scholarly journals Electrostatically assisted macroion association

2021 ◽  
Vol 24 (3) ◽  
pp. 33502
Author(s):  
J. Reščiš
Keyword(s):  
Monte Carlo ◽  
Molecular Docking ◽  
Binding Energy ◽  
Short Range ◽  
Dynamic Equilibrium ◽  
Model System ◽  
Binding Energies ◽  
Effective Attraction ◽  
Theoretical Results ◽  
Good Agreement

A model system of highly asymmetric polyelectrolyte with directional short-range attractive interactions was studied by canonical Monte Carlo computer simulations. Comparison of MC data with previously published theoretical results shows good agreement. For moderate values of binding energies, which matches those of molecular docking, a dynamic equilibrium between free and dimerized macroions is observed. Fraction of dimerized macroions depends on macroion concentration, binding energy magnitude, and on the valency of small counterions. Divalent counterions induce an effective attraction between macroions and enhance dimerization. This effect is most notable at low to moderate macroion concentrations.

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

scholarly journals Combinatorial Library Designing and Virtual Screening of Cryptolepine Derivatives against Topoisomerase II by Molecular Docking

2020 ◽  
Author(s):  
Maria ◽  
Zahid Khan
Keyword(s):  
Molecular Docking ◽  
Cell Division ◽  
Binding Energy ◽  
Cancer Cells ◽  
Anticancer Agents ◽  
Combinatorial Library ◽  
Topoisomerase Ii ◽  
Computational Study ◽  
Binding Energies ◽  
Potential Inhibitors

AbstractComputational approaches have emerging role for designing potential inhibitors against topoisomerase 2 for treatment of cancer. TOP2A plays a key role in DNA replication before cell division and thus facilitates the growth of cells. This function of TOP2A can be suppressed by targeting with potential inhibitors in cancer cells to stop the uncontrolled cell division. Among potential inhibitors cryptolepine is more selective and has the ability to intercalate into DNA, effectively block TOP2A and cease cell division in cancer cells. However, cryptolepine is non-specific and have low affinity, therefore, a combinatorial library was designed and virtually screened for identification of its derivatives with greater TOP2A binding affinities.A combinatorial library of 31114 derivatives of cryptolepine was formed and the library was virtually screened by molecular docking to predict the molecular interactions between cryptolepine derivatives and TOP2A taking cryptolepine as standard. The overall screening and docking approach explored all the binding poses of cryptolepine for TOP2A to calculate binding energy. The compounds are given database number 8618, 907, 147, 16755, and 8186 scored lowest binding energies of −9.88kcal/mol, −9.76kcal/mol, −9.75kcal/mol, −9.73kcal/mol, and −9.72kcal/mol respectively and highest binding affinity while cryptolepine binding energy is −6.09kcal/mol. The good binding interactions of the derivatives showed that they can be used as potent TOP2A inhibitors and act as more effective anticancer agents than cryptolepine itself. The interactions of derivatives with different amino acid residues were also observed. A comprehensive understanding of the interactions of proposed derivatives with TOP2A helped for searching more novel and potent drug-like molecules for anticancer therapy. This Computational study suggests useful references to understand inhibition mechanisms that will help in the modification of TOP2A inhibitors.

scholarly journals RADII AND BINDING ENERGIES OF NUCLEI IN THE ALPHA-CLUSTER MODEL

2007 ◽  
Vol 22 (03) ◽  
pp. 227-242 ◽  
Author(s):  
G. K. NIE
Keyword(s):  
Experimental Data ◽  
Cluster Model ◽  
Short Range ◽  
Binding Energies ◽  
Coulomb Energy ◽  
Number Of Clusters ◽  
Charge Radii ◽  
Neutron Pair ◽  
Alpha Cluster ◽  
Good Agreement

The α-cluster model is based on two assumptions that the proton–neutron pair interactions are responsible for adherence between α-clusters and that the NN-interaction in the α-clusters is isospin independent. It allows one to estimate the Coulomb energy and the short range inter-cluster bond energy in dependence on the number of clusters. The charge radii are calculated from the number of α-clusters too. Unlike the Weizsäcker formula in this model the binding energies of alpha-clusters and excess neutrons are estimated separately. The calculated values are in a good agreement with the experimental data.

KINETIC ROUGHENING AND INTERACTING REACTING SPECIES: NONLINEAR ASPECTS

Fractals ◽  
1993 ◽  
Vol 01 (03) ◽  
pp. 470-474 ◽  
Author(s):  
I.M. SOKOLOV ◽  
P. ARGYRAKIS ◽  
A. BLUMEN
Keyword(s):  
Monte Carlo ◽  
Theoretical Analysis ◽  
Diffusion Process ◽  
Monte Carlo Simulations ◽  
Short Range ◽  
Reaction Diffusion ◽  
Kinetic Roughening ◽  
Constant Rate ◽  
Good Agreement

We consider the A+B→0 reaction, in which particles interact through short-range forces. The analysis leads to expressions akin in form to those which describe kinetic roughening. In a situation in which particles are generated with a constant rate j0, their concentration n(t) grows as [Formula: see text] in d=1. Here the theoretical analysis predicts γ=1/5 and β=2/5, in very good agreement with direct Monte-Carlo simulations of the reaction-diffusion process.

