Considering all data gathered and study findings available, we agreed to investigate using GMP-Cd-bpe, a precursor complex by varying the pH, to construct supramolecular species with noncovalent interactions (Hydrogen bonding and π-π interactions) as nucleotides may coordinate closely with the number of metal ions. Nucleotide fragments, metal ions and mixed N-donor ligands play an important function in supramolecule for structural chirality. The role of hydroxyl groups and pH in the assembly of GMP-Cd-bpe, and GMP-Cd chiral supramolecular complexes has also been addressed in pentose sugar, N-donor bridging ligand bpe, and noncovalent interactions. The ligands of guanosine (GMP, dGMP, GDP etc.) are coordinated with metal ions in acidic and neutral pH varying from 4-9.[36, 38]
The complexes 1 and 2 both are composed of Cd(II) metal ions and nucleotide ligand expect for supplementary N-donor ligands in complex 1. In complex 1, the metal ions combine to bpe to create a similar independent unit with two neighbouring bpe ligands while in complex 2 each Cd (II) is coordinated with one nucleotide ligand through nitrogen N6 of guanine base ring and five water molecules through oxygen atoms due to the variation in pH=6-8 shown in figure 1(a-b). Complex 1 single crystals (GMP-Cd-bpe) have been synthesized at pH= 6; GMP demonstrates the greater potential for coordination through oxygen of phosphate in the crystalline state with Cd(II) ions, for supramolecular chiral complex. Cadmium metal, three water molecules and two bpe ligands organize the complex 1. Nucleotide GMP provides better stability in organized complexes with slightly acidic to neutral and slight basic pH values. The pH is a very significant and effective approach for regulating supramolecular structure forming in complex 1. The slight acidic pH=6 favours the coordination of GMP, bpe with Cadmium metal in complex 1. The relationship between pyridine rings of the bpe and GMP intrachain and interchain π-π stacking has tuned the orientation for GMP (figure 2, S2). The space group of complex 1 is P1, suggesting the chirality of the crystalline complex 1. A Cd(II) ion coordinated with one GMP ligand, two bpe ligands and three coordinated water molecules to form the molecular structure of complex 1. (Fig. 1, Tables S1 and S2). In complex 2, Cd (II) is coordinated with one GMP through N6 of Guanine Base and five water molecules at pH 8. The synthesis of complexes 1-2 suggested that the GMP ligand can coordinate through oxygen of phosphate group at slight acidic pH=6 in complex 1 and in complex 2 GMP is coordinated with Cadmium at slight basic pH=8 through N6 of guanine base of GMP. The basic pH favours the metal coordination of GMP through Nitrogen of guanine base while Acidic pH favours the Coordination of GMP through Oxygen of phosphate group. The purine AMP ligand coordinated with copper metal through oxygen of phosphate group at pH 3.65-5.82.[37] While in this work we synthesize the two GMP coordination supramolecular complexes at pH 6 and 8 for complex 1 and complex 2 respectively.
It must be mentioned that the same structure of complex 2 has been reported in 1976 by Katsuyuki Aoki and was measured by Cu Kα radiation (0.15406 nm). [47] Compare to the structure reported before, diffraction data of complex 2 were collected by Mo Kα radiation (0.071073 nm), and more independent reflections were observed in experiment, which mean the locations of the non-hydrogen atoms and hydrogen atoms can be determined more accurately. Additionally, all the hydrogen atoms of GMP and solvent molecules have been added and refined in complex 2, which is helpful to study the structure of complex 2 and the chirality of the supramolecular helical chains formed by hydrogen bonding.
The chirality of the GMP ligand persisted based on the octahedral geometry of the Cd(II) centre in molecules 1-2 and molecular chirality. In complex 1, the nucleotide ratio with bpe is 1:2, rendering GMP ligand wide freedom, especially for the phosphate group metal coordination. It contributes to several H-bonding structures in molecular crystal structure packaging from the perspective of supramolecular chemistry. The molecules are connected to form a 1D chain by strong intermolecular forces H-bonds among, O6 — H6C ...N2, O6 — H6D...O3, O7-H7A...O10, O12- H12A...O13, and N7 — H7 … O12 in complex 1(Figure 3, Table S6) and in complex 2 the H-bonds are O4-H4A...O171 , O7-H7A…O152 , O10-H10A…O123 , O10-H10B…O1, O12-H12…O115 which stabilize the structure of supramolecular design and these intermolecular interactions are responsible for construction of these complexes (figure 2 a-b).
The chain and the 3D structure arose primarily from the versatility of the sugar motif, organization of phosphates and water molecules which coordinated with metal and form Hydrogen bonding to pack the neighbouring chains. The twisting angles between sugar motif and guanine base are 67.939(155)o in Complex 1, and 79.506(377)o in complex 2 (figure S1 c-d). These angles are responsible for orientation of ligands around the Cd (II) in both complexes and for the construction of such supramolecular coordination complexes. In complex 1 hydroxyl of sugar motif creates hydrogen bonding with water molecules coordinated with Cd (II) metal this hydrogen bonding connects two parallel layers of coordination polymers. These 1D chains are then installed in H-binding to create the 3D supramolecular chiral architectures in the presence of solvent water molecules. The 1D chain composed of half the bpe and half the GMP chain shown in (figure 2a-b, S2 a-d). The molecules are unequivocally intertwined through H-bonding to expand the structure of the 2D supramolecule. In addition, these 2D sheets are wrapped based on packaging and H-bonding. The 3D topology of complex 1 with one node and intermolecular interactions as a connection is the network that clearly shows the link between complex molecules packaging in the crystal lattice (figure 2a-b). Chiral dichroism (CD) experiments have verified both the ligand chirality and complex 1 (Fig. 6).
