Unusual Coordination of the Rare Neutral Imine Tautomer of 9-Methyladenine Chelating in theN6,N7-Mode to Ruthenium(II) Complexes

Abstract

The coordination of the DNA model base 9‐methyladenine (9‐MeAde) to both complexes cis‐[Ru(bpy)2Cl2] and α‐[Ru(azpy)2(NO3)2] is reported. Structural characterisation using 2D NMR techniques and variable‐temperature NMR studies between 25 and −55 °C show that in the compounds α‐[Ru(azpy)2(9‐MeAde)](PF6)2 (1) and cis‐[Ru(bpy)2(9‐MeAde)](PF6)2 (2), 9‐MeAde is coordinated to the ruthenium ion in a chelating mode via its N7 and exocyclic N6 atoms. The NMR spectroscopic data unambiguously prove the occurrence of the rare imine tautomer of 9‐MeAde in these complexes, which is clearly stabilised by the bidentate coordination of 9‐MeAde in both complexes. Variable‐temperature NMR spectra and 2D COSY data show that the H2 resonance of 9‐MeAde in 1 and 2 appears as a doublet at low temperatures and shows a COSY cross peak to the NH1 resonance of 9‐MeAde, which confirms the protonation at the N1 site. This protonated N1 site, together with an observed pKa of ca. 6.5 of compound 1 is in agreement with the presence of the imine tautomeric form of 9‐MeAde. As the binding mode of 9‐MeAde to both cis‐[Ru(bpy)2] and α‐[Ru(azpy)2] moieties is the same, this binding mode does not explain the earlier observed difference in cytotoxicity between cis‐[Ru(bpy)2Cl2] and α‐[Ru(azpy)2Cl2].

Binding to DNA Purine Base and Structure−Activity Relationship of a Series of Structurally Related Ru(II) Antitumor Complexes: A Theoretical Study

“…Meanwhile, the fact that the bond dissociation free energies of Ru-A7 adducts in solution are much lower, or even become negative values, suggests that binding of hydrolyzed Ru(II) species to adenine at N7 site is a quite unfavorable process. It is also in agreement with the experimental observation that the coordination of adenine bases to the α-[Ru(azpy) 2 ] moiety results in didentate coordination via the N6 and N7 atoms. , …”

Binding to DNA Purine Base and Structure−Activity Relationship of a Series of Structurally Related Ru(II) Antitumor Complexes: A Theoretical Study

“…Meanwhile, the fact that the bond dissociation free energies of Ru-A7 adducts in solution are much lower, or even become negative values, suggests that binding of hydrolyzed Ru(II) species to adenine at N7 site is a quite unfavorable process. It is also in agreement with the experimental observation that the coordination of adenine bases to the α-[Ru(azpy) 2 ] moiety results in didentate coordination via the N6 and N7 atoms. , …”

Head‐to‐Head Right‐Handed Cross‐Links of the Antitumor‐Active Bis(μ‐N,N′‐di‐p‐tolylformamidinato)dirhodium(II,II) Unit with the Dinucleotides d(GpA) and d(ApG)

“…Although the NMR data for [Rh 2 (DTolF) 2 {d(GpA)}] and d(GpA) were collected in different solvents (the complex is not soluble in D 2 O only), a comparison of the aromatic proton chemical shifts is still useful: the resonance of 5′‐G H8 is shifted downfield (Δ δ ≈1 ppm), whereas the 3′‐A H8 and H2 protons are shifted upfield by Δ δ ≈0.40 and 0.13 ppm, respectively, as compared to the corresponding protons in free d(GpA). Similar changes to the chemical shifts of the aromatic proton resonances of metalated adenine rings have been previously recorded in the literature 47. 48 Additionally, downfield shifts of the guanine H8 proton indicate metal binding to site N7 of the base 22.…”

