Reversible thermo-sensitivity induced from varying the hydrogen bonding between the side residues of rationally designed polypeptides

2015 ◽  
Vol 51 (50) ◽  
pp. 10174-10177 ◽  
Author(s):  
Hong Liu ◽  
Yan Xiao ◽  
Heng Xu ◽  
Yebin Guan ◽  
Jun Zhang ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bond Acceptor ◽  
Thermo Sensitivity

Balancing the ratio of the hydrogen bond acceptor/donor in the side residues of poly(l-glutamate) derivatives endows the copolypeptide obtained with reversible thermosensitivity.

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.

Sulfur as hydrogen-bond acceptor in cocrystals of 2-thio-modified thymine

2018 ◽  
Vol 74 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Engineering ◽  
Rational Design ◽  
Three Dimensional ◽  
Good Reliability ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bonding Interactions ◽  
Hydrogen Bonding Site ◽  
Hydrogen Bonded

Doubly and triply hydrogen-bonded supramolecular synthons are of particular interest for the rational design of crystal and cocrystal structures in crystal engineering since they show a high robustness due to their high stability and good reliability. The compound 5-methyl-2-thiouracil (2-thiothymine) contains an ADA hydrogen-bonding site (A = acceptor and D = donor) if the S atom is considered as an acceptor. We report herein the results of cocrystallization experiments with the coformers 2,4-diaminopyrimidine, 2,4-diamino-6-phenyl-1,3,5-triazine, 6-amino-3H-isocytosine and melamine, which contain complementary DAD hydrogen-bonding sites and, therefore, should be capable of forming a mixed ADA–DAD N—H...S/N—H...N/N—H...O synthon (denoted synthon 3s N·S;N·N;N·O), consisting of three different hydrogen bonds with 5-methyl-2-thiouracil. The experiments yielded one cocrystal and five solvated cocrystals, namely 5-methyl-2-thiouracil–2,4-diaminopyrimidine (1/2), C5H6N2OS·2C4H6N4, (I), 5-methyl-2-thiouracil–2,4-diaminopyrimidine–N,N-dimethylformamide (2/2/1), 2C5H6N2OS·2C4H6N4·C3H7NO, (II), 5-methyl-2-thiouracil–2,4-diamino-6-phenyl-1,3,5-triazine–N,N-dimethylformamide (2/2/1), 2C5H6N2OS·2C9H9N5·C3H7NO, (III), 5-methyl-2-thiouracil–6-amino-3H-isocytosine–N,N-dimethylformamide (2/2/1), (IV), 2C5H6N2OS·2C4H6N4O·C3H7NO, (IV), 5-methyl-2-thiouracil–6-amino-3H-isocytosine–N,N-dimethylacetamide (2/2/1), 2C5H6N2OS·2C4H6N4O·C4H9NO, (V), and 5-methyl-2-thiouracil–melamine (3/2), 3C5H6N2OS·2C3H6N6, (VI). Synthon 3s N·S;N·N;N·O was formed in three structures in which two-dimensional hydrogen-bonded networks are observed, while doubly hydrogen-bonded interactions were formed instead in the remaining three cocrystals whereby three-dimensional networks are preferred. As desired, the S atoms are involved in hydrogen-bonding interactions in all six structures, thus illustrating the ability of sulfur to act as a hydrogen-bond acceptor and, therefore, its value for application in crystal engineering.

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.

Intramolecular OH⋅⋅⋅FC Hydrogen Bonding in Fluorinated Carbohydrates: CHF is a Better Hydrogen Bond Acceptor than CF2

2013 ◽  
Vol 125 (40) ◽  
pp. 10718-10722 ◽  
Author(s):  
Guy T. Giuffredi ◽  
Véronique Gouverneur ◽  
Bruno Bernet
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bond Acceptor

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.

6-Propyl-2-thiouracilversus6-methoxymethyl-2-thiouracil: enhancing the hydrogen-bonded synthon motif by replacement of a methylene group with an O atom

2016 ◽  
Vol 72 (8) ◽  
pp. 634-646 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Ernst Egert ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Engineering ◽  
Rational Design ◽  
Antithyroid Drug ◽  
Chemical Properties ◽  
Structural Similarity ◽  
Molecular Solids ◽  
Hydrogen Bond Acceptor ◽  
Methylene Group

The understanding of intermolecular interactions is a key objective of crystal engineering in order to exploit the derived knowledge for the rational design of new molecular solids with tailored physical and chemical properties. The tools and theories of crystal engineering are indispensable for the rational design of (pharmaceutical) cocrystals. The results of cocrystallization experiments of the antithyroid drug 6-propyl-2-thiouracil (PTU) with 2,4-diaminopyrimidine (DAPY), and of 6-methoxymethyl-2-thiouracil (MOMTU) with DAPY and 2,4,6-triaminopyrimidine (TAPY), respectively, are reported. PTU and MOMTU show a high structural similarity and differ only in the replacement of a methylene group (–CH2–) with an O atom in the side chain, thus introducing an additional hydrogen-bond acceptor in MOMTU. Both molecules contain anADAhydrogen-bonding site (A= acceptor andD= donor), while the coformers DAPY and TAPY both show complementaryDADsites and therefore should be capable of forming a mixedADA/DADsynthon with each other,i.e. N—H...O, N—H...N and N—H...S hydrogen bonds. The experiments yielded one solvated cocrystal salt of PTU with DAPY, four different solvates of MOMTU, one ionic cocrystal of MOMTU with DAPY and one cocrystal salt of MOMTU with TAPY, namely 2,4-diaminopyrimidinium 6-propyl-2-thiouracilate–2,4-diaminopyrimidine–N,N-dimethylacetamide–water (1/1/1/1) (the systematic name for 6-propyl-2-thiouracilate is 6-oxo-4-propyl-2-sulfanylidene-1,2,3,6-tetrahydropyrimidin-1-ide), C4H7N4+·C7H9N2OS−·C4H6N4·C4H9NO·H2O, (I), 6-methoxymethyl-2-thiouracil–N,N-dimethylformamide (1/1), C6H8N2O2S·C3H7NO, (II), 6-methoxymethyl-2-thiouracil–N,N-dimethylacetamide (1/1), C6H8N2O2S·C4H9NO, (III), 6-methoxymethyl-2-thiouracil–dimethyl sulfoxide (1/1), C6H8N2O2S·C2H6OS, (IV), 6-methoxymethyl-2-thiouracil–1-methylpyrrolidin-2-one (1/1), C6H8N2O2S·C5H9NO, (V), 2,4-diaminopyrimidinium 6-methoxymethyl-2-thiouracilate (the systematic name for 6-methoxymethyl-2-thiouracilate is 4-methoxymethyl-6-oxo-2-sulfanylidene-1,2,3,6-tetrahydropyrimidin-1-ide), C4H7N4+·C6H7N2O2S−, (VI), and 2,4,6-triaminopyrimidinium 6-methoxymethyl-2-thiouracilate–6-methoxymethyl-2-thiouracil (1/1), C4H8N5+·C6H7N2O2S−·C6H8N2O2S, (VII). Whereas in (I) only anAA/DDhydrogen-bonding interaction was formed, the structures of (VI) and (VII) both display the desiredADA/DADsynthon. Conformational studies on the side chains of PTU and MOMTU also revealed a significant deviation for cocrystals (VI) and (VII), leading to the desired enhancement of the hydrogen-bond pattern within the crystal.

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.

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