Table 1: Structural Refinement and Crystalline Data for Complexes 1 & 2.
Complexes
|
Complex 1 (GMP-Cd-bpe)
|
Complex 2 (GMP-Cd)
|
Empirical formula
|
C22H38CdN7O21P
|
C10H28CdN5O16P
|
Formula weight
|
879.96
|
617.74
|
Temperature/K
|
296.15
|
296.15
|
Crystal system
|
Triclinic
|
Monoclinic
|
Space group
|
P1
|
C2
|
a/Å
|
7.045(3)
|
27.891(4)
|
b/Å
|
10.127(4)
|
11.3556(17)
|
c/Å
|
13.508(5)
|
6.7542(10)
|
α/°
|
109.007(11)
|
90
|
β/°
|
90.834(14)
|
92.737(4)
|
γ/°
|
91.751(16)
|
90
|
Volume/Å3
|
910.4(6)
|
2136.8(5)
|
Z
|
1
|
4
|
ρcalcg/cm3
|
1.605
|
1.920
|
μ/mm‑1
|
0.734
|
1.187
|
F(000)
|
450.0
|
1256.0
|
Crystal size/mm3
|
0.25 × 0.23 × 0.2
|
0.25 × 0.21 × 0.18
|
Radiation
|
MoKα (λ = 0.71073)
|
MoKα (λ = 0.71073)
|
2Θ range for data collection/°
|
3.19 to 62.898
|
3.874 to 62.886
|
Index ranges
|
-9 ≤ h ≤ 10, -13 ≤ k ≤ 14, -19 ≤ l ≤ 15
|
-38 ≤ h ≤ 39, -15 ≤ k ≤ 15, -9 ≤ l ≤ 9
|
Reflections collected
|
8160
|
13772
|
Independent reflections
|
7218 [Rint = 0.0440, Rsigma = 0.1559]
|
6186 [Rint = 0.0447, Rsigma = 0.0576]
|
Data/restraints/parameters
|
7218/45/489
|
6186/2/317
|
Goodness-of-fit on F2
|
0.956
|
1.075
|
Final R indexes [I>=2σ (I)]
|
R1 = 0.0593, wR2 = 0.1209
|
R1 = 0.0408, wR2 = 0.0947
|
Final R indexes [all data]
|
R1 = 0.1006, wR2 = 0.1475
|
R1 = 0.0440, wR2 = 0.0962
|
Largest diff. peak/hole / e Å-3
|
1.19/-1.93
|
2.00/-1.05
|
Flack parameter
|
-0.01(3)
|
0.067(15)
|
In complex 1, each cadmium is coordinated with three oxygen atoms of three water molecules, two nitrogen atoms of two neighbouring bpe molecules and one GMP by the phosphate group's oxygen. The organized distances are Å (Figure S1 f), Cd1-N4 = 2.3121(93) Å, Cd1-O7 = 2.2987(96) Å, Cd1-O4 = 2.3551(88) Å, Cd1-O3 = 2.3021 Å, Cd1-O1 = 2.2308(89) Å and Cd1-N3 = 2.3640(89) Å in Complex 1. In Complex 1, the distances between coordinated Guanine base ring and 1.2-Di(4-pyridyl) ethylene (bpe) rings are 3.4559 (196) Å. O1-P1 = 1.5205(92)Å, O9-P1 = 1.5902(74)Å, O13-P1 = 1.4964(108)Å and O10-P1 = 1.5001(77)Å as shown in Table S1, figure S5, are the bond lengths of phosphate and oxygen in the phosphate group. In complex 2, each cadmium is coordinated with five oxygen atoms of five water molecules, one nitrogen atoms N6 of guanine base. The organized distances are Å (Figure S1 f), Cd1-O4 = 2.304(4) Å, Cd1-O7 = 2.304(4) Å, Cd1-O10 = 2.273(4) Å, Cd1-O13 = 2.368(5)Å, Cd1-O14 = 2.253(5) Å and Cd1-N6 = 2.294(5) Å in Complex 2. In Complex 2, the distances between P-O in coordinated Guanosine monophosphate are P1-O3 = 1.519(4) Å, P1-O5 = 1.617(4) Å, P1-O17 = 1.521(4) Å and P1-O15 = 1.515(4) Å as shown in Table S2, figure S6 are the bond lengths of phosphate and oxygen in the phosphate group.
