Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

Abstract

Adenosine diphosphate (ADP) plays a crucial role in cell biochemistry, especially in metabolic pathways and energy storage. ADP itself, as well as many of its analogues, such as adenosine hypodiphosphate (AhDP), has been studied extensively, in particular in terms of enzymatic activity. However, structural studies in the solid state, especially for AhDP, are still missing. An analogue of ADP, i.e. adenosine hypodiphosphate ester, has been synthesized and characterized in the crystalline form as two hydrated sodium salts of 2':3'-isopropylideneadenosine 5'-hypodiphosphate (HAhDP, CHNOP for the neutral form), namely pentasodium tetrakis(2':3'-isopropylideneadenosine 5'-hypodiphosphate) tetracosahydrate, 5Na·3CHNOP·CHNOP·24HO or Na(HAhDP)(HAhDP)·24HO, (I), and sodium tetrakis(2':3'-isopropylideneadenosine 5'-hypodiphosphate) pentadecahydrate, Na·CHNOP·2CHNOP·CHNOP·15HO or Na(HAhDP)(HAhDP)(HAhDP)·15HO, (II). Crystal structure analyses of (I) and (II) reveal two nucleoside hypodiphosphate ions in the asymmetric units with different ionization states of the hypodiphosphate unit and adenine base. For all AhDP nucleotides, the same anti conformation about the N-glycosidic bond and similar puckering of the ribose ring have been found. AhDP geometry and interactions have been compared to ADP nucleotides deposited in the Cambridge Structural Database. The adenine-hypodiphosphate interactions, identified as defining nucleotide self-assembly, have been analysed in model systems, i.e. the adenine (Ade) salts of hypodiphosphoric acid, namely bis(adeninium) hypodiphosphate dihydrate, 2CHN·HPO·2HO or (AdeH)(HPO)·2HO, (III), and bis(adeninium) hypodiphosphate, 2CHN·HPO or (AdeH)(HPO), (IV).

Synthesis, structural elucidation, spectroscopic, Hirshfeld surface analysis and theoretical simulation of a new adeninium orthoperiodate (1−) bis(hydrate) organic–inorganic hybrid crystals

“…This homosynthon (10) motif that mimics the Hoogsteen pattern has been observed in similar adenine-based hybrid compounds formed with different oxoanions, namely; bis adeninium dinitrate monohydrate [36], adeninium perchlorate adenine dihydrate [50] and adeninium perchlorate [51]. Despite the fact that the adeninium-anion supramolecular heterosynthon motifs are one of the classic motifs frequently observed in similar structures [52], we however note their total absence in the title compounds. Moreover, it should be noted that the planar edge-to-edge Ade-Ade non-Watson-Crick base pairing in the trans-sugar/sugar homosynthon mode is not present in (I) although it is commonly observed in similar adeninium-based structures [53,54].…”

Crystal engineering and structural diversity of 2-aminopyridinium hypodiphosphates obtained by crystallization and dehydration

“…3). Despite some differences in the environment of the anions within the inorganic substructure, both mono-and dianions are involved in the formation of inter-anionic R 2 2 (10) rings 25 (20) rings are formed (Fig. 3).…”

“…Moreover, the tendency of hypodiphosphates to form networks stabilized by strong O–H⋯O hydrogen bonds, composed exclusively of hypodiphosphate anions and/or acid molecules, has been clearly indicated. 20–24 Hypodiphosphate substructures are stabilized by the formation of one, two or three hydrogen bond bridges between anions or acid molecules. In most of the known crystals of organic hypodiphosphates, two hydrogen bonds link adjacent anions giving rise to motifs as shown in Fig.…”

The supramolecular behavior and molecular recognition of adeninium cations on anionic hydrogen selenite/diselenite frameworks: A structural and theoretical analysis

“…The structural investigation shows that the 1H,9H-adeninium in both crystal structures generate cationic ribbons, where they are formed from centrosymmetric homosynthons in (I) and heterosynthons in (II). Therefore, the supramolecular homo and hetero-synthon motifs are one of the classical motifs frequently observed in similar adenine-based hybrid compounds formed with different oxoanions [61][62][63][64][65].…”