scholarly journals Decoding conformational polymorphism in organic substances

2014 ◽  
Vol 70 (a1) ◽  
pp. C557-C557
Author(s):  
Ahmed Orlando ◽  
Laura Loconte ◽  
Emanuele Ortoleva ◽  
Carlo Gatti ◽  
Leonardo Lo Presti
Keyword(s):  
Molecular Conformation ◽  
Crystal Packing ◽  
X Ray Diffraction ◽  
Self Recognition ◽  
Crystallization Conditions ◽  
Polymorphic Forms ◽  
Non Covalent Interactions ◽  
Cohesive Energies ◽  
Covalent Interactions

Different polymorphs have different intensive physical properties and it is still impossible to predict from scratch if a change in the crystallization conditions will result in different crystal structures or not. In this contribution, possible correlations are highlighted among charge density features, molecular conformation and interaction energetics in the two known polymorphic forms of (DTC)[1,2], an isothiazole β-sultamic derivative. A tentative rationale is provided for the relative stability of the two forms on the basis of their different self-recognition patterns. Both polymorphs crystallize in the same P21/n space group and show very different non-covalent networks of weak C-H–X (X = N,O,π) interactions due to the dissimilar conformation of the asymmetric units (ASU). Accurate multi-temperature (100 K ≤ T ≤ 298 K) single-crystal X-Ray diffraction experiments were carried out and the evolution of crystal packing and self-recognition energetics were monitored through periodic quantum-mechanical calculations at fixed geometries. Preliminary results show that dispersive/repulsive and electrostatic non-covalent interactions dominate the crystal packing in both polymorphs. At T=100 K the form A have a tighter packing, as it shows a greater propensity in being involved in H bonds than B (see the Hirshfeld surface fingerprint plots[3] of forms A -left- and B -right- here reported). This reflects in greater density, whereas the estimated DFT cohesive energies of the two forms are similar. DTC has enough molecular flexibility to access various favourable arrangements during the nucleation, as the interconversion between the A and B conformers in the gas phase takes place with a very small activation energy. The possible role of the solvent in favouring either of the two observed conformations is discussed.

scholarly journals A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC)

RSC Advances ◽  
2018 ◽  
Vol 8 (67) ◽  
pp. 38445-38454 ◽  
Author(s):  
Andrea Gionda ◽  
Giovanni Macetti ◽  
Laura Loconte ◽  
Silvia Rizzato ◽  
Ahmed M. Orlando ◽  
...  
Keyword(s):  
Theoretical Study ◽  
Crystal Packing ◽  
Variable Temperature ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Complex Organic Molecule ◽  
Non Covalent Interactions ◽  
Complex Organic ◽  
Covalent Interactions

A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.

scholarly journals Uracil Derivatives for Halogen-Bonded Cocrystals

2021 ◽  
Vol 22 (19) ◽  
pp. 10663
Author(s):  
Mónica Benito ◽  
Yannick Roselló ◽  
Miquel Barceló-Oliver ◽  
Antonio Frontera ◽  
Elies Molins
Keyword(s):  
Self Assembly ◽  
Crystal Packing ◽  
Halogen Bonding ◽  
X Ray Diffraction ◽  
Thermal Methods ◽  
Uracil Derivatives ◽  
Fourier Transformed Infrared Spectroscopy ◽  
Solution Methods ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Among non-covalent interactions, halogen bonding is emerging as a new powerful tool for supramolecular self-assembly. Here, along with a green and effective method, we report three new halogen-bonded cocrystals containing uracil derivatives and 1,2,4,5-tetrafluoro-3,6-diiodobenzene as X-bond donor coformer. These multicomponent solids were prepared both by solvent-drop grinding and solution methods and further characterized by powder and single-crystal X-ray diffraction, Fourier-transformed infrared spectroscopy, and thermal methods (TGA-DSC). In order to study the relative importance of hydrogen versus halogen bonds in the crystal packing, computational methods were applied.

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.

Role of non-covalent interactions in the supramolecular architectures of mercury(ii) diphenyldithiophosphates: An experimental and theoretical investigation

2021 ◽  
Vol 45 (4) ◽  
pp. 2249-2263
Author(s):  
Pretam Kumar ◽  
Snehasis Banerjee ◽  
Anu Radha ◽  
Tahira Firdoos ◽  
Subash Chandra Sahoo ◽  
...  
Keyword(s):  
Theoretical Investigation ◽  
Supramolecular Organization ◽  
Π Interactions ◽  
Supramolecular Architectures ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The H-bond, spodium bond and CH⋯π interactions playing an important role in the supramolecular organization of two mercury(ii) diphenyldithiophosphate complexes have been discussed.

The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution

2021 ◽  
Author(s):  
Sascha Jähnigen ◽  
Daniel Sebastiani ◽  
Rodolphe Vuilleumier
Keyword(s):  
Lactic Acid ◽  
Circular Dichroism ◽  
Computational Study ◽  
Bulk Water ◽  
Vibrational Circular Dichroism ◽  
Ab Initio Molecular Dynamics ◽  
Non Covalent Interactions ◽  
Circular Dichroïsm ◽  
Covalent Interactions

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss...

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 Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall

2018 ◽  
Author(s):  
Alister T. Boags ◽  
Firdaus Samsudin ◽  
Syma Khalid
Keyword(s):  
Cell Wall ◽  
Electrostatic Interactions ◽  
Cell Envelope ◽  
Binding Domain ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
E Coli ◽  
Non Covalent Interactions ◽  
Covalent Interactions

SUMMARYWe present a molecular modeling and simulation study of the of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. We show that non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. When OmpA is truncated to remove the peptidoglycan binding domain, TolR is able to pull the cell wall down towards the inner membrane. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.

Sign in / Sign up

Export Citation Format

Share Document