Mechanisms of Ligand Hyperfine Coupling in Transition-Metal Complexes: σ and π Transmission Pathways.

Theoretical interpretation of hyperfine interactions was pioneered in the 1950s-1960s by the seminal works of McConnell, Karplus, and others for organic radicals and by Watson and Freeman for transition-metal (TM) complexes. In this work, we investigate a series of octahedral Ru(III) complexes with aromatic ligands to understand the mechanism of transmission of the spin density from the d-orbital of the metal to the s-orbitals of the ligand atoms. Spin densities and spin populations underlying ligand hyperfine couplings are analyzed in terms of π-conjugative or σ-hyperconjugative delocalization vs spin polarization based on symmetry considerations and restricted open-shell vs unrestricted wave function analysis. The transmission of spin density is shown to be most efficient in the case of symmetry-allowed π-conjugative delocalization, but when the π-conjugation is partially or fully symmetry-forbidden, it can be surpassed by σ-hyperconjugative delocalization. Despite a lower spin population of the ligand in σ-hyperconjugative transmission, the hyperfine couplings can be larger because of the direct involvement of the ligand s-orbitals in this delocalization pathway. We demonstrate a quantitative correlation between the hyperfine couplings of aromatic ligand atoms and the characteristics of the metal-ligand bond modulated by the trans substituent, a hyperfine trans effect.

Paramagnetic Effects in NMR Spectroscopy of Transition-Metal Complexes: Principles and Chemical Concepts.

ConspectusMagnetic resonance techniques represent a fundamental class of spectroscopic methods used in physics, chemistry, biology, and medicine. Electron paramagnetic resonance (EPR) is an extremely powerful technique for characterizing systems with an open-shell electronic nature, whereas nuclear magnetic resonance (NMR) has traditionally been used to investigate diamagnetic (closed-shell) systems. However, these two techniques are tightly connected by the electron-nucleus hyperfine interaction operating in paramagnetic (open-shell) systems. Hyperfine interaction of the nuclear spin with unpaired electron(s) induces large temperature-dependent shifts of nuclear resonance frequencies that are designated as hyperfine NMR shifts (δHF).Three fundamental physical mechanisms shape the total hyperfine interaction: Fermi-contact, paramagnetic spin-orbit, and spin-dipolar. The corresponding hyperfine NMR contributions can be interpreted in terms of through-bond and through-space effects. In this Account, we provide an elemental theory behind the hyperfine interaction and NMR shifts and describe recent progress in understanding the structural and electronic principles underlying individual hyperfine terms.The Fermi-contact (FC) mechanism reflects the propagation of electron-spin density throughout the molecule and is proportional to the spin density at the nuclear position. As the imbalance in spin density can be thought of as originating at the paramagnetic metal center and being propagated to the observed nucleus via chemical bonds, FC is an excellent indicator of the bond character. The paramagnetic spin-orbit (PSO) mechanism originates in the orbital current density generated by the spin-orbit coupling interaction at the metal center. The PSO mechanism of the ligand NMR shift then reflects the transmission of the spin polarization through bonds, similar to the FC mechanism, but it also makes a substantial through-space contribution in long-range situations. In contrast, the spin-dipolar (SD) mechanism is relatively unimportant at short-range with significant spin polarization on the spectator atom. The PSO and SD mechanisms combine at long-range to form the so-called pseudocontact shift, traditionally used as a structural and dynamics probe in paramagnetic NMR (pNMR). Note that the PSO and SD terms both contribute to the isotropic NMR shift only at the relativistic spin-orbit level of theory.We demonstrate the advantages of calculating and analyzing the NMR shifts at relativistic two- and four-component levels of theory and present analytical tools and approaches based on perturbation theory. We show that paramagnetic NMR effects can be interpreted by spin-delocalization and spin-polarization mechanisms related to chemical bond concepts of electron conjugation in π-space and hyperconjugation in σ-space in the framework of the molecular orbital (MO) theory. Further, we discuss the effects of environment (supramolecular interactions, solvent, and crystal packing) and demonstrate applications of hyperfine shifts in determining the structure of paramagnetic Ru(III) compounds and their supramolecular host-guest complexes with macrocycles.In conclusion, we provide a short overview of possible pNMR applications in the analysis of spectra and electronic structure and perspectives in this field for a general chemical audience.

