Non-covalent interactions in the multicomponent crystal of 1-aminocyclopentane carboxylic acid, oxalic acid and water: a crystallographic and a theoretical approach

2017 ◽  
Vol 73 (5) ◽  
pp. 968-980 ◽  
Author(s):  
Asiloé J. Mora ◽  
Lusbely M. Belandria ◽  
Gerzon E. Delgado ◽  
Luis E. Seijas ◽  
Angel Lunar ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Critical Points ◽  
Three Dimensional ◽  
Dispersion Interactions ◽  
X Ray Diffraction ◽  
Carboxylate Groups ◽  
Non Covalent Interactions ◽  
A Charge ◽  
Covalent Interactions

Single-crystal X-ray diffraction and quantum mechanical theories were used to examine in detail the subtle nature of non-covalent interactions in the [2:1:1] multicomponent crystal of 1,1-aminocyclopentanecarboxylic acid:oxalic acid:water. The crystal, which is a hydrate salt of the amino acid with the hydrogen-oxalate ion, also contains the zwitterion of the amino acid in equal proportions. It was found that a dimeric cation [Acc5(Z)...Acc5(C)]+bonded by an O—H...O hydrogen bond exists due to a charge transfer between acid and carboxylate groups. The three-dimensional crystal is built by blocks stacked along the [101] direction by dispersion interactions, with each block growing along two directions: a hydrogen oxalate HOX−...HOX−catameric supramolecular structure along the [010] direction; and double ...HOX−—W—[Acc5(Z)... Acc5(C)]+... chains related by inversion centers along the [1 0 {\bar 1}] direction. A PBE-DFT optimization, under periodic boundary conditions, was carried out. The fully optimized structure obtained was used to extract the coordinates to calculate the stabilization energy between the dimers under the crystal field, employing the M062X/aug-cc-pVTZ level of theory. The non-covalent index isosurfaces employed here allow the visualization of where the hydrogen bond and dispersion interactions contribute within the crystal. The crystal atomic arrangements are analyzed by employing the Atoms in Molecules and electron localization function theories. Within this context, the presence of density bond critical points is employed as a criterion for proving the existence of the hydrogen bond and it was found that these results agree with those rendered by the crystallographic geometrical analysis, with only three exceptions, for which bond critical points were not found.

scholarly journals Synthesis, Characterization, and Non-Covalent Interactions of Palladium(II)-Amino Acid Complexes

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4331
Author(s):  
David B. Hobart ◽  
Michael A. G. Berg ◽  
Hannah M. Rogers ◽  
Joseph S. Merola
Keyword(s):  
Amino Acid ◽  
High Resolution Mass Spectrometry ◽  
Resonance Spectroscopy ◽  
Spectroscopic Techniques ◽  
X Ray Diffraction ◽  
Amino Acid Complexes ◽  
Acetone Water ◽  
Square Planar ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The reaction of palladium(II) acetate with acyclic amino acids in acetone/water yields square planar bis-chelated palladium amino acid complexes that exhibit interesting non-covalent interactions. In all cases, complexes were examined by multiple spectroscopic techniques, especially HRMS (high resolution mass spectrometry), IR (infrared spectroscopy), and 1H NMR (nuclear magnetic resonance) spectroscopy. In some cases, suitable crystals for single crystal X-ray diffraction were able to be grown and the molecular structure was obtained. The molecular geometries of the products are discussed. Except for the alanine complex, all complexes incorporate water molecules into the extended lattice and exhibit N-H···O and/or O···(HOH)···O hydrogen bonding interactions. The non-covalent interactions are discussed in terms of the extended lattice structures exhibited by the structures.

scholarly journals Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 328
Author(s):  
Raquel Álvarez-Vidaurre ◽  
Alfonso Castiñeiras ◽  
Antonio Frontera ◽  
Isabel García-Santos ◽  
Diego M. Gil ◽  
...  
Keyword(s):  
Density Functional ◽  
Glycolic Acid ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Functional Theory ◽  
Molecular Systems ◽  
X Ray Crystallography ◽  
Hydroxycarboxylic Acids ◽  
Non Covalent Interactions ◽  
Covalent Interactions

