CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine

2007 ◽  
Vol 127 (14) ◽  
pp. 145102 ◽  
Author(s):  
Luis Alberto Montero-Cabrera ◽  
Ute Röhrig ◽  
Juan A. Padrón-Garcia ◽  
Rachel Crespo-Otero ◽  
Ana L. Montero-Alejo ◽  
...  
Keyword(s):  
Electronic Properties ◽  
Gas Phase ◽  
Reliable Method ◽  
Binding Pocket ◽  
Large Systems ◽  
Retinal Binding Pocket

scholarly journals Absorption mechanism, structural and electronic properties of MC19 (M = B and Si) fullerenes with 1-acetylpiperazine

2017 ◽  
Vol 36 (1-2) ◽  
pp. 797-804
Author(s):  
Özgür Alver ◽  
Cemal Parlak ◽  
Mohamed I Elzagheid ◽  
Ponnadurai Ramasami
Keyword(s):  
Electronic Properties ◽  
Gas Phase ◽  
Basis Set ◽  
Stable Complex ◽  
Absorption Mechanism ◽  
Boron Doped ◽  
Structural And Electronic Properties ◽  
Influence Of Water ◽  
Vibrational Bands ◽  
Silicon Doped

The interaction mechanisms of undoped, silicon- and boron-doped C20 fullerenes and 1-acetylpiperazine (1-ap) were investigated. Stability, electronic properties, influence of water on the solubility and stability, molecular parameters, descriptive vibrational bands and nuclear magnetic resonance shielding values are reported. The quantum mechanical calculations were carried out using the M06-2X functional and the 6-31G(d) basis set. It is observed that all the complexes are more stabilized in water compared to the gas phase. The most stable complex was found as silicon-doped fullerene interacting with the carbonyl edge of 1-ap releasing energy of 64.13 kcal/mol in water.

scholarly journals 1JCH couplings in Group 14/IVA tetramethyls from the gas-phase NMR and DFT structural study: a search for the best computational protocol

2014 ◽  
Vol 16 (29) ◽  
pp. 15699-15708 ◽  
Author(s):  
Ryszard B. Nazarski ◽  
Włodzimierz Makulski
Keyword(s):  
Dft Calculations ◽  
Electronic Properties ◽  
Gas Phase ◽  
Structural Study ◽  
Group 14 ◽  
Computational Protocol ◽  
Isolated Molecules

The gas-phase 1J0,CHs in ‘isolated’ molecules of EMe4 were determined and discussed in terms of their geometric/electronic properties obtained from DFT calculations.

Steric constraints in the retinal binding pocket of sensory rhodopsin I

Biochemistry ◽  
1993 ◽  
Vol 32 (38) ◽  
pp. 10224-10232 ◽  
Author(s):  
Bing Yan ◽  
Aihua Xie ◽  
G. Ulrich Nienhaus ◽  
Yuko Katsuta ◽  
John L. Spudich
Keyword(s):  
Binding Pocket ◽  
Sensory Rhodopsin ◽  
Sensory Rhodopsin I ◽  
Retinal Binding Pocket ◽  
Steric Constraints

Study on the Gas Phase Stability of Heme-binding Pocket in Cytochrome Tb5 and Its Mutants by Electrospray Mass Spectrometry

2010 ◽  
Vol 20 (12) ◽  
pp. 1540-1545 ◽  
Author(s):  
Chong-Tian Yu ◽  
Yin-Long Guo ◽  
Long Lü ◽  
Yun-Hua Wang ◽  
Ping Yao ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Phase Stability ◽  
Electrospray Mass Spectrometry ◽  
Binding Pocket ◽  
Heme Binding

scholarly journals Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces

2011 ◽  
Vol 2 ◽  
pp. 427-447 ◽  
Author(s):  
David M Benoit ◽  
Bruno Madebene ◽  
Inga Ulusoy ◽  
Luis Mancera ◽  
Yohann Scribano ◽  
...  
Keyword(s):  
Gas Phase ◽  
First Principles ◽  
Gold Clusters ◽  
Computational Grids ◽  
Consistent Field ◽  
Self Consistent Field ◽  
Quantum Approach ◽  
Large Systems ◽  
Correlation Corrections ◽  
Thiophene Molecule

We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters.

scholarly journals Conserved amino acids in F-helix of bacteriorhodopsin form part of a retinal binding pocket

FEBS Letters ◽  
1989 ◽  
Vol 250 (2) ◽  
pp. 448-452 ◽  
Author(s):  
K.J. Rothschild ◽  
M.S. Braiman ◽  
T. Mogi ◽  
L.J. Stern ◽  
H.G. Khorana
Keyword(s):  
Amino Acids ◽  
Binding Pocket ◽  
Form Part ◽  
Retinal Binding Pocket ◽  
Conserved Amino Acids

Modification of graphene electronic properties via controllable gas-phase doping with copper chloride

2018 ◽  
Vol 112 (3) ◽  
pp. 033107 ◽  
Author(s):  
Maxim G. Rybin ◽  
Vera R. Islamova ◽  
Ekaterina A. Obraztsova ◽  
Elena D. Obraztsova
Keyword(s):  
Electronic Properties ◽  
Gas Phase ◽  
Copper Chloride
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