Conformational space analysis of neutral and deprotonated forms of benzoic acid, salicylic acid and phthalic acid using a genetic algorithm

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Genetic Algorithm ◽  
Salicylic Acid ◽  
Benzoic Acid ◽  
Phthalic Acid ◽  
Conformational Space ◽  
Am1 Method ◽  
The Stability ◽  
Intramolecular Hydrogen ◽  
Semi Empirical ◽  
Global And Local

In this paper we present a detailed conformational study of three aromatic systems constituting the basic units of humic acids namely benzoic acid, salicylic acid and phthalic acid. The genetic algorithm, based on the multi-niche crowding (MNC) method, coupled with the semi-empirical AM1 method is used to analyze the potential energy surface (PES) of these systems. This algorithm, implemented in the MOPAC program and piloted by scripts, provides better detection of global and local minima in a reasonable time. The results obtained are comparable with those of previous studies. Three factors can be cited to justify the stability of conformations i.e. effects of conjugation, steric interactions and intramolecular hydrogen bonds.

Polyalanine gas phase acidities determination and conformational space analysis by genetic algorithm assessment

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Genetic Algorithm ◽  
Gas Phase ◽  
Energy Surface ◽  
Conformational Space ◽  
Am1 Method ◽  
The One ◽  
Semi Empirical ◽  
Global And Local ◽  
Formation Energies ◽  
Good Agreement

The genetic algorithm, based on the Multi-Niche Crowding (MNC) method, coupled with the semi-empirical AM1 method is used to analyze the potential energy surface of some polypeptides containing cysteine. Calculating the formation energies of these systems in both neutral and deprotonated states, we deducted their enthalpy of deprotonation (ΔHacid) and we identified the types of rearrangement of these systems when isolated. Deprotonation occurs at the level of the alone acid site characterizing these peptides namely the thiol. The values obtained for the deprotonation enthalpies of polypeptides AlaCysNH2, Ala2CysNH2, Ala3CysNH2, Ala4CysNH2, CysAlaNH2 and CysAla2NH2 are in the order of 331.3 kcal/mol, 322.9 kcal/mol, 313.8 kcal/mol, 312.9 kcal/mol, 325.1 kcal/mol and 317.3 kcal/mol, respectively. The location of global and local minima of these polypeptides shows that they are rearranged in two forms of secondary structures namely helical and globular forms. The obtained results are in good agreement with the experimental ones, on the one hand, and with those from other methods in the theoretical calculation, on the other hand. Therefore, the N-cysteine is more acidic than their homologous C-Cysteine and for this series of plolyalanines, the acidity in the gas phase increased with the peptide chain length.

scholarly journals Theoretical study of the potential energy surface of N-formyl-L-cysteine-amide by using a genetic algorithm multi niche crowding

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Genetic Algorithm ◽  
Energy Surface ◽  
Energy Analysis ◽  
Theoretical Study ◽  
Molecular Structures ◽  
Conformational Space ◽  
Side Chain ◽  
Am1 Method ◽  
The Subject ◽  
Semi Empirical

The generation of molecular structures constituting the conformational space of trans-N-For-L-Cys-NH2 was accomplished using the genetic algorithm MNC coupled to the semi-empirical AM1 method, AM1/GA-MNC. The structural and energy analysis of the obtained conformational space E=E(,ψ) locates 7 regions or minima ɣL, ɣD, L, D, L, ɛD and ɛL. The combination of these folds to structuring modes adopted by the side chain CH2-SH has allowed us to identify 27 stable geometric structures. The regions corresponding to helical folds αD and αL are not favorable for the system that is the subject of current study.

scholarly journals Theoretical study of the potential energy surface of N-formyl-L-cysteine-amide by using a genetic algorithm multi niche crowding

2019 ◽  
Author(s):  
Chem Int ◽  
Malika Bourjila
Keyword(s):  
Genetic Algorithm ◽  
Energy Surface ◽  
Energy Analysis ◽  
Theoretical Study ◽  
Molecular Structures ◽  
Conformational Space ◽  
Side Chain ◽  
Am1 Method ◽  
The Subject ◽  
Semi Empirical

The generation of molecular structures constituting the conformational space of trans-N-For-L-Cys-NH2 was accomplished using the genetic algorithm MNC coupled to the semi-empirical AM1 method, AM1/GA-MNC. The structural and energy analysis of the obtained conformational space E=E(,ψ) locates 7 regions or minima ɣL, ɣD, L, D, L, ɛD and ɛL. The combination of these folds to structuring modes adopted by the side chain CH2-SH has allowed us to identify 27 stable geometric structures. The regions corresponding to helical folds αD and αL are not favorable for the system that is the subject of current study.

