scholarly journals Unraveling the structural and chemical features of biological short hydrogen bonds

2019 ◽  
Vol 10 (33) ◽  
pp. 7734-7745 ◽  
Author(s):  
Shengmin Zhou ◽  
Lu Wang
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Biological Macromolecules ◽  
Proton Potential ◽  
Energy Surfaces ◽  
Short Hydrogen Bonds

Short hydrogen bonds are ubiquitous in biological macromolecules and exhibit distinctive proton potential energy surfaces and proton sharing properties.

Global and local minima of protonated acetonitrile clusters

2020 ◽  
Vol 44 (40) ◽  
pp. 17558-17569 ◽  
Author(s):  
Alhadji Malloum ◽  
Jeanet Conradie
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Local Minima ◽  
Energy Surfaces ◽  
Global And Local

Potential energy surfaces of protonated acetonitrile clusters have been explored to locate global and local minima energy structures. The structures are stabilized by strong hydrogen bonds, anti-parallel dimers, dipole–dipole and CH⋯N interactions.

scholarly journals Theoretical Studies of Dynamic Interactions in Excited States of Hydrogen-Bonded Systems

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Marek J. Wójcik ◽  
Marek Boczar ◽  
Łukasz Boda
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy ◽  
Benzoic Acid ◽  
Excited States ◽  
Potential Energy Surfaces ◽  
Low Frequency ◽  
Fermi Resonance ◽  
Tunneling Splittings ◽  
Energy Surfaces ◽  
Hydrogen Bonded

Theoretical model for vibrational interactions in the hydrogen-bonded benzoic acid dimer is presented. The model takes into account anharmonic-type couplings between the high-frequency O–H and the low-frequency O⋯O stretching vibrations in two hydrogen bonds, resonance interactions between two hydrogen bonds in the dimer, and Fermi resonance between the O–H stretching fundamental and the first overtone of the O–H in-plane bending vibrations. The model is used for theoretical simulation of the O–H stretching IR absorption bands of benzoic acid dimers in the gas phase in the first excited singlet state. Ab initio CIS and CIS(D)/CIS/6-311++G(d,p) calculations have been carried out in the à state of tropolone. The grids of potential energy surfaces along the coordinates of the tunneling vibration and the low-frequency coupled vibration have been calculated. Two-dimensional model potentials have been fitted to the calculated potential energy surfaces. The tunneling splittings for vibrationally excited states have been calculated and compared with the available experimental data. The model potential energy surfaces give good estimation of the tunneling splittings in the vibrationally ground and excited states of tropolone, and explain monotonic decrease in tunneling splittings with the excitation of low-frequency out-of-plane modes and increase of the tunneling splittings with the excitation of low-frequency planar modes.

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.]

Asymmetric hydrogen bonds in a centrosymmetric environment. III. Quantum mechanical calculations of the potential-energy surfaces for the very short hydrogen bonds in potassium hydrogen dichloromaleate

2007 ◽  
Vol 63 (5) ◽  
pp. 748-752 ◽  
Author(s):  
I. Majerz ◽  
I. Olovsson
Keyword(s):  
Hydrogen Bonds ◽  
Potential Energy Surfaces ◽  
Bond Order ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Acta Cryst ◽  
Reaction Coordinates ◽  
Potassium Hydrogen ◽  
Energy Surfaces ◽  
Short Hydrogen Bonds

In the crystal structure of potassium hydrogen dichloromaleate there are two short hydrogen bonds of 2.44 Å. The `heavy-atom' structure is centrosymmetric (space group P\bar 1) with centers of symmetry in the middle of the O—O bonds, suggesting centered hydrogen bonds. However, earlier unconventional types of refinements of the extensive neutron data taken at 30, 90, 135, 170 and 295 K demonstrated that the H atoms are actually non-centered in the hydrogen bonds, although the environment is centrosymmetric. Traditionally it has been assumed that the hydrogen distribution adopts the same symmetry as the environment. Reviewing these unusual results it was considered of great interest to verify that the non-centered locations of the H atoms are reasonable from an energy point of view. Quantum mechanical calculations have now been carried out for the potential-energy surfaces (PES) for both the centered and non-centered locations of the H atoms. In all cases the non-centered positions are closer to the energy minima in the PES than the centered positions, and this result confirms that the structure is best described with non-centered H atoms. There is virtually perfect agreement between the quantum-mechanically derived reaction coordinates (QMRC) and the bond-order reaction coordinates (BORC) derived using Pauling's bond-order concept together with the principle of conservation of bond order. [Part I: Olovsson et al. (2001). Acta Cryst. B57, 311–316; Part II: Olovsson et al. (2002). Acta Cryst. B58, 627–631.]

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