobases and nucleosides that included 9-methyladenine (9-MA), 9-ethylguanine (9-EG), 9-methylhypoxanthine (9-MH), 9-ethylhypoxanthine (9-EH), 1-methylcytosine (1-MC), 1-methylthymine (1-MT), adenosine (Ado), and guanosine (Guo) provided new bonding modes, all as a function of pH. The 9-MA nucleobase provided a novel cyclic trimer, at pH 6, characteristic for all Ado complexes: [Cp*Rh(μ2- η1(N1): η2(N6,N7)-9-MA/Ado)]3(OTf) 3. The Cp*Rh(9-EG) and Cp*Rh(Guo) complexes showed N7 and 6-C-O binding modes in water, [Cp*Rh((η2(N7,O6)-9-EG/Guo) (OH)](OTf), and no cyclic trimer products, due to a pronounced steric effect of the 2-amino group. This was shown convincingly by the results with 9-MH and 9-EH, which did form cyclic trimers at pH 6.1, [Cp*Rh(μ2- η1(N1):η2(N7,O6)-9-MH/9-EH)]3(OTf) 3, with a structure similar to that of 9-EG, but with no 2-amino group available. At pH 10.2, the pKa of the 9-MH's NH1 hydrogen dictated the structure, providing a μ-hydroxy dimer, trans- [Cp*Rh(η1(N1)-9-MH)(μ-OH)]2(OTf) 2, while in methanol the same reaction provided a mononuclear complex, [Cp*Rh(η1(N7)-9-MH)(MeOH)2](OTf) 2. The reaction of 1 and 1-MC, at pH 5.4, provided another μ-hydroxy dimer with intramolecular H bonding of the O and H atoms of the μ-OH groups (H-acceptor and H-donor, respectively), trans- [Cp*Rh(η1(N3)-1-MC)(μ-OH)]2(OTf) 2, while in acetone, the product was a monomeric complex, [(η5-Cp*Rh)(η1(N3)-1-MC)( η2(O2,N3)-1-MC)](OTf)2. The reaction of 1 and 1-MT at pH 10 showed the initial complex 1 being converted to its equilibrium complex, [(Cp*Rh)2(μ-OH)3]+, and this led to two components being formed. The anionic component was a linear [(η1(N3)-MT)-RhI-(η1(N3)-MT)] - (12e RhI center) assembly, formed via a presumed reductive elimination of Cp*OH, and included an orthogonal array of two thymine planes. The cationic component was [(Cp*Rh)2(μ-OH) 3]+, with its Cp* moiety being π-π stacked with thymine rings, as well as the π-π interactions of two thymine rings: {[RhI1(N3)-1-MT)2]2[(Cp* Rh)2(μ-OH)3]3}OH. The competitive order of nucleoside reactivity was Ado ≫ Guo, while for the nucleotides it was GMP > AMP ≫ CMP ≈ TMP. Finally, we also discuss several examples of the utilization of these unique Cp*Rh-DNA base complexes, as aqueous hosts for molecular recognition of aromatic amino acids and as NMR shift reagents for many organic compounds.

Original languageEnglish
Pages (from-to)2389-2404
Number of pages16
JournalOrganometallics
Volume33
Issue number10
DOIs
Publication statusPublished - May 27 2014

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nucleosides
nucleotides
Nucleosides
Guanosine
guanosines
adenosines
Nucleotides
deoxyribonucleic acid
Adenosine
Thymine
chemistry
X rays
thymine
DNA
trimers
x rays
Dimers
Thymidine Monophosphate
Cytidine Monophosphate
Molecular recognition

