Adsorption Conformation of Comb-Shaped Polycarboxylate Ethers on Ettringite (100) Surface: An Atomic Scales Simulation

2020 ◽  
pp. 2150007
Author(s):  
Hongxia Zhao ◽  
Yong Yang ◽  
Shenyou Song ◽  
Xin Shu ◽  
Weile Chen ◽  
...  
Keyword(s):  
Dynamic Equilibrium ◽  
Ion Pairs ◽  
Md Simulations ◽  
Distribution Functions ◽  
Side Chain ◽  
Side Chains ◽  
Distribution Profile ◽  
Coverage Area ◽  
Carboxylate Groups ◽  
Adsorption Energies

The adsorption of five polycarboxylate ethers (PCEs) oligomers with different side-chain number and side-chain length on the ettringite (100) surface in explicit solution is studied by all-atom molecular dynamics (MD) simulations. The adsorption conformations, adsorption energies, the radial distribution functions (RDF) between PCEs and ettringite surface and density distribution profile of water perpendicular to the substrate are analyzed. After dynamic equilibrium, negatively charged carboxylate groups are absorbed on the surface of the disordered ettringite crystal and the side-chains are extended to solution. The influence of the number of side-chain on the adsorption strength of PCEs on the ettringite (100) surface is more significant than that of the length of side-chain. The less number of grafted side-chains, the weaker electrostatic shielding, the electrostatic interaction between PCEs and ettringite (100) surface is stronger, which is favorable for the adsorption. The conformation of adsorbed PCEs is closely related to the length of side chain. The greater the length of side-chains is, the larger will be the coverage area of PCE on surface and the degree of water reduction. The mechanism of adsorption of PCEs on ettringite surface is concluded and the major contribution to the adsorption includes ion pairs, hydrogen bonds and an entropic compensation.

scholarly journals The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: molecular dynamics simulations.

2000 ◽  
Vol 47 (1) ◽  
pp. 47-57 ◽  
Author(s):  
J Mazerski ◽  
I Antonini ◽  
S Martelli
Keyword(s):  
Molecular Dynamics ◽  
Rational Design ◽  
Md Simulations ◽  
Ring System ◽  
Side Chain ◽  
Side Chains ◽  
Intercalation Complex ◽  
Highly Active ◽  
Simulation Techniques ◽  
Dynamics Simulations

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.

scholarly journals Effect of perfluorosulfonic acid side chains on oxygen permeation in hydrated ionomers of PEMFCs: Molecular dynamics simulation approach

2020 ◽  
Author(s):  
Sung Hyun Kwon ◽  
Haisu Kang ◽  
Young-Jun Sohn ◽  
Jinhee Lee ◽  
Sunbo Shim ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water Content ◽  
Polymer Electrolyte Membrane ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Side Chain ◽  
Side Chains ◽  
Perfluorosulfonic Acid ◽  
Short Side ◽  
Water Contents

Abstract We prepared two types of perfluorosulfonic acid (PFSA) ionomers with Aquivion (short side chain) and Nafion (long side chain) on a Pt surface and varied their water contents (2.92 ≤ λ ≤ 13.83) to calculate the solubility and permeability of O2 in hydrated PFSA ionomers on a Pt surface using full atomistic molecular dynamics (MD) simulations. The solubility and permeability of O2 molecules in hydrated Nafion ionomers were greater than those of O2 molecules in hydrated Aquivion ionomers at the same water content, indicating that the permeation of O2 molecules in the ionomers is affected not only by the diffusion coefficient of O2 but also by the solubility of O2. Notably, O2 molecules are more densely distributed in regions where water and hydronium ions have a lower density in hydrated Pt/PFSA ionomers. Radial distribution function (RDF) analysis was performed to investigate where O2 molecules preferentially dissolve in PFSA ionomers on a Pt surface. The results showed that O2 molecules preferentially dissolved between hydrophilic and hydrophobic regions in a hydrated ionomer. The RDF analysis was performed to provide details of the O2 location in hydrated PFSA ionomers on a Pt surface to evaluate the influence of O2 solubility in ionomers with side chains of different lengths. The coordination number of C(center)–O(O2) and O(side chain)–O(O2) pairs in hydrated Nafion ionomers was higher than that of the same pairs in hydrated Aquivion ionomers with the same water content. Our investigation provides detailed information about the properties of O2 molecules in different PFSA ionomers on a Pt surface and with various water contents, potentially enabling the design of better-performing PFSA ionomers for use in polymer electrolyte membrane fuel cells.

