scholarly journals Diversifying molecular and topological space via a supramolecular solid-state synthesis: a purely organic mok net sustained by hydrogen bonds

IUCrJ ◽  
2019 ◽  
Vol 6 (6) ◽  
pp. 1032-1039 ◽  
Author(s):  
Shalisa M. Oburn ◽  
Michael A. Sinnwell ◽  
Devin P. Ericson ◽  
Eric W. Reinheimer ◽  
Davide M. Proserpio ◽  
...  

A three-dimensional hydrogen-bonded network based on a rare mok topology has been constructed using an organic molecule synthesized in the solid state. The molecule is obtained using a supramolecular protecting-group strategy that is applied to a solid-state [2+2] photodimerization. The photodimerization affords a novel head-to-head cyclobutane product. The cyclobutane possesses tetrahedrally disposed cis-hydrogen-bond donor (phenolic) and cis-hydrogen-bond acceptor (pyridyl) groups. The product self-assembles in the solid state to form a mok network that exhibits twofold interpenetration. The cyclobutane adopts different conformations to provide combinations of hydrogen-bond donor and acceptor sites to conform to the structural requirements of the mok net.

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Christoph A. Bauer ◽  
Gisbert Schneider ◽  
Andreas H. Göller

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.


Author(s):  
William Levason ◽  
David Pugh ◽  
Gillian Reid

Tribenzylphosphane, PBz3(C21H21P), crystallizes in a notably different unit cell to its Group 15 analogues NBz3and SbBz3. The packing is dominated by face–edge π-interactions which result in infinite columns of molecules parallel to thebaxis; these columns are linked by further face–edge π-interactions into sheets of columns parallel to the [101] direction. Its hydrochloride salt, tribenzylphosphonium hydrogen dichloride–tribenzylphosphane (1/1), lies on a threefold axis within a trigonal crystal system. It exists in the solid state as a hydrogen-bridged dimer with the composition [H(PBz3)2]+[HCl2]−(C42H43P2+·HCl2−). The cation is the first structurally authenticated example of a phosphane acting as a hydrogen-bond acceptor to a phosphonium group and the cations are linked into a three-dimensional network through intermolecular face–edge π-interactions.


2016 ◽  
Vol 72 (8) ◽  
pp. 612-618
Author(s):  
Marisiddaiah Girisha ◽  
Hemmige S. Yathirajan ◽  
Jerry P. Jasinski ◽  
Christopher Glidewell

Pyrazole and isoxazole rings differ only in the notional replacement of a potential hydrogen-bond-donor NH unit in pyrazole by a potential hydrogen-bond-acceptor O atom in isoxazole. It is thus of interest to compare the hydrogen-bonding characteristics of these rings. (4-Fluorophenyl)pyrazole undergoes protonation in the presence of 2,4,6-trinitrophenol to yield the salt 3-(4-fluorophenyl)-1H-pyrazolium 2,4,6-trinitrophenolate, C9H8FN2+·C6H2N3O7−, (I), whereas there is no proton transfer between 4-amino-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzenesulfonamide and 3,5-dinitrobenzoic acid, whose reaction gives the 1:1 cocrystal, C11H13N3O3S·C7H4N2O6, (II). The bond lengths in salt (I) provide evidence for aromatic-type delocalization in the pyrazolium ring and for extensive delocalization of the negative charge into the ring of the trinitrophenolate anion. The O atoms of one of the nitro groups in the trinitrophenolate anion are disordered over two sets of atomic sites having occupancies of 0.571 (6) and 0.429 (6), but all of the other substituents on the carbocyclic rings are fully ordered. The ions in salt (I) are linked by an extensive series of N—H...O hydrogen bonds to form a three-dimensional framework structure, and in cocrystal (II), the molecular components are linked by a combination of O—H...N and N—H...O hydrogen bonds to form complex bilayers. Comparisons are made with some related compounds.


Author(s):  
Ankit Dhaundiyal ◽  
Puja Kumari ◽  
Shasta Kalra

Abstract:: Human Acyl-CoA cholesterol acyltransferase (ACAT) plays an important role in catalysis of reaction which converts cholesterol into cholesteryl esters and long-chain fatty acyl coenzyme A. The inhibition of ACAT has therapeutically potential roles in hypercholestrolemia, atherosclerosis and coronary heart disease. For better understanding of essential chemical features for ACAT inhibition and identifying novel inhibitors, a three-dimensional (3D) chemical-feature-based quantitative QSAR pharmacophore model for available ACAT inhibitors have been developed for first time using Discovery Studio 2.5. The best model (Hypo1) having lowest total cost (84.14), highest cost difference (69.67), highest correlation coefficient (0.94), and lowest RMS (1.15Å), constitutes of one hydrogen bond acceptor, one hydrogen bond donor, two hydrophobic aromatic and one hydrophobic aliphatic feature. Validation of Hypo1 was further done using test set activity prediction, Fischer’s randomization method and decoy data set to check the reliability of the model. The validated Hypo1 was then used as a 3D search query for virtual screening to retrieve potential inhibitors from National cancer institute (NCI), ChemDiv and Specs databases. Finally, ADMET properties of selected compounds were calculated. The result shows the good potential of the newly found ACAT inhibitors. Finally, the two compounds have been obtained as novel hits to design the Novel ACAT inhibitors.


2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu

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.


