Self‐assembly of Unprotected Dipeptides into Hydrogels: Water‐Channels Make the Difference.

In this work, we report the synthesis of a new bis(tris(2-aminoethyl)amine) azacryptand L with triphenyl spacers. The binding properties of its dicopper complex for aromatic dicarboxylate anions (as TBA salts) were investigated, with the aim to obtain potential building blocks for supramolecular structures like rotaxanes and pseudo-rotaxanes. As expected, UV-Vis and emission studies of [Cu2L]4+ in water/acetonitrile mixture (pH = 7) showed a high affinity for biphenyl-4,4′-dicarboxylate (dfc2−), with a binding constant of 5.46 log units, due to the best match of the anion bite with the Cu(II)-Cu(II) distance in the cage’s cavity. Compared to other similar bistren cages, the difference of the affinity of [Cu2L]4+ for the tested anions was not so pronounced: conformational changes of L seem to promote a good interaction with both long (e.g., dfc2−) and short anions (e.g., terephthalate). The good affinity of [Cu2L]4+ for these dicarboxylates, together with hydrophobic interactions within the cage’s cavity, may promote the self-assembly of a stable 1:1 complex in water mixture. These results represent a good starting point for the application of these molecular systems as building units for the design of new supramolecular architectures based on non-covalent interactions, which could be of interest in all fields related to supramolecular devices.

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Development of an Electron Scattering Model to Detect Differences in DNA Base Molecules

ASME-JSME-KSME 2011 Joint Fluids Engineering Conference: Volume 2, Fora ◽

10.1115/ajk2011-36031 ◽

2011 ◽

Author(s):

Yuki Nishioka ◽

Kentaro Doi ◽

Satoyuki Kawano

Keyword(s):

Theoretical Model ◽

Electric Conductivity ◽

Electron Scattering ◽

Self Assembly ◽

High Speed ◽

Classical Electrodynamics ◽

Base Pairs ◽

Novel Technologies ◽

Dna Base ◽

The Difference

In recent, novel technologies which apply bio-macromolecules to bio-nanodevices attract much attention. Particularly, DNAs have several desirable characteristics: complementary base pairs, self assembly, and electric conductivity. It is expected that high-speed DNA sequencers can be developed by using these specific characteristics of DNAs. In the present study, we develop a theoretical model to analyze the difference of DNA base molecules, in which electron scattering is simulated based on classical electrodynamics and scattering angles are evaluated. Consequently, it is found that scattering angles of the scattered electrons are clearly different from each other.

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Exploring the Adsorption Mechanism of Tetracene on Ag(110) by STM and Dispersion-Corrected DFT

Crystals ◽

10.3390/cryst10010013 ◽

2019 ◽

Vol 10 (1) ◽

pp. 13 ◽

Cited By ~ 1

Author(s):

Zhaofeng Liang ◽

Qiwei Tian ◽

Huan Zhang ◽

Jinping Hu ◽

Pimo He ◽

...

Keyword(s):

Molecular Electronics ◽

Self Assembly ◽

Density Functional ◽

Scanning Tunneling ◽

Dispersion Force ◽

Tunneling Microscopy ◽

Functional Theory ◽

Silver Substrate ◽

The Difference ◽

Low Dimensional

Self-assembled strategy has been proven to be a promising vista in constructing organized low-dimensional nanostructures with molecular precision and versatile functionalities on solid surfaces. Herein, we investigate by a combination of scanning tunneling microscopy (STM) and dispersion-corrected density functional theory (DFT), the adsorption of tetracene molecules on the silver substrate and the mechanism mediating the self-assembly on Ag(110). As expected, ordered domain is formed on Ag(110) after adsorption with adjacent molecules being imaged with alternating bright or dim pattern regularly. While such behavior has been assigned previously to the difference of molecular adsorption height, herein, it is possible to investigate essentially the mechanism leading to the periodic alternation of brightness and dimness for tetracene adsorbed on Ag(110) thanks to the consideration of Van der Waals (vdW) dispersion force. It is demonstrated that the adsorption height in fact is same for both bright and dim molecules, while the adsorption site and the corresponding interfacial charge transfer play an important role in the formation of such pattern. Our report reveals that vdW dispersion interaction is crucial to appropriately describe the adsorption of tetracene on the silver substrate, and the formation of delicate molecular architectures on metal surfaces might also offers a promising approach towards molecular electronics.