The Impact of ortho-substituents on Bonding in Silver(I) and Halogen(I) Complexes of 2-Mono- and 2,6-Disubstituted Pyridines: An In-Depth Experimental and Theoretical Study.

The coordination nature of 2-mono- and 2,6-disubstituted pyridines with electron-withdrawing halogen and electron-donating methyl groups for [N-X-N]+ (X=I, Br) complexations have been studied using 15 N NMR, X-ray crystallography, and Density Functional Theory (DFT) calculations. The 15 N NMR chemical shifts reveal iodine(I) and bromine(I) prefer to form complexes with 2-substituted pyridines and only 2,6-dimethylpyridine. The crystalline halogen(I) complexes of 2-substituted pyridines were characterized by using X-ray diffraction analysis, but 2,6-dihalopyridines were unable to form stable crystalline halogen(I) complexes due to the lower nucleophilicity of the pyridinic nitrogen. In contrast, the halogen(I) complexes of 2,6-dimethylpyridine, which has a more basic nitrogen, are characterized by X-crystallography, which complements the 15 N NMR studies. DFT calculations reveal that the bond energies for iodine(I) complexes vary between -291 and -351 kJ mol-1 and for bromine between -370 and -427 kJ mol-1 . The bond energies of halogen(I) complexes of 2-halopyridines with more nucleophilic nitrogen are 66-76 kJ mol-1 larger than those of analogous 2,6-dihalopyridines with less nucleophilic nitrogen. The experimental and DFT results show that the electronic influence of ortho-halogen substituents on pyridinic nitrogen leads to a completely different preference for the coordination bonding of halogen(I) ions, providing new insights into bonding in halogen(I) chemistry.

Quadratic Spin-Orbit Mechanism of the Electronic g-Tensor.

Understanding how the electronic g-tensor is linked to the electronic structure is desirable for the correct interpretation of electron paramagnetic resonance spectra. For heavy-element compounds with large spin-orbit (SO) effects, this is still not completely clear. We report our investigation of quadratic SO contributions to the g-shift in heavy transition metal complexes. We implemented third-order perturbation theory in order to analyze the contributions arising from frontier molecular spin orbitals (MSOs). We show that the dominant quadratic SO term─spin-Zeeman (SO2/SZ)─generally makes a negative contribution to the g-shift, irrespective of the particular electronic configuration or molecular symmetry. We further analyze how the SO2/SZ contribution adds to or subtracts from the linear orbital-Zeeman (SO/OZ) contribution to the individual principal components of the g-tensor. Our study suggests that the SO2/SZ mechanism decreases the anisotropy of the g-tensor in early transition metal complexes and increases it in late transition metal complexes. Finally, we apply MSO analysis to the investigation of g-tensor trends in a set of closely related Ir and Rh pincer complexes and evaluate the influence of different chemical factors (the nuclear charge of the central atom and the terminal ligand) on the magnitudes of the g-shifts. We expect our conclusions to aid the understanding of spectra in magnetic resonance investigations of heavy transition metal compounds.

Nature of NMR Shifts in Paramagnetic Octahedral Ru(III) Complexes with Axial Pyridine-Based Ligands.