Molecular structure, reorientational dynamics, and intermolecular interactions in the neat ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

2004 ◽  
Vol 76 (1) ◽  
pp. 255-261 ◽  
Author(s):  
J. H. Antony ◽  
D. Mertens ◽  
Tobias Breitenstein ◽  
Andreas Dölle ◽  
P. Wasserscheid ◽  
...  
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Ion Pairs ◽  
Md Simulations ◽  
Liquid Structure ◽  
Distribution Functions ◽  
Reorientational Dynamics ◽  
Pair Distribution Functions

Results on the molecular and liquid structure and the reorientational dynamics are reported for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]). In quantum-chemical calculations for [BMIM][PF6] in the gas phase, hydrogen bonding between the proton at carbon 2 in the aromatic ring and the fluorine atoms of the hexafluorophosphate anion was found. From the analysis of 13C relaxation data, the reorientational motions were evaluated, and the Vogel-Fulcher-Tammann and Arrhenius activation energies for the overall and internal reorientational motions, respectively, of the different 13C-1H vectors are given as well as correlation times at 300 K. By performing molecular dynamics (MD) simulations, pair distribution functions between moieties in the cation and the phosphorous atom in the anion were determined. The pair distribution function for the proton at carbon 2 exhibits a particular sharp and strong maximum indicating a strong interaction with the anion. The quantum-chemical calculations, the motional parameters, and the results from the MD simulations support the existence of hydrogen bonding and the formation of ion pairs in the ionic liquid.

scholarly journals Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems

2020 ◽  
Author(s):  
Soumendranath Bhakat ◽  
Pär Söderhjelm
Keyword(s):  
Dynamic Equilibrium ◽  
Sequence Similarity ◽  
Experimental Studies ◽  
Md Simulations ◽  
Model Systems ◽  
Side Chain ◽  
Aspartic Proteases ◽  
Plasmepsin Ii ◽  
Normal States ◽  
Bace 1

AbstractFlexibility of β hairpin structure known as flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequence similarity. Tyrosine is a conserved residue present in the flap region of pepsin-like aspartic proteases. In apo protease, tyrosine remains in a dynamic equilibrium between normal and flipped states due to rotation of χ1 angle (distributions of the χ1 angle centred around radian or radian are denoted as normal, whereas distribution centred around ±π radian is denoted as flipped). In this study, we have used apo Plm-II and BACE-1 as model systems. Independent MD simulations starting with Plm-II and BACE-1 remained stuck either in normal or flipped state. Metadynamics simulations using torsion angles (χ1 and χ2 of Tyr) as CVs sampled transition between normal and flipped states. Qualitatively, flipped and normal states predicted to be equally populated. These states were stabilised by H-bond interactions to tryptophan (normal) and catalytic aspartate (flipped) respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine; reduced flap flexibility and resulted in a flap collapse. This is in accordance with previous experimental studies which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Using apo plasmepsin-II and BACE-1 as model systems, we have hypothesised that the rotation of tyrosine side-chain is the key movement which governs the flap dynamics in all pepsin-like aspartic proteases.

scholarly journals Molecular dynamics simulation study on the effect of perfluorosulfonic acid side chains on oxygen permeation in hydrated ionomers of PEMFCs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sung Hyun Kwon ◽  
Haisu Kang ◽  
Young-Jun Sohn ◽  
Jinhee Lee ◽  
Sunbo Shim ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water Content ◽  
Polymer Electrolyte Membrane ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Side Chain ◽  
Side Chains ◽  
Perfluorosulfonic Acid ◽  
Short Side ◽  
Water Contents

