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>

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.

N—H...S and N—H...O hydrogen bonds: `pure' and `mixed'R22(8) patterns in the crystal structures of eight 2-thiouracil derivatives

2014 ◽  
Vol 70 (2) ◽  
pp. 241-249 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Ernst Egert
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Dimethyl Sulfoxide ◽  
Crystal Structures ◽  
Thiouracil Derivatives ◽  
Bonding Patterns

The preferred hydrogen-bonding patterns in the crystal structures of 5-propyl-2-thiouracil, C7H10N2OS, (I), 5-methoxy-2-thiouracil, C5H6N2O2S, (II), 5-methoxy-2-thiouracil–N,N-dimethylacetamide (1/1), C5H6N2O2S·C4H9NO, (IIa), 5,6-dimethyl-2-thiouracil, C6H8N2OS, (III), 5,6-dimethyl-2-thiouracil–1-methylpyrrolidin-2-one (1/1), C6H8N2OS·C5H9NO, (IIIa), 5,6-dimethyl-2-thiouracil–N,N-dimethylformamide (2/1), 2C6H8N2OS·C3H7NO, (IIIb), 5,6-dimethyl-2-thiouracil–N,N-dimethylacetamide (2/1), 2C6H8N2OS·C4H9NO, (IIIc), and 5,6-dimethyl-2-thiouracil–dimethyl sulfoxide (2/1), 2C6H8N2OS·C2H6OS, (IIId), were analysed. All eight structures containR22(8) patterns. In (II), (IIa), (III) and (IIIa), they are formed by two N—H...S hydrogen bonds, and in (I) by alternating pairs of N—H...S and N—H...O hydrogen bonds. In contrast, the structures of (IIIb), (IIIc) and (IIId) contain `mixed'R22(8) patterns with one N—H...S and one N—H...O hydrogen bond, as well asR22(8) motifs with two N—H...O hydrogen bonds.

A Comparison of the Enamino Carbonyl Conjugation Efficiency for Hydrogen Bonding Formation in Pyridone and Dihydropyridone Systems

2000 ◽  
Vol 55 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Teresa Borowiak ◽  
Irena Wolska ◽  
Artur Korzański ◽  
Wolfgang Milius ◽  
Wolfgang Schnick ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Steric Hindrance ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Asymmetric Unit ◽  
Intermolecular Hydrogen Bonds

The crystal structures of two compounds containing enaminone heterodiene systems and forming intermolecular hydrogen bonds N-H·O are reported: 1) 3-ethoxycarbonyl-2-methyl-4-pyridone (hereafter ETPY) and 2) 3-ethoxycarbonyl-2-phenyl-6-methoxycarbonyl-5,6-di-hydro-4-pyridone (hereafter EPPY). The crystal packing is controlled by intermolecular hydro­ gen bonds N-H·O = C connecting the heteroconjugated enaminone groups in infinite chains. In ETPY crystals the intermolecular hydrogen bond involves the heterodienic pathway with the highest π-delocalization that is effective for a very short N·O distance of 2.701(9) Å (average from two molecules in the asymmetric unit). Probably due to the steric hindrance, the hydrogen bond in EPPY is formed following the heterodienic pathway that involves the ester C = O group, although π-delocalization along this pathway is less than that along the pyridone-part pathway resulting in a longer N·O distance of 2.886(3) Å

Extensive analysis of N—H...O hydrogen bonding in four classes of phosphorus compounds: a combined experimental and database study

2017 ◽  
Vol 73 (3) ◽  
pp. 287-297 ◽  
Author(s):  
Farahnaz Hamzehee ◽  
Mehrdad Pourayoubi ◽  
Marek Nečas ◽  
Duane Choquesillo-Lazarte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Neutral Hydrogen ◽  
The Other ◽  
Phosphorus Compounds ◽  
Database Study ◽  
Extensive Analysis ◽  
Structural Database