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Periodically Birefringent Thin Films Grown out of the Isotropic Phase of a Bent-Core Banana-Shaped Liquid Crystal

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.428-429.228 ◽

2010 ◽

Vol 428-429 ◽

pp. 228-231 ◽

Cited By ~ 11

Author(s):

Qing Lan Ma ◽

Yuan Ming Huang

Keyword(s):

Thin Films ◽

Liquid Crystal ◽

Optical Microscopy ◽

Self Assembly ◽

Driving Forces ◽

Isotropic Phase ◽

Periodic Modulation ◽

Polarized Optical Microscopy ◽

Self Assembled ◽

The Difference

Periodically birefringent thin films growing out of the isotropic phase of the banana-shaped liquid crystal 1,3-phenylene-bis (4-butoxybenzyldiamine) were investigated with polarized optical microscopy. The gown thin films of the periodic modulation of the birefringent index self-assembled by the banana-shaped LC molecules were attributed to the difference of the molecular composing structures. Further the driving forces of the banana-shaped molecular self-assembly were discussed.

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Water-Induced Self-Assembly of Amphiphilic Discotic Molecules for Adaptive Artificial Water Channels

ACS Nano ◽

10.1021/acsnano.1c04994 ◽

2021 ◽

Author(s):

Hsi-Yen Chang ◽

Kuan-Yi Wu ◽

Wei-Chun Chen ◽

Jing-Ting Weng ◽

Chin-Yi Chen ◽

...

Keyword(s):

Self Assembly ◽

Water Channels ◽

Artificial Water

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Thermodynamic aspects of the self-assembly of DsrA, a small noncoding RNA from Escherichia coli.

Acta Biochimica Polonica ◽

10.18388/abp.2014_1941 ◽

2014 ◽

Vol 61 (1) ◽

Cited By ~ 1

Author(s):

Frédéric Geinguenaud ◽

Maeva Gesson ◽

Véronique Arluison

Keyword(s):

Escherichia Coli ◽

Self Assembly ◽

Noncoding Rna ◽

The Self ◽

Functional Consequence ◽

Small Noncoding Rna ◽

The Difference ◽

First Time ◽

Thermodynamic Basis

DsrA is an Escherichia coli small noncoding RNA that acts by base pairing to some mRNAs in order to control their translation and turnover. It was recently shown that DsrA is able to self-associate in a way similar to DNA and to build nanostructures. Although functional consequence of this RNA self-assembly in vivo is not yet understood, the formation of such an assemblage more than likely influences the noncoding RNA function. We report here for the first time the thermodynamic basis of this natural RNA self-assembly. In particular we show that assembling of the ribonucleic acid is enthalpy driven and that the versatility of the RNA molecule is important for the polymerisation; indeed, an equivalent DNA sequence is unable to make a nanoassembly. The origin of the difference is discussed herein.

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Growth and Removal Behavior of Magnesium Oxide Microspheres towards Methyl Orange and Methylene Blue in Aqueous Solution

10.3762/bxiv.2020.5.v1 ◽

2020 ◽

Author(s):

Saeed Ahmed ◽

Jingsong Pan ◽

Dianqing Li ◽

Pinggui Tang ◽

Xin Shu ◽

...