AbstractWe prepared two types of perfluorosulfonic acid (PFSA) ionomers with Aquivion (short side chain) and Nafion (long side chain) on a Pt surface and varied their water contents (2.92 ≤ λ ≤ 13.83) to calculate the solubility and permeability of O2 in hydrated PFSA ionomers on a Pt surface using full atomistic molecular dynamics (MD) simulations. The solubility and permeability of O2 molecules in hydrated Nafion ionomers were greater than those of O2 molecules in hydrated Aquivion ionomers at the same water content, indicating that the permeation of O2 molecules in the ionomers is affected not only by the diffusion coefficient of O2 but also by the solubility of O2. Notably, O2 molecules are more densely distributed in regions where water and hydronium ions have a lower density in hydrated Pt/PFSA ionomers. Radial distribution function (RDF) analysis was performed to investigate where O2 molecules preferentially dissolve in PFSA ionomers on a Pt surface. The results showed that O2 molecules preferentially dissolved between hydrophilic and hydrophobic regions in a hydrated ionomer. The RDF analysis was performed to provide details of the O2 location in hydrated PFSA ionomers on a Pt surface to evaluate the influence of O2 solubility in ionomers with side chains of different lengths. The coordination number of C(center)–O(O2) and O(side chain)–O(O2) pairs in hydrated Nafion ionomers was higher than that of the same pairs in hydrated Aquivion ionomers with the same water content. Our investigation provides detailed information about the properties of O2 molecules in different PFSA ionomers on a Pt surface and with various water contents, potentially enabling the design of better-performing PFSA ionomers for use in polymer electrolyte membrane fuel cells.

Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

2020 ◽  
Author(s):  
Julian Keupp ◽  
Johannes P. Dürholt ◽  
Rochus Schmid
Keyword(s):  
First Principles ◽  
Good Accuracy ◽  
Field Investigation ◽  
Square Lattice ◽  
Side Chain ◽  
Second Step ◽  
Side Chains ◽  
Dynamics Simulations ◽  
Complex Phenomena ◽  
Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br>wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br>transition by a “wine-rack” type motion of the square lattice. We studied this not<br>yet fully understood behavior using an accurate first principles parameterized force<br>field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br>benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br>cations for an interface between a closed and an open pore phase traveling through<br>the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br>conventional simulations in small supercells this mechanism is prevented by periodic<br>boundary conditions (PBC), enforcing a synchronous transformation of the entire<br>crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br>side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br>tally known to have different properties with the side-chains acting as fixed guest<br>molecules. First, in order to extend the parameterization for such flexible groups,<br>1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br>structure force based fit method. The resulting parametrization for a library of<br>fu-MOFs is then validated with respect to a set of reference systems and shows very<br>good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br>length is studied with respect to the influence of the side-chains on the breathing<br>behavior. For small supercells in PBC a systematic trend of the closed pore volume<br>with the chain length is observed. However, for a nanocrystallite model a distinct<br>interface between a closed and an open pore phase is visible only for the short chain<br>length, whereas for longer chains the interface broadens and a nearly concerted trans-<br>formation is observed. Only by molecular dynamics simulations using accurate force<br>fields such complex phenomena can be studied on a molecular level.

Polysaccharide Structures in the Outer Mucilage of Arabidopsis Seeds Visualized by AFM

2020 ◽  
Author(s):  
MAK Williams ◽  
V Cornuault ◽  
AH Irani ◽  
VV Symonds ◽  
J Malmström ◽  
...  
Keyword(s):  
Average Length ◽  
American Chemical Society ◽  
Md Simulations ◽  
Chemical Society ◽  
Side Chains ◽  
Rhamnogalacturonan I ◽  
Afm Imaging ◽  
Minor Population ◽  
The Stability ◽  
A Minor

© 2020 American Chemical Society. Evidence is presented that the polysaccharide rhamnogalacturonan I (RGI) can be biosynthesized in remarkably organized branched configurations and surprisingly long versions and can self-assemble into a plethora of structures. AFM imaging has been applied to study the outer mucilage obtained from wild-type (WT) and mutant (bxl1-3 and cesa5-1) Arabidopsis thaliana seeds. For WT mucilage, ordered, multichain structures of the polysaccharide RGI were observed, with a helical twist visible in favorable circumstances. Molecular dynamics (MD) simulations demonstrated the stability of several possible multichain complexes and the possibility of twisted fibril formation. For bxl1-3 seeds, the imaged polymers clearly showed the presence of side chains. These were surprisingly regular and well organized with an average length of ∼100 nm and a spacing of ∼50 nm. The heights of the side chains imaged were suggestive of single polysaccharide chains, while the backbone was on average 4 times this height and showed regular height variations along its length consistent with models of multichain fibrils examined in MD. Finally, in mucilage extracts from cesa5-1 seeds, a minor population of chains in excess of 30 μm long was observed.

scholarly journals Effects of Amino Acid Side-Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1789
Author(s):  
Dmitry Tolmachev ◽  
George Mamistvalov ◽  
Natalia Lukasheva ◽  
Sergey Larin ◽  
Mikko Karttunen
Keyword(s):  
Glutamic Acid ◽  
Chain Length ◽  
Chemical Structure ◽  
Side Chain ◽  
Side Chains ◽  
Side Chain Length ◽  
Polyelectrolyte Brushes ◽  
Grafting Density ◽  
The Difference ◽  
Cellulose Surface

