scholarly journals 2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

2019 ◽  
Vol 15 ◽  
pp. 1460-1467 ◽  
Author(s):  
Li-Li Wang ◽  
Yi-Kuan Tu ◽  
Huan Yao ◽  
Wei Jiang
Keyword(s):  
Hydrogen Bonds ◽  
Precious Metal ◽  
Electrostatic Interactions ◽  
Fluorescent Sensor ◽  
Coordination Complexes ◽  
Metal Chloride ◽  
Binding Affinities ◽  
Chloride Complexes ◽  
Square Planar ◽  
Intramolecular Hydrogen

Two new tetralactam macrocycles with 2,3-dibutoxynaphthalene groups as sidewalls have been synthesized and characterized. The macrocycle containing isophthalamide bridges can bind square-planar chloride coordination complexes of gold(III), platinum(II), and palladium(II) in CDCl3, while the macrocycle with 2,6-pyridine dicarboxamide bridging units cannot. This may be due to the shrunken cavity caused by intramolecular hydrogen bonds in the latter tetralactam macrocycle. The binding of the isophthalamide-based macrocycle is mainly driven by hydrogen bonds and electrostatic interactions. This naphthalene-based macrocycle has similar binding affinities to all the three abovementioned precious metal chloride complexes. This is in contrast to the fact that the tetralactam macrocycle with anthracene as the sidewalls only show good binding affinities to AuCl4 −. The superior binding to all three complexes may be due to the conformational diversity of the naphthalene-based macrocycle, which make it conformationally adaptive to maximize the binding affinities. In addition, the macrocycle shows fluorescent quenching when adding the chloride metal complexes in its solution and may be used as a fluorescent sensor for the detection of these coordination complexes.

Synthesis of a series of M(ii) (M = Mn, Fe, Co) chloride complexes with both inter- and intra-ligand hydrogen bonding interactions

2021 ◽  
Vol 50 (35) ◽  
pp. 12088-12092
Author(s):  
Clare A. Leahy ◽  
Michael J. Drummond ◽  
Josh Vura-Weis ◽  
Alison R. Fout
Keyword(s):  
Hydrogen Bonding ◽  
Transition Metal ◽  
Intramolecular Hydrogen Bonding ◽  
Metal Chloride ◽  
Chloride Complexes ◽  
Hydrogen Bonding Interactions ◽  
Transition Metal Chloride ◽  
Hydrogen Bonding Networks ◽  
Intramolecular Hydrogen

Hydrogen bonding networks are vital for metallo-enzymes to function; however, modeling these systems is non-trivial. The development of 1st-row transition metal chloride complexes with intramolecular hydrogen-bonding interactions are detailed herein.

scholarly journals E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

2021 ◽  
Author(s):  
Wei Bu Wang ◽  
Yu Liang ◽  
Yu Qin Jin ◽  
Jing Zhang ◽  
Ji Guo Su ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Binding Affinity ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Electrostatic Interactions ◽  
Tight Binding ◽  
Energy Calculation ◽  
Binding Affinities ◽  
Loop Region ◽  
Binding Interface

AbstractThe pandemic of the COVID-19 disease caused by SARS-CoV-2 has led to more than 100 million infections and over 2 million deaths worldwide. The progress in the developments of effective vaccines and neutralizing antibody therapeutics brings hopes to eliminate the threat of COVID-19. However, SARS-CoV-2 continues to mutate, and several new variants have been emerged. Among the various naturally-occurring mutations, the E484K mutation shared by both the 501Y.V2 and 501Y.V3 variants attracted serious concerns, which may potentially enhance the receptor binding affinity and reduce the immune response. In the present study, the molecular mechanism behind the impacts of E484K mutation on the binding affinity of the receptor-binding domain (RBD) with the receptor human angiotensin-converting enzyme 2 (hACE2) was investigated by using the molecular dynamics (MD) simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method. Our results indicate that the E484K mutation results in more favorable electrostatic interactions compensating the burial of the charged and polar groups upon the binding of RBD with hACE2, which significantly improves the RBD-hACE2 binding affinity. Besides that, the E484K mutation also causes the conformational rearrangements of the loop region containing the mutant residue, which leads to more tight binding interface of RBD with hACE2 and formation of some new hydrogen bonds. The more tight binding interface and the new hydrogen bonds formation also contribute to the improved binding affinity of RBD to the receptor hACE2. In addition, six neutralizing antibodies and nanobodies complexed with RBD were selected to explore the effects of E484K mutation on the recognition of these antibodies to RBD. The simulation results show that the E484K mutation significantly reduces the binding affinities to RBD for most of the studied neutralizing antibodies, and the decrease in the binding affinities is mainly owing to the unfavorable electrostatic interactions caused by the mutation. Our studies revealed that the E484K mutation may improve the binding affinity between RBD and the receptor hACE2, implying more transmissibility of the E484K-containing variants, and weaken the binding affinities between RBD and the studied neutralizing antibodies, indicating reduced effectiveness of these antibodies. Our results provide valuable information for the effective vaccine development and antibody drugs design.