The N—H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N′-(p-tolyl)phosphonic diamide, C20H21N2OP or (C6H5)P(O)(NHCH2C6H5)(NHC6H4-p-CH3), (I), diphenylphosphinic 1-methylpropylamide, C16H20NOP or (C6H5)2P(O)[NHCH(CH3)(C2H5)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C8H12N+·C14H15NO2P− or [S-(C6H5)CH(CH3)NH3][(C6H5)P(O){S-NHCH(CH3)(C6H5)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C8H12N+·C12H10O2P− or [4-CH3-C6H4CH2NH3][(C6H5)2P(O)(O)], (IV). This article focuses on the N—H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)2, 102 (C)2P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)2P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)2 segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)2P(O)(O) structures were particularly noticeable for a high number of cation–anion compounds. The overall tendencies of N...O distances in neutral and cation–anion compounds were compared. The N—H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.

Structure of the adducts methylthiourea: 1,4-dioxane (2:1) and 1,1-dimethylthiourea: morpholine (1:1)

2016 ◽  
Vol 71 (8) ◽  
pp. 905-907 ◽  
Author(s):  
Christina Taouss ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Crystal Structures ◽  
Sulfur Atom ◽  
Layer Structure ◽  
Blocking Effect ◽  
Methyl Groups ◽  
Inversion Symmetry

AbstractThe adducts methylthiourea:1,4-dioxane (2:1) (1) and 1,1-dimethylthiourea:morpholine (1:1) (2) were prepared and their crystal structures determined. In 1, hydrogen bonding involving the methylthiourea molecules leads to the formation of ${\rm{R}}_2^2(8)$ rings and thence to molecular ribbons parallel to [110]. The dioxane molecules accept hydrogen bonds from the remaining NH groups, and their inversion symmetry means that they connect adjacent methylthiourea ribbons, forming a layer structure parallel to (11̅1). In the packing of 2, dimethylthiourea dimers cannot link to each other because of the blocking effect of their methyl groups, but instead are linked indirectly via morpholine molecules, the NH groups of which are simultaneously hydrogen bond acceptors from the remaining NH function of dimethylthiourea and donors towards the sulfur atom of a neighbouring dimer. The overall effect is to form broad ribbons parallel to the a axis, with the morpholine molecules occupying the peripheral positions. The morpholine oxygen atom of 2 is not involved in classical hydrogen bonds.

Interplay between steric and electronic factors in determining the strength of intramolecular N—H...O resonance-assisted hydrogen bonds in β-enaminones

2006 ◽  
Vol 62 (6) ◽  
pp. 1112-1120 ◽  
Author(s):  
Valerio Bertolasi ◽  
Loretta Pretto ◽  
Valeria Ferretti ◽  
Paola Gilli ◽  
Gastone Gilli
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Features ◽  
Membered Ring ◽  
Resonance Assisted Hydrogen Bond ◽  
Electronic Resonance ◽  
Hydrogen Bonded

The crystal structures of five β-enaminones are reported: (2Z)-3-(benzylamino)-1,3-diphenyl-prop-2-en-1-one, (2Z)-3-(benzylamino)-3-(2-hydroxyphenyl)-1-phenyl-prop-2-en-1-one, (2Z)-3-(benzylamino)-3-(4-methoxyphenyl)-1-(3-nitrophenyl)-prop-2-en-1-one, 2-{1-[(4-methoxyphenyl)amino]ethylidene}cyclohexene-1,3-dione and 2-{1-[(3-methoxyphenyl)amino]ethylidene}cyclohexene-1,3-dione. The structures were analysed and compared with those of similar compounds in order to establish which factors determine the range (2.53–2.72 Å) of N...O hydrogen-bond distances in intramolecularly hydrogen-bonded β-enaminones. It has been shown that, beyond electronic resonance-assisted hydrogen-bond effects modulated by substituents, the necessary requirements to produce very short N—H...O hydrogen bonding are steric intramolecular repulsions, including the embedding of an enaminonic C—C or C—N bond in an aliphatic six-membered ring. By considering the structural features it is possible to expect the strength of N—H...O hydrogen bonds adopted by specific β-enaminones.

