Two conformational polymorphs of 4-methylhippuric acid

2020 ◽  
Vol 76 (6) ◽  
pp. 1077-1091
Author(s):  
Marilia Guillén ◽  
Asiloé J. Mora ◽  
Lusbely M. Belandria ◽  
Luis E. Seijas ◽  
Jeans W. Ramírez ◽  
...  
Keyword(s):  
Electron Density ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Local Level ◽  
Acid Amide ◽  
Closed Shell ◽  
Ethanoic Acid ◽  
Delocalized Electron ◽  
Methylhippuric Acid ◽  
Van Der Waals Radii

4-Methylhippuric acid {systematic name: 2-[(4-methylbenzoyl)amino]ethanoic acid}, a p-xylene excreted metabolite with a backbone containing three rotatable bonds (R-bonds), is likely to produce more than one stable molecular structure in the solid state. In this work, we prepared polymorph I by slow solvent evaporation (plates with Z′ = 1) and polymorph II by mechanical grinding (plates with Z′ = 2). Potential energy surface (PES) analysis, rotating the molecule about the C—C—N—C torsion angle, shows four conformational energy basins. The second basin, with torsion angles near −73°, agree with the conformations adopted by polymorph I and molecules A of polymorph II, and the third basin at 57° matched molecules B of polymorph II. The energy barrier between these basins is 27.5 kJ mol−1. Superposition of the molecules of polymorphs I and II rendered a maximum r.m.s. deviation of 0.398 Å. Polymorphs I and II are therefore true conformational polymorphs. The crystal packing of polymorph I consists of C(5) chains linked by N—H...O interactions along the a axis and C(7) chains linked by O—H...O interactions along the b axis. In polymorph II, two molecules (A with A or B with B) are connected by two acid–amide O—H...O interactions rendering R 2 2(14) centrosymmetric dimers. These dimers alternate to pile up along the b axis linked by N—H...O interactions. A Hirshfeld surface analysis localized weaker noncovalent interactions, C—H...O and C—H...π, with contact distances close to the sum of the van der Waals radii. Electron density at a local level using the Quantum Theory of Atoms in Molecules (QTAIM) and the Electron Localization Function (ELF), or a semi-local level using noncovalent interactions, was used to rank interactions. Strong closed shell interactions in classical O—H...O and N—H...O hydrogen bonds have electron density highly localized on bond critical points. Weaker delocalized electron density is seen around the p-methylphenyl rings associated with dispersive C—H...π and H...H interactions.

Role of halogen-involved intermolecular interactions and existence of isostructurality in the crystal packing of —CF3 and halogen (Cl or Br or I) substituted benzamides

2018 ◽  
Vol 74 (6) ◽  
pp. 574-591 ◽  
Author(s):  
Pradip Kumar Mondal ◽  
Rahul Shukla ◽  
Subha Biswas ◽  
Deepak Chopra
Keyword(s):  
Solid State ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
X Ray Diffraction ◽  
Substituted Benzamides ◽  
Size Type ◽  
Substituted Benzamide ◽  
Van Der Waals Radii

A total of 23 benzamides are obtained through a simple reaction between chloro-/bromo-/iodoaniline and trifluoromethylbenzoyl chloride and characterized using single-crystal X-ray diffraction. Crystal structures of three series of benzamides based on N-chlorophenyl–trifluoromethyl–benzamide (nine compounds), N-bromophenyl–trifluoromethyl–benzamide (six compounds), and N-iodophenyl–trifluoromethyl–benzamide (eight compounds) are prepared to analyse the halogen-mediated noncovalent interactions. The influences of Cl/Br/I and trifluoromethyl substituents on the respective interactions are examined in the presence of a strong N—H...O hydrogen bond. This exercise has resulted in the documentation of frequently occurring supramolecular synthons involving halogen atoms in the crystal packing of benzamide molecules in the solid state. In the present study, a detailed quantitative evaluation has been performed on the nature, energetics, electrostatic contributions, and topological properties of short and directional intermolecular interactions derived from the electron density on halogenated benzamides in the solid state. Besides these, the occurrence of three-, two- and one-dimensional isostructurality in halogen (Cl or Br or I) substituted benzamide analogues is also investigated. A `region of co-existence' involving halogen-based intermolecular interactions in the vicinity of the sum of the van der Waals radii has been identified. Thus, the nature of the halogen (effective size), type of interaction and the packing characteristics via presence of additional interactions establish the subtle, yet important, role of cooperativity in intermolecular interactions in crystal packing.

