Exploiting hydrogen bonding interactions to probe smaller linear and cyclic diamines binding to G-quadruplexes: a DFT and molecular dynamics study

2017 ◽  
Vol 19 (18) ◽  
pp. 11474-11484 ◽  
Author(s):  
Mrinal Kanti Si ◽  
Anik Sen ◽  
Bishwajit Ganguly
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Binding Motif ◽  
Stacking Interactions ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking ◽  
G Quadruplex

This report reveals that hydrogen bonding interactions between the ligand and G-quadruplex can initiate an alternative binding motif to typical π-stacking interactions.

scholarly journals The role of π–π stacking and hydrogen-bonding interactions in the assembly of a series of isostructural group IIB coordination compounds

2019 ◽  
Vol 75 (2) ◽  
pp. 178-188 ◽  
Author(s):  
Taraneh Hajiashrafi ◽  
Roghayeh Zekriazadeh ◽  
Keith J. Flanagan ◽  
Farnoush Kia ◽  
Antonio Bauzá ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Coordination Compounds ◽  
Spectroscopic Techniques ◽  
Stacking Interactions ◽  
X Ray Crystallography ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking ◽  
Research Domain

The supramolecular chemistry of coordination compounds has become an important research domain of modern inorganic chemistry. Herein, six isostructural group IIB coordination compounds containing a 2-{[(2-methoxyphenyl)imino]methyl}phenol ligand, namely dichloridobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)zinc(II), [ZnCl2(C28H26N2O4)], 1, diiodidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)zinc(II), [ZnI2(C28H26N2O4)], 2, dibromidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)cadmium(II), [CdBr2(C28H26N2O4)], 3, diiodidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)cadmium(II), [CdI2(C28H26N2O4)], 4, dichloridobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)mercury(II), [HgCl2(C28H26N2O4)], 5, and diiodidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)mercury(II), [HgI2(C28H26N2O4)], 6, were synthesized and characterized by X-ray crystallography and spectroscopic techniques. All six compounds exhibit an infinite one-dimensional ladder in the solid state governed by the formation of hydrogen-bonding and π–π stacking interactions. The crystal structures of these compounds were studied using geometrical and Hirshfeld surface analyses. They have also been studied using M06-2X/def2-TZVP calculations and Bader's theory of `atoms in molecules'. The energies associated with the interactions, including the contribution of the different forces, have been evaluated. In general, the π–π stacking interactions are stronger than those reported for conventional π–π complexes, which is attributed to the influence of the metal coordination, which is stronger for Zn than either Cd or Hg. The results reported herein might be useful for understanding the solid-state architecture of metal-containing materials that contain M II X 2 subunits and aromatic organic ligands.

scholarly journals 3-(2-Pyridyl)-5-(4-pyridyl)-4-(p-tolyl)-1H-1,2,4-triazole

2009 ◽  
Vol 65 (6) ◽  
pp. o1225-o1225
Author(s):  
Lu-Tong Yuan ◽  
Hai Zhang ◽  
Zuo-Xiang Wang ◽  
Zhi-Rong Qu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Title Compound ◽  
Triazole Ring ◽  
Dihedral Angles ◽  
Stacking Interactions ◽  
Compound C ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking ◽  
Centroid Distance

In the molecule of the title compound, C19H15N5, the dihedral angles formed by the plane of the triazole ring with those of the 2-pyridyl, 4-pyridyl andp-tolyl rings are 28.12 (10), 34.62 (10) and 71.43 (9)°, respectively. The crystal structure is consolidated by C—H...π hydrogen-bonding interactions and by π–π stacking interactions, with a centroid–centroid distance of 3.794 (4) Å.

