scholarly journals Comprehensive Modelling of the Self-Folding Cavitand Dynamics

2020 ◽  
Author(s):  
Ricard López-Coll ◽  
Rubén Álvarez-Yebra ◽  
Ferran Feixas ◽  
Agustí Lledó
Keyword(s):  
Rational Design ◽  
Exchange Process ◽  
Md Simulations ◽  
High Energy ◽  
Design Tool ◽  
Dynamic Features ◽  
High Energy Barrier ◽  
Dynamics Simulations ◽  
Good Agreement

<div>The conformational equilibria and guest exchange process of a resorcin[4]arene derived self‐folding cavitand receptor have been modelled in detail by molecular dynamics simulations (MD). A multi‐timescale strategy for exploring the fluxional behavior of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and c) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by 1H NMR. These results constitute the first comprehensive computational characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host‐guest systems.</div>

scholarly journals Comprehensive Modelling of the Self-Folding Cavitand Dynamics

2020 ◽  
Author(s):  
Ricard López-Coll ◽  
Rubén Álvarez-Yebra ◽  
Ferran Feixas ◽  
Agustí Lledó
Keyword(s):  
Rational Design ◽  
Exchange Process ◽  
Md Simulations ◽  
High Energy ◽  
Design Tool ◽  
Dynamic Features ◽  
High Energy Barrier ◽  
Dynamics Simulations ◽  
Good Agreement

<div>The conformational equilibria and guest exchange process of a resorcin[4]arene derived self‐folding cavitand receptor have been modelled in detail by molecular dynamics simulations (MD). A multi‐timescale strategy for exploring the fluxional behavior of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and c) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by 1H NMR. These results constitute the first comprehensive computational characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host‐guest systems.</div>

scholarly journals Comprehensive Characterization of the Self-Folding Cavitand Dynamics

2021 ◽  
Author(s):  
Ricard López-Coll ◽  
Rubén Álvarez-Yebra ◽  
Ferran Feixas ◽  
Agustí Lledó
Keyword(s):  
Rational Design ◽  
Exchange Process ◽  
Md Simulations ◽  
High Energy ◽  
Design Tool ◽  
Dynamic Features ◽  
H Nmr ◽  
High Energy Barrier ◽  
Dynamics Simulations

The conformational equilibria and guest exchange process of a resorcin[4]arene derived self-folding cavitand receptor have been characterized in detail by molecular dynamics simulations (MD) and <sup>1</sup>H EXSY experiments. A multi-timescale strategy for exploring the fluxional behavior of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high-energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales from ns to s: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and c) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by <sup>1</sup>H NMR. These results constitute the first comprehensive computational characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host-guest systems.<br>

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.

Filler-Elastomer Interactions. Part VI. Characterization of Carbon Blacks by Inverse Gas Chromatography at Finite Concentration

1992 ◽  
Vol 65 (5) ◽  
pp. 890-907 ◽  
Author(s):  
Meng-Jiao Wang ◽  
Siegfried Wolff
Keyword(s):  
Gas Chromatography ◽  
Energy Distribution ◽  
Inverse Gas Chromatography ◽  
General Trend ◽  
High Energy ◽  
Carbon Blacks ◽  
Finite Concentration ◽  
Good Agreement

Abstract Carbon blacks ranging from N110 to N990 were characterized by means of inverse gas chromatography at finite concentration. The isotherms, net heat, and spreading pressures for benzene and cyclohexane adsorption suggest a general trend of increasing surface activity with increases in specific surface area. This is in good agreement with surface-energy measurements reported previously. The energy-distribution function of adsorption shows that while the concentrations of low-energy sites are comparable for most of the carbon blacks, differences exist with regard to high-energy sites. These suggest that small-particle-size blacks possess a greater number of high-energy centers. The graphitization of carbon blacks results in a considerable reduction in their adsorption capacity and narrows the energy distribution of their surfaces. One can therefore conclude that high-energy sites play an important role in the determination of the surface energies and reinforcing ability of carbon blacks.

Molecular dynamics simulations for CL-20/TNT co-crystal based polymer-bonded explosives

2017 ◽  
Vol 16 (08) ◽  
pp. 1750072
Author(s):  
Qiang Cao ◽  
Ji Jun Xiao ◽  
Pei Gao ◽  
Shen Shen Li ◽  
Feng Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pair Correlation ◽  
Md Simulations ◽  
High Energy ◽  
Binding Energies ◽  
Polymer Binders ◽  
Polymer Bonded Explosives ◽  
Dynamics Simulations ◽  
Theoretical Results ◽  
Crystal Compound

Molecular dynamics (MD) simulations were carried out to study the polymer-bonded explosives (PBXs) where the explosive base was the well-known high energy co-crystal compound, 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT), and the polymer binders were fluorine rubber (F[Formula: see text], fluorine resin (F[Formula: see text], polyvinyl acetate (PVAc) and polystyrene (PS), respectively. The binding energies, pair correlation functions (PCFs) and mechanical properties of the PBXs were reported. According to our theoretical results of binding energies, the compatibility of the PBXs is predicted to be in the following order: CL-20/TNT/PVAc[Formula: see text] CL-20/TNT/F[Formula: see text] [Formula: see text] CL-20/TNT/PS [Formula: see text] CL-20/TNT/F[Formula: see text]. The binding energies of the PBXs on three crystalline surfaces, (100), (001), (010), of the CL-20/TNT co-crystal were also compared: CL-20/TNT(100)[Formula: see text]CL-20/TNT(001)[Formula: see text]CL-20/TNT(010) for F[Formula: see text], F[Formula: see text], and PS; CL-20/TNT(001)[Formula: see text]CL-20/TNT(100)[Formula: see text]CL-20/TNT(010) for PVAc. The PCF analysis reveals that there exist H-bonds between H and O, F, and N atoms on all three interfaces and among all H-bonds, N H-bond has the fewest number. For the CL-20/TNT co-crystal, the moduli can be reduced by adding a small amount of the polymer binders but the ductility can be prolonged only by F[Formula: see text] and F[Formula: see text].

