scholarly journals Elucidating the Aromatic Properties of Covalent Organic Frameworks Surface for Enhanced Polar Solvent Adsorption

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1861
Author(s):  
Mostafa Yousefzadeh Borzehandani ◽  
Emilia Abdulmalek ◽  
Mohd Basyaruddin Abdul Rahman ◽  
Muhammad Alif Mohammad Latif
Keyword(s):  
Electrostatic Interactions ◽  
Selective Adsorption ◽  
Van Der Waals Interactions ◽  
Covalent Organic Frameworks ◽  
Aromatic Character ◽  
Good Surface ◽  
Phenyl Rings ◽  
Adsorption Of Water ◽  
Dynamics Simulations ◽  
Solvent Adsorption

Covalent organic frameworks (COFs) have a distinguished surface as they are mostly made by boron, carbon, nitrogen and oxygen. Many applications of COFs rely on polarity, size, charge, stability and hydrophobicity/hydrophilicity of their surface. In this study, two frequently used COFs sheets, COF-1 and covalent triazine-based frameworks (CTF-1), are studied. In addition, a theoretical porous graphene (TPG) was included for comparison purposes. The three solid sheets were investigated for aromaticity and stability using quantum mechanics calculations and their ability for water and ethanol adsorption using molecular dynamics simulations. COF-1 demonstrated the poorest aromatic character due to the highest energy delocalization interaction between B–O bonding orbital of sigma type and unfilled valence-shell nonbonding of boron. CTF-1 was identified as the least kinetically stable and the most chemically reactive. Both COF-1 and CTF-1 showed good surface properties for selective adsorption of water via hydrogen bonding and electrostatic interactions. Among the three sheets, TPG’s surface was mostly affected by aromatic currents and localized π electrons on the phenyl rings which in turn made it the best platform for selective adsorption of ethanol via van der Waals interactions. These results can serve as guidelines for future studies on solvent adsorption for COFs materials.

Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Secondary Structure ◽  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Heterogeneous Polymer ◽  
Non Local ◽  
Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

scholarly journals Characterization of design grammar of peptides for regulating liquid droplets and aggregates of FUS

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kiyoto Kamagata ◽  
Rika Chiba ◽  
Ichiro Kawahata ◽  
Nanako Iwaki ◽  
Saori Kanbayashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Electrostatic Interactions ◽  
Amyloid Fibrils ◽  
Droplet Formation ◽  
Liquid Droplets ◽  
Proof Of Concept ◽  
Aggregate Formation ◽  
Fused In Sarcoma ◽  
Dynamics Simulations

AbstractLiquid droplets of aggregation-prone proteins, which become hydrogels or form amyloid fibrils, are a potential target for drug discovery. In this study, we proposed an experiment-guided protocol for characterizing the design grammar of peptides that can regulate droplet formation and aggregation. The protocol essentially involves investigation of 19 amino acid additives and polymerization of the identified amino acids. As a proof of concept, we applied this protocol to fused in sarcoma (FUS). First, we evaluated 19 amino acid additives for an FUS solution and identified Arg and Tyr as suppressors of droplet formation. Molecular dynamics simulations suggested that the Arg additive interacts with specific residues of FUS, thereby inhibiting the cation–π and electrostatic interactions between the FUS molecules. Second, we observed that Arg polymers promote FUS droplet formation, unlike Arg monomers, by bridging the FUS molecules. Third, we found that the Arg additive suppressed solid aggregate formation of FUS, while Arg polymer enhanced it. Finally, we observed that amyloid-forming peptides induced the conversion of FUS droplets to solid aggregates of FUS. The developed protocol could be used for the primary design of peptides controlling liquid droplets and aggregates of proteins.

scholarly journals Spatial segregation of mixed-sized counterions in dendritic polyelectrolytes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. S. Kłos ◽  
J. Paturej
Keyword(s):  
Electrostatic Interactions ◽  
Spatial Separation ◽  
Excluded Volume ◽  
The Core ◽  
Bjerrum Length ◽  
Two Component ◽  
Conformational Properties ◽  
Dynamics Simulations ◽  
Two Parameters ◽  
Swelling Factor