In recent decades, transition-metal coordination compounds have been extensively studied for their antitumor and antimetastatic activities. In this work, we synthesized a set of symmetric and asymmetric Ru(III) and Rh(III) coordination compounds of the general structure (Na+/K+/PPh4+/LH+) [trans-MIIIL(eq)nL(ax)2]- (M = RuIII or RhIII; L(eq) = Cl, n = 4; L(eq) = ox, n = 2; L(ax) = 4-R-pyridine, R = CH3, H, C6H5, COOH, CF3, CN; L(ax) = DMSO-S) and systematically investigated their structure, stability, and NMR properties. 1H and 13C NMR spectra measured at various temperatures were used to break down the total NMR shifts into the orbital (temperature-independent) and hyperfine (temperature-dependent) contributions. The hyperfine NMR shifts for paramagnetic Ru(III) compounds were analyzed in detail using relativistic density functional theory (DFT). The effects of (i) the 4-R substituent of pyridine, (ii) the axial trans ligand L(ax), and (iii) the equatorial ligands L(eq) on the distribution of spin density reflected in the "through-bond" (contact) and the "through-space" (pseudocontact) contributions to the hyperfine NMR shifts of the individual atoms of the pyridine ligands are rationalized. Further, we demonstrate the large effects of the solvent on the hyperfine NMR shifts and discuss our observations in the general context of the paramagnetic NMR spectroscopy of transition-metal complexes.

Relativistic Spin-Orbit Electronegativity and the Chemical Bond Between a Heavy Atom and a Light Atom.

Radek Marek and his co-workers at Masaryk University, Brno, Czechia have been invited to prepare the cover of this issue. The image depicts the relativistic spin-orbit coupling that is associated with the presence of a heavy atom in a molecule influencing the electron density around a light atom and modulating the chemical bond between these two atoms. Read the full text of the article at 10.1002/chem.202200277.

Relativistic Spin-Orbit Electronegativity and the Chemical Bond Between a Heavy Atom and a Light Atom.

Relativistic effects are known to alter the chemical bonds and spectroscopic properties of heavy-element compounds. In this work, we introduce the concept of spin-orbit (SO) electronegativity of a heavy atom, as reflected by an SO-induced change in the interatomic distance between the heavy atom (HA) and a neighboring light atom (LA). We provide a transparent interpretation of these SO effects by using the concept of spin-orbit electron deformation density (SO-EDD). Spin-orbit coupling at the HA induces rearrangement of the electron density for the scalar-relativistically optimized geometry that, in turn, exerts a new force on the LA. The resulting expansion or contraction of the HA-LA bond depends on the nature and electron configuration of the HA. In addition, we quantify the change in atomic electronegativity induced by SO coupling for a series of hydrides, thereby complementing the SO-EDD picture. The trends in the SO-induced electronegativity and the HA-LA bond length across the periodic table of elements are demonstrated and interpreted, and also linked, intuitively, with the SO-induced NMR shielding at the LA.

Supramolecular Coronation of Platinum(II) Complexes by Macrocycles: Structure, Relativistic DFT Calculations, and Biological Effects.

Platinum-based anticancer drugs are actively developed utilizing lipophilic ligands or drug carriers for the efficient penetration of biomembranes, reduction of side effects, and tumor targeting. We report the development of a supramolecular host-guest system built on cationic platinum(II) compounds bearing ligands anchored in the cavity of the macrocyclic host. The host-guest binding and hydrolysis process on the platinum core were investigated in detail by using NMR, MS, X-ray diffraction, and relativistic DFT calculations. The encapsulation process in cucurbit[7]uril unequivocally promotes the stability of hydrolyzed dicationic cis-[PtII(NH3)2(H2O)(NH2-R)]2+ compared to its trans isomer. Biological screening on the ovarian cancer lines A2780 and A2780/CP shows time-dependent toxicity. Notably, the reported complex and its ß-cyclodextrin (ß-CD) assembly achieve the same cellular uptake as cisplatin and cisplatin@ß-CD, respectively, while maintaining a significantly lower toxicity profile.

Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip.

Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence-structure-stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.

c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry.

Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π-π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.

Crystal and Substituent Effects on Paramagnetic NMR Shifts in Transition-Metal Complexes.

