scholarly journals On the Polymorph-Selective Role of Hydrogen Bonding and π - π Stacking in Para-Aminobenzoic Acid Solutions

2020 ◽  
Author(s):  
Raitis Bobrovs ◽  
Laura Drunka ◽  
Andrievis Auseklis Auzins ◽  
Kristaps Jaudzems ◽  
Matteo Salvalaglio
Keyword(s):  
Hydrogen Bonds ◽  
Single Molecule ◽  
Md Simulations ◽  
Crystal Form ◽  
Crystal Nucleation ◽  
Growth Unit ◽  
Aminobenzoic Acid ◽  
Crystal Forms ◽  
Π Stacking ◽  
Hydrogen Bonded

<div><div><div><p>Understanding molecular self-association in solution is vital for uncovering polymorph- selective crystal nucleation pathways. In this paper, we combine solution NMR spectroscopy and molecular dynamics simulations to shed light on the structural and dynamical features of para-aminobenzoic acid (pABA) in solution, and on their role in pABA crystals nucleation. pABA is known to yield different crystal forms (α, and β) depending on solvent choice and su- persaturation conditions. NMR reveals that dominant interactions stabilising pABA oligomers are markedly solvent-dependent: in organic solvents, hydrogen bonds dominate, while water promotes π - π stacking. Despite this clear preference, both types of interactions contribute to the variety of self-associated species in all solvents considered. MD simulations support this observation and show that pABA oligomers are short-lived and display a fluxional character, therefore indicating that the growth unit involved in pABA crystallisation is likely to be a single molecule. Nevertheless, we note that the interactions dominating in pABA oligomers are indicative of the polymorph obtained from precipitation. In water, at low pABA concen- trations - conditions that are known to yield crystals of the β form - carboxylic-carboxylic hydrogen bonds are exclusively asymmetric. At higher pABA concentration conditions in which the crystallisation is known to yield the α form - a small but statistically significant fraction of symmetric carboxylic-carboxylic hydrogen-bonded dimers is present. We interpret the presence of these interactions in solvated pABA oligomers as indicative of the fact that a simultaneous and complete desolvation of two carboxylic groups, necessary to form the sym- metric hydrogen-bonded dimer typical of the α crystal form, is accessible, therefore directing the nucleation pathway towards the nucleation of α-pABA.</p></div></div></div>

scholarly journals On The Polymorph-Selective Role of Hydrogen Bonding and π - π Stacking in Para-Aminobenzoic Acid Solutions

2020 ◽  
Author(s):  
Raitis Bobrovs ◽  
Laura Drunka ◽  
Andrievis Auseklis Auzins ◽  
Kristaps Jaudzems ◽  
Matteo Salvalaglio
Keyword(s):  
Hydrogen Bonds ◽  
Single Molecule ◽  
Md Simulations ◽  
Crystal Form ◽  
Crystal Nucleation ◽  
Growth Unit ◽  
Aminobenzoic Acid ◽  
Crystal Forms ◽  
Π Stacking ◽  
Hydrogen Bonded

<div><div><div><p>Understanding molecular self-association in solution is vital for uncovering polymorph- selective crystal nucleation pathways. In this paper, we combine solution NMR spectroscopy and molecular dynamics simulations to shed light on the structural and dynamical features of para-aminobenzoic acid (pABA) in solution, and on their role in pABA crystals nucleation. pABA is known to yield different crystal forms (α, and β) depending on solvent choice and su- persaturation conditions. NMR reveals that dominant interactions stabilising pABA oligomers are markedly solvent-dependent: in organic solvents, hydrogen bonds dominate, while water promotes π - π stacking. Despite this clear preference, both types of interactions contribute to the variety of self-associated species in all solvents considered. MD simulations support this observation and show that pABA oligomers are short-lived and display a fluxional character, therefore indicating that the growth unit involved in pABA crystallisation is likely to be a single molecule. Nevertheless, we note that the interactions dominating in pABA oligomers are indicative of the polymorph obtained from precipitation. In water, at low pABA concen- trations - conditions that are known to yield crystals of the β form - carboxylic-carboxylic hydrogen bonds are exclusively asymmetric. At higher pABA concentration conditions in which the crystallisation is known to yield the α form - a small but statistically significant fraction of symmetric carboxylic-carboxylic hydrogen-bonded dimers is present. We interpret the presence of these interactions in solvated pABA oligomers as indicative of the fact that a simultaneous and complete desolvation of two carboxylic groups, necessary to form the sym- metric hydrogen-bonded dimer typical of the α crystal form, is accessible, therefore directing the nucleation pathway towards the nucleation of α-pABA.</p></div></div></div>

