Determining the Geometry of Hydrogen Bonds in Solids with Picometer Accuracy by Quantum-Chemical Calculations and NMR Spectroscopy

ChemPhysChem ◽  
2005 ◽  
Vol 6 (2) ◽  
pp. 315-327 ◽  
Author(s):  
Martin Schulz-Dobrick ◽  
Thorsten Metzroth ◽  
Hans Wolfgang Spiess ◽  
J�rgen Gauss ◽  
Ingo Schnell
Keyword(s):  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical

Problems with a conformation assignment of aryl-substituted resorc[4]arenes

2011 ◽  
Vol 76 (10) ◽  
pp. 1199-1222 ◽  
Author(s):  
Jakub Kaminský ◽  
Hana Dvořáková ◽  
Jan Štursa ◽  
Jitka Moravcová
Keyword(s):  
Hydrogen Bonding ◽  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Quantum Chemical Calculations ◽  
Dynamic Process ◽  
Quantum Chemical ◽  
Energy Barrier ◽  
Π Interactions ◽  
Temperature Range ◽  
Acid Catalyzed

Acid-catalyzed condensation of resorcinol with 3,5-diisopropoxybenzaldehyde and 3,5-dihydroxybenzaldehyde afforded aryl substituted resorc[4]arenes 1a and 1b, respectively. All 16 hydroxyls in 1b were acetylated providing resorc[4]arene 1c. The conformational behaviour of 1a, 1b and 1c was studied by NMR spectroscopy and quantum chemical calculations. It was found that the stabilization of their conformations is an effect of competing π-π and OH-π interactions, hydrogen bonding and steric features, respectively. As a result, C2 symmetrical boat conformations 1a, 1b and 1c with aryls in axial positions were identified in all cases. In case of 1c also the formation of C2 symmetrical conformation with aryls in equatorial positions (boat-eq) was identified. Moreover, compounds 1a and 1b being able to create hydrogen bonds, adopt also symmetrical C4 crown conformations. For 1c(boat-ax), the boat-boat conversion with energy barrier of 80 kJ/mol was observed, while the 1c(boat-eq) was found to be rigid in the whole accessible temperature range. Both conformers of 1c exhibit also second dynamic process – rotation of bridge aryl rings (ΔG‡ = 66 kJ/mol).

Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds

2019 ◽  
Vol 75 (3) ◽  
pp. 301-309
Author(s):  
Jelena M. Andrić ◽  
Ivana M. Stanković ◽  
Snežana D. Zarić
Keyword(s):  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Nucleic Acids ◽  
Metal Ions ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Metal Ion ◽  
Water Molecules ◽  
Nucleic Acid Bases ◽  
Coordinated Water

The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.

Hydrogen-Bonding and the Dissolution Mechanism of Uracil in an Acetate Ionic Liquid: New Insights from NMR Spectroscopy and Quantum Chemical Calculations

2013 ◽  
Vol 117 (15) ◽  
pp. 4109-4120 ◽  
Author(s):  
João M. M. Araújo ◽  
Ana B. Pereiro ◽  
José N. Canongia Lopes ◽  
Luís P. N. Rebelo ◽  
Isabel M. Marrucho
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Nmr Spectroscopy ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Dissolution Mechanism
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