We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side-chain length, the chemical structure and their interplay are required. It was found that in the case of glutamic acid oligomers, the longer side chains facilitate attractive interactions with the cellulose surface, which forces the grafted chains to lie down on the surface. The additional methylene group in the side chain enables side-chain rotation, enhancing this effect. On the other hand, the shorter and more restricted side chains of aspartic acid oligomers prevent attractive interactions to a large degree and push the grafted chains away from the surface. The difference in side-chain length also leads to differences in other properties of the brush in divalent salt solutions. At a low grafting density, the longer side chains of glutamic acid allow the adsorbed cations to be spatially distributed inside the brush resulting in a charge inversion. With an increase in grafting density, the difference in the total charge of the aspartic and glutamine brushes disappears, but new structural features appear. The longer sides allow for ion bridging between the grafted chains and the cellulose surface without a significant change in main-chain conformation. This leads to the brush structure being less sensitive to changes in salt concentration.

scholarly journals Unusual Structural Features in the Adduct of Dirhodium Tetraacetate with Lysozyme

2021 ◽  
Vol 22 (3) ◽  
pp. 1496
Author(s):  
Domenico Loreto ◽  
Giarita Ferraro ◽  
Antonello Merlino
Keyword(s):  
Anticancer Agents ◽  
Structural Features ◽  
Side Chain ◽  
Side Chains ◽  
Valuable Insight ◽  
Experimental Conditions ◽  
Egg White Lysozyme ◽  
Potential Applications ◽  
Model Protein ◽  
Hen Egg White

The structures of the adducts formed upon reaction of the cytotoxic paddlewheel dirhodium complex [Rh2(μ-O2CCH3)4] with the model protein hen egg white lysozyme (HEWL) under different experimental conditions are reported. Results indicate that [Rh2(μ-O2CCH3)4] extensively reacts with HEWL:it in part breaks down, at variance with what happens in reactions with other proteins. A Rh center coordinates the side chains of Arg14 and His15. Dimeric Rh–Rh units with Rh–Rh distances between 2.3 and 2.5 Å are bound to the side chains of Asp18, Asp101, Asn93, and Lys96, while a dirhodium unit with a Rh–Rh distance of 3.2–3.4 Å binds the C-terminal carboxylate and the side chain of Lys13 at the interface between two symmetry-related molecules. An additional monometallic fragment binds the side chain of Lys33. These data, which are supported by replicated structural determinations, shed light on the reactivity of dirhodium tetracarboxylates with proteins, providing useful information for the design of new Rh-containing biomaterials with an array of potential applications in the field of catalysis or of medicinal chemistry and valuable insight into the mechanism of action of these potential anticancer agents.

scholarly journals Synthesis of New Derivatives of BEDT-TTF: Installation of Alkyl, Ethynyl, and Metal-Binding Side Chains and Formation of Tris(BEDT-TTF) Systems

2021 ◽  
Vol 7 (8) ◽  
pp. 110
Author(s):  
Songjie Yang ◽  
Matteo Zecchini ◽  
Andrew Brooks ◽  
Sara Krivickas ◽  
Desiree Dalligos ◽  
...  
Keyword(s):  
Metal Binding ◽  
Tricarboxylic Acid ◽  
Metal Salts ◽  
Side Chain ◽  
Side Chains ◽  
Ethynyl Group ◽  
X Ray ◽  
Transition Metal Salts ◽  
Alkyl Side Chains ◽  
Derivatives Of

The syntheses of new BEDT-TTF derivatives are described. These comprise BEDT-TTF with one ethynyl group (HC≡C-), with two (n-heptyl) or four (n-butyl) alkyl side chains, with two trans acetal (-CH(OMe)2) groups, with two trans aminomethyl (-CH2NH2) groups, and with an iminodiacetate (-CH2N(CH2CO2−)2 side chain. Three transition metal salts have been prepared from the latter donor, and their magnetic properties are reported. Three tris-donor systems are reported bearing three BEDT-TTF derivatives with ester links to a core derived from benzene-1,3,5-tricarboxylic acid. The stereochemistry and molecular structure of the donors are discussed. X-ray crystal structures of two BEDT-TTF donors are reported: one with two CH(OMe)2 groups and with one a -CH2N(CH2CO2Me)2 side chain.

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