Hydrogen-bonding properties of galanthamine: an investigation through crystallographic database observations and computational chemistry

2008 ◽  
Vol 64 (3) ◽  
pp. 338-347 ◽  
Author(s):  
Soleymane Koné ◽  
Nicolas Galland ◽  
El-Hadji Sawaliho Bamba ◽  
Jean-Yves Le Questel
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Data Bank ◽  
Spatial Proximity ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Oh Groups ◽  
Interaction Sites ◽  
Bonding Properties

The hydrogen-bonding properties of galanthamine have been investigated experimentally from a thorough analysis of crystallographic data retrieved from the Protein Data Bank and Cambridge Structural Database databases and theoretically through ab initio [MP2/6-311++G(2d,p)] and density functional theory [MPWB1K/6-31++G(d,p)] calculations. The main hydrogen-bond acceptor (HBA) interaction sites of the molecule are the O atoms and their spatial proximity allows multi-centered hydrogen-bond (HB) motifs. The hydrogen-bond donor (HBD) sites of the molecule are the NH+ and OH groups as well as several CH donors. Among them, the preferred ones are those directly linked to the ammonium nitrogen, followed by aromatic CH and finally the methyl group of the methoxy substituent. All these observations are in fairly good agreement with the computed positions of the molecular electrostatic potential (MEP) minima and maxima of various galanthamine species. The galanthamine HBD and HBA properties, investigated through the MEP analysis, appear sensitive to the degree of neutralization of the ammonium NH+ positive charge.

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 Salicylaldehyde Hydrazones: Buttressing of Outer-Sphere Hydrogen-Bonding and Copper Extraction Properties

2017 ◽  
Vol 70 (5) ◽  
pp. 556 ◽  
Author(s):  
Benjamin D. Roach ◽  
Tai Lin ◽  
Heiko Bauer ◽  
Ross S. Forgan ◽  
Simon Parsons ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Outer Sphere ◽  
Copper Extraction ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Oxime Derivatives ◽  
Intramolecular Hydrogen

Salicylaldehyde hydrazones are weaker copper extractants than their oxime derivatives, which are used in hydrometallurgical processes to recover ~20 % of the world’s copper. Their strength, based on the extraction equilibrium constant Ke, can be increased by nearly three orders of magnitude by incorporating electron-withdrawing or hydrogen-bond acceptor groups (X) ortho to the phenolic OH group of the salicylaldehyde unit. Density functional theory calculations suggest that the effects of the 3-X substituents arise from a combination of their influence on the acidity of the phenol in the pH-dependent equilibrium, Cu2+ + 2Lorg ⇌ [Cu(L–H)2]org + 2H+, and on their ability to ‘buttress’ interligand hydrogen bonding by interacting with the hydrazone N–H donor group. X-ray crystal structure determination and computed structures indicate that in both the solid state and the gas phase, coordinated hydrazone groups are less planar than coordinated oximes and this has an adverse effect on intramolecular hydrogen-bond formation to the neighbouring phenolate oxygen atoms.

Sub-Pharmacophore Generation of JNK3 Inhibitors

2013 ◽  
Vol 444-445 ◽  
pp. 1756-1760 ◽  
Author(s):  
Yan Ling Zhang ◽  
Yuan Ming Wang ◽  
Yan Jiang Qiao
Keyword(s):  
Hydrogen Bond ◽  
Pharmacophore Model ◽  
High Specificity ◽  
Data Bank ◽  
Chinese Herbs ◽  
Mitogen Activated Protein Kinase ◽  
Specific Class ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Appraisal Index

The structure-based pharmacophore (SBP) model is consisted by the complementarity of the chemical features and space of the interaction between the ligand and receptor. The SBP models always have a high specificity which can only represent the specific class of the ligand. To simplify the models, sub-pharmacophore was then proposed in present study, and was expected to have and only have the most important or the common chemical features which play the major role in the interaction of ligand and receptor. Sub-pharmacophore should contain 4-6 features, the higher specificity with more features, and vice versa. The sub-pharmacophore was generated by the random combination of features from the structure-based models. With the MDL Drug Data Report database used as the testing database, a new metric CAI (comprehensive appraisal index), which integrated the metrics of E and A%, was defined and used to determine the best sub-pharmacophore model. C-Jun N-terminal kinase (JNKs) is one of the mitogen-activated protein kinase family, and widely involved in immune response and inflammatory response, and other pathological processes. JNK3 is mainly distributed in the brain and nervous system. In present study, twenty-five initial SBP models of JNK3 inhibitors were directly constructed from the Protein Data Bank (PDB) complexes by the LigandScout software. Then, 1018 sub-pharmacophore models were obtained from the 25 initial models. Finally, the best sub-pharmacophore was determined which was simplified from the initial model generated from the 3FI2 complex, and included four features: one hydrogen bond donor, one hydrogen bond acceptor, and two hydrophobic groups. The metrics of E, A% and CAI value of the best sub-pharmacophore model are 17.47, 31.15 and 5.44, respectively. The potential JNK3 inhibitors were then identified from Chinese herbs with the best sub-pharmacophore model, and 286 compounds were obtained.

