Nucleophilic properties of purine bases: inherent reactivity versus reaction conditions

Stachowicz‐Kuśnierz, Anna; Korchowiec, Jacek

doi:10.1007/s11224-015-0583-y

Cited by 24 publications

(16 citation statements)

References 92 publications

(100 reference statements)

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“…The analysis of interatomic distances suggests that the electron density is delocalized between N7-C8-N9 atoms in the imidazole fragment and between the N1-C2-N3 atoms in the pyrimidine fragment, rather than ascribe a localized negative charge to any single N atom. This agrees with the theoretical work of Stachowicz-Kuśnierz & Korchowiec (2016), according to which the negative charge should be distributed among all the electronegative atoms in the doubly deprotonated guanine anion. To get more details about charge distribution in guanine monoand di-cations quantum-chemical calculations would be necessary.…”

Section: Resultssupporting

confidence: 91%

A new guaninate hydrate K⁺·C₅H₄N₅O⁻·H₂O: crystal structure from 100 to 300 K in a comparison with 2Na⁺·C₅H₃N₅O²⁻·7H₂O

Gaydamaka¹,

Arkhipov²,

Boldyreva³

2021

Acta Crystallogr B Struct Sci Cryst Eng Mater

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A new guanine salt hydrate, K+·C5H4N5O−·H2O, was obtained and characterized by single-crystal X-ray diffraction in the temperature range 100 K–300 K and compared with that of the previously documented sodium salt hydrate (2Na+·C5H3N5O2−·7H2O) [Gur & Shimon (2015). Acta Cryst. E71, 281–283; Gaydamaka et al. (2019). CrystEngComm, 21, 4484–4492]. Both sodium and potassium salt hydrates have channels. However, the structure of the channels, the cation coordination, the protonation (and, respectively, the charge) of the guanine anions, as well as the role of water molecules in the crystal structure are different for the two salt hydrates. In the crystal structures of the potassium salt, the guanine anions are linked via hydrogen bonds into quartets that form open cylindrical channels in a honeycomb framework. Water molecules `line the walls' of the channels, whereas the potassium cations fill the intra-channel space. This contrasts with the structure of the sodium salt hydrate in which guanine anions form channels with water molecules filling in the channel space together with sodium cations coordinating them. The 1D anionic assembly generated through numerous hydrogen bonds and cation interactions with guanine anions and water molecules is energetically the most distinctive part of the structure of the potassium salt hydrate. In the case of the guanine sodium salt, the structure contains purely inorganic polymeric fragments – sodium cations coordinated to a water molecule forming a 1D polymeric structure and guanine anions interconnecting these polymers via hydrogen bonds with water molecules. The structural differences account for the difference in the anisotropy of strain on temperature variation for the two salt hydrates: whereas in both structures the values of the bulk thermal expansion coefficients are similar in the two structures and the major expansion is observed along the channel axes, the degree of anisotropy for the K salt is more than four times higher than that for the Na salt.

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Section: Resultssupporting

confidence: 91%

A new guaninate hydrate K⁺·C₅H₄N₅O⁻·H₂O: crystal structure from 100 to 300 K in a comparison with 2Na⁺·C₅H₃N₅O²⁻·7H₂O

Gaydamaka¹,

Arkhipov²,

Boldyreva³

2021

Acta Crystallogr B Struct Sci Cryst Eng Mater

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“…The electrophilic activity of the alcohol hydroxyl oxygen atom of the two molecules follows the order water < formic acid < acetic acid < benzene, whereas the carboxyl oxygen atom follows the order gas phase < lactic acid < ethanol. This proves that the polarity of the solvent affects the electrophilic nucleophilic activity of the molecular functional groups [46].…”

Section: Resultsmentioning

confidence: 92%

Theoretical Studies on the Electronic Structure Parameters and Reactive Activity of Neu5Gc and Neu5Ac under Food Processing Solvent Environment

