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Coordination Patterns of the Diphosphate in IDP Coordination Complexes: Crystal Structure and Chirality
Inorganic Chemistry ( IF 4.6 ) Pub Date : 2022-11-22 , DOI: 10.1021/acs.inorgchem.2c03285 Yanhong Zhu 1, 2 , Zhongkui Li 1 , Xue Zhong 1 , Xuan Wu 1 , Yongqiu Lu 1 , Maroof Ahmad Khan 1 , Hui Li 1
Inorganic Chemistry ( IF 4.6 ) Pub Date : 2022-11-22 , DOI: 10.1021/acs.inorgchem.2c03285 Yanhong Zhu 1, 2 , Zhongkui Li 1 , Xue Zhong 1 , Xuan Wu 1 , Yongqiu Lu 1 , Maroof Ahmad Khan 1 , Hui Li 1
Affiliation
The knowledge of accurate geometrical parameters from X-ray diffraction studies in the solid state of metal nucleotide is very important for understanding the relationship between structures and properties, including biochemical processes and even enzyme–metal–substrate interactions. The research is also very necessary to precisely and controllably design the functional materials. Here, seven types of coordination polymers of inosine 5′-diphosphate nucleotide (IDP) with transition metals, {[Zn(HIDP)(azpy)(H2O)2]·4H2O}n (1), {[Cd2(IDP)2(bpda)2]·[Cd(H2O)6]·11H2O}n (2), {[Cd3(IDP)2(4,4′-bipy)2(H2O)3]·6H2O}n (3), {[Cd2(IDP)2(bpe)2(H2O)2]·(H2bpe)·26H2O}n (4), {[Cu3(IDP)2(azpy)2(H2O)5]·5H2O}n (5), {[Cu3(IDP)2(bpe)2(H2O)5]·9H2O}n (6), and {[Co(HIDP)(azpy)(H2O)2]·7H2O}n (7) [4,4′-bipy = 4,4′-bipyridine, azpy = 4,4′-azopyridine, bpe = 1,2-bis(4-pyridyl)ethene, and bpda = 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene], were designed, synthesized, and firmly characterized using single-crystal X-ray diffraction. The coordination patterns of the diphosphate group of IDP in these complexes were studied by crystallographic analysis, namely, open, close, and open–close hybrid types. We have investigated the diverse coordination patterns of the diphosphate group and its spatial relationship relative to the pentose ring on the basis of two conformational parameters, the pseudorotation phase angle and the degree of puckering. Crystallographic studies clearly reveal the correlation between the backbone torsion angle (ω′ and φ) of the sugar–diphosphate and the conformational preference of the pentose ring, i.e., the signs of the backbone torsion angles ω′ and φ are both plus (+) or minus (−), the conformation of the pentose ring is envelope form (E), while when one of the two signs is plus (+) and the other is minus (−), the pentose ring is in the twist form (T). This is the first time elucidation of the coordination pattern of diphosphate relative to the conformation of the pentose ring in nucleotide metal complexes, which are different from the other inorganic or organic diphosphate compounds. The chirality of these coordination polymers was examined by combining solid-state circular dichroism spectroscopy measurements with the explanation of their crystal structures. The results presented in this paper are very important for understanding their nucleotide coordination chemistry, their supramolecular chemistry, and even their biochemistry.
