An intraresidue H-bonding motif in selenocysteine and cysteine, revealed by gas phase laser spectroscopy and quantum chemistry calculations

2020 ◽  
Vol 22 (36) ◽  
pp. 20409-20420 ◽  
Author(s):  
Gildas Goldsztejn ◽  
Venkateswara Rao Mundlapati ◽  
Jérémy Donon ◽  
Benjamin Tardivel ◽  
Eric Gloaguen ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Gas Phase ◽  
Laser Spectroscopy ◽  
Side Chain ◽  
Quantum Chemistry Calculations ◽  
Bonding Properties

Models of protein chains containing a seleno-cysteine (Sec) residue have been investigated by gas phase laser spectroscopy in order to document the effect of the H-bonding properties of the SeH group in the folding of the Sec side chain, by comparison with recent data on Ser- and Cys-containing sequences.

Gas-phase models of γ turns: Effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

2005 ◽  
Vol 123 (8) ◽  
pp. 084301 ◽  
Author(s):  
Wutharath Chin ◽  
François Piuzzi ◽  
Jean-Pierre Dognon ◽  
Iliana Dimicoli ◽  
Michel Mons
Keyword(s):  
Quantum Chemistry ◽  
Gas Phase ◽  
Uv Spectroscopy ◽  
Side Chain ◽  
Phase Models

scholarly journals Unravelling the electronic structure and dynamics of an isolated molecular rotary motor in the gas-phase

2017 ◽  
Vol 8 (9) ◽  
pp. 6141-6148 ◽  
Author(s):  
Reece Beekmeyer ◽  
Michael A. Parkes ◽  
Luke Ridgwell ◽  
Jamie W. Riley ◽  
Jiawen Chen ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Quantum Chemistry ◽  
Gas Phase ◽  
Photoelectron Spectroscopy ◽  
Structure And Dynamics ◽  
Quantum Chemistry Calculations ◽  
Anion Photoelectron Spectroscopy ◽  
Rotary Motor

Anion photoelectron spectroscopy and quantum chemistry calculations are employed to probe the electronic structure and dynamics of a unidirectional molecular rotary motor anion in the gas-phase.

On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins

2018 ◽  
Vol 20 (5) ◽  
pp. 3411-3423 ◽  
Author(s):  
S. Habka ◽  
W. Y. Sohn ◽  
V. Vaquero-Vara ◽  
M. Géléoc ◽  
B. Tardivel ◽  
...  
Keyword(s):  
Gas Phase ◽  
Laser Spectroscopy ◽  
Protein Structures ◽  
Side Chain ◽  
Amide Side Chain ◽  
Model Peptides

The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Thomas Hamelryck ◽  
Jan H Jensen
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Jan H Jensen ◽  
Thomas Hamelryck
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

Mechanisms and kinetic parameters for the gas-phase reactions of anthracene and pyrene with Cl atoms in the presence of NOx

RSC Advances ◽  
2016 ◽  
Vol 6 (21) ◽  
pp. 17345-17353 ◽  
Author(s):  
Juan Dang ◽  
Maoxia He
Keyword(s):  
Quantum Chemistry ◽  
Kinetic Parameters ◽  
Gas Phase ◽  
Atmospheric Oxidation ◽  
Gas Phase Reactions ◽  
Quantum Chemistry Calculations ◽  
Cl Atoms

The mechanisms of the Cl radical-initiated atmospheric oxidation of anthracene (Ant) and pyrene (Pyr) were investigated by using quantum chemistry calculations.

The nature of selenium hydrogen bonding: gas phase spectroscopy and quantum chemistry calculations

2017 ◽  
Vol 19 (35) ◽  
pp. 24179-24187 ◽  
Author(s):  
Kamal K. Mishra ◽  
Santosh K. Singh ◽  
Paulami Ghosh ◽  
Debashree Ghosh ◽  
Aloke Das
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Charge Transfer ◽  
Quantum Chemistry ◽  
Gas Phase ◽  
Quantum Chemistry Calculations ◽  
Gas Phase Spectroscopy

Charge transfer interactions, along with electrostatic and polarization interactions, are important for the strength of hydrogen bonding when poorly electronegative atoms act as hydrogen bond acceptors.

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