Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study

2015 ◽  
Vol 17 (35) ◽  
pp. 22736-22748 ◽  
Author(s):  
João R. Robalo ◽  
J. P. Prates Ramalho ◽  
Daniel Huster ◽  
Luís M. S. Loura
Keyword(s):  
Molecular Dynamics ◽  
Membrane Properties ◽  
Side Chain ◽  
Side Chains ◽  
Aliphatic Side Chain ◽  
Acyl Chains ◽  
Hydrophobic Matching ◽  
Phospholipid Acyl Chains

Cholesterol provides best hydrophobic matching, induces maximal membrane ordering, and displays highest preference for saturated phospholipid acyl chains, among a homologous ser ies of sterols with side chains of varying lengths.

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 Cholesterol's Aliphatic Side Chain Structure Modulates Membrane Properties

2016 ◽  
Vol 110 (3) ◽  
pp. 84a
Author(s):  
Daniel Huster ◽  
Thomas Meyer ◽  
Jörg Nikolaus ◽  
Dong Jae Baek ◽  
Ivan Haralampiev ◽  
...  
Keyword(s):  
Chain Structure ◽  
Membrane Properties ◽  
Side Chain ◽  
Aliphatic Side Chain

scholarly journals Membrane properties of cholesterol analogs with an unbranched aliphatic side chain

2014 ◽  
Vol 184 ◽  
pp. 1-6 ◽  
Author(s):  
Thomas Meyer ◽  
Dong Jae Baek ◽  
Robert Bittman ◽  
Ivan Haralampiev ◽  
Peter Müller ◽  
...  
Keyword(s):  
Membrane Properties ◽  
Side Chain ◽  
Aliphatic Side Chain

scholarly journals Cholesterol’s Aliphatic Side Chain Modulates Membrane Properties

2013 ◽  
Vol 52 (49) ◽  
pp. 12848-12851 ◽  
Author(s):  
Holger A. Scheidt ◽  
Thomas Meyer ◽  
Jörg Nikolaus ◽  
Dong Jae Baek ◽  
Ivan Haralampiev ◽  
...  
Keyword(s):  
Membrane Properties ◽  
Side Chain ◽  
Aliphatic Side Chain

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.

Simultaneous enhancement of the molecular planarity and the solubility of non-fullerene acceptors: effect of aliphatic side-chain substitution on the photovoltaic performance

2017 ◽  
Vol 5 (17) ◽  
pp. 7776-7783 ◽  
Author(s):  
Zhe Zhang ◽  
Miao Li ◽  
Yahui Liu ◽  
Jicheng Zhang ◽  
Shiyu Feng ◽  
...  
Keyword(s):  
Photovoltaic Performance ◽  
Side Chain ◽  
Side Chains ◽  
Aliphatic Side Chain

By incorporating aliphatic side chains and adjusting their lengths, non-fullerene acceptors can obtain an improved morphology and photovoltaic performance.

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.

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