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

Cite this

@article{85785ff92e4f419b9efb7a5916f61f05,
title = "Bioorganometallic chemistry. 27. Synthetic, x-ray crystallographic, and competitive binding studies in the reactions of nucleobases, nucleosides, and nucleotides with [Cp*Rh(H2O)3](OTf)2, as a function of pH, and the utilization of several Cp*Rh-DNA base complexes in host-guest chemistry",
abstract = "The reactions of the air- and water-stable tris(aqua) complex [Cp*Rh(H2O)3](OTf)2 (1; OTf = trifluoromethanesulfonate) with nucleobases and nucleosides that included 9-methyladenine (9-MA), 9-ethylguanine (9-EG), 9-methylhypoxanthine (9-MH), 9-ethylhypoxanthine (9-EH), 1-methylcytosine (1-MC), 1-methylthymine (1-MT), adenosine (Ado), and guanosine (Guo) provided new bonding modes, all as a function of pH. The 9-MA nucleobase provided a novel cyclic trimer, at pH 6, characteristic for all Ado complexes: [Cp*Rh(μ2- η1(N1): η2(N6,N7)-9-MA/Ado)]3(OTf) 3. The Cp*Rh(9-EG) and Cp*Rh(Guo) complexes showed N7 and 6-C-O binding modes in water, [Cp*Rh((η2(N7,O6)-9-EG/Guo) (OH)](OTf), and no cyclic trimer products, due to a pronounced steric effect of the 2-amino group. This was shown convincingly by the results with 9-MH and 9-EH, which did form cyclic trimers at pH 6.1, [Cp*Rh(μ2- η1(N1):η2(N7,O6)-9-MH/9-EH)]3(OTf) 3, with a structure similar to that of 9-EG, but with no 2-amino group available. At pH 10.2, the pKa of the 9-MH's NH1 hydrogen dictated the structure, providing a μ-hydroxy dimer, trans- [Cp*Rh(η1(N1)-9-MH)(μ-OH)]2(OTf) 2, while in methanol the same reaction provided a mononuclear complex, [Cp*Rh(η1(N7)-9-MH)(MeOH)2](OTf) 2. The reaction of 1 and 1-MC, at pH 5.4, provided another μ-hydroxy dimer with intramolecular H bonding of the O and H atoms of the μ-OH groups (H-acceptor and H-donor, respectively), trans- [Cp*Rh(η1(N3)-1-MC)(μ-OH)]2(OTf) 2, while in acetone, the product was a monomeric complex, [(η5-Cp*Rh)(η1(N3)-1-MC)( η2(O2,N3)-1-MC)](OTf)2. The reaction of 1 and 1-MT at pH 10 showed the initial complex 1 being converted to its equilibrium complex, [(Cp*Rh)2(μ-OH)3]+, and this led to two components being formed. The anionic component was a linear [(η1(N3)-MT)-RhI-(η1(N3)-MT)] - (12e RhI center) assembly, formed via a presumed reductive elimination of Cp*OH, and included an orthogonal array of two thymine planes. The cationic component was [(Cp*Rh)2(μ-OH) 3]+, with its Cp* moiety being π-π stacked with thymine rings, as well as the π-π interactions of two thymine rings: {[RhI(η1(N3)-1-MT)2]2[(Cp* Rh)2(μ-OH)3]3}OH. The competitive order of nucleoside reactivity was Ado ≫ Guo, while for the nucleotides it was GMP > AMP ≫ CMP ≈ TMP. Finally, we also discuss several examples of the utilization of these unique Cp*Rh-DNA base complexes, as aqueous hosts for molecular recognition of aromatic amino acids and as NMR shift reagents for many organic compounds.",
author = "Smith, {David P.} and Hong Chen and Seiji Ogo and Elduque, {Ana I.} and Miriam Eisenstein and Olmstead, {Marilyn M.} and Fish, {Richard H.}",
year = "2014",
month = "5",
day = "27",
doi = "10.1021/om500106r",
language = "English",
volume = "33",
pages = "2389--2404",
journal = "Organometallics",
issn = "0276-7333",
publisher = "American Chemical Society",
number = "10",

}

TY - JOUR

T1 - Bioorganometallic chemistry. 27. Synthetic, x-ray crystallographic, and competitive binding studies in the reactions of nucleobases, nucleosides, and nucleotides with [Cp*Rh(H2O)3](OTf)2, as a function of pH, and the utilization of several Cp*Rh-DNA base complexes in host-guest chemistry

AU - Smith, David P.

AU - Chen, Hong

AU - Ogo, Seiji

AU - Elduque, Ana I.

AU - Eisenstein, Miriam

AU - Olmstead, Marilyn M.

AU - Fish, Richard H.