2011 ◽  
Vol 22 (5) ◽  
pp. 1015-1030 ◽  
Author(s):  
Damanjit Kaur ◽  
Ritika Sharma ◽  
Darpandeep Aulakh

2000 ◽  
Vol 55 (8) ◽  
pp. 738-752 ◽  
Author(s):  
Oliver Moers ◽  
Karna Wijaya ◽  
Ilona Lange ◽  
Armand Blaschette ◽  
Peter G. Jones

As an exercise in crystal engineering, low-temperature X-ray structures were determined for six rationally designed ionic solids of general formula BH+(MeSO2)2N−, where BH+ is 2-aminopyridinium (2, monoclinic, space group P21/c, Z = 4), 2-aminopyrimidinium (3, orthorhombic, Pbca, Z = 8), 2-aminothiazolium (4, orthorhombic, Pbcn, Z = 8), 2-amino-6-methylpyridinium (5, solvated with 0.5 H20, monoclinic, C2/c, Z = 8), 2-amino-1,3,4-thiadiazolium (6, triclinic, P1̄, Z = 2), or 2-amino-4,6-dimethylpyrimidinium (7, orthorhombic. Fdd2, Z = 16). The onium cations in question exhibit a trifunctional hydrogen-bond donor sequence H − N (H*)-C (sp2) − N − H , which is complementary to an O − S (sp3)−N fragment of the anion and simultaneously expected to form a third hydrogen bond via the exocyclic N − H* donor. Consequently, all the crystal packings contain cation-anion pairs assembled by an N − H ∙∙∙ N and an N −H ∙∙∙ O hydrogen bond, these substructures being mutually associated through an N − H* ∙∙∙ O bond. For the robust eight-membered ring synthon within the ion pairs [graph set N2 = R22(8), antidromic], two supramolecular isomers were observed: In 2 and 3, N − H ∙∙∙ N originates from the ring NH donor and N − H ∙∙∙ O from the exocyclic amino group, whereas in 4-7 these connectivities are reversed. The third hydrogen bond, N − H*∙∙∙ O , leads either to chains of ion pairs (generated by a 21 transformation in 2-4 or by a glide plane in 5) or to cyclic dimers of ion pairs (Ci symmetric in 6, C2-symmetric in 7). The overall variety of motifs observed in a small number of structures reflects the limits imposed on the prediction of hydrogen bonding patterns. Owing to the excess of potential acceptors over traditional hydrogen-bond donors, several of the structures display prominent non-classical secondary bonding. Thus, the cyclodimeric units of 6 are associated into strands through short antiparallel O ∙∙∙ S(cation) interactions. In the hemihydrate 5, two independent C-H(cation) ∙∙∙ O bonds generate a second antidromic R22(8) pattern, leading to sheets composed of N − H ∙∙∙ N/O connected catemers; the water molecules are alternately sandwiched between and O - H ∙∙∙ O bonded to the sheets to form bilayers, which are cross-linked by a third C − H (cation ) ∙∙∙ O contact. The roof-shaped cyclodimers occurring in 7 occupy the polar C2 axes parallel to z and build up hollow Car− H ∙∙∙ O bonded tetrahedral lattices; in order to fill their large empty cavities, five translationally equivalent lattices mutually interpenetrate.


Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1940 ◽  
Author(s):  
Yanwen Zhong ◽  
Xuanyi Li ◽  
Hequan Yao ◽  
Kejiang Lin

The programmed cell death ligand protein 1 (PD-L1) is a member of the B7 protein family and consists of 290 amino acid residues. The blockade of the PD-1/PD-L1 immune checkpoint pathway is effective in tumor treatment. Results: Two pharmacophore models were generated based on peptides and small molecules. Hypo 1A consists of one hydrogen bond donor, one hydrogen bond acceptor, two hydrophobic points and one aromatic ring point. Hypo 1B consists of one hydrogen bond donor, three hydrophobic points and one positive ionizable point. Conclusions: The pharmacophore model consisting of a hydrogen bond donor, hydrophobic points and a positive ionizable point may be helpful for designing small-molecule inhibitors targeting PD-L1.


2013 ◽  
Vol 91 (12) ◽  
pp. 1292-1302 ◽  
Author(s):  
Osama Y. Ali ◽  
Elyse Jewer ◽  
Travis D. Fridgen

The infrared absorption spectra of hydrogen-bonded complexes of propylene oxide with either ethanol or 2-fluoroethanol have been recorded in neon matrices. Mixtures of propylene oxide and ethanol or propylene oxide and 2-fluoroethanol vapors were mixed with an excess of neon gas and deposited onto a KBr substrate at 4.2 K. The results indicate that hydrogen-bonded complexes were formed with propylene oxide as the hydrogen bond acceptor and either ethanol or 2-fluoroethanol as the hydrogen bond donors. The features assigned to the O−H stretch were red-shifted by 175 and 193 cm−1 for the ethanol- and 2-fluoroethanol-containing complexes, respectively. The difference in red shifts can be accounted for due to the greater acidity of 2-fluroethanol. Deuterium isotope experiments were conducted to help confirm the assignment of the O–H stretch for the complexes. As well, structures and infrared spectra were calculated using B3LYP/6-311++G(2d,2p) calculations and were used to compare with the experimental spectra. A “scaling equation” rather than a scaling factor was used and is shown to greatly increase the utility of the calculations when comparing with experimental spectra. An examination of the O–H stretching red shifts for many hydrogen-bound complexes reveals a relationship between the shift and the difference between the acidity of the hydrogen bond donor and the basicity of the hydrogen bond acceptor (the enthalpy of proton transfer). Both hydrogen-bonded complexes and proton-bound complexes appear to have a maximum in the reduced frequency value that corresponds to complexes where the hydrogen/proton are equally shared between the two bases.


2018 ◽  
Vol 74 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte

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.


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