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.

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.

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.

scholarly journals Side-Chain to Main-Chain Hydrogen Bonding Controls the Intrinsic Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix

2014 ◽  
Vol 106 (6) ◽  
pp. 1318-1326 ◽  
Author(s):  
Christina Scharnagl ◽  
Oxana Pester ◽  
Philipp Hornburg ◽  
Daniel Hornburg ◽  
Alexander Götz ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Amyloid Precursor Protein ◽  
Main Chain ◽  
Transmembrane Helix ◽  
Precursor Protein ◽  
Backbone Dynamics ◽  
Side Chain

scholarly journals A semi-empirical method for predicting GOC in oil reservoirs with limited PVT dataset

2020 ◽  
Vol 2 (7) ◽  
Author(s):  
Oluchukwu M. Okoh ◽  
Kazeem A. Lawal ◽  
Asekhame U. Yadua ◽  
Mathilda I. Ovuru ◽  
Stella I. Eyitayo ◽  
...  
Keyword(s):  
Empirical Method ◽  
Oil Reservoirs ◽  
Semi Empirical

HYDROGEN BONDING IN DIASTEREOISOMERIC α-β AMINOALCOHOLS: A REINVESTIGATION OF THE EPHEDRINES BY N.M.R

1960 ◽  
Vol 38 (1) ◽  
pp. 125-130 ◽  
Author(s):  
James B. Hyne
Keyword(s):  
Hydrogen Bonding ◽  
Polar Solvents ◽  
Relative Stabilities ◽  
Hydrogen Bonded

The results of an n.m.r. study of the diastereoisomeric ephedrine and ψ-ephedrine molecules in non-polar solvents are interpreted and discussed in terms of the relative stabilities of the intramolecularly hydrogen-bonded conformers.

A semi-empirical method for the calculation of the electronic structure of glass

1970 ◽  
Vol 2 (4) ◽  
pp. 865-874 ◽  
Author(s):  
I. V. Abarenkov ◽  
A. V. Amosov ◽  
V. F. Bratsev ◽  
D. M. Yudin
Keyword(s):  
Electronic Structure ◽  
Empirical Method ◽  
Semi Empirical
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