中文翻译：
IDP 配位化合物中二磷酸盐的配位模式：晶体结构和手性
从固态金属核苷酸的 X 射线衍射研究中获得准确的几何参数知识对于理解结构和性质之间的关系非常重要，包括生化过程甚至酶-金属-底物相互作用。该研究对于精确可控地设计功能材料也非常必要。这里，七种类型的肌苷 5'-二磷酸核苷酸 (IDP) 与过渡金属配位聚合物，{[Zn(HIDP)(azpy)(H 2 O) 2 ]·4H 2 O} n ( 1 )，{[Cd 2 (IDP) 2 (bpda) 2 ]·[Cd(H 2 O) 6 ]·11H 2O} n ( 2 ), {[Cd 3 (IDP) 2 (4,4'-bipy) 2 (H 2 O) 3 ]·6H 2 O} n ( 3 ), {[Cd 2 (IDP) 2 ( bpe) 2 (H 2 O) 2 ]·(H 2 bpe)·26H 2 O} n ( 4 ), {[Cu 3 (IDP) 2 (azpy) 2 (H 2 O) 5 ]·5H 2 O} n ( 5 ), {[铜3 (IDP) 2 (bpe) 2 (H 2 O) 5 ]·9H 2 O} n ( 6 ), 和 {[Co(HIDP)(azpy)(H 2 O) 2 ]·7H 2 O} n ( 7) [4,4'-bipy = 4,4'-联吡啶，azpy = 4,4'-偶氮吡啶，bpe = 1,2-双(4-吡啶基)乙烯，bpda = 1,4-双(4- pyridyl)-2,3-diaza-1,3-butadiene]，被设计、合成并使用单晶 X 射线衍射进行了表征。通过晶体学分析研究了这些配合物中 IDP 二磷酸基团的配位模式，即开型、闭型和开闭杂化型。我们根据假旋转相位角和褶皱程度这两个构象参数研究了二磷酸基团的不同配位模式及其与戊糖环的空间关系。晶体学研究清楚地揭示了糖-二磷酸的骨架扭转角（ω' 和 φ）与戊糖环的构象偏好之间的相关性，即，骨架扭转角ω′和φ的符号均为正（+）或负（-），戊糖环的构象为包络型（E），而当两个符号之一为正（+）且另一个是减号（-），戊糖环是扭曲形式（T）。这是首次阐明核苷酸金属配合物中二磷酸盐相对于戊糖环构象的配位模式，这与其他无机或有机二磷酸盐化合物不同。这些配位聚合物的手性通过将固态圆二色谱测量与其晶体结构的解释相结合来检验。本文中的结果对于理解它们的核苷酸配位化学、超分子化学甚至生物化学非常重要。
更新日期：2022-11-22
中文翻译：
IDP 配位化合物中二磷酸盐的配位模式：晶体结构和手性
从固态金属核苷酸的 X 射线衍射研究中获得准确的几何参数知识对于理解结构和性质之间的关系非常重要，包括生化过程甚至酶-金属-底物相互作用。该研究对于精确可控地设计功能材料也非常必要。这里，七种类型的肌苷 5'-二磷酸核苷酸 (IDP) 与过渡金属配位聚合物，{[Zn(HIDP)(azpy)(H 2 O) 2 ]·4H 2 O} n ( 1 )，{[Cd 2 (IDP) 2 (bpda) 2 ]·[Cd(H 2 O) 6 ]·11H 2O} n ( 2 ), {[Cd 3 (IDP) 2 (4,4'-bipy) 2 (H 2 O) 3 ]·6H 2 O} n ( 3 ), {[Cd 2 (IDP) 2 ( bpe) 2 (H 2 O) 2 ]·(H 2 bpe)·26H 2 O} n ( 4 ), {[Cu 3 (IDP) 2 (azpy) 2 (H 2 O) 5 ]·5H 2 O} n ( 5 ), {[铜3 (IDP) 2 (bpe) 2 (H 2 O) 5 ]·9H 2 O} n ( 6 ), 和 {[Co(HIDP)(azpy)(H 2 O) 2 ]·7H 2 O} n ( 7) [4,4'-bipy = 4,4'-联吡啶，azpy = 4,4'-偶氮吡啶，bpe = 1,2-双(4-吡啶基)乙烯，bpda = 1,4-双(4- pyridyl)-2,3-diaza-1,3-butadiene]，被设计、合成并使用单晶 X 射线衍射进行了表征。通过晶体学分析研究了这些配合物中 IDP 二磷酸基团的配位模式，即开型、闭型和开闭杂化型。我们根据假旋转相位角和褶皱程度这两个构象参数研究了二磷酸基团的不同配位模式及其与戊糖环的空间关系。晶体学研究清楚地揭示了糖-二磷酸的骨架扭转角（ω' 和 φ）与戊糖环的构象偏好之间的相关性，即，骨架扭转角ω′和φ的符号均为正（+）或负（-），戊糖环的构象为包络型（E），而当两个符号之一为正（+）且另一个是减号（-），戊糖环是扭曲形式（T）。这是首次阐明核苷酸金属配合物中二磷酸盐相对于戊糖环构象的配位模式，这与其他无机或有机二磷酸盐化合物不同。这些配位聚合物的手性通过将固态圆二色谱测量与其晶体结构的解释相结合来检验。本文中的结果对于理解它们的核苷酸配位化学、超分子化学甚至生物化学非常重要。
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