“…The previous H2/N1H DQF‐COSY cross‐peaks provide unambiguous evidence that the N1 sites of the adenine bases in [Rh 2 (DTolF) 2 {d(GpA)}] and [Rh 2 (DTolF) 2 {d(ApG)}] are protonated and thus present in the rare imino form, which is stabilized by the bidentate metalation of the N7 and N6 sites 25. 47, 49 Moreover, in the ROESY spectra in CD 3 CN at−38 °C, ROESY cross‐peaks are observed between the 3′‐A N1H ( δ =10.32 ppm) with 3′‐A N6H ( δ =6.98 ppm) resonances (for [Rh 2 (DTolF) 2 {d(GpA)}]) and between 5′‐A N1H ( δ =7.29 ppm) with 5′‐A N6H ( δ =7.10 ppm) resonances (for [Rh 2 (DTolF) 2 {d(ApG)}]), further confirming protonation of the adenine N1H sites of the adducts (the X‐ray crystallographic study of cis ‐[Rh 2 (DTolF) 2 (9‐EtAdeH) 2 ](BF 4 ) 2 showed that the adenine N1H–N6H distance is 2.25 Å40, 41).…”

Unprecedented Head-to-Head Right-Handed Cross-Links between the Antitumor Bis(μ-N,N‘-di-p-tolylformamidinate) Dirhodium(II,II) Core and the Dinucleotide d(ApA) with the Adenine Bases in the Rare Imino Form

“…Although the NMR data for Rh 2 (DTolF) 2 {d(ApA)} and d(ApA) were collected in different solvents (the complex is not soluble in D 2 O only), a comparison of the aromatic proton chemical shifts is still useful: the resonance of 5′-A H8 is downfield shifted (∆δ ≈ 0.5 ppm), the 3′-A H8 is upfield shifted (∆δ ≈ 0.1 ppm), whereas both the H2 protons are upfield shifted by ∆δ ≈ 0.2 ppm, as compared to free d(ApA). Similar changes to the chemical shifts of the aromatic proton resonances of metalated adenine rings have been previously recorded in the literature, 42,44,85 and ∼0.2 ppm upfield shifts of the nonexchangeable proton resonances of deoxyadenosine have been associated with formation of the imino tautomer of the base. 78 As will be inferred from the 2D NMR spectroscopic data (vide infra), the adenine bases in Rh 2 (DTolF) 2 {d(ApA)} have a HH orientation (Chart 4), and it has been established from d(GpG) metalated adducts that HH orientation of the bases gives rise to disparate and downfield H8 resonances.…”

“…The presence of the adenine bases in the rare imino form due to bidentate metalation of the N6/N7 sites is further corroborated by the H2/N1H cross-peaks (with a doublet coupling pattern) in the [ 1 H− 1 H] DQF-COSY spectrum of Rh 2 (DTolF) 2 {d(ApA)} in CD 3 CN- d 3 at −38 °C (Figure ) and the N1H/N6H cross-peaks in the ROESY spectrum of Rh 2 (DTolF) 2 {d(ApA)}; the latter provide unambiguous evidence that the N1 sites of the adenine bases in Rh 2 (DTolF) 2 {d(ApA)} are protonated below the determined p K a value (∼7.0), which is considerably reduced as compared to the imino form of the free base (vide supra). Furthermore, the downfield shifts of the C2 and C6 NMR resonances due to metalation of the adenine rings are compensated by the opposite upfield effect due to protonation of the N1H sites and support the formation of the rare imino tautomer of the bases. , …”

Binding to DNA Purine Base and Structure−Activity Relationship of a Series of Structurally Related Ru(II) Antitumor Complexes: A Theoretical Study

“…Meanwhile, the fact that the bond dissociation free energies of Ru-A7 adducts in solution are much lower, or even become negative values, suggests that binding of hydrolyzed Ru(II) species to adenine at N7 site is a quite unfavorable process. It is also in agreement with the experimental observation that the coordination of adenine bases to the α-[Ru(azpy) 2 ] moiety results in didentate coordination via the N6 and N7 atoms. , …”

Head‐to‐Head Right‐Handed Cross‐Links of the Antitumor‐Active Bis(μ‐N,N′‐di‐p‐tolylformamidinato)dirhodium(II,II) Unit with the Dinucleotides d(GpA) and d(ApG)

“…Although the NMR data for [Rh 2 (DTolF) 2 {d(GpA)}] and d(GpA) were collected in different solvents (the complex is not soluble in D 2 O only), a comparison of the aromatic proton chemical shifts is still useful: the resonance of 5′‐G H8 is shifted downfield (Δ δ ≈1 ppm), whereas the 3′‐A H8 and H2 protons are shifted upfield by Δ δ ≈0.40 and 0.13 ppm, respectively, as compared to the corresponding protons in free d(GpA). Similar changes to the chemical shifts of the aromatic proton resonances of metalated adenine rings have been previously recorded in the literature 47. 48 Additionally, downfield shifts of the guanine H8 proton indicate metal binding to site N7 of the base 22.…”