Statistical analysis of noncovalent interactions of anion groups in crystal structures. I. Hydrogen bonding of sulfate anions

1996 ◽  
Vol 52 (4) ◽  
pp. 677-684 ◽  
Author(s):  
L. Chertanova ◽  
C. Pascard
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Small Molecules ◽  
Crystal Structures ◽  
Noncovalent Interactions ◽  
Data Set ◽  
Hydrogen Bond Acceptor ◽  
Covalently Bonded ◽  
Different Types

The hydrogen-bond acceptor characteristics of sulfate dianions are analyzed in crystal structures of small molecules. For 85 anions, neither coordinated to metal ions nor covalently bonded, 697 hydrogen bonds are faund. Of these, 266 (38%) are the O...H—O type and 431 (62%) are the O...H—N type, proportions that correspond well to the stoichiometry of the compounds studied and indicate no preference for a particular donor. The analysis of the data set, after classifying the hydrogen bonds according to the different types of donors, shows that O...H—O bonds are more linear than O...H—N. The anion oxygen–acceptor function is characterized by multiple hydrogen bonding. Only in 56 cases does a sulfate oxygen participate in a single hydrogen bond. In most cases every sulfate oxygen is coordinated by two (187 cases) or three (89 cases) hydrogen bonds. For three H donors, the preferred coordination geometry of the sulfate oxygen is pyramidal. The most frequent coordination around a sulfate dianion is with eight to ten H donors. Thus, sulfate dianions can play a significant cohesive role in molecular aggregation.

scholarly journals Crystal structures and supramolecular features of 9,9-dimethyl-3,7-diazabicyclo[3.3.1]nonane-2,4,6,8-tetraone, 3,7-diazaspiro[bicyclo[3.3.1]nonane-9,1′-cyclopentane]-2,4,6,8-tetraone and 9-methyl-9-phenyl-3,7-diazabicyclo[3.3.1]nonane-2,4,6,8-tetraone dimethylformamide monosolvate

2017 ◽  
Vol 73 (7) ◽  
pp. 1097-1101 ◽  
Author(s):  
Sergey Z. Vatsadze ◽  
Marina A. Manaenkova ◽  
Evgeny V. Vasilev ◽  
Nikolai U. Venskovsky ◽  
Victor N. Khrustalev
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Dihedral Angle ◽  
Mirror Symmetry ◽  
Solvent Molecule ◽  
Twofold Axis ◽  
The Mean ◽  
Methyl Analog

Compounds (I), C9H10N2O4, (II), C11H12N2O4, and (III), C14H12N2O4·C3H7NO represent 9,9-disubstituted-3,7-diazabicyclo[3.3.1]nonane-2,4,6,8-tetraone derivatives with very similar molecular geometries for the bicyclic framework: the dihedral angle between the planes of the imide groups is 74.87 (6), 73.86 (3) and 74.83 (6)° in (I)–(III), respectively. The dimethyl derivative (I) is positioned on a crystallographic twofold axis and its overall geometry deviates only slightly from idealizedC2vsymmetry. The spiro-cyclopentane derivative (II) and the phenyl/methyl analog (III) retain only internalCssymmetry, which in the case of (II) coincides with crystallographic mirror symmetry. The cyclopentane moiety in (II) adopts an envelope conformation, with the spiro C atom deviating from the mean plane of the rest of the ring by 0.548 (2) Å. In compound (III), an N—H...O hydrogen bond is formed with the dimethylformamide solvent molecule. In the crystal, both (I) and (II) form similar zigzag hydrogen-bonded ribbons through double intermolecular N—H...O hydrogen bonds. However, whereas in (I) the ribbons are formed by twotrans-arranged O=C—N—H amide fragments, the amide fragments arecis-positioned in (II). The formation of ribbons in (III) is apparently disrupted by participation of one of its N—H groups in hydrogen bonding with the solvent molecule. As a result, the molecules of (III) form zigzag chains rather than the ribbons through intermolecular N—H...O hydrogen bonds. The crystal of (I) was a pseudo-merohedral twin.

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.

Sign in / Sign up

Export Citation Format

Share Document