Selective encapsulation and extraction of hydrogenphosphate by a hydrogen bond donor tripodal receptor

CrystEngComm ◽  
2020 ◽  
Vol 22 (37) ◽  
pp. 6152-6160
Author(s):  
Sandeep Kumar Dey ◽  
Archana ◽  
Sybil Pereira ◽  
Sarvesh S. Harmalkar ◽  
Shashank N. Mhaldar ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Hydrogen Bond Donor ◽  
Tripodal Receptor ◽  
Multiple Hydrogen Bonds

Intramolecular N–H⋯OC hydrogen bonding between the inner amide groups dictates the receptor–anion complementarity in a tripodal receptor towards selective encapsulation of hydrogenphosphate in the outer urea cavity by multiple hydrogen bonds.

scholarly journals Hydrogen Bonding Guests Direct the Packing of a Small Organic Cage Molecule

2019 ◽  
Author(s):  
Thomas Anglim Lagones ◽  
Stephanie Boer ◽  
Nicholas White
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Hydrogen Bond Donor ◽  
Crystalline Phases ◽  
Cage Molecule

<div> <p>A small organic cage molecule (<b>1</b>) containing six nitrile groups was crystallized in the presence of a number of guests with hydrogen bond donor groups, and from different solvents. In total, eight crystal structures of <b>1</b> were obtained, six of which are guest-free and two of which are co-crystals. When the guest was resorcinol or pyrogallol co-crystals did not form, but the presence of the guests directed formation of new crystalline phases that were not observed when the cage was crystallized alone. When the guest was hydroquinone or diaminobenzene, it was possible to isolate co-crystals where the guest hydrogen bonds to some of the nitrile groups of the cage. </p> </div> <br>

scholarly journals Hydrogen Bonding Guests Direct the Packing of a Small Organic Cage Molecule

2019 ◽  
Author(s):  
Thomas Anglim Lagones ◽  
Stephanie Boer ◽  
Nicholas White
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Hydrogen Bond Donor ◽  
Crystalline Phases ◽  
Cage Molecule

<div> <p>A small organic cage molecule (<b>1</b>) containing six nitrile groups was crystallized in the presence of a number of guests with hydrogen bond donor groups, and from different solvents. In total, eight crystal structures of <b>1</b> were obtained, six of which are guest-free and two of which are co-crystals. When the guest was resorcinol or pyrogallol co-crystals did not form, but the presence of the guests directed formation of new crystalline phases that were not observed when the cage was crystallized alone. When the guest was hydroquinone or diaminobenzene, it was possible to isolate co-crystals where the guest hydrogen bonds to some of the nitrile groups of the cage. </p> </div> <br>

scholarly journals Reconciling solvent effects on rotamer populations in carbohydrates — A joint MD and NMR analysis

2006 ◽  
Vol 84 (4) ◽  
pp. 569-579 ◽  
Author(s):  
Jorge Gonzalez-Outeiriño ◽  
Karl N Kirschner ◽  
Smita Thobhani ◽  
Robert J Woods
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Solvent Polarity ◽  
Local Environment ◽  
Dynamics Simulation ◽  
Hydrogen Bond Donor ◽  
Hydroxymethyl Group ◽  
Internal Hydrogen

The rotational preferences of the hydroxymethyl group in pyranosides is known to depend on the local environment, whether in solid, solution, or gas phase. By combining molecular dynamics (MD) simulations with NMR spectroscopy the rotational preferences for the ω angle in methyl 2,3-di-O-methyl-α-D-glucopyranoside (3) and methyl 2,3-di-O-methyl-α-D-galactopyranoside (6) in a variety of solvents, with polarities ranging from 80 to 2.3 D have been determined. The effects of solvent polarity on intramolecular hydrogen bonding have been identified and quantified. In water, the internal hydrogen bonding networks are disrupted by competition with hydrogen bonds to the solvent. When the internal hydrogen bonds are differentially disrupted, the rotamer populations associated with the ω angle may be altered. In the case of 3 in water, the preferential disruption of the interaction between HO6 and O4 destabilizes the tg rotamer, leading to the observed preference for gauche rotamers. Without the hydrogen bond enhancement offered by a low polarity environment, both 3 and 6 display rotamer populations that are consistent with expectations based on the minimization of repulsive intramolecular oxygen–oxygen interactions. In a low polarity environment, HO6 prefers to interact with O4, however, in water these interactions are markedly weakened, indicating that HO6 acts as a hydrogen bond donor to water.Key words: carbohydrate, rotamer, molecular dynamics simulation, MD, NMR.