Nuclear magnetic resonance (NMR) spectroscopy of paramagnetic molecules provides detailed information about their molecular and electron-spin structure. The paramagnetic NMR spectrum is a very rich source of information about the hyperfine interaction between the atomic nuclei and the unpaired electron density. The Fermi-contact contribution to ligand hyperfine NMR shifts is particularly informative about the nature of the metal-ligand bonding and the structural arrangements of the ligands coordinated to the metal center. In this account, we provide a detailed experimental and theoretical NMR study of compounds of Cr(III) and Cu(II) coordinated with substituted acetylacetonate (acac) ligands in the solid state. For the first time, we report the experimental observation of extremely paramagnetically deshielded 13C NMR resonances for these compounds in the range of 900-1200 ppm. We demonstrate an excellent agreement between the experimental NMR shifts and those calculated using relativistic density-functional theory. Crystal packing is shown to significantly influence the NMR shifts in the solid state, as demonstrated by theoretical calculations of various supramolecular clusters. The resonances are assigned to individual atoms in octahedral Cr(acac)3 and square-planar Cu(acac)2 compounds and interpreted by different electron configurations and magnetizations at the central metal atoms resulting in different spin delocalizations and polarizations of the ligand atoms. Further, effects of substituents on the 13C NMR resonance of the ipso carbon atom reaching almost 700 ppm for Cr(acac)3 compounds are interpreted based on the analysis of Fermi-contact hyperfine contributions.

Modes of Micromolar Host-Guest Binding of ß-Cyclodextrin Complexes Revealed by NMR Spectroscopy in Salt Water.

Multitopic supramolecular guests with finely tuned affinities toward widely explored cucurbit[n]urils (CBs) and cyclodextrins (CDs) have been recently designed and tested as functional components of advanced supramolecular systems. We employed various spacers between the adamantane cage and a cationic moiety as a tool for tuning the binding strength toward CB7 to prepare a set of model guests with KCB7 and Kß-CD values of (0.6-5.0) × 1010 M-1 and (0.6-2.6) × 106 M-1, respectively. These accessible adamantylphenyl-based binding motifs open a way toward supramolecular components with an outstanding affinity toward ß-cyclodextrin. 1H NMR experiments performed in 30% CaCl2/D2O at 273 K along with molecular dynamics simulations allowed us to identify two arrangements of the guest@ß-CD complexes. The approach, joining experimental and theoretical methods, provided a better understanding of the structure of cyclodextrin complexes and related molecular recognition, which is highly important for the rational design of drug delivery systems, molecular sensors and switches.

Anatomy of Base Pairing in DNA by Interacting Quantum Atoms.

The formation of purine and pyrimidine base pairs (BPs), which contributes to shaping of the canonical and noncanonical 3D structures of nucleic acids, is one the most investigated phenomena in chemistry and life sciences. In this contribution, the anatomy of the bond energy (BDE) of the base-pairing interaction in 39 different arrangements found experimentally or predicted for DNA structures containing the four common nucleobases (A, C, G, T) in their neutral or protonated forms is described in light of the theory of interacting quantum atoms within the context of the quantum theory of atoms in molecules. The interplay of individual energy components involved in the three stages of the bond formation process (structural deformation, electron-density promotion, and intermolecular interaction) is studied. We recognized that for the neutral BPs, variations in the kinetic and electrostatic contributions to the BDE are rather negligible, leaving the exchange-correlation energy as the main stabilizing component. It is shown that the contribution of the exchange-correlation term can be recovered by including atoms that are formally assumed to be hydrogen bonded (primary interaction). In contrast, to recover the electrostatic component of interaction, one must consider both the primary and secondary (formally nonbonded atoms) interatomic interactions. The results of our study were employed to design new types of BPs with altered bonding anatomy. We demonstrate that improving the electrostatic characteristics of the BPs does not necessarily result in greater interaction energies if weak secondary hydrogen bonding is destroyed. However, the main tuning factor for systems with conserved interacting faces (primary interactions) is the electrostatic component of the interaction energy resulting from the secondary atom-atom electrostatics.

Zwitterionic Ru(III) Complexes: Stability of Metal-Ligand Bond and Host-Guest Binding with Cucurbit[7]uril.

