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.

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.

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.

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.

Conformational analysis of diamide system HCO-L-Phenylalanine-NH2 by genetic algorithm

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Genetic Algorithm ◽  
Hydrogen Bonding ◽  
Conformational Analysis ◽  
Electrostatic Interactions ◽  
Main Chain ◽  
Empirical Method ◽  
Relative Stabilities ◽  
Semi Empirical

Present work reports a detailed conformational and energy study of diamide system HCO-L-Phenylalanine-NH2 using genetic algorithm based on multi-Niche crowding technique (MNC) coupled with semi-empirical method AM1. Analysis showed the existence of 28 conformations covering 6 folds among 9 predicted with multi-dimensional conformational analysis MDCA. The relative stabilities are discussed in terms of hydrogen bonding established within the main chains, and various other types of electrostatic interactions between the main chain and the side one.

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.

Modeling the Effects of O-sulfonation on the CID of Serine

2020 ◽  
Author(s):  
Kenneth Lucas ◽  
George Barnes
Keyword(s):  
Sulfo Group ◽  
High Energy ◽  
Empirical Method ◽  
Side Chain ◽  
Energy Structure ◽  
Direct Dynamics ◽  
Theoretical Mass ◽  
Intermolecular Proton Transfer ◽  
Dynamics Simulations ◽  
Semi Empirical

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of \textit{O}-sulfonation on the collision induced dissociation for serine. Towards this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m\z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m\z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The \mz 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also seen that the RM1 semi empirical method was not able to obtain all of the major peaks seen in experiment for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

scholarly journals How Good Is the STW Sensor? An Account from a Larger Shipping Company

2021 ◽  
Vol 9 (5) ◽  
pp. 465
Author(s):  
Angelos Ikonomakis ◽  
Ulrik Dam Nielsen ◽  
Klaus Kähler Holst ◽  
Jesper Dietz ◽  
Roberto Galeazzi
Keyword(s):  
High Frequency ◽  
Additional Data ◽  
Empirical Method ◽  
Influential Factor ◽  
Sensor Data ◽  
Sea State ◽  
Shipping Company ◽  
Frequency Sensor ◽  
Semi Empirical

This paper examines the statistical properties and the quality of the speed through water (STW) measurement based on data extracted from almost 200 container ships of Maersk Line’s fleet for 3 years of operation. The analysis uses high-frequency sensor data along with additional data sources derived from external providers. The interest of the study has its background in the accuracy of STW measurement as the most important parameter in the assessment of a ship’s performance analysis. The paper contains a thorough analysis of the measurements assumed to be related with the STW error, along with a descriptive decomposition of the main variables by sea region including sea state, vessel class, vessel IMO number and manufacturer of the speed-log installed in each ship. The paper suggests a semi-empirical method using a threshold to identify potential error in a ship’s STW measurement. The study revealed that the sea region is the most influential factor for the STW accuracy and that 26% of the ships of the dataset’s fleet warrant further investigation.

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