Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer

2014 ◽  
Vol 141 (10) ◽  
pp. 101105 ◽  
Author(s):  
Matthias Heger ◽  
Martin A. Suhm ◽  
Ricardo A. Mata
Keyword(s):  
Hydrogen Bond ◽  
Binding Energy ◽  
Red Shift

Observation of an Unusually Large IR Red-Shift in an Unconventional S–H···S Hydrogen-Bond

2021 ◽  
Vol 12 (4) ◽  
pp. 1228-1235
Author(s):  
Kamal K. Mishra ◽  
Kshetrimayum Borish ◽  
Gulzar Singh ◽  
Prakash Panwaria ◽  
Surajit Metya ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Red Shift

scholarly journals A theoretical study on the red- and blue-shift hydrogen bonds of cis-trans formic acid dimer in excited states

2013 ◽  
Vol 11 (2) ◽  
pp. 171-179 ◽  
Author(s):  
Dapeng Yang ◽  
Yonggang Yang ◽  
Yufang Liu
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Formic Acid ◽  
Excited States ◽  
Density Functional ◽  
Blue Shift ◽  
Red Shift ◽  
Functional Theory ◽  
Photophysical Study ◽  
Tddft Method

AbstractThe excited states of cis-trans formic acid dimer and its monomers have been investigated by time-dependent density functional theory (TDDFT) method. The formation of intermolecular hydrogen bonds O1-H1...O2=C2 and C2-H2...O4=C1 induces bond length lengthening of the groups related to the hydrogen bond, while that of the C2-H2 group is shortened. It is demonstrated that the red-shift hydrogen bond O1-H1...O2=C2 and blue-shift hydrogen bond C2-H2...O4=C1 are both weakened when excited to the S1 state. Moreover, it is found that the groups related to the formation of red-shift hydrogen bond O1-H1...O2=C2 are both strengthened in the S1 state, while the groups related to the blue-shift hydrogen bond C2-H2...O4=C1 are both weakened. This will provide information for the photochemistry and photophysical study of red- and blue-shift hydrogen bond.

scholarly journals The Computational Calculation and Molecular Docking of Aeroplysinin-1 As Antibacterial

2021 ◽  
Vol 9 (2) ◽  
pp. 124-128
Author(s):  
Mirella Fonda Maahury ◽  
Veliyana Londong Allo
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Binding Energy ◽  
Gas Phase ◽  
Geometry Optimization ◽  
Dna Gyrase ◽  
Marine Sponges ◽  
E Coli ◽  
Free Binding Energy ◽  
Computational Calculation

Aeroplysinin-1 is naturally found from marine sponges as an anti-bacterial compound. Computational calculation and molecular docking were performed for aeroplysinin. Aeroplysinin as an inhibitor has optimized in the gas phase using DFT with 6-31G(d) functional. The structure from geometry optimization of aeroplysinin-1is, not in one plane. The interaction of aeroplysinin-1 with two different DNA gyrase from E. Coli and S. Aureus. In this research,aeroplysinin-1 can inhibit the protein with the free binding energy of about -5.7 kcal/mol and -6.35 kcal/mol, respectively, for E. Coli and S. Aureus. The dominant molecular interaction is the hydrogen bond.

scholarly journals MOLECULAR DOCKING OF ANTITRYPANOSOMAL INHIBITORS FROM EUCALYPTUS TERETICORNIS FOR SLEEPING SICKNESS

2019 ◽  
pp. 191-195
Author(s):  
AARTHI RASHMI B ◽  
HARISHCHANDER A ◽  
PRIYANKA K ◽  
VASANTH NIRMAL BOSCO
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Binding Energy ◽  
Sleeping Sickness ◽  
Betulonic Acid ◽  
Eucalyptus Tereticornis ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Interactions ◽  
Bond Interaction ◽  
Pure Compounds