Recognition of a Flavin Analogue by Novel Bile Acid-Based Receptors: Effects of Hydrogen Bonding and Aromatic π-Stacking Interactions

2017 ◽  
Vol 70 (12) ◽  
pp. 1263 ◽  
Author(s):  
Pradeep Kumar Muwal ◽  
Rajesh Kumar Chhatra ◽  
Shubhajit Das ◽  
Pramod S. Pandey
Keyword(s):  
Hydrogen Bonding ◽  
Bile Acid ◽  
Molecular Recognition ◽  
Stacking Interactions ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking ◽  
Fused Ring ◽  
Bile Acid Receptors ◽  
Binding Behaviour

Molecular recognition properties are reported for novel bile acid-based receptors that incorporate 2,6-diaminopyridine as a recognition unit. Apart from hydrogen-bonding interactions, the bile acid receptors exhibit significant aromatic π-stacking interactions with the aromatic fused ring of the flavin derivative. These studies provide rationalisation for the differences in binding behaviour of bile acid receptors having differing aromatic arm lengths towards a flavin analogue.

2-Diethylamino-6-ethyl-6-methyl-3-phenylthieno[2,3-d]pyrimidin-4(3H)-one

2006 ◽  
Vol 62 (7) ◽  
pp. o2862-o2863
Author(s):  
Zheng-Dong Fang ◽  
Ming-Wu Ding
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Title Compound ◽  
Van Der Waals ◽  
Van Der Waals Forces ◽  
Stacking Interactions ◽  
Intermolecular Hydrogen Bonding ◽  
Compound C ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking

In the title compound, C19H23N3OS, the two fused rings of the thieno[2,3-d]pyrimidin-4(3H)-one system are almost coplanar. The packing of the molecules in the crystal structure is determined by van der Waals forces. No intermolecular hydrogen-bonding interactions or π–π stacking interactions are present in the crystal structure.

scholarly journals High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A π-stacking interactions for small-molecule recognition

2020 ◽  
Vol 48 (10) ◽  
pp. 5766-5776 ◽  
Author(s):  
Arnold Ou ◽  
Jason W Schmidberger ◽  
Katie A Wilson ◽  
Cameron W Evans ◽  
Jessica A Hargreaves ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
High Resolution ◽  
Molecular Dynamics Simulations ◽  
Small Molecule ◽  
Rational Design ◽  
Stacking Interactions ◽  
Π Stacking ◽  
G Quadruplex ◽  
Dynamics Simulations

Abstract Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 Å) of a KRAS G-quadruplex as a 5′-head-to-head dimer with extensive poly-A π-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A π-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indicated the poly-A loop was a binding site for these ligands in addition to the 5′-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of specific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.

Hydrogen-bonded chains in threecis-dichloridoplatinum(II) complexes bearing piperidine and amine ligands

2014 ◽  
Vol 70 (3) ◽  
pp. 297-301 ◽  
Author(s):  
Chi Nguyen Thi Thanh ◽  
Ngan Nguyen Bich ◽  
Luc Van Meervelt
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Stacking Interactions ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking ◽  
Amine Ligands ◽  
Hydrogen Bonded

The crystal structures ofcis-dichlorido(ethylamine-κN)(piperidine-κN)platinum(II), [PtCl2(C2H7N)(C5H11N)], (I),cis-dichlorido(3-methoxyaniline-κN)(piperidine-κN)platinum(II), [PtCl2(C5H11N)(C7H9NO)], (II), andcis-dichlorido(piperidine-κN)(quinoline-κN)platinum(II), [PtCl2(C5H11N)(C9H7N)], (III), have been determined at 100 K in order to verify the influence of the nonpiperidine ligand on the geometry and crystal packing. The crystal packing is characterized by N—H...Cl hydrogen bonding, resulting in the formation of chains of molecules connected in a head-to-tail fashion. Hydrogen-bonding interactions play a major role in the packing of (I), where the chains further aggregate into planes, but less so in the case of (II) and (III), where π–π stacking interactions are of greater importance.

