scholarly journals Self-Assembly of Hydrogen-Bonded Cage Tetramers of Phosphonic Acid

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 258 ◽  
Author(s):  
Ivan S. Giba ◽  
Peter M. Tolstoy
Keyword(s):  
Hydrogen Bonds ◽  
Phosphonic Acid ◽  
Self Assembly ◽  
Density Functional ◽  
Proton Donor ◽  
The Self ◽  
Proton Acceptor ◽  
31P Nmr Spectroscopy ◽  
Phosphonic Acids ◽  
Self Association

The self-association of phosphonic acids with general formula RP(O)(OH)2 in solution state remains largely unexplored. The general understanding is that such molecules form multiple intermolecular hydrogen bonds, but the stoichiometry of self-associates and the bonding motifs are unclear. In this work, we report the results of the study of self-association of tert-butylphosphonic acid using low temperature liquid-state 1H and 31P NMR spectroscopy (100 K; CDF3/CDF2Cl) and density functional theory (DFT) calculations. For the first time, we demonstrate conclusively that polar aprotic medium tert-butylphosphonic acid forms highly symmetric cage-like tetramers held by eight OHO hydrogen bonds, which makes the complex quite stable. In these associates. each phosphonic acid molecule is bonded to three other molecules by forming two hydrogen bonds as proton donor and two hydrogen bonds as proton acceptor. Though the structure of such cage-like tetramers is close to tetrahedral, the formal symmetry of the self-associate is C2.

scholarly journals Insight into the Self-Assembly of Water-Soluble Perylene Bisimide Derivatives Through a Combined Computational and Experimental Approach

2019 ◽  
Author(s):  
Emily R. Draper ◽  
Liam Wilbraham ◽  
Dave J. Adams ◽  
Matthew Wallace ◽  
Martijn Zwijnenburg
Keyword(s):  
Density Functional Theory ◽  
Self Assembly ◽  
Density Functional ◽  
Colloidal Stability ◽  
Water Soluble ◽  
The Self ◽  
Functional Theory ◽  
Perylene Bisimide ◽  
Aggregate Growth ◽  
Perylene Bisimides

We use a combination of computational and experimental techniques to study the self-assembly and gelation of water-soluble perylene bisimides derivatised at the imide position with an amino acid. Specifically, we study the likely structure of self-assembled aggregates of the alanine-functionalised perylene bisimide (PBI-A) and the thermodynamics of their formation using density functional theory and predict the UV-vis spectra of such aggregates using time-dependent density functional theory. We compare these predictions to experiments in which we study the evolution of the UV-Vis and NMR spectra and rheology of alkaline PBI-A solutions when gradually decreasing the pH. Based on the combined computational and experimental results, we show that PBI-A self-assembles at all pH values but that aggregates grow in size upon protonation. Gelation is driven not by aggregate growth but reduction of the aggregation surface-charge and a decrease in the colloidal stability of the aggregation with respect to agglomeration.

scholarly journals Unveiling the self-association and desolvation in crystal nucleation

IUCrJ ◽  
2021 ◽  
Vol 8 (3) ◽  
pp. 468-479
Author(s):  
Danning Li ◽  
Yongli Wang ◽  
Shuyi Zong ◽  
Na Wang ◽  
Xin Li ◽  
...  
Keyword(s):  
Density Functional ◽  
Interaction Strength ◽  
Solution Chemistry ◽  
The Self ◽  
Crystal Nucleation ◽  
Nucleation Kinetics ◽  
Molecular Conformations ◽  
Self Association ◽  
Induction Times ◽  
The Relationship

As the first step in the crystallization process, nucleation has been studied by many researchers. In this work, phenacetin (PHEN) was selected as a model compound to investigate the relationship between the solvent and nucleation kinetics. Induction times at different supersaturation in six solvents were measured. FTIR and NMR spectroscopy were employed to explore the solvent–solute interactions and the self-association properties in solution. Density functional theory (DFT) was adopted to evaluate the strength of solute–solvent interactions and the molecular conformations in different solvents. Based on these spectroscopy data, molecular simulation and nucleation kinetic results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics is discussed. Both the solute–solvent interaction strength and the supramolecular structure formed by the self-association of solute molecules affect the nucleation rate. The findings reported here shed new light on the molecular mechanism of nucleation in solution.

scholarly journals Self-assembly of nucleopeptides to interact with DNAs

2017 ◽  
Vol 7 (6) ◽  
pp. 20160116 ◽  
Author(s):  
Xuewen Du ◽  
Jie Zhou ◽  
Xinming Li ◽  
Bing Xu
Keyword(s):  
Hydrogen Bonds ◽  
Plasmid Dna ◽  
Self Assembly ◽  
Unique Property ◽  
The Self ◽  
Proteinase K ◽  
Rational Approach ◽  
Proteolytic Resistance ◽  
Soft Biomaterials

As a novel class of biomaterials, nucleopeptides, via the conjugation of nucleobases and peptides, usually self-assemble to form nanofibres driven mainly by hydrogen bonds. Containing nucleobase(s), nucleopeptides have a unique property—interacting with nucleic acids. Here we report the design and characterization of nucleopeptides that self-assemble in water and are able to interact with single-stranded DNAs (ssDNAs). Containing nucleobases on their side chains, these nucleopeptides bind with the ssDNAs, and the ssDNAs reciprocally affect the self-assembly of nucleopeptides. In addition, the interactions between nucleopeptides and ssDNAs also decrease their proteolytic resistance against proteinase K, which further demonstrates the binding with ssDNAs. The nucleopeptides also interact with plasmid DNA and deliver hairpin DNA into cells. This work illustrates a new and rational approach to create soft biomaterials by the integration of nucleobases and peptides to bind with DNA, which may lead to the development of nucleopeptides for controlling DNA in cells.