PY - 2014/5/27

Y1 - 2014/5/27

N2 - The reactions of the air- and water-stable tris(aqua) complex [Cp*Rh(H2O)3](OTf)2 (1; OTf = trifluoromethanesulfonate) with nucleobases and nucleosides that included 9-methyladenine (9-MA), 9-ethylguanine (9-EG), 9-methylhypoxanthine (9-MH), 9-ethylhypoxanthine (9-EH), 1-methylcytosine (1-MC), 1-methylthymine (1-MT), adenosine (Ado), and guanosine (Guo) provided new bonding modes, all as a function of pH. The 9-MA nucleobase provided a novel cyclic trimer, at pH 6, characteristic for all Ado complexes: [Cp*Rh(μ2- η1(N1): η2(N6,N7)-9-MA/Ado)]3(OTf) 3. The Cp*Rh(9-EG) and Cp*Rh(Guo) complexes showed N7 and 6-C-O binding modes in water, [Cp*Rh((η2(N7,O6)-9-EG/Guo) (OH)](OTf), and no cyclic trimer products, due to a pronounced steric effect of the 2-amino group. This was shown convincingly by the results with 9-MH and 9-EH, which did form cyclic trimers at pH 6.1, [Cp*Rh(μ2- η1(N1):η2(N7,O6)-9-MH/9-EH)]3(OTf) 3, with a structure similar to that of 9-EG, but with no 2-amino group available. At pH 10.2, the pKa of the 9-MH's NH1 hydrogen dictated the structure, providing a μ-hydroxy dimer, trans- [Cp*Rh(η1(N1)-9-MH)(μ-OH)]2(OTf) 2, while in methanol the same reaction provided a mononuclear complex, [Cp*Rh(η1(N7)-9-MH)(MeOH)2](OTf) 2. The reaction of 1 and 1-MC, at pH 5.4, provided another μ-hydroxy dimer with intramolecular H bonding of the O and H atoms of the μ-OH groups (H-acceptor and H-donor, respectively), trans- [Cp*Rh(η1(N3)-1-MC)(μ-OH)]2(OTf) 2, while in acetone, the product was a monomeric complex, [(η5-Cp*Rh)(η1(N3)-1-MC)( η2(O2,N3)-1-MC)](OTf)2. The reaction of 1 and 1-MT at pH 10 showed the initial complex 1 being converted to its equilibrium complex, [(Cp*Rh)2(μ-OH)3]+, and this led to two components being formed. The anionic component was a linear [(η1(N3)-MT)-RhI-(η1(N3)-MT)] - (12e RhI center) assembly, formed via a presumed reductive elimination of Cp*OH, and included an orthogonal array of two thymine planes. The cationic component was [(Cp*Rh)2(μ-OH) 3]+, with its Cp* moiety being π-π stacked with thymine rings, as well as the π-π interactions of two thymine rings: {[RhI(η1(N3)-1-MT)2]2[(Cp* Rh)2(μ-OH)3]3}OH. The competitive order of nucleoside reactivity was Ado ≫ Guo, while for the nucleotides it was GMP > AMP ≫ CMP ≈ TMP. Finally, we also discuss several examples of the utilization of these unique Cp*Rh-DNA base complexes, as aqueous hosts for molecular recognition of aromatic amino acids and as NMR shift reagents for many organic compounds.

AB - The reactions of the air- and water-stable tris(aqua) complex [Cp*Rh(H2O)3](OTf)2 (1; OTf = trifluoromethanesulfonate) with nucleobases and nucleosides that included 9-methyladenine (9-MA), 9-ethylguanine (9-EG), 9-methylhypoxanthine (9-MH), 9-ethylhypoxanthine (9-EH), 1-methylcytosine (1-MC), 1-methylthymine (1-MT), adenosine (Ado), and guanosine (Guo) provided new bonding modes, all as a function of pH. The 9-MA nucleobase provided a novel cyclic trimer, at pH 6, characteristic for all Ado complexes: [Cp*Rh(μ2- η1(N1): η2(N6,N7)-9-MA/Ado)]3(OTf) 3. The Cp*Rh(9-EG) and Cp*Rh(Guo) complexes showed N7 and 6-C-O binding modes in water, [Cp*Rh((η2(N7,O6)-9-EG/Guo) (OH)](OTf), and no cyclic trimer products, due to a pronounced steric effect of the 2-amino group. This was shown convincingly by the results with 9-MH and 9-EH, which did form cyclic trimers at pH 6.1, [Cp*Rh(μ2- η1(N1):η2(N7,O6)-9-MH/9-EH)]3(OTf) 3, with a structure similar to that of 9-EG, but with no 2-amino group available. At pH 10.2, the pKa of the 9-MH's NH1 hydrogen dictated the structure, providing a μ-hydroxy dimer, trans- [Cp*Rh(η1(N1)-9-MH)(μ-OH)]2(OTf) 2, while in methanol the same reaction provided a mononuclear complex, [Cp*Rh(η1(N7)-9-MH)(MeOH)2](OTf) 2. The reaction of 1 and 1-MC, at pH 5.4, provided another μ-hydroxy dimer with intramolecular H bonding of the O and H atoms of the μ-OH groups (H-acceptor and H-donor, respectively), trans- [Cp*Rh(η1(N3)-1-MC)(μ-OH)]2(OTf) 2, while in acetone, the product was a monomeric complex, [(η5-Cp*Rh)(η1(N3)-1-MC)( η2(O2,N3)-1-MC)](OTf)2. The reaction of 1 and 1-MT at pH 10 showed the initial complex 1 being converted to its equilibrium complex, [(Cp*Rh)2(μ-OH)3]+, and this led to two components being formed. The anionic component was a linear [(η1(N3)-MT)-RhI-(η1(N3)-MT)] - (12e RhI center) assembly, formed via a presumed reductive elimination of Cp*OH, and included an orthogonal array of two thymine planes. The cationic component was [(Cp*Rh)2(μ-OH) 3]+, with its Cp* moiety being π-π stacked with thymine rings, as well as the π-π interactions of two thymine rings: {[RhI(η1(N3)-1-MT)2]2[(Cp* Rh)2(μ-OH)3]3}OH. The competitive order of nucleoside reactivity was Ado ≫ Guo, while for the nucleotides it was GMP > AMP ≫ CMP ≈ TMP. Finally, we also discuss several examples of the utilization of these unique Cp*Rh-DNA base complexes, as aqueous hosts for molecular recognition of aromatic amino acids and as NMR shift reagents for many organic compounds.

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