This work deals with the preparation of pyridine-3-carbohydrazide (isoniazid, inh) cocrystals with two α-hydroxycarboxylic acids. The interaction of glycolic acid (H2ga) or d,l-mandelic acid (H2ma) resulted in the formation of cocrystals or salts of composition (inh)·(H2ga) (1) and [Hinh]+[Hma]–·(H2ma) (2) when reacted with isoniazid. An N′-(propan-2-ylidene)isonicotinic hydrazide hemihydrate, (pinh)·1/2(H2O) (3), was also prepared by condensation of isoniazid with acetone in the presence of glycolic acid. These prepared compounds were well characterized by elemental analysis, and spectroscopic methods, and their three-dimensional molecular structure was determined by single crystal X-ray crystallography. Hydrogen bonds involving the carboxylic acid occur consistently with the pyridine ring N atom of the isoniazid and its derivatives. The remaining hydrogen-bonding sites on the isoniazid backbone vary based on the steric influences of the derivative group. These are contrasted in each of the molecular systems. Finally, Hirshfeld surface analysis and Density-functional theory (DFT) calculations (including NCIplot and QTAIM analyses) have been performed to further characterize and rationalize the non-covalent interactions.

Self-assembly mode and supramolecular framework of cyclopentanocucurbit[6]uril and aromatic amines

2021 ◽  
Vol 25 ◽  
Author(s):  
Jun Zheng ◽  
Yan Mei Jin ◽  
Xi Nan Yang ◽  
Lin Zhang ◽  
Dao Fa Jiang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Functional Materials ◽  
Supramolecular Interactions ◽  
X Ray Diffraction ◽  
Guest Molecules ◽  
Characterization Methods ◽  
Potential Applications ◽  
Non Covalent Interactions ◽  
Multi Level ◽  
Covalent Interactions

: Single-crystal X-ray diffraction analysis, nuclear magnetic resonance (NMR), and other characterization methods are used to characterize the complexes formed by cyclopentano-cucurbit[6]uril (abbreviated as CyP6Q[6]) as a host interacting with p-aminobenzenesulfonamide (G1), 4,4'-diaminobiphenyl (G2), and (E)-4,4'-diamino-1,2-diphenylethene (G3) as guests, respectively. The experimental results show that these three aromatic amine molecules have the same interaction mode with CyP6Q[6], interacting with its negatively electric potential portals. The supramolecular interactions include non-covalent interactions of hydrogen bonding and ion-dipole between host and guest molecules. CdCl2 acts as a structureinducing agent to form self-assemblies of multi-dimensional and multi-level supramolecular frameworks that may have potential applications in various functional materials.

scholarly journals Solid-State Structures and Photoluminescence of Lamellar Architectures of Cu(I) and Ag(I) Paddlewheel Clusters with Hydrogen-Bonded Polar Guests

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6731
Author(s):  
Haruki Inoue ◽  
Yuga Yamashita ◽  
Yoshiki Ozawa ◽  
Toshikazu Ono ◽  
Masaaki Abe
Keyword(s):  
Solid State ◽  
Diffuse Reflectance Spectroscopy ◽  
X Ray Diffraction ◽  
Uv Illumination ◽  
Near Ir ◽  
Carboxylic Groups ◽  
Dta Analysis ◽  
Non Covalent Interactions ◽  
Solid State Structures ◽  
Covalent Interactions