scholarly journals Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa

2005 ◽  
Vol 61 (1) ◽  
pp. 58-68 ◽  
Author(s):  
Stephen A. Moggach ◽  
David R. Allan ◽  
Carole A. Morrison ◽  
Simon Parsons ◽  
Lindsay Sawyer
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Ambient Pressure ◽  
Crystal Form ◽  
Hydroxyl Groups ◽  
Orthorhombic Space Group ◽  
Crystal Forms ◽  
Hydrogen Bonded

The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed L-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH...carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the —CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O...O separation of 2.918 (4) Å and an O...O...O angle of 148.5 (2)°; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7)°. Elsewhere in the structure one NH...O interaction reaches an N...O separation of 2.691 (13) Å at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate L-serine-II. The OH...OH hydrogen-bonded chains of L-serine-I are replaced in L-serine-II by shorter OH...carboxyl interactions, which have an O...O separation of 2.62 (2) Å. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCαCO torsion angle from −178.1 (2)° at 4.8 GPa to −156.3 (10)° at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to L-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH...O hydrogen bonding in both phases relative to L-serine-I at ambient pressure.

Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network

2021 ◽  
Vol 77 (2) ◽  
pp. 211-218
Author(s):  
Ivica Cvrtila ◽  
Vladimir Stilinović
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Two Dimensional ◽  
Structural Motifs ◽  
Supramolecular Isomerism ◽  
Other Hand ◽  
Π Stacking ◽  
Hydrogen Bonded

The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.

Synthesis, crystallization, X-ray structural characterization and solid-state assembly of a cyclic hexapeptoid with propargyl and methoxyethyl side chains

2017 ◽  
Vol 73 (3) ◽  
pp. 399-412 ◽  
Author(s):  
Consiglia Tedesco ◽  
Eleonora Macedi ◽  
Alessandra Meli ◽  
Giovanni Pierri ◽  
Giorgio Della Sala ◽  
...  
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Structural Characterization ◽  
Crystal Form ◽  
Side Chains ◽  
Crystal Forms ◽  
Hydrate Crystal ◽  
The Stability ◽  
Efficient Packing

The synthesis and the structural characterization of a cyclic hexapeptoid with four methoxyethyl and two propargyl side chains have disclosed the presence of a hydrate crystal form [form (I)] and an anhydrous crystal form [form (II)]. The relative amounts of form (I) and form (II) in the as-purified product were determined by Rietveld refinement and depend on the purification procedures. In crystal form (I), peptoid molecules assemble in a columnar arrangement by means of side-chain-to-backbone C=CH...OC hydrogen bonds. In the anhydrous crystal form (II), cyclopeptoid molecules form ribbons by means of backbone-to-backbone CH2...OC hydrogen bonds, thus mimicking β-sheet secondary structures in proteins. In both crystal forms side chains act as joints among the columns or the ribbons and contribute to the stability of the whole solid-state assembly. Water molecules in the hydrate crystal form (I) bridge columns of cyclic peptoid molecules, providing a more efficient packing.

scholarly journals Hydrogen-bonding patterns in 2-amino-4,6-dimethoxypyrimidine–4-aminobenzoic acid (1/1)

