A new view of the quantum dynamics for proton transfer along hydrogen bonds: Vibrational spectroscopy with neutrons

1998 ◽  
Vol 102 (3) ◽  
pp. 384-392 ◽  
Author(s):  
F. Fillaux ◽  
B. Nicolaï ◽  
M. H. Baron ◽  
A. Lautié ◽  
J. Tomkinson ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Vibrational Spectroscopy ◽  
Quantum Dynamics ◽  
New View

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

scholarly journals 5-Nitrosalicylic Acid and its Proton-Transfer Compounds with Aliphatic Lewis Bases

2005 ◽  
Vol 58 (1) ◽  
pp. 47 ◽  
Author(s):  
Graham Smith ◽  
Andy W. Hartono ◽  
Urs D. Wermuth ◽  
Peter C. Healy ◽  
Jonathan M. White ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Lewis Base ◽  
Unusual Structure ◽  
Lewis Bases ◽  
Carboxylate Oxygen ◽  
Hydrogen Bonding Interactions ◽  
Polymer Compound ◽  
Proton Transfer Compounds ◽  
Centrosymmetric Dimers

The crystal structures of the proton-transfer compounds of 5-nitrosalicylic acid (5-nsa) with morpholine (morph), hexamethylenetetramine (hmt), and ethylenediamine (en) have been determined and their solid-state packing structures described. The compounds are [(morph)+(5-nsa)–] 1, [(hmt)+(5-nsa)–·H2O] 2, and [(en)2+2(5-nsa)–·H2O] 3. In all compounds, protonation of the hetero-nitrogen of the Lewis base occurs. With 1, the 5-nsa anions and the morpholine cations lie, respectively, in or across crystallographic mirror planes and are linked within the planes by hydrogen-bonding interactions through the aminium group and the carboxylic and phenolic oxygens of the anionic 5-nsa species giving a two-dimensional sheet polymer. Compound 2 is an unusual structure with the planar 5-nsa anions lying within pseudo mirror planes and cyclically linked by duplex water bridges through a single carboxylate oxygen into centrosymmetric dimers. The hmt cation molecules are disordered across the pseudo mirror and are strongly linked by N+–H···O hydrogen bonds only to the water molecules with peripheral weak hmt C–H···O hydrogen bonds extending the dimer within and between the dimer planes. Compound 3 is a network polymer comprised of the 5-nsa anions, the en dianions, and the water molecule in an extensive hydrogen-bonded structure.

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

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