Two hexanuclear paddlewheel-like clusters appending six carboxylic-acid pendants have been isolated with the inclusion of polar solvent guests: [Cu6(Hmna)6]·7DMF (1·7DMF) and [Ag6(Hmna)6]·8DMSO (2·8DMSO), where H2mna = 2-mercaptonicotininc acid, DMF = N,N’-dimethylformamide, and DMSO = dimethyl sulfoxide. The solvated clusters, together with their fully desolvated forms 1 and 2, have been characterized by FTIR, UV–Vis diffuse reflectance spectroscopy, TG-DTA analysis, and DFT calculations. Crystal structures of two solvated clusters 1·7DMF and 2·8DMSO have been unambiguously determined by single-crystal X-ray diffraction analysis. Six carboxylic groups appended on the clusters trap solvent guests, DMF or DMSO, through H-bonds. As a result, alternately stacked lamellar architectures comprising of a paddlewheel cluster layer and H-bonded solvent layer are formed. Upon UV illumination (λex = 365 nm), the solvated hexasilver(I) cluster 2·8DMSO gives intense greenish-yellow photoluminescence in the solid state (λPL = 545 nm, ΦPL = 0.17 at 298 K), whereas the solvated hexacopper(I) cluster 1·7DMF displays PL in the near-IR region (λPL = 765 nm, ΦPL = 0.38 at 298 K). Upon complete desolvation, a substantial bleach in the PL intensity (ΦPL < 0.01) is observed. The desorption–sorption response was studied by the solid-state PL spectroscopy. Non-covalent interactions in the crystal including intermolecular H-bonds, CH···π interactions, and π···π stack were found to play decisive roles in the creation of the lamellar architectures, small-molecule trap-and-release behavior, and guest-induced luminescence enhancement.

scholarly journals 2-Methyl-3-(3-methylisoxazol-5-yl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-1-ium chloride

IUCrData ◽  
2016 ◽  
Vol 1 (12) ◽  
Author(s):  
Sanae Lahmidi ◽  
Latifa El Ouasif ◽  
Alae Eddine Jilalat ◽  
Wedad Al-Garadi ◽  
El Mokhtar Essassi ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Three Dimensional ◽  
Extended Structure ◽  
Dimensional Network ◽  
A Charge ◽  
Molecular Salt

In the title molecular salt, C13H12N3O2+·Cl−, the oxazolyl ring is disordered over two orientations in a 0.536 (15):0.464 (15) ratio, both of which approximate to envelopes with the N atom as the flap in each case. The cation and anion are linked by a charge-assisted N—H...Cl hydrogen bond. In the extended structure, C—H...N, C—H...O and C—H...Cl interactions link the components into a three-dimensional network.

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.

Synthesis, structure and selective luminescence sensing for iron(III) ions of a three-dimensional zinc(II) (4,6)-connected coordination network

2019 ◽  
Vol 75 (2) ◽  
pp. 141-149 ◽  
Author(s):  
Feng Su ◽  
Cheng-Yong Zhou ◽  
Lin-Tao Wu ◽  
Xi Wu ◽  
Chun Han ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Electronic Configuration ◽  
Organic Ligands ◽  
Tetracarboxylic Acid ◽  
X Ray Diffraction ◽  
X Ray ◽  
Carboxylate Groups ◽  
Dimensional Network ◽  
Solvent Stability ◽  
Solvothermal Conditions

Coordination polymers constructed from conjugated organic ligands and metal ions with a d 10 electronic configuration exhibit intriguing properties for chemical sensing and photochemistry. A ZnII-based coordination polymer, namely poly[aqua(μ6-biphenyl-3,3′,5,5′-tetracarboxylato)(μ2-4,4′-bipyridine)dizinc(II)], [Zn2(C16H6O8)(C10H8N2)(H2O)2] n or [Zn2(m,m-bpta)(4,4′-bipy)(H2O)2] n , was synthesized from a mixture of biphenyl-3,3′,5,5′-tetracarboxylic acid [H4(m,m-bpta)], 4,4′-bipyridine (4,4′-bipy) and Zn(NO3)2·6H2O under solvothermal conditions. The title complex has been structurally characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction and powder X-ray diffraction analysis, and features a μ6-coordination mode. The ZnII ions adopt square-pyramidal geometries and are bridged by two syn–syn carboxylate groups to form [Zn2(COO)2] secondary buildding units (SBUs). The SBUs are crosslinked by (m,m-bpta)4− ligands to produce a two-dimensional grid-like layer that exhibits a stair-like structure along the a axis. Adjacent layers are linked by 4,4′-bipy ligands to form a three-dimensional network with a {44.610.8}{44.62} topology. In the solid state, the complex displays a strong photoluminescence and an excellent solvent stability. In addition, the luminescence sensing results indicate a highly selective and sensitive sensing for Fe3+ ions.

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