scholarly journals The Stability of a Nanoparticle Diamond Lattice Linked by DNA

Nanomaterials ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 661 ◽  
Author(s):  
Hamed Emamy ◽  
Oleg Gang ◽  
Francis W. Starr
Keyword(s):  
Free Energy ◽  
Self Assembly ◽  
Lattice Structure ◽  
Diamond Lattice ◽  
Structure Stability ◽  
Lattice Stability ◽  
Wulff Construction ◽  
Crystallite Shape ◽  
The Stability ◽  
Relative Gibbs Free Energy

The functionalization of nanoparticles (NPs) with DNA has proven to be an effective strategy for self-assembly of NPs into superlattices with a broad range of lattice symmetries. By combining this strategy with the DNA origami approach, the possible lattice structures have been expanded to include the cubic diamond lattice. This symmetry is of particular interest, both due to the inherent synthesis challenges, as well as the potential valuable optical properties, including a complete band-gap. Using these lattices in functional devices requires a robust and stable lattice. Here, we use molecular simulations to investigate how NP size and DNA stiffness affect the structure, stability, and crystallite shape of NP superlattices with diamond symmetry. We use the Wulff construction method to predict the equilibrium crystallite shape of the cubic diamond lattice. We find that, due to reorientation of surface particles, it is possible to create bonds at the surface with dangling DNA links on the interior, thereby reducing surface energy. Consequently, the crystallite shape depends on the degree to which such surface reorientation is possible, which is sensitive to DNA stiffness. Further, we determine dependence of the lattice stability on NP size and DNA stiffness by evaluating relative Gibbs free energy. We find that the free energy is dominated by the entropic component. Increasing NP size or DNA stiffness increases free energy, and thus decreases the relative stability of lattices. On the other hand, increasing DNA stiffness results in a more precisely defined lattice structure. Thus, there is a trade off between structure and stability of the lattice. Our findings should assist experimental design for controlling lattice stability and crystallite shape.

Structure, Stability and Water Adsorption on Ultra-Thin TiO2 Supported on TiN

2019 ◽  
Author(s):  
Jose Julio Gutierrez Moreno ◽  
Marco Fronzi ◽  
Pierre Lovera ◽  
alan O'Riordan ◽  
Mike J Ford ◽  
...  
Keyword(s):  
Density Functional ◽  
Water Adsorption ◽  
Chemical Potential ◽  
Energy Gap ◽  
Molecular Water ◽  
Structure Stability ◽  
Ambient Conditions ◽  
Rutile Structure ◽  
The Stability ◽  
The One

<p></p><p>Interfacial metal-oxide systems with ultrathin oxide layers are of high interest for their use in catalysis. In this study, we present a density functional theory (DFT) investigation of the structure of ultrathin rutile layers (one and two TiO<sub>2</sub> layers) supported on TiN and the stability of water on these interfacial structures. The rutile layers are stabilized on the TiN surface through the formation of interfacial Ti–O bonds. Charge transfer from the TiN substrate leads to the formation of reduced Ti<sup>3+</sup> cations in TiO<sub>2.</sub> The structure of the one-layer oxide slab is strongly distorted at the interface, while the thicker TiO<sub>2</sub> layer preserves the rutile structure. The energy cost for the formation of a single O vacancy in the one-layer oxide slab is only 0.5 eV with respect to the ideal interface. For the two-layer oxide slab, the introduction of several vacancies in an already non-stoichiometric system becomes progressively more favourable, which indicates the stability of the highly non-stoichiometric interfaces. Isolated water molecules dissociate when adsorbed at the TiO<sub>2</sub> layers. At higher coverages the preference is for molecular water adsorption. Our ab initio thermodynamics calculations show the fully water covered stoichiometric models as the most stable structure at typical ambient conditions. Interfacial models with multiple vacancies are most stable at low (reducing) oxygen chemical potential values. A water monolayer adsorbs dissociatively on the highly distorted 2-layer TiO<sub>1.75</sub>-TiN interface, where the Ti<sup>3+</sup> states lying above the top of the valence band contribute to a significant reduction of the energy gap compared to the stoichiometric TiO<sub>2</sub>-TiN model. Our results provide a guide for the design of novel interfacial systems containing ultrathin TiO<sub>2</sub> with potential application as photocatalytic water splitting devices.</p><p></p>

