Hydrogen Bonding: From Biological Systems To Interstellar Medium

2018 ◽  
Author(s):  
Emmanuel E. Etim ◽  
Prasanta Gorai ◽  
Ankan Das ◽  
Sandip K. Chakrabarti ◽  
Elangannan Arunan
Keyword(s):  
Hydrogen Bonding ◽  
Interstellar Medium ◽  
Biological Systems

CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?

2009 ◽  
Vol 08 (04) ◽  
pp. 691-711 ◽  
Author(s):  
FENG FENG ◽  
HUAN WANG ◽  
WEI-HAI FANG ◽  
JIAN-GUO YU
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Density Functional ◽  
Biological Systems ◽  
Binding Energies ◽  
Semiempirical Model ◽  
Hydrogen Bonded Systems ◽  
High Level ◽  
Hydrogen Bonded

A modified semiempirical model named RM1BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

scholarly journals Physical Meanings of Fractal Behaviors of Water in Aqueous and Biological Systems with Open-Ended Coaxial Electrodes

Sensors ◽  
2019 ◽  
Vol 19 (11) ◽  
pp. 2606
Author(s):  
Shin Yagihara ◽  
Rio Kita ◽  
Naoki Shinyashiki ◽  
Hironobu Saito ◽  
Yuko Maruyama ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Relaxation Time ◽  
Relaxation Process ◽  
Fractal Analysis ◽  
Biological Systems ◽  
Polymer Networks ◽  
Dispersion Systems ◽  
Dispersion State ◽  
Frequency Relaxation ◽  
Average Relaxation Time

The dynamics of a hydrogen bonding network (HBN) relating to macroscopic properties of hydrogen bonding liquids were observed as a significant relaxation process by dielectric spectroscopy measurements. In the cases of water and water rich mixtures including biological systems, a GHz frequency relaxation process appearing at around 20 GHz with the relaxation time of 8.2 ps is generally observed at 25 °C. The GHz frequency process can be explained as a rate process of exchanges in hydrogen bond (HB) and the rate becomes higher with increasing HB density. In the present work, this study analyzed the GHz frequency process observed by suitable open-ended coaxial electrodes, and physical meanings of the fractal nature of water structures were clarified in various aqueous systems. Dynamic behaviors of HBN were characterized by a combination of the average relaxation time and the distribution of the relaxation time. This fractal analysis offered an available approach to both solution and dispersion systems with characterization of the aggregation or dispersion state of water molecules. In the case of polymer-water mixtures, the HBN and polymer networks penetrate each other, however, the HBN were segmented and isolated more by dispersed and aggregated particles in the case of dispersion systems. These HBN fragments were characterized by smaller values of the fractal dimension obtained from the fractal analysis. Some examples of actual usages suggest that the fractal analysis is now one of the most effective tools to understand the molecular mechanism of HBN in aqueous complex materials including biological systems.

scholarly journals Self-assembling peptide semiconductors

Science ◽  
2017 ◽  
Vol 358 (6365) ◽  
pp. eaam9756 ◽  
Author(s):  
Kai Tao ◽  
Pandeeswar Makam ◽  
Ruth Aizen ◽  
Ehud Gazit
Keyword(s):  
Hydrogen Bonding ◽  
Biological Systems ◽  
Band Gaps ◽  
Short Peptides ◽  
Promising Candidate ◽  
Supramolecular Materials ◽  
Self Assembling ◽  
The Family ◽  
Nanoscale Semiconductors ◽  
Inorganic Semiconductor

Semiconductors are central to the modern electronics and optics industries. Conventional semiconductive materials bear inherent limitations, especially in emerging fields such as interfacing with biological systems and bottom-up fabrication. A promising candidate for bioinspired and durable nanoscale semiconductors is the family of self-assembled nanostructures comprising short peptides. The highly ordered and directional intermolecular π-π interactions and hydrogen-bonding network allow the formation of quantum confined structures within the peptide self-assemblies, thus decreasing the band gaps of the superstructures into semiconductor regions. As a result of the diverse architectures and ease of modification of peptide self-assemblies, their semiconductivity can be readily tuned, doped, and functionalized. Therefore, this family of electroactive supramolecular materials may bridge the gap between the inorganic semiconductor world and biological systems.

Accessibility of the Lone Pair and Hydrogen Bonding Site in Biological Systems

1987 ◽  
pp. 275-278
Author(s):  
S. Toppet ◽  
J. De Taeye ◽  
M. Ruyssen ◽  
C. Laureys ◽  
Th. Zeegers-Huyskens
Keyword(s):  
Hydrogen Bonding ◽  
Biological Systems ◽  
Lone Pair ◽  
Hydrogen Bonding Site ◽  
Bonding Site

Spectral Properties of Fluorescein in Solvent-Water Mixtures: Applications as a Probe of Hydrogen Bonding Environments in Biological Systems

1998 ◽  
Vol 67 (5) ◽  
pp. 500-510 ◽  
Author(s):  
Nectarios Klonis ◽  
Andrew H. A. Clayton ◽  
Edward W. Voss ◽  
William H. Sawyer
Keyword(s):  
Hydrogen Bonding ◽  
Spectral Properties ◽  
Biological Systems ◽  
Solvent Water

Boosting Performance by Water Solvation Shell with Hydrogen Bonds on Protonic Ionic Liquid: Insights into the Acid Catalysis of Glycosidic Bond

2021 ◽  
Author(s):  
Kaixin Li ◽  
Limin Deng ◽  
Shun Yi ◽  
Yabo Wu ◽  
Guangjie Xia ◽  
...  
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Hydrogen Bonds ◽  
Acid Catalysis ◽  
Biological Systems ◽  
Solvation Shell ◽  
Water Molecules ◽  
Binding Behavior ◽  
Chemical And Biological Systems

Hydrogen-bonding (HB) induced by water solvation shell is vital in the chemical and biological systems. Herein, HBs related to the binding behavior of protonic ionic liquids (PIL) with water molecules...

scholarly journals A comparative study of tough hydrogen bonding dissipating hydrogels made with different network structures.

2021 ◽  
Author(s):  
Badri Narayanan Narasimhan ◽  
Gerrit Sjoerd Deijs ◽  
Sesha Manuguri ◽  
Matthew S. Ting ◽  
Bill Williams ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Hydrogen Bonding ◽  
Comparative Study ◽  
Biological Systems ◽  
Soft Materials ◽  
Network Structures ◽  
Engineering Applications ◽  
Precise Control

Hydrogels are excellent soft materials to interface with biological systems. Precise control and tunability of dissipative properties of gels are particularly interesting in tissue engineering applications. In this work, we...

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