scholarly journals A simple predictor of interface orientation of mesogenic fluids and its implications for organic semiconductors

Author(s):  
Belinda Boehm ◽  
David Huang

From classical molecular dynamics simulations, we identify a simple and general predictor of molecular orientation at solid and vapour interfaces of isotropic fluids of anisotropic particles based on their shape and interaction anisotropy. For a wide variety of inter-particle interactions, temperatures, and substrate types within the range of typical organic semiconductors and their processing conditions, we find remarkable universal scaling of the orientation at the interface with the free energy calculated from pair interactions between close-packed nearest neighbours and an empirically derived universal relationship between the entropy and the shape anisotropy and bulk volume fraction of the fluid particles. The face-on orientation of fluid particles at the solid interface is generally predicted to be the equilibrium structure, although the alignment can be controlled by tuning the particle shape and substrate type, while changing the strength of fluid--fluid interactions is likely to play a less effective role. At the vapour interface, only the side-on structure is predicted, and conditions for which the face-on structure may be preferred, such as low temperature, low interaction anisotropy, or low shape anisotropy, are likely to result in little orientation preference (due to the low anisotropy) or be associated with a phase transition to an anisotropic bulk phase for systems with interactions in the range of typical organic semiconductors. Based on these results, we propose a set of guidelines for the rational design and processing of organic semiconductors to achieve a target orientation at a solid or vapour interface.

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.


2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.


Author(s):  
Suryakanti Debata ◽  
Smruti R. Sahoo ◽  
Rudranarayan Khatua ◽  
Sridhar Sahu

In this study, we present an effective molecular design strategy to develop the n-type charge transport characteristics in organic semiconductors, using ring-fused double perylene diimides (DPDIs) as the model compounds.


2006 ◽  
Vol 510-511 ◽  
pp. 358-361
Author(s):  
Won Yong Kim ◽  
Han Sol Kim ◽  
In Dong Yeo ◽  
Mok Soon Kim

We report on advanced Ni3Al based high temperature structural alloys with refractory alloying elements such as Zr and Mo to be apllied in the fields of die-casting and high temperature press forming as die materials. The duplex microstructure consisting of L12 structured Ni3Al phase and Ni5Zr intermetallic dispersoids was observed to display the microstructural feature for the present alloys investigated. Depending on alloying elements, the volume fraction of 2nd phase was measured to be different, indicating a difference in solid solubility of alloying elements in the matrix γ’ phase. Lattice parameter of matrix phase increased with increasing content of alloying elements. In the higher temperature region more than 973K, the present alloys appeared to show their higher strength compared to those obtained in conventional superalloys. On the basis of experimental results obtained, it is suggested that refractory alloying elements have an effective role to improve the high temperature strength in terms of enhanced thermal stability and solid solution hardening.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Annika Meiners ◽  
Sandra Bäcker ◽  
Inesa Hadrović ◽  
Christian Heid ◽  
Christine Beuck ◽  
...  

AbstractSurvivin’s dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein–protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin’s nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.


2000 ◽  
Vol 47 (1) ◽  
pp. 47-57 ◽  
Author(s):  
J Mazerski ◽  
I Antonini ◽  
S Martelli

Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.


COVID-19 has become a pandemic affecting the most of countries in the world. One of the most difficult decisions doctors face during the Covid-19 epidemic is determining which patients will stay in hospital, and which are safe to recover at home. In the face of overcrowded hospital capacity and an entirely new disease with little data-based evidence for diagnosis and treatment, the old rules for determining which patients should be admitted have proven ineffective. But machine learning can help make the right decision early, save lives and lower healthcare costs. So, there is therefore an urgent and imperative need to collect data describing clinical presentations, risks, epidemiology and outcomes. On the other side, artificial intelligence(AI) and machine learning(ML) are considered a strong firewall against outbreaks of diseases and epidemics due to its ability to quickly detect, examine and diagnose these diseases and epidemics.AI is being used as a tool to support the fight against the epidemic that swept the entire world since the beginning of 2020.. This paper presents the potential for using data engineering, ML and AI to confront the Coronavirus, predict the evolution of disease outbreaks, and conduct research in order to develop a vaccine or effective treatment that protects humanity from these deadly diseases.


2020 ◽  
Author(s):  
Anirban Das ◽  
Anju Yadav ◽  
Mona Gupta ◽  
R Purushotham ◽  
Vishram L. Terse ◽  
...  

AbstractProtein folding can go wrong in vivo and in vitro, with significant consequences for the living cell and the pharmaceutical industry, respectively. Here we propose a general design principle for constructing small peptide-based protein-specific folding modifiers. We construct a ‘xenonucleus’, which is a pre-folded peptide that resembles the folding nucleus of a protein, and demonstrate its activity on the folding of ubiquitin. Using stopped-flow kinetics, NMR spectroscopy, Förster Resonance Energy transfer, single-molecule force measurements, and molecular dynamics simulations, we show that the ubiquitin xenonucleus can act as an effective decoy for the native folding nucleus. It can make the refolding faster by 33 ± 5% at 3 M GdnHCl. In principle, our approach provides a general method for constructing specific, genetically encodable, folding modifiers for any protein which has a well-defined contiguous folding nucleus.


2019 ◽  
Author(s):  
Ian H. Kimball ◽  
Phuong T. Nguyen ◽  
Baldomero M. Olivera ◽  
Jon T. Sack ◽  
Vladimir Yarov-Yarovoy

AbstractThe voltage-gated sodium (Nav) channel subtype Nav1.7 plays a critical role in pain signaling, making it an important drug target. Here we studied the molecular interactions between μ-conotoxin KIIIA (KIIIA) and the human Nav1.7 channel (hNav1.7). We developed a structural model of hNav1.7 using Rosetta computational modeling and performed in silico docking of KIIIA using RosettaDock to predict residues forming specific pairwise contacts between KIIIA and hNav1.7. We experimentally validated these contacts using mutant cycle analysis. Comparison between our KIIIA-hNav1.7 model and the recently published cryo-EM structure of KIIIA-hNav1.2 revealed key similarities and differences between channel subtypes with potential implications for the molecular mechanism of toxin block. Our integrative approach, combining structural data with computational modeling, experimental validation, and molecular dynamics simulations will be useful for engineering molecular probes to study Nav channel function, and for rational design of novel biologics targeting specific Nav channels.


2018 ◽  
Vol 293 (21) ◽  
pp. 7969-7981 ◽  
Author(s):  
Thomas E. Bohl ◽  
Pek Ieong ◽  
John K. Lee ◽  
Thomas Lee ◽  
Jayakanth Kankanala ◽  
...  

Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen–deuterium exchange MS provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic, thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors.


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