2006 ◽  
Vol 62 (7) ◽  
pp. o2976-o2978 ◽  
Author(s):  
Kaliyaperumal Thanigaimani ◽  
Packianathan Thomas Muthiah ◽  
Daniel E. Lynch
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Carboxyl Group ◽  
Acid Molecule ◽  
Aminobenzoic Acid ◽  
Graph Set ◽  
Supramolecular Chain ◽  
Bonding Patterns ◽  
Hydrogen Bonded

In the title cocrystal, C6H9N3O2·C7H7NO2, the 2-amino-4,6-dimethoxypyrimidine molecule interacts with the carboxyl group of the 4-aminobenzoic acid molecule through N—H...O and O—H...N hydrogen bonds, forming a cyclic hydrogen-bonded motif [R 2 2(8)]. This motif further self-organizes through N—H...O hydrogen bonds to generate an array of six hydrogen bonds with the rings having the graph-set notation R 2 3(6), R 2 2(8), R 4 2(8), R 2 2(8) and R 2 3(6). The 4-aminobenzoic acid molecules self-assemble via N—H...O hydrogen bonds to form a supramolecular chain along the c axis.

Bis{4-[(4-pyridyl)ethenyl]pyridinium} 4-sulfonatobenzoate trihydrate

2006 ◽  
Vol 62 (4) ◽  
pp. o1529-o1531 ◽  
Author(s):  
Li-Ping Zhang ◽  
Long-Guan Zhu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Water Molecules ◽  
Stacking Interactions ◽  
Two Dimensional ◽  
One Dimensional ◽  
Π Stacking ◽  
Dimensional Network ◽  
Hydrogen Bonded

In the crystal structure of the title organic proton-transfer complex, 2C12H11N2 +·C7H4O5S2−·3H2O, the cations form one-dimensional chains via intermolecular N—H...N hydrogen bonds and these chains, in turn, form a two-dimensional network through π–π stacking interactions. In addition, the anions and water molecules are connected into a two-dimensional hydrogen-bonded network through intermolecular O—H...O hydrogen bonds. The two motifs result in sheets of cations and anions stacked alternately.

Two drimane lactones, valdiviolide and 11-epivaldiviolide, in the form of a 1:1 cocrystal obtained fromDrimys winteriextracts

2014 ◽  
Vol 70 (12) ◽  
pp. 1112-1115
Author(s):  
Cristian Paz Robles ◽  
Darío Mercado ◽  
Sebastián Suarez ◽  
Ricardo Baggio
Keyword(s):  
Hydrogen Bonds ◽  
Sesquiterpene Lactones ◽  
Crystal Form ◽  
Stacking Interactions ◽  
Π Stacking ◽  
Weakly Interacting ◽  
Drimys Winteri

A cocrystal, C15H22O3·C15H22O3, (I), obtained fromDrimys winteri, is composed of two isomeric drimane sesquiterpene lactones, namely valdiviolide, (Ia), and 11-epivaldiviolide, (Ib), neither of which has been reported in the crystal form. Both diastereoisomers present three chiral centres at sites 5, 10 and 11, with anSSRsequence in (Ia) and anSSSsequence in (Ib). O—H...O hydrogen bonds bind molecules into chains running along [\overline{1}20] and the chains are in turn linked by π–π stacking interactions to define planar weakly interacting arrays parallel to (001).

