Adsorption of 2-Chloroethyl Ethyl Sulfide on Silica: Binding Mechanism and Energy of a Bifunctional Hydrogen-Bond Acceptor at the Gas–Surface Interface

2014 ◽  
Vol 119 (1) ◽  
pp. 365-372 ◽  
Author(s):  
Joshua Abelard ◽  
Amanda R. Wilmsmeyer ◽  
Angela C. Edwards ◽  
Wesley O. Gordon ◽  
Erin M. Durke ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Binding Mechanism ◽  
Hydrogen Bond Acceptor

scholarly journals Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer’s Disease: Computational Refining and Biochemical Evaluation

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1946
Author(s):  
Nitin Chitranshi ◽  
Ashutosh Kumar ◽  
Samran Sheriff ◽  
Veer Gupta ◽  
Angela Godinez ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Hydrogen Bond ◽  
Virtual Screening ◽  
Cathepsin B ◽  
Amyloid Β ◽  
Proteolytic Degradation ◽  
Hydrogen Bond Acceptor ◽  
Starting Point ◽  
The Brain

Amyloid precursor protein (APP), upon proteolytic degradation, forms aggregates of amyloid β (Aβ) and plaques in the brain, which are pathological hallmarks of Alzheimer’s disease (AD). Cathepsin B is a cysteine protease enzyme that catalyzes the proteolytic degradation of APP in the brain. Thus, cathepsin B inhibition is a crucial therapeutic aspect for the discovery of new anti-Alzheimer’s drugs. In this study, we have employed mixed-feature ligand-based virtual screening (LBVS) by integrating pharmacophore mapping, docking, and molecular dynamics to detect small, potent molecules that act as cathepsin B inhibitors. The LBVS model was generated by using hydrophobic (HY), hydrogen bond acceptor (HBA), and hydrogen bond donor (HBD) features, using a dataset of 24 known cathepsin B inhibitors of both natural and synthetic origins. A validated eight-feature pharmacophore hypothesis (Hypo III) was utilized to screen the Maybridge chemical database. The docking score, MM-PBSA, and MM-GBSA methodology was applied to prioritize the lead compounds as virtual screening hits. These compounds share a common amide scaffold, and showed important interactions with Gln23, Cys29, His110, His111, Glu122, His199, and Trp221. The identified inhibitors were further evaluated for cathepsin-B-inhibitory activity. Our study suggests that pyridine, acetamide, and benzohydrazide compounds could be used as a starting point for the development of novel therapeutics.

On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules

1998 ◽  
Vol 279 (5) ◽  
pp. 1123-1136 ◽  
Author(s):  
Ben Luisi ◽  
Modesto Orozco ◽  
Jiri Sponer ◽  
Francisco J Luque ◽  
Zippora Shakked
Keyword(s):  
Hydrogen Bond ◽  
Nitrogen Atom ◽  
Potential Role ◽  
Amino Nitrogen ◽  
Hydrogen Bond Acceptor ◽  
Amino Nitrogen Atom

6,9-Dibromo-2a,10b-diphenyl-2a,5,10,10b-tetrahydro-2H,3H-2,3,4a,10a-tetraazabenzo[g]cyclopenta[cd]azulene-1,4-dione monohydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Supramolecular Structure ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Compound C ◽  
Bifurcated Hydrogen Bond

The title compound, C24H18Br2N4O2·H2O, forms a supramolecular structure via N—H...O, O—H...O and C—H...O hydrogen bonds. In the crystal structure, the water molecule serves as a bifurcated hydrogen-bond acceptor and as a hydrogen-bond donor.

scholarly journals (2,3-Di-2-pyridylpyrazine-κ2 N 2,N 3)diiodidoplatinum(II)

