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.

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.

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.

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.

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 Compilation and evaluation of gas phase diffusion coefficients of halogenated organic compounds

2018 ◽  
Vol 5 (7) ◽  
pp. 171936 ◽  
Author(s):  
Wenjun Gu ◽  
Peng Cheng ◽  
Mingjin Tang
Keyword(s):  
Gas Phase ◽  
Diffusion Coefficients ◽  
Input Parameter ◽  
Empirical Method ◽  
Trace Gas ◽  
Temperature And Pressure ◽  
Organic Halogens ◽  
Semi Empirical ◽  
Method Show ◽  
Good Agreement

Organic halogens are of great environmental and climatic concern. In this work, we have compiled their gas phase diffusivities (pressure-normalized diffusion coefficients) in a variety of bath gases experimentally measured by previous studies. It is found that diffusivities estimated using Fuller's semi-empirical method agree very well with measured values for organic halogens. In addition, we find that at a given temperature and pressure, different molecules exhibit very similar mean free paths in the same bath gas, and then propose a method to estimate mean free paths in different bath gases. For example, the pressure-normalized mean free paths are estimated to be 90, 350, 90, 80, 120 nm atm in air (and N 2 /O 2 ), He, argon, CO 2 and CH 4 , respectively, with estimated errors of around ±25%. A generic method, which requires less input parameter than Fuller's method, is proposed to calculate gas phase diffusivities. We find that gas phase diffusivities in He (and air as well) calculated using our method show fairly good agreement with those measured experimentally and estimated using Fuller's method. Our method is particularly useful for the estimation of gas phase diffusivities when the trace gas contains atoms whose diffusion volumes are not known.

scholarly journals A comparative study of AumRhn (4 ≤ m + n ≤ 6) clusters in the gas phase versus those deposited on (100) MgO

2016 ◽  
Vol 18 (32) ◽  
pp. 22122-22128 ◽  
Author(s):  
Fernando Buendía ◽  
Jorge A. Vargas ◽  
Marcela R. Beltrán ◽  
Jack B. A. Davis ◽  
Roy L. Johnston
Keyword(s):  
Genetic Algorithm ◽  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Surface ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Functional Theory ◽  
Phase Versus ◽  
Combined Use

The combined use of a genetic algorithm and Density Functional Theory (DFT) calculations allows us to explore the potential energy surface. Our results show interesting effects on the geometries of the clusters on deposition. Two-dimensional clusters in the gas phase become three-dimensional and vice versa.

New Semi-Empirical Method for Alloys

1992 ◽  
Vol 278 ◽  
Author(s):  
Guillermo Bozzolo ◽  
John Ferrante
Keyword(s):  
Defect Formation ◽  
Empirical Method ◽  
Experimental Results ◽  
New Method ◽  
Surface Energies ◽  
Computational Simplicity ◽  
Alloy Properties ◽  
Semi Empirical ◽  
Formation Energies ◽  
Good Agreement

AbstractWe introduce a new semi-empirical method for calculating alloy properties. The method Is based on the concepts of equivalent crystal theory of defect formation energies in elemental solids. With this new method we predict heats of formation, lattice parameters, surface energies, segregation senergies and other properties of several binary alloys of fcc (Cu, NI, Ag, Au, Al, Fe, Pd and Pt) and bcc (Cr, Mo, Fe, V) elements. The method is characterized for its extreme computational simplicity and good agreement with experimental results. Several applications of the method are discussed.

Statistical Mechanics Approximation of Biogeography-Based Optimization

2016 ◽  
Vol 24 (3) ◽  
pp. 427-458 ◽  
Author(s):  
Haiping Ma ◽  
Dan Simon ◽  
Minrui Fei
Keyword(s):  
Genetic Algorithm ◽  
Statistical Mechanics ◽  
Evolutionary Algorithm ◽  
Mathematical Description ◽  
Fitness Function ◽  
Statistical Properties ◽  
Separable Functions ◽  
The One ◽  
Good Agreement ◽  
Population Fitness

Biogeography-based optimization (BBO) is an evolutionary algorithm inspired by biogeography, which is the study of the migration of species between habitats. This paper derives a mathematical description of the dynamics of BBO based on ideas from statistical mechanics. Rather than trying to exactly predict the evolution of the population, statistical mechanics methods describe the evolution of statistical properties of the population fitness. This paper uses the one-max problem, which has only one optimum and whose fitness function is the number of 1s in a binary string, to derive equations that predict the statistical properties of BBO each generation in terms of those of the previous generation. These equations reveal the effect of migration and mutation on the population fitness dynamics of BBO. The results obtained in this paper are similar to those for the simple genetic algorithm with selection and mutation. The paper also derives equations for the population fitness dynamics of general separable functions, and we find that the results obtained for separable functions are the same as those for the one-max problem. The statistical mechanics theory of BBO is shown to be in good agreement with simulation.

INTRAMOLECULAR CHARGE TRANSFER AND PHOTOISOMERIZATION OF THE DCM STYRENE DYE: A THEORETICAL STUDY

2008 ◽  
Vol 07 (04) ◽  
pp. 719-736 ◽  
Author(s):  
XUEFEI XU ◽  
RUIQIN ZHANG ◽  
ZEXING CAO ◽  
QIANER ZHANG
Keyword(s):  
Gas Phase ◽  
Energy Surface ◽  
Theoretical Study ◽  
Potential Surface ◽  
Polar Solvent ◽  
Intramolecular Charge Transfer ◽  
Structures And Properties ◽  
Experimental Values ◽  
Intramolecular Rotation ◽  
Good Agreement

Structures and properties of the low-lying states in 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran (DCM) have been investigated theoretically. Calculations show that the dimethylamino and dimethylanilino twisted conformations of DCM on the potential energy surface of the first excited state ( S 1) have relatively high stabilities and remarkable intramolecular charge transfers (ICT). Both structures can serve as candidates for the red-shifted emissive state in polar solvent. In particular, the dimethylanilino twisted ICT state has been predicted to have a dipole moment increment of 20 Debye with respect to the ground state by CASSCF calculations, in good agreement with the suggested experimental values. The optimized geometry of the S 1 state exhibits a long central CC bond of 1.458 Å, which makes the trans–cis isomerization quite facile through intramolecular rotation around the central CC bond on the S 1 potential surface. The S 1 state is a precursor to the formation of the ICT emissive state and photoinduced trans–cis isomerization. The S 1/ S 0 crossing in polar solvent and avoid-crossing in the gas phase as well as in non-polar solvent are involved in the trans–cis isomerization process. The presence of an early S 1/ S 0 crossing in the strong polar solvent reduces the isomerization efficiency.

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