Crystal structure of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis

2021 ◽  
Vol 77 (11) ◽  
Author(s):  
Kohei Sasamoto ◽  
Tomoki Himiyama ◽  
Kunihiko Moriyoshi ◽  
Takashi Ohmoto ◽  
Koichi Uegaki ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cellulose Acetate ◽  
Electron Density ◽  
Active Site ◽  
Catalytic Domain ◽  
Crystal Packing ◽  
Signal Sequence ◽  
Industrial Applications ◽  
Side Chain ◽  
Active Site Conformation

The acetylxylan esterases (AXEs) classified into carbohydrate esterase family 4 (CE4) are metalloenzymes that catalyze the deacetylation of acetylated carbohydrates. AXE from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866), which belongs to CE4, is composed of three parts: a signal sequence (residues 1–22), an N-terminal region (NTR; residues 23–135) and a catalytic domain (residues 136–324). TTE0866 catalyzes the deacetylation of highly substituted cellulose acetate and is expected to be useful for industrial applications in the reuse of resources. In this study, the crystal structure of TTE0866 (residues 23–324) was successfully determined. The crystal diffracted to 1.9 Å resolution and belonged to space group I212121. The catalytic domain (residues 136–321) exhibited a (β/α)7-barrel topology. However, electron density was not observed for the NTR (residues 23–135). The crystal packing revealed the presence of an intermolecular space without observable electron density, indicating that the NTR occupies this space without a defined conformation or was truncated during the crystallization process. Although the active-site conformation of TTE0866 was found to be highly similar to those of other CE4 enzymes, the orientation of its Trp264 side chain near the active site was clearly distinct. The unique orientation of the Trp264 side chain formed a different-shaped cavity within TTE0866, which may contribute to its reactivity towards highly substituted cellulose acetate.

scholarly journals Rationalizing the diverse reactivity of [1.1.1]propellane through sigma-pi-delocalization

2020 ◽  
Author(s):  
Alistair Sterling ◽  
Alexander Durr ◽  
Russell C. Smith ◽  
Edward Anderson ◽  
Fernanda Duarte
Keyword(s):  
Charge Transfer ◽  
Electron Density ◽  
Computational Study ◽  
Unified Framework ◽  
Delocalized Electron ◽  
Materials Research ◽  
Pauli Repulsion ◽  
Opening Up

<p>[1.1.1]Propellane has gained increased attention due to its utility as a precursor to bicyclo[1.1.1]pentanes (BCPs) – motifs of high value in pharmaceutical and materials research – by addition of nucleophiles, radicals and electrophiles across its inter-bridgehead C–C bond. However, the origin of this broad reactivity profile is not well-understood. Here, we present a comprehensive computational study that attributes the omniphilicity of [1.1.1]propellane to a moldable, delocalized electron density, characterized by the mixing of the inter-bridgehead C–C bonding and antibonding orbitals. Reactions with anions and radicals are facilitated by stabilization of the adducts through sigma-pi-delocalization of electron density over the cage, while reactions with cations involve charge transfer that relieves Pauli repulsion inside the cage. These results provide a unified framework to rationalize propellane reactivity, opening up opportunities for the exploration of new chemistry of [1.1.1]propellane and related strained systems. </p>

Salt formation, hydrogen-bonding patterns and supramolecular architectures of acridine with salicylic and hippuric acid molecules

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Suresh Suganya ◽  
Kandasamy Saravanan ◽  
Ramakrishnan Jaganathan ◽  
Poomani Kumaradhas
Keyword(s):  
Hydrogen Bonding ◽  
Intermolecular Interactions ◽  
Hippuric Acid ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Salt Formation ◽  
Aminosalicylic Acid ◽  
Dispersion Interactions ◽  
Supramolecular Architectures ◽  
Quantitative Contributions

The intermolecular interactions and salt formation of acridine with 4-aminosalicylic acid, 5-chlorosalicylic acid and hippuric acid were investigated. The salts obtained were acridin-1-ium 4-aminosalicylate (4-amino-2-hydroxybenzoate), C13H10N+·C7H6NO3 − (I), acridin-1-ium 5-chlorosalicylate (5-chloro-2-hydroxybenzoate), C13H10N+·C7H4ClO3 − (II), and acridin-1-ium hippurate (2-benzamidoacetate) monohydrate, C13H10N+·C9H8NO3 −·H2O (III). Acridine is involved in strong intermolecular interactions with the hydroxy group of the three acids, enabling it to form supramolecular assemblies. Hirshfeld surfaces, fingerprint plots and enrichment ratios were generated and investigated, and the intermolecular interactions were analyzed, revealing their quantitative contributions in the crystal packing of salts I, II and III. A quantum theory of atoms in molecules (QTAIM) analysis shows the charge–density distribution of the intermolecular interactions. The isosurfaces of the noncovalent interactions were studied, which allows visualization of where the hydrogen-bonding and dispersion interactions contribute within the crystal.