A wide range of ruthenium-based coordination compounds have been reported to possess potential as metallodrugs with anticancer or antimetastatic activity. In this work, we synthesized a set of new zwitterionic Ru(III) compounds bearing ligands derived from N-alkyl (R) systems based on pyridine, 4,4'-bipyridine, or 1,4-diazabicyclo[2.2.2]octane (DABCO). The effects of the ligand(s) and their environment on the coordination stability have been investigated. Whereas the [DABCO-R]+ ligand is shown to be easily split out of a negative [RuCl4]- core, positively charged R-pyridine and R-bipyridine ligands form somewhat more stable Ru(III) complexes and can be used as supramolecular anchors for binding with macrocycles. Therefore, supramolecular host-guest assemblies between the stable zwitterionic Ru(III) guests and the cucurbit[7]uril host were investigated and characterized in detail by using NMR spectroscopy and single-crystal X-ray diffraction. Paramagnetic 1H NMR experiments supplemented by relativistic DFT calculations of the structure and hyperfine NMR shifts were performed to determine the host-guest binding modes in solution. In contrast to the intramolecular hyperfine shifts, dominated by the through-bond Fermi-contact mechanism, supramolecular hyperfine shifts were shown to depend on the "through-space" spin-dipole contributions with structural trends being satisfactorily reproduced by a simple point-dipole approximation.

Relativistic Heavy-Neighbor-Atom Effects on NMR Shifts: Concepts and Trends Across the Periodic Table.

Chemical shifts present crucial information about an NMR spectrum. They show the influence of the chemical environment on the nuclei being probed. Relativistic effects caused by the presence of an atom of a heavy element in a compound can appreciably, even drastically, alter the NMR shifts of the nearby nuclei. A fundamental understanding of such relativistic effects on NMR shifts is important in many branches of chemical and physical science. This review provides a comprehensive overview of the tools, concepts, and periodic trends pertaining to the shielding effects by a neighboring heavy atom in diamagnetic systems, with particular emphasis on the "spin-orbit heavy-atom effect on the light-atom" NMR shift (SO-HALA effect). The analyses and tools described in this review provide guidelines to help NMR spectroscopists and computational chemists estimate the ranges of the NMR shifts for an unknown compound, identify intermediates in catalytic and other processes, analyze conformational aspects and intermolecular interactions, and predict trends in series of compounds throughout the Periodic Table. The present review provides a current snapshot of this important subfield of NMR spectroscopy and a basis and framework for including future findings in the field.

Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA.

BACKGROUND: The i-motif is a tetrameric DNA structure based on the formation of hemiprotonated cytosine-cytosine (C+.C) base pairs. i-motifs are widely used in nanotechnology. In biological systems, i-motifs are involved in gene regulation and in control of genome integrity. In vivo, the i-motif forming sequences are subjects of epigenetic modifications, particularly 5-cytosine methylation. In plants, natively occurring methylation patterns lead to a complex network of C+.C, 5mC+.C and 5mC+.5mC base-pairs in the i-motif stem. The impact of complex methylation patterns (CMPs) on i-motif formation propensity is currently unknown. METHODS: We employed CD and UV-absorption spectroscopies, native PAGE, thermal denaturation and quantum-chemical calculations to analyse the effects of native, native-like, and non-native CMPs in the i-motif stem on the i-motif stability and pKa. RESULTS: CMPs have strong influence on i-motif stability and pKa and influence these parameters in sequence-specific manner. In contrast to a general belief, i) CMPs do not invariably stabilize the i-motif, and ii) when the CMPs do stabilize the i-motif, the extent of the stabilization depends (in a complex manner) on the number and pattern of symmetric 5mC+.5mC or asymmetric 5mC+.C base pairs in the i-motif stem. CONCLUSIONS: CMPs can be effectively used to fine-tune i-motif properties. Our data support the notion of epigenetic modifications as a plausible control mechanism of i-motif formation in vivo. GENERAL SIGNIFICANCE: Our results have implications in epigenetic regulation of telomeric DNA in plants and highlight the potential and limitations of engineered patterning of cytosine methylations on the i-motif scaffold in nanotechnological applications.

Locked and Loaded: Ruthenium(II)-Capped Cucurbit[n]uril-Based Rotaxanes with Antimetastatic Properties.