“…The previous H2/N1H DQF‐COSY cross‐peaks provide unambiguous evidence that the N1 sites of the adenine bases in [Rh 2 (DTolF) 2 {d(GpA)}] and [Rh 2 (DTolF) 2 {d(ApG)}] are protonated and thus present in the rare imino form, which is stabilized by the bidentate metalation of the N7 and N6 sites 25. 47, 49 Moreover, in the ROESY spectra in CD 3 CN at−38 °C, ROESY cross‐peaks are observed between the 3′‐A N1H ( δ =10.32 ppm) with 3′‐A N6H ( δ =6.98 ppm) resonances (for [Rh 2 (DTolF) 2 {d(GpA)}]) and between 5′‐A N1H ( δ =7.29 ppm) with 5′‐A N6H ( δ =7.10 ppm) resonances (for [Rh 2 (DTolF) 2 {d(ApG)}]), further confirming protonation of the adenine N1H sites of the adducts (the X‐ray crystallographic study of cis ‐[Rh 2 (DTolF) 2 (9‐EtAdeH) 2 ](BF 4 ) 2 showed that the adenine N1H–N6H distance is 2.25 Å40, 41).…”

Unprecedented Head-to-Head Right-Handed Cross-Links between the Antitumor Bis(μ-N,N‘-di-p-tolylformamidinate) Dirhodium(II,II) Core and the Dinucleotide d(ApA) with the Adenine Bases in the Rare Imino Form

“…Although the NMR data for Rh 2 (DTolF) 2 {d(ApA)} and d(ApA) were collected in different solvents (the complex is not soluble in D 2 O only), a comparison of the aromatic proton chemical shifts is still useful: the resonance of 5′-A H8 is downfield shifted (∆δ ≈ 0.5 ppm), the 3′-A H8 is upfield shifted (∆δ ≈ 0.1 ppm), whereas both the H2 protons are upfield shifted by ∆δ ≈ 0.2 ppm, as compared to free d(ApA). Similar changes to the chemical shifts of the aromatic proton resonances of metalated adenine rings have been previously recorded in the literature, 42,44,85 and ∼0.2 ppm upfield shifts of the nonexchangeable proton resonances of deoxyadenosine have been associated with formation of the imino tautomer of the base. 78 As will be inferred from the 2D NMR spectroscopic data (vide infra), the adenine bases in Rh 2 (DTolF) 2 {d(ApA)} have a HH orientation (Chart 4), and it has been established from d(GpG) metalated adducts that HH orientation of the bases gives rise to disparate and downfield H8 resonances.…”

“…The presence of the adenine bases in the rare imino form due to bidentate metalation of the N6/N7 sites is further corroborated by the H2/N1H cross-peaks (with a doublet coupling pattern) in the [ 1 H− 1 H] DQF-COSY spectrum of Rh 2 (DTolF) 2 {d(ApA)} in CD 3 CN- d 3 at −38 °C (Figure ) and the N1H/N6H cross-peaks in the ROESY spectrum of Rh 2 (DTolF) 2 {d(ApA)}; the latter provide unambiguous evidence that the N1 sites of the adenine bases in Rh 2 (DTolF) 2 {d(ApA)} are protonated below the determined p K a value (∼7.0), which is considerably reduced as compared to the imino form of the free base (vide supra). Furthermore, the downfield shifts of the C2 and C6 NMR resonances due to metalation of the adenine rings are compensated by the opposite upfield effect due to protonation of the N1H sites and support the formation of the rare imino tautomer of the bases. , …”

Binding to DNA Purine Base and Structure−Activity Relationship of a Series of Structurally Related Ru(II) Antitumor Complexes: A Theoretical Study

“…Meanwhile, the fact that the bond dissociation free energies of Ru-A7 adducts in solution are much lower, or even become negative values, suggests that binding of hydrolyzed Ru(II) species to adenine at N7 site is a quite unfavorable process. It is also in agreement with the experimental observation that the coordination of adenine bases to the α-[Ru(azpy) 2 ] moiety results in didentate coordination via the N6 and N7 atoms. , …”

Head‐to‐Head Right‐Handed Cross‐Links of the Antitumor‐Active Bis(μ‐N,N′‐di‐p‐tolylformamidinato)dirhodium(II,II) Unit with the Dinucleotides d(GpA) and d(ApG)