2012 ◽  
Vol 68 (6) ◽  
pp. m834-m834 ◽  
Author(s):  
Kwang Ha
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Least Squares ◽  
Dihedral Angle ◽  
Layer Structure ◽  
Title Complex ◽  
Maximum Deviation ◽  
Hydrogen Bond Acceptor ◽  
Pyrazine Ring ◽  
Square Planar

The PtII ion in the title complex, [PtI2(C14H10N4)], exists in a distorted square-planar environment defined by the two pyridine N atoms of the chelating 2,3-di-2-pyridylpyrazine ligand and two iodide anions. The pyridine rings are inclined to the least-squares plane of the PtI2N2 unit [maximum deviation = 0.070 (3) Å] at 66.1 (2) and 65.9 (2)°; the pyrazine ring is perpendicular to this plane [dihedral angle = 89.7 (2)°]. Two intermolecular C—H...I hydrogen bonds, both involving the same I atom as hydrogen-bond acceptor, generate a layer structure extending parallel to (001). Molecules are stacked in columns along the a axis. Along the b axis, successive molecules stack in opposite directions.

Gaussian Process Regression Models for the Prediction of Hydrogen Bond Acceptor Strengths

2018 ◽  
Vol 38 (4) ◽  
pp. 1800115 ◽  
Author(s):  
Christoph A. Bauer ◽  
Gisbert Schneider ◽  
Andreas H. Göller
Keyword(s):  
Hydrogen Bond ◽  
Gaussian Process ◽  
Regression Models ◽  
Gaussian Process Regression ◽  
Hydrogen Bond Acceptor

Gold setting the “gold standard” among transition metals as a hydrogen bond acceptor – a theoretical investigation

2017 ◽  
Vol 46 (15) ◽  
pp. 4960-4967 ◽  
Author(s):  
Ferdinand Groenewald ◽  
Helgard G. Raubenheimer ◽  
Jan Dillen ◽  
Catharine Esterhuysen
Keyword(s):  
Hydrogen Bond ◽  
Transition Metals ◽  
Theoretical Investigation ◽  
Gold Standard ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Donors

MP2/aug-cc-pVTZ-pp calculations show that the Au(i) atom of dimethylaurate behaves as a hydrogen-bond acceptor to a range of hydrogen-bond donors.

scholarly journals Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Christoph A. Bauer ◽  
Gisbert Schneider ◽  
Andreas H. Göller
Keyword(s):  
Machine Learning ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Training Data ◽  
Free Energies ◽  
Hydrogen Bond Donor ◽  
Chemical Application ◽  
Hydrogen Bond Acceptor ◽  
Donor And Acceptor ◽  
Target Values

Abstract We present machine learning (ML) models for hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) strengths. Quantum chemical (QC) free energies in solution for 1:1 hydrogen-bonded complex formation to the reference molecules 4-fluorophenol and acetone serve as our target values. Our acceptor and donor databases are the largest on record with 4426 and 1036 data points, respectively. After scanning over radial atomic descriptors and ML methods, our final trained HBA and HBD ML models achieve RMSEs of 3.8 kJ mol−1 (acceptors), and 2.3 kJ mol−1 (donors) on experimental test sets, respectively. This performance is comparable with previous models that are trained on experimental hydrogen bonding free energies, indicating that molecular QC data can serve as substitute for experiment. The potential ramifications thereof could lead to a full replacement of wetlab chemistry for HBA/HBD strength determination by QC. As a possible chemical application of our ML models, we highlight our predicted HBA and HBD strengths as possible descriptors in two case studies on trends in intramolecular hydrogen bonding.

scholarly journals DESIGN AND SYNTHESIS OF SOME NEWER IMIDAZOLYL HETEROCYCLES AS POTENT BTK INHIBITORS FOR THE TREATMENT OF RHEUMATOID ARTHRITIS