scholarly journals Does Antibody Stabilize the Ligand Binding in GP120 of HIV-1 Envelope Protein? Evidence from MD Simulation

Molecules ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 239
Author(s):  
Shalini Yadav ◽  
Vishnudatt Pandey ◽  
Rakesh Kumar Tiwari ◽  
Rajendra Prasad Ojha ◽  
Kshatresh Dutta Dubey
Keyword(s):  
Conformational Dynamics ◽  
Md Simulations ◽  
Conformational Flexibility ◽  
Free Energy Calculations ◽  
Titration Calorimetry ◽  
Entry Inhibitors ◽  
Binding Enthalpy ◽  
Dynamics Simulations ◽  
Hiv 1 ◽  
Good Agreement

CD4-mimetic HIV-1 entry inhibitors are small sized molecules which imitate similar conformational flexibility, in gp120, to the CD4 receptor. However, the mechanism of the conformational flexibility instigated by these small sized inhibitors is little known. Likewise, the effect of the antibody on the function of these inhibitors is also less studied. In this study, we present a thorough inspection of the mechanism of the conformational flexibility induced by a CD4-mimetic inhibitor, NBD-557, using Molecular Dynamics Simulations and free energy calculations. Our result shows the functional importance of Asn425 in substrate induced conformational dynamics in gp120. The MD simulations of Asn425Gly mutant provide a less dynamic gp120 in the presence of NBD-557 without incapacitating the binding enthalpy of NBD-557. The MD simulations of complexes with the antibody clearly show the enhanced affinity of NBD-557 due to the presence of the antibody, which is in good agreement with experimental Isothermal Titration Calorimetry results (Biochemistry2006, 45, 10973–10980).

scholarly journals Highly efficient binary copper−iron catalyst for photoelectrochemical carbon dioxide reduction toward methane

2020 ◽  
Vol 117 (3) ◽  
pp. 1330-1338 ◽  
Author(s):  
Baowen Zhou ◽  
Pengfei Ou ◽  
Nick Pant ◽  
Shaobo Cheng ◽  
Srinivas Vanka ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Density Functional ◽  
Rational Design ◽  
Iron Catalyst ◽  
High Current Density ◽  
Density Functional Theory Calculations ◽  
High Energy ◽  
Faradaic Efficiency ◽  
High Energy Barrier ◽  
Linear Configuration

A rational design of an electrocatalyst presents a promising avenue for solar fuels synthesis from carbon dioxide (CO2) fixation but is extremely challenging. Herein, we use density functional theory calculations to study an inexpensive binary copper−iron catalyst for photoelectrochemical CO2 reduction toward methane. The calculations of reaction energetics suggest that Cu and Fe in the binary system can work in synergy to significantly deform the linear configuration of CO2 and reduce the high energy barrier by stabilizing the reaction intermediates, thus spontaneously favoring CO2 activation and conversion for methane synthesis. Experimentally, the designed CuFe catalyst exhibits a high current density of −38.3 mA⋅cm−2 using industry-ready silicon photoelectrodes with an impressive methane Faradaic efficiency of up to 51%, leading to a distinct turnover frequency of 2,176 h−1 under air mass 1.5 global (AM 1.5G) one-sun illumination.

scholarly journals A detailed picture of a protein–carbohydrate hydrogen-bonding network revealed by NMR and MD simulations

Glycobiology ◽  
2020 ◽  
Author(s):  
Gustav Nestor ◽  
Alessandro Ruda ◽  
Taigh Anderson ◽  
Stefan Oscarson ◽  
Göran Widmalm ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Antiviral Agents ◽  
Md Simulations ◽  
Protein Backbone ◽  
Carbohydrate Ligands ◽  
Hydrogen Bonding Network ◽  
Dynamics Simulations ◽  
Hydroxyl Protons

Abstract Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Manα(1→2)ManαOMe and Manα(1→2) Manα(1→6)ManαOMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Manα(1→2)Manα(1→6)ManαOMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.

Lanthanoids(III) and actinoids(III) in water: Diffusion coefficients and hydration enthalpies from polarizable molecular dynamics simulations

2012 ◽  
Vol 85 (1) ◽  
pp. 237-246 ◽  
Author(s):  
Fausto Martelli ◽  
Sacha Abadie ◽  
Jean-Pierre Simonin ◽  
Rodolphe Vuilleumier ◽  
Riccardo Spezia
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Heavy Ions ◽  
Md Simulations ◽  
Contradictory Result ◽  
Dielectric Friction ◽  
Water Interaction ◽  
Diffusive Regime ◽  
Dynamics Simulations ◽  
Good Agreement

By using polarizable molecular dynamics (MD) simulations of lanthanoid(III) and actinoid(III) ions in water, we obtained ionic diffusion coefficients and hydration enthalpies for both series. These values are in good agreement with experiments. Simulations thus allow us to relate them to microscopic structure. In particular, across the series the diffusion coefficients decrease, reflecting the increase of ion–water interaction. Hydration enthalpies also show that interactions increase from light to heavy ions in agreement with experiment. The apparent contradictory result of the decrease of the diffusion coefficient with decreasing ionic radius is tentatively explained in terms of dielectric friction predominance on Stokes’ diffusive regime.

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