scholarly journals Kinetically Trapped Liquid-State Conformers of a Sodiated Model Peptide Observed in the Gas Phase

2017 ◽  
Vol 121 (36) ◽  
pp. 6838-6844 ◽  
Author(s):  
Markus Schneider ◽  
Chiara Masellis ◽  
Thomas Rizzo ◽  
Carsten Baldauf
Keyword(s):  
Gas Phase ◽  
Liquid State ◽  
Model Peptide

scholarly journals N-ethylformamide dimer. A β-turn model peptide in the gas phase

2017 ◽  
Vol 335 ◽  
pp. 102-107 ◽  
Author(s):  
V. Vaquero-Vara ◽  
V. Alstadt ◽  
T.P. Sewatsky ◽  
J.L. Claughton ◽  
I.A. Finneran ◽  
...  
Keyword(s):  
Gas Phase ◽  
Model Peptide

CONFORMATIONAL PREFERENCES OF N-ACETYL–GLYCINE–GLYCINE–N′-METHYLAMIDE: A THEORETICAL STUDY

2009 ◽  
Vol 08 (05) ◽  
pp. 799-811 ◽  
Author(s):  
HO-JIN LEE ◽  
HYUN-MEE PARK ◽  
KANG-BONG LEE
Keyword(s):  
Protein Folding ◽  
Force Field ◽  
Gas Phase ◽  
Relative Position ◽  
Theoretical Study ◽  
Minimum Energy ◽  
Energy Profile ◽  
Model Peptide ◽  
Conformational Preferences ◽  
Peptide Models

The conformational preferences of peptide models have been investigated to understand the protein folding mechanism and to develop the force field. Here, we report the minimum energy conformations for a model peptide, N-acetyl–glycine–glycine–N′-methylamide ( Ac–1Gly–2Gly–NHMe(I) ) at the HF/3-21G, HF/6-31G*, and the B3LYP/6-31G* level of theory. At the B3LYP/6-31G* level, the 31 minima were identified and the 10 β-turn structures among the minima were observed in gas-phase. The conformational preferences of Gly residue in the model peptide, I depend on its relative position and conformation of neighboring Gly residue. The Gly residue in this model dipeptide has an asymmetric energy profile as one of Gly residue adopts a specific conformation. This study sheds some lights on understanding the unique conformational preferences of Gly residue in protein including two consecutive Gly residues.

scholarly journals Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions

The Analyst ◽  
2015 ◽  
Vol 140 (20) ◽  
pp. 6933-6944 ◽  
Author(s):  
Chunying Xiao ◽  
Lisa M. Pérez ◽  
David H. Russell
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Gas Phase ◽  
Dynamics Simulation ◽  
Side Chain ◽  
Peptide Ions ◽  
Conformational Preference ◽  
Model Peptide ◽  
Factors Affecting ◽  
Conformational Preferences

The factors affecting conformational preference of gas phase peptide ions are investigated by IM-MS and molecular dynamics simulation.

Electrostatic interactions as a factor in the determination of the HOMO in the liquid state

1986 ◽  
Vol 64 (12) ◽  
pp. 2353-2358 ◽  
Author(s):  
Enrique Sánchez Marcos ◽  
Joaquín Maraver ◽  
Manuel F. Ruíz-López ◽  
Juan Bertrán
Keyword(s):  
Gas Phase ◽  
Molecular Orbital ◽  
Perturbation Analysis ◽  
Liquid State ◽  
Electrostatic Interactions ◽  
Orbital Evolution ◽  
Benzene Derivatives ◽  
Cavity Model ◽  
Ellipsoidal Cavity

An ellipsoidal cavity model has been used to study the energy changes in occupied molecular orbitals induced by solute–solvent electrostatic interactions. Some benzene derivatives have been selected as solutes. Calculations have been carried out at the CNDO and abinitio STO-4G levels. Important variations in the molecular orbital sequence, involving a change in the HOMO nature, have been observed. A perturbation analysis is employed to understand the orbital evolution from gas phase to solution.

Gas-Phase Folding of a Two-Residue Model Peptide Chain: On the Importance of an Interplay between Experiment and Theory

2010 ◽  
Vol 132 (34) ◽  
pp. 11860-11863 ◽  
Author(s):  
E. Gloaguen ◽  
B. de Courcy ◽  
J.-P. Piquemal ◽  
J. Pilmé ◽  
O. Parisel ◽  
...  
Keyword(s):  
Gas Phase ◽  
Peptide Chain ◽  
Model Peptide

scholarly journals Optimized Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters Based on Liquid-State Data

2019 ◽  
Author(s):  
Samuel Kantonen ◽  
Hari S. Muddana ◽  
Niel M. Henriksen ◽  
Lee-Ping Wang ◽  
Michael Gilson
Keyword(s):  
Experimental Data ◽  
Force Field ◽  
Gas Phase ◽  
Liquid State ◽  
Quantum Calculations ◽  
Minimal Basis ◽  
State Data ◽  
Lennard Jones ◽  
Mapping Parameters ◽  
General Force

We utilize a previously described Minimal Basis Iterative Stockholder (MBIS) method to carry out an atoms-in-molecules partitioning of electron densities. Information from these atomic densities is then mapped to Lennard-Jones parameters using a set of mapping parameters much smaller than the typical number of atom types in a force field. This approach is advantageous in two ways: it eliminates atom types by allowing each atom to have unique Lennard-Jones parameters, and it greatly reduces the number of parameters to be optimized. We show that this approach yields results comparable to those obtained with the typed GAFF force field, even when trained on a relatively small amount of experimental data.

Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase

2010 ◽  
Vol 132 (6) ◽  
pp. 2085-2093 ◽  
Author(s):  
Peter Kupser ◽  
Kevin Pagel ◽  
Jos Oomens ◽  
Nick Polfer ◽  
Beate Koksch ◽  
...  
Keyword(s):  
Gas Phase ◽  
Model Peptide ◽  
Gramicidin S ◽  
Β Sheet

Gas-phase and liquid-state properties of esters, nitriles, and nitro compounds with the OPLS-AA force field

2001 ◽  
Vol 22 (13) ◽  
pp. 1340-1352 ◽  
Author(s):  
Melissa L. P. Price ◽  
Dennis Ostrovsky ◽  
William L. Jorgensen
Keyword(s):  
Force Field ◽  
Gas Phase ◽  
Liquid State ◽  
Nitro Compounds

Infrared and Raman Studies of Ortho- and Meta-Substituted Styrenes

1968 ◽  
Vol 22 (6) ◽  
pp. 650-658 ◽  
Author(s):  
W. G. Fateley ◽  
G. L. Carlson ◽  
F. E. Dickson
Keyword(s):  
Gas Phase ◽  
Raman Spectra ◽  
Spectral Region ◽  
Liquid State ◽  
Infrared And Raman Spectra ◽  
Nitro Derivatives

Infrared and Raman spectra have been obtained over the region 4000 cm−1 to 33 cm−1 on ortho-and meta-substituted styrenes including F, Br, Cl, methyl, and meta-nitro derivatives. The entire spectral region has been investigated in the liquid state while selected regions and isomers have been studied in the solid and gas phase. Gas phase and interferometric spectra in the far ir of ortho-and meta-fluorostyrene did not reveal the torsional modes. Assignment of most fundamental modes of vibrations are reported and discussed.

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