On the transfer of theoretical multipole parameters for restoring static electron density and revealing and treating atomic anharmonic motion. Features of chemical bonding in crystals of an isocyanuric acid derivative

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Sergey A. Shteingolts ◽  
Julia K. Voronina ◽  
Liliya F. Saifina ◽  
Marina M. Shulaeva ◽  
Vyacheslav E. Semenov ◽  
...  
Keyword(s):  
Electron Density ◽  
Acid Derivative ◽  
Noncovalent Interactions ◽  
Initial Guess ◽  
Atomic Motion ◽  
Total Probability ◽  
Electronic Temperature ◽  
Covalent Bonds ◽  
Isocyanuric Acid ◽  
Static Electron

The crystal and electronic structure of an isocyanuric acid derivative was studied by high-resolution single-crystal X-ray diffraction within the Hansen–Coppens multipole formalism. The observed deformation electron density shows signs of thermal smearing. The experimental picture meaningfully assigned to the consequences of unmodelled anharmonic atomic motion. Straightforward simultaneous refinement of all parameters, including Gram–Charlier coefficients, resulted in more significant distortion of apparent static electron density, even though the residual density became significantly flatter and more featureless. Further, the method of transferring multipole parameters from the model refined against theoretical structure factors as an initial guess was employed, followed by the subsequent block refinement of Gram–Charlier coefficients and the other parameters. This procedure allowed us to appropriately distinguish static electron density from the contaminant smearing effects of insufficiently accounted atomic motion. In particular, some covalent bonds and the weak π...π interaction between isocyanurate moieties were studied via the mutual penetration of atomic-like kinetic and electrostatic potential φ-basins with complementary atomic ρ-basins. Further, local electronic temperature was applied as an advanced descriptor for both covalent bonds and noncovalent interactions. Total probability density function (PDF) of nuclear displacement showed virtually no negative regions close to and around the atomic nuclei. The distribution of anharmonic PDF to a certain extent matched the residual electron density from the multipole model before anharmonic refinement. No signs of disordering of the sulfonyl group hidden in the modelled anharmonic motion were found in the PDF.

scholarly journals Noncovalent Bonds, Spectral and Thermal Properties of Substituted Thiazolo[2,3-b][1,3]thiazinium Triiodides

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 506 ◽  
Author(s):  
Irina Yushina ◽  
Natalya Tarasova ◽  
Dmitry Kim ◽  
Vladimir Sharutin ◽  
Ekaterina Bartashevich
Keyword(s):  
Electron Density ◽  
Noncovalent Interactions ◽  
Material Design ◽  
Spectroscopic Properties ◽  
Structural Features ◽  
Halogen Bonds ◽  
X Ray Diffraction ◽  
Raman Spectroscopic ◽  
Pairwise Interactions ◽  
Noncovalent Bonds

The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.

scholarly journals Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4′-Bipyridine Derivatives

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4409
Author(s):  
Carlo Gatti ◽  
Alessandro Dessì ◽  
Roberto Dallocchio ◽  
Victor Mamane ◽  
Sergio Cossu ◽  
...  
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Source Function ◽  
Noncovalent Interactions ◽  
Conformational Search ◽  
Atomic Group ◽  
Group Contributions ◽  
Conformational Freedom ◽  
Molecular Patterns ◽  
The Impact

Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader–Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4′-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C–Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.

Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

2015 ◽  
Vol 71 (10) ◽  
pp. 921-928 ◽  
Author(s):  
Kulsoom Kamal ◽  
Hardesh K. Maurya ◽  
Atul Gupta ◽  
Prema G. Vasudev
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Cambridge Structural Database ◽  
Database Analysis ◽  
Molecular Conformations ◽  
Keto Esters ◽  
Organic Molecular Crystals ◽  
Structural Database

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013).RSC Adv.3, 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014).Angew. Chem. Int. Ed.53, 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple-bond]C interaction (X = F, Cl, Br or I),viz.the N...Xdistance and the C—X...N and C—N...Xangles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

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