Examining sharp restart in a Monte Carlo method for the linearized Poisson–Boltzmann equation

2020 ◽  
Vol 26 (3) ◽  
pp. 223-244
Author(s):  
W. John Thrasher ◽  
Michael Mascagni
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Algorithm ◽  
Significant Bias ◽  
Poisson Boltzmann ◽  
Electrostatic Free Energy ◽  
Poisson Boltzmann Equation ◽  
The Stability ◽  
Potential Methods ◽  
The Individual

AbstractIt has been shown that when using a Monte Carlo algorithm to estimate the electrostatic free energy of a biomolecule in a solution, individual random walks can become entrapped in the geometry. We examine a proposed solution, using a sharp restart during the Walk-on-Subdomains step, in more detail. We show that the point at which this solution introduces significant bias is related to properties intrinsic to the molecule being examined. We also examine two potential methods of generating a sharp restart point and show that they both cause no significant bias in the examined molecules and increase the stability of the run times of the individual walks.

Use of Minimal Free Energy and Self-Assembly To Form Shapes

1995 ◽  
Vol 7 (6) ◽  
pp. 1257-1264 ◽  
Author(s):  
Enoch Kim ◽  
George M. Whitesides
Keyword(s):  
Free Energy ◽  
Self Assembly ◽  
Minimal Free Energy

scholarly journals High stability of trehalose/maltose binding protein fromThermococcus litoralismakes it a good candidate as a sensitive element in biosensor systems for sugar control

2010 ◽  
Vol 24 (3-4) ◽  
pp. 349-353 ◽  
Author(s):  
Olga I. Povarova ◽  
Olga V. Stepanenko ◽  
Anna I. Sulatskaya ◽  
Irina M. Kuznetsova ◽  
Konstantin K. Turoverov ◽  
...  
Keyword(s):  
Free Energy ◽  
Sensitive Element ◽  
High Stability ◽  
Binding Protein ◽  
Maltose Binding Protein ◽  
Thermococcus Litoralis ◽  
Thermophilic Archaeon ◽  
Unfolded State ◽  
The Stability ◽  
Innate Ability

Fluorescence and circular dichroism in far-UV region were used to study the stability of trehalose/maltose binding protein (TMBP) from hyper thermophilic archaeonThermococcus litoralisand its complex with glucose (TMBP/Glc). The evaluation of difference between free energy of native and unfolded state for TMBP and TMBP/Glc showed that both of them are several times higher than that of proteins from mesophilic organisms. Due to the high stability and innate ability to bind glucose this protein is a good candidate as a sensitive element in biosensor systems for sugar control.

Correlation of the solid-state reactivities of racemic 2,4(6)-di-O-benzoyl-myo-inositol 1,3,5-orthoformate and its 4,4′-bipyridine cocrystal with their crystal structures

2014 ◽  
Vol 70 (11) ◽  
pp. 1040-1045 ◽  
Author(s):  
Majid I. Tamboli ◽  
Vir Bahadur ◽  
Rajesh G. Gonnade ◽  
Mysore S. Shashidhar
Keyword(s):  
Solid State ◽  
Self Assembly ◽  
Transfer Reaction ◽  
Acyl Transfer ◽  
Transfer Reactions ◽  
Group Transfer ◽  
Hydrogen Bonding Interactions ◽  
Benzoyl Group ◽  
The Stability ◽  
Group Migration