“…Although the NMR data for [Rh 2 (DTolF) 2 {d(GpA)}] and d(GpA) were collected in different solvents (the complex is not soluble in D 2 O only), a comparison of the aromatic proton chemical shifts is still useful: the resonance of 5′‐G H8 is shifted downfield (Δ δ ≈1 ppm), whereas the 3′‐A H8 and H2 protons are shifted upfield by Δ δ ≈0.40 and 0.13 ppm, respectively, as compared to the corresponding protons in free d(GpA). Similar changes to the chemical shifts of the aromatic proton resonances of metalated adenine rings have been previously recorded in the literature 47. 48 Additionally, downfield shifts of the guanine H8 proton indicate metal binding to site N7 of the base 22.…”

“…The previous H2/N1H DQF‐COSY cross‐peaks provide unambiguous evidence that the N1 sites of the adenine bases in [Rh 2 (DTolF) 2 {d(GpA)}] and [Rh 2 (DTolF) 2 {d(ApG)}] are protonated and thus present in the rare imino form, which is stabilized by the bidentate metalation of the N7 and N6 sites 25. 47, 49 Moreover, in the ROESY spectra in CD 3 CN at−38 °C, ROESY cross‐peaks are observed between the 3′‐A N1H ( δ =10.32 ppm) with 3′‐A N6H ( δ =6.98 ppm) resonances (for [Rh 2 (DTolF) 2 {d(GpA)}]) and between 5′‐A N1H ( δ =7.29 ppm) with 5′‐A N6H ( δ =7.10 ppm) resonances (for [Rh 2 (DTolF) 2 {d(ApG)}]), further confirming protonation of the adenine N1H sites of the adducts (the X‐ray crystallographic study of cis ‐[Rh 2 (DTolF) 2 (9‐EtAdeH) 2 ](BF 4 ) 2 showed that the adenine N1H–N6H distance is 2.25 Å40, 41).…”

Unprecedented Head-to-Head Right-Handed Cross-Links between the Antitumor Bis(μ-N,N‘-di-p-tolylformamidinate) Dirhodium(II,II) Core and the Dinucleotide d(ApA) with the Adenine Bases in the Rare Imino Form

“…Although the NMR data for Rh 2 (DTolF) 2 {d(ApA)} and d(ApA) were collected in different solvents (the complex is not soluble in D 2 O only), a comparison of the aromatic proton chemical shifts is still useful: the resonance of 5′-A H8 is downfield shifted (∆δ ≈ 0.5 ppm), the 3′-A H8 is upfield shifted (∆δ ≈ 0.1 ppm), whereas both the H2 protons are upfield shifted by ∆δ ≈ 0.2 ppm, as compared to free d(ApA). Similar changes to the chemical shifts of the aromatic proton resonances of metalated adenine rings have been previously recorded in the literature, 42,44,85 and ∼0.2 ppm upfield shifts of the nonexchangeable proton resonances of deoxyadenosine have been associated with formation of the imino tautomer of the base. 78 As will be inferred from the 2D NMR spectroscopic data (vide infra), the adenine bases in Rh 2 (DTolF) 2 {d(ApA)} have a HH orientation (Chart 4), and it has been established from d(GpG) metalated adducts that HH orientation of the bases gives rise to disparate and downfield H8 resonances.…”

“…The presence of the adenine bases in the rare imino form due to bidentate metalation of the N6/N7 sites is further corroborated by the H2/N1H cross-peaks (with a doublet coupling pattern) in the [ 1 H− 1 H] DQF-COSY spectrum of Rh 2 (DTolF) 2 {d(ApA)} in CD 3 CN- d 3 at −38 °C (Figure ) and the N1H/N6H cross-peaks in the ROESY spectrum of Rh 2 (DTolF) 2 {d(ApA)}; the latter provide unambiguous evidence that the N1 sites of the adenine bases in Rh 2 (DTolF) 2 {d(ApA)} are protonated below the determined p K a value (∼7.0), which is considerably reduced as compared to the imino form of the free base (vide supra). Furthermore, the downfield shifts of the C2 and C6 NMR resonances due to metalation of the adenine rings are compensated by the opposite upfield effect due to protonation of the N1H sites and support the formation of the rare imino tautomer of the bases. , …”