Emissive and birefringent Hg(CN)2-based coordination polymer materials with very distorted coordination geometries

2018 ◽  
Vol 96 (2) ◽  
pp. 226-234 ◽  
Author(s):  
David Guan ◽  
John R. Thompson ◽  
Daniel B. Leznoff
Keyword(s):  
Optical Properties ◽  
Hydrogen Bonding ◽  
Coordination Polymer ◽  
Coordination Polymers ◽  
Polymer Materials ◽  
Stacking Interactions ◽  
One Dimensional ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking ◽  
New Compounds

New compounds and coordination polymers with highly polarizable metals (M = Hg, Pb) and 2,2′;6′2′-terpyridine (terpy) and 2,6-bis(benzimidazol-2-yl)pyridine (bbp) ligands have been synthesized and characterized for their photo-physical and optical properties. Hg(L)(CN)2 (L = terpy, bbp) exhibit π-stacking interactions, which form a supramolecular alignment of the planar terpy and bbp units. Pb(terpy)X2[Hg(CN)2]0.5 (X = Cl, Br) generate one-dimensional coordination polymers through bridging Hg(CN)2 linkers and hydrogen-bonding interactions. All of the metal centres have very distorted coordination geometries. Hg(L)(CN)2 (L = terpy, bbp) and Pb(terpy)Br2[Hg(CN)2]0.5 show terpy or bbp based emission. The materials are very birefringent, with Δn ranging from 0.37(2) to 0.45(2). The magnitude of the observed birefringence depends on the orientation of the highly polarizable terpy and bbp units in relation to the viewing axis of the crystals. These materials represent rare examples of multifunctional emissive and birefringent systems.

scholarly journals Crystal structure of bis(1,10-phenanthroline-κ2N,N′)(1,3-thiazole-2-thiolato-κ2S2,N)nickel(II) hexafluoridophosphate 1,4-dioxane sesquisolvate

2017 ◽  
Vol 73 (4) ◽  
pp. 590-593
Author(s):  
Keisuke Kai ◽  
Tomohiko Hamaguchi ◽  
Isao Ando
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Zigzag Chain ◽  
Stacking Interactions ◽  
Hydrogen Bonding Interactions ◽  
Π Stacking ◽  
Chelating Ligand ◽  
Solvent Molecules ◽  
Unexpected Product

The title salt, [Ni(C3H2NS2)(C12H8N2)2]PF6·1.5C4H8O2, was the unexpected product on making an attempt to prepare an [Ni(2-mercaptothiazolate)(1,10-phenanthroline)]+complex by reaction of [NiCl2(1,10-phenanthroline)] with 2-mercaptothiazolate. In the resulting complex, the 2-mercaptothiazolate anion acts as a chelating ligand, which coordinates to the NiIIion with the thiazolyl N and thiolate S atoms. In the crystal, π–π stacking interactions between the coordinating 1,10-phenanthroline molecules of adjacent complexes result in a zigzag chain running parallel to thecaxis. Weak C—H...X(X= O, F) hydrogen-bonding interactions between the chains and 1,4-dioxane solvent molecules and PF6−counter-anions lead to the formation of sheets parallel to theacplane.

3-n-Butyl-2-methoxy-1-benzothieno[3,2-d]pyrimidin-4(3H)-one

2006 ◽  
Vol 62 (4) ◽  
pp. o1319-o1320 ◽  
Author(s):  
Min-Hui Cao ◽  
Sheng-Zhen Xu ◽  
Yang-Gen Hu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Benzene Ring ◽  
Title Compound ◽  
Thiophene Ring ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Compound C ◽  
Π Stacking ◽  
Independent Molecules

The title compound, C15H16N2O2S, contains a five-membered thiophene ring fused to a benzene ring and a substituted pyrimidinone ring. All three rings in each of the independent molecules of the asymmetric unit lie in approximately the same plane. The crystal structure is stabilized by intermolecular C—H...O hydrogen bonding and π–π stacking interactions.

Sign in / Sign up

Export Citation Format

Share Document