In silico investigation of Alliin as potential activator for AMPA receptor

2021 ◽  
Author(s):  
Hilal Ozturk ◽  
N. Yorulmaz ◽  
Mustafa Durgun ◽  
Harun Basoglu
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Ampa Receptor ◽  
Docking Study ◽  
Binding Energies ◽  
Molecular Docking Study ◽  
Gaba A ◽  
Docking Method ◽  
Ampa And Nmda Receptors ◽  
The Central Nervous System

Abstract Natural products from plants, such as flavonoids, arouse immense interest in medicine because of the therapeutic and many other bioactive properties. The molecular docking is a very useful method to screen the molecules based on their free binding energies and give important structural suggestions about how molecules might activate or inhibit the target receptor by comparing reference molecules. Alliin and Allicin differ from many other flavonoids because of containing no benzene rings and having nitrogen and sulfur atoms in their structure. In this study Alliin and Allicin affinity on AMPA, NMDA and GABA-A receptors were evaluated in the central nervous system by using the molecular docking method. Both Alliin and Allicin indicated no inhibitory effects. However Alliin showed significant selectivity to human AMPA receptor (3RN8) as an excitatory. The binding energy of glutamate to 3RN8 was -6.61 kcal/mol, while the binding energy of Allin was -8.08 kcal/mol. Furthermore Alliin’s affinity to the other AMPA and NMDA receptors is quite satisfactory compared to the reference molecule glutamate. In conclusion based on the molecular docking study, Alliin can be useful for synaptic plasticity studies whereas might be enhance seizure activity because of the increased permeability to cations. It also can be beneficial to improve learning and memory and can be used as a supportive product to the hypofunction of NMDA associated problems.

The electrostatic calculation of molecurlar energies - III. The binding energies of saturated molecules

1954 ◽  
Vol 226 (1165) ◽  
pp. 193-205 ◽  
Keyword(s):  
Binding Energy ◽  
Valence Bond ◽  
Binding Energies ◽  
Wave Functions ◽  
Complex Molecules ◽  
Electron Orbital ◽  
Hydride Molecule ◽  
Paired Electron ◽  
Bond Functions ◽  
Good Agreement

A technique for calculating the binding energy of any saturated molecule is developed.The method is based on an application of the electrostatic theorem, discussed in earlier parts, to paired-electron orbital wave functions.These wave functions include both molecular-orbital and valence-bond functions as special cases.The resulting numerical computations are sufficiently simple to be carried through without approximation even for complex molecules. The method is applied to the lithium molecule and the lithium hydride molecule, and yields results in good agreement with experiment. The choice of wave functions for calculations on other molecules is discussed.

J/ψ PRODUCTION IN A GLAUBER MONTE CARLO FRAMEWORK

2010 ◽  
Vol 25 (05) ◽  
pp. 1009-1018 ◽  
Author(s):  
HONG-MIN WANG ◽  
ZHAO-YU HOU ◽  
BEN-AI ZHANG ◽  
XIAN-JING SUN
Keyword(s):  
Experimental Data ◽  
Monte Carlo ◽  
Center Of Mass ◽  
Nuclear Modification Factor ◽  
Center Of Mass Energy ◽  
Modification Factor ◽  
Energy Formula ◽  
Theoretical Results ◽  
Monte Carlo Framework ◽  
Good Agreement

By means of a Glauber Monte Carlo framework, the J/ψ production at RHIC energies is studied with the EKS98, EPS09 and HKN07 shadowing parameters. With a χ2 analysis of the experimental data given by PHENIX, a significant dependence of the absorption cross-section, σ abs , on the J/ψ-nucleon center-of-mass energy, [Formula: see text], is revealed with the HKN07 shadowing, but an unconspicuous dependence is shown with the EKS98 and EPS09 shadowing. In this paper, the nuclear modification factor Rd Au vs y, pT and N coll are also calculated and the theoretical results are in good agreement with the experimental data.

Lattice Dynamical Properties of Potassium

1981 ◽  
Vol 36 (11) ◽  
pp. 1242-1245
Author(s):  
O. P. Gupta
Keyword(s):  
Equilibrium Condition ◽  
Short Range ◽  
Phonon Dispersion ◽  
Waller Factor ◽  
Crystal Stability ◽  
Debye Waller Factor ◽  
Dynamical Properties ◽  
Experimental Values ◽  
Theoretical Results ◽  
Good Agreement

The phonon dispersion, temperature dependence of the Debye temperature, Debye-Waller factor, and Grüneisen parameter of potassium are calculated using a realistic lattice dynamical model. The model considers short range pairwise forces effective upto second neighbors and an improved electron ion interaction on the lines of Bhatia. An equilibrium condition, which preserves the crystal stability, is obtained. The theoretical results are found to be in good agreement with the experimental values.

BINDING ENERGIES OF HYPERNUCLEI FROM 2.3 BeV/c K− INTERACTIONS

1967 ◽  
Vol 45 (9) ◽  
pp. 2939-2942
Author(s):  
R. Huang ◽  
J. P. Roalsvig ◽  
R. J. Sahni ◽  
P. H. Steinberg
Keyword(s):  
Short Range ◽  
Binding Energies ◽  
Good Agreement

Hypernuclear binding energies obtained from 43 uniquely identified mesic decays are reported here. The values are in good agreement with the previous data. Reported also are binding energies of two short-range mesic spallation hyperfragments.

scholarly journals Binding Energy of Exciton in Quantum Dots with the Central-cell Correction Depending on the Dot Sizes

2007 ◽  
Vol 14 (2) ◽  
pp. 95-99 ◽  
Author(s):  
To Thi Thao ◽  
Nguyen Ai Viet
Keyword(s):  
Quantum Dots ◽  
Binding Energy ◽  
Variational Methods ◽  
Effective Mass ◽  
Short Range ◽  
Central Cell ◽  
Short Range Potential ◽  
Two Parameters ◽  
Center Cell ◽  
Good Agreement

The binding energy of exciton in quantum dots with a parabolic confinement potential was calculated by variational methods beyond the Kohn-Luttinger effective mass theory, when the central-cell correction was taken into account.We have assumed that a short range potential with two parameters for strength and range for exciton, representing the center-cell effect also depends on dot size. Our result is in good agreement with experiment.

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