Hydrogen-Bonded Networks Featuring Yttrium(III) Complexes of N,N’-Dimethylurea (DMU): Preparation and Characterization of [Y(DMU)6][YCl6] and [Y(NO3)3(DMU)3]

2005 ◽  
Vol 60 (4) ◽  
pp. 363-372 ◽  
Author(s):  
Athanassios K. Boudalis ◽  
Vassilios Nastopoulos ◽  
Catherine P. Raptopoulou ◽  
Aris Terzis ◽  
Spyros P. Perlepes
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Crystal Engineering ◽  
Coordination Complexes ◽  
3D Network ◽  
3D Architecture ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

In order to examine the possibility of using yttrium(III) in the crystal engineering of hydrogenbonded coordination complexes and to compare the molecular and supramolecular YIII/Cl3 or NO3-/DMU chemistry with the already well-developed LnIII/Cl− or NO3−/DMU chemistry (LnIII = lanthanide, DMU = N,N’-dimethylurea), compounds [Y(DMU)6][YCl6] (1) and [Y(NO3)3(DMU)3] (2) have been prepared. The structures of both compounds have been determined by single-crystal Xray diffraction. The structure of 1 consists of octahedral [Y(DMU)6]3+ and [YCl6]3− ions. The YIII ion in 2 is nine-coordinate and ligation is provided by three O-bonded DMU ligands and three bidentate chelating nitrato groups; the coordination polyhedron about the metal can be viewed as a distorted, monocapped square antiprism. The [Y(DMU)6]3+ cations and [YCl6]3− anions self-assemble to form a hydrogen-bonded 3D architecture in 1. Most of the hydrogen-bonding functionalities on the components of 2 create also a 3D network. Two motifs of interionic/intramolecular hydrogen-bonds have been observed: N-H···Cl in 1 and N-H···O(NO3−) in 2. The IR data are discussed in terms of the nature of bonding and the structures of the two complexes

A THEORETICAL COMPARISON OF CONFORMATIONAL FEATURES OF CALIX[4]AROMATICS

2004 ◽  
Vol 03 (01) ◽  
pp. 51-68 ◽  
Author(s):  
DI-FEI WANG ◽  
YUN-DONG WU
Keyword(s):  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Conformational Preference ◽  
Cone Conformation ◽  
Structural Modifications ◽  
Hydrogen Bonding Interactions ◽  
Partial Cone ◽  
Conformational Preferences ◽  
Intramolecular Hydrogen ◽  
Electrostatic Repulsions

Although there are tremendous studies about the conformational feature of calix[4]arenes and its analogies, no theoretical study has been done systematically about why some structural modifications could completely lead to a change of conformational preference. For example, calix[4]arene 1 adopts a cone conformation while its analogue calix[4]pyrrole 7 only adopts a 1,3-alternate conformation. So if this is only because of the effect of OH—OH hydrogen bonds, then why does O-methyl substituted calix[4]arene 2 still has cone conformation? In this paper, the conformational features of a series of seven calix[4]aromatics, calix[4]arene and calix[4]pyrrole related structures, have been investigated at BLYP/6–31G* level both in the gas phase and in CH 2 Cl 2 solution. The calculations demonstrated that three main factors influence the conformational preference of these calix[4]aromatics, i.e. the intramolecular hydrogen bond, the adjacent ring-ring electrostatic interaction and the intrinsic flexibility of the [14] metacyclophane framework. Calix[4]benzene 3 and calix[4]pyridine 4 have little conformational preferences due to their flexible [14] metacyclophane framework, the lack of hydrogen-bonding interactions and weak ring-ring electrostatic interactions. In contrast, calix[4]aromatics 1 and 5–7 have either intramolecular hydrogen bonds (1) or ring-ring electrostatic interactions (5–7). Consequently, calix[4]arene 1 has the cone preference and calix[4]pyrrole, calix[4]furan, and calixthiophene (5–7) have the 1,3-alternate preference. Methoxy calix[4]arene prefers a cone or partial cone conformation, because the 1,3-alternate and 1,2-alternate conformations are destabilized by electrostatic repulsions involving the methoxy group and the adjacent phenyl ring.