scholarly journals Prediction of solvation properties of low transition temperature mixtures (LTTMs) using COSMO-RS and NMR approach

2021 ◽  
Vol 1195 (1) ◽  
pp. 012006
Author(s):  
N R Yusuf ◽  
S Yusup ◽  
C L Yiin ◽  
P J Ratri ◽  
A A Halim ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Transition Temperature ◽  
Environmental Science ◽  
Choline Chloride ◽  
Monosodium Glutamate ◽  
Experimental Studies ◽  
Green Solvent ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor

Abstract The concept of sustainable and green solvent has always highlighted in the field of energy and environmental science. The synthesis and application of natural-based Low Transition Temperature Mixture (LTTM) as a novel and green solvent for the lignocellulose biomass pre-treatment such as delignification of Oil-Palm Empty Fruit Bunch (EFB) have been greatly emphasized. In this present work, the investigation of LTTM efficiency as green solvent in delignification process was conducted using both theoretical and experimental studies. Initially, screening of solvation properties of different types of hydrogen bond acceptor (HBA) and predicted hydrogen bond donor (HBD) for synthesis of LTTMs was conducted using conductor-like screening model (COSMO-RS) software and formation of hydrogen bonding was evidenced using NMR spectroscopy analysis. Three types of HBA namely sucrose, choline chloride and monosodium glutamate were mixed with malic acids as HBD and their charge density distribution on the surface was determined through sigma profile (σ). The COSMO-RS results determined the σ profile of pure component malic acid to be 11.42, sucrose to be 25.37 and the total value of σ profile for mixtures is 14.19 as the best combination of LTTM composition compared to LTTM from choline chloride and monosodium glutamate (MSG). The reliability of the COSMO-RS predictions data was correlated with Nuclear Magnetic Resonance (NMR) analysis through determination of peaks with chemical shifts hydrogen bonding that suggested existence of potential interaction between malic acids and sucrose has occurred.

42 salt forms of tyramine: structural comparison and the occurrence of hydrate formation

2012 ◽  
Vol 68 (4) ◽  
pp. 453-464 ◽  
Author(s):  
Naomi E. B. Briggs ◽  
Alan R. Kennedy ◽  
Catriona A. Morrison
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Single Crystal ◽  
Hydrate Formation ◽  
Structural Comparison ◽  
Hydrogen Bond Donor ◽  
Single Crystal Diffraction ◽  
Hydrogen Bond Acceptor ◽  
First Time ◽  
Salt Forms

The single-crystal diffraction structures of 38 salt forms of the base tyramine (4-hydroxyphenethylamine) are reported for the first time. Together with literature examples, these structures are discussed with respect to cation conformation, cation packing, hydrogen bonding and hydrate formation. It is found that isostructural cation packing can occur even with structurally different anions, with different hydration states and with different hydrogen bonding. Hydrate formation is found to be more likely both (i) when there is an increase in the total number of potential hydrogen bond acceptor and donor atoms; and (ii) when the ratio of potential hydrogen bond donor to acceptor atoms is low.

scholarly journals A Theoretical and Experimental Study on Hydrogen-bonding Interactions between 4H-1,2,4-triazole-3,5-diamine and DMSO/water

2020 ◽  
Vol 39 (1) ◽  
pp. 65
Author(s):  
Mustafa Tuğfan Bilkan
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Energy Difference ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Hydrogen Bond Acceptor ◽  
Functional Theory ◽  
Hydrogen Bonding Interactions ◽  
Aqueous Complexes