We report here the first coupling of Ru(II) units with cucurbit[6/7]uril-based pseudorotaxane ligands meant for biological application. The resulting ruthenium-capped rotaxanes were fully characterized, and a structure of one supramolecular system was determined by X-ray diffraction. Because the biological properties of Ru-based metallodrugs are tightly linked to the ligand-exchange processes, the effect of salt concentration on the hydrolysis of chlorides from the Ru(II) center was monitored by using 1H NMR spectroscopy. The biological activity of Ru(II)-based rotaxanes was evaluated for three selected mammalian breast cell lines, HBL-100, MCF-7, and MDA-MB-231. The antimetastatic activity of the assembled cationic Ru(II)-rotaxane systems, evaluated in migration assays against MCF-7 and MDA-MB-231 cell lines, is notably enhanced compared to that of RAPTA-C, a reference that was used. The indicated synergistic effect of combining Ru(II) with a pseudorotaxane unit opens a new direction in searching for anticancer supramolecular metallodrugs.

Electron-Spin Structure and Metal-Ligand Bonding in Open-Shell Systems from Relativistic EPR and NMR: A Case Study of Square-Planar Iridium Catalysts.

Electron and nuclear magnetic resonance spectroscopies are indispensable and powerful methods for investigating the molecular and electronic structures of open-shell systems. We demonstrate that the NMR and EPR parameters are extremely sensitive quantitative probes for the electronic spin density around heavy-metal atoms and the metal-ligand bonding. Using relativistic density-functional theory, we have analyzed the relation between the spin density and the EPR and NMR parameters in paramagnetic iridium(II/IV) complexes with a PNP pincer ligand. As the magnetic-response parameters for compounds containing 5d transition metal(s) are heavily affected by spin-orbit coupling, relativistic effects must be included in the calculations. We have used a recent implementation of the fully relativistic Dirac-Kohn-Sham (DKS) method employing the hybrid PBE0 functional and an implicit solvent model to calculate EPR parameters and hyperfine NMR shifts. The modulation of the metal-ligand bond by the trans substituent (-Cl or ≡N) and the electronic spin structure around the central metal atom and ligands are shown to be reflected in the "long-range" through-bond Fermi-contact (FC) contributions to the ligand 13C and 1H hyperfine couplings. Interestingly, the hyperfine coupling constant of the ligand atom L ( AL) bonded directly to the iridium center changes its sign because of the dominating role of the paramagnetic spin-orbit (PSO) term. Furthermore, the electronic g-shift and the PSO contribution to the ligand AL are shown to invert their signs when nitrogen is substituted for chlorine, reflecting the different formal metal oxidation states and the change in metal-ligand bond character. A full understanding of the substituent effects is provided by using chemical bond concepts in combination with a molecular-orbital (MO) theory analysis of the second-order perturbation theory expression for the EPR parameters. Our findings are easily transferable to other systems containing d-block elements and beyond. Relativistic DFT calculations of magnetic-resonance parameters are expected to frequently assist in future experimental observations and the characterization of hitherto unknown unstable or exotic species.

Protonation of Nucleobases in Single- and Double-Stranded DNA.

Single-stranded model oligodeoxyribonucleotides, each containing a single protonatable base-cytosine, adenine, guanine, or 5-methylcytosine-centrally located in a background of non-protonatable thymine residues, were acid-titrated in aqueous solution, with UV monitoring. The basicity of the central base was shown to depend on the type of the central base and its nearest neighbours and to rise with increasing oligonucleotide length and decreasing ionic strength of the solution. More complex model oligonucleotides, each containing a centrally located 5-methylcytosine base, were comparatively evaluated in single-stranded and double-stranded form, by UV spectroscopy and high-field NMR. The N3 protonation of the 5-methylcytosine moiety in the double-stranded case occurred at much lower pH, at which the duplex was already experiencing general dissociation, than in the single-stranded case. The central guanine:5-methylcytosine base pair remained intact up to this point, possibly due to an unusual alternative protonation on O2 of the 5-methylcytosine moiety, already taking place at neutral or weakly basic pH, as indicated by UV spectroscopy, thus suggesting that 5-methylcytosine sites in double-stranded DNA might be protonated to a significant extent under physiological conditions.