AbstractLangevin dynamics simulations are utilized to study the structure of a dendritic polyelectrolyte embedded in two component mixtures comprised of conventional (small) and bulky counterions. We vary two parameters that trigger conformational properties of the dendrimer: the reduced Bjerrum length, $$\lambda _B^*$$ λ B ∗ , which controls the strength of electrostatic interactions and the number fraction of the bulky counterions, $$f_b$$ f b , which impacts on their steric repulsion. We find that the interplay between the electrostatic and the counterion excluded volume interactions affects the swelling behavior of the molecule. As compared to its neutral counterpart, for weak electrostatic couplings the charged dendrimer exists in swollen conformations whose size remains unaffected by $$f_b$$ f b . For intermediate couplings, the absorption of counterions into the pervaded volume of the dendrimer starts to influence its conformation. Here, the swelling factor exhibits a maximum which can be shifted by increasing $$f_b$$ f b . For strong electrostatic couplings the dendrimer deswells correspondingly to $$f_b$$ f b . In this regime a spatial separation of the counterions into core–shell microstructures is observed. The core of the dendrimer cage is preferentially occupied by the conventional ions, whereas its periphery contains the bulky counterions.

scholarly journals Adsorption in Mixtures with Competing Interactions

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4532
Author(s):  
Marek Litniewski ◽  
Alina Ciach
Keyword(s):  
Short Range ◽  
Selective Adsorption ◽  
Similar Amount ◽  
Particle Interactions ◽  
Near Surface ◽  
Gas Density ◽  
Short Range Repulsion ◽  
Adsorbed Layers ◽  
Dynamics Simulations ◽  
Oppositely Charged

A binary mixture of oppositely charged particles with additional short-range attraction between like particles and short-range repulsion between different ones in the neighborhood of a substrate preferentially adsorbing the first component is studied by molecular dynamics simulations. The studied thermodynamic states correspond to an approach to the gas–crystal coexistence. Dependence of the near-surface structure, adsorption and selective adsorption on the strength of the wall–particle interactions and the gas density is determined. We find that alternating layers or bilayers of particles of the two components are formed, but the number of the adsorbed layers, their orientation and the ordered patterns formed inside these layers could be quite different for different substrates and gas density. Different structures are associated with different numbers of adsorbed layers, and for strong attraction the thickness of the adsorbed film can be as large as seven particle diameters. In all cases, similar amount of particles of the two components is adsorbed, because of the long-range attraction between different particles.

scholarly journals Optimization of Mordenite Membranes Using Sucrose Precursor for Pervaporation of Water-Ethanol Mixtures

Membranes ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 160
Author(s):  
Abdulaziz A. Alomair ◽  
Yousef Alqaheem
Keyword(s):  
Pyrolysis Temperature ◽  
Operating Temperature ◽  
Selective Adsorption ◽  
Sucrose Concentration ◽  
Low Cost ◽  
Water Flux ◽  
Separation Performance ◽  
Carbon Membranes ◽  
Adsorption Of Water ◽  
High Separation

Post-treated mordenite membranes were prepared using sucrose (C12H22O11) as a carbon precursor to block any pinholes and defects in the zeolite layer. The pervaporation (PV) process was used to separate ethanol from the water. The effects of the sucrose concentration and the pyrolysis temperature (650–850 °C) were investigated, and the resulting high separation performance compared to those post/pre-treated membranes was reported in the literature. In this study, mordenite carbon membranes yielded a water/ethanol separation factor of 990.37 at a water flux of 9.10 g/m2h. The influence of the operating temperature on the performance of the membrane also was considered. It was concluded that the selective adsorption of water through zeolite pores was achieved. The entire preparation procedure was achieved using a rapid, low-cost preparation process.

scholarly journals Dynamical strengthening of covalent and non-covalent molecular interactions by nuclear quantum effects at finite temperature

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Huziel E. Sauceda ◽  
Valentin Vassilev-Galindo ◽  
Stefan Chmiela ◽  
Klaus-Robert Müller ◽  
Alexandre Tkatchenko
Keyword(s):  
Finite Temperature ◽  
Electrostatic Interactions ◽  
Zero Point ◽  
Quantum Effects ◽  
Van Der Waals Interactions ◽  
Interatomic Distances ◽  
Point Energy ◽  
Molecular Bond ◽  
Energy Surfaces ◽  
Nuclear Quantum Effects