In this paper, 4TZDA-DMSO/water complexes formed by hydrogen bonding interactions were investigated by a combined experimental and computational approach. Two conformations of 4TZDA molecule were considered. Seven hydrogen-bonded 4TZDA-DMSO/H2O complexes were characterized in terms of geometries, energies and vibrational frequencies. The optimizations and calculations were performed for the complexes by Density Functional Theory. In the experimental part, the DMSO/H2O solutions of 4TZDA were prepared and infrared spectra of the solutions were recorded. After the solvation process, significant shifts in the existing bands and new band rising were observed in the experimental spectra of 4TZDA. Following results are found from this study: 1) 4TZDA (I) is more stable than 4TZDA (II). 2) Seven 4TZDA-DMSO and 4TZDA-H2O complexes are investigated and it is seen that all nitrogen atoms of 4TZDA are hydrogen bond acceptor and all hydrogen atoms are hydrogen bond donors. 3) Aqueous complexes of 4TZDA are found to form stronger hydrogen bonds compared to DMSO complexes. 4) It is determined that the most stable structures are intermolecular interactions of lpO⋯H-N and lpN⋯H-O type for the complexes. For these interactions, h-bond lengths are calculated as 1.78 and 1.90 Å and interaction energies are -7.10 kJ/mol for 4TZDA-DMSO and -50.5 kJ/mol for 4TZDA-H2O. Because of this energy difference in the complexes, it can be said 4TZDA forms more stable complexes with water molecules compared to DMSO molecules and with this property, it is an ideal molecule for pharmacological purposes.

Defining the hydrogen bond: An account (IUPAC Technical Report)

2011 ◽  
Vol 83 (8) ◽  
pp. 1619-1636 ◽  
Author(s):  
Elangannan Arunan ◽  
Gautam R. Desiraju ◽  
Roger A. Klein ◽  
Joanna Sadlej ◽  
Steve Scheiner ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Bond Formation ◽  
Blue Shift ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Technical Report ◽  
Definition Of ◽  
Covalent Nature

The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.

Statistical Analysis of Noncovalent Interactions of Anion Groups in Crystal Structures. III. Metal Complexes of Thiocyanate and their Hydrogen-Donor Accepting Function

1997 ◽  
Vol 53 (6) ◽  
pp. 904-915 ◽  
Author(s):  
L. Tchertanov ◽  
C. Pascard
Keyword(s):  
Hydrogen Bonding ◽  
Metal Complexes ◽  
Noncovalent Interactions ◽  
Data Bank ◽  
Hydrogen Bond Acceptor ◽  
Acceptor Atom ◽  
Anionic Charge ◽  
Bonding Properties ◽  
Structural Database ◽  
Good Agreement

The bidentate function of the thiocyanate anion was studied using the Cambridge Structural Database System. Complexing properties (metal–thiocyanate interactions) with respect to metal cations were analysed. Two main classes were distinguished: (a) alkali and alkaline earth metals, and (b) metals of Zn and Cu groups and transition metals (group VIII). Good correlations were found between the nature of the metal (radius, oxidation state and charge) and its position relative to the thiocyanate unit. Hydrogen-bond acceptor properties of discrete and complexed SCN units were compared. The extraordinarily active hydrogen-bonding behaviour allows this anion to act as a powerful bridge between different molecular fragments. In metal complexes the cation provokes a redistribution of anionic charge in SCN and the distribution of electron density, in turn, controls the hydrogen-bonding properties of the terminal acceptor atom. Binding properties of thiocyanate in biological systems were illustrated using the Brookhaven Protein Data Bank. A comparison of anion binding in small-molecule structures and in macromolecular structures shows good agreement.

Removal of thiophene from model oil by polyethylene glycol via forming deep eutectic solvents

2021 ◽  
Vol 10 (1) ◽  
pp. 893-901
Author(s):  
Yingna Cui ◽  
Wenqing Xu ◽  
Yingping Jia ◽  
Shenmin Li ◽  
Jingmei Yin
Keyword(s):  
Hydrogen Bond ◽  
Polyethylene Glycol ◽  
Density Functional ◽  
Extraction Efficiency ◽  
Kinetic Constant ◽  
Deep Eutectic Solvents ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Peg 400 ◽  
Model Oil

Abstract The removal of organosulfurs from liquid fuel has become a hot issue due to the serious environmental pollution by sulfur oxide gases. In this study, the removal of thiophene from model oil was carried out using polyethylene glycol (PEG). It was found that deep eutectic solvents formed by PEG as hydrogen bond donor and thiophene as hydrogen bond acceptor could efficiently separate thiophene from model oil. The influencing parameters in this process were discussed, such as extraction time, temperature, mass ratio of PEG to oil, and initial sulfur concentration. The results showed that the single extraction efficiency of PEG-200 and PEG-400 could reach up to 89.0% and 97.1% in optimal conditions, respectively. The extraction efficiency as high as 95.7% and 99.9% could be achieved after three extraction cycles. The kinetic equation of the extractive desulfurization was studied by in situ infrared (IR), and the kinetic constant k 1 of PEG-400 and PEG-200 was compared (k 1(PEG-400) > k 1(PEG-200)). The desulfurization mechanism of PEG was studied by IR, 1H NMR spectra, and density functional theory (DFT). The results showed that the hydrogen bond formed between hydroxyl hydrogen in PEG and sulfur atom in thiophene accounted for the high extraction efficiency.

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.

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