Structural Characterization of the Metalized Radical Cations of Adenosine ([Ade+Li-H]•+ and [Ade+Na-H]•+) by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Studies

Nucleoside radicals are key intermediates in the process of DNA damage, and alkali metal ions are a common group of ions in living organisms. However, so far, there has been a significant lack of research on the structural effects of alkali metal ions on nucleoside free radicals. In this study, we report a new method for generating metalized nucleoside radical cations in the gas phase. The radical cations [Ade+M-H]•+ (M = Li, Na) are generated by the 280 nm ultraviolet photodissociation (UVPD) of the precursor ions of lithiated and sodiated ions of 2-iodoadenine in a Fourier transform ion cyclotron resonance (FT ICR) cell. Further infrared multiphoton dissociation (IRMPD) spectra of both radical cations were recorded in the region of 2750-3750 cm-1. By combining these results with theoretical calculations, the most stable isomers of both radicals can be identified, which share the common characteristics of triple coordination patterns of the metal ions. For both radical species, the lowest-energy isomers undergo hydrogen transfer. Although the sugar ring in the most stable isomer of [Ade+Li-H]•+ is in a (South, syn) conformation similar to that of [Ado+Na]+, [Ade+Na-H]•+ is distinguished by the unexpected opening of the sugar ring. Their theoretical spectra are in good agreement with experimental spectra. However, due to the flexibility of the structures and the complexity of their potential energy surfaces, the hydrogen transfer pathways still need to be further studied. Considering that the free radicals formed directly after C-I cleavage have some similar spectral characteristics, the existence of these corresponding isomers cannot be ruled out. The findings imply that the structures of nucleoside radicals may be significantly influenced by the attached alkali metal ions. More detailed experiments and theoretical calculations are still crucial.

Structure-activity features of purines and their receptors: implications in cell physiopathology

The purine molecular structure consists of fused pyrimidine and imidazole rings. Purines are main pieces that conform the structure of nucleic acids which rule the inheritance processes. Purines also work as metabolic intermediates in different cell functions and as messengers in the signaling pathways throughout cellular communication. Purines, mainly ATP and adenosine (ADO), perform their functional and pharmacological properties because of their structural/chemical characteristics that make them either targets of mutagenesis, mother frameworks for designing molecules with controlled effects (e.g. anti-cancer), or chemical donors (e.g., of methyl groups, which represent a potential chemoprotective action against cancer). Purines functions also come from their effect on specific receptors, channel-linked and G-protein coupled for ATP, and exclusively G-coupled receptors for ADO (also known as ADORAs), which are involved in cell signaling pathways, there, purines work as chemical messengers with autocrine, paracrine, and endocrine actions that regulate cell metabolism and immune response in tumor progression which depends on the receptor types involved in these signals. Purines also have antioxidant and anti-inflammatory properties and participate in the cell energy homeostasis. Therefore, purine physiology is important for a variety of functions relevant to cellular health; thus, when these molecules present a homeostatic imbalance, the stability and survival of the cellular systems become compromised.

Substituent effects of nitro group in cyclic compounds

Numerous studies on nitro group properties are associated with its high electron-withdrawing ability, by means of both resonance and inductive effect. The substituent effect of the nitro group may be well described using either traditional substituent constants or characteristics based on quantum chemistry, i.e., cSAR, SESE, and pEDA/sEDA models. Interestingly, the cSAR descriptor allows to describe the electron-attracting properties of the nitro group regardless of the position and the type of system. Analysis of classical and reverse substituent effects of the nitro group in various systems indicates strong pi-electron interactions with electron-donating substituents due to the resonance effect. This significantly affects the pi-electron delocalization of the aromatic ring decreasing the aromatic character, evidenced clearly by HOMA values. Use of the pEDA/sEDA model allows to measure the population of electrons transferred from the ring to the nitro group.

Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs

For many years, non-covalently bonded complexes of nucleobases have attracted considerable interest. However, there is a lack of information about the nature of hydrogen bonding between nucleobases when the bonding is affected by metal coordination to one of the nucleobases, and how the individual hydrogen bonds and aromaticity of nucleobases respond to the presence of the metal cation. Here we report a DFT computational study of nucleobase pairs interacting with alkali metal cations. The metal cations contribute to the stabilization of the base pairs to varying degrees depending on their position. The energy decomposition analysis revealed that the nature of bonding between nucleobases does not change much upon metal coordination. The effect of the cations on individual hydrogen bonds were described by changes in VDD charges on frontier atoms, H-bond length, bond energy from NBO analysis, and the delocalization index from QTAIM calculations. The aromaticity changes were determined by a HOMA index.

Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity

Adenine, one of the components of DNA/RNA helices, has the ability to form self-organizing structures with cyclic hydrogen bonds (A₄), similar to guanine quartets. Here, we report a computational investigation of the effect of substituents (X = NO₂, Cl, F, H, Me, and NH₂) on the electronic structure of 9H-adenine and its quartets (A₄-N1, A₄-N3, and A₄-N7). DFT calculations were used to show the relationships between the electronic nature of the substituents, strength of H-bonds in the quartets, and aromaticity of five- and six-membered rings of adenine. We demonstrated how the remote substituent X modifies the proton-donating properties of the NH₂ group involved in the H-bonds within quartets and how the position of the substituent and its electronic nature affect the stability of the quartets. We also showed the possible changes in electronic properties of the substituent and aromaticity of adenine rings caused by tetramer formation. The results indicate that the observed relationships depend on the A₄ type. Moreover, the same substituent can both strengthen and weaken intermolecular interactions, depending on the substitution position.

Substituent effects on hydrogen bonds in adenine quartets and aromaticity of adenine rings depend on the quartet type. A₄-N3 and A₄-N7 quartets are more responsive to the electronic nature of substituents than A₄-N1.

Impact of the Substituents on the Electronic Structure of the Four Most Stable Tautomers of Purine and Their Adenine Analogues

Substituent effects at the C2-, C8-, and N-positions of adenine and purine on the structural and π-electronic changes in their four tautomers were studied using the B97D3/aug-cc-pvdz computational level. The effect of various substituents (NO2, CN, CHO, Cl, F, H, Me, OMe, OH, and NH2) was characterized by the charge of the substituent active region (cSAR) approach and Hammett substituent constants σ. It has been found that for both adenine and purine derivatives, substituents from the C8-X position have a stronger influence on their electronic structure than from the C2-X and N-X positions. The presence of the amino group in adenine enhances the substituent effect compared to that which occurs in purine. In addition, its electronic structure is more sensitive to the effect of the substituent in 3H and 1H than in the 9H and 7H adenine tautomers. For a given substituent, a large variation in cSAR(X) values is observed, strongly dependent on the substitution position. For 7H and 9H adenine tautomers for C8-X systems, substituents reduce the aromaticity of the five-membered rings but increase the aromaticity of the six-membered rings.

Hydrogen bond design principles

Hydrogen bonding principles are at the core of supramolecular design. This overview features a discussion relating molecular structure to hydrogen bond strengths, highlighting the following electronic effects on hydrogen bonding: electronegativity, steric effects, electrostatic effects, π-conjugation, and network cooperativity. Historical developments, along with experimental and computational efforts, leading up to the birth of the hydrogen bond concept, the discovery of nonclassical hydrogen bonds (C-H…O, O-H…π, dihydrogen bonding), and the proposal of hydrogen bond design principles (e.g., secondary electrostatic interactions, resonance-assisted hydrogen bonding, and aromaticity effects) are outlined. Applications of hydrogen bond design principles are presented.

Application of the Extended HOMED (Harmonic Oscillator Model of Aromaticity) Index to Simple and Tautomeric Five-Membered Heteroaromatic Cycles with C, N, O, P, and S Atoms

The geometry-based HOMA (Harmonic Oscillator Model of Aromaticity) descriptor, based on the reference compounds of different delocalizations of n- and π-electrons, can be applied to molecules possessing analogous bonds, e.g., only CC, only CN, only CO, etc. For compounds with different heteroatoms and a different number of CC, CX, XX, and XY bonds, its application leads to some discrepancies. For this reason, the structural descriptor was modified and the HOMED (Harmonic Oscillator Model of Electron Delocalization) index defined. In 2010, the HOMED index was parameterized for compounds with C, N and O atoms. For parametrization, the reference molecules of similar delocalizations of n- and π-electrons were employed. In this paper, the HOMED index was extended to compounds containing the CP, CS, NN, NP, PP, NO, NS, PO, and PS bonds. For geometrical optimization of all reference molecules and of all investigated heterocompounds, the same quantum–chemical method {B3LYP/6-311+G(d,p)} was used to eliminate errors of the HOMED estimation. For some tautomeric systems, the Gn methods were also employed to confirm tautomeric preferences. The extended HOMED index was applied to five-membered heterocycles, simple furan and thiophene, and their N and P derivatives as well as for tautomeric pyrrole and phosphole and their N and P derivatives. The effects of additional heteroatom(s) in the ring on the HOMED values for furan are parallel to those for thiophene. For pyrroles, aromaticity dictates the tautomeric preferences. An additional N atom in the ring only slightly affects the HOMED values for the favored and well delocalized NH tautomers. Significant changes take place for their rare CH forms. When intramolecular proton-transfer is considered for phosphole and its P derivatives, the PH tautomers seem to be favored only for 1,2,3-triphosphole/1,2,5-triphosphole and for 1,2,3,5-tetraphosphole. For other phospholes, the CH forms have smaller Gibbs energies than the PH isomers. For phosphazoles, the labile proton in the favored form is linked to the N atom. The PH forms have smaller HOMED indices than the NH tautomers but higher than the CH ones.

Geometric and energetic consequences of prototropy for adenine and its structural models – a review

Prototropy for adenine and its convenient models causes parallel changes of geometric (HOMED) and energetic (ΔE) parameters for neutral tautomers.

Tautomerisation of thymine acts against the Hückel 4N + 2 rule. The effect of metal ions and H-bond complexations on the electronic structure of thymine

Not necessarily the π-electron delocalization is responsible for the stability of thymine tautomers.