Keyword(s):

Methylene Blue ◽

Methyl Orange ◽

Self Assembly ◽

Order Kinetic ◽

Isothermal Model ◽

Benefit Design ◽

Order Kinetic Model ◽

Pseudo Second Order ◽

The Difference ◽

Maximum Removal

The adsorption of dyes from the industrial influent has attracted great interest to overcome water pollution. In this work, we carefully investigated the growth process of hierarchical MgO microspheres and the difference in the corresponding removal behavior towards two dyes: anionic methyl orange and cationic methylene blue. The MgO microspheres were formed by the self-assembly of thin nanosheets following the reaction time and exhibited the maximum removal capacities are 940.14 mg g-1 for methyl orange and 354.00 mg g-1 for methylene blue. The anionic methyl orange and cationic methylene blue adsorption follow the pseudo-second-order kinetic model, Freundlich isothermal model. The difference in the removal behavior towards two dyes is strongly related to the surface charge of MgO and the charge of pollutants. This work will benefit design and improvement in the removal performance of novel porous adsorbents.

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Milliseconds Make the Difference in the Far-from-Equilibrium Self-Assembly of Supramolecular Chiral Nanostructures

Journal of the American Chemical Society ◽

10.1021/jacs.6b02538 ◽

2016 ◽

Vol 138 (22) ◽

pp. 6920-6923 ◽

Cited By ~ 39

Author(s):

Alessandro Sorrenti ◽

Romen Rodriguez-Trujillo ◽

David B. Amabilino ◽

Josep Puigmartí-Luis

Keyword(s):

Self Assembly ◽

Far From Equilibrium ◽

The Difference ◽

Chiral Nanostructures

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The Knot Spectrum of Confined Random Equilateral Polygons

Computational and Mathematical Biophysics ◽

10.2478/mlbmb-2014-0002 ◽

2014 ◽

Vol 2 (1) ◽

Cited By ~ 4

Author(s):

Y. Diao ◽

C. Ernst ◽

A. Montemayor ◽

E. Rawdon ◽

U. Ziegler

Keyword(s):

Self Assembly ◽

Viral Capsids ◽

Benchmark Data ◽

Random Polygons ◽

Circular Dnas ◽

Bacteriophage P4 ◽

Topological Characteristics ◽

The Difference ◽

Living Organisms ◽

Dna Packing

Abstract It is well known that genomic materials (long DNA chains) of living organisms are often packed compactly under extreme confining conditions using macromolecular self-assembly processes but the general DNA packing mechanism remains an unsolved problem. It has been proposed that the topology of the packed DNA may be used to study the DNA packing mechanism. For example, in the case of (mutant) bacteriophage P4, DNA molecules packed inside the bacteriophage head are considered to be circular since the two sticky ends of the DNA are close to each other. The DNAs extracted from the capsid without separating the two ends can thus preserve the topology of the (circular) DNAs. It turns out that the circular DNAs extracted from bacteriophage P4 are non-trivially knotted with very high probability and with a bias toward chiral knots. In order to study this problem using a systematic approach based on mathematical modeling, one needs to introduce a DNA packing model under extreme volume confinement condition and test whether such a model can produce the kind of knot spectrum observed in the experiments. In this paper we introduce and study a model of equilateral random polygons con_ned in a sphere. This model is not meant to generate polygons that model DNA packed in a virus head directly. Instead, the average topological characteristics of this model may serve as benchmark data for totally randomly packed circular DNAs. The difference between the biologically observed topological characteristics and our benchmark data might reveal the bias of DNA packed in the viral capsids and possibly lead to a better understanding of the DNA packing mechanism, at least for the bacteriophage DNA. The purpose of this paper is to provide information about the knot spectrum of equilateral random polygons under such a spherical confinement with length and confinement ratios in a range comparable to circular DNAs packed inside bacteriophage heads.

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Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

Nanomaterials ◽

10.3390/nano11020299 ◽

2021 ◽

Vol 11 (2) ◽

pp. 299

Author(s):

Silvio Osella

Keyword(s):

Self Assembly ◽

Artificial Photosynthesis ◽

Light Harvesting ◽

Point Of View ◽

Experimental Point ◽

Redox Active ◽

Surface Assembly ◽

Recent Developments ◽

The Difference ◽

Artificial Photosynthetic

A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.

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