2017 ◽  
Vol 9 (3) ◽  
pp. 80
Author(s):  
R. Priyadarsini ◽  
Anandhan Menaka
Keyword(s):  
Rheumatoid Arthritis ◽  
Hydrogen Bond ◽  
Molecular Docking ◽  
Tyrosine Kinase ◽  
Pharmacophore Model ◽  
Spectral Studies ◽  
Bruton’S Tyrosine Kinase ◽  
Bruton's Tyrosine Kinase ◽  
Hydrogen Bond Acceptor ◽  
Btk Inhibitors

Objective: The rheumatoid arthritis as a global health problem over the past few decades, Emphasizes the need for discovery of new therapeutic disease modifying anti-rheumatoid Arthritis drugs (DMARD’s). Bruton’s tyrosine kinase (BTK) is a cytoplasmic, non-receptor, tyrosine kinase which is expressed in most of the hematopoietic cells and plays an important role in the development, differentiation and proliferation of B-lineage cells, thus making BTK an efficient therapeutic target for the treatment of rheumatoid arthritis. This prompted us to synthesise a novel series of Imidazolyl Heterocycles as potent BTK (Bruton’s Tyrosine Kinase) inhibitors with alleged Anti-Rheumatoid Arthritis properties. Methods: Newer BTK inhibitors containing one hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD) and three hydrophobic features based on that pharmacophore model for BTK were designed. The designed compounds were sorted by applying ADMET properties, Lipinski rule of five, molecular docking and Novelty prediction to refine the designed ligands. Finally, different five compounds containing Imidazole as the heterocyclic nucleus have been synthesized and characterized by different analytical methods like Chromatographic data, Elemental analysis and Spectral studies by IR, 1H NMR, 13C NMR, GC-MS. Molecular docking studies were performed against BTK using GLIDE 10.2. Results: Several important hydrogen bonds with BTK were revealed, which include the gatekeeper residue Glu475 and Met477 at the hinge region. Conclusion: Overall, this study suggests that the proposed ligands are found to be more effective BTK inhibitor as Anti-Rheumatoid arthritis agents.

scholarly journals Reactivity of cyclohex-1-enylcarboxylic and 2-methylcyclohex-1-enylcarboxylic acids with diazodiphenylmethane in aprotic solvents

2000 ◽  
Vol 65 (12) ◽  
pp. 839-846
Author(s):  
Jasmina Nikolic ◽  
Gordana Uscumlic ◽  
Vera Krstic
Keyword(s):  
Hydrogen Bond ◽  
Rate Constants ◽  
Kinetic Data ◽  
Linear Regression Analysis ◽  
Spectroscopic Method ◽  
Reaction Rates ◽  
Aprotic Solvents ◽  
Experimental Conditions ◽  
Hydrogen Bond Acceptor ◽  
Protic Solvents

Rate constants for the reaction of diazodiphenylmethane with cyclohex-1-enylcarboxylic acid and 2-methylcyclohex-1-enylcarboxylic acid were determined in nine aprotic solvents, as well as in seven protic solvents, at 30?C using the appropriate UV-spectroscopic method. In protic solvents the unsubsituted acid displayed higher reaction rates than the methyl-substituted one. The results in aprotic solvents showed quite the opposite, and the reaction rates were considerably lower. In order to explain the obtained results through solvent effects, reaction rate constants (k) of the examined acids were correlated using the total solvatochromic equation of the form: log k=logk0+s?*+a?+b?, where ?* is the measure of the solvent polarity, a represents the scale of the solvent hydrogen bond donor acidities (HBD) and b represents the scale of the solvent hydrogen bond acceptor basicities (HBA). The correlation of the kinetic data were carried out by means of multiple linear regression analysis and the opposite effects of aprotic solvents, as well as the difference in the influence of protic and aprotic solvents on the reaction of the two examined acids with DDM were discussed. The results presented in this paper for cyclohex-1-enylcarboxylic and 2-methylcyclohex-1-enylcarboxylic acids were compared with the kinetic data for benzoic acid obtained in the same chemical reaction, under the same experimental conditions.

Sign in / Sign up

Export Citation Format

Share Document