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 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.

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

scholarly journals Crystal structures of butyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate and 2-methoxyethyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate

2019 ◽  
Vol 75 (6) ◽  
pp. 880-887 ◽  
Author(s):  
Rosita Diana ◽  
Angela Tuzi ◽  
Barbara Panunzi ◽  
Antonio Carella ◽  
Ugo Caruso
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Molecular Structures ◽  
Antitumoral Activity ◽  
Space Group ◽  
One Dimensional ◽  
Axis Direction ◽  
Hydrogen Bonding Pattern ◽  
Butyl Group

The title benzofuran derivatives 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate (BF1), C19H18N2O6, and 2-methoxyethyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate (BF2), C18H16N2O7, recently attracted attention because of their promising antitumoral activity. BF1 crystallizes in the space group P\overline{1}. BF2 in the space group P21/c. The nitrophenyl group is inclined to benzofuran moiety with a dihedral angle between their mean planes of 69.2 (2)° in BF1 and 60.20 (6)° in BF2. A common feature in the molecular structures of BF1 and BF2 is the intramolecular N—H...Ocarbonyl hydrogen bond. In the crystal of BF1, the molecules are linked head-to-tail into a one-dimensional hydrogen-bonding pattern along the a-axis direction. In BF2, pairs of head-to-tail hydrogen-bonded chains of molecules along the b-axis direction are linked by O—H...Omethoxy hydrogen bonds. In BF1, the butyl group is disordered over two orientations with occupancies of 0.557 (13) and 0.443 (13).

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

scholarly journals New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

2016 ◽  
Vol 12 ◽  
pp. 2834-2848 ◽  
Author(s):  
Pavel Nagorny ◽  
Zhankui Sun
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Recent Progress ◽  
Halogen Bonds ◽  
Hydrogen Bond Donor ◽  
New Approaches ◽  
Substrate Activation ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Hydrogen Bond Donors

Hydrogen bond donor catalysis represents a rapidly growing subfield of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new organic catalysts for electrophile activation through the formation of C–H hydrogen bonds and C–X halogen bonds.

Secondary Interactions in Gold(I) Complexes with Thione Ligands, 3. Three Ionic Dimesylamides [1, 2]

2004 ◽  
Vol 59 (11-12) ◽  
pp. 1429-1437 ◽  
Author(s):  
Friedrichsa Friedrichsa ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Layer Structure ◽  
Chain Structure ◽  
Hydrogen Bond Donor ◽  
Weak Hydrogen Bonds ◽  
Ribbon Structure ◽  
A Chain ◽  
Aurophilic Interactions ◽  
Short Contacts

Three structures of the form bis(thione)gold(I) di(methanesulfonyl)amide [thione = imidazolidine- 2-thione, 1; 1-methyl-imidazolidine-2-thione, 2; thiazolidine-2-thione, 3] were determined; all crystallize with one formula unit in the asymmetric unit. Each N-H hydrogen bond donor forms one classical two-centre hydrogen bond with an anion acceptor. Compound 1 thereby forms a complex layer structure with a layer thickness of 10.17 Å ; the packing may be analysed in terms of thinner subunit layers consisting of interlinked, hydrogen-bonded chains and rings. Compound 2 forms a chain structure consisting of a series of “hairpin bends”, a common feature in the gold complexes of 1-alkyl-imidazolidine-2-thiones. Compound 3 forms a corrugated ribbon structure in which the central region consists of parallel S-Au-S axes linked by aurophilic interactions; the anions exercise a “clamping” function by forming hydrogen bonds at the periphery of the ribbons. Further short contacts can be classed as weak hydrogen bonds C-H ··· X, with X = N, O, S or Au.

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