A crucial consideration for the construction of noncovalent interactions, i.e. π-π interactions and hydrogen bonding in relation with GMP and bpe, is the molecular length orientation of the ligand bpe and pH value. The orientation of the base ring, sugar ring and solvent molecules stabilize the structure and create the noncovalent interactions among the layers and within the layer of complex 1. Nucleotide linking displays a peculiar activity to create π-π connections and lateral interactions at slight acidic pH in complex 1 and slight basic pH in complex 2. The continuous Hydrogen bonding and π-π interactions (3.388 Å), (3.482 Å) are about to transfer the chirality in supramolecular structure in complex 2. These 2D layers packed in such a way to form 3D structure and shows that network of complex with single node demonstrating crystal lattice packing of compound (figure 3, S4). Hydrogen bonding among the nitrogenous base of Guanine, metal coordinated water molecules and π-π interactions orient the complex molecule in such a way to form butterfly like structure as shown in figure 3 (a-d). This is one of the best example, to representing the chiral GMP ligand develop the Chiral Coordination supramolecules which are biomimetic materials. The chiral biomimetic materials could be used in fields of fluorescent materials, bioimaging and drug delivery etc.
In purine (Adenosine and Guanosine) nucleotides, the oxygen of Phosphate group, hydroxyl of sugar motif, Nitrogen atoms of nucleobases are capable binding spots for transition metals like (Cd, Cu, Ag, Ni, Mn, Co etc.).[36, 44]
The pH sensitivity of nucleotides plays vital role for coordination abilities of nucleotides, stability of supramolecular complexes.[37-46, 48] The metal recognition through N-binding sites of monophosphate nucleotide shows different binding sites due to endocyclic nitrogen. The Nitrogen N6 is favourably coordinated with metals ( Mn, Cd, Pt, Ni) at basic pH = 8-9.[37, 38, 43, 41, 44, 46] 2D layers are produced in complexes by the bridging ligand bpe and solvent molecules through comprehensive π-π interactions and hydrogen bonding in 3D supramolecular frameworks. These interactions occur between the phosphate oxygen atom, organized solvent molecules, purine base (guanine) and ribose sugar hydroxy (figure 2, S3). These intermolecular interactions transform 2D chirality into 3D supramolecular architecture. The crucial factor for building noncovalent interactions, i.e. π-π interactions and hydrogen bonding between purine base ring, hydroxyl groups of sugar motif, phosphate group of GMP in both complexes 1-2 and the length as well as orientation of bridging ligand in complex 2 by tuning the pH=6-8.
The orientation of the base ring, sugar ring and solvent molecules stabilizes the arrangement and induces noncovalent interactions between layers of complexes 1-2. The mixture of nucleotide demonstrates a peculiar activity in constructing π-π interactions and side-chain interactions. Nucleotide GMP is twisted in complex 1 along the bpe axis. We have proposed the perception of organic chemistry as axial chirality into a coordination polymer which creatively enhances extending axial chirality (EAC) based on controllable pH conditions.
Now the complex 2 offer great examples for understanding the EAC. In complex 2, the chiral character of GMP makes bpe a chiral environment and locks up the axial chirality through the coordination link to the infinite chain. The Superamolecular Chirality is based on the GMP orientation and the direction of the sugar motif of GMP, and structure and binding ability of phosphate group.
CD Spectra:
Spectroscopy of Circular Dichroism (CD). Superamolecular chirality and the EAC were present in complex 1 and 2 according to the structural analysis. The solid-state CD spectrum was recorded to identify the new chirality and EAC of GMP in complexes 1-2. All samples were phased pure and tested with a single crystal by measuring X-ray powder diffraction (XRPD). For GMP, the CD spectrum of the solid samples had two typical large peaks centred near 220 and 280 nm. Specifically, for the intermolecular π-π* and n-π* transitions, the stronger and broader negative envelope is about 260nm for complex 1 and 280 nm for complex 2 were observed. The positive absorption of about 220 nm in GMP is related to the intermolecular π-π* interaction of nucleotide bases, which shows that GMP is ribonucleotide. There was a net positive absorption of 330 nm in complex 1 compared to the ligand. This positive peak also indicating the presence of auxiliary ligand in complex 1 which shows π-π interactions with nucleotide bases. Because coordinating Cd(II) with GMP prevents ligand mutarotation, ligands are kept in their complexes. Compared to GMP, the solid-CD (Fig. 6) for complex 1-2 was significantly similar. A positive and new peak of 330 nm indicated a further chiral source due to the supramolecular chiral structure of complex 1.[9-10] The complex 1 and GMP CD spectrums can be attributed to the EAC of bpe, and complex 2 also shows the extended chirality which is due to π-π* transitions between bpe and purine of GMP and GMP structural research can be confirmed.
This work has confirmed the experimental findings that GMP chirality can be well-preserved when coordinated into Cd(II). The chirality of this centrally complex molecule can be transmitted by hydrogen bonding and π-π interactions to its supramolecule architecture. Spectroscopy of solid-state circular dichroism has been performed for the GMP complexes and proposes an effective method for study of delivering chirality. It offers a new way of delivering chiral from nucleotide-metallic complex molecules to its supramolecular architecture, which is important to understand life's origin. Preparation of appropriate nucleotide-metal complexes in future.