2019

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The animal product hazard factor N-glycolylneuraminic (Neu5Gc) and brain nutrient substance N-acetylneuraminic acid (Neu5Ac) were studied at the M062X/6-311 + G(d,p) geometry optimization level. We considered the electronic structure parameters with different solvents: (benzene ε = 2.27, acetic acid ε = 6.25, ethanol ε = 24.85, lactic acid ε = 22.00, formic acid ε = 51.1, water ε = 78.35). The maximum molecular surface electrostatic potentials, which were 62.77 for Neu5Gc and 60.90 kcal/mol for Neu5Ac, are both located on the carboxyl group hydrogen. The orbital analysis showed that the amide group and carboxyl group confer the sites with susceptibility to nucleophilic and electrophilic attack, respectively. The solvent effect showed that polar solvents, such as formic acid and water, can enhance the two molecules’ nucleophilic activity. To better understand the roles of the hydroxyl group in the two molecules, the independent gradient model theory confirmed the four intramolecular hydrogen bonds of Neu5Gc at gas phase, whereas Neu5Ac only has two. The lowest bond dissociation energy in solvent occurs at O7-H, which is 104.03 kcal/mol in water for Neu5Gc and 104.57 kcal/mol in lactic acid for Neu5Ac. The lowest proton affinity value for Neu5Gc (20.34 kcal/mol) and Neu5Ac (20.76 kcal/mol) was both occur at the carboxyl group O6-H under ethanol. The antioxidant mechanisms of the two sialic acid are prone to sequential proton-loss electron transfer under polar or non-polar solvents.

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“…When cisPt coordinates with DNA, it predominantly platinates the N7 position of dGuo [60, 62]. In this work, we sought to determine the binding site preferences and to characterize the types of adducts formed by AAPt compounds.…”

Section: Resultsmentioning

confidence: 99%

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

Kimutai

Roberts

et al. 2019

J Biol Inorg Chem

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Nucleobases serve as ideal targets where drugs bind and exert their anticancer activities. Cisplatin (cisPt) preferentially coordinates to 2′-deoxyguanosine (dGuo) residues within DNA. The dGuo adducts that are formed alter the DNA structure, contributing to inhibition of function and ultimately cancer cell death. Despite its success as an anticancer drug, cisPt has a number of drawbacks that reduce its efficacy, including repair of adducts and drug resistance. Some approaches to overcome this problem involve development of compounds that coordinate to other purine nucleobases, including those found in RNA. In this work, amino acid-linked platinum(II) (AAPt) compounds of alanine and ornithine (AlaPt and OrnPt, respectively) were studied. Their reactivity preferences for DNA and RNA purine nucleosides (i.e., 2′-deoxyadenosine (dAdo), adenosine (Ado), dGuo, and guanosine (Guo)) were determined. The chosen compounds form predominantly monofunctional adducts by reacting at the N1, N3, or N7 positions of purine nucleobases. In addition, features of AAPt compounds that impact the glycosidic bond stability of Ado residues were explored. The glycosidic bond cleavage is activated differentially for AlaPt-Ado and OrnPt-Ado isomers. Formation of unique adducts at non-canonical residues and subsequent destabilization of the glycosidic bonds are important features that could circumvent platinum-based drug resistance.Graphic abstract Electronic supplementary materialThe online version of this article (10.1007/s00775-019-01693-y) contains supplementary material, which is available to authorized users.

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Nucleophilic properties of purine bases: inherent reactivity versus reaction conditions

Cited by 24 publications

References 92 publications

A new guaninate hydrate K⁺·C₅H₄N₅O⁻·H₂O: crystal structure from 100 to 300 K in a comparison with 2Na⁺·C₅H₃N₅O²⁻·7H₂O

A new guaninate hydrate K⁺·C₅H₄N₅O⁻·H₂O: crystal structure from 100 to 300 K in a comparison with 2Na⁺·C₅H₃N₅O²⁻·7H₂O

Theoretical Studies on the Electronic Structure Parameters and Reactive Activity of Neu5Gc and Neu5Ac under Food Processing Solvent Environment

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

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Nucleophilic properties of purine bases: inherent reactivity versus reaction conditions

Cited by 24 publications

References 92 publications

A new guaninate hydrate K+·C5H4N5O−·H2O: crystal structure from 100 to 300 K in a comparison with 2Na+·C5H3N5O2−·7H2O

A new guaninate hydrate K+·C5H4N5O−·H2O: crystal structure from 100 to 300 K in a comparison with 2Na+·C5H3N5O2−·7H2O

Theoretical Studies on the Electronic Structure Parameters and Reactive Activity of Neu5Gc and Neu5Ac under Food Processing Solvent Environment

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

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A new guaninate hydrate K⁺·C₅H₄N₅O⁻·H₂O: crystal structure from 100 to 300 K in a comparison with 2Na⁺·C₅H₃N₅O²⁻·7H₂O

A new guaninate hydrate K⁺·C₅H₄N₅O⁻·H₂O: crystal structure from 100 to 300 K in a comparison with 2Na⁺·C₅H₃N₅O²⁻·7H₂O