AbstractNuclear quantum effects (NQE) tend to generate delocalized molecular dynamics due to the inclusion of the zero point energy and its coupling with the anharmonicities in interatomic interactions. Here, we present evidence that NQE often enhance electronic interactions and, in turn, can result in dynamical molecular stabilization at finite temperature. The underlying physical mechanism promoted by NQE depends on the particular interaction under consideration. First, the effective reduction of interatomic distances between functional groups within a molecule can enhance the n → π* interaction by increasing the overlap between molecular orbitals or by strengthening electrostatic interactions between neighboring charge densities. Second, NQE can localize methyl rotors by temporarily changing molecular bond orders and leading to the emergence of localized transient rotor states. Third, for noncovalent van der Waals interactions the strengthening comes from the increase of the polarizability given the expanded average interatomic distances induced by NQE. The implications of these boosted interactions include counterintuitive hydroxyl–hydroxyl bonding, hindered methyl rotor dynamics, and molecular stiffening which generates smoother free-energy surfaces. Our findings yield new insights into the versatile role of nuclear quantum fluctuations in molecules and materials.

scholarly journals Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

2018 ◽  
Author(s):  
Giovanni B. Brandani ◽  
Shoji Takada
Keyword(s):  
Genome Organization ◽  
Electrostatic Interactions ◽  
Defect Formation ◽  
Energy Landscape ◽  
Molecular Machines ◽  
Biological Processes ◽  
Complete Understanding ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna ◽  
Dynamics Simulations

ABSTRACTATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning, ejecting, or editing nucleosomes, activities that confer them essential regulatory roles on gene expression and DNA replication. Here, we investigate the molecular mechanism of active nucleosome sliding by means of molecular dynamics simulations of the Snf2 remodeler in complex with a nucleosome. During its inchworm motion driven by ATP consumption, the remodeler overwrites the original nucleosome energy landscape via steric and electrostatic interactions to induce sliding of nucleosomal DNA unidirectionally. The sliding is initiated at the remodeler binding location via the generation of twist defects, which then spontaneously propagate to complete sliding throughout the entire nucleosome. We also reveal how remodeler mutations and DNA sequence control active nucleosome repositioning, explaining several past experimental observations. These results offer a detailed mechanistic picture of remodeling important for the complete understanding of these important biological processes.

scholarly journals The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.

2000 ◽  
Vol 47 (1) ◽  
pp. 65-78 ◽  
Author(s):  
J Mazerski ◽  
K Muchewicz
Keyword(s):  
Conformational Changes ◽  
Ring System ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Intercalation Complex ◽  
Highly Active ◽  
Antitumor Compounds ◽  
Chemical Constitution ◽  
Modelling Techniques ◽  
Dynamics Simulations

Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.

scholarly journals Synthesis of a magnetic C@Co material via the design of a MOF precursor for efficient and selective adsorption of water pollutants

2021 ◽  
Author(s):  
Yu Liu ◽  
Yan Wang ◽  
Xiao-Sa Zhang ◽  
Wen-Ze Li ◽  
Ai-Ai Yang ◽  
...  
Keyword(s):  
Active Sites ◽  
Organic Dyes ◽  
Selective Adsorption ◽  
Catalytic Performance ◽  
Adsorption Processes ◽  
Carbon Coated ◽  
Adsorption Of Water ◽  
Metal Organic ◽  
Cobalt Nanoparticle ◽  
Fast Acting

Abstract 3D metal-organic frameworks (MOFs) can be appropriate templates for the fabrication of nanomaterials due to they have active sites exposed on the channel or surface, which thus provide them with improved catalytic performance. In this study, a 3D cobalt-based MOF [Co(H2bpta)]n (Co-MOF), where H4bpta denotes 2,2′,4,4′-biphenyltetracarboxylic acid, has been constructed with the use of a ligand with a high carbon content. On this basis, a 2D magnetic carbon-coated cobalt nanoparticle composite (C@Co) was prepared by using the title MOF. Magnetic C@Co can readily absorb dye from the solution and can thus act as an inexpensive and fast-acting adsorbent. Moreover, we have explored the adsorption isotherms, kinetics and thermodynamics of the anion dyes in detail. The adsorption capacity of the C@Co for investigated methyl orange (MO) and congo red (CR) dyes were 773.48 and 495.66 mg g− 1, respectively. It is noteworthy that MO adsorption is higher in existing materials. Thermodynamic studies suggest that the adsorption processes are spontaneous and exothermic. This study opens a new insight into the synthesis and application of carbon-based materials that enable the selective removal of organic dyes.

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