Supramolecular networks via hydrogen bonding and stacking interactions for adenosine 5′-diphosphate. Synthesis and crystal structure of diaqua(2,2′∶6′,2″-terpyridine)copper(II) [adenosine 5′-diphosphato(3−)](2,2′∶6′,2″-terpyridine)cuprate(II) adenosine 5′-diphosphate(1−) hexadecahydrate and density functional geometry optimization analysis of copper(II)- and zinc(II)-pyrophosphate complexes

Supramolecular Assembly of Uridine Monophosphate (UMP) and Thymidine Monophosphate (TMP) with a Dinuclear Copper(II) Receptor

“…In recent years, there has been a growing interest in designing artificial receptors that recognize nucleotides as target substrates, − with the goal to mimic their biological interactions with enzymes. , Nucleotides are the fundamental building blocks of DNA and RNA, playing many critical roles in biology. For instance, adenosine triphosphate (ATP) is used in generating universal chemical energy for cellular functions, guanosine triphosphate (GTP) is involved in the synthesis of DNA and proteins, and uridine monophosphate (UMP) is the central building block in the synthesis of RNA. , Although an abundance of information is available on solution binding studies and theoretical calculations predicting the binding modes of nucleotides, − structural reports of nucleotide complexes with synthetic receptors are indeed limited. − In 2008, Bianchi and co-workers reported the first structure of a nucleoside triphosphate complex with a synthetic receptor, showing hydrogen bonding and π–π stacking interactions between a thymidine 5′-triphosphate and a polyamine-based receptor . Several structures of nucleotides, nucleosides, or nucleobases as pure or mixed ligands with transition metal ions were also reported. − In particular, the central role played by nucleoside monophosphates (NMPs) in many biological events mak...…”

“…For instance, adenosine triphosphate (ATP) is used in generating universal chemical energy for cellular functions, guanosine triphosphate (GTP) is involved in the synthesis of DNA and proteins, and uridine monophosphate (UMP) is the central building block in the synthesis of RNA. , Although an abundance of information is available on solution binding studies and theoretical calculations predicting the binding modes of nucleotides, − structural reports of nucleotide complexes with synthetic receptors are indeed limited. − In 2008, Bianchi and co-workers reported the first structure of a nucleoside triphosphate complex with a synthetic receptor, showing hydrogen bonding and π–π stacking interactions between a thymidine 5′-triphosphate and a polyamine-based receptor . Several structures of nucleotides, nucleosides, or nucleobases as pure or mixed ligands with transition metal ions were also reported. − In particular, the central role played by nucleoside monophosphates (NMPs) in many biological events makes them attractive targets for mimicking their biological interactions. − For instance, as characterized by X-ray analysis, UMP was found within the cavity of a Bacillus subtilis orotidine 5′-monophosphate decarboxylase via hydrogen bonds and salt bridges between the nucleotide and the protein . However, to the best of our knowledge, a crystallographically characterized NMP complex with a macrocycle-based synthetic receptor has not been reported yet.…”

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

“…It is clear that all the corresponding values are equal within 2σ, and are equal within 3σ to those from the work on TTP by Bianchi et al [28], even though the chemical environment for the triphosphate chain is different in the two structures. The absence of significant discrepancies between terminal P- 2 O, ADP = adenosine 5'-diphosphate, TERPY = 2,2':2"-terpyridine [30] confirms that diphosphate chain has terminal Pα-O and Pβ-O, and (Cu)O-P bond lengths that agree with the finding presented above for NTPs that P-Ot lengths do not vary significantly upon complex formation to Cu(II) (and to other divalent cations from alkaline earth group and first row block-d of the periodic table). On the other hands, in case an oxygen atom from phosphate groups is protonated the relevant O-P bond distance is significantly elongated with respect to the not protonated ones.…”

The Research of G–Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes

“…They are measured by the C (8)–N (1)–C (5)–O (5) and C (18)–N (6)–C (15)–O (12) (χ) torsion angle, which is –76 (1)° for the N (1)–bound Co(II) central and –82 (1)°for the N (6)–bound Co(II) central, respectively. This special conformation can be described as high anti , – sc ( Cini and Pifferi, 1999 ; Asami et al, 2012 ) for the coordinated nucleotide ( Supplementary Figure S2 ). To the best of our knowledge, this extreme position described as high anti is not frequent for nucleoside and has never been found before for the solid-state structures of dGMP nucleotides.…”