Intermolecular interactions in dictating the self-assembly of halogen derivatives of bis-(N-substituted oxamato)palladate(ii) complexes

RSC Advances ◽  
2016 ◽  
Vol 6 (8) ◽  
pp. 6164-6170 ◽  
Author(s):  
Francisco Ramón Fortea-Pérez ◽  
Nadia Marino ◽  
Giovanni de Munno ◽  
Donatella Armentano ◽  
Miguel Julve ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Self Assembly ◽  
Supramolecular Assemblies ◽  
The Self ◽  
Derivatives Of

The reaction of aqueous [PdCl4]2−withN-4-Xphenyloxamate ligands (X = F, Cl, Br) afforded three non-isostructural compounds exhibiting intriguing diverse supramolecular assemblies driven by hydrogen bonds and/or halogen⋯halogen interactions.

scholarly journals Stacks of Azobenzene Stars: Self-Assembly Scenario and Stabilising Forces Quantified in Computer Modelling

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4387 ◽  
Author(s):  
Vladyslav Savchenko ◽  
Markus Koch ◽  
Aleksander S. Pavlov ◽  
Marina Saphiannikova ◽  
Olga Guskova
Keyword(s):  
Self Assembly ◽  
Density Functional ◽  
Computer Modelling ◽  
Light Stimulus ◽  
Dipole Moments ◽  
Intermolecular Forces ◽  
Binding Energies ◽  
The Self ◽  
Assembly Mechanism ◽  
Lateral Displacements

In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analyzed theoretically by applying a combination of computer simulation techniques. Without a light stimulus, the azobenzene arms adopt the trans-state and build one-dimensional columns of stacked molecules during the first stage of the noncovalent association. These columnar aggregates represent the structural elements of more complex experimentally observed morphologies—fibers, spheres, gels, and others. Here, we determine the most favorable mutual orientations of the trans-stars in the stack in terms of (i) the π – π distance between the cores lengthwise the aggregate, (ii) the lateral displacements due to slippage and (iii) the rotation promoting the helical twist and chirality of the aggregate. To this end, we calculate the binding energy diagrams using density functional theory. The model predictions are further compared with available experimental data. The intermolecular forces responsible for the stability of the stacks in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of the stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moments and the binding energies as functions of the columnar length. For this, molecular dynamics trajectories are analyzed. Finally, we conclude about the cooperative nature of the self-assembly of star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core in aqueous solution.

Intramolecular hydrogen bonds and the orientation of amino groupsin o-phenylenediamines

1967 ◽  
Vol 45 (19) ◽  
pp. 2135-2141 ◽  
Author(s):  
P. J. Krueger
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Infrared Absorption ◽  
Substituent Effect ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Amino Groups ◽  
Intramolecular Hydrogen Bonds ◽  
Infrared Absorption Spectra ◽  
Intramolecular Hydrogen

The infrared absorption spectra of partially deuterated o-phenylenediamine and 4,5-di-methyl-, 4-methyl-, and 4-chloro-o-phenylenediamine in dilute CCl4 solution show double intramolecular [Formula: see text] hydrogen bonds in which the two NHD groups are equivalent and each group acts as both a proton donor and a proton acceptor. The ring substituent effect on this interaction in these compounds is small. In 4-methoxy-o-phenylenediamine, the amino groups are not equivalent, but double intramolecular hydrogen bonds are still present. In 4-nitro-o-phenylenediamine, only one intramolecular [Formula: see text] hydrogen bond appears to exist. The effect of N-substitution on some of these observations is discussed.

The self-assembly mechanism of the Lindqvist anion [W6O19]2− in aqueous solution: a density functional theory study

2012 ◽  
Vol 41 (37) ◽  
pp. 11361 ◽  
Author(s):  
Zhong-Ling Lang ◽  
Wei Guan ◽  
Li-Kai Yan ◽  
Shi-Zheng Wen ◽  
Zhong-Min Su ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Density Functional Theory ◽  
Self Assembly ◽  
Density Functional ◽  
The Self ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Assembly Mechanism

Multiple Hydrogen Bonds in the Self-Assembly of Aminotriazine and Glutarimide. Decisive Role of the Triazine Substituents

2008 ◽  
Vol 8 (5) ◽  
pp. 1585-1594 ◽  
Author(s):  
Blanca R. Manzano ◽  
Félix A. Jalón ◽  
M. Laura Soriano ◽  
Ana M. Rodríguez ◽  
Antonio de la Hoz ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Self Assembly ◽  
Decisive Role ◽  
The Self ◽  
Multiple Hydrogen Bonds
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