Hydrogen-bonded and π-interaction assembly in two 8-alkoxycarbonyl-1,8-diazabicyclo[5.4.0]undec-7-enium chloride salts

2013 ◽  
Vol 69 (4) ◽  
pp. 444-447
Author(s):  
E. Mesto ◽  
E. Quaranta
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Space Group ◽  
Π Stacking ◽  
Chloride Salts ◽  
Crystal Packings ◽  
Chloride Monohydrate ◽  
Hydrogen Bonded

The crystal structures of 8-phenoxycarbonyl-1,8-diazabicyclo[5.4.0]undec-7-enium chloride, C16H21N2O2+·Cl−, (I), and 8-methoxycarbonyl-1,8-diazabicyclo[5.4.0]undec-7-enium chloride monohydrate, C11H19N2O2+·Cl−·H2O, (II), recently reported by Carafa, Mesto & Quaranta [Eur. J. Org. Chem.(2011), pp. 2458–2465], are analysed and discussed with a focus on crystal interaction assembly. Both compounds crystallize in the space groupP21/c. The crystal packings are characterized by dimers linked through π–π stacking interactions and intermolecular nonclassical hydrogen bonds, respectively. Additional intermolecular C—H...Cl interactions [in (I) and (II)] and classical O—H...Cl hydrogen bonds [in (II)] are also evident and contribute to generating three-dimensional hydrogen-bonded networks.

Polymorphism in 3-acetyl-4-hydroxy-2H-chromen-2-one

2015 ◽  
Vol 71 (10) ◽  
pp. 873-877 ◽  
Author(s):  
Afef Ghouili ◽  
Ameni Brahmia ◽  
Rached Ben Hassen
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Stacking Interactions ◽  
Π Stacking ◽  
Hydrogen Bonded

A new polymorph (denoted polymorph II) of 3-acetyl-4-hydroxy-2H-chromen-2-one, C11H8O4, was obtained unexpectedly during an attempt to recrystallize the compound from salt–melted ice, and the structure is compared with that of the original polymorph (denoted polymorph I) [Lyssenko & Antipin (2001).Russ. Chem. Bull.50, 418–431]. Strong intramolecular O—H...O hydrogen bonds are observed equally in the two polymorphs [O...O = 2.4263 (13) Å in polymorph II and 2.442 (1) Å in polymorph I], with a slight delocalization of the hydroxy H atom towards the ketonic O atom in polymorph II [H...O = 1.32 (2) Å in polymorph II and 1.45 (3) Å in polymorph I]. In both crystal structures, the packing of the molecules is dominated and stabilized by weak intermolecular C—H...O hydrogen bonds. Additional π–π stacking interactions between the keto–enol hydrogen-bonded rings stabilize polymorph I [the centres are separated by 3.28 (1) Å], while polymorph II is stabilized by interactions between α-pyrone rings, which are parallel to one another and separated by 3.670 (5) Å.

scholarly journals Supramolecular Architecture of Chloranilate Salts with Organic Cations

2019 ◽  
Vol 92 (2) ◽  
pp. 297-305
Author(s):  
Krešimir Molčanov ◽  
Marijana Jurić ◽  
Lidija Androš Dubraja
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Organic Cations ◽  
Supramolecular Architecture ◽  
Aromatic Rings ◽  
Chloranilic Acid ◽  
Π Stacking ◽  
Different Types ◽  
1D Chains ◽  
Hydrogen Bonded

Four novel salts of chloranilic acid (H2CA; 3,6-dichloro-2,5-dihydroxy-1,4-quinone) with organic cations pyridinium (Hpy+), piperazinediium (H2ppz2+), 4,4'-bipyridinediium (H2bpy2+) and 1,10-phenanthrolinium (Hphen+) were prepared and structurally characterised: (Hpy)2CA (1), (H2ppz)CA (2), (H2bpy)CA·4H2O (3) and (Hphen)HCA·MeOH (4). Supramolecular architecture is based on extensive hydrogen bonding and π-stacking. The central motive is chloranilate dianion which acts as an acceptor of two bifurcated hydrogen bonds. Topology and dimensionality of hydrogen bonded networks can be tuned by use of different cations: thus discrete motives, 1D chains and 2D layers were observed. Three different types of π-stacks are present: aromatic stacks, quinoid stacks and stacks of alternating quinoid and aromatic rings.

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