scholarly journals Crystal structure ofcis-diamminebis(nitrito-κN)platinum(II)

2015 ◽  
Vol 71 (4) ◽  
pp. 366-370 ◽  
Author(s):  
Volker Kahlenberg ◽  
Thomas Gelbrich ◽  
Richard Tessadri ◽  
Frederik Klauser
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Single Crystals ◽  
Packed Column ◽  
Intramolecular Hydrogen Bonding ◽  
Coordination Environment ◽  
Connected Node ◽  
Square Planar ◽  
Intramolecular Hydrogen

Single crystals ofcis-[Pt(NO2)2(NH3)2], were obtained by means of hypersaturation directly out of a plating electrolyte. The square-planar coordination environment of the divalent PtIIatom is formed by four N atoms belonging to two ammine and two monodentate nitrite ligands. The ligands adopt acisconfiguration. The crystal structure contains stacks of close-packed molecules which run parallel to [001]. There are nine crystallographically independent intermolecular N—H...O hydrogen bonds, resulting in a hydrogen-bondedhxl-type framework in which each molecule serves as an eight-connected node. Four of the nine distinct hydrogen bonds connect complexes which belong to the same close-packed column parallel to [001]. In contrast to the previously reported crystal structure of thetransisomer, the title structure does not display intramolecular hydrogen bonding.

Synthesis, Crystal Structure And Spectroscopic Studies Of A Mixed Ligand Copper (Ii) Complex: Trans-Bis(Succinimidato)-Bis(Benzylamino)Cu(Ii)

2006 ◽  
Vol 61 (8) ◽  
pp. 979-982 ◽  
Author(s):  
Murat Taş ◽  
Hanife Saraçoğlu ◽  
Hümeyra Bati ◽  
Nezihe Çalışkan ◽  
Orhan Büyükgüngör
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Spectroscopic Studies ◽  
Mixed Ligand ◽  
Interplanar Angle ◽  
Space Group ◽  
Square Planar

The molecules of the title compound, [Cu(C11H13N2O2)2], lie across centres of inversion in space group P21/c and are linked by intermolecular N-H···O and C-H···O hydrogen bonds. The central Cu atom has a slightly distorted square-planar coordination comprised of four N atoms. Cu-N bond distances are 1.975(2) and 2.020(2) Å . The interplanar angle between the phenyl and succinimidato ring is 87.34(10)°

Controlling emissive properties by intramolecular hydrogen bonds: alkyl and aryl meso‐substituted porphycenes

2021 ◽  
Author(s):  
Jacek Waluk ◽  
Arkadiusz Listkowski ◽  
Natalia Masiera ◽  
Michał Kijak ◽  
Roman Luboradzki ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

Energies of intramolecular hydrogen bonds in some alcohols

1974 ◽  
Vol 20 (3) ◽  
pp. 414-415
Author(s):  
Ya. A. Shuster ◽  
V. A. Granzhan ◽  
P. M. Zaitsev
Keyword(s):  
Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

scholarly journals Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

Symmetry ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 766
Author(s):  
Barbara Bankiewicz ◽  
Marcin Palusiak
Keyword(s):  
Complex Formation ◽  
Hydrogen Bonds ◽  
Dft Calculations ◽  
Electrostatic Interactions ◽  
Dipole Moments ◽  
Main Role ◽  
Halogen Bonds ◽  
Topological Parameters ◽  
Leading Role ◽  
The Impact

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

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