Objectives: This study aims to investigate the antitrypanosomal inhibitors of Eucalyptus tereticornis for sleeping sickness through molecular docking and studies on Absorption distribution metabolism excursion and toxicology (ADMET). Methods: In silico molecular docking in ArgusLab software and ADMET analysis in AdmetSAR software was performed for the antitrypanosomal inhibitors of E. tereticornis for sleeping sickness. Results: Interactions were studied for the ten proteins responsible for sleeping sickness with the 50 antitrypanosomal inhibitors of E. tereticornis. Docking was performed to see the interaction and the best binding energy of compounds with the proteins involved in sleeping sickness. The docking scores were highest for betulonic acid with −15.66 kcal/mol followed by euglobal with −12.24 kcal/mol, B-pinene with −10.313 kcal/mol, A-pinene with −10.3418 kcal/mol, and the least docking score for P-cymene with −10.6045 kcal/mol. Docking results showed that only betulonic acid and euglobal showed that hydrogen bond interaction was as b-pinene, a-pinene, and p-cymene yielded no hydrogen bond interactions so we will be taking the former docking results for further studies. The best docking result was shown by betulonic acid with trypanothione reductase giving binding energy of −15.66 kcal/mol with hydrogen bond interaction of 2.9, so this result was taken for further analysis. Conclusion: The results of the compound extracted from E. tereticornis will become physiological relevant only when (i) the pure compounds of this plant is available in large quantities; (ii) the Eucalyptus is biochemically stabilized to avoid degradation and enhance absorption in the gastrointestinal tract; and (iii) special delivery methods for this drug to reach the areas of treatment. In this work, the efficacy of E. tereticornis to act against trypanosomal protein was initiated and thus further research in this process would help us to take full advantage of the remedial effects of the compounds extracted from this plant.

scholarly journals Pemodelan Farmakofor untuk Identifikasi Inhibitor Heat Shock Proteins-90 (HSP-90)

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Muhammad Arba ◽  
Arfan ◽  
Ayu Trisnawati ◽  
Desi Kurniawati
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Heat Shock ◽  
Binding Energy ◽  
Heat Shock Proteins ◽  
Cancer Cells ◽  
Operating Characteristics ◽  
Hydrogen Bond Donor ◽  
Shock Proteins ◽  
Hsp 90

Heat shock proteins-90 (HSP-90) is a protein that plays an important role in the life cycle of normal and cancer cells for their self protection from thermal stress, oxidative damage, and cell hypoxia. Inhibition of HSP90 is one way to suppress the growth of cancer cells. In this study, pharmacophore modeling and molecular docking were conducted to identify hit compounds as inhibitors of HSP-90. The pharmacophore feature consists of three hydrogen bond acceptors, one hydrogen bond donor and one hydrophobic feature with Area Under Curve of Receiver Operating Characteristics (AUCROC) is 0.5 and the Goodness of Hit (GH) value is 0.752. Screening in the ZINC database generated 1,500 hit compounds, were subjected to molecular docking to determine their binding energy and interactions with HSP-90. The range of binding energy (E) of all hit compounds is -5.68 to -12.24 kcal/mol and there are four best hit compounds namely lig_543, lig_527, lig_1337 and lig_337, when compared to native ligands (PU2, E=-8.25 kkal/mol) based on the binding energy and orientation, which indicate their potential as new HSP-90 inhibitors.     

scholarly journals Theoretical Study on Cyclopeptides as the Nanocarriers for Li+, Na+, K+and F−, Cl−, Br−

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Lili Liu ◽  
Shimou Chen
Keyword(s):  
Hydrogen Bond ◽  
Binding Energy ◽  
Metal Ions ◽  
Theoretical Calculation ◽  
Theoretical Study ◽  
Interaction Process ◽  
Stable Complex ◽  
Electron Population ◽  
Monovalent Ions ◽  
Potential Use

The interaction process between a series of cyclopeptide compounds cyclo(Gly)n  (n=4,6,8)and monovalent ions (Li+, Na+, K+, F−, Cl−, and Br−) was studied using theoretical calculation. The mechanism of combination between the cyclo(Gly)nand ions was discussed through binding energy, Mulliken electron population, and hydrogen bond. It was found that for the same cyclopeptide the binding energy has the order of cyclo(Gly)n–Li+> cyclo(Gly)n–Na+> cyclo(Gly)n–K+and cyclo(Gly)n–F−> cyclo(Gly)n–Br−> cyclo(Gly)n–Cl−. The binding energy manifests the stable complex of cyclo(Gly)nand ions can be formed, and the different energy shows the potential use of cyclo(Gly)nas nanocarriers for metal ions or the extractant for ions separation.

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