Search results for "molecular model"
showing 10 items of 274 documents
Molecular structures of chlorophyll a aggregates: spectroscopic and molecular modeling study
1993
Molecular structures of chlorophyll a aggregates have been studied. Spectroscopic properties of these aggregates have been studied by absorption and fluorescence spectroscopy in hydrocarbon solution at various temperatures. Observed spectroscopic shifts were interpreted in terms of simple exciton theory. Exciton splittings were estimated from computer optimized models of previously suggested Chl a aggregate structures.
Indole-substituted 2,4-diamino-5,8-dihydropyrido[2,3-d]pyrimidines from one-pot process and evaluation of their ability to bind dopamine receptors
2018
A series of novel 7-indole substituted 2,4-diamino-5,8-dihydropyrido[2,3-d]pyrimidine analogous to the 2,4-diaminopteridine core were synthesized by the three-component one-pot cyclocondensation between 2,4,6-triaminopyrimidine, 3-(2-cyanoacetyl)indole and aromatic aldehydes. The reactions, which exhibited good performance, proceeded in EtOH using indium (III) chloride as catalyst under microwave irradiation, in short reaction times. On the basis of certain structural similarity of these compounds with known ligands of the D2 dopamine receptors (D2DR), the study of these compounds as possible ligands of dopamine D2 and D1 receptors was carried out. Three of them showed moderate affinity to …
Predicting antitrichomonal activity: A computational screening using atom-based bilinear indices and experimental proofs
2006
Existing Trichomonas vaginalis therapies are out of reach for most trichomoniasis people in developing countries and, where available, they are limited by their toxicity (mainly in pregnant women) and their cost. New antitrichomonal agents are needed to combat emerging metronidazole-resistant trichomoniasis and reduce the side effects associated with currently available drugs. Toward this end, atom-based bilinear indices, a new TOMOCOMD-CARDD molecular descriptor, and linear discriminant analysis (LDA) were used to discover novel, potent, and non-toxic lead trichomonacidal chemicals. Two discriminant functions were obtained with the use of non-stochastic and stochastic atom-type bilinear in…
Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects
2015
We have studied the alkaline hydrolysis of p-nitrophenylmethylphosphate (p-NPmP) in aqueous solution by means of polarizable continuum models and by hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods. The theoretical predictions of kinetic isotope effects (KIEs) are in very good agreement with the experimental data, confirming a concerted asynchronous molecular mechanism. In addition, comparison of high level DFT theory with semiempirical AM1/d Hamiltonian has allowed checking the reliability of the later to be used in modeling very large molecular models containing phosphorus atoms.
Statistical characterization of self-assembled charged nanoparticle structures
2013
We propose a novel approach for description of dynamics of nanostructure formation for a system consisting of oppositely charged particles. The combination of numerical solution of analytical Bogolyubov–Born–Green–Kirkwood–Yvon (BBGKY) type equation set with reverse Monte Carlo (RMC) method allows us to overcome difficulties of standard approaches, such as kinetic Monte Carlo or Molecular Dynamics, to describe effects of long-range Coulomb interactions. Moreover, this allows one to study the system dynamics on realistic time and length scales. We applied this method to a simple short-range Lenard–Jones (LJ)-like three- (3D) and two-dimensional (2D) system combining the long-range Coulomb an…
New ligand-based approach for the discovery of antitrypanosomal compounds.
2005
The antitrypanosomal activity of 10 already synthesized compounds was in silico predicted as well as in vitro and in vivo explored against Trypanosoma cruzi. For the computational study, an approach based on non-stochastic linear fingerprints to the identification of potential antichagasic compounds is introduced. Molecular structures of 66 organic compounds, 28 with antitrypanosomal activity and 38 having other clinical uses, were parameterized by means of the TOMOCOMD-CARDD software. A linear classification function was derived allowing the discrimination between active and inactive compounds with a confidence of 95%. As predicted, seven compounds showed antitrypanosomal activity (%AE > 7…
Nautilus pompilius Hemocyanin: 9 Å Cryo-EM Structure and Molecular Model Reveal the Subunit Pathway and the Interfaces between the 70 Functional Units
2007
Hemocyanins are giant extracellular oxygen carriers in the hemolymph of many molluscs. Nautilus pompilius (Cephalopoda) hemocyanin is a cylindrical decamer of a 350 kDa polypeptide subunit that in turn is a "pearl-chain" of seven different functional units (FU-a to FU-g). Each globular FU has a binuclear copper centre that reversibly binds one O(2) molecule, and the 70-FU decamer is a highly allosteric protein. Its primary structure and an 11 A cryo-electron microscopy (cryo-EM) structure have recently been determined, and the crystal structures of two related FU types are available in the databanks. However, in molluscan hemocyanin, the precise subunit pathway within the decamer, the inter…
Structural Characterization of Glycoconjugate Polystyrene in Aqueous Solution
1999
Maltopentaose-carrying polystyrene was synthesized by the homopolymerization of vinylbenzyl maltopentaose amide. Resulted amphiphilc polymacromonomer was dissolved in 0.1 M urea aqueous solution, and its structure was characterized by small-angle X-ray scattering and molecular modeling. Maltopentaose-carrying polystyrene polymacromonomer was found to be represented by a molecular bottlebrush, composed of a large helix of polystyrene backbone and maltopentaose brushes. The molecular bottlebrush seems to be distributed randomly or many even be broken once or twice in segments with no apparent intersegmental spatial correlation. A large helix of polystyrene backbone is formed by a random seque…
Theoretical Foundations of the Monte Carlo Method and Its Applications in Statistical Physics
2002
In this chapter we first introduce the basic concepts of Monte Carlo sampling, give some details on how Monte Carlo programs need to be organized, and then proceed to the interpretation and analysis of Monte Carlo results.
Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
2019
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics‐generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…