Theoretical investigation of Ramachandran plot of N-formyl-L-alanine-amide

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Genetic Algorithm ◽  
Theoretical Investigation ◽  
Energy Analysis ◽  
Empirical Method ◽  
Conformational Space ◽  
Ramachandran Plot ◽  
Global Minima ◽  
Reasonable Time ◽  
Semi Empirical

The full conformational space of N-formyl-L-alanine-amide was explored by the semi-empirical method AM1 coupled to the Multi Niche Crowding (MNC) genetic algorithm implemented in a package of programs developed in our laboratory. The structural and energy analysis of the resulting conformational space E(,ψ) exhibits 5 regions or minima ɣL, ɣD, ɛL, D and αD. The technique provides better detection of local and global minima within a reasonable time.

Conformational space analysis of neutral and protonated glycine using a genetic algorithm for multi-modal search

2014 ◽  
Vol 13 (08) ◽  
pp. 1450067 ◽  
Author(s):  
B. El Merbouh ◽  
M. Bourjila ◽  
R. Tijar ◽  
R. Drissi El Bouzaidi ◽  
A. El Gridani ◽  
...  
Keyword(s):  
Genetic Algorithm ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Protonated Form ◽  
Conformational Space ◽  
Empirical Methods ◽  
Space Analysis ◽  
Semi Empirical

The genetic algorithm based on the Multi-Niche Crowding (MNC) method is used with the semi-empirical methods AM1 and PM3 in order to scan the potential energy surface (PES) of neutral and protonated glycine. The algorithm is implemented as a package of programs interfaced with MOPAC and piloted by scripts. Both methods AM1 and PM3 located six minima on the PES of neutral glycine and seven on the protonated glycine one, of which three are those of the N -protonated form and four of the O -protonated one.

scholarly journals Adsorption Equilibrium and Kinetic Studies of Effect of ortho-Substitution to Benzoic Acid in Aqueous Phase Using Granular Activated Carbon

2019 ◽  
Vol 31 (8) ◽  
pp. 1667-1674
Author(s):  
Roy George
Keyword(s):  
Salicylic Acid ◽  
Activated Carbon ◽  
Benzoic Acid ◽  
Aqueous Phase ◽  
Phthalic Acid ◽  
Adsorption Equilibrium ◽  
Granular Activated Carbon ◽  
Kinetic Studies ◽  
Equilibrium And Kinetics ◽  
Adsorption Equilibrium And Kinetics

Adsorption equilibrium and kinetics studies of effect of ortho-substituted benzoic acid in aqueous phase using granular activated carbon were investigated. The granular activated carbon (GAC) obtained from bituminous type coal having a surface area of 998 m2/g and loosely bounded and open pores morphology. The adorbates selected for this study was benzoic acid and its ortho-derivatives namely; salicylic acid, phthalic acid and o-toluic acid. The solubility of adsorbate in solvent affected the adsorption behaviour more pronouncly. The order of adsorption for adsorbates was found to be as: benzoic acid > salicylic acid > o-toluic acid > phthalic acid.

Rapid removal of salicylic acid, 4-nitroaniline, benzoic acid and phthalic acid from wastewater using magnetized fast pyrolysis biochar from waste Douglas fir

2017 ◽  
Vol 319 ◽  
pp. 75-88 ◽  
Author(s):  
Akila G. Karunanayake ◽  
Olivia A. Todd ◽  
Morgan L. Crowley ◽  
Lindsey B. Ricchetti ◽  
Charles U. Pittman ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Benzoic Acid ◽  
Phthalic Acid ◽  
Fast Pyrolysis ◽  
Douglas Fir ◽  
Rapid Removal

scholarly journals Free and Conjugated Benzoic Acid in Tobacco Plants and Cell Cultures. Induced Accumulation upon Elicitation of Defense Responses and Role as Salicylic Acid Precursors

2001 ◽  
Vol 125 (1) ◽  
pp. 318-328 ◽  
Author(s):  
Julie Chong ◽  
Marie-Agnès Pierrel ◽  
Rossitza Atanassova ◽  
Danièle Werck-Reichhart ◽  
Bernard Fritig ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Benzoic Acid ◽  
Cell Cultures ◽  
Defense Responses ◽  
Tobacco Plants

Benzoic Acid and Phthalic Acid on Atomically Well-Defined MgO(100) Thin Films: Adsorption, Interface Reaction, and Thin Film Growth

2015 ◽  
Vol 119 (48) ◽  
pp. 26968-26979 ◽  
Author(s):  
Tao Xu ◽  
Susanne Mohr ◽  
Max Amende ◽  
Mathias Laurin ◽  
Tibor Döpper ◽  
...  
Keyword(s):  
Thin Film ◽  
Thin Films ◽  
Benzoic Acid ◽  
Phthalic Acid ◽  
Film Growth ◽  
Interface Reaction ◽  
Thin Film Growth
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