Racemic 2,4(6)-di-O-benzoyl-myo-inositol 1,3,5-orthoformate, C21H18O8,(1), shows a very efficient intermolecular benzoyl-group migration reaction in its crystals. However, the presence of 4,4′-bipyridine molecules in its cocrystal, C21H18O8·C10H8N2,(1)·BP, inhibits the intermolecular benzoyl-group transfer reaction. In(1), molecules are assembled around the crystallographic twofold screw axis (baxis) to form a helical self-assembly through conventional O—H...O hydrogen-bonding interactions. This helical association places the reactive C6-O-benzoyl group (electrophile, El) and the C4-hydroxy group (nucleophile, Nu) in proximity, with a preorganized El...Nu geometry favourable for the acyl transfer reaction. In the cocrystal(1)·BP, the dibenzoate and bipyridine molecules are arranged alternately through O—H...N interactions. The presence of the bipyridine molecules perturbs the regular helical assembly of the dibenzoate molecules and thus restricts the solid-state reactivity. Hence, unlike the parent dibenzoate crystals, the cocrystals do not exhibit benzoyl-transfer reactions. This approach is useful for increasing the stability of small molecules in the crystalline state and could find application in the design of functional solids.

scholarly journals Surface modification and adhesion improvement of polyester films

2013 ◽  
Vol 11 (1) ◽  
pp. 35-45 ◽  
Author(s):  
Aniello Cammarano ◽  
Giovanna Luca ◽  
Eugenio Amendola
Keyword(s):  
Free Energy ◽  
Surface Modification ◽  
Surface Free Energy ◽  
Self Assembly ◽  
Treatment Time ◽  
Solution Treatment ◽  
Film Surface ◽  
Critical Surface ◽  
Hydrolysis Time ◽  
Critical Surface Tension

AbstractFacile surface modification of polyester films was performed via chemical solutions treatment. Surface hydrolysis was carried out by means of sodium hydroxide solutions, leading to the formation of carboxylate groups. Three commercial polyester films of 100 μm in thickness were used in this work: AryLite™, Mylar™, and Teonex™, hydrolysis time being the main modification parameter. FTIR-ATR analysis, topography and contact angle (CA) measurements, surface free energy (SFE) and T-Peel adhesion tests were carried out to characterize the modified films. A quantitative estimate of the carboxylates surface coverage as a function of treatment time was obtained through a supramolecular approach, i.e. the ionic self-assembly of a tetracationic porphyrin chromophore onto the film surface. The surface free energy and critical surface tension of the hydrolyzed polyesters was evaluated by means of Zisman, Saito, Berthelot and Owens-Wendt methods. It was shown that NaOH solution treatment increases roughness, polarity and surface free energy of polymers. As a result, T-Peel strengths for modified Mylar™ and Teonex™ films were respectively 2.2 and 1.8 times higher than that for the unmodified films, whereas AryLite™ adhesion test failed.

scholarly journals Conserved Motifs within Ebola and Marburg Virus VP40 Proteins Are Important for Stability, Localization, and Subsequent Budding of Virus-Like Particles

2009 ◽  
Vol 84 (5) ◽  
pp. 2294-2303 ◽  
Author(s):  
Yuliang Liu ◽  
Luis Cocka ◽  
Atsushi Okumura ◽  
Yong-An Zhang ◽  
J. Oriol Sunyer ◽  
...  
Keyword(s):  
Self Assembly ◽  
Mammalian Cells ◽  
Ebola Virus ◽  
Intracellular Localization ◽  
Gel Filtration ◽  
Point Mutations ◽  
Marburg Virus ◽  
Structure Stability ◽  
Wild Type ◽  
Virus Like Particles

