Polarizability, proton transfer, and symmetry of energy surfaces of phenol-propylamine hydrogen bonds. Infrared investigation

1978 ◽  
Vol 82 (6) ◽  
pp. 685-689 ◽  
Author(s):  
Georg Zundel ◽  
Anton Nagyrevi
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Energy Surfaces

Comparison of the proton-transfer path in hydrogen bonds from theoretical potential-energy surfaces and the concept of conservation of bond order. II. (N—H...N)+ hydrogen bonds

2007 ◽  
Vol 63 (4) ◽  
pp. 650-662 ◽  
Author(s):  
Irena Majerz ◽  
Ivar Olovsson
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surfaces ◽  
Bond Order ◽  
Theoretical Calculations ◽  
Perfect Agreement ◽  
Reaction Coordinates ◽  
Donor And Acceptor ◽  
Energy Surfaces

The quantum-mechanically derived reaction coordinates (QMRC) for the proton transfer in (N—H—N)+ hydrogen bonds have been derived from ab initio calculations of potential-energy surfaces. A comparison is made between the QMRC and the corresponding bond-order reaction coordinates (BORC) derived by applying the Pauling bond-order concept together with the principle of conservation of bond order. We find virtually perfect agreement between the QMRC and the BORC for intermolecular (N—H—N)+ hydrogen bonds. In contrast, for intramolecular (N—H—N)+ hydrogen bonds, the donor and acceptor parts of the molecule impose strong constraints on the N—N distance and the QMRC does not follow the BORC relation in the whole range. The X-ray determined hydrogen positions are not located exactly at the theoretically calculated potential-energy minima, but instead at the point where the QMRC and the BORC coincide with each other. On the other hand, the optimized hydrogen positions, with other atoms in the cation fixed as in the crystal structure, are closer to these energy minima. Inclusion of the closest neighbours in the theoretical calculations has a rather small effect on the optimized hydrogen positions. [Part I: Olovsson (2006). Z. Phys. Chem. 220, 797–810.]

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.

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