ABSTRACT The filovirus VP40 protein is capable of budding from mammalian cells in the form of virus-like particles (VLPs) that are morphologically indistinguishable from infectious virions. Ebola virus VP40 (eVP40) contains well-characterized overlapping L domains, which play a key role in mediating efficient virus egress. L domains represent only one component required for efficient budding and, therefore, there is a need to identify and characterize additional domains important for VP40 function. We demonstrate here that the 96LPLGVA101 sequence of eVP40 and the corresponding 84LPLGIM89 sequence of Marburg virus VP40 (mVP40) are critical for efficient release of VP40 VLPs. Indeed, deletion of these motifs essentially abolished the ability of eVP40 and mVP40 to bud as VLPs. To address the mechanism by which the 96LPLGVA101 motif of eVP40 contributes to egress, a series of point mutations were introduced into this motif. These mutants were then compared to the eVP40 wild type in a VLP budding assay to assess budding competency. Confocal microscopy and gel filtration analyses were performed to assess their pattern of intracellular localization and ability to oligomerize, respectively. Our results show that mutations disrupting the 96LPLGVA101 motif resulted in both altered patterns of intracellular localization and self-assembly compared to wild-type controls. Interestingly, coexpression of either Ebola virus GP-WT or mVP40-WT with eVP40-ΔLPLGVA failed to rescue the budding defective eVP40-ΔLPLGVA mutant into VLPs; however, coexpression of eVP40-WT with mVP40-ΔLPLGIM successfully rescued budding of mVP40-ΔLPLGIM into VLPs at mVP40-WT levels. In sum, our findings implicate the LPLGVA and LPLGIM motifs of eVP40 and mVP40, respectively, as being important for VP40 structure/stability and budding.

Estimation of pKa values for carboxylic acids, alcohols, phenols and amines using changes in the relative Gibbs free energy

2012 ◽  
Vol 313 ◽  
pp. 148-155 ◽  
Author(s):  
Yue Zeng ◽  
Xianglan Chen ◽  
Dongbo Zhao ◽  
Haitao Li ◽  
Youyu Zhang ◽  
...  
Keyword(s):  
Free Energy ◽  
Carboxylic Acids ◽  
Gibbs Free Energy ◽  
Pka Values ◽  
Relative Gibbs Free Energy

scholarly journals REMOVAL OF CU (II) FROM DYE EFFLUENT USING NATURAL AND PHOSPHATE-MODIFIED NIGERIAN KAOLINITE CLAY

2019 ◽  
Vol 7 (8) ◽  
pp. 402-414
Author(s):  
S. C. Olu ◽  
P. E. Dim ◽  
J. O. Okafor
Keyword(s):  
Free Energy ◽  
Metal Ion ◽  
Fourier Transforms ◽  
Lattice Structure ◽  
Enthalpy Change ◽  
Free Energy Change ◽  
Energy Change ◽  
Order Model ◽  
Acid Modification ◽  
Kaolinite Clay

This study indicates kaolinite clay as an effective adsorbent for the uptake of Cu (II) from wastewater. The adsorption process was studied with variation of time, temperature and adsorbent dosage at the effluent pH of 6. X-ray diffraction (XRD), Fourier transforms infrared spectroscopy (FTIR), Brunauer Emmett and Teller (BET) and Scanning electron microscopy (SEM) were used to characterize the adsorbents. XRD spectra showed that modification with KH2PO4 did not significantly change the crystal spacing on the lattice structure of the clay mineral; however, there were shifts in the intensity of the peaks for the modified kaolinite clay. The FTIR spectra showed that certain functional groups are responsible for binding the metal ions from solution. SEM indicated an increase in the porosity of the modified adsorbent as compared with the unmodified kaolinite, which enhances metal ion adsorption on modified kaolinite clay. The BET indicate that acid modification increased the surface area and total pore volume of the kaolinite clay. The kinetic study revealed that the pseudo-first-order model fitted poorly to the equilibrium data, however, the pseudo-second-order model had a good fit for all reaction time at different initial concentrations. The mechanism of the sorption process was evaluated using thermodynamic properties such as enthalpy change (ΔH), Gibbs free energy change (ΔG), and entropy change (ΔS), which were evaluated using Van’t Hoff equations. The negative values of free energy change (ΔG), suggests spontaneity and feasibility of the process. The positive values